Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009330.1 Hibiscus syriacus cultivar Beakdansim tig00113096_pilon, whole genome shotgun sequence
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: 1820295
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1164602 original size:61 final size:62
Alignment explanation
Indices: 1164491--1164669 Score: 209
Period size: 61 Copynumber: 2.9 Consensus size: 62
1164481 TCAACTTTTG
* * *
1164491 TTATTCCTGACTCCCCAATAGAGTCAATCCTTGACTTTCTCGTGAAGAGAAATCAAGCTTTA
1 TTATCCCTGACTCCCCAATAGAGTCAATCCTTGACTTCCTCGTGAAGAGAAATCAAGCCTTA
* * * * * *
1164553 TTATCCCTGACTCCTCAGTAGAGTCAAT-CTTGACTTCCTCGTTAAGAGAAGTCAATCCTTG
1 TTATCCCTGACTCCCCAATAGAGTCAATCCTTGACTTCCTCGTGAAGAGAAATCAAGCCTTA
* * ** *
1164614 TTATCCCTGACTCCCCAAAAGAGTCAATTCC-TGACTCCCTCACGAAGAGAAGTCAA
1 TTATCCCTGACTCCCCAATAGAGTCAA-TCCTTGACTTCCTCGTGAAGAGAAATCAA
1164670 TCCCTGACTT
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
61 51 0.52
62 47 0.47
63 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (62 bp):
TTATCCCTGACTCCCCAATAGAGTCAATCCTTGACTTCCTCGTGAAGAGAAATCAAGCCTTA
Found at i:1164693 original size:29 final size:29
Alignment explanation
Indices: 1164616--1164700 Score: 72
Period size: 29 Copynumber: 3.1 Consensus size: 29
1164606 AATCCTTGTT
1164616 ATCCCTGACT-CC-C-C-AAAAG-AGTCA
1 ATCCCTGACTCCCTCACAAAAAGAAGTCA
* * *
1164640 ATTCCTGACTCCCTCACGAAGAGAAGTCA
1 ATCCCTGACTCCCTCACAAAAAGAAGTCA
* ** *
1164669 ATCCCTGACTTCCTCGTAAAAAGAAGTAA
1 ATCCCTGACTCCCTCACAAAAAGAAGTCA
1164698 ATC
1 ATC
1164701 TTTCTTATTT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
24 9 0.19
25 2 0.04
26 1 0.02
27 1 0.02
28 4 0.09
29 30 0.64
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.21
Consensus pattern (29 bp):
ATCCCTGACTCCCTCACAAAAAGAAGTCA
Found at i:1165933 original size:16 final size:15
Alignment explanation
Indices: 1165906--1165939 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1165896 TAGTCCCCCA
*
1165906 AATTTTAATATTTTT
1 AATTTTAATATTATT
1165921 AATTTTAAATATTATT
1 AATTTT-AATATTATT
1165937 AAT
1 AAT
1165940 GGTTTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTTTAATATTATT
Found at i:1170101 original size:3 final size:3
Alignment explanation
Indices: 1170093--1170118 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1170083 ACACTATACG
1170093 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1170119 AATTACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1171438 original size:5 final size:5
Alignment explanation
Indices: 1171428--1171471 Score: 63
Period size: 5 Copynumber: 8.6 Consensus size: 5
1171418 ATATATGTTT
1171428 TTTTA TTTTA TTTTA TTTTA TTTTAA TTTTAA TTTT- TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTT-A TTTT-A TTTTA TTTTA TTT
1171472 CTTTTAACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.11
5 22 0.59
6 11 0.30
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:1171451 original size:21 final size:21
Alignment explanation
Indices: 1171427--1171471 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1171417 TATATATGTT
*
1171427 TTTTTATTTT-ATTTTATTTTA
1 TTTTAATTTTAATTTT-TTTTA
1171448 TTTTAATTTTAATTTTTTTTA
1 TTTTAATTTTAATTTTTTTTA
1171469 TTT
1 TTT
1171472 CTTTTAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTAATTTTAATTTTTTTTA
Found at i:1171493 original size:2 final size:2
Alignment explanation
Indices: 1171486--1171512 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1171476 TAACATTGTT
1171486 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1171513 GTTTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1171611 original size:21 final size:22
Alignment explanation
Indices: 1171553--1171624 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 22
1171543 GACTGAACAT
1171553 TTTTCTTC-ATTTTTATTTTTA
1 TTTTCTTCAATTTTTATTTTTA
1171574 TTTTCTTCTTAACATTTTTATTTTTA
1 TTTTCTTC---A-ATTTTTATTTTTA
*
1171600 TTTTC-TCAATTTATT-TATTTA
1 TTTTCTTCAATTT-TTATTTTTA
1171621 TTTT
1 TTTT
1171625 TTCTCTCTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
21 21 0.48
22 3 0.07
25 2 0.05
26 18 0.41
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTCTTCAATTTTTATTTTTA
Found at i:1171616 original size:23 final size:24
Alignment explanation
Indices: 1171560--1171630 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 24
1171550 CATTTTTCTT
1171560 CATTTTTATTTTTATTTTCTTCTTAA
1 CATTTTTATTTTTATTTTC-TC-TAA
1171586 CATTTTTATTTTTATTTTCTC-AA
1 CATTTTTATTTTTATTTTCTCTAA
*
1171609 -TTTATTTATTTATT-TTTTCTCT
1 CATT-TTTATTT-TTATTTTCTCT
1171631 CTTCGATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
22 2 0.05
23 16 0.39
24 2 0.05
25 2 0.05
26 19 0.46
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.70
Consensus pattern (24 bp):
CATTTTTATTTTTATTTTCTCTAA
Found at i:1171742 original size:12 final size:13
Alignment explanation
Indices: 1171722--1171750 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1171712 TGAATTGAAT
1171722 TTTTAAATTTTAA
1 TTTTAAATTTTAA
1171735 TTTT-AATTTTAA
1 TTTTAAATTTTAA
1171747 TTTT
1 TTTT
1171751 CGCAACTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:1183915 original size:16 final size:16
Alignment explanation
Indices: 1183876--1183917 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
1183866 TTTTAAAACG
*
1183876 TGATTTTCTGAAATTT
1 TGATTTACTGAAATTT
*
1183892 TGGATTTACTGATATTT
1 T-GATTTACTGAAATTT
1183909 TGATTTACT
1 TGATTTACT
1183918 TTTAACTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (16 bp):
TGATTTACTGAAATTT
Found at i:1185207 original size:69 final size:69
Alignment explanation
Indices: 1185134--1185272 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
1185124 AATTATAAAT
1185134 TGTTTTATGATTTTACGCGTTTTAACAAAATTTTAATTTTTTCTAGATTTTTATAGTGGGTCGTT
1 TGTTTTATGATTTTACGCGTTTTAACAAAATTTTAATTTTTTCTAGATTTTTATAGTGGGTCGTT
1185199 TCGG
66 TCGG
1185203 TGTTTTATGATTTTACGCGTTTTAACAAAATTTTAATTTTTTCTAGATTTTTATAGTGGGTCGTT
1 TGTTTTATGATTTTACGCGTTTTAACAAAATTTTAATTTTTTCTAGATTTTTATAGTGGGTCGTT
1185268 TCGG
66 TCGG
1185272 T
1 T
1185273 AATCCTAATG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.22, C:0.09, G:0.17, T:0.53
Consensus pattern (69 bp):
TGTTTTATGATTTTACGCGTTTTAACAAAATTTTAATTTTTTCTAGATTTTTATAGTGGGTCGTT
TCGG
Found at i:1186533 original size:46 final size:47
Alignment explanation
Indices: 1186483--1186573 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 47
1186473 AAGTAATTTG
* **
1186483 TATAAAATTAAATTTATAAATAGTATTT-TAATATATATATATATAA
1 TATAAAAATAAATAAATAAATAGTATTTATAATATATATATATATAA
* * * *
1186529 TATAAAAATAAGTAAATAAATATTATTTATTATATATATTTATAT
1 TATAAAAATAAATAAATAAATAGTATTTATAATATATATATATAT
1186574 GACTACATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
46 23 0.62
47 14 0.38
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (47 bp):
TATAAAAATAAATAAATAAATAGTATTTATAATATATATATATATAA
Found at i:1187744 original size:18 final size:17
Alignment explanation
Indices: 1187690--1187738 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1187680 TGACACTCTT
* *
1187690 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
1187708 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1187726 AGTGCATTCGATG
1 AGTGCA-TCGATG
1187739 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1187844 original size:65 final size:64
Alignment explanation
Indices: 1187710--1187835 Score: 182
Period size: 64 Copynumber: 2.0 Consensus size: 64
1187700 TGCACTAAGA
* *
1187710 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * *
1187774 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGG
1187836 TATGTGCATA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
64 28 0.51
65 24 0.44
66 3 0.05
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.29
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:1187851 original size:65 final size:64
Alignment explanation
Indices: 1187718--1187852 Score: 157
Period size: 65 Copynumber: 2.1 Consensus size: 64
1187708 GAGTGCATCG
* * **
1187718 ATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGGTGCATCG
1 ATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGGTGCATAA
* * * *
1187782 ATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-TATGTGCAT
1 ATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGGCT-GGTGCAT
1187845 AA
63 AA
1187847 ATGCAT
1 ATGCAT
1187853 TTGATGTTCA
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
64 21 0.35
65 36 0.60
66 3 0.05
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (64 bp):
ATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGGTGCATAA
Found at i:1188373 original size:2 final size:2
Alignment explanation
Indices: 1188366--1188414 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1188356 AATTGATTAA
1188366 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1188408 AT AT AT A
1 AT AT AT A
1188415 GCTTAAGCTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1190145 original size:23 final size:22
Alignment explanation
Indices: 1190114--1190189 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
1190104 GACCCTGTGC
1190114 ATCGATGCACATTCAAGGCGTGT
1 ATCGATGCACATTCAAGG-GTGT
* * *
1190137 ATCGGTGCACCTTC-ATGGTGT
1 ATCGATGCACATTCAAGGGTGT
*
1190158 ATCGATGCACATTCAAGGATGT
1 ATCGATGCACATTCAAGGGTGT
1190180 ATCGATGCAC
1 ATCGATGCAC
1190190 TGTTAGGTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
21 16 0.36
22 17 0.38
23 12 0.27
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (22 bp):
ATCGATGCACATTCAAGGGTGT
Found at i:1190202 original size:20 final size:21
Alignment explanation
Indices: 1190114--1190208 Score: 104
Period size: 21 Copynumber: 4.4 Consensus size: 21
1190104 GACCCTGTGC
1190114 ATCGATGCACATTCAAGGCGTGT
1 ATCGATGCACATTCAA-G-GTGT
* * *
1190137 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGTGT
1190158 ATCGATGCACATTCAAGGATGT
1 ATCGATGCACATTCAAGG-TGT
*
1190180 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
1190200 ATCGATGCA
1 ATCGATGCA
1190209 TGAAGCACAA
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
20 12 0.19
21 23 0.37
22 15 0.24
23 13 0.21
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:1193428 original size:59 final size:59
Alignment explanation
Indices: 1193328--1193446 Score: 222
Period size: 59 Copynumber: 2.0 Consensus size: 59
1193318 TGTATGGAAG
1193328 AGGTATTAGATATATTACCTATACCTTCAATGTACCTTTTTGAATAATCACCAAAAGTC
1 AGGTATTAGATATATTACCTATACCTTCAATGTACCTTTTTGAATAATCACCAAAAGTC
1193387 AGGTATTAGATATATTACCTATACCTTCAATGTGACC-TTTTGAATAATCACCAAAAGTC
1 AGGTATTAGATATATTACCTATACCTTCAATGT-ACCTTTTTGAATAATCACCAAAAGTC
1193446 A
1 A
1193447 CTTCTCCTCC
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 56 0.95
60 3 0.05
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (59 bp):
AGGTATTAGATATATTACCTATACCTTCAATGTACCTTTTTGAATAATCACCAAAAGTC
Found at i:1195802 original size:36 final size:36
Alignment explanation
Indices: 1195757--1195835 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
1195747 GTTTCTAGTT
*
1195757 GCTTGTTGTTTCTTGTTCTTGATCAATGGGTTCTAA
1 GCTTGTTGTTTCTTGTTCTTGATCAATGGCTTCTAA
1195793 GCTTGTTGTTTCTTGTTCTTGATCAATGGCTTCTAA
1 GCTTGTTGTTTCTTGTTCTTGATCAATGGCTTCTAA
1195829 GCTTGTT
1 GCTTGTT
1195836 TAAATATACC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.13, C:0.15, G:0.22, T:0.51
Consensus pattern (36 bp):
GCTTGTTGTTTCTTGTTCTTGATCAATGGCTTCTAA
Found at i:1196118 original size:46 final size:45
Alignment explanation
Indices: 1196020--1196125 Score: 133
Period size: 45 Copynumber: 2.3 Consensus size: 45
1196010 GTGCACTAAG
* * *
1196020 AGTGCATCTATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
* *
1196065 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTC
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCAC
*
1196111 AGTGCATCGGTGCAT
1 AGTGCATCGATGCAT
1196126 GGTATGTGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
45 28 0.53
46 22 0.42
47 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (45 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
Found at i:1196201 original size:65 final size:63
Alignment explanation
Indices: 1196066--1196191 Score: 157
Period size: 65 Copynumber: 2.0 Consensus size: 63
1196056 AATAGCCAGA
*
1196066 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGTAT
* **
1196131 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG
1196192 ATTGGTGCAT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
62 3 0.06
63 3 0.06
64 20 0.37
65 28 0.52
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTAT
Found at i:1197250 original size:3 final size:3
Alignment explanation
Indices: 1197242--1197316 Score: 75
Period size: 3 Copynumber: 26.0 Consensus size: 3
1197232 GCCTAAAATG
* ** * *
1197242 TAA TAA TAA TAT TTT TAA TAA TAA TAA TAA TAA -AA AAA AAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1197288 AAA TAA TAA TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1197317 AAGCAAATGG
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 6 0.10
3 57 0.90
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1197298 original size:14 final size:14
Alignment explanation
Indices: 1197264--1197318 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
1197254 TTTTAATAAT
1197264 AATAATAATAAAAA
1 AATAATAATAAAAA
*
1197278 AAAAATAA-AAAAA
1 AATAATAATAAAAA
* *
1197291 TAATAATAATATAAT
1 -AATAATAATAAAAA
1197306 AATAATAATAAAA
1 AATAATAATAAAA
1197319 GCAAATGGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
13 5 0.15
14 26 0.76
15 3 0.09
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AATAATAATAAAAA
Found at i:1197304 original size:11 final size:11
Alignment explanation
Indices: 1197257--1197312 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
1197247 ATAATATTTT
1197257 TAATAATAATAA
1 TAATAATAAT-A
* *
1197269 TAATAAAAAAA
1 TAATAATAATA
* * *
1197280 AAATAAAAAAA
1 TAATAATAATA
1197291 TAATAATAATA
1 TAATAATAATA
1197302 TAATAATAATA
1 TAATAATAATA
1197313 ATAAAAGCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
11 30 0.79
12 8 0.21
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAATAATAATA
Found at i:1197839 original size:123 final size:123
Alignment explanation
Indices: 1197686--1198490 Score: 982
Period size: 123 Copynumber: 6.7 Consensus size: 123
1197676 GAATCAAGCT
* * * *
1197686 AAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTGTTTCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * *
1197751 GAACTTTATCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAA
66 GAACTTTCTCTGGAAAAGTTGATGATGATCTATCTCCTTCTGTGATAGAGTCATGCAA
1197809 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1197874 GAACTTTCTCTGGAAAAGTTGATGATGATCTATCTCCTTCTGTGATAGAGTCATGCAA
66 GAACTTTCTCTGGAAAAGTTGATGATGATCTATCTCCTTCTGTGATAGAGTCATGCAA
* *
1197932 AATGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCCTTAT
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * *
1197997 GAACTTTCTCTGGAAAATTTGATGCTAATCTATCTCCTTCTGTGATAGAGTCATGCAA
66 GAACTTTCTCTGGAAAAGTTGATGATGATCTATCTCCTTCTGTGATAGAGTCATGCAA
*
1198055 AAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* *
1198120 GAACTTTCTCTGGAAAAG-TGTATGATGATCTATCTCCTTCTGTGATAGAGTCAAGAAA
66 GAACTTTCTCTGGAAAAGTTG-ATGATGATCTATCTCCTTCTGTGATAGAGTCATGCAA
* *
1198178 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAA
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * ** *
1198243 GAACATTCTCTGGAAAA--T--T--TGATCCA--T-C--AAGTGAT-GAATTCGA-GCAA
66 GAACTTTCTCTGGAAAAGTTGATGATGATCTATCTCCTTCTGTGATAG-AGTC-ATGCAA
** * *
1198290 AAGACTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTA
* * * ** * *
1198355 TGAACTCTAC-CTGG-CAA--TG-T--TGATCCA--T-C--GAGTGAT-GAATTCAAGCAA
65 TGAACT-TTCTCTGGAAAAGTTGATGATGATCTATCTCCTTCTGTGATAG-AGTCATGCAA
* * ** *
1198403 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGAGGAGTTATTCTCATTA
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTA
* *
1198468 TGAACTCT-TCTGGAAATGTTGAT
65 TGAACTTTCTCTGGAAAAGTTGAT
1198491 CCATTGAGTG
Statistics
Matches: 623, Mismatches: 47, Indels: 31
0.89 0.07 0.04
Matches are distributed among these distances:
111 1 0.00
112 57 0.09
113 125 0.20
114 3 0.00
115 3 0.00
116 1 0.00
117 6 0.01
119 1 0.00
122 3 0.00
123 423 0.68
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (123 bp):
AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
GAACTTTCTCTGGAAAAGTTGATGATGATCTATCTCCTTCTGTGATAGAGTCATGCAA
Found at i:1198392 original size:113 final size:112
Alignment explanation
Indices: 1198183--1198503 Score: 477
Period size: 113 Copynumber: 2.9 Consensus size: 112
1198173 AGAAAAAGGT
* *
1198183 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTAAGAAC
1 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
* *
1198247 AT-TCTCTGGAAAAT-TTGATCCATCAAGTGATGAATTCGAGCAAAAGAC
66 -TCTC-CTGG-AAATGTTGATCCATCGAGTGATGAATTCAAGCAAAAGAC
1198295 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
* **
1198360 TCTACCTGGCAATGTTGATCCATCGAGTGATGAATTCAAGCAAAAGGT
66 TCT-CCTGGAAATGTTGATCCATCGAGTGATGAATTCAAGCAAAAGAC
* * *
1198408 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGAGGAGTTATTCTCATTATGAAC
1 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
* *
1198473 TCTTCTGGAAATGTTGATCCATTGAGTGATG
66 TCTCCTGGAAATGTTGATCCATCGAGTGATG
1198504 GATTTGATTC
Statistics
Matches: 192, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
112 64 0.33
113 127 0.66
114 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.37
Consensus pattern (112 bp):
TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
TCTCCTGGAAATGTTGATCCATCGAGTGATGAATTCAAGCAAAAGAC
Found at i:1199447 original size:18 final size:18
Alignment explanation
Indices: 1199424--1199469 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1199414 ACCGGTCATA
* *
1199424 ACCCGACCCGACCTGTTT
1 ACCCGACCCGACCCGTTG
1199442 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1199460 ACCCGACCCG
1 ACCCGACCCG
1199470 TTGACCGGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.17, C:0.50, G:0.20, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1199462 original size:13 final size:13
Alignment explanation
Indices: 1199446--1199475 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1199436 CTGTTTACCC
1199446 GACCCGACCCGTT
1 GACCCGACCCGTT
1199459 GACCCGACCCGTT
1 GACCCGACCCGTT
1199472 GACC
1 GACC
1199476 GGCGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1200261 original size:26 final size:26
Alignment explanation
Indices: 1200208--1200262 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
1200198 CTTGGATGAG
* *
1200208 AAATTATGAGAATACTCCGTAGGGTA
1 AAATTATGAAAATACTCCGTAGGATA
*
1200234 AAATTATGAAAATAC-CCGTATGTATA
1 AAATTATGAAAATACTCCGTA-GGATA
1200260 AAA
1 AAA
1200263 AGACAAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.27
Consensus pattern (26 bp):
AAATTATGAAAATACTCCGTAGGATA
Found at i:1201944 original size:12 final size:11
Alignment explanation
Indices: 1201880--1201944 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 11
1201870 TCCGAATTGA
1201880 ATTCTGTTCTG
1 ATTCTGTTCTG
*
1201891 ATAC-GTTACCTG
1 ATTCTGTT--CTG
1201903 AATTCTGTTCTG
1 -ATTCTGTTCTG
*
1201915 ATTCTGATCTGG
1 ATTCTGTTCT-G
1201927 ATTCTGTTCTG
1 ATTCTGTTCTG
1201938 ATATCTG
1 AT-TCTG
1201945 ATATGAATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
10 3 0.07
11 15 0.34
12 20 0.45
13 3 0.07
14 3 0.07
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.46
Consensus pattern (11 bp):
ATTCTGTTCTG
Found at i:1201952 original size:47 final size:47
Alignment explanation
Indices: 1201863--1201970 Score: 114
Period size: 47 Copynumber: 2.3 Consensus size: 47
1201853 AAATATTTTA
* * * *
1201863 TCTGATTTCCGAAT-TGAATTCTGTTCTGATACGTTACCTGAATTCTGT
1 TCTGATTTCTG-ATCTGGATTCTGTTCTGATACGATA-CTGAATTCTAT
1201911 TCTGA-TTCTGATCTGGATTCTGTTCTGATATCTGATA-TGAATTCTAT
1 TCTGATTTCTGATCTGGATTCTGTTCTGATA-C-GATACTGAATTCTAT
*
1201958 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1201971 ATCTCCGTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
46 2 0.04
47 33 0.65
48 13 0.25
49 3 0.06
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.47
Consensus pattern (47 bp):
TCTGATTTCTGATCTGGATTCTGTTCTGATACGATACTGAATTCTAT
Found at i:1201963 original size:24 final size:23
Alignment explanation
Indices: 1201877--1201972 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 23
1201867 ATTTCCGAAT
* *
1201877 TGAATTCTGTTCTGATAC-GTTA
1 TGAATTCTGTTCTGATTCTGATA
*
1201899 CCTGAATTCTGTTCTGATTCTGATC
1 --TGAATTCTGTTCTGATTCTGATA
*
1201924 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGAT-TCTGATA
* *
1201948 TGAATTCTATTTTGATTTCTGATA
1 TGAATTCTGTTCTGA-TTCTGATA
1201972 T
1 T
1201973 CTCCGTTTAC
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
23 15 0.25
24 43 0.70
25 3 0.05
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (23 bp):
TGAATTCTGTTCTGATTCTGATA
Found at i:1203331 original size:54 final size:53
Alignment explanation
Indices: 1203247--1203379 Score: 162
Period size: 54 Copynumber: 2.5 Consensus size: 53
1203237 AACTGATTCA
* * * *
1203247 TAAAATATTTGACAACACATTCATTCTTTCCTGTGGTTTCTGC-TCAGATGTTC-G
1 TAAAACATTTGACAACACATTCA-TCTTTCCAGTGATTTCTACAT-AGAT-TTCTG
1203301 TAAAACATTTGACAACACATTCATCATTTCCAGTGATTTCTACATAGATTTCTG
1 TAAAACATTTGACAACACATTCATC-TTTCCAGTGATTTCTACATAGATTTCTG
* *
1203355 TAAAACATTTGACAATAAATTCATC
1 TAAAACATTTGACAACACATTCATC
1203380 CAGATGTGGC
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
53 5 0.07
54 64 0.91
55 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (53 bp):
TAAAACATTTGACAACACATTCATCTTTCCAGTGATTTCTACATAGATTTCTG
Found at i:1204584 original size:14 final size:14
Alignment explanation
Indices: 1204565--1204591 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1204555 GGAAAAGTTG
1204565 AAATTTGGTTTATT
1 AAATTTGGTTTATT
1204579 AAATTTGGTTTAT
1 AAATTTGGTTTAT
1204592 GCTTTTGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (14 bp):
AAATTTGGTTTATT
Found at i:1204884 original size:16 final size:16
Alignment explanation
Indices: 1204863--1204896 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1204853 ATAATGAAAT
*
1204863 TATATGTATATGTGAA
1 TATATGTATATGAGAA
*
1204879 TATATGTTTATGAGAA
1 TATATGTATATGAGAA
1204895 TA
1 TA
1204897 CATAAGAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (16 bp):
TATATGTATATGAGAA
Found at i:1205153 original size:21 final size:21
Alignment explanation
Indices: 1205136--1205175 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1205126 TACGTGACAT
1205136 AAAATAAGAGATATGTGAAAG
1 AAAATAAGAGATATGTGAAAG
1205157 AAAATAAGAGATATGTGAA
1 AAAATAAGAGATATGTGAA
1205176 TTGTTATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (21 bp):
AAAATAAGAGATATGTGAAAG
Found at i:1205288 original size:31 final size:31
Alignment explanation
Indices: 1205249--1205388 Score: 226
Period size: 31 Copynumber: 4.5 Consensus size: 31
1205239 AGGGTCGAGG
1205249 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1205280 ATTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1205311 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1205342 GTTTACCTATGTTCTTCGAGATATATGGAAT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1205373 GTTTACCTAGGTTCTT
1 GTTTACCTATGTTCTT
1205389 TAGAATCTCT
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 101 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1210502 original size:8 final size:7
Alignment explanation
Indices: 1210462--1210501 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
1210452 AATTTTTCAT
1210462 TTTTTCC
1 TTTTTCC
1210469 TTTTTCC
1 TTTTTCC
1210476 TTTTTCC
1 TTTTTCC
* *
1210483 CTTTTCT
1 TTTTTCC
1210490 TTTTTCC
1 TTTTTCC
1210497 TTTTT
1 TTTTT
1210502 TTTAATATAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTCC
Found at i:1213600 original size:20 final size:20
Alignment explanation
Indices: 1213572--1213610 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1213562 GCAAAGATGC
* *
1213572 AAATGCAAAAATGAAAATGT
1 AAATACAAAAATAAAAATGT
*
1213592 AAATACAAACATAAAAATG
1 AAATACAAAAATAAAAATG
1213611 AAAAGATGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.08, G:0.10, T:0.18
Consensus pattern (20 bp):
AAATACAAAAATAAAAATGT
Found at i:1213709 original size:7 final size:7
Alignment explanation
Indices: 1213699--1213739 Score: 59
Period size: 6 Copynumber: 6.0 Consensus size: 7
1213689 AGCAAACAAC
1213699 AAATGCA
1 AAATGCA
1213706 AAATG-A
1 AAATGCA
1213712 AAATGCA
1 AAATGCA
1213719 AAGATGCA
1 AA-ATGCA
1213727 AAATGC-
1 AAATGCA
1213733 AAATGCA
1 AAATGCA
1213740 TGTACGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 12 0.39
7 12 0.39
8 7 0.23
ACGTcount: A:0.56, C:0.12, G:0.17, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:1215811 original size:33 final size:33
Alignment explanation
Indices: 1215774--1215836 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
1215764 AAATGAAAAT
*
1215774 GGATTTTGAA-AATCAAAATGAAATCTTGAAGAA
1 GGATTTAGAACAATCAAAATGAAAT-TTGAAGAA
**
1215807 GGATTTAGAACTCTCAAAATGAAATTTGAA
1 GGATTTAGAACAATCAAAATGAAATTTGAA
1215837 AGTATTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 14 0.54
34 12 0.46
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (33 bp):
GGATTTAGAACAATCAAAATGAAATTTGAAGAA
Found at i:1219622 original size:21 final size:21
Alignment explanation
Indices: 1219596--1219678 Score: 80
Period size: 23 Copynumber: 3.8 Consensus size: 21
1219586 TATAGGGCAG
1219596 AGGGAATCGATACCCCCTTGA
1 AGGGAATCGATACCCCCTTGA
* *
1219617 AGGGAAACCGATTCCCCCTTTGA
1 AGGG-AATCGATACCCCC-TTGA
*
1219640 ATGGGAA-CTGATTCCCTCCTT-A
1 A-GGGAATC-GATACCC-CCTTGA
1219662 AGGGAATCGATACCCCC
1 AGGGAATCGATACCCCC
1219679 AATGGGTTCT
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
20 2 0.04
21 15 0.28
22 15 0.28
23 16 0.30
24 5 0.09
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.22
Consensus pattern (21 bp):
AGGGAATCGATACCCCCTTGA
Found at i:1224380 original size:4 final size:4
Alignment explanation
Indices: 1224328--1224360 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
1224318 AATATTAATA
1224328 TATT TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT T
1224361 TTATAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1226087 original size:3 final size:3
Alignment explanation
Indices: 1226081--1226131 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
1226071 TATTTTTTAT
* *
1226081 TAA TAA TAA TAA TAA TAA TAA TAAA TAA T-A TTA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
1226126 TAA TAA
1 TAA TAA
1226132 AAGCAAATGG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1230347 original size:90 final size:89
Alignment explanation
Indices: 1230194--1230370 Score: 318
Period size: 90 Copynumber: 2.0 Consensus size: 89
1230184 CCTAATACAC
1230194 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
* *
1230259 TTTAATTAATTGGAATTTAATAAT
66 TTTAATTAATTGAAATTAAATAAT
*
1230283 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTAT
1230348 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTGAAATTAAATA
1230371 TTCGGGATTA
Statistics
Matches: 84, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
89 34 0.40
90 50 0.60
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAAATAAT
Found at i:1233945 original size:31 final size:31
Alignment explanation
Indices: 1233878--1233937 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
1233868 CAATTTAAGG
*
1233878 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
*
1233909 CAAAAT-GTATTTGGACTT-AATTTAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1233938 TTCAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 11 0.41
31 6 0.22
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:1234219 original size:21 final size:21
Alignment explanation
Indices: 1234186--1234225 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1234176 TTTTTGCAGA
*
1234186 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1234208 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1234226 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1248781 original size:27 final size:27
Alignment explanation
Indices: 1248751--1248803 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1248741 TATGATTTTA
1248751 ATATA-AAATACAAAAAATATTTAAAAT
1 ATATATAAATACAAAAAAT-TTTAAAAT
**
1248778 ATATATAAATTTAAAAAATTTTAAAA
1 ATATATAAATACAAAAAATTTTAAAA
1248804 AGAGGATCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (27 bp):
ATATATAAATACAAAAAATTTTAAAAT
Found at i:1249681 original size:17 final size:18
Alignment explanation
Indices: 1249645--1249684 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1249635 TTATTAATAG
1249645 AAAATATAAAAAATATTT
1 AAAATATAAAAAATATTT
* *
1249663 AAAATATATAAGA-ATTT
1 AAAATATAAAAAATATTT
1249680 AAAAT
1 AAAAT
1249685 TTTCAGAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
AAAATATAAAAAATATTT
Found at i:1254050 original size:15 final size:16
Alignment explanation
Indices: 1254012--1254051 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1254002 ACAGAGCCTA
*
1254012 TGAATCATTCAACATT
1 TGAATCATTCAACACT
*
1254028 TGAATCATTCAACGCT
1 TGAATCATTCAACACT
1254044 T-AATCATT
1 TGAATCATT
1254052 TTGAAGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (16 bp):
TGAATCATTCAACACT
Found at i:1255450 original size:23 final size:23
Alignment explanation
Indices: 1255423--1255469 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1255413 TTTTAAAGTG
1255423 ACATGGCACAACCAAAAAATGAC
1 ACATGGCACAACCAAAAAATGAC
* * *
1255446 ACATGGCACTACGAAAAAGTGAC
1 ACATGGCACAACCAAAAAATGAC
1255469 A
1 A
1255470 TGTGGAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.23, G:0.17, T:0.11
Consensus pattern (23 bp):
ACATGGCACAACCAAAAAATGAC
Found at i:1255470 original size:21 final size:21
Alignment explanation
Indices: 1255417--1255471 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 21
1255407 CTACATTTTT
1255417 AAAGTGACATGGCACAACCAA
1 AAAGTGACATGGCACAACCAA
* * *
1255438 AAAATGACACATGGCACTACGAA
1 AAAGTG--ACATGGCACAACCAA
1255461 AAAGTGACATG
1 AAAGTGACATG
1255472 TGGAATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 10 0.36
23 18 0.64
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (21 bp):
AAAGTGACATGGCACAACCAA
Found at i:1255551 original size:27 final size:28
Alignment explanation
Indices: 1255509--1255561 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
1255499 TATCAGAATA
*
1255509 TTTTAAAAATATATTA-AAAT-TTTTAT
1 TTTTAAAAATAAATTATAAATATTTTAT
1255535 TTTTAAAAAATAAATTATAAATATTTT
1 TTTT-AAAAATAAATTATAAATATTTT
1255562 GAATTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 11 0.48
28 4 0.17
29 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTTAAAAATAAATTATAAATATTTTAT
Found at i:1258907 original size:11 final size:11
Alignment explanation
Indices: 1258891--1258915 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1258881 TGTGAGATAG
1258891 TTAACGATTTT
1 TTAACGATTTT
1258902 TTAACGATTTT
1 TTAACGATTTT
1258913 TTA
1 TTA
1258916 TAATATACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (11 bp):
TTAACGATTTT
Found at i:1264469 original size:25 final size:27
Alignment explanation
Indices: 1264441--1264491 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
1264431 CTTTCTATTT
1264441 TCTCTTATTTCTT-CCCT-TTTTTTTC
1 TCTCTTATTTCTTCCCCTCTTTTTTTC
*
1264466 TCTCTTCTTTCTTCCCCTCTTTTTTT
1 TCTCTTATTTCTTCCCCTCTTTTTTT
1264492 TCATTTCCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.52
26 4 0.17
27 7 0.30
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (27 bp):
TCTCTTATTTCTTCCCCTCTTTTTTTC
Found at i:1265057 original size:15 final size:15
Alignment explanation
Indices: 1265037--1265067 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1265027 GGAAGACGCA
*
1265037 TGGACTTTAATACGT
1 TGGACTCTAATACGT
1265052 TGGACTCTAATACGT
1 TGGACTCTAATACGT
1265067 T
1 T
1265068 TTTAGTGTTT
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:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (15 bp):
TGGACTCTAATACGT
Found at i:1267065 original size:2 final size:2
Alignment explanation
Indices: 1267060--1267136 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
1267050 GCGCACACAC
1267060 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1267102 AT AT AT 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 AT AT AT A
1267137 GGTTGAAAAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1269762 original size:24 final size:24
Alignment explanation
Indices: 1269730--1269778 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1269720 AGTCTTCCTG
1269730 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
1269754 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
1269778 A
1 A
1269779 ATGTCATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:1271390 original size:4 final size:4
Alignment explanation
Indices: 1271361--1273467 Score: 2485
Period size: 4 Copynumber: 528.8 Consensus size: 4
1271351 GCCACTCCTA
* * * * * *
1271361 GATG GATA GATG GAAG GATA GATG GATG GATA GATG GATA GATA GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * * *
1271409 GATA GATG GATA GATA GATG AATA GATG GATG GATG GATA GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * * * * * *
1271457 GATT GATA GATG GATA GATA GATA GATG GATA GATA GATG GATA GATA
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * * * *
1271505 GATG GATA GATA GATG AATA GATG GATG GATG GATA GATG GATA GATT
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * *
1271553 GATG GATG GATG GATG GATG AATA GATG GATG GATG GATA GATA GATA
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * * * * *
1271601 GATA GATG GATA GATA GATG GATA GATA GATG AATA GATG GATG GATT
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * * * * *
1271649 GATA GATG GATA GATA GATT GATA GATG GATA GATA GATG GATA GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * * * * *
1271697 GATA GATA GATG AATA GATG GATG GATG GATA GATG GATA GATA GATT
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * * * * * *
1271745 GATA GATG GATA GATA GATA GATG GATA GATG GATA GATA GATG AATA
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * *
1271793 GATG GATG GATG GATA GATG GATA GATT GTTG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * * * * * * *
1271841 AATA GATG GATG GATA GATA AATA GATA GATG GATA GATA GATG GATA
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * * *
1271889 GATA GATG AATA GATG GATG GATG GATA GATG GATA GATT GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * * *
1271937 GATG GATG AATA GATG GATG GATG GATA GATA GATA GATA GATAG G-TAG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GAT-G GAT-G
* *
1271986 G-TAG G-TAG G-TAG G-TAG G-TAG G-TAG G-TAG G-TA GATA GATAG G-TAG
1 GAT-G GAT-G GAT-G GAT-G GAT-G GAT-G GAT-G GATG GATG GAT-G GAT-G
* *
1272030 G-TAG G-TAG G-TAG G-TA GATA GATAG G-TAG G-TAG G-TAG G-TAG G-TAG
1 GAT-G GAT-G GAT-G GATG GATG GAT-G GAT-G GAT-G GAT-G GAT-G GAT-G
* * * * * * * * *
1272074 G-TAG G-TG GGTG GGTG GGTG GGTG GGTG GGTG GGTG GGTG GGTG G-TG
1 GAT-G GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * *
1272120 G--G GGTG GGTG GGTG GGTG G-TG GTATG TA-G G-TAG G-TAG G-TAG
1 GATG GATG GATG GATG GATG GATG G-ATG GATG GAT-G GAT-G GAT-G
* * * * *
1272161 G-TAG G-TAG G-TAG G-TAG G-TAG GGTGG GGTG GGTG G-TG GGTG GGTG
1 GAT-G GAT-G GAT-G GAT-G GAT-G GAT-G GATG GATG GATG GATG GATG
* * * * * * * * *
1272205 GGTG GGTG GGTG G-TG GGTG GGTG GGTG G-TG GGTG GGTG G-TG GGTG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * *
1272250 G-TG GGTG G-TG GATG GGTG GATG GATG GGTG GGTG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1272296 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1272344 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1272392 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1272440 GATG GATG GATG GATGG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GAT-G GATG GATG GATG GATG GATG GATG GATG GATG
1272489 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1272537 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1272585 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1272633 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1272681 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1272729 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1272777 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1272825 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1272873 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1272921 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1272969 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1273017 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1273065 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1273113 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1273161 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
*
1273209 GATG GATG GATG GATG GATG GAGG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1273257 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1273305 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1273353 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1273401 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1273449 GATG GATG GATG GATG GAT
1 GATG GATG GATG GATG GAT
1273468 AAGATCCTGT
Statistics
Matches: 1949, Mismatches: 134, Indels: 40
0.92 0.06 0.02
Matches are distributed among these distances:
2 2 0.00
3 29 0.01
4 1904 0.98
5 14 0.01
ACGTcount: A:0.27, C:0.00, G:0.47, T:0.25
Consensus pattern (4 bp):
GATG
Found at i:1274808 original size:20 final size:20
Alignment explanation
Indices: 1274783--1274835 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1274773 GAGGCACGAG
1274783 GAAGAAGAGGCAATTATTAA
1 GAAGAAGAGGCAATTATTAA
1274803 GAAGAAGAGGCAATTATTAA
1 GAAGAAGAGGCAATTATTAA
*
1274823 GAGGAAGA-GCAAT
1 GAAGAAGAGGCAAT
1274836 GATATTCATC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 5 0.16
20 27 0.84
ACGTcount: A:0.49, C:0.06, G:0.28, T:0.17
Consensus pattern (20 bp):
GAAGAAGAGGCAATTATTAA
Found at i:1275763 original size:24 final size:24
Alignment explanation
Indices: 1275735--1275796 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
1275725 CGTTCGTGAA
1275735 CGTTCAGTTATGTTCGTTTATGTT
1 CGTTCAGTTATGTTCGTTTATGTT
* * *
1275759 TGTTCGGTTATATTCGTTTATGTT
1 CGTTCAGTTATGTTCGTTTATGTT
* *
1275783 CATTCATTTATGTT
1 CGTTCAGTTATGTT
1275797 TAAGCCAATC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.15, C:0.11, G:0.18, T:0.56
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATGTT
Found at i:1276260 original size:16 final size:16
Alignment explanation
Indices: 1276239--1276278 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1276229 AATCCAATAA
1276239 TCGAGTTCAATCCTTT
1 TCGAGTTCAATCCTTT
1276255 TCGAGTTCAATCCTTT
1 TCGAGTTCAATCCTTT
1276271 TCGAGTTC
1 TCGAGTTC
1276279 GAGTCGAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.17, C:0.25, G:0.15, T:0.42
Consensus pattern (16 bp):
TCGAGTTCAATCCTTT
Found at i:1276432 original size:10 final size:10
Alignment explanation
Indices: 1276417--1276490 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 10
1276407 GGTCTCCAAT
1276417 GTTTATGTTC
1 GTTTATGTTC
1276427 GTTTATGTTC
1 GTTTATGTTC
1276437 G----TGTTC
1 GTTTATGTTC
*
1276443 ATTTATGTTC
1 GTTTATGTTC
* *
1276453 GTGTT-CGTTTAT
1 GT-TTATG-TT-C
*
1276465 GTTTGTGTTC
1 GTTTATGTTC
1276475 GTTTATGTTC
1 GTTTATGTTC
1276485 GTTTAT
1 GTTTAT
1276491 TTATTAAATG
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.10
10 33 0.67
11 8 0.16
12 3 0.06
ACGTcount: A:0.09, C:0.09, G:0.22, T:0.59
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:1276441 original size:16 final size:16
Alignment explanation
Indices: 1276422--1276486 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
1276412 CCAATGTTTA
1276422 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1276438 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1276454 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
1276470 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1276486 T
1 T
1276487 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1287239 original size:36 final size:36
Alignment explanation
Indices: 1287198--1287300 Score: 179
Period size: 36 Copynumber: 2.9 Consensus size: 36
1287188 ATTTATCCAT
*
1287198 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1287234 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* *
1287270 TATCAGCTTTGGTATATTCGTGTACCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
1287301 CCAGTACCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:1293325 original size:19 final size:19
Alignment explanation
Indices: 1293294--1293346 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
1293284 ACCAACAAAA
*
1293294 TCGCAATGCGATCTCTAAT
1 TCGCATTGCGATCTCTAAT
*
1293313 TCGCATTGTGATCTCTAAT
1 TCGCATTGCGATCTCTAAT
1293332 TCGCATTGCGATCTC
1 TCGCATTGCGATCTC
1293347 CATTATCGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (19 bp):
TCGCATTGCGATCTCTAAT
Found at i:1293418 original size:21 final size:21
Alignment explanation
Indices: 1293392--1293445 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
1293382 ATTTTCCAGT
1293392 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
1293413 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
1293434 TAGCGTTGCGAT
1 TCGCGTTGCGAT
1293446 TTTCATTTCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:1293484 original size:22 final size:22
Alignment explanation
Indices: 1293456--1293571 Score: 89
Period size: 22 Copynumber: 5.4 Consensus size: 22
1293446 TTTCATTTCG
1293456 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * *
1293478 CGTTGCGAT--TTTCCAATTCGTT
1 CGTTGCGATAGTCTACAGTT-G-T
* * **
1293500 GCGTTGCGAT--TTTCCAAAT-T
1 -CGTTGCGATAGTCTACAGTTGT
*
1293520 CGTTGTGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
1293542 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1293564 CGTTGCGA
1 CGTTGCGA
1293572 AAATCCGTTG
Statistics
Matches: 76, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
19 8 0.11
20 7 0.09
21 6 0.08
22 38 0.50
23 17 0.22
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.40
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:1293508 original size:23 final size:25
Alignment explanation
Indices: 1293473--1293525 Score: 92
Period size: 23 Copynumber: 2.2 Consensus size: 25
1293463 ATAGTCTACA
1293473 GTTGTCGTTGCGATTTTCC-AATTC
1 GTTGTCGTTGCGATTTTCCAAATTC
1293497 GTTG-CGTTGCGATTTTCCAAATTC
1 GTTGTCGTTGCGATTTTCCAAATTC
1293521 GTTGT
1 GTTGT
1293526 GATAGTCTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (25 bp):
GTTGTCGTTGCGATTTTCCAAATTC
Found at i:1293661 original size:6 final size:6
Alignment explanation
Indices: 1293650--1293682 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1293640 GACAAGTATT
1293650 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1293683 CGAGACGAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1294179 original size:11 final size:11
Alignment explanation
Indices: 1294163--1294199 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
1294153 GCCGTCTGTC
*
1294163 TCGGGTCGGGG
1 TCGGGTCGTGG
1294174 TCGGGTCGTGG
1 TCGGGTCGTGG
1294185 TCGTGGTCGTGG
1 TCG-GGTCGTGG
1294197 TCG
1 TCG
1294200 TGGTAATACG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.00, C:0.19, G:0.54, T:0.27
Consensus pattern (11 bp):
TCGGGTCGTGG
Found at i:1294200 original size:6 final size:6
Alignment explanation
Indices: 1294166--1294203 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
1294156 GTCTGTCTCG
*
1294166 GGTCGG GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1294204 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.00, C:0.16, G:0.55, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:1294200 original size:18 final size:17
Alignment explanation
Indices: 1294166--1294203 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1294156 GTCTGTCTCG
1294166 GGTCGGGGTCGGGTCGT
1 GGTCGGGGTCGGGTCGT
*
1294183 GGTCGTGGTCGTGGTCGT
1 GGTCGGGGTCG-GGTCGT
1294201 GGT
1 GGT
1294204 AATACGTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.00, C:0.16, G:0.55, T:0.29
Consensus pattern (17 bp):
GGTCGGGGTCGGGTCGT
Found at i:1294325 original size:22 final size:22
Alignment explanation
Indices: 1294299--1294348 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 22
1294289 GATTTGGAAA
1294299 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
1294321 ATCGC-A--ACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
1294340 ATTGCAACG
1 ATCGCAACG
1294349 CGAAATGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 17 0.71
20 1 0.04
21 1 0.04
22 5 0.21
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:1294332 original size:19 final size:19
Alignment explanation
Indices: 1294308--1294347 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1294298 AATCGCAACG
1294308 ACAACTGTAGACTATCGCA
1 ACAACTGTAGACTATCGCA
*
1294327 ACAACTGTAGACTATTGCA
1 ACAACTGTAGACTATCGCA
1294346 AC
1 AC
1294348 GCGAAATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.23
Consensus pattern (19 bp):
ACAACTGTAGACTATCGCA
Found at i:1294433 original size:21 final size:21
Alignment explanation
Indices: 1294409--1294473 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
1294399 AAATCGCGTT
1294409 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
* ** * **
1294430 GCGA-ATGGAA-AATCGCATT
1 GCGATTTTCAACTATCGCAAC
1294449 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
1294470 GCGA
1 GCGA
1294474 AATGCAACGC
Statistics
Matches: 30, Mismatches: 12, Indels: 4
0.65 0.26 0.09
Matches are distributed among these distances:
19 10 0.33
20 6 0.20
21 14 0.47
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
GCGATTTTCAACTATCGCAAC
Found at i:1294451 original size:40 final size:41
Alignment explanation
Indices: 1294337--1294477 Score: 239
Period size: 41 Copynumber: 3.5 Consensus size: 41
1294327 ACAACTGTAG
* *
1294337 ACTATTGCAACGCGAAATGGAAAATCGCGTTGCGATTTTTA
1 ACTATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
*
1294378 ACTATCGCAACTCGAAATGGAAAATCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
*
1294419 ACTATCGCAACGCG-AATGGAAAATCGCATTGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
1294459 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
1294478 CAACGCGAAT
Statistics
Matches: 94, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
40 39 0.41
41 55 0.59
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
Found at i:1294481 original size:21 final size:21
Alignment explanation
Indices: 1294417--1294481 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
1294407 TTGCGATTTT
1294417 CAACTATCGCAACGCG-AATG
1 CAACTATCGCAACGCGAAATG
* * ** ** *
1294437 GAA-AATCGCATTGCGATTTT
1 CAACTATCGCAACGCGAAATG
1294457 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
1294478 CAAC
1 CAAC
1294482 GCGAATTTGC
Statistics
Matches: 29, Mismatches: 14, Indels: 3
0.63 0.30 0.07
Matches are distributed among these distances:
19 9 0.31
20 5 0.17
21 15 0.52
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:1294517 original size:28 final size:28
Alignment explanation
Indices: 1294477--1294544 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
1294467 AACGCGAAAT
1294477 GCAACGCGAATTTGCGATAGTGGAGATC
1 GCAACGCGAATTTGCGATAGTGGAGATC
1294505 GCAACGCGAATTTGCGATAGTGGAGATC
1 GCAACGCGAATTTGCGATAGTGGAGATC
*
1294533 GCAATGCGAATT
1 GCAACGCGAATT
1294545 AGAGATCGCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (28 bp):
GCAACGCGAATTTGCGATAGTGGAGATC
Found at i:1294551 original size:19 final size:19
Alignment explanation
Indices: 1294527--1294579 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
1294517 TGCGATAGTG
1294527 GAGATCGCAATGCGAATTA
1 GAGATCGCAATGCGAATTA
1294546 GAGATCGCAATGCGAATTA
1 GAGATCGCAATGCGAATTA
*
1294565 GAGATCGCATTGCGA
1 GAGATCGCAATGCGA
1294580 TTTTGTTGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (19 bp):
GAGATCGCAATGCGAATTA
Found at i:1294996 original size:226 final size:219
Alignment explanation
Indices: 1294563--1295009 Score: 815
Period size: 226 Copynumber: 2.0 Consensus size: 219
1294553 CAATGCGAAT
1294563 TAGAGATCGCATTGCGATTTTGTTGTCATTTTCACAAATCCAAAAAAGTTGGTCAAAATCGTATA
1 TAGAGATCGCATTGCGATTTTGTTGTCATTTTCACAAATCCAAAAAAGTTGGTCAAAATCGTATA
1294628 TTAGGATTTTGGTCACTGAGGTTATTTTCTCTATACAAAAGGTATGAATTTCTAACCGATGAAAG
66 TTAGGATTTTGGTCACTGAGGTTATTTTCTCTATACAAAAGGTATGAATTTCTAACCGATGAAAG
1294693 GTCAAAAACGGGCAGCAGATTCTGCACAAAACAGATTATGTCGGTCAATTTTGAAAATTCACCAT
131 GTCAAAAACGGGCAGCAGATTCTGCACAAAACAGATTATGTCGGTCAATTTTGAAAATTCACCAT
1294758 AAATTGTATGGAATGGACTAGAAG
196 AAATTGTATGGAATGGACTAGAAG
1294782 TAGAGATCGCATTGCGATTTTGTTGGTCATTTTCACAAATCCAAAAAAAGTTGGTCAAAATCGTA
1 TAGAGATCGCATTGCGATTTTGTT-GTCATTTTCACAAATCC-AAAAAAGTTGGTCAAAATCG--
1294847 TATTATCTAGGATTTTGGTCACTGAGGTTATTTTCTCTATACAAAAGGTATGAATTTCTAACCGA
62 TA-TAT-TAGGATTTTGGTCACTGAGGTTATTTTCTCTATACAAAAGGTATGAATTTCTAACCGA
1294912 TGAAAGGTCAGAAAAAC-GGCAGCAGATTCTGCACAAAACAGATTATGTCGGTCAATTTTGAAAA
125 TGAAAGGTC--AAAAACGGGCAGCAGATTCTGCACAAAACAGATTATGTCGGTCAATTTTGAAAA
1294976 TTCACCATAAATTGTATGGAATGGACTAGAAG
188 TTCACCATAAATTGTATGGAATGGACTAGAAG
1295008 TA
1 TA
1295010 TTTATTTATA
Statistics
Matches: 220, Mismatches: 0, Indels: 9
0.96 0.00 0.04
Matches are distributed among these distances:
219 24 0.11
220 17 0.08
221 20 0.09
223 2 0.01
224 3 0.01
225 67 0.30
226 81 0.37
227 6 0.03
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (219 bp):
TAGAGATCGCATTGCGATTTTGTTGTCATTTTCACAAATCCAAAAAAGTTGGTCAAAATCGTATA
TTAGGATTTTGGTCACTGAGGTTATTTTCTCTATACAAAAGGTATGAATTTCTAACCGATGAAAG
GTCAAAAACGGGCAGCAGATTCTGCACAAAACAGATTATGTCGGTCAATTTTGAAAATTCACCAT
AAATTGTATGGAATGGACTAGAAG
Found at i:1296101 original size:35 final size:35
Alignment explanation
Indices: 1296061--1296159 Score: 155
Period size: 35 Copynumber: 2.8 Consensus size: 35
1296051 ATTTATCCAT
* *
1296061 TATCAGCTTTGATACATTCGTGTATC-ATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAAT-ATATCA
1296096 TATCAGCTTTGGTACATTCGTGTATCAATATATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATATATCA
*
1296131 TATCAGCTTTGGTACATTCGTGTACCAAT
1 TATCAGCTTTGGTACATTCGTGTATCAAT
1296160 GTCCAGCACC
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
35 58 0.97
36 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.40
Consensus pattern (35 bp):
TATCAGCTTTGGTACATTCGTGTATCAATATATCA
Found at i:1297190 original size:380 final size:381
Alignment explanation
Indices: 1296534--1297294 Score: 1442
Period size: 380 Copynumber: 2.0 Consensus size: 381
1296524 TTATATTAGT
1296534 TAATGATTTCATACGTAGGGTCTGATTGAGATACATACGTTTTATGAGAAGCCTACCAAGCATCA
1 TAATGATTTCATACGTAGGGTCTGATTGAGATACATACGTTTTATGAGAAGCCTACCAAGCATCA
1296599 TGTGCAGATCATCTATAATACCAGTATCAGTAAGACATCATTAAAGTGTCTTTTGACTAGTTGTG
66 TGTGCAGATCATCTATAATACCAGTATCAGTAAGACATCATTAAAGTGTCTTTTGACTAGTTGTG
1296664 GTTGTGGCATATATAATATGTCAGTAATTCTATTTATCGTATTTACTTTAAATAATAGTAATAGT
131 GTTGTGGCATATATAATATGTCAGTAATTCTATTTATCGTATTTACTTTAAATAATAGTAATAGT
1296729 AAATTAGAACTATTTAGTTTATTTTACTTAGTTTAGTTTTATCAGTATCTATGCATGAAAAGAAT
196 AAATTAGAACTATTTAGTTTATTTTACTTAGTTTAGTTTTATCAGTATCTATGCATG-AAAGAAT
1296794 ATATTACGTTATTATGTTTTTAAAAGATTTCACGAAAAGACATGGTTTAGTAAAATTATTGATTA
260 ATATTACGTTATTATGTTTTTAAAAGATTTCACGAAAAGACATGGTTTAGTAAAATTATTGATTA
1296859 ACAAATG-ATTTA-TTTTCTCTGACAAAGGAA-AAATTATAGTTGAGATACACTTTG
325 ACAAATGAATTTATTTTTCTCTGACAAAGGAATAAATTATAGTTGAGATACACTTTG
1296913 TAATGATTTTCATACGTAGGGTCTGATTGAGATACATACGTTTTATGAGAAGCCTACCAAGCATC
1 TAATGA-TTTCATACGTAGGGTCTGATTGAGATACATACGTTTTATGAGAAGCCTACCAAGCATC
1296978 ATGTGCAGATCATCTATAATACCAGTATCA-TAAGACATCATTAAAGTGTCTTTTGACTAGTTGT
65 ATGTGCAGATCATCTATAATACCAGTATCAGTAAGACATCATTAAAGTGTCTTTTGACTAGTTGT
1297042 GGTTGTGGCATATATAATTATGTCAGTAATTTCTATTTATCGTATTTACTTTAAATAATATGTAA
130 GGTTGTGGCATATATAA-TATGTCAGTAA-TTCTATTTATCGTATTTACTTTAAATAATA-GTAA
1297107 TAGTAAATTAGAACTATTTAGTTTATTTTACTTAGTTTAGTTTTATCAGTATCTATGCATG-AAG
192 TAGTAAATTAGAACTATTTAGTTTATTTTACTTAGTTTAGTTTTATCAGTATCTATGCATGAAAG
1297171 AATATATTACGTTATTATGTTTTTAAAAGATTTCACGAAAAGACATGGTTTAGTAAAATTATTGA
257 AATATATTACGTTATTATGTTTTTAAAAGATTTCACGAAAAGACATGGTTTAGTAAAATTATTGA
1297236 TTAACAAATGAATTTATTTTTCTCTGACAAAGGAATAAATTATAGTTGAGATACACTTT
322 TTAACAAATGAATTTATTTTTCTCTGACAAAGGAATAAATTATAGTTGAGATACACTTT
1297295 AAAATAGATT
Statistics
Matches: 375, Mismatches: 0, Indels: 10
0.97 0.00 0.03
Matches are distributed among these distances:
379 57 0.15
380 177 0.47
381 35 0.09
382 83 0.22
383 23 0.06
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (381 bp):
TAATGATTTCATACGTAGGGTCTGATTGAGATACATACGTTTTATGAGAAGCCTACCAAGCATCA
TGTGCAGATCATCTATAATACCAGTATCAGTAAGACATCATTAAAGTGTCTTTTGACTAGTTGTG
GTTGTGGCATATATAATATGTCAGTAATTCTATTTATCGTATTTACTTTAAATAATAGTAATAGT
AAATTAGAACTATTTAGTTTATTTTACTTAGTTTAGTTTTATCAGTATCTATGCATGAAAGAATA
TATTACGTTATTATGTTTTTAAAAGATTTCACGAAAAGACATGGTTTAGTAAAATTATTGATTAA
CAAATGAATTTATTTTTCTCTGACAAAGGAATAAATTATAGTTGAGATACACTTTG
Found at i:1304193 original size:23 final size:24
Alignment explanation
Indices: 1304135--1304193 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
1304125 TTATATTCAC
1304135 TTTATTT-TTTATTACTTTCCTTA
1 TTTATTTATTTATTACTTTCCTTA
1304158 TTTCATTTA--TATTAC-TTCCTT-
1 TTT-ATTTATTTATTACTTTCCTTA
1304179 TATTATTTATTTATT
1 T-TTATTTATTTATT
1304194 TAATCTCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
21 6 0.19
22 8 0.26
23 13 0.42
24 4 0.13
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTATTTATTTATTACTTTCCTTA
Found at i:1314457 original size:46 final size:48
Alignment explanation
Indices: 1314382--1314472 Score: 123
Period size: 46 Copynumber: 1.9 Consensus size: 48
1314372 AATACTTCGC
* * * *
1314382 TTAGGATGAAAACCCGAGAGTGCGTCCTAAGTTG-GAAAA-AAAATGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAATGT
*
1314428 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAA
1314473 AGAAAAAGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
46 29 0.76
47 5 0.13
48 4 0.11
ACGTcount: A:0.42, C:0.14, G:0.26, T:0.18
Consensus pattern (48 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAATGT
Found at i:1315639 original size:105 final size:105
Alignment explanation
Indices: 1315262--1315714 Score: 786
Period size: 105 Copynumber: 4.3 Consensus size: 105
1315252 AGGTTTTACC
* * *
1315262 CAGAGTCAGTTTCAACTTCACAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1315327 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTTAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
1315367 CGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1315432 ACG-AGGGACCGCTGGTTGTCAACAAACA-TTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
1315470 CAGAGCCAGTTTCAACTTCAC-ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1315534 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
**
1315574 CAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1315639 ACAAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
1315679 CAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1315715 CCTCGAAACA
Statistics
Matches: 332, Mismatches: 13, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
102 46 0.14
103 53 0.16
104 55 0.17
105 178 0.54
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:1316176 original size:2 final size:2
Alignment explanation
Indices: 1316171--1316213 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
1316161 CCGAAAGAAC
*
1316171 AT AT AT AT AT AT AT AT AT AT -T AT AT -T AC AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1316210 AT AT
1 AT AT
1316214 CAGTATTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1316220 original size:24 final size:24
Alignment explanation
Indices: 1316175--1316221 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1316165 AAGAACATAT
*
1316175 ATATATATATATATATTATATTAC
1 ATATATATATATATATCATATTAC
1316199 ATATATATAT-TATATCAGTATTA
1 ATATATATATATATATCA-TATTA
1316222 TTATTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (24 bp):
ATATATATATATATATCATATTAC
Found at i:1317848 original size:23 final size:23
Alignment explanation
Indices: 1317790--1317853 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 23
1317780 TTATATTCAC
1317790 TTTATTT-TTTATTACTTTCCTTA
1 TTTATTTATTTATTAC-TTCCTTA
1317813 TTTCATTTA--TATTACTTCCTT-
1 TTT-ATTTATTTATTACTTCCTTA
*
1317834 TATTATTTATTTATTTCTTC
1 T-TTATTTATTTATTACTTC
1317854 TCTTCTAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
21 6 0.17
22 8 0.23
23 17 0.49
24 4 0.11
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTATTTATTTATTACTTCCTTA
Found at i:1324534 original size:22 final size:22
Alignment explanation
Indices: 1324506--1324550 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1324496 CTATTTTATA
1324506 ATTTCTAATAGTTAGGAGACTC
1 ATTTCTAATAGTTAGGAGACTC
1324528 ATTTCTAATAGTTAGGAGACTC
1 ATTTCTAATAGTTAGGAGACTC
1324550 A
1 A
1324551 GTAACCTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (22 bp):
ATTTCTAATAGTTAGGAGACTC
Found at i:1325413 original size:29 final size:29
Alignment explanation
Indices: 1325371--1325532 Score: 272
Period size: 29 Copynumber: 5.6 Consensus size: 29
1325361 CCGTTGACTC
* *
1325371 GGGTGTTATTTTCGTAAATATTGTTAAAA
1 GGGTGTTAGTTTCGTAAATATTTTTAAAA
*
1325400 GGGTGTTAGTTTCGTAAATATTTTAAAAA
1 GGGTGTTAGTTTCGTAAATATTTTTAAAA
1325429 GGGTGTTAGTTTCGTAAATATTTTTAAAA
1 GGGTGTTAGTTTCGTAAATATTTTTAAAA
1325458 -GGTGTTAGTTTCGTAAATATTTTTAAAAA
1 GGGTGTTAGTTTCGTAAATATTTTT-AAAA
1325487 GGGTGTTAGTTTCGTAAATATTTTTAAAA
1 GGGTGTTAGTTTCGTAAATATTTTTAAAA
*
1325516 GGGTGTTAGTTTTGTAA
1 GGGTGTTAGTTTCGTAA
1325533 TTAATTTCTG
Statistics
Matches: 126, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
28 24 0.19
29 78 0.62
30 24 0.19
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.44
Consensus pattern (29 bp):
GGGTGTTAGTTTCGTAAATATTTTTAAAA
Found at i:1327481 original size:25 final size:25
Alignment explanation
Indices: 1327446--1327498 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1327436 AAGGTAACAC
* *
1327446 TTTTATAAGATTTACTGCATTATGA
1 TTTTATAAGATTTACTGAACTATGA
*
1327471 TTTTATGAGATTTACTGAACTATGA
1 TTTTATAAGATTTACTGAACTATGA
1327496 TTT
1 TTT
1327499 GTTTAGTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (25 bp):
TTTTATAAGATTTACTGAACTATGA
Found at i:1334223 original size:24 final size:24
Alignment explanation
Indices: 1334210--1334328 Score: 177
Period size: 24 Copynumber: 5.0 Consensus size: 24
1334200 AAACATAATT
* *
1334210 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCAGATCAGAATC
*
1334234 CAGGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
*
1334258 CAAGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
1334282 CATGTC-AGATATCAGATCAGAATC
1 CATGTCAAG-TATCAGATCAGAATC
*
1334306 CATGTCAAGTATCAAATCAGAAT
1 CATGTCAAGTATCAGATCAGAAT
1334329 TCAAATCTGA
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
23 2 0.02
24 83 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
CATGTCAAGTATCAGATCAGAATC
Found at i:1337127 original size:19 final size:19
Alignment explanation
Indices: 1337103--1337145 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1337093 TTGACTGGCT
* *
1337103 TGACCGGTCTAAACTAGTC
1 TGACCGATCTAAACCAGTC
*
1337122 TGACCGATCTGAACCAGTC
1 TGACCGATCTAAACCAGTC
1337141 TGACC
1 TGACC
1337146 CGACCCCCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (19 bp):
TGACCGATCTAAACCAGTC
Found at i:1337184 original size:22 final size:22
Alignment explanation
Indices: 1337156--1337202 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1337146 CGACCCCCCA
*
1337156 ACCCGACAGTTGAC-CTGACCCG
1 ACCCGACAGTTAACTC-GACCCG
*
1337178 ACCCGACCGTTAACTCGACCCG
1 ACCCGACAGTTAACTCGACCCG
1337200 ACC
1 ACC
1337203 GTTTACCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.23, C:0.45, G:0.19, T:0.13
Consensus pattern (22 bp):
ACCCGACAGTTAACTCGACCCG
Found at i:1337217 original size:24 final size:24
Alignment explanation
Indices: 1337183--1337242 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
1337173 ACCCGACCCG
*
1337183 ACCGTTAACTCGACCCGACCGTTT
1 ACCGTTGACTCGACCCGACCGTTT
1337207 ACCGTTGACTCGACCCGACCGTTT
1 ACCGTTGACTCGACCCGACCGTTT
*
1337231 ACCATTGACTCG
1 ACCGTTGACTCG
1337243 GGTGTTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.20, C:0.37, G:0.18, T:0.25
Consensus pattern (24 bp):
ACCGTTGACTCGACCCGACCGTTT
Found at i:1337310 original size:30 final size:30
Alignment explanation
Indices: 1337243--1337347 Score: 160
Period size: 30 Copynumber: 3.5 Consensus size: 30
1337233 CATTGACTCG
* *
1337243 GGTGTTATTTTCGTAAATATTGTT--AAAA
1 GGTGTTAGTTTCGTAAATATTTTTAAAAAA
1337271 GGATGTTAGTTTCGTAAATATTTTTAAAAAA
1 GG-TGTTAGTTTCGTAAATATTTTTAAAAAA
1337302 GGTGTTAGTTTCGTAAATATTTTTAAAAAA
1 GGTGTTAGTTTCGTAAATATTTTTAAAAAA
*
1337332 GGTGTTAGTTTTGTAA
1 GGTGTTAGTTTCGTAA
1337348 TTAATTTATA
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
28 2 0.03
29 20 0.28
30 43 0.61
31 6 0.08
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.45
Consensus pattern (30 bp):
GGTGTTAGTTTCGTAAATATTTTTAAAAAA
Found at i:1338441 original size:25 final size:25
Alignment explanation
Indices: 1338406--1338456 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1338396 AGGGTAACTC
*
1338406 TTTTATAAGATTTACTGCAGTATGA
1 TTTTATAAGATTTACTGCACTATGA
* *
1338431 TTTTATGAGATTTACTGGACTATGA
1 TTTTATAAGATTTACTGCACTATGA
1338456 T
1 T
1338457 ATGTTTAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (25 bp):
TTTTATAAGATTTACTGCACTATGA
Found at i:1342569 original size:22 final size:22
Alignment explanation
Indices: 1342544--1342587 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1342534 AATTTATTAG
1342544 TATGAATTGATTTATTTCAAAA
1 TATGAATTGATTTATTTCAAAA
*
1342566 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTCAAAA
1342588 AAATTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (22 bp):
TATGAATTGATTTATTTCAAAA
Found at i:1342648 original size:31 final size:31
Alignment explanation
Indices: 1342611--1342669 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1342601 AGTTGTATGG
* *
1342611 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
1342642 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
1342670 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:1342728 original size:223 final size:223
Alignment explanation
Indices: 1342339--1342954 Score: 1101
Period size: 223 Copynumber: 2.8 Consensus size: 223
1342329 AGAACATTAA
1342339 AAAATATGGATTGATTTATTTTAAAAAAATTATTATTGTAGTTGTATGGATTATTTAAATTTCAG
1 AAAATATGGATTGATTTATTTTAAAAAAATTATTATTGTAGTTGTATGGATTATTTAAATTTCAG
*
1342404 TATTGTAAAACTAAAATTATTTAAATTTCAGTATTGCAAAATTCTTTTAAGTTTAAAAAATCAGT
66 TATTGTAAAACTAAAATTATTTAAATTTCAGTATTGCAAAACTCTTTTAAGTTTAAAAAATCAGT
*
1342469 TTATTTATATTTCAGTTTATTTTAGCCGTCTGCAGACGTTAATTTAATAAGGTTATTTATTAAAT
131 TTATTTATATTTCAGTTTATTTTAGCAGTCTGCAGACGTTAATTTAATAAGGTTATTTATTAAAT
1342534 AATTTATTAGTATGAATTGATTTATTTC
196 AATTTATTAGTATGAATTGATTTATTTC
*
1342562 AAAATATGAATTGATTTATTTTAAAAAAATTATTATTGTAGTTGTATGGATTATTTAAATTTCAG
1 AAAATATGGATTGATTTATTTTAAAAAAATTATTATTGTAGTTGTATGGATTATTTAAATTTCAG
*
1342627 TATTGTAAAACTAAAATTATTTAAATCTCAGTATTGCAAAACTCTTTTAAGTTTAAAAAATCAGT
66 TATTGTAAAACTAAAATTATTTAAATTTCAGTATTGCAAAACTCTTTTAAGTTTAAAAAATCAGT
* * *
1342692 TTATTTATATTTTAGTTTATTTTAGTAGTTTGCAGACGTTAATTTAATAAGGTTATTTATTAAAT
131 TTATTTATATTTCAGTTTATTTTAGCAGTCTGCAGACGTTAATTTAATAAGGTTATTTATTAAAT
* *
1342757 AATTTATTAGTATGGATTGATTTATTTT
196 AATTTATTAGTATGAATTGATTTATTTC
*
1342785 AAAATATGGATTGATTTATTTAAAAAAAATTATTATTGTAGTTGTATGGATTATTT-AATTTCAG
1 AAAATATGGATTGATTTATTTTAAAAAAATTATTATTGTAGTTGTATGGATTATTTAAATTTCAG
* *
1342849 TTTTATAAAACTAAAATTA-TTAAATTTCAGTATTGCAAAACTCTTTTAAGTTTAAAAAATCAGT
66 TATTGTAAAACTAAAATTATTTAAATTTCAGTATTGCAAAACTCTTTTAAGTTTAAAAAATCAGT
*
1342913 TTATTTATATTTCAGTTTTTTTTAGCAGTCTGCAGACGTTAA
131 TTATTTATATTTCAGTTTATTTTAGCAGTCTGCAGACGTTAA
1342955 AAAACAAACA
Statistics
Matches: 375, Mismatches: 18, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
221 82 0.22
222 25 0.07
223 268 0.71
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (223 bp):
AAAATATGGATTGATTTATTTTAAAAAAATTATTATTGTAGTTGTATGGATTATTTAAATTTCAG
TATTGTAAAACTAAAATTATTTAAATTTCAGTATTGCAAAACTCTTTTAAGTTTAAAAAATCAGT
TTATTTATATTTCAGTTTATTTTAGCAGTCTGCAGACGTTAATTTAATAAGGTTATTTATTAAAT
AATTTATTAGTATGAATTGATTTATTTC
Found at i:1342792 original size:22 final size:22
Alignment explanation
Indices: 1342767--1342810 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1342757 AATTTATTAG
*
1342767 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTAAAAA
1342789 TATGGATTGATTTATTTAAAAA
1 TATGGATTGATTTATTTAAAAA
1342811 AAATTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.48
Consensus pattern (22 bp):
TATGGATTGATTTATTTAAAAA
Found at i:1342889 original size:30 final size:30
Alignment explanation
Indices: 1342834--1342890 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1342824 AGTTGTATGG
* * *
1342834 ATTATTTAATTTCAGTTTTATAAAACTAAA
1 ATTATTAAATTTCAGTATTACAAAACTAAA
*
1342864 ATTATTAAATTTCAGTATTGCAAAACT
1 ATTATTAAATTTCAGTATTACAAAACT
1342891 CTTTTAAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (30 bp):
ATTATTAAATTTCAGTATTACAAAACTAAA
Found at i:1345784 original size:2 final size:2
Alignment explanation
Indices: 1345777--1345809 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1345767 TTTAAAAAGC
1345777 AT AT 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 AT AT A
1345810 GGGAAAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1350404 original size:19 final size:19
Alignment explanation
Indices: 1350362--1350411 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
1350352 TTGACTGATC
1350362 CATT-ACTTTGACCCGACT
1 CATTGACTTTGACCCGACT
* * *
1350380 TATTGAGTTTGACCTGACT
1 CATTGACTTTGACCCGACT
*
1350399 CGTTGACTTTGAC
1 CATTGACTTTGAC
1350412 ATAAAAAGTA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (19 bp):
CATTGACTTTGACCCGACT
Found at i:1350471 original size:20 final size:20
Alignment explanation
Indices: 1350448--1350490 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1350438 GAACCGATTT
*
1350448 GAACCAGTCCGAGTCAACCC
1 GAACCAATCCGAGTCAACCC
* *
1350468 GAACCAATCTGAGTCAACTC
1 GAACCAATCCGAGTCAACCC
1350488 GAA
1 GAA
1350491 TCGGTCTGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.33, G:0.19, T:0.14
Consensus pattern (20 bp):
GAACCAATCCGAGTCAACCC
Found at i:1350516 original size:14 final size:14
Alignment explanation
Indices: 1350497--1350529 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1350487 CGAATCGGTC
1350497 TGACCCATTGAA-TT
1 TGACCCATT-AACTT
1350511 TGACCCATTAACTT
1 TGACCCATTAACTT
1350525 TGACC
1 TGACC
1350530 TGATCCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.33
Consensus pattern (14 bp):
TGACCCATTAACTT
Found at i:1350564 original size:173 final size:169
Alignment explanation
Indices: 1350272--1350607 Score: 620
Period size: 173 Copynumber: 2.0 Consensus size: 169
1350262 AACTGGCCCG
1350272 ACCGATTTGAACCAGTCCGAGTCACCGAACCAATCTGAGTCAACTCGAATCGGTCTGACCATTGA
1 ACCGATTTGAACCAGTCCGAGTCACCGAACCAATCTGAGTCAACTCGAATCGGTCTGACCATTGA
1350337 ATTTGACCCATTAACTTGACTGATCCATTACTTTGACCCGACTTATTGAGTTTGACCTGACTCGT
66 ATTTGACCCATTAACTTGACTGATCCATTACTTTGACCCGACTTATTGAGTTTGACCTGACTCGT
1350402 TGACTTTGACATAAAAAGT-AAATTATTTGAAAGTCCGA
131 TGACTTTGACATAAAAAGTAAAATTATTTGAAAGTCCGA
1350440 ACCGATTTGAACCAGTCCGAGTCAACCCGAACCAATCTGAGTCAACTCGAATCGGTCTGACCCAT
1 ACCGATTTGAACCAGTCCGAGTC-A-CCGAACCAATCTGAGTCAACTCGAATCGGTCTGA-CCAT
1350505 TGAATTTGACCCATTAACTTTGACCTGATCCATTACTTTGACCCGACTTATTGAGTTTGACCTGA
63 TGAATTTGACCCATTAAC-TTGA-CTGATCCATTACTTTGACCCGACTTATTGAGTTTGACCTGA
1350570 CTCGTTGACTTTGACATAAAAAGTAAAATTATTTGAAA
126 CTCGTTGACTTTGACATAAAAAGTAAAATTATTTGAAA
1350608 AGTCATATTT
Statistics
Matches: 162, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
168 23 0.14
169 1 0.01
170 34 0.21
171 22 0.14
172 4 0.02
173 65 0.40
174 13 0.08
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (169 bp):
ACCGATTTGAACCAGTCCGAGTCACCGAACCAATCTGAGTCAACTCGAATCGGTCTGACCATTGA
ATTTGACCCATTAACTTGACTGATCCATTACTTTGACCCGACTTATTGAGTTTGACCTGACTCGT
TGACTTTGACATAAAAAGTAAAATTATTTGAAAGTCCGA
Found at i:1350577 original size:19 final size:19
Alignment explanation
Indices: 1350516--1350584 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
1350506 GAATTTGACC
* *
1350516 CATTAACTTTGACCTGA-T
1 CATTGACTTTGACCCGACT
1350534 CCATT-ACTTTGACCCGACT
1 -CATTGACTTTGACCCGACT
* * *
1350553 TATTGAGTTTGACCTGACT
1 CATTGACTTTGACCCGACT
*
1350572 CGTTGACTTTGAC
1 CATTGACTTTGAC
1350585 ATAAAAAGTA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
18 14 0.34
19 27 0.66
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.38
Consensus pattern (19 bp):
CATTGACTTTGACCCGACT
Found at i:1351799 original size:13 final size:14
Alignment explanation
Indices: 1351765--1351801 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1351755 GAGTCAACCT
1351765 ATTAACTTTGACCC
1 ATTAACTTTGACCC
*
1351779 ATT-GCTTTGA-CC
1 ATTAACTTTGACCC
1351791 ATTAACTTTGA
1 ATTAACTTTGA
1351802 TCGAAAAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
12 5 0.25
13 12 0.60
14 3 0.15
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (14 bp):
ATTAACTTTGACCC
Found at i:1359052 original size:16 final size:16
Alignment explanation
Indices: 1359033--1359092 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 16
1359023 TTTAAATTTT
1359033 AAATATAAAAATATTC
1 AAATATAAAAATATTC
*
1359049 AAATATTTAAAAAT-TTT
1 AAATA--TAAAAATATTC
* *
1359066 AATTATAAAAATACTC
1 AAATATAAAAATATTC
*
1359082 ATA-ATAAAAAT
1 AAATATAAAAAT
1359093 TAAATTACTA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
15 15 0.43
16 7 0.20
17 6 0.17
18 7 0.20
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATATAAAAATATTC
Found at i:1359538 original size:15 final size:14
Alignment explanation
Indices: 1359490--1359538 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
1359480 GTTTTAATAT
1359490 ATATTTATTTTTTA
1 ATATTTATTTTTTA
*
1359504 GTATTT-TTTTTT-
1 ATATTTATTTTTTA
*
1359516 TTATTTATTTTTTA
1 ATATTTATTTTTTA
1359530 ATATCTTAT
1 ATAT-TTAT
1359539 ATTTAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 5 0.17
13 12 0.41
14 8 0.28
15 4 0.14
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (14 bp):
ATATTTATTTTTTA
Found at i:1362749 original size:32 final size:31
Alignment explanation
Indices: 1362713--1362830 Score: 137
Period size: 32 Copynumber: 3.7 Consensus size: 31
1362703 GATTATTTTG
* *
1362713 GGGCCTGAGAGCCTACCCAAGGGAGTACCTT
1 GGGCCTTAGAGCCTACCCAAGGAAGTACCTT
* * *
1362744 AGGGCCTAATAGCCTACTCAAGGAAGTACCTT
1 -GGGCCTTAGAGCCTACCCAAGGAAGTACCTT
* * *
1362776 GGGGCCTTAGAGCCTACCCAAGAAAATTCCTT
1 -GGGCCTTAGAGCCTACCCAAGGAAGTACCTT
1362808 GAGGCCTTAGAGCCTACCCAAGG
1 G-GGCCTTAGAGCCTACCCAAGG
1362831 TCACTTTAGG
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
31 1 0.01
32 72 0.99
ACGTcount: A:0.27, C:0.28, G:0.26, T:0.19
Consensus pattern (31 bp):
GGGCCTTAGAGCCTACCCAAGGAAGTACCTT
Found at i:1362814 original size:64 final size:64
Alignment explanation
Indices: 1362710--1362830 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 64
1362700 AGAGATTATT
** * * *
1362710 TTGGGGCCTGAGAGCCTACCCAAGGGAGTACCTTAGGGCCTAATAGCCTACTCAAGGAAGTACC
1 TTGGGGCCTGAGAGCCTACCCAAGAAAATACCTTAGGGCCTAAGAGCCTACCCAAGGAAGTACC
* * *
1362774 TTGGGGCCTTAGAGCCTACCCAAGAAAATTCCTT-GAGGCCTTAGAGCCTACCCAAGG
1 TTGGGGCCTGAGAGCCTACCCAAGAAAATACCTTAG-GGCCTAAGAGCCTACCCAAGG
1362831 TCACTTTAGG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 1 0.02
64 47 0.98
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.20
Consensus pattern (64 bp):
TTGGGGCCTGAGAGCCTACCCAAGAAAATACCTTAGGGCCTAAGAGCCTACCCAAGGAAGTACC
Found at i:1363837 original size:27 final size:28
Alignment explanation
Indices: 1363796--1363859 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
1363786 TCTAAGGCTG
1363796 GGGGTATTTTGGGTCATTTCACACTTCA
1 GGGGTATTTTGGGTCATTTCACACTTCA
* * *
1363824 GGGGTATTTT-GGTCATTTTATAGTTCA
1 GGGGTATTTTGGGTCATTTCACACTTCA
*
1363851 AGGGTATTT
1 GGGGTATTT
1363860 CAGTCCTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 22 0.69
28 10 0.31
ACGTcount: A:0.19, C:0.11, G:0.27, T:0.44
Consensus pattern (28 bp):
GGGGTATTTTGGGTCATTTCACACTTCA
Found at i:1366958 original size:137 final size:138
Alignment explanation
Indices: 1366769--1367069 Score: 364
Period size: 137 Copynumber: 2.2 Consensus size: 138
1366759 CAAATTACAT
* ** * *
1366769 AATTGATTAGGATTAATATTAGAGCCTCCACCTTAGGCGTAATTTTATATTTAGTCCTTAAATTA
1 AATTAATTAGGATTAATATTAGAGCCTCCACCTTAAACCTAATTTTACATTTAGTCCTTAAATTA
* *
1366834 GG-TGAATTCTTAATTTGGTCAT-CGCTTTTGCTCGAGGTTCCAATTTAATTATTCAAATAGCAC
66 GGAT-AATTCTTAATTTGGT-ATGCGCTTTTCCTCGAGGATCCAATTTAATTATTCAAATAGCAC
1366897 AATTGATTAA
129 AATTGATTAA
* *
1366907 AATTAATTATGATTAATATTAGA-CCTCCATCTTAAACCTAATTTTACATTTAGTCCTTAAATTA
1 AATTAATTAGGATTAATATTAGAGCCTCCACCTTAAACCTAATTTTACATTTAGTCCTTAAATTA
* * * * *
1366971 GGATAATTTTTAATTTGGTATGCGCTTTTCCTTGAGGATCCAATTTAATAATT-AGAGTTA-CAT
66 GGATAATTCTTAATTTGGTATGCGCTTTTCCTCGAGGATCCAATTTAATTATTCA-A-ATAGCAC
* *
1367034 AATCGAATAA
129 AATTGATTAA
1367044 AATTGAA-TAGG-TTAATATTAGAGCCT
1 AATT-AATTAGGATTAATATTAGAGCCT
1367070 ACATTTTTAG
Statistics
Matches: 140, Mismatches: 17, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
136 14 0.10
137 100 0.71
138 26 0.19
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (138 bp):
AATTAATTAGGATTAATATTAGAGCCTCCACCTTAAACCTAATTTTACATTTAGTCCTTAAATTA
GGATAATTCTTAATTTGGTATGCGCTTTTCCTCGAGGATCCAATTTAATTATTCAAATAGCACAA
TTGATTAA
Found at i:1367309 original size:19 final size:19
Alignment explanation
Indices: 1367285--1367329 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
1367275 CGAAGTAAAT
1367285 CAACATCCTTTTCAAAACC
1 CAACATCCTTTTCAAAACC
1367304 CAACATCCTTTTCAAAACC
1 CAACATCCTTTTCAAAACC
1367323 CAACATC
1 CAACATC
1367330 ATTATTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.24
Consensus pattern (19 bp):
CAACATCCTTTTCAAAACC
Found at i:1369673 original size:22 final size:22
Alignment explanation
Indices: 1369648--1369710 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
1369638 ATATTTAACC
*
1369648 TTTTTAGTAATTCAAT-TTCTAT
1 TTTTTAAT-ATTCAATATTCTAT
* *
1369670 TTTTTAATATTTAATATTTTAT
1 TTTTTAATATTCAATATTCTAT
*
1369692 TTTTTAATATATGAATATT
1 TTTTTAATAT-TCAATATT
1369711 TTATATTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.17
22 22 0.63
23 7 0.20
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (22 bp):
TTTTTAATATTCAATATTCTAT
Done.