Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold247
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4737410
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 22 of 29
Found at i:3422930 original size:154 final size:151
Alignment explanation
Indices: 3422612--3422948 Score: 415
Period size: 154 Copynumber: 2.2 Consensus size: 151
3422602 CAATCTTTCA
* * * * * *
3422612 TCTCGGGGATACTCTAACCCTATCAATTCCGAGGGGATACTCCAACCCCGTTTTTATTTTCAAAA
1 TCTCGGGGATACTCCAACCCTGTTATTTTCGAGGAGATACTCCAACCCCGTTTTTATTTTCAAAA
* * * * * *
3422677 TATTAAATTTTCTCAAGGATACTCAAATCCTATTATTTTCGAGGGAATACTCTAACCCCATTTTT
66 TATTAAATTTTCTCAAGGATACTCAAACCCCATCAATTCCGAGGGAATACTCCAACCCCATTTTT
* *
3422742 ATTTCCAAAATTATGAATTTT
131 AGTTCCAAAATTATAAATTTT
*
3422763 TTTCGGGGATACTCCAACCCTGTTATTTTCGAGGAGATACTCCAACCCCGTTTTTATTTTCAAAA
1 TCTCGGGGATACTCCAACCCTGTTATTTTCGAGGAGATACTCCAACCCCGTTTTTATTTTCAAAA
** ** * *
3422828 TATTAAATTTTCATCTTGGGGATACTCTGACCCCATCAATTCCGAGGGGATACTCCAACCCTATT
66 TATTAAATTTTC-TC--AAGGATACTCAAACCCCATCAATTCCGAGGGAATACTCCAACCCCATT
*
3422893 TTTAGTTCTAAAA-TATTAAATTTT
128 TTTAGTTCCAAAATTA-TAAATTTT
* *
3422917 TCTCGGGGGTACTCCAACCCCGTTATTTTCGA
1 TCTCGGGGATACTCCAACCCTGTTATTTTCGA
3422949 ACAGACACTT
Statistics
Matches: 157, Mismatches: 25, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
151 70 0.45
152 2 0.01
153 2 0.01
154 83 0.53
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.36
Consensus pattern (151 bp):
TCTCGGGGATACTCCAACCCTGTTATTTTCGAGGAGATACTCCAACCCCGTTTTTATTTTCAAAA
TATTAAATTTTCTCAAGGATACTCAAACCCCATCAATTCCGAGGGAATACTCCAACCCCATTTTT
AGTTCCAAAATTATAAATTTT
Found at i:3432159 original size:20 final size:20
Alignment explanation
Indices: 3432134--3432191 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
3432124 GTAAAAAGAC
3432134 AGAATGTATAGATACATTGA
1 AGAATGTATAGATACATTGA
3432154 AGAATGTATAGATACATTGA
1 AGAATGTATAGATACATTGA
*
3432174 AGAATGTATCGATACATT
1 AGAATGTATAGATACATT
3432192 CATACATGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (20 bp):
AGAATGTATAGATACATTGA
Found at i:3432250 original size:20 final size:20
Alignment explanation
Indices: 3432225--3432262 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3432215 GTAAAAAGAT
3432225 AGAATGTATCGACACATTGA
1 AGAATGTATCGACACATTGA
*
3432245 AGAATGTATCGATACATT
1 AGAATGTATCGACACATT
3432263 CTTACATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (20 bp):
AGAATGTATCGACACATTGA
Found at i:3432278 original size:91 final size:89
Alignment explanation
Indices: 3432090--3432262 Score: 276
Period size: 91 Copynumber: 1.9 Consensus size: 89
3432080 TTTAACTAGG
* *
3432090 TGTATCGATACATT-TAATGTATGGATATATCTGGGTAAAAAGACAGAATGTATAGATACATTGA
1 TGTATCGATACATTATAATGTATCGATATATCTGGGTAAAAAGACAGAATGTATAGACACATTGA
3432154 AGAATGTATAGATACATTGAAGAA
66 AGAATGTATAGATACATTGAAGAA
* *
3432178 TGTATCGATACATTCATACATGTATCGATATATCTGGGTAAAAAGATAGAATGTATCGACACATT
1 TGTATCGATACATT-ATA-ATGTATCGATATATCTGGGTAAAAAGACAGAATGTATAGACACATT
*
3432243 GAAGAATGTATCGATACATT
64 GAAGAATGTATAGATACATT
3432263 CTTACATGTA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
88 14 0.18
90 2 0.03
91 61 0.79
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (89 bp):
TGTATCGATACATTATAATGTATCGATATATCTGGGTAAAAAGACAGAATGTATAGACACATTGA
AGAATGTATAGATACATTGAAGAA
Found at i:3433387 original size:19 final size:19
Alignment explanation
Indices: 3433360--3433411 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
3433350 CGATACAATA
* *
3433360 TATCGATACATGTTCATTG
1 TATCGATACATGATAATTG
*
3433379 TATCTATACATGGATAATTG
1 TATCGATACAT-GATAATTG
3433399 TATCGATACATGA
1 TATCGATACATGA
3433412 AACTGGCAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
TATCGATACATGATAATTG
Found at i:3433464 original size:20 final size:20
Alignment explanation
Indices: 3433439--3433492 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
3433429 CTACCACTGT
* * *
3433439 TTGTATCAATACATGGCGCA
1 TTGTATCGATACATGACGAA
*
3433459 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGACGAA
3433479 TTGTATCGATACAT
1 TTGTATCGATACAT
3433493 TGCTTCAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGACGAA
Found at i:3435106 original size:15 final size:15
Alignment explanation
Indices: 3435086--3435122 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3435076 ACCATCAAAG
3435086 ATGATGAAGATGATA
1 ATGATGAAGATGATA
*
3435101 ATGATGATGATGATA
1 ATGATGAAGATGATA
*
3435116 ATAATGA
1 ATGATGA
3435123 CTCGGATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (15 bp):
ATGATGAAGATGATA
Found at i:3441619 original size:29 final size:28
Alignment explanation
Indices: 3441567--3441650 Score: 105
Period size: 29 Copynumber: 2.8 Consensus size: 28
3441557 AAATAAATTT
3441567 TTATCAAGGGAGAGAAAATCTTTTTAACCAA
1 TTATCAAGGG-G-GAAAAT-TTTTTAACCAA
* *
3441598 TTATCAAGGGGGAAAATATTTTTAATCGA
1 TTATCAAGGGGGAAAAT-TTTTTAACCAA
3441627 TTATCAAGGGGGAGAAATTTTTTA
1 TTATCAAGGGGGA-AAATTTTTTA
3441651 TCAAAGGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 34 0.69
30 5 0.10
31 10 0.20
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.33
Consensus pattern (28 bp):
TTATCAAGGGGGAAAATTTTTTAACCAA
Found at i:3442260 original size:13 final size:13
Alignment explanation
Indices: 3442242--3442266 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3442232 CATTATGCTC
3442242 TGTATCGATACAA
1 TGTATCGATACAA
3442255 TGTATCGATACA
1 TGTATCGATACA
3442267 TGTTCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3444010 original size:15 final size:14
Alignment explanation
Indices: 3443959--3444013 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
3443949 AATATTTTAG
*
3443959 TATT-AAATATTAT
1 TATTAAAATATTAA
* *
3443972 TAATAAAATATTAC
1 TATTAAAATATTAA
*
3443986 TATTTGAAATATTAA
1 TA-TTAAAATATTAA
3444001 TATTAAAA-ATTAA
1 TATTAAAATATTAA
3444014 ATGTTTAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
13 8 0.24
14 15 0.44
15 11 0.32
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (14 bp):
TATTAAAATATTAA
Found at i:3444093 original size:8 final size:8
Alignment explanation
Indices: 3444082--3444150 Score: 58
Period size: 8 Copynumber: 8.9 Consensus size: 8
3444072 AAATATAAAA
3444082 TAATATAT
1 TAATATAT
3444090 TAATATATT
1 TAATATA-T
*
3444099 TAATATTT
1 TAATATAT
3444107 TAATA-AT
1 TAATATAT
*
3444114 GAATAATAT
1 TAAT-ATAT
3444123 T-AT-T-T
1 TAATATAT
3444128 TAA-ATATT
1 TAATATA-T
3444136 TAATATAT
1 TAATATAT
3444144 TAATATA
1 TAATATA
3444151 ATATTTTAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
5 2 0.04
6 3 0.06
7 4 0.08
8 28 0.57
9 12 0.24
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (8 bp):
TAATATAT
Found at i:3444139 original size:29 final size:30
Alignment explanation
Indices: 3444090--3444158 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
3444080 AATAATATAT
3444090 TAATATATTT-AATATTTTAATA-ATGAATAA
1 TAATAT-TTTAAATATTTTAATATATGAAT-A
* *
3444120 TATTATTTTAAATA-TTTAATATATTAATA
1 TAATATTTTAAATATTTTAATATATGAATA
3444149 TAATATTTTA
1 TAATATTTTA
3444159 GTATTACATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 20 0.59
30 14 0.41
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (30 bp):
TAATATTTTAAATATTTTAATATATGAATA
Found at i:3444140 original size:22 final size:20
Alignment explanation
Indices: 3444102--3444145 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3444092 ATATATTTAA
3444102 TATTTTAATAATGAATAATAT
1 TATTTTAATAATGAAT-ATAT
* *
3444123 TATTTTAAATATTTAATATAT
1 TATTTT-AATAATGAATATAT
3444144 TA
1 TA
3444146 ATATAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TATTTTAATAATGAATATAT
Found at i:3444172 original size:19 final size:18
Alignment explanation
Indices: 3444128--3444174 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 18
3444118 AATATTATTT
3444128 TAAATATTTAATATATTAA
1 TAAATATTT-ATATATTAA
3444147 TATAATATTT-TAGTATTACA
1 TA-AATATTTATA-TATTA-A
3444167 TAAATATT
1 TAAATATT
3444175 ATTAAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.08
19 13 0.52
20 10 0.40
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
TAAATATTTATATATTAA
Found at i:3444275 original size:18 final size:18
Alignment explanation
Indices: 3444252--3444322 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
3444242 TCTAAATACA
3444252 TATTTTATTATTTATTTT
1 TATTTTATTATTTATTTT
**
3444270 TATTTTAAAATTATAATATTT
1 TATTTTATTATT-T-AT-TTT
* *
3444291 AATTTTATTA-TTAATTT
1 TATTTTATTATTTATTTT
3444308 TATTTTTATTATTTA
1 TA-TTTTATTATTTA
3444323 CTCAAATAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
17 4 0.10
18 19 0.46
19 5 0.12
20 3 0.07
21 10 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTTTATTATTTATTTT
Found at i:3454183 original size:21 final size:21
Alignment explanation
Indices: 3454157--3454199 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3454147 CCATGGTGCT
*
3454157 TCCTTCATCTTGCTTCTTTCG
1 TCCTTCACCTTGCTTCTTTCG
3454178 TCCTTCACCTTGCTTCTTTCG
1 TCCTTCACCTTGCTTCTTTCG
3454199 T
1 T
3454200 GGCTCTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.05, C:0.35, G:0.09, T:0.51
Consensus pattern (21 bp):
TCCTTCACCTTGCTTCTTTCG
Found at i:3454574 original size:2 final size:2
Alignment explanation
Indices: 3454567--3454595 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3454557 CGCCACGTGA
3454567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3454596 GGAGTCCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3455696 original size:78 final size:78
Alignment explanation
Indices: 3455413--3455976 Score: 387
Period size: 78 Copynumber: 7.1 Consensus size: 78
3455403 AAAATCATTT
* * ** * * * * *
3455413 ATTTTTTA-TTTTTTTAATAAAATA-TAATATTGGTACATTTTCATTTTCTTTACATTTGTTAGT
1 ATTTTTTACTCTTTCTAATAAAA-AGTAATATTATTGCATTTTCAATATCTTTACATCTATTAGT
*
3455476 TATCAAATTTCTTA
65 TATCAAATTACTTA
* ** * * * * *
3455490 ATTTCTTACT-TTTGAAATGAAAAGTAATATAGCTATTGCATTTT-AGTATTTTTATAT-TAAAT
1 ATTTTTTACTCTTTCTAATAAAAAGTAATAT---TATTGCATTTTCAATATCTTTACATCT-ATT
3455552 AGTT-TCAAATTACTTAA
62 AGTTATCAAATTACTT-A
* * * ** * *
3455569 ATTTTTTACT-TTATATATTACAAAAATAATATTATTATATTTT-ACTATCTTTATATCTATTAG
1 ATTTTTTACTCTT-TCTAATA-AAAAGTAATATTATTGCATTTTCAATATCTTTACATCTATTAG
*
3455632 CTATCAAATTACTTA
64 TTATCAAATTACTTA
* * *
3455647 ATTTTTTACTCTTTCTAATAAAAAGTAATATCACTGCATTTTCAATATCTTTACATTTATTAGTT
1 ATTTTTTACTCTTTCTAATAAAAAGTAATATTATTGCATTTTCAATATCTTTACATCTATTAGTT
*
3455712 ATCAAATTATTTA
66 ATCAAATTACTTA
* * * * *
3455725 ATTCTTTA-TGCTTTTTAAT-AAAAGTAATATTTTTGCATTTTCATTATTTTTACATCTATTAGT
1 ATTTTTTACT-CTTTCTAATAAAAAGTAATATTATTGCATTTTCAATATCTTTACATCTATTAGT
3455788 TATCAAATTACTTA
65 TATCAAATTACTTA
* * * *
3455802 ATTTTTTTCCTTTTTTACTTTTCT-TTAAAAAGATTAATATTATTGCATGTTCAATATCTTTCCA
1 A-TTTTTTAC-----T-C-TTTCTAATAAAAAG--TAATATTATTGCATTTTCAATATCTTTACA
*
3455866 TCTATTAGTTATCAAATTACTCA
56 TCTATTAGTTATCAAATTACTTA
* * * * ** * * * **
3455889 A-TTATCACTCTTTCTAATAAAAATTAATATTAATATATTTTTAATTATCATTACGTCTATTAAC
1 ATTTTTTACTCTTTCTAATAAAAAGTAATATTATTGCATTTTCAA-TATCTTTACATCTATTAGT
*
3455953 TATTAAATTACTTA
65 TATCAAATTACTTA
3455967 TATTTTTTAC
1 -ATTTTTTAC
3455977 CTAACACAAA
Statistics
Matches: 381, Mismatches: 77, Indels: 55
0.74 0.15 0.11
Matches are distributed among these distances:
76 1 0.00
77 107 0.28
78 134 0.35
79 48 0.13
80 17 0.04
81 10 0.03
84 3 0.01
85 13 0.03
87 48 0.13
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.51
Consensus pattern (78 bp):
ATTTTTTACTCTTTCTAATAAAAAGTAATATTATTGCATTTTCAATATCTTTACATCTATTAGTT
ATCAAATTACTTA
Found at i:3455717 original size:157 final size:154
Alignment explanation
Indices: 3455423--3455808 Score: 386
Period size: 157 Copynumber: 2.5 Consensus size: 154
3455413 ATTTTTTATT
* ** * * * * *
3455423 TTTTTAATAAAATATAATATTGGTACATTTTCATTTTCTTTACATTTGTTAGTTATCAAATTTCT
1 TTTTTAACAAAA-ATAATATTATTACATTTTCACTATCTTTACATCTATTAGTTATCAAATTACT
* * * * * * *
3455488 TAATTTCTTACTTTTGAAATGAAAAGTAATATAGCTATTGCATTTTAGTATTTTTATATTAAATA
65 TAATTTTTTACTTTTCAAATAAAAAGTAATATA-CTACTGCATTTTAATATCTTTACATTAAATA
3455553 GTTTCAAATTACTTAAATT-TTT-TAC
129 GTTTCAAATTA-TTAAATTCTTTATAC
* * *
3455578 TTTATATATTACAAAAATAATATTATTATATTTT-ACTATCTTTATATCTATTAGCTATCAAATT
1 TTT-T-TA--ACAAAAATAATATTATTACATTTTCACTATCTTTACATCTATTAGTTATCAAATT
* *
3455642 ACTTAATTTTTTACTCTTTCTAATAAAAAGTAATAT-C-ACTGCATTTTCAATATCTTTACATTT
62 ACTTAATTTTTTACT-TTTCAAATAAAAAGTAATATACTACTGCATTTT-AATATCTTTACATTA
* * *
3455705 ATTAGTTATCAAATTATTTAATTCTTTATGC
125 AATAGTT-TCAAATTATTAAATTCTTTATAC
* * * * * *
3455736 TTTTTAATAAAAGTAATATTTTTGCATTTTCATTATTTTTACATCTATTAGTTATCAAATTACTT
1 TTTTTAACAAAAATAATATTATTACATTTTCACTATCTTTACATCTATTAGTTATCAAATTACTT
3455801 AATTTTTT
66 AATTTTTT
3455809 TCCTTTTTTA
Statistics
Matches: 189, Mismatches: 32, Indels: 20
0.78 0.13 0.08
Matches are distributed among these distances:
154 19 0.10
155 50 0.26
156 27 0.14
157 51 0.27
158 37 0.20
159 5 0.03
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (154 bp):
TTTTTAACAAAAATAATATTATTACATTTTCACTATCTTTACATCTATTAGTTATCAAATTACTT
AATTTTTTACTTTTCAAATAAAAAGTAATATACTACTGCATTTTAATATCTTTACATTAAATAGT
TTCAAATTATTAAATTCTTTATAC
Found at i:3455718 original size:235 final size:231
Alignment explanation
Indices: 3455304--3455814 Score: 531
Period size: 233 Copynumber: 2.2 Consensus size: 231
3455294 TATTATTATA
* * * * *
3455304 ATTTTTATAATAAATAATTATTAAATTACTT-AATTTTTTATTTTTTAAAAATAAAAAATAATAT
1 ATTTTTATATTAAATAGTTATCAAATTACTTAAATTTTTTACTTTATAAAAATAAAAAATAATAT
* * * * * *
3455368 TATTATATTTTTATCATCTTTGTATTTAAAACTGTAAAATCATTTATTTTTTATTTTTTTAATAA
66 TATTATATTTTTATCATCTTTATATCTAAAACTATAAAATCATTAATTTTTTATCTTTCTAATAA
*** * * *
3455433 AATATAATATTGGTACATTTTCATTTTCTTTACATTTGTTAGTTATCAAATT-TCTTAATT-TCT
131 AATATAATATCACTACATTTTCAATATCTTTACATTTATTAGTTATCAAATTAT-TTAATTCT-T
3455496 TA-CTTTTGAAATGAAAAGTAATATAGCTATTGCATTTT-AGT
194 TAGCTTTT-AAAT-AAAAGTAATAT---TATTGCATTTTCAGT
* *
3455537 ATTTTTATATTAAATAGTT-TCAAATTACTTAAATTTTTTACTTTAT-ATATTACAAAAATAATA
1 ATTTTTATATTAAATAGTTATCAAATTACTTAAATTTTTTACTTTATAAAAATA-AAAAATAATA
* * * *
3455600 TTATTATA-TTTTA-CTATCTTTATATCTATTAGCTATCAAATTACTTAATTTTTTACTCTTTCT
65 TTATTATATTTTTATC-ATCTTTATATCTA-AAACTATAAAATCA-TTAATTTTTTA-TCTTTCT
*
3455663 AATAAAA-AGTAATATCACTGCATTTTCAATATCTTTACATTTATTAGTTATCAAATTATTTAAT
126 AATAAAATA-TAATATCACTACATTTTCAATATCTTTACATTTATTAGTTATCAAATTATTTAAT
* * *
3455727 TCTTTATGCTTTTTAATAAAAGTAATATTTTTGCATTTTCATT
190 TCTTTA-GCTTTTAAATAAAAGTAATATTATTGCATTTTCAGT
* * * *
3455770 ATTTTTACATCT-ATTAGTTATCAAATTACTTAATTTTTTTCCTTT
1 ATTTTTATAT-TAAATAGTTATCAAATTACTTAAATTTTTTACTTT
3455815 TTTACTTTTC
Statistics
Matches: 233, Mismatches: 31, Indels: 27
0.80 0.11 0.09
Matches are distributed among these distances:
231 1 0.00
232 40 0.17
233 74 0.32
234 35 0.15
235 73 0.31
236 5 0.02
237 5 0.02
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (231 bp):
ATTTTTATATTAAATAGTTATCAAATTACTTAAATTTTTTACTTTATAAAAATAAAAAATAATAT
TATTATATTTTTATCATCTTTATATCTAAAACTATAAAATCATTAATTTTTTATCTTTCTAATAA
AATATAATATCACTACATTTTCAATATCTTTACATTTATTAGTTATCAAATTATTTAATTCTTTA
GCTTTTAAATAAAAGTAATATTATTGCATTTTCAGT
Found at i:3456945 original size:16 final size:16
Alignment explanation
Indices: 3456924--3456970 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
3456914 TGAGTTAATT
3456924 GTTCGGGTCATTTCGA
1 GTTCGGGTCATTTCGA
*
3456940 GTTCGGGTCATTTTGA
1 GTTCGGGTCATTTCGA
*
3456956 GTTCAGGTCATTTCG
1 GTTCGGGTCATTTCG
3456971 GGTTTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.13, C:0.17, G:0.30, T:0.40
Consensus pattern (16 bp):
GTTCGGGTCATTTCGA
Found at i:3457008 original size:16 final size:16
Alignment explanation
Indices: 3456989--3457029 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
3456979 TTCGGATTCA
*
3456989 GGTCATTTTGGGTTCG
1 GGTCATTTTGAGTTCG
*
3457005 GGTCATTTTAAGTTCG
1 GGTCATTTTGAGTTCG
*
3457021 GGTTATTTT
1 GGTCATTTT
3457030 CAGGTTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.12, C:0.10, G:0.29, T:0.49
Consensus pattern (16 bp):
GGTCATTTTGAGTTCG
Found at i:3458229 original size:20 final size:20
Alignment explanation
Indices: 3458204--3458242 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
3458194 CTACTGCCAG
3458204 TTTCATGTATCGATACAATT
1 TTTCATGTATCGATACAATT
3458224 TTTCATGTATCGATACAAT
1 TTTCATGTATCGATACAAT
3458243 GAACATGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (20 bp):
TTTCATGTATCGATACAATT
Found at i:3458251 original size:19 final size:19
Alignment explanation
Indices: 3458207--3458262 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
3458197 CTGCCAGTTT
***
3458207 CATGTATCGATACAATTTTT
1 CATGTATCGATACAA-TGAA
3458227 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
3458246 CATGTATCGATATAATG
1 CATGTATCGATACAATG
3458263 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:3460845 original size:13 final size:13
Alignment explanation
Indices: 3460827--3460851 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3460817 ATAGTACCCC
3460827 TTGTATCGATACA
1 TTGTATCGATACA
3460840 TTGTATCGATAC
1 TTGTATCGATAC
3460852 TAAGATCCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3472041 original size:65 final size:65
Alignment explanation
Indices: 3471965--3472091 Score: 236
Period size: 65 Copynumber: 2.0 Consensus size: 65
3471955 TAGGTTGGTA
*
3471965 TTTGTGAAAGTTTAAGTACAAAGAAAATGAAAGAGCTTAACAAAAAATTACAACAATAGAAAGTG
1 TTTGTGAAAGTTTAAGTACAAAGAAAATGAAAGAGCTTAACAAAAAATAACAACAATAGAAAGTG
*
3472030 TTTGTGAAAGTTTAAGTACAAAGAAAATGAAAGAGCTTAACAAAGAATAACAACAATAGAAA
1 TTTGTGAAAGTTTAAGTACAAAGAAAATGAAAGAGCTTAACAAAAAATAACAACAATAGAAA
3472092 CCTTGAATAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.54, C:0.08, G:0.17, T:0.22
Consensus pattern (65 bp):
TTTGTGAAAGTTTAAGTACAAAGAAAATGAAAGAGCTTAACAAAAAATAACAACAATAGAAAGTG
Found at i:3472410 original size:21 final size:21
Alignment explanation
Indices: 3472362--3472440 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 21
3472352 CTGTTGGGCC
*
3472362 AAATGTATCGATAAAATTCTT-
1 AAATGTATCGATACAA-TCTTA
*
3472383 -GATGTATCGATACAATCTTA
1 AAATGTATCGATACAATCTTA
*
3472403 AAATGTATCGATACACT-TTCA
1 AAATGTATCGATACAATCTT-A
*
3472424 ACATGTATCGATACAAT
1 AAATGTATCGATACAAT
3472441 TATAGGGTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.08
20 15 0.31
21 30 0.61
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.34
Consensus pattern (21 bp):
AAATGTATCGATACAATCTTA
Found at i:3473115 original size:21 final size:20
Alignment explanation
Indices: 3473078--3473116 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3473068 GTTGATCTTG
*
3473078 TGTTTAGTGTTAGTTGTTGA
1 TGTTTAGTGTTAATTGTTGA
*
3473098 TGTTTCGTGGTTAATTGTT
1 TGTTTAGT-GTTAATTGTT
3473117 CTTAATTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.13, C:0.03, G:0.28, T:0.56
Consensus pattern (20 bp):
TGTTTAGTGTTAATTGTTGA
Found at i:3477795 original size:20 final size:21
Alignment explanation
Indices: 3477747--3477800 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
3477737 GATGCATGTT
* *
3477747 GAATTGCATCGATACATTTTAA
1 GAATTGTATCGATACA-TTCAA
3477769 G-ATTGTATCGATACA-TCAA
1 GAATTGTATCGATACATTCAA
3477788 GAATTGTATCGAT
1 GAATTGTATCGAT
3477801 TTGGCCCAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 11 0.38
21 13 0.45
22 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
GAATTGTATCGATACATTCAA
Found at i:3477840 original size:59 final size:59
Alignment explanation
Indices: 3477770--3477900 Score: 262
Period size: 59 Copynumber: 2.2 Consensus size: 59
3477760 ACATTTTAAG
3477770 ATTGTATCGATACATCAAGAATTGTATCGATTTGGCCCAACGGCTAGAATTTCAAATGC
1 ATTGTATCGATACATCAAGAATTGTATCGATTTGGCCCAACGGCTAGAATTTCAAATGC
3477829 ATTGTATCGATACATCAAGAATTGTATCGATTTGGCCCAACGGCTAGAATTTCAAATGC
1 ATTGTATCGATACATCAAGAATTGTATCGATTTGGCCCAACGGCTAGAATTTCAAATGC
3477888 ATTGTATCGATAC
1 ATTGTATCGATAC
3477901 TTTTTGAAAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 72 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (59 bp):
ATTGTATCGATACATCAAGAATTGTATCGATTTGGCCCAACGGCTAGAATTTCAAATGC
Found at i:3479981 original size:20 final size:20
Alignment explanation
Indices: 3479958--3479995 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3479948 TACATGTATG
3479958 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
* *
3479978 AATGTATTGATATATTCT
1 AATGTATCGATACATTCT
3479996 ATCTTTTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:3486932 original size:9 final size:11
Alignment explanation
Indices: 3486906--3486939 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
3486896 GAAGTTTTTA
3486906 TGAAAAATATT
1 TGAAAAATATT
3486917 TGAAAAAT-TT
1 TGAAAAATATT
3486927 TGAAAAATCATT
1 TGAAAAAT-ATT
3486939 T
1 T
3486940 AATAGGACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.48
11 8 0.38
12 3 0.14
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (11 bp):
TGAAAAATATT
Found at i:3491627 original size:19 final size:19
Alignment explanation
Indices: 3491603--3491643 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3491593 ATTACATAAA
*
3491603 ATTTAAAT-AGATTATTTAT
1 ATTTAAATAAG-TTAATTAT
3491622 ATTTAAATAAGTTAATTAT
1 ATTTAAATAAGTTAATTAT
3491641 ATT
1 ATT
3491644 ATTTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
ATTTAAATAAGTTAATTAT
Found at i:3492363 original size:32 final size:35
Alignment explanation
Indices: 3492294--3492370 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 35
3492284 AAACTAGTAT
3492294 AATATTATTATTATTATTATGTGAATAAAATATTTA
1 AATATTATTATTATTATTA-GTGAATAAAATATTTA
*
3492330 AATATTATTA-TATT-TTA-TGAAT-AAATGTCTTA
1 AATATTATTATTATTATTAGTGAATAAAATAT-TTA
3492362 AATA-TATTA
1 AATATTATTA
3492371 CCTATTTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
31 10 0.26
32 12 0.31
34 3 0.08
35 4 0.10
36 10 0.26
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.49
Consensus pattern (35 bp):
AATATTATTATTATTATTAGTGAATAAAATATTTA
Found at i:3492763 original size:2 final size:2
Alignment explanation
Indices: 3492722--3492746 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3492712 ATATAAGGTG
3492722 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3492747 AAACATAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3492769 original size:21 final size:22
Alignment explanation
Indices: 3492736--3492776 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3492726 ATATATATAT
3492736 ATATATATATAAAACATAATCA
1 ATATATATATAAAACATAATCA
*
3492758 ATATAT-TATAAAGCATAAT
1 ATATATATATAAAACATAAT
3492777 GTATTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.34
Consensus pattern (22 bp):
ATATATATATAAAACATAATCA
Found at i:3493809 original size:8 final size:9
Alignment explanation
Indices: 3493792--3493833 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
3493782 AATAATAATT
3493792 AAAAGAAAA
1 AAAAGAAAA
3493801 AAAAGAAAA
1 AAAAGAAAA
*
3493810 AAAA-AACA
1 AAAAGAAAA
*
3493818 AAAACAAAGA
1 AAAAGAAA-A
3493828 AAAAGA
1 AAAAGA
3493834 TAGAGAGAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
8 7 0.25
9 15 0.54
10 6 0.21
ACGTcount: A:0.86, C:0.05, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:3493826 original size:21 final size:20
Alignment explanation
Indices: 3493792--3493831 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
3493782 AATAATAATT
*
3493792 AAAAGAAAAAAAAGAAAAAA
1 AAAACAAAAAAAAGAAAAAA
3493812 AAAACAAAAACAAAGAAAAA
1 AAAACAAAAA-AAAGAAAAA
3493832 GATAGAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00
Consensus pattern (20 bp):
AAAACAAAAAAAAGAAAAAA
Found at i:3495488 original size:33 final size:33
Alignment explanation
Indices: 3495446--3495512 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
3495436 TGTTGTGTAC
3495446 TTAGCGTTTTAAAAGCTTGTTTTCTTTGAACTT
1 TTAGCGTTTTAAAAGCTTGTTTTCTTTGAACTT
3495479 TTAGCGTTTTAAAAGCTTGTTTTCTTTGAACTT
1 TTAGCGTTTTAAAAGCTTGTTTTCTTTGAACTT
3495512 T
1 T
3495513 ATTTTACTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.21, C:0.12, G:0.15, T:0.52
Consensus pattern (33 bp):
TTAGCGTTTTAAAAGCTTGTTTTCTTTGAACTT
Found at i:3501492 original size:2 final size:2
Alignment explanation
Indices: 3501487--3501515 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3501477 TATATATATA
3501487 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3501516 ACATATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3505407 original size:49 final size:50
Alignment explanation
Indices: 3505295--3505407 Score: 149
Period size: 50 Copynumber: 2.3 Consensus size: 50
3505285 TTTCACAATT
** * * *
3505295 TGTATCGGCACATTGTTCATTGTATCGATACATTCTGAGTTTTACCTAGA
1 TGTATCGATACATTGTTCACTATATCGATACATTCTGAGGTTTACCTAGA
*
3505345 TGTATCGATACATTGTTCACTATATCGATACATTTTG-GGTTTA-CTCAGA
1 TGTATCGATACATTGTTCACTATATCGATACATTCTGAGGTTTACCT-AGA
3505394 TGTATCGATACATT
1 TGTATCGATACATT
3505408 AAAAAATGTA
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
48 2 0.04
49 22 0.39
50 32 0.57
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.41
Consensus pattern (50 bp):
TGTATCGATACATTGTTCACTATATCGATACATTCTGAGGTTTACCTAGA
Found at i:3505420 original size:49 final size:50
Alignment explanation
Indices: 3505315--3505428 Score: 133
Period size: 49 Copynumber: 2.3 Consensus size: 50
3505305 CATTGTTCAT
* **** *
3505315 TGTATCGATACATTCTGAGTTTTACCTAGATGTATCGATACATTGTTCAC
1 TGTATCGATACATTCTGAGGTTTACCTAGATGTATCGATACATTAAAAAA
* *
3505365 TATATCGATACATTTTG-GGTTTA-CTCAGATGTATCGATACATTAAAAAA
1 TGTATCGATACATTCTGAGGTTTACCT-AGATGTATCGATACATTAAAAAA
3505414 TGTATCGATACATTC
1 TGTATCGATACATTC
3505429 AGGCATTTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
48 2 0.04
49 36 0.68
50 15 0.28
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (50 bp):
TGTATCGATACATTCTGAGGTTTACCTAGATGTATCGATACATTAAAAAA
Found at i:3507779 original size:50 final size:50
Alignment explanation
Indices: 3507714--3507845 Score: 167
Period size: 50 Copynumber: 2.6 Consensus size: 50
3507704 TAAATTTCTA
* * * *
3507714 GATTTTTTATTTCGGGGATACTCCAACCCCGGCTTTATTTCTAAAATATT
1 GATTTTTCATCTCGGGGATACTCCAACCCCGGCTTTATTTCTAAAACATC
* *
3507764 GATTTTTCATCTCGGGGATACTCCAACCTCGGCTTTATTTCTAAAGCATC
1 GATTTTTCATCTCGGGGATACTCCAACCCCGGCTTTATTTCTAAAACATC
* *
3507814 GATTTTCCA-CAATCGGGGATACTCCAATCCCG
1 GATTTTTCATC--TCGGGGATACTCCAACCCCG
3507846 TTATTTCCAA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
49 1 0.01
50 52 0.73
51 18 0.25
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (50 bp):
GATTTTTCATCTCGGGGATACTCCAACCCCGGCTTTATTTCTAAAACATC
Found at i:3507879 original size:78 final size:77
Alignment explanation
Indices: 3507778--3508154 Score: 336
Period size: 79 Copynumber: 4.8 Consensus size: 77
3507768 TTTCATCTCG
*
3507778 GGGATACTCCAA-CCTCGGCTTTATTTCTAAAGCATCGATTTTCCACAATCGGGGATACTCCAAT
1 GGGATACTCCAACCCT-GACTTTATTTCTAAAGCATCGATTTTCCACAATCGGGGATACTCCAA-
*
3507842 CCCGTTATTTCCAA
64 CCCGTTATTTCCGA
* *
3507856 GGGATACTCCAACCCTGACTTTATTTCT-AAGATATTGA-TTTCTCACAATCGGGGATA-TCCCA
1 GGGATACTCCAACCCTGACTTTATTTCTAAAG-CATCGATTTTC-CACAATCGGGGATACT-CCA
*
3507918 ACCTCGTTATTTTGGCG-
63 ACC-CGTTA-TTT-CCGA
* * * * * *
3507935 GGGATAGTCCAACCCCGACCTTATTGCTAAAGCATCGATTTTTCACAATCGGGGATACTTCAACC
1 GGGATACTCCAACCCTGACTTTATTTCTAAAGCATCGATTTTCCACAATCGGGGATACTCCAA-C
**
3508000 CCGTTATTTTTGA
65 CCGTTATTTCCGA
* * * * * * **
3508013 GAGGATACTCCAACCCAGATTTTATTT-TCAAAACGTCGATTTTCTATAATCAAGGATACTCCAA
1 G-GGATACTCCAACCCTGACTTTATTTCT-AAAGCATCGATTTTCCACAATCGGGGATACTCCAA
*
3508077 CCCTGTTATTTCTGA
64 CCC-GTTATTTCCGA
* * * * *
3508092 GGGAATACTCCAACCCTGATTTTATTT-TCAAAACATCGATTTTTCATAATCGGAGATACTCCA
1 GGG-ATACTCCAACCCTGACTTTATTTCT-AAAGCATCGATTTTCCACAATCGGGGATACTCCA
3508155 GCCTCGTTGT
Statistics
Matches: 247, Mismatches: 36, Indels: 31
0.79 0.11 0.10
Matches are distributed among these distances:
77 11 0.04
78 60 0.24
79 166 0.67
80 10 0.04
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (77 bp):
GGGATACTCCAACCCTGACTTTATTTCTAAAGCATCGATTTTCCACAATCGGGGATACTCCAACC
CGTTATTTCCGA
Found at i:3508104 original size:158 final size:156
Alignment explanation
Indices: 3507781--3508154 Score: 389
Period size: 158 Copynumber: 2.4 Consensus size: 156
3507771 CATCTCGGGG
* * * *
3507781 ATACTCCAACCTCGGCTTTATTTCTAAAGCATCGATTTTCCACAATCGGGGATACTCCAATCCCG
1 ATACTCCAACCCCGACTTTA-TTCTAAAGCATCGATTTTTCACAATCGGGGATACTCCAACCCCG
* * * * **
3507846 TTATTTCCAAGGGATACTCCAACCCTGACTTTATTTCTAAGATATTGATTTCTCACAATCGGGGA
65 TTATTTCCAAGGGATACTCCAACCCAGACTTTATTTCTAAAACATCGATTTCTCACAATCAAGGA
* *
3507911 TATCCCAACCTCGTTATTTTGGCGGGG
130 TATCCCAACCTCGTTATTTTGGAGGGA
* * *
3507938 ATAGTCCAACCCCGACCTTATTGCTAAAGCATCGATTTTTCACAATCGGGGATACTTCAACCCCG
1 ATACTCCAACCCCGACTTTATT-CTAAAGCATCGATTTTTCACAATCGGGGATACTCCAACCCCG
*** * * *
3508003 TTATTTTTGAGAGGATACTCCAACCCAGATTTTATTT-TCAAAACGTCGATTT-TCTATAATCAA
65 TTATTTCCAAG-GGATACTCCAACCCAGACTTTATTTCT-AAAACATCGATTTCTC-ACAATCAA
3508066 GGATA-CTCCAACC-CTGTTATTTCT-GAGGGA
127 GGATATC-CCAACCTC-GTTATTT-TGGAGGGA
* * * * * *
3508096 ATACTCCAACCCTGATTTTATTTTCAAAACATCGATTTTTCATAATCGGAGATACTCCA
1 ATACTCCAACCCCGACTTTATTCT-AAAGCATCGATTTTTCACAATCGGGGATACTCCA
3508155 GCCTCGTTGT
Statistics
Matches: 179, Mismatches: 30, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
156 2 0.01
157 69 0.39
158 107 0.60
159 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.33
Consensus pattern (156 bp):
ATACTCCAACCCCGACTTTATTCTAAAGCATCGATTTTTCACAATCGGGGATACTCCAACCCCGT
TATTTCCAAGGGATACTCCAACCCAGACTTTATTTCTAAAACATCGATTTCTCACAATCAAGGAT
ATCCCAACCTCGTTATTTTGGAGGGA
Found at i:3508836 original size:33 final size:33
Alignment explanation
Indices: 3508799--3508865 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3508789 TTCAACGATT
3508799 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
3508832 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
3508865 T
1 T
3508866 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:3508837 original size:13 final size:13
Alignment explanation
Indices: 3508819--3508843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3508809 CATAAAATGT
3508819 TGTATCGATACAA
1 TGTATCGATACAA
3508832 TGTATCGATACA
1 TGTATCGATACA
3508844 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3508927 original size:13 final size:13
Alignment explanation
Indices: 3508909--3508933 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3508899 ATTACTCACA
3508909 TGTATCGATACAT
1 TGTATCGATACAT
3508922 TGTATCGATACA
1 TGTATCGATACA
3508934 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3509070 original size:52 final size:52
Alignment explanation
Indices: 3508942--3509062 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
3508932 CACTGATCTT
*
3508942 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
3508994 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
3509046 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
3509063 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:3517424 original size:27 final size:27
Alignment explanation
Indices: 3517333--3517419 Score: 84
Period size: 33 Copynumber: 3.0 Consensus size: 27
3517323 GGCATTTTTT
*
3517333 CTTTAAAGCCCACAACTCCGTGGCACCTTGTTC
1 CTTTTAAGCCCACAACTCCGTGGCA-C-----C
*
3517366 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGCCCACAACTCCGTGGCACC
*
3517393 CTTTTAAAGCCCACAATTCCGTGGCAC
1 CTTTT-AAGCCCACAACTCCGTGGCAC
3517420 TTTTTTCATC
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
27 6 0.12
28 19 0.39
32 1 0.02
33 23 0.47
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (27 bp):
CTTTTAAGCCCACAACTCCGTGGCACC
Found at i:3517441 original size:34 final size:32
Alignment explanation
Indices: 3517311--3518638 Score: 964
Period size: 34 Copynumber: 40.6 Consensus size: 32
3517301 TTTTCAAAGT
* * *
3517311 CCACGACTCAGTGGCA-TTTTTTCTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTTAAGC
* * *
3517342 CCACAACTCCGTGGCACCTTGTTCCTTTTAAGT
1 CCACAACTCCGTGGCA-CTTTTTTCTTTTAAGC
*
3517375 CCACAACTCCGTGGCAC-----CCTTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT-AAGC
* *
3517403 CCACAATTCCGTGGCACTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTC-T-TTTAAGC
*
3517437 CCACAACTCCGTGGCACCTTTTTCTGTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCT-TTT-AAGC
3517471 CCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGC
1 CCACAACTCCGTGGCA--CTTTTT-TCTTTT--AAGC
* *
3517508 CCACGACTCCGTGGCAC-----TCTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTTAAGC
* *
3517535 CCACAACTCCGTGGCACCTTCTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT--AAGC
* * *
3517569 CCACAACTCTGTGGCACCTTCTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT--AAGC
* * *
3517603 CCACAACTCTGTGGCACCTTCTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT--AAGC
* * *
3517637 CCACAACTCTGTGGCACCTTCTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT--AAGC
* * *
3517671 CCACGACTCCGTGGCAC--TCTT-TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTTAAGC
**
3517700 CCACAACTCCGTGGCACTCTTTTTCCTCCTAAGC
1 CCACAACTCCGTGGCACT-TTTTT-CTTTTAAGC
* *
3517734 CCACAACTCTGTGGCACTCTTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACT-TTTTT-CTTTTAAGC
*
3517768 CCACAACTCCGTGGCAC-----CCTTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT-AAGC
* *
3517796 CCACAATTCCGTGGCACTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTC-T-TTTAAGC
*
3517830 CCACAACTCCGTGGCACCTTTTTCTGTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCT-TTT-AAGC
*
3517864 CCATAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGC
1 CCACAACTCCGTGGCA--CTTTTT-TCTTTT--AAGC
* *
3517901 CCACGACTCCGTGGCAC-----TCTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTTAAGC
* *
3517928 CCACAACTCCGTGGCACCTTCTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT--AAGC
* * *
3517962 CCACAACTCTGTGGCACCTTCTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT--AAGC
* * *
3517996 CCACAACTCTGTGGCACCTTCTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT--AAGC
* * *
3518030 CCACAACTCTGTGGCACCTTCTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT--AAGC
* * *
3518064 CCACGACTCCGTGGCAC--TCTT-TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTTAAGC
**
3518093 CCACAACTCCGTGGCACTCTTTTTCCTCCTAAGC
1 CCACAACTCCGTGGCACT-TTTTT-CTTTTAAGC
* *
3518127 CCACAACTCTGTGGCACTCTTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACT-TTTTT-CTTTTAAGC
*
3518161 CCACAACTCCGTGGCAC-----CCTTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT-AAGC
* *
3518189 CCACAATTCCGTGGCACTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTC-T-TTTAAGC
*
3518223 CCACAACTCCGTGGCACCTTTTTCTGTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCT-TTT-AAGC
3518257 CCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGC
1 CCACAACTCCGTGGCA--CTTTTT-TCTTTT--AAGC
* *
3518294 CCACGACTCCGTGGCAC-----TCTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTTAAGC
* *
3518321 CCACAACTCCGTGGCACCTTCTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT--AAGC
* * *
3518355 CCACAACTCTGTGGCACCTTCTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT--AAGC
* * *
3518389 CCACGACTCCGTGGCAC--TCTT-TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTTAAGC
**
3518418 CCACAACTCCGTGGCACTCTTTTTCCTCCTAAGC
1 CCACAACTCCGTGGCACT-TTTTT-CTTTTAAGC
* *
3518452 CCACAACTCTGTGGCACTCTTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACT-TTTTT-CTTTTAAGC
*
3518486 CCACAACTCCGTGGCAC-----CCTTTTAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTTAAGC
* *
3518513 CCATAACTCCGTGGCACTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTC-T-TTTAAGC
* *
3518547 CCATAACTCCGTGACACCTTTTTTTTCTTTTAAAGC
1 CCACAACTCCGTGGCA-C--TTTTTTCTTTT-AAGC
*
3518583 CCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGT
1 CCACAACTCCGTGGCACT-TTTTT--CTTTTAAGC
*
3518618 CCACAACTCCATGGCATCTTT
1 CCACAACTCCGTGGCA-CTTT
3518639 CTCCCTTCCT
Statistics
Matches: 1109, Mismatches: 96, Indels: 180
0.80 0.07 0.13
Matches are distributed among these distances:
27 98 0.09
28 59 0.05
29 75 0.07
31 23 0.02
32 38 0.03
33 44 0.04
34 611 0.55
35 37 0.03
36 49 0.04
37 75 0.07
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.32
Consensus pattern (32 bp):
CCACAACTCCGTGGCACTTTTTTCTTTTAAGC
Found at i:3517788 original size:27 final size:28
Alignment explanation
Indices: 3517758--3517812 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
3517748 CACTCTTTTT
3517758 CCTTCT-AAGCCCACAACTCCGTGGCAC
1 CCTTCTAAAGCCCACAACTCCGTGGCAC
* *
3517785 CCTTTTAAAGCCCACAATTCCGTGGCAC
1 CCTTCTAAAGCCCACAACTCCGTGGCAC
3517813 TTTTTTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.24, C:0.40, G:0.15, T:0.22
Consensus pattern (28 bp):
CCTTCTAAAGCCCACAACTCCGTGGCAC
Found at i:3518046 original size:359 final size:361
Alignment explanation
Indices: 3517300--3518636 Score: 1567
Period size: 359 Copynumber: 3.7 Consensus size: 361
3517290 CTTCAAATAC
* * ** * *
3517300 CTTTTCAAAGTCCACGACTCAGTGGCATTTTTTCTTTAAAGCCCACAACTCCGTGGCAC-CTTGT
1 CTTTTCAAAGCCCACGACTCCGTGGCACCTCTT-TTTAAAGCCCACAACTCCGTGGCACTCTTTT
** * * * * **
3517364 TCCTTTTAAGTCCACAACTCCGTGGCAC-C--CTT--TT-AAAGCCCACAATTCCGTGGCACTTT
65 TCCTCCTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCCT
* *
3517423 TTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTC-TGTTTAAAGCCCACAACTCCGTGGCA
130 TTTCA-----AAGCCCACAACTCCGTGGCACCTTTTTCATCTTT-AAGCCCACAACTCCGTGGCA
*
3517487 CTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCA-------CTC-TTTAAAGCCCACAACTC
189 C-C-TTTT-TCTTTT-AAAGCCCACAACTCCGTGGCACCTTTTTCTCTTTTAAAGCCCACAACTC
*
3517544 CGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAA
250 CGTGGCA---TC-TCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAA
3517609 CTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTT
311 CTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTT
3517660 CTTTTCAAAGCCCACGACTCCGTGGCA-CTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CTTTTCAAAGCCCACGACTCCGTGGCACCTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
*
3517724 CCTCCTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCCTT
66 CCTCCTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCCTT
* * *
3517789 TT-AAAGCCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTT
131 TTCAAAGCCCACAACTCCGTGGCACCTTTTTCATCTTTAAGCCCACAACTCCGTGGCACCTTTTT
* *
3517853 CTGTTTAAAGCCCATAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCA-
196 CT-TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCTCTTTT-AAAGCCCACAACTCCGTGGCAT
3517917 CTC-TTT-AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACC
258 CTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACC
3517980 TTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTT
323 TTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTT
* * *
3518019 CTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACGACTCCGTGGCACTC-
1 CTTTTCAAAGCCCACGACTCCGTGGCACC-TC-T-TTTT-AAAGCCCACAACTCCGTGGCACTCT
* * *
3518083 TTTT--T--AAAGCCCACAACTCCGTGGCACTCTTTTTCCTCCTAAGCCCACAACTCTGTGGCAC
62 TTTTCCTCCTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCAC
* * * *
3518144 TCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCCTTTT-A-----AAGCCCACAATTCCGTGG
127 -C--CTT--TTCAAAGCCCACAACTCCGTGGCACCTTTTTCATCTTTAAGCCCACAACTCCGTGG
* * *
3518203 CACTTTTTTCATCTTT-AAGTCCACAACTCCGTGGCACCTTTTTCT-GTTTAAAGCCCACAACTC
187 CACCTTTTTC-T-TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTCTTTTAAAGCCCACAACTC
*
3518266 CGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCA----C-TC-TTT-AAAGCCCA
250 CGTGGCA-------TCTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCA
*
3518324 CAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTT
308 CAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTT
3518378 CTTTTCAAAGCCCACGACTCCGTGGCA-CTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CTTTTCAAAGCCCACGACTCCGTGGCACCTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
*
3518442 CCTCCTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCCTT
66 CCTCCTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCCTT
* * * * *
3518507 TT--AAGCCCATAACTCCGTGGCACTTTTTTCATCTTTAAGTCCATAACTCCGTGACACCTTTTT
131 TTCAAAGCCCACAACTCCGTGGCACCTTTTTCATCTTTAAGCCCACAACTCCGTGGCACC---TT
* * *
3518570 TTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT-AAGTCCACAACTCCATGGCA
193 TTTCTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCTCTTTTAAAGCCCACAACTCCGTGGCA
3518634 TCT
257 TCT
3518637 TTCTCCCTTC
Statistics
Matches: 853, Mismatches: 66, Indels: 122
0.82 0.06 0.12
Matches are distributed among these distances:
352 24 0.03
353 1 0.00
354 28 0.03
355 8 0.01
356 45 0.05
357 13 0.02
358 53 0.06
359 433 0.51
360 63 0.07
361 38 0.04
362 10 0.01
363 8 0.01
364 35 0.04
365 54 0.06
366 40 0.05
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.32
Consensus pattern (361 bp):
CTTTTCAAAGCCCACGACTCCGTGGCACCTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
CCTCCTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCCTT
TTCAAAGCCCACAACTCCGTGGCACCTTTTTCATCTTTAAGCCCACAACTCCGTGGCACCTTTTT
CTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTCTTTTAAAGCCCACAACTCCGTGGCATCTC
TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTC
TTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTT
Found at i:3518100 original size:393 final size:393
Alignment explanation
Indices: 3517338--3518638 Score: 2096
Period size: 393 Copynumber: 3.3 Consensus size: 393
3517328 TTTTTCTTTA
* * *
3517338 AAGCCCACAACTCCGTGGCAC-CTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAG
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCCTTTTAAAG
3517402 CCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTCTGTTTA
66 CCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTCTGTTTA
3517467 AAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCACTCTTTAA
131 AAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCACTCTTTAA
3517532 AGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTTTT
196 AGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTTTT
3517597 CAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCT
261 CAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCT
3517662 TTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
326 TTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
3517727 CCT
391 CCT
*
3517730 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCCTTTTAAAG
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCCTTTTAAAG
3517795 CCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTCTGTTTA
66 CCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTCTGTTTA
*
3517860 AAGCCCATAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCACTCTTTAA
131 AAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCACTCTTTAA
3517925 AGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTTTT
196 AGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTTTT
3517990 CAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCT
261 CAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCT
3518055 TTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
326 TTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
3518120 CCT
391 CCT
*
3518123 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCCTTTTAAAG
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCCTTTTAAAG
3518188 CCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTCTGTTTA
66 CCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTCTGTTTA
3518253 AAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCACTCTTTAA
131 AAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCACTCTTTAA
3518318 AGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTTTT
196 AGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTTTT
* * * *
3518383 CAAAGCCCACGACTCCGTGGCA-C-TC-T-TTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTC
261 CAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCAC-CTTCTTC
* * * * * *
3518443 -CTCCTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCAC-C--
325 TTTTCAAAGCCCACGACTCCGTGGCACTC--TTT--TT-AAAGCCCACAACTCCGTGGCACTCTT
*
3518504 CTT--T--T
385 TTTCCTCCT
* * * *
3518509 AAGCCCATAACTCCGTGGCACT-TTTTTCATCTT-TAAGTCCATAACTCCGTGACACCTTTTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTC--CTTCTAAGCCCACAACTCCGTGGCACC-------
* * * *
3518572 TCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC-CCTTTTAAGTCCACAACTCCATGGCATC
57 -CTTTTAAAGCCCACAATTCCGTGGCACT-TTTTTCATC-TTTAAGTCCACAACTCCGTGGCACC
3518636 TTT
119 TTT
3518639 CTCCCTTCCT
Statistics
Matches: 864, Mismatches: 26, Indels: 35
0.93 0.03 0.04
Matches are distributed among these distances:
385 6 0.01
386 41 0.05
387 3 0.00
388 45 0.05
389 10 0.01
390 6 0.01
391 2 0.00
392 24 0.03
393 667 0.77
394 28 0.03
395 32 0.04
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.32
Consensus pattern (393 bp):
AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCCTTTTAAAG
CCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTCTGTTTA
AAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCACTCTTTAA
AGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTTTT
CAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCT
TTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
CCT
Found at i:3518535 original size:27 final size:27
Alignment explanation
Indices: 3518476--3518529 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
3518466 CACTCTTTTT
*
3518476 CCTTCTAAGCCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
*
3518503 CCTTTTAAGCCCATAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
3518530 TTTTTTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCCGTGGCAC
Found at i:3518573 original size:97 final size:95
Alignment explanation
Indices: 3517333--3518605 Score: 994
Period size: 97 Copynumber: 13.1 Consensus size: 95
3517323 GGCATTTTTT
* * * *
3517333 CTTTAAAGCCCACAACTCCGTGGCACCTTGTTC-CTTTTAAGTCCACAACTCCGTGGCACC--C-
1 CTTTTAAGCCCACAACTCCGTGGCACCTTTTTCTCTTTAAAGCCCACAACTCCGTGGCACCTTCT
*
3517394 --TTTT-AAAGCCCACAATTCCGTGGCACTTTTTTC
66 TTTTTTCAAAGCCCACAACTCCGTGGCAC------C
* * *
3517427 ATCTTTAAGTCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTT
1 CT-TTTAAGCCCACAACTCCGTGGCACCTTTTTCTCTTTAAAGCCCACAACTCCGTGGCAC-CTT
* * *
3517492 TTTCTCTTTTCAAAGCCCACGACTCCGTGGCACT
64 CTT-T-TTTTCAAAGCCCACAACTCCGTGGCACC
* * *
3517526 CTTTAAAGCCCACAACTCCGTGGCACCTTCTTCT-TTTCAAAGCCCACAACTCTGTGGCACCTTC
1 CTTTTAAGCCCACAACTCCGTGGCACCTTTTTCTCTTT-AAAGCCCACAACTCCGTGGCACCTTC
* *
3517590 TTCTTTTCAAAGCCCACAACTCTGTGGCACCTTC
65 TTTTTTTCAAAGCCCACAACTCCGTGGCA-C--C
* * *
3517624 TTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCT-TTTCAAAGCCCACGACTCCGTGGCA-
1 --CTTTT--AAGCCCACAACTCCGTGGCACCTTTTTCTCTTT-AAAGCCCACAACTCCGTGGCAC
3517687 C-TC--TTTTT-AAAGCCCACAACTCCGTGGCACTC
61 CTTCTTTTTTTCAAAGCCCACAACTCCGTGGCAC-C
* *
3517719 TTTTTCCTCCTAAGCCCACAACTCTGTGGCACTCTTTTTC-CTTCT-AAGCCCACAACTCCGTGG
1 --CTT--T--TAAGCCCACAACTCCGTGGCAC-CTTTTTCTCTT-TAAAGCCCACAACTCCGTGG
*
3517782 CACC--C---TTTT-AAAGCCCACAATTCCGTGGCACTTTTTTC
58 CACCTTCTTTTTTTCAAAGCCCACAACTCCGTGGCAC------C
* * * *
3517820 ATCTTTAAGTCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCATAACTCCGTGGCACTCTT
1 CT-TTTAAGCCCACAACTCCGTGGCACCTTTTTCTCTTTAAAGCCCACAACTCCGTGGCAC-CTT
* * *
3517885 TTTCTCTTTTCAAAGCCCACGACTCCGTGGCACT
64 CTT-T-TTTTCAAAGCCCACAACTCCGTGGCACC
* * *
3517919 CTTTAAAGCCCACAACTCCGTGGCACCTTCTTCT-TTTCAAAGCCCACAACTCTGTGGCACCTTC
1 CTTTTAAGCCCACAACTCCGTGGCACCTTTTTCTCTTT-AAAGCCCACAACTCCGTGGCACCTTC
* *
3517983 TTCTTTTCAAAGCCCACAACTCTGTGGCACCTTC
65 TTTTTTTCAAAGCCCACAACTCCGTGGCA-C--C
* * *
3518017 TTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCT-TTTCAAAGCCCACGACTCCGTGGCA-
1 --CTTTT--AAGCCCACAACTCCGTGGCACCTTTTTCTCTTT-AAAGCCCACAACTCCGTGGCAC
3518080 C-TC--TTTTT-AAAGCCCACAACTCCGTGGCACTC
61 CTTCTTTTTTTCAAAGCCCACAACTCCGTGGCAC-C
* *
3518112 TTTTTCCTCCTAAGCCCACAACTCTGTGGCACTCTTTTTC-CTTCT-AAGCCCACAACTCCGTGG
1 --CTT--T--TAAGCCCACAACTCCGTGGCAC-CTTTTTCTCTT-TAAAGCCCACAACTCCGTGG
*
3518175 CACC--C---TTTT-AAAGCCCACAATTCCGTGGCACTTTTTTC
58 CACCTTCTTTTTTTCAAAGCCCACAACTCCGTGGCAC------C
* * *
3518213 ATCTTTAAGTCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTT
1 CT-TTTAAGCCCACAACTCCGTGGCACCTTTTTCTCTTTAAAGCCCACAACTCCGTGGCAC-CTT
* * *
3518278 TTTCTCTTTTCAAAGCCCACGACTCCGTGGCACT
64 CTT-T-TTTTCAAAGCCCACAACTCCGTGGCACC
* * *
3518312 CTTTAAAGCCCACAACTCCGTGGCACCTTCTTCT-TTTCAAAGCCCACAACTCTGTGGCACCTTC
1 CTTTTAAGCCCACAACTCCGTGGCACCTTTTTCTCTTT-AAAGCCCACAACTCCGTGGCACCTTC
* *
3518376 TTCTTTTCAAAGCCCACGACTCCGTGGCACTC
65 TTTTTTTCAAAGCCCACAACTCCGTGGCAC-C
* * *
3518408 TTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC-CTCCT-AAGCCCACAACTCTGTGGCA-C-
1 CTTTT-AAGCCCACAACTCCGTGGCAC-CTTTTTCTCT-TTAAAGCCCACAACTCCGTGGCACCT
*
3518469 TCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACC
63 TCTTTTT--TTCAAAGCCCACAACTCCGTGGCACC
* * * * *
3518504 CTTTTAAGCCCATAACTCCGTGGCACTTTTTTCATCTTT-AAGTCCATAACTCCGTGACACCTTT
1 CTTTTAAGCCCACAACTCCGTGGCACCTTTTTC-TCTTTAAAGCCCACAACTCCGTGGCACC-TT
* * *
3518568 TTTTTCTTTTAAAGCCCACAACTCCGTGGCACT
64 CTTTT-TTTCAAAGCCCACAACTCCGTGGCACC
3518601 CTTTT
1 CTTTT
3518606 TCCCTTTTAA
Statistics
Matches: 992, Mismatches: 96, Indels: 179
0.78 0.08 0.14
Matches are distributed among these distances:
94 7 0.01
95 174 0.18
96 174 0.18
97 243 0.24
98 189 0.19
99 11 0.01
100 14 0.01
101 6 0.01
102 102 0.10
104 12 0.01
105 60 0.06
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.32
Consensus pattern (95 bp):
CTTTTAAGCCCACAACTCCGTGGCACCTTTTTCTCTTTAAAGCCCACAACTCCGTGGCACCTTCT
TTTTTTCAAAGCCCACAACTCCGTGGCACC
Found at i:3518591 original size:36 final size:34
Alignment explanation
Indices: 3518504--3518638 Score: 137
Period size: 35 Copynumber: 3.9 Consensus size: 34
3518494 CCGTGGCACC
*
3518504 CTTTTAAGCCCATAACTCCGTGGCACTTTTTTCAT
1 CTTTTAAGCCCACAACTCCGTGGCACTTTTTT-AT
* * * *
3518539 C-TTTAAGTCCATAACTCCGTGACACCTTTTTTTT
1 CTTTTAAGCCCACAACTCCGTGGCA-CTTTTTTAT
**
3518573 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 CTTTT-AAGCCCACAACTCCGTGGCACT-TTTTTAT
* *
3518609 CTTTTAAGTCCACAACTCCATGGCATCTTT
1 CTTTTAAGCCCACAACTCCGTGGCA-CTTT
3518639 CTCCCTTCCT
Statistics
Matches: 85, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
34 23 0.27
35 33 0.39
36 29 0.34
ACGTcount: A:0.21, C:0.30, G:0.10, T:0.39
Consensus pattern (34 bp):
CTTTTAAGCCCACAACTCCGTGGCACTTTTTTAT
Found at i:3518644 original size:34 final size:34
Alignment explanation
Indices: 3518502--3518645 Score: 137
Period size: 36 Copynumber: 4.1 Consensus size: 34
3518492 CTCCGTGGCA
*
3518502 CCCTTTTAAGCCCATAACTCCGTGGCA-CTTTTT
1 CCCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
* * * * * *
3518535 TCATCTTTAAGTCCATAACTCCGTGACACCTTTTTT
1 CCCT-TTTAAGCCCACAACTCCGTGGCATC-TTTTT
**
3518571 TTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCCTTTT-AAGCCCACAACTCCGTGGCA-TCTTTTT
* * *
3518607 CCCTTTTAAGTCCACAACTCCATGGCATCTTTCT
1 CCCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
3518641 CCCTT
1 CCCTT
3518646 CCTAAAGCCC
Statistics
Matches: 91, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
33 2 0.02
34 32 0.35
35 22 0.24
36 34 0.37
37 1 0.01
ACGTcount: A:0.19, C:0.33, G:0.10, T:0.38
Consensus pattern (34 bp):
CCCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
Found at i:3518652 original size:71 final size:70
Alignment explanation
Indices: 3518509--3518658 Score: 169
Period size: 71 Copynumber: 2.1 Consensus size: 70
3518499 GCACCCTTTT
* * * * **
3518509 AAGCCCATAACTCCGTGGCACTTTTTTCATCTTTAAGTCCATAACTCCGTGACACCTTTTTTTTC
1 AAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCATGACACCTTTTCTCCC
*
3518574 TTTTA
66 TTCTA
* * *
3518579 AAGCCCACAACTCCGTGGCACTCTTTTTC-CCTTTTAAGTCCACAACTCCATGGCATC-TTTCTC
1 AAGCCCACAACTCCGTGGCACT-TTTTTCATC-TTTAAGTCCACAACTCCATGACACCTTTTCTC
3518642 CCTTCCTA
64 CCTT-CTA
3518650 AAGCCCACA
1 AAGCCCACA
3518659 CAAGTCGGTG
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
70 29 0.43
71 38 0.57
ACGTcount: A:0.22, C:0.33, G:0.10, T:0.35
Consensus pattern (70 bp):
AAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCATGACACCTTTTCTCCC
TTCTA
Found at i:3518686 original size:33 final size:35
Alignment explanation
Indices: 3518643--3518712 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 35
3518633 ATCTTTCTCC
3518643 CTTCCTAAAGCCCACACAAGTCGGTGGCAA-CCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
3518677 CTTCC-AAAGCCCACACAAGTCGGTGGCAACCCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
3518711 CT
1 CT
3518713 AAGCCCAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 24 0.69
34 11 0.31
ACGTcount: A:0.26, C:0.37, G:0.17, T:0.20
Consensus pattern (35 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
Found at i:3518776 original size:49 final size:49
Alignment explanation
Indices: 3518712--3519186 Score: 536
Period size: 49 Copynumber: 9.9 Consensus size: 49
3518702 GCAACCCTTC
*
3518712 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* *
3518761 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* *
3518804 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
*
3518853 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* * *
3518902 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
*
3518945 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* *
3518994 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
*
3519037 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTT
* * ** *
3519089 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAT-C----T-TCATCTT
* * * * *
3519144 TAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTT
3519187 TATCACTCTT
Statistics
Matches: 361, Mismatches: 38, Indels: 54
0.80 0.08 0.12
Matches are distributed among these distances:
43 115 0.32
45 5 0.01
47 2 0.01
49 160 0.44
50 5 0.01
52 35 0.10
54 1 0.00
55 37 0.10
56 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
Found at i:3518870 original size:92 final size:88
Alignment explanation
Indices: 3518712--3519120 Score: 435
Period size: 92 Copynumber: 4.4 Consensus size: 88
3518702 GCAACCCTTC
* *
3518712 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATAGCT
*
3518777 GGCCTTGAATCAGCACATTGGCA-C-CTT
60 GGCCTTGAATCAGCATATTGGCATCACTT
* *
3518804 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCT
1 TAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATAGCT
3518869 GGCCTTGAATCAGCATATTGGCATCTTCATCTT
60 GGCCTTGAATCAGCATATTGGCA---TCA-CTT
* * * *
3518902 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
1 TAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
3518967 GAATCAGCATATTGGCATCTTCATCTT
66 GAATCAGCATATTGGCA---TCA-CTT
* *
3518994 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
1 TAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
3519059 GAATCAGCATATTGGCACATTTTCCATCTT
66 GAATCAGCATATTGG--CA---T-CA-CTT
** *
3519089 TAAGTTCAATGTAGCTGGCCTTGAATCAGCAC
1 TAAGCCCAATATAGCTGGCCTTGAATCAGCAC
3519121 GTTGACATCC
Statistics
Matches: 296, Mismatches: 12, Indels: 15
0.92 0.04 0.05
Matches are distributed among these distances:
92 214 0.72
94 6 0.02
95 37 0.12
96 1 0.00
98 38 0.13
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (88 bp):
TAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
GAATCAGCATATTGGCATCACTT
Found at i:3518971 original size:141 final size:141
Alignment explanation
Indices: 3518712--3519076 Score: 598
Period size: 141 Copynumber: 2.6 Consensus size: 141
3518702 GCAACCCTTC
*
3518712 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCT
3518777 GGCCTTGAATCAGCACATTGGCACCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGC
66 GGCCTTGAATCAGCACATTGGCACCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGC
3518842 ACCTTCATCTT
131 ACCTTCATCTT
*
3518853 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCT
* * *
3518918 GGCCTTGACTCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
66 GGCCTTGAATCAGCACATTGGCACCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGC
*
3518983 ATCTTCATCTT
131 ACCTTCATCTT
* * *
3518994 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCT
*
3519053 GGCCTTGAATCAGCATATTGGCAC
66 GGCCTTGAATCAGCACATTGGCAC
3519077 ATTTTCCATC
Statistics
Matches: 212, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
135 40 0.19
137 1 0.00
141 171 0.81
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (141 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCT
GGCCTTGAATCAGCACATTGGCACCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGC
ACCTTCATCTT
Found at i:3519104 original size:52 final size:54
Alignment explanation
Indices: 3519034--3519182 Score: 176
Period size: 52 Copynumber: 2.8 Consensus size: 54
3519024 ACATTGGCAC
3519034 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
* * ** * *
3519086 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCATTTTCTCAT
* * * * *
3519141 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
3519183 TCTTTATCAC
Statistics
Matches: 78, Mismatches: 16, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
52 37 0.47
54 6 0.08
55 35 0.45
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.34
Consensus pattern (54 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
Found at i:3519324 original size:171 final size:171
Alignment explanation
Indices: 3519034--3519428 Score: 691
Period size: 171 Copynumber: 2.3 Consensus size: 171
3519024 ACATTGGCAC
*
3519034 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTTCAAT
3519099 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
63 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
3519164 ATGAATCAACATATTGGCATCTTTATCACTCTTCTCATCATCAT
128 ATGAATCAACATATTGGCATCTTTATCACTCTTCTCATCATCAT
* *
3519208 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
*
3519273 GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATG
66 GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
* *
3519338 AATCAACATATTGGCATCTTTATCACTTTTCTCATCTTCAT
131 AATCAACATATTGGCATCTTTATCACTCTTCTCATCATCAT
* *
3519379 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
3519429 ATCTCTAAAA
Statistics
Matches: 212, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
171 169 0.80
172 5 0.02
174 38 0.18
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (171 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
AATCAACATATTGGCATCTTTATCACTCTTCTCATCATCAT
Found at i:3520264 original size:33 final size:33
Alignment explanation
Indices: 3520227--3520293 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3520217 TTCAACGATT
3520227 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
3520260 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
3520293 T
1 T
3520294 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:3520265 original size:13 final size:13
Alignment explanation
Indices: 3520247--3520271 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3520237 CATAAAATGT
3520247 TGTATCGATACAA
1 TGTATCGATACAA
3520260 TGTATCGATACA
1 TGTATCGATACA
3520272 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3520355 original size:13 final size:13
Alignment explanation
Indices: 3520337--3520361 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3520327 ATTACTCACA
3520337 TGTATCGATACAT
1 TGTATCGATACAT
3520350 TGTATCGATACA
1 TGTATCGATACA
3520362 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3520498 original size:52 final size:52
Alignment explanation
Indices: 3520370--3520490 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
3520360 CACTGATCTT
*
3520370 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
3520422 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
3520474 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
3520491 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:3522216 original size:33 final size:33
Alignment explanation
Indices: 3522179--3522245 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3522169 TTCAACGATT
3522179 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
3522212 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
3522245 T
1 T
3522246 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:3522217 original size:13 final size:13
Alignment explanation
Indices: 3522199--3522223 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3522189 CATAAAATGT
3522199 TGTATCGATACAA
1 TGTATCGATACAA
3522212 TGTATCGATACA
1 TGTATCGATACA
3522224 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3522307 original size:13 final size:13
Alignment explanation
Indices: 3522289--3522313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3522279 ATTACTCACA
3522289 TGTATCGATACAT
1 TGTATCGATACAT
3522302 TGTATCGATACA
1 TGTATCGATACA
3522314 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3532917 original size:13 final size:13
Alignment explanation
Indices: 3532899--3532928 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3532889 GTAAACCCAG
3532899 AATGTATCCATAC
1 AATGTATCCATAC
*
3532912 AATGTATCGATAC
1 AATGTATCCATAC
3532925 AATG
1 AATG
3532929 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (13 bp):
AATGTATCCATAC
Found at i:3532952 original size:62 final size:63
Alignment explanation
Indices: 3532850--3532978 Score: 197
Period size: 62 Copynumber: 2.1 Consensus size: 63
3532840 AAAATGCTTG
* * * *
3532850 AATGTATCGATACATTGAAAAATGTATTGATACATTTGGGT-AAACCCAGAATGTATCCATAC
1 AATGTATCGATACAATGAAAAATGTATCGATACATCTGGGTAAAACCCAAAATGTATCCATAC
* *
3532912 AATGTATCGATACAATGAACAATGTATCGATACATCTGGGTAAAACCCAAAATGTATCGATAC
1 AATGTATCGATACAATGAAAAATGTATCGATACATCTGGGTAAAACCCAAAATGTATCCATAC
3532975 AATG
1 AATG
3532979 AACAATATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
62 37 0.62
63 23 0.38
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (63 bp):
AATGTATCGATACAATGAAAAATGTATCGATACATCTGGGTAAAACCCAAAATGTATCCATAC
Found at i:3533048 original size:21 final size:21
Alignment explanation
Indices: 3533022--3533067 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3533012 AATTTTTGAC
*
3533022 CATTAAGACCTTGTATCGATA
1 CATTAAGACCATGTATCGATA
**
3533043 CATTAAGGGCATGTATCGATA
1 CATTAAGACCATGTATCGATA
3533064 CATT
1 CATT
3533068 TTGGAAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (21 bp):
CATTAAGACCATGTATCGATA
Found at i:3540325 original size:20 final size:20
Alignment explanation
Indices: 3540278--3540352 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
3540268 AAAAAGACAT
*
3540278 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
3540297 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
3540318 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
3540338 AATGTATCGATACAT
1 AATGTATCGATACAT
3540353 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:3540346 original size:40 final size:39
Alignment explanation
Indices: 3540275--3540352 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
3540265 GGTAAAAAGA
* *
3540275 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
3540314 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
3540353 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:3541401 original size:229 final size:229
Alignment explanation
Indices: 3540866--3541764 Score: 1339
Period size: 229 Copynumber: 3.9 Consensus size: 229
3540856 ATAGGGGTGA
* * * * *
3540866 TTTGAAAAGGGTTGCCATTGACTTGCATGGGCTTT-AAAAGGGTGCCACTGACTTGCGTGGACTT
1 TTTG-AAAGGG-TGCCACTAACTTG--TGGGCTTTGAAAAGAGTGCCACTGACTT-TGTGGGCTT
* * * * *
3540930 TGAAAGAATGCCACTAACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGT
61 TGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGT
* * *
3540995 GCCACTGACTTGTGGGCTTTGAAAAG-GTACCACTGACTTGCGTGAGCTTT-AAAAGGAGTGCCA
126 GCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGA-TT-TGTGGGCTTTGAAAA-GAGTGCCA
*
3541058 CTGACTTGTGTGGGCTTTAAAAGG-GTGCCACTGACTTGTGGGC
188 CTGAC-T-TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
** * * *
3541101 TTTGAAAAAGTGCCACTGAA-TTGTGGGCTTTGCAATG-GTGCCACTGAC-TTGTGGGCTTCGAA
1 TTTGAAAGGGTGCCACT-AACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTTGTGGGCTTTGAA
* * *
3541163 AGGGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCA
65 AGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
3541228 CTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTT
130 CTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTT
*
3541293 GTGGGCTTTGAAAGGAGTGCCACTAACTTGTGGGC
195 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
3541328 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGA-TTTGTGGGCTTTGAAA
1 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTTGTGGGCTTTG-AA
* *
3541392 AGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGGCACTGAGTTGTGGGCTTTGAAAGGGTGCCA
65 AGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
*
3541457 CTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTT
130 CTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTT
3541522 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
195 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* *
3541557 TTTGAAAGGGTGCCACTCACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTT-TGGGCTTTGAAA
1 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTTGTGGGCTTTGAAA
*
3541621 GGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCAC
66 GAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCAC
* * *
3541686 TGACTTATGGGCTTTGAAAAGAGTGCCATTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTG
131 TGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
3541751 TGGGCTTTGAAAGG
196 TGGGCTTTGAAAGG
3541765 GATGAACATT
Statistics
Matches: 613, Mismatches: 41, Indels: 27
0.90 0.06 0.04
Matches are distributed among these distances:
226 17 0.03
227 49 0.08
228 184 0.30
229 310 0.51
230 13 0.02
231 19 0.03
232 3 0.00
233 9 0.01
234 5 0.01
235 4 0.01
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (229 bp):
TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTTGTGGGCTTTGAAA
GAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCAC
TGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
Found at i:3541763 original size:29 final size:29
Alignment explanation
Indices: 3540878--3541764 Score: 1252
Period size: 28 Copynumber: 30.9 Consensus size: 29
3540868 TGAAAAGGGT
* *
3540878 TGCCATTGACTTGCATGGGCTTTAAAAGG-G
1 TGCCACTGACTTG--TGGGCTTTGAAAGGAG
* *
3540908 TGCCACTGACTTGCGTGGACTTTGAAA-GAA
1 TGCCACTGACTT--GTGGGCTTTGAAAGGAG
* *
3540938 TGCCACTAACTCGTGGGCTTTGAAAGGA-
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3540966 TGCCACTGACTTGTGGGCTTTGAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3540994 TGCCACTGACTTGTGGGCTTTGAAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
3541022 TACCACTGACTTGCGTGAGCTTTAAAAGGAG
1 TGCCACTGACTT--GTGGGCTTTGAAAGGAG
*
3541053 TGCCACTGACTTGTGTGGGCTTTAAAAGG-G
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGGAG
*
3541083 TGCCACTGACTTGTGGGCTTTGAAA-AAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
3541111 TGCCACTGAATTGTGGGCTTTGCAATG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3541139 TGCCACTGACTTGTGGGCTTCGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3541167 TGCCACTGACTTGTGGGCTCTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3541195 TGCCACTAACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3541223 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3541252 TGCCACTGATTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3541281 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3541310 TGCCACTAACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3541338 TGCCACTAACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3541367 TGCCACTGATTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3541396 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3541424 TGGCACTGAGTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3541452 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3541481 TGCCACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3541510 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3541539 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3541567 TGCCACTCACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3541596 TGCCACTGACTTTTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3541624 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3541652 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3541680 TGCCACTGACTTATGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3541709 TGCCATTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3541738 TGCCACTGACTTGTGGGCTTTGAAAGG
1 TGCCACTGACTTGTGGGCTTTGAAAGG
3541765 GATGAACATT
Statistics
Matches: 780, Mismatches: 59, Indels: 37
0.89 0.07 0.04
Matches are distributed among these distances:
27 2 0.00
28 397 0.51
29 300 0.38
30 54 0.07
31 24 0.03
32 2 0.00
33 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (29 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGAG
Found at i:3542421 original size:18 final size:18
Alignment explanation
Indices: 3542400--3542435 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3542390 TTTTTGCTAT
3542400 TTTTTTTCTTTTTTTTTG
1 TTTTTTTCTTTTTTTTTG
*
3542418 TTTTTTTGTTTTTTTTTG
1 TTTTTTTCTTTTTTTTTG
3542436 GGTGTAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (18 bp):
TTTTTTTCTTTTTTTTTG
Found at i:3542435 original size:10 final size:10
Alignment explanation
Indices: 3542389--3542435 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
3542379 GACCCTTCTA
3542389 TTTTTTGCTATT
1 TTTTTTG-T-TT
*
3542401 TTTTTTCTTT
1 TTTTTTGTTT
3542411 TTTTTTG--T
1 TTTTTTGTTT
3542419 TTTTTTGTTT
1 TTTTTTGTTT
3542429 TTTTTTG
1 TTTTTTG
3542436 GGTGTAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
8 8 0.26
10 16 0.52
11 1 0.03
12 6 0.19
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:3556477 original size:40 final size:39
Alignment explanation
Indices: 3556429--3556506 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
3556419 GGTAAAAAGA
* * *
3556429 CATAATGTATCGATACATTGTAGAATTTATCGATACATT
1 CATAATGTATCGATACATTGAAAAATGTATCGATACATT
*
3556468 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATGTATCGATACAT
3556507 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATGTATCGATACATT
Found at i:3556479 original size:20 final size:20
Alignment explanation
Indices: 3556432--3556506 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
3556422 AAAAAGACAT
*
3556432 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
3556451 GAATTTATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
3556472 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
3556492 AATGTATCGATACAT
1 AATGTATCGATACAT
3556507 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:3558541 original size:13 final size:12
Alignment explanation
Indices: 3558519--3558553 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
3558509 CCTTCTTTTT
3558519 AAAAAAAAAACA
1 AAAAAAAAAACA
3558531 AAAAAACAAAACA
1 AAAAAA-AAAACA
3558544 AAGAAAAAAA
1 AA-AAAAAAA
3558554 GAGAGAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.29
13 11 0.52
14 4 0.19
ACGTcount: A:0.89, C:0.09, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:3559904 original size:60 final size:60
Alignment explanation
Indices: 3559661--3560005 Score: 383
Period size: 60 Copynumber: 5.9 Consensus size: 60
3559651 GAGTAGGACG
*
3559661 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAATCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * *
3559721 CGTTTTAAAGCTCACACAAGTTGGTGGCACTTTTTTAGTCCTCAAAGAGCAGGACG------
1 CCTTTCAAAGCCCACACAAGTTGGTGGCAC--CTTCAGTCCTCAAAGAGCAGGACGCCTTTT
** *
3559777 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCATGACG------
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
3559832 CCTTTCAAAGCCCATACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTT
** * * * *
3559892 CCTTTCAAAGCCCACGTAAGCTGGTGGCACCTTCAATCCTCAAAGAGCAGGACACCTTCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTT
*
3559952 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGAC
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT--CAGTCCTCAAAGAGCAGGAC
3560006 ACTCTCTCCT
Statistics
Matches: 244, Mismatches: 30, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
54 22 0.09
55 48 0.20
56 26 0.11
59 3 0.01
60 105 0.43
61 19 0.08
62 21 0.09
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.24
Consensus pattern (60 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:3560057 original size:269 final size:271
Alignment explanation
Indices: 3559754--3560275 Score: 760
Period size: 269 Copynumber: 1.9 Consensus size: 271
3559744 GTGGCACTTT
* *
3559754 TTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
1 TTTAGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
* * * * *
3559819 AAAGAGCATGACGCCTTTCAAAGCCCATACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGA
66 AAAGAGCAAGACACCTTCCAAAGCCCACACAAGCTGGTGGCACCTTCAATCCTCAAAGAGCAGGA
** * ** *
3559884 TGCCTTTTCC-TTTCAAAGCCCACGTAAGCTGGTGGCACCTTC-AATCCTCAAAGAGCAGGACAC
131 CACCTTTTCCTTTTAAAAGCCCACACAAGCTGGAGGCACCTTCTAATCCTCAAAGAGCAGGACAC
3559947 CTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACACTCTC
196 CTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACACTCTC
3560012 TCCTTTCACCC
261 TCCTTTCACCC
* *
3560023 TTTAGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACATGTTGGTGGCATTTTCTAGTCCTC
1 TTTAGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
* * *
3560088 AAAGAGCAAGACACCTTCCAAAGCTCACCCAAGCTGGTGGCACCTTCAATTCTCAAAGAGCAGGA
66 AAAGAGCAAGACACCTTCCAAAGCCCACACAAGCTGGTGGCACCTTCAATCCTCAAAGAGCAGGA
* * * **
3560153 CATCTTTTCCTTTTAAAAGCCCACACAAGTTGGAGGCACCTTCTAGTCCTCAAAGAGCAGGACGT
131 CACCTTTTCCTTTTAAAAGCCCACACAAGCTGGAGGCACCTTCTAATCCTCAAAGAGCAGGACAC
* * * ** * *
3560218 TTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTTAAGGAGCAGGA
196 CTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGA
3560276 TGCCTTTTCC
Statistics
Matches: 221, Mismatches: 30, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
269 125 0.57
270 27 0.12
271 69 0.31
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (271 bp):
TTTAGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
AAAGAGCAAGACACCTTCCAAAGCCCACACAAGCTGGTGGCACCTTCAATCCTCAAAGAGCAGGA
CACCTTTTCCTTTTAAAAGCCCACACAAGCTGGAGGCACCTTCTAATCCTCAAAGAGCAGGACAC
CTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACACTCTC
TCCTTTCACCC
Found at i:3560239 original size:61 final size:62
Alignment explanation
Indices: 3560106--3560474 Score: 385
Period size: 61 Copynumber: 6.0 Consensus size: 62
3560096 AGACACCTTC
* * * * * *
3560106 CAAAGCTCACCCAAGCTGGTGGCACCTTC-AATTCTCAAAGAGCAGGACATCTTTTCCTTTT
1 CAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTT
* * *
3560167 AAAAGCCCACACAAGTTGGAGGCACCTTCTAGTCCTCAAAGAGCAGGACGTTTTTTCCTTTT
1 CAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTT
* * * * * *
3560229 -AAAGCCCACACAAGTTGGTGGCA-TTTTTCAGTCCTTAAGGAGCAGGATGCCTTTTCC-TTT
1 CAAAGCCCACACAAGTTGGTGGCACCTTCT-AGTCCTCAAAGAGCAGGACGTCTTTTCCTTTT
* * * ** *
3560289 CAAAGCCCACATAAGCTGGTGGCACCTTC-AGTCCTCAAAAAAGCAGGACACCTTTTTCTTTT
1 CAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTC-AAAGAGCAGGACGTCTTTTCCTTTT
* * *
3560351 CAAAGCCCACACAAGTTGGTGGCACC-TCTTAGTCCTCAAAGAGTAGGAC-ACCTTTCCTTTT
1 CAAAGCCCACACAAGTTGGTGGCACCTTC-TAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTT
* * * * *
3560412 CAAAGCCCATACGAGTTGGTGGCA-CTTTTCAGTCCTTAAAGAGCAAGACGTCTTTTCCTTTT
1 CAAAGCCCACACAAGTTGGTGGCACCTTCT-AGTCCTCAAAGAGCAGGACGTCTTTTCCTTTT
3560474 C
1 C
3560475 TCCTTTGTCC
Statistics
Matches: 255, Mismatches: 42, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
60 14 0.05
61 156 0.61
62 78 0.31
63 7 0.03
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28
Consensus pattern (62 bp):
CAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTT
Found at i:3560368 original size:184 final size:183
Alignment explanation
Indices: 3560048--3560472 Score: 535
Period size: 184 Copynumber: 2.3 Consensus size: 183
3560038 ACAGGACACC
* * *
3560048 TTTCAAAGCCCACACATGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAAGACACC--TT-C---
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTTAAAGAGCAAGACGCCTTTTCCTTT
* ** * * *
3560106 CAAAGCTCACCCAAGCTGGTGGCACCTTCAATTCTCAAAGAGCAGGACATCTTTTCCTTTTAAAA
65 CAAAGCCCACATAAGCTGGTGGCACCTTCAATCCTCAAAAAGCAGGACACCTTTTCCTTTTAAAA
***
3560171 GCCCACACAAGTTGGAGGCACCT-TCTAGTCCTCAAAGAGCAGGACGTTTTTTCCT
130 GCCCACACAAGTTGGAGGCACCTCT-TAGTCCTCAAAGAGCAGGAC-ACCTTTCCT
* * * *
3560226 TTT-AAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTTAAGGAGCAGGATGCCTTTTCCTTTC
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTTAAAGAGCAAGACGCCTTTTCCTTTC
* * *
3560290 AAAGCCCACATAAGCTGGTGGCACCTTCAGTCCTCAAAAAAGCAGGACACCTTTTTCTTTTCAAA
66 AAAGCCCACATAAGCTGGTGGCACCTTCAATCCTC-AAAAAGCAGGACACCTTTTCCTTTTAAAA
* *
3560355 GCCCACACAAGTTGGTGGCACCTCTTAGTCCTCAAAGAGTAGGACACCTTTCCT
130 GCCCACACAAGTTGGAGGCACCTCTTAGTCCTCAAAGAGCAGGACACCTTTCCT
* * *
3560409 TTTCAAAGCCCATACGAGTTGGTGGCACTTTTCAGTCCTTAAAGAGCAAGACGTCTTTTCCTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTTAAAGAGCAAGACGCCTTTTCCTTT
3560473 TCTCCTTTGT
Statistics
Matches: 210, Mismatches: 27, Indels: 14
0.84 0.11 0.06
Matches are distributed among these distances:
177 39 0.19
178 8 0.04
179 2 0.01
180 1 0.00
183 40 0.19
184 119 0.57
185 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28
Consensus pattern (183 bp):
TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTTAAAGAGCAAGACGCCTTTTCCTTTC
AAAGCCCACATAAGCTGGTGGCACCTTCAATCCTCAAAAAGCAGGACACCTTTTCCTTTTAAAAG
CCCACACAAGTTGGAGGCACCTCTTAGTCCTCAAAGAGCAGGACACCTTTCCT
Found at i:3560385 original size:123 final size:122
Alignment explanation
Indices: 3560048--3560473 Score: 392
Period size: 123 Copynumber: 3.5 Consensus size: 122
3560038 ACAGGACACC
* ** * *
3560048 TTTCAAAGCCCACACATGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAAGACACC---TTCC---
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTC-AGTCCTCAAAAAGCAGGAC-CCTTTTTCCTTT
* * * * * *
3560107 -AAAGCTCACCCAAGCTGGTGGCAC-CTTCAATTCTCAAAGAGCAGGACATCTTTTCCT
64 TAAAGCCCACACAAGTTGGTGGCACTCTTCAGTCCTCAAAGAGCAGGACACCTTTTCCT
* * * **
3560164 TTTAAAAGCCCACACAAGTTGGAGGCACCTTCTAGTCCTCAAAGAGCAGGACGTTTTTTCCTTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTC-AGTCCTCAAAAAGCAGGACCCTTTTTCCTTTT
* * * * **
3560229 AAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTTAAGGAGCAGGATGCCTTTTCC-
65 AAAGCCCACACAAGTTGGTGGCACTCTTCAGTCCTCAAAGAGCAGGACACCTTTTCCT
* *
3560286 TTTCAAAGCCCACATAAGCTGGTGGCACCTTCAGTCCTCAAAAAAGCAGGACACCTTTTT-CTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTC-AAAAAGCAGGAC-CCTTTTTCCTTT
*
3560350 TCAAAGCCCACACAAGTTGGTGGCACCTCTT-AGTCCTCAAAGAGTAGGACACC-TTTCCT
64 T-AAAGCCCACACAAGTTGGTGGCA-CTCTTCAGTCCTCAAAGAGCAGGACACCTTTTCCT
* * * * * * *
3560409 TTTCAAAGCCCATACGAGTTGGTGGCACTTTTCAGTCCTTAAAGAGCAAGA-CGTCTTTTCCTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAAAGCAGGACCCT-TTTTCCTTT
3560473 T
64 T
3560474 CTCCTTTGTC
Statistics
Matches: 251, Mismatches: 43, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
116 46 0.18
118 4 0.02
121 9 0.04
122 73 0.29
123 107 0.43
124 12 0.05
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28
Consensus pattern (122 bp):
TTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAAAGCAGGACCCTTTTTCCTTTTA
AAGCCCACACAAGTTGGTGGCACTCTTCAGTCCTCAAAGAGCAGGACACCTTTTCCT
Found at i:3560474 original size:123 final size:121
Alignment explanation
Indices: 3560106--3560474 Score: 400
Period size: 123 Copynumber: 3.0 Consensus size: 121
3560096 AGACACCTTC
* * * * * * * *
3560106 CAAAGCTCACCCAAGCTGGTGGCACCTTCAATTCTCAAAGAGCAGGACATCTTTTCCTTTTAAAA
1 CAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACA-CCTTTCCTTTTCAAA
* * *
3560171 GCCCACACAAGTTGGAGGCACCTTCTAGTCCTCAAAGAGCAGGACGTTTTTTCCTTTT
65 GCCCACACAAGTTGGTGGCACCTTC-AGTCCTAAAAGAGCAGGACGTCTTTTCCTTTT
** * * **
3560229 -AAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTTAAGGAGCAGGATGCCTTTTCC-TTTCAA
1 CAAAGCCCACACAAGTTGGTGGCACCTTT-AGTCCTCAAAGAGCAGGACACC-TTTCCTTTTCAA
* * * ** *
3560292 AGCCCACATAAGCTGGTGGCACCTTCAGTCCTCAAAAAAGCAGGACACCTTTTTCTTTT
64 AGCCCACACAAGTTGGTGGCACCTTCAGTCCT-AAAAGAGCAGGACGTCTTTTCCTTTT
*
3560351 CAAAGCCCACACAAGTTGGTGGCACCTCTTAGTCCTCAAAGAGTAGGACACCTTTCCTTTTCAAA
1 CAAAGCCCACACAAGTTGGTGGCACCT-TTAGTCCTCAAAGAGCAGGACACCTTTCCTTTTCAAA
* * * * *
3560416 GCCCATACGAGTTGGTGGCACTTTTCAGTCCTTAAAGAGCAAGACGTCTTTTCCTTTT
65 GCCCACACAAGTTGGTGGCAC-CTTCAGTCCTAAAAGAGCAGGACGTCTTTTCCTTTT
3560474 C
1 C
3560475 TCCTTTGTCC
Statistics
Matches: 198, Mismatches: 41, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
121 6 0.03
122 76 0.38
123 105 0.53
124 11 0.06
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28
Consensus pattern (121 bp):
CAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACACCTTTCCTTTTCAAAG
CCCACACAAGTTGGTGGCACCTTCAGTCCTAAAAGAGCAGGACGTCTTTTCCTTTT
Found at i:3560527 original size:45 final size:43
Alignment explanation
Indices: 3560469--3560687 Score: 182
Period size: 45 Copynumber: 5.0 Consensus size: 43
3560459 ACGTCTTTTC
3560469 CTTTTCTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTT
1 CTTTTC-CCTTTGTCCTCAAAGAGCAGGACACATTT-ATTTCCTT
* * ** * *
3560514 CTTTTCCCTTTTGTCCTCAAAAAGCATGATGCCTTT-TTTTCTT
1 CTTTTCCC-TTTGTCCTCAAAGAGCAGGACACATTTATTTCCTT
* *
3560557 -TTTT-CCTTTGTCCTCAAAGAGCAGGACGA-ACTTCATTTACTT
1 CTTTTCCCTTTGTCCTCAAAGAGCAGGAC-ACA-TTTATTTCCTT
*
3560599 CTTTTCCCTTCTAGTTCTCAAAGAGCAGGATGCAC-TTTA-TT-CTT
1 CTTTTCCCTT-T-GTCCTCAAAGAGCAGGA--CACATTTATTTCCTT
* * *
3560643 CTTTTTCCTTTGTCCTAAAAAATGCAGGACACATTTAATTTCCTT
1 CTTTTCCCTTTGTCCTCAAAGA-GCAGGACACATTT-ATTTCCTT
3560688 TTTCTTTTAT
Statistics
Matches: 139, Mismatches: 19, Indels: 32
0.73 0.10 0.17
Matches are distributed among these distances:
40 18 0.13
41 7 0.05
42 21 0.15
43 18 0.13
44 20 0.14
45 34 0.24
46 19 0.14
47 1 0.01
48 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.42
Consensus pattern (43 bp):
CTTTTCCCTTTGTCCTCAAAGAGCAGGACACATTTATTTCCTT
Found at i:3560579 original size:85 final size:87
Alignment explanation
Indices: 3560464--3560687 Score: 285
Period size: 85 Copynumber: 2.6 Consensus size: 87
3560454 GCAAGACGTC
* * *
3560464 TTTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTTCCCTT-TTGT
1 TTTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTTCCCTTCTAGT
*
3560528 CCTCAAAAAGCATGATGC-CTT
66 CCTCAAAAAGCAGGATGCACTT
* *
3560549 TTTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGA-ACTTCATTTACTTCTTTTCCCTTCTAG
1 TTTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGAC-ACATTTCATTTCCTTCTTTTCCCTTCTAG
* *
3560613 TTCTCAAAGAGCAGGATGCACTT
65 TCCTCAAAAAGCAGGATGCACTT
* * *
3560636 TATTCTTC-TTTTTCCTTTGTCCTAAAAAATGCAGGACACATTTAATTTCCTT
1 T-TT-TTCTTTTTTCCTTTGTCCTCAAAGA-GCAGGACACATTTCATTTCCTT
3560688 TTTCTTTTAT
Statistics
Matches: 119, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
85 54 0.45
86 19 0.16
87 4 0.03
88 22 0.18
89 20 0.17
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.43
Consensus pattern (87 bp):
TTTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTTCCCTTCTAGT
CCTCAAAAAGCAGGATGCACTT
Found at i:3561451 original size:50 final size:49
Alignment explanation
Indices: 3561375--3561483 Score: 173
Period size: 50 Copynumber: 2.2 Consensus size: 49
3561365 TTTCACAATT
*
3561375 TGTATCGATACATTATTCATTATATCGATACATTCTGAGTTTCACCCAGA
1 TGTATCGATACATTATTCACTATATCGATACATTCTGAGTTT-ACCCAGA
* * *
3561425 TGTATCGATACATTGTTCACTGTATCGATACATTCTGGGTTTACCCAGA
1 TGTATCGATACATTATTCACTATATCGATACATTCTGAGTTTACCCAGA
3561474 TGTATCGATA
1 TGTATCGATA
3561484 TAATCGATAC
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
49 17 0.31
50 38 0.69
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (49 bp):
TGTATCGATACATTATTCACTATATCGATACATTCTGAGTTTACCCAGA
Found at i:3563924 original size:79 final size:78
Alignment explanation
Indices: 3563793--3564179 Score: 318
Period size: 79 Copynumber: 4.9 Consensus size: 78
3563783 TTTTCATCTC
*
3563793 GGGGATACTCCAACCCTGACTTTATTTCTAAAGTATCGATTTTCTACAATCGGAGATACTCCAAT
1 GGGGATACTCCAACCCCGACTTTATTTCTAAAGTATCGATTTTC-ACAATCGGAGATACTCCAAT
**
3563858 CCCGTTATTTTTTA
65 CCCGTTATTTTCCA
* * * * *
3563872 GGGGATACTCTAAGCCCGGCTTTATTTCT-ATGATATTGATTTCTCACAATCGGAGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCTAAAG-TATCGATTT-TCACAATCGGAGATACTCCAA
* *
3563936 TCTCGTTATTTTGGCA
64 TCCCGTTATTTT-CCA
* * * * * * *
3563952 -GGGATACTCCAACCCCGGCCTTATTGCTAAAGCATCAATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGACTTTATTTCTAAAGTATCGA-TTTTCACAATCGGAGATACTCCAAT
*
3564016 CCCGTTATTTTCGA
65 CCCGTTATTTTCCA
* * ** * * *
3564030 GGGGATACTCTAACCCCGATTTTATTT-TCAAAGCGTCAATTTTCTATAATCAGG-GATGCTCCA
1 GGGGATACTCCAACCCCGACTTTATTTCT-AAAGTATCGATTTTC-ACAATC-GGAGATACTCCA
**
3564093 A-CCCTGTTATTTTTGA
63 ATCCC-GTTATTTTCCA
* * * * * * *
3564109 GAGGATACTCCAACCCCGATTTTATTTCCTGAA-CATCGATTTTTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTT-CTAAAGTATCGA-TTTTCACAATCGGAGATACTCCAA
*
3564173 CCCCGTT
64 TCCCGTT
3564180 GTTATCCCCA
Statistics
Matches: 255, Mismatches: 38, Indels: 30
0.79 0.12 0.09
Matches are distributed among these distances:
78 14 0.05
79 220 0.86
80 20 0.08
81 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.34
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGACTTTATTTCTAAAGTATCGATTTTCACAATCGGAGATACTCCAATC
CCGTTATTTTCCA
Found at i:3564092 original size:158 final size:156
Alignment explanation
Indices: 3563794--3564179 Score: 406
Period size: 158 Copynumber: 2.4 Consensus size: 156
3563784 TTTCATCTCG
* * * * *
3563794 GGGATACTCCAACCCTGACTTTATTTCTAAAGTATCGA-TTTTCTACAATCGGAGATACTCCAAT
1 GGGATACTCCAACCCCGACTTTATTCCTAAAGCATCGATTTTTC-ACAATCGGGGATACTCCAAC
** * * * * *
3563858 CCCGTTATTTTTTAGGGGATACTCTAAGCCCGGCTTTATTTCTATGATATTGATTTCTCACAATC
65 CCCGTTATTTTCGAGGGGATACTCTAACCCCGACTTTATTTCAAAGATAAT-ATTTCTCACAATC
*
3563923 GGAGATACTCCAA-TCTCGTTATTTTGGCA
129 GGAGATACTCCAACCCT-GTTATTTTGG-A
* * * *
3563952 GGGATACTCCAACCCCGGCCTTATTGCTAAAGCATCAATTTTTCACAATCGGGGATACTCCAACC
1 GGGATACTCCAACCCCGACTTTATTCCTAAAGCATCGATTTTTCACAATCGGGGATACTCCAACC
* * *
3564017 CCGTTATTTTCGAGGGGATACTCTAACCCCGATTTTATTTTCAAAGCGTCAAT-TTTCT-ATAAT
66 CCGTTATTTTCGAGGGGATACTCTAACCCCGACTTTA-TTTCAAAG-AT-AATATTTCTCACAAT
* *
3564080 CAGG-GATGCTCCAACCCTGTTATTTTTGA
128 C-GGAGATACTCCAACCCTGTTATTTTGGA
* * * *
3564109 GAGGATACTCCAACCCCGATTTTATTTCCTGAA-CATCGATTTTTCATAATTGGGGATACTCCAA
1 G-GGATACTCCAACCCCGACTTTA-TTCCTAAAGCATCGATTTTTCACAATCGGGGATACTCCAA
3564173 CCCCGTT
64 CCCCGTT
3564180 GTTATCCCCA
Statistics
Matches: 191, Mismatches: 29, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
157 2 0.01
158 160 0.84
159 26 0.14
160 1 0.01
161 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.34
Consensus pattern (156 bp):
GGGATACTCCAACCCCGACTTTATTCCTAAAGCATCGATTTTTCACAATCGGGGATACTCCAACC
CCGTTATTTTCGAGGGGATACTCTAACCCCGACTTTATTTCAAAGATAATATTTCTCACAATCGG
AGATACTCCAACCCTGTTATTTTGGA
Found at i:3566566 original size:13 final size:13
Alignment explanation
Indices: 3566548--3566572 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3566538 CAATTCTTCA
3566548 TGTATCGATACAT
1 TGTATCGATACAT
3566561 TGTATCGATACA
1 TGTATCGATACA
3566573 ATGTCCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3566583 original size:33 final size:33
Alignment explanation
Indices: 3566528--3566594 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
3566518 TTGCACATAA
*
3566528 TGTATCGATACAATTCTTCATGTATCGATACAT
1 TGTATCGATACAATTCTCCATGTATCGATACAT
* *
3566561 TGTATCGATACAATGTC-CCATGTATTGATGCAT
1 TGTATCGATACAAT-TCTCCATGTATCGATACAT
3566594 T
1 T
3566595 TCGCTTAGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATTCTCCATGTATCGATACAT
Found at i:3566665 original size:19 final size:20
Alignment explanation
Indices: 3566621--3566671 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
3566611 CTACCAGTTT
*
3566621 CATGTATCGATACAATTGAG
1 CATGTATTGATACAATTGAG
**
3566641 TGTGTATTGATACAA-TGAG
1 CATGTATTGATACAATTGAG
3566660 CATGTATTGATA
1 CATGTATTGATA
3566672 GATTGTATCG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (20 bp):
CATGTATTGATACAATTGAG
Found at i:3578225 original size:11 final size:10
Alignment explanation
Indices: 3578203--3578270 Score: 73
Period size: 11 Copynumber: 6.4 Consensus size: 10
3578193 CATATAAATC
*
3578203 TTTTTCAATT
1 TTTTTCATTT
3578213 TTTTTCACTTT
1 TTTTTCA-TTT
3578224 TTTTTCATTT
1 TTTTTCATTT
*
3578234 TTTATTTATTTT
1 TTT-TTCA-TTT
3578246 TTTTTCAGTTT
1 TTTTTCA-TTT
*
3578257 TTTTACATTT
1 TTTTTCATTT
3578267 TTTT
1 TTTT
3578271 CATAGAATCA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
10 20 0.40
11 24 0.48
12 6 0.12
ACGTcount: A:0.13, C:0.09, G:0.01, T:0.76
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:3582703 original size:21 final size:21
Alignment explanation
Indices: 3582673--3582725 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
3582663 ATAACAATTG
3582673 CATT-TTTCATCCAAAAAATA
1 CATTATTTCATCCAAAAAATA
**
3582693 CA-TACTTTCATCCAACTAATA
1 CATTA-TTTCATCCAAAAAATA
3582714 CATTATTTCATC
1 CATTATTTCATC
3582726 TAAATACACA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 1 0.04
20 2 0.07
21 23 0.82
22 2 0.07
ACGTcount: A:0.38, C:0.25, G:0.00, T:0.38
Consensus pattern (21 bp):
CATTATTTCATCCAAAAAATA
Found at i:3584386 original size:126 final size:126
Alignment explanation
Indices: 3584216--3584468 Score: 443
Period size: 126 Copynumber: 2.0 Consensus size: 126
3584206 CTGGTTTAAT
* *
3584216 GGTGTACAAGAGGGTAACTATTCCAAGAATGGAACGAACAGTAATATCATGATCTTAGATAGTTT
1 GGTGTACAAGAGGGTAACTATTCCAAGAATGGAACAAACAGTAATATCATGATCTTAGACAGTTT
* * *
3584281 TCTTAGAAGAGGTGAACTTTTCTTACTTCAGCTTTAGAATATTGGAGATCCTTAGAAGCTA
66 GCTTAGAAGAGGTGAACTTTTCTTACTTCAGCTTTAAAATATTAGAGATCCTTAGAAGCTA
* *
3584342 GGTGTACAAGAGGGTGACTATTCCAAGAATGGAACAAACAGTAATATCATGATCTTAGACGGTTT
1 GGTGTACAAGAGGGTAACTATTCCAAGAATGGAACAAACAGTAATATCATGATCTTAGACAGTTT
3584407 GCTTAGAAGAGGTGAACTTTTCTTACTTCAGCTTTAAAATATTAGAGATCCTTAGAAGCTA
66 GCTTAGAAGAGGTGAACTTTTCTTACTTCAGCTTTAAAATATTAGAGATCCTTAGAAGCTA
3584468 G
1 G
3584469 ATATTTAAAG
Statistics
Matches: 120, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 120 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.31
Consensus pattern (126 bp):
GGTGTACAAGAGGGTAACTATTCCAAGAATGGAACAAACAGTAATATCATGATCTTAGACAGTTT
GCTTAGAAGAGGTGAACTTTTCTTACTTCAGCTTTAAAATATTAGAGATCCTTAGAAGCTA
Found at i:3590340 original size:6 final size:6
Alignment explanation
Indices: 3590319--3590412 Score: 54
Period size: 6 Copynumber: 15.7 Consensus size: 6
3590309 CATTTTCACC
* * *
3590319 AAAAGA AAAAGGA GAAAA-A GAAAGA AAAA-A AAGGAA-A AAAAGG AAAAGG
1 AAAAGA AAAA-GA -AAAAGA AAAAGA AAAAGA AA--AAGA AAAAGA AAAAGA
* * *
3590368 AAAAGG AAAAGA AAAA-A AAGAA-A AAAGGA AAAATA AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AA-AAGA AAAAGA AAAAGA AAAAGA AAAA
3590413 TAGAAAAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
5 12 0.17
6 49 0.68
7 7 0.10
8 4 0.06
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (6 bp):
AAAAGA
Found at i:3590352 original size:22 final size:21
Alignment explanation
Indices: 3590324--3590412 Score: 76
Period size: 22 Copynumber: 4.1 Consensus size: 21
3590314 TCACCAAAAG
3590324 AAAAAGGAGAAAAAGAAAGAAA
1 AAAAAGGA-AAAAAGAAAGAAA
*
3590346 AAAAAGG-AAAAA-AAGGAAA
1 AAAAAGGAAAAAAGAAAGAAA
*
3590365 AGGAAAAGGAAAAGAA-AAAAAAGA
1 A--AAAAGGAAAA-AAGAAAGAA-A
*
3590389 AAAAAGGAAAAATAAAAAGAAA
1 AAAAAGGAAAAA-AGAAAGAAA
3590411 AA
1 AA
3590413 TAGAAAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
19 7 0.12
20 5 0.09
21 7 0.12
22 24 0.43
23 11 0.20
24 2 0.04
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (21 bp):
AAAAAGGAAAAAAGAAAGAAA
Found at i:3590405 original size:28 final size:27
Alignment explanation
Indices: 3590319--3590420 Score: 98
Period size: 28 Copynumber: 3.7 Consensus size: 27
3590309 CATTTTCACC
** *
3590319 AAAAGAAAAAGGAGAAAAAGAAAGAAAA
1 AAAAGAAAAAAAAGAAAAAGGAA-AAAA
* * **
3590347 AAAAGGAAAAAAAGGAAAAGGAAAAGG
1 AAAAGAAAAAAAAGAAAAAGGAAAAAA
3590374 AAAAGAAAAAAAAGAAAAAAGGAAAAATA
1 AAAAGAAAAAAAAG-AAAAAGGAAAAA-A
*
3590403 AAAAG-AAAAATAGAAAAA
1 AAAAGAAAAAAAAGAAAAA
3590421 AATTAGCTTG
Statistics
Matches: 60, Mismatches: 12, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
27 20 0.33
28 35 0.58
29 5 0.08
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (27 bp):
AAAAGAAAAAAAAGAAAAAGGAAAAAA
Found at i:3590407 original size:35 final size:36
Alignment explanation
Indices: 3590331--3590422 Score: 102
Period size: 36 Copynumber: 2.6 Consensus size: 36
3590321 AAGAAAAAGG
3590331 AGAAAAAG--AAAGAAAAAAAAGGAAAAAAAGGAAA
1 AGAAAAAGAAAAAGAAAAAAAAGGAAAAAAAGGAAA
* *
3590365 AGGAAAAGGAAAAGAAAAAAAA-G-AAAAAAGGAAAA
1 AGAAAAAGAAAAAGAAAAAAAAGGAAAAAAAGG-AAA
* *
3590400 ATAAAAAGAAAAATAGAAAAAAA
1 AGAAAAAGAAAAAGA-AAAAAAA
3590423 TTAGCTTGGG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
34 15 0.31
35 15 0.31
36 19 0.39
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.02
Consensus pattern (36 bp):
AGAAAAAGAAAAAGAAAAAAAAGGAAAAAAAGGAAA
Found at i:3590411 original size:34 final size:36
Alignment explanation
Indices: 3590331--3590411 Score: 114
Period size: 34 Copynumber: 2.3 Consensus size: 36
3590321 AAGAAAAAGG
3590331 AGAAAAAG-AAAGAAAAAAAAGGAAAAAAAGGAAAA
1 AGAAAAAGAAAAGAAAAAAAAGGAAAAAAAGGAAAA
* *
3590366 GGAAAAGGAAAAGAAAAAAAA-G-AAAAAAGGAAAA
1 AGAAAAAGAAAAGAAAAAAAAGGAAAAAAAGGAAAA
*
3590400 ATAAAAAGAAAA
1 AGAAAAAGAAAA
3590412 ATAGAAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
34 21 0.52
35 7 0.17
36 12 0.30
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (36 bp):
AGAAAAAGAAAAGAAAAAAAAGGAAAAAAAGGAAAA
Found at i:3590417 original size:8 final size:7
Alignment explanation
Indices: 3590319--3590421 Score: 70
Period size: 7 Copynumber: 14.6 Consensus size: 7
3590309 CATTTTCACC
3590319 AAAAGAA
1 AAAAGAA
*
3590326 AAAGGAGA
1 AAAAGA-A
3590334 AAAAGAA
1 AAAAGAA
3590341 AGAAA-AA
1 A-AAAGAA
*
3590348 AAAGGAA
1 AAAAGAA
*
3590355 AAAA-AGG
1 AAAAGA-A
*
3590362 AAAAGGA
1 AAAAGAA
*
3590369 AAAGGAA
1 AAAAGAA
3590376 AAGAA-AA
1 AA-AAGAA
3590383 AAAAGAA
1 AAAAGAA
*
3590390 AAAAGGA
1 AAAAGAA
*
3590397 AAAA-TA
1 AAAAGAA
3590403 AAAAGAA
1 AAAAGAA
3590410 AAATAGAA
1 AAA-AGAA
3590418 AAAA
1 AAAA
3590422 ATTAGCTTGG
Statistics
Matches: 74, Mismatches: 13, Indels: 18
0.70 0.12 0.17
Matches are distributed among these distances:
6 10 0.14
7 47 0.64
8 17 0.23
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:3595169 original size:13 final size:13
Alignment explanation
Indices: 3595151--3595175 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3595141 CAATTTTTTG
3595151 TGTATCGATACAT
1 TGTATCGATACAT
3595164 TGTATCGATACA
1 TGTATCGATACA
3595176 AGTTTGGCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3595896 original size:21 final size:21
Alignment explanation
Indices: 3595855--3595898 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3595845 CTCCCTTTTA
* *
3595855 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
3595876 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
3595897 TC
1 TC
3595899 ATATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:3597731 original size:13 final size:13
Alignment explanation
Indices: 3597703--3597740 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3597693 ATAATCACCC
3597703 TGTATCGATA-AA
1 TGTATCGATACAA
3597715 TGTATCGATACAA
1 TGTATCGATACAA
3597728 TGTATCGATACAA
1 TGTATCGATACAA
3597741 AGAAAATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3599839 original size:15 final size:15
Alignment explanation
Indices: 3599819--3599849 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3599809 ATTTCGTTTG
*
3599819 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3599834 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3599849 G
1 G
3599850 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3601680 original size:21 final size:21
Alignment explanation
Indices: 3601651--3601695 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3601641 AAGTTTTCAT
*
3601651 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
3601671 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
3601693 TTT
1 TTT
3601696 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:3603931 original size:13 final size:13
Alignment explanation
Indices: 3603913--3603937 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3603903 CAATTTTTTG
3603913 TGTATCGATACAT
1 TGTATCGATACAT
3603926 TGTATCGATACA
1 TGTATCGATACA
3603938 AGTTTGGCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3607404 original size:20 final size:22
Alignment explanation
Indices: 3607379--3607433 Score: 80
Period size: 20 Copynumber: 2.6 Consensus size: 22
3607369 AAAACCCAGA
3607379 ATGTATCGATACAA-TG--AGAC
1 ATGTATCGATACAATTGTAAG-C
3607399 ATGTATCGATACAATTGTAAGC
1 ATGTATCGATACAATTGTAAGC
3607421 ATGTATCGATACA
1 ATGTATCGATACA
3607434 TTTCCTTGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.44
21 2 0.06
22 14 0.44
23 2 0.06
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (22 bp):
ATGTATCGATACAATTGTAAGC
Found at i:3607426 original size:22 final size:20
Alignment explanation
Indices: 3607379--3607433 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 20
3607369 AAAACCCAGA
3607379 ATGTATCGATACAATGAGAC
1 ATGTATCGATACAATGAGAC
3607399 ATGTATCGATACAATTGTA-AGC
1 ATGTATCGATACAA-TG-AGA-C
3607421 ATGTATCGATACA
1 ATGTATCGATACA
3607434 TTTCCTTGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.44
21 3 0.09
22 15 0.47
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (20 bp):
ATGTATCGATACAATGAGAC
Found at i:3607498 original size:19 final size:20
Alignment explanation
Indices: 3607474--3607527 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
3607464 ATCAATACAT
3607474 TGTATCGATACAAAACT-TA
1 TGTATCGATACAAAACTGTA
** *
3607493 TGTATCGATACATTTACTGTT
1 TGTATCGATACA-AAACTGTA
3607514 TGTATCGATACAAA
1 TGTATCGATACAAA
3607528 TTGTAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTATCGATACAAAACTGTA
Found at i:3610989 original size:12 final size:12
Alignment explanation
Indices: 3610972--3611005 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3610962 ATTGGCCAAA
3610972 AAATAATAAAAT
1 AAATAATAAAAT
3610984 AAATAATAAAAT
1 AAATAATAAAAT
3610996 -AATAA-AAAAT
1 AAATAATAAAAT
3611006 GCTAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 5 0.23
11 5 0.23
12 12 0.55
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAATAAAAT
Found at i:3611774 original size:155 final size:153
Alignment explanation
Indices: 3611477--3611805 Score: 378
Period size: 155 Copynumber: 2.1 Consensus size: 153
3611467 TATTTGCAAT
* * *
3611477 TTTAGAAAGTTCAAGGACTAAATTACAAAATGTTCAAAATGTTTTCTTAGGTATCCTTGCTTGAC
1 TTTA-AAAGTTCAAAGACTAAATTACAAAAAGTTCAAAATGTTTTCTTAGGTATCCTTACTTGAC
** ** * *
3611542 CGAGAGTCTTTAGTGCCATAGGAGGACTATTTCATGCATTTTTAAACATATTTTAGTCTTTTTAA
65 CGAGAGTCCCTAGTGCCATAGGAGGACTATTTCATGCATTTTTAAACATATTCAAGGCTTTTCAA
3611607 CATGTTAAGGACCTTTTGGCA-AA
130 CATGTTAAGGACCTTTTGGCACAA
* * *
3611630 TTTCAAAAAGTTTAAAGACTAAATTACAAAAAGTT-TAAATCTTTTTCCTT-GAGTATCCTTACT
1 TTT--AAAAGTTCAAAGACTAAATTACAAAAAGTTCAAAAT-GTTTT-CTTAG-GTATCCTTACT
* * *
3611693 TGGCTGAGAGTCCCTAGTG-CATTAGGAGGACTATTTCATGCATTTTTAAACTTATTCAAGGCTT
61 TGACCGAGAGTCCCTAGTGCCA-TAGGAGGACTATTTCATGCATTTTTAAACATATTCAAGGCTT
** ** *
3611757 TTCAATGTGTTGGGGACCTTTTTGCACAA
125 TTCAACATGTTAAGGACCTTTTGGCACAA
*
3611786 TTTAAAAGTTCAGAGACTAA
1 TTTAAAAGTTCAAAGACTAA
3611806 TTTATACATT
Statistics
Matches: 147, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
153 7 0.05
154 48 0.33
155 87 0.59
156 5 0.03
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (153 bp):
TTTAAAAGTTCAAAGACTAAATTACAAAAAGTTCAAAATGTTTTCTTAGGTATCCTTACTTGACC
GAGAGTCCCTAGTGCCATAGGAGGACTATTTCATGCATTTTTAAACATATTCAAGGCTTTTCAAC
ATGTTAAGGACCTTTTGGCACAA
Found at i:3613428 original size:154 final size:154
Alignment explanation
Indices: 3612792--3613687 Score: 786
Period size: 154 Copynumber: 5.9 Consensus size: 154
3612782 GTGGTCACCA
* * *
3612792 AGTCACTTTTATGCCAAAGATGCGTATTTAGGATAGGTTCATCCTCTTACTTATC---TTGT-TC
1 AGTCACTTTTATGCCAAAGGTGTGTATTTAGGATAGGTTCATCCTTTTACTTATCTTTTTGTGTC
* * ** *
3612853 CTTTAA-AGTTACTGAGACA-TGTTTATGTCAAAGGTATACCCTA-GGGCATTTTAGTAATGTTC
66 CTTTAAGA-TTACCGAGATACT-TTTACATCAAAGGTATACCCTAGGGGCATTTTAGTAAT-TTT
*
3612915 TTAGAATCGAGTCCTAGGTAGTCAAC-
128 TTAGAATCGAGTCCTAGGTAGTCATCG
*** * * * * *
3612941 AGTTTTTTTTATGCCAAAGGTGTGTATTTAGGATAGGTTTAT-CTTTTATTTATCTTTTCGAGCC
1 AGTCACTTTTATGCCAAAGGTGTGTATTTAGGATAGGTTCATCCTTTTACTTATCTTTTTGTGTC
** * **
3613005 CTTTAAGATTGTCGAGATA-TTTTCACATCAAAGGTATACCCGAGGGGTGTTTTAGTAATTTTCT
66 CTTTAAGATTACCGAGATACTTTT-ACATCAAAGGTATACCCTAGGGGCATTTTAGTAATTTT-T
*
3613069 TAGAATCGAGTCATAGGTAGTCATCG
129 TAGAATCGAGTCCTAGGTAGTCATCG
* * * **
3613095 AGTCACTTTTATGCCAAAGGTGTGTATTCAGAATAGGTTCATCCTTTTACATATCTTTTCATGTC
1 AGTCACTTTTATGCCAAAGGTGTGTATTTAGGATAGGTTCATCCTTTTACTTATCTTTTTGTGTC
* * * * * * * * * * *
3613160 TTTTAGGGTTATCGGGATACTTCATA-TTGAAA-GTATA-CTTAGGGGCATTTTGGTAGTTTTCT
66 CTTTAAGATTACCGAGATACTT-TTACATCAAAGGTATACCCTAGGGGCATTTTAGTAATTTT-T
** *
3613222 TAGAATTAAGTCCTAGGTAGTCACCG
129 TAGAATCGAGTCCTAGGTAGTCATCG
** * *
3613248 AGTTGCTTCTATGCCAAAGATGTGTATTTAGGATAGGTTCATCCTTTTACTTATCTTTTTGTGTC
1 AGTCACTTTTATGCCAAAGGTGTGTATTTAGGATAGGTTCATCCTTTTACTTATCTTTTTGTGTC
* * * * *
3613313 CTTCAAGATTACCGAAATACTTTTACATTAAAGGTGTACCCTATGGGCATTTTAGTAATTTTTTA
66 CTTTAAGATTACCGAGATACTTTTACATCAAAGGTATACCCTAGGGGCATTTTAGTAATTTTTTA
* * *
3613378 -AAGCCAAGTCCAAGGTAGTCATCG
131 GAA-TCGAGTCCTAGGTAGTCATCG
* *
3613402 AGTCACTTTTATGCCAAAGGTGTGTATTTAGGATAGGTTCATCCTCTTACTTATCTTTTTATGTC
1 AGTCACTTTTATGCCAAAGGTGTGTATTTAGGATAGGTTCATCCTTTTACTTATCTTTTTGTGTC
* ** * * * * * ** ** *
3613467 TTTTGGGGTTACTGAGATACTTTCACATCGAAGATATACTTTAAAGGTATTTTAGTAATTTTTTT
66 CTTTAAGATTACCGAGATACTTTTACATCAAAGGTATACCCTAGGGGCATTTTAGTAA-TTTTTT
* *
3613532 AGAA-CTGAGTCTTAGGTAGTCAT-T
130 AGAATC-GAGTCCTAGGTAGTCATCG
* * ** *
3613556 AGGTCATTTTTATGCCAAAGGTGTGTATTTATGATAGGTTCAT-CTTTTACTTATCTTTTCATAT
1 A-GTCACTTTTATGCCAAAGGTGTGTATTTAGGATAGGTTCATCCTTTTACTTATCTTTTTGTGT
* * * * * ** * *
3613620 CTTTTAGGGTTACCGTGATACTTTTACATTGAAA-GTATA-CCTAGAAGCATTTTGGTAATTTCT
65 CCTTTAAGATTACCGAGATACTTTTACA-TCAAAGGTATACCCTAGGGGCATTTTAGTAATTTTT
3613683 TAGAA
129 TAGAA
3613688 CCAAGTCACT
Statistics
Matches: 600, Mismatches: 126, Indels: 39
0.78 0.16 0.05
Matches are distributed among these distances:
148 10 0.02
149 36 0.06
151 5 0.01
152 44 0.07
153 169 0.28
154 213 0.35
155 117 0.19
156 5 0.01
157 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.41
Consensus pattern (154 bp):
AGTCACTTTTATGCCAAAGGTGTGTATTTAGGATAGGTTCATCCTTTTACTTATCTTTTTGTGTC
CTTTAAGATTACCGAGATACTTTTACATCAAAGGTATACCCTAGGGGCATTTTAGTAATTTTTTA
GAATCGAGTCCTAGGTAGTCATCG
Found at i:3613672 original size:307 final size:305
Alignment explanation
Indices: 3612792--3613694 Score: 940
Period size: 307 Copynumber: 3.0 Consensus size: 305
3612782 GTGGTCACCA
* * *
3612792 AGTCACTTTTATGCCAAAGATGCGTATTTAGGATAGGTTCATCCTCTTACTTATC---TTGT-TC
1 AGTCACTTTTATGCCAAAGGTGTGTATTTAGGATAGGTTCATCCTCTTACTTATCTTTTTATGTC
* ** * * * * * * *
3612853 CTTTAAAGTTACTGAGACA-TGTTTATGTCAAAGGTATACCCT-AGGGCATTTTAGTAATGTTCT
66 TTTTAGGGTTACTGAGATACT-TTCATATCGAAGATATA-CTTAAGGGCATTTTAGTAATTTTCT
* * *
3612916 TAGAATCGAGTCCTAGGTAGTCAACAGTTTTTTTTATGCCAAAGGTGTGTATTTAGGATAGGTTT
129 TAGAAT-GAGTCCTAGGTAGTCAACAGGTCTTTTTATGCCAAAGGTGTGTATTTAGGATAGGTTC
* * ** *
3612981 ATCTTTTATTTATCTTTTCGA-GCCCTTTAAGATTGTCGAGATA-TTTTCACATCAAAGGTATAC
193 ATCTTTTACTTATCTTTTC-ATGTCCTTTAAGATTACCGAGATACTTTT-ACATTAAAGGTATAC
* ** * *
3613044 CCGAGGGGTGTTTTAGTAATTTTCTTAGAATCGAGT-CATAGGTAGTCATCG
256 CCTA-GGGCATTTTAGTAATTTT-TTAGAACCAAGTCCATAGGTAGTCATCG
* * * * *
3613095 AGTCACTTTTATGCCAAAGGTGTGTATTCAGAATAGGTTCATCCTTTTACATATCTTTTCATGTC
1 AGTCACTTTTATGCCAAAGGTGTGTATTTAGGATAGGTTCATCCTCTTACTTATCTTTTTATGTC
* * * * *
3613160 TTTTAGGGTTA-TCGGGATAC-TTCATATTGAA-AGTATACTTAGGGGCATTTTGGTAGTTTTCT
66 TTTTAGGGTTACT-GAGATACTTTCATATCGAAGA-TATACTTAAGGGCATTTTAGTAATTTTCT
* * * * *
3613222 TAGAATTAAGTCCTAGGTAGTCACCGAGTTGC-TTCTATGCCAAAGATGTGTATTTAGGATAGGT
129 TAGAA-TGAGTCCTAGGTAGTCAAC-AGGT-CTTTTTATGCCAAAGGTGTGTATTTAGGATAGGT
** * * *
3613286 TCATCCTTTTACTTATCTTTTTGTGTCCTTCAAGATTACCGAAATACTTTTACATTAAAGGTGTA
191 TCAT-CTTTTACTTATCTTTTCATGTCCTTTAAGATTACCGAGATACTTTTACATTAAAGGTATA
3613351 CCCTATGGGCATTTTAGTAATTTTTTA-AAGCCAAGTCCA-AGGTAGTCATCG
255 CCCTA-GGGCATTTTAGTAATTTTTTAGAA-CCAAGTCCATAGGTAGTCATCG
3613402 AGTCACTTTTATGCCAAAGGTGTGTATTTAGGATAGGTTCATCCTCTTACTTATCTTTTTATGTC
1 AGTCACTTTTATGCCAAAGGTGTGTATTTAGGATAGGTTCATCCTCTTACTTATCTTTTTATGTC
* * * * *
3613467 TTTTGGGGTTACTGAGATACTTTCACATCGAAGATATACTTTAAAGGTATTTTAGTAATTTTTTT
66 TTTTAGGGTTACTGAGATACTTTCATATCGAAGATATAC-TTAAGGGCATTTTAGTAATTTTCTT
* ** *
3613532 AGAACTGAGTCTTAGGTAGTCATTAGGTCATTTTTATGCCAAAGGTGTGTATTTATGATAGGTTC
130 AGAA-TGAGTCCTAGGTAGTCAACAGGTC-TTTTTATGCCAAAGGTGTGTATTTAGGATAGGTTC
* * * * *
3613597 ATCTTTTACTTATCTTTTCATATCTTTTAGGGTTACCGTGATACTTTTACATTGAAA-GTATA-C
193 ATCTTTTACTTATCTTTTCATGTCCTTTAAGATTACCGAGATACTTTTACATT-AAAGGTATACC
* * *
3613660 CTAGAAGCATTTTGGTAATTTCTTAGAACCAAGTC
257 CTAG-GGCATTTTAGTAATTTTTTAGAACCAAGTC
3613695 ACTGAGTCAG
Statistics
Matches: 493, Mismatches: 82, Indels: 46
0.79 0.13 0.07
Matches are distributed among these distances:
303 49 0.10
305 2 0.00
306 55 0.11
307 176 0.36
308 132 0.27
309 79 0.16
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.41
Consensus pattern (305 bp):
AGTCACTTTTATGCCAAAGGTGTGTATTTAGGATAGGTTCATCCTCTTACTTATCTTTTTATGTC
TTTTAGGGTTACTGAGATACTTTCATATCGAAGATATACTTAAGGGCATTTTAGTAATTTTCTTA
GAATGAGTCCTAGGTAGTCAACAGGTCTTTTTATGCCAAAGGTGTGTATTTAGGATAGGTTCATC
TTTTACTTATCTTTTCATGTCCTTTAAGATTACCGAGATACTTTTACATTAAAGGTATACCCTAG
GGCATTTTAGTAATTTTTTAGAACCAAGTCCATAGGTAGTCATCG
Done.