Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold373
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: 3053563
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 20
Found at i:2929143 original size:20 final size:20
Alignment explanation
Indices: 2929120--2929192 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
2929110 ACAATTCAAA
2929120 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
*****
2929140 GTATCGATACATAAAAAAAAT
1 GTATCGATACAT-GTTGCAAT
2929161 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2929181 GTATCGATACAT
1 GTATCGATACAT
2929193 AAAAAGGATG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2929163 original size:21 final size:21
Alignment explanation
Indices: 2929137--2929213 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
2929127 TACATGTTGC
2929137 AATGTATCGATACATAAAAAA
1 AATGTATCGATACATAAAAAA
*****
2929158 AATGTATCGATACAT-GTTGC
1 AATGTATCGATACATAAAAAA
*
2929178 AATGTATCGATACATAAAAAG
1 AATGTATCGATACATAAAAAA
*
2929199 GATGTATCGATACAT
1 AATGTATCGATACAT
2929214 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATAAAAAA
Found at i:2929171 original size:41 final size:41
Alignment explanation
Indices: 2929120--2929213 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2929110 ACAATTCAAA
2929120 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAAT
**
2929161 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAAT
2929202 GTATCGATACAT
1 GTATCGATACAT
2929214 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAAT
Found at i:2929270 original size:13 final size:13
Alignment explanation
Indices: 2929252--2929277 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2929242 TACAGCAAGT
2929252 ATGTATCGATACA
1 ATGTATCGATACA
2929265 ATGTATCGATACA
1 ATGTATCGATACA
2929278 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2932592 original size:11 final size:11
Alignment explanation
Indices: 2932578--2932602 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2932568 ATTTTTCCTC
2932578 TTTTTCTTTCT
1 TTTTTCTTTCT
2932589 TTTTTCTTTCT
1 TTTTTCTTTCT
2932600 TTT
1 TTT
2932603 CTCTCTAATT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTCTTTCT
Found at i:2932972 original size:16 final size:18
Alignment explanation
Indices: 2932936--2932974 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
2932926 AATAAACCAA
*
2932936 TAAAAATAAATTTAGAAT
1 TAAAAATAAATTTAAAAT
2932954 TAAAAA-AAA-TTAAAAT
1 TAAAAATAAATTTAAAAT
2932970 TAAAA
1 TAAAA
2932975 TCAATTCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 3 0.15
18 6 0.30
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
TAAAAATAAATTTAAAAT
Found at i:2933357 original size:167 final size:166
Alignment explanation
Indices: 2933082--2933503 Score: 460
Period size: 167 Copynumber: 2.5 Consensus size: 166
2933072 AACATATACA
* * * * * * *
2933082 AAAAAAATTCAAAAATTCATG-AAATAATTTAAAATTTTCAAAGCTGATTTAATGTGAATTTAAT
1 AAAAAAATTC-AAAACTCATGAAAATAA-ATAAATTTTTAAAAACTGATTTAATATGAATTAAAT
* ** **
2933146 GAA-AATATTAGATG---TTTAAAAATTTTAAACCAAGAAAAATCCCCTCGAAAACATTTATGGA
64 -AATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCTCGAAAACATTTA-CAA
** * *
2933207 A-TTGAAAACTTGATTTTTCGAAAATAGGAAAATTTCAAAG
127 AGCAGAAAACTTCAGTTTTCGAAAATAGGAAAATTTC-AAG
*
2933247 AAAAAAATTCAAAACTCATGAAAATAAATGAATTTTTAAAAACTGATTTAATATGAATTAAATAA
1 AAAAAAATTCAAAACTCATGAAAATAAATAAATTTTTAAAAACTGATTTAATATGAATTAAATAA
* * * *
2933312 TAATTTTTGATGAATTTTAAAAATTAAAAACTAAGGAAAATCCCCTTGAAAACATTTACAAAGCA
66 TAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCTCGAAAACATTTACAAAGCA
* *
2933377 GAAAACTTCAGTTTTCGAAAATATGAGAATTTCAAG
131 GAAAACTTCAGTTTTCGAAAATAGGAAAATTTCAAG
* ** * * * *
2933413 GAAAAAATAAAAAAACTCATGAAAATGAATAAATTTTTAAAAAATAATATAATATGAATTAAATA
1 AAAAAAAT-TCAAAACTCATGAAAATAAATAAATTTTTAAAAACTGATTTAATATGAATTAAATA
* *
2933478 ATAGTATTTGATAAATTTTAAAAATT
65 ATAATATTTGATGAATTTTAAAAATT
2933504 TTGGATCAAT
Statistics
Matches: 216, Mismatches: 34, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
163 2 0.01
164 47 0.22
165 16 0.07
166 12 0.06
167 139 0.64
ACGTcount: A:0.51, C:0.08, G:0.09, T:0.32
Consensus pattern (166 bp):
AAAAAAATTCAAAACTCATGAAAATAAATAAATTTTTAAAAACTGATTTAATATGAATTAAATAA
TAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCTCGAAAACATTTACAAAGCA
GAAAACTTCAGTTTTCGAAAATAGGAAAATTTCAAG
Found at i:2933549 original size:167 final size:165
Alignment explanation
Indices: 2933160--2933552 Score: 423
Period size: 167 Copynumber: 2.3 Consensus size: 165
2933150 ATATTAGATG
** * * * * *
2933160 TTTAAAAATTTTAAACCAAGAAAAATCCCCTCGAAAACATTTATGGAA-TTGAAAACTTGATTTT
1 TTTAAAAATTAAAAACTAAGGAAAAT-CCC-CGAAAACATTTAT-GAAGTAGAAAACTTCAGTTT
** *
2933224 TCGAAAATAGGAAAATTTCAAAGAAAAAAATTCAAAACTCATGAAAATAAATGAATTTTTAAAAA
63 TCGAAAATAGGAAAATTTCAAAGAAAAAAATAAAAAACTCATGAAAATAAATAAATTTTTAAAAA
* * * * *
2933289 CTGATTTAATATGAATTAAATAATAATTTTTGATGAAT
128 ATAATATAATATGAATTAAATAATAATATTTGATAAAT
** *
2933327 TTTAAAAATTAAAAACTAAGGAAAATCCCCTTGAAAACATTTACAAAGCAGAAAACTTCAGTTTT
1 TTTAAAAATTAAAAACTAAGGAAAATCCCC--GAAAACATTTATGAAGTAGAAAACTTCAGTTTT
* * * *
2933392 CGAAAATATGAGAATTTC-AAGGAAAAAATAAAAAAACTCATGAAAATGAATAAATTTTTAAAAA
64 CGAAAATAGGAAAATTTCAAAGAAAAAAAT-AAAAAACTCATGAAAATAAATAAATTTTTAAAAA
*
2933456 ATAATATAATATGAATTAAATAATAGTATTTGATAAAT
128 ATAATATAATATGAATTAAATAATAATATTTGATAAAT
**** * *
2933494 TTTAAAAATTTTGGA-TCAATGAAAATCTTCCCGAAAAAATTTATGAAGTAGAAAACTTC
1 TTTAAAAATTAAAAACT-AAGGAAAATC--CCCGAAAACATTTATGAAGTAGAAAACTTC
2933553 GTATTTTAAA
Statistics
Matches: 187, Mismatches: 32, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
165 1 0.01
166 16 0.09
167 167 0.89
169 3 0.02
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (165 bp):
TTTAAAAATTAAAAACTAAGGAAAATCCCCGAAAACATTTATGAAGTAGAAAACTTCAGTTTTCG
AAAATAGGAAAATTTCAAAGAAAAAAATAAAAAACTCATGAAAATAAATAAATTTTTAAAAAATA
ATATAATATGAATTAAATAATAATATTTGATAAAT
Found at i:2935932 original size:79 final size:79
Alignment explanation
Indices: 2935811--2936534 Score: 584
Period size: 79 Copynumber: 9.2 Consensus size: 79
2935801 GAAAAATTGA
* * * ** * * *
2935811 TGTTTTA-AAATAAAACCGGGGGCTAGAGTATCCCCTAAAAAATAACAGGGTTGAAGTGTCCCCA
1 TGTTTTAGAAATAAAACC-GAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCG
2935875 ATGGTGAAAAATCAG
65 ATGGTGAAAAATCAG
* * * * *
2935890 TGTTTTAGAAATAAAACCGAGGTTAGAGTATTCTCTCGAAAATAACGGGGTTGGAGTGTCCCCGA
1 TGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGA
**
2935955 TGGT-AGAAAATTGG
66 TGGTGA-AAAATCAG
* ** * * * * * *
2935969 TATTTTAGAAATAAAATTGGGGTTGAAGTATCCCTTCAAAAATAACGGGGTTGGAGTGTCCCCGA
1 TGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGA
*
2936034 TGGTGAAAAATCGG
66 TGGTGAAAAATCAG
*** *
2936048 TGTTTTAGAAA-AAAAATAAGGGTTGGAGTATCCCCTC-AGAAACAAC-GGTGTTGGAGTATCCC
1 TGTTTTAGAAATAAAACCGA-GGTTGGAGTATCCCCTCGA-AAATAACAGG-GTTGGAGTATCCC
**
2936110 CGATGGTGAAAAATTGG
63 CGATGGTGAAAAATCAG
* * * * **
2936127 TGTTTTAGAAATAAAATCGAAGTTGGAGTATCTCGTCGAAAATAAC-GGTGTTGGAGTAT-CTAG
1 TGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAATAACAGG-GTTGGAGTATCCCCG
2936190 -TGGTGAAAAATCAG
65 ATGGTGAAAAATCAG
* * * * * **
2936204 TGTTTTTGTAATAAAACC-AGGGTTGGAGTATCCCCTCAAAAATAACAAGGTTAGAGTATCCCAA
1 TGTTTTAGAAATAAAACCGA-GGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCG
* *
2936268 ATGGTGGAAAATCAA
65 ATGGTGAAAAATCAG
* *** *
2936283 TGTTTTAGAAATAAAACC-AGGGTTGGAGTATCCCCTCGAAAA-AATA-GGTCATAGTATCCTCG
1 TGTTTTAGAAATAAAACCGA-GGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCG
2936345 ATGGTGAAAAATC-G
65 ATGGTGAAAAATCAG
* * * ** * *
2936359 ATATTTTAGAAAT-AAAGCTAGGGTTGGAGTATCCTTTCGAAAATAACGGGGTTGGAGTATCCTC
1 -TGTTTTAGAAATAAAACCGA-GGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCC
2936423 GATGGT-AGAAAATC-G
64 GATGGTGA-AAAATCAG
* * ** * * *
2936438 ATATTTTAGAAATGAAGTCGGGGTTGGAGTATCTCCTCGAAAATAA-TGAGGTTGGAGTATCCCC
1 -TGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAATAACAG-GGTTGGAGTATCCCC
2936502 GATGGTGAAGAAAATCA-
64 GATGGTG-A-AAAATCAG
* *
2936519 TATTTTGGAAATAAAA
1 TGTTTTAGAAATAAAA
2936535 ACATCAATGA
Statistics
Matches: 536, Mismatches: 87, Indels: 43
0.80 0.13 0.06
Matches are distributed among these distances:
76 5 0.01
77 114 0.21
78 21 0.04
79 355 0.66
80 33 0.06
81 8 0.01
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (79 bp):
TGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGA
TGGTGAAAAATCAG
Found at i:2936095 original size:158 final size:158
Alignment explanation
Indices: 2935803--2936510 Score: 662
Period size: 156 Copynumber: 4.5 Consensus size: 158
2935793 GGAGTAGTGA
* * * * * ** * *
2935803 AAAATTGATGTTTTA-AAATAAAACCGGGGGCTAGAGTATCCCCTAAAAAATAACAGGGTTGAAG
1 AAAATCGATATTTTAGAAATAAAATC-GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAG
* * * * * * *
2935867 TGTCCCCAATGGTGAAAAATCAGTGTTTTAGAAATAAAA-CCGAGGTTAGAGTATTCTCTCGAAA
65 TATCCCCGATGGTGAAAAATCAGTGTTTTAGAAAAAAAATCAG-GGTTGGAGTATCCCCTCGAAA
*
2935931 ATAACGGGGTTGGAGTGTCCCCGATGGTAG
129 ATAACGGGGTTGGAGTATCCCCGATGGTAG
* * * * * *
2935961 AAAATTGGTATTTTAGAAATAAAATTGGGGTTGAAGTATCCCTTCAAAAATAACGGGGTTGGAGT
1 AAAATCGATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGT
* * *
2936026 GTCCCCGATGGTGAAAAATCGGTGTTTTAGAAAAAAAATAAGGGTTGGAGTATCCCCTC-AGAAA
66 ATCCCCGATGGTGAAAAATCAGTGTTTTAGAAAAAAAATCAGGGTTGGAGTATCCCCTCGA-AAA
* *
2936090 CAACGGTGTTGGAGTATCCCCGATGGT-G
130 TAACGGGGTTGGAGTATCCCCGATGGTAG
* * * ** * * *
2936118 AAAAATTGGTGTTTTAGAAATAAAATCGAAGTTGGAGTATCTCGTCGAAAATAACGGTGTTGGAG
1 -AAAATCGATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAG
** * * * * *
2936183 TAT-CTAG-TGGTGAAAAATCAGTGTTTTTGTAATAAAACCAGGGTTGGAGTATCCCCTCAAAAA
65 TATCCCCGATGGTGAAAAATCAGTGTTTTAGAAAAAAAATCAGGGTTGGAGTATCCCCTCGAAAA
** * ** *
2936246 TAACAAGGTTAGAGTATCCCAAATGGTGG
130 TAACGGGGTTGGAGTATCCCCGATGGTAG
* * * * ** ***
2936275 AAAATCAATGTTTTAGAAATAAAACCAGGGTTGGAGTATCCCCTCGAAAA-AA-TAGGTCATAGT
1 AAAATCGATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGT
* * * * **
2936338 ATCCTCGATGGTGAAAAATC-GATATTTTAG-AAATAAAGCTAGGGTTGGAGTATCCTTTCGAAA
66 ATCCCCGATGGTGAAAAATCAG-TGTTTTAGAAAAAAAATC-AGGGTTGGAGTATCCCCTCGAAA
*
2936401 ATAACGGGGTTGGAGTATCCTCGATGGTAG
129 ATAACGGGGTTGGAGTATCCCCGATGGTAG
* * * * *
2936431 AAAATCGATATTTTAGAAATGAAGTCGGGGTTGGAGTATCTCCTCGAAAATAATGAGGTTGGAGT
1 AAAATCGATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGT
2936496 ATCCCCGATGGTGAA
66 ATCCCCGATGGTGAA
2936511 GAAAATCATA
Statistics
Matches: 448, Mismatches: 90, Indels: 24
0.80 0.16 0.04
Matches are distributed among these distances:
154 7 0.02
155 12 0.03
156 213 0.48
157 8 0.02
158 199 0.44
159 9 0.02
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (158 bp):
AAAATCGATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGT
ATCCCCGATGGTGAAAAATCAGTGTTTTAGAAAAAAAATCAGGGTTGGAGTATCCCCTCGAAAAT
AACGGGGTTGGAGTATCCCCGATGGTAG
Found at i:2938988 original size:51 final size:51
Alignment explanation
Indices: 2938904--2939038 Score: 207
Period size: 51 Copynumber: 2.6 Consensus size: 51
2938894 AAAAATGCCT
* * * *
2938904 GAATGTATCGATACATTGAGAAATGTATGGATACATCTGGGTTAAAACCTA
1 GAATGTATCGATACAATGAAAAATGTATCGATACATCTGGGTTAAAACCCA
*
2938955 GAATGTATCGATACAATGAAAAATATATCGATACATCTGGGTTAAAACCCA
1 GAATGTATCGATACAATGAAAAATGTATCGATACATCTGGGTTAAAACCCA
* *
2939006 GAATGTATCGATATAATAAAAAATGTATCGATA
1 GAATGTATCGATACAATGAAAAATGTATCGATA
2939039 AAAACAGTAA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 76 1.00
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (51 bp):
GAATGTATCGATACAATGAAAAATGTATCGATACATCTGGGTTAAAACCCA
Found at i:2940025 original size:13 final size:13
Alignment explanation
Indices: 2940007--2940032 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2939997 TACACCAAGT
2940007 ATGTATCGATACA
1 ATGTATCGATACA
2940020 ATGTATCGATACA
1 ATGTATCGATACA
2940033 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2940030 original size:32 final size:33
Alignment explanation
Indices: 2939989--2940052 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2939979 TAGCCAAACT
* **
2939989 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2940021 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2940053 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2944111 original size:15 final size:15
Alignment explanation
Indices: 2944091--2944121 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2944081 TAAAAATATC
*
2944091 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2944106 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2944121 C
1 C
2944122 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2946204 original size:13 final size:13
Alignment explanation
Indices: 2946186--2946222 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
2946176 ACATTTTTCT
2946186 TTGTATCGATACA
1 TTGTATCGATACA
2946199 TTGTATCGATACA
1 TTGTATCGATACA
*
2946212 CTGTATCGATA
1 TTGTATCGATA
2946223 TAGGGGGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2946389 original size:20 final size:20
Alignment explanation
Indices: 2946346--2946392 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
2946336 AAATCTTTTG
2946346 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
2946367 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
2946387 CAAAAT
1 CAAAAT
2946393 CGTCCCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:2948577 original size:13 final size:13
Alignment explanation
Indices: 2948559--2948584 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2948549 TACACCAAGT
2948559 ATGTATCGATACA
1 ATGTATCGATACA
2948572 ATGTATCGATACA
1 ATGTATCGATACA
2948585 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2948584 original size:32 final size:33
Alignment explanation
Indices: 2948541--2948604 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 33
2948531 TAGCCAAACT
* **
2948541 TGTATCAATACACCAAGTA-TGTATCGATACAA
1 TGTATCAATACACAAAAAATTGTATCGATACAA
*
2948573 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCAATACACAAAAAATTGTATCGATACA
2948605 TTGGCTTGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCAATACACAAAAAATTGTATCGATACAA
Found at i:2953536 original size:15 final size:17
Alignment explanation
Indices: 2953505--2953536 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2953495 AGCAAGATGA
2953505 AAGTGTCCAAAATGAAG
1 AAGTGTCCAAAATGAAG
2953522 AAGT-TCCAAAA-GAAG
1 AAGTGTCCAAAATGAAG
2953537 TTGATGAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 7 0.47
17 4 0.27
ACGTcount: A:0.50, C:0.12, G:0.22, T:0.16
Consensus pattern (17 bp):
AAGTGTCCAAAATGAAG
Found at i:2955631 original size:13 final size:13
Alignment explanation
Indices: 2955613--2955649 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
2955603 ACAATATTCC
2955613 TTGTATCGATACA
1 TTGTATCGATACA
2955626 TTGTATCGATACA
1 TTGTATCGATACA
*
2955639 CTGTATCGATA
1 TTGTATCGATA
2955650 TATTAGGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2958191 original size:20 final size:20
Alignment explanation
Indices: 2958148--2958202 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2958138 GTATCGATAC
* **
2958148 ATTGTATCAATACAT-GTTA
1 ATTGTATCGATACATGGACA
2958167 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
2958187 ATTGTATCGATACATG
1 ATTGTATCGATACATG
2958203 AGATTGGCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:2962590 original size:138 final size:137
Alignment explanation
Indices: 2962336--2962615 Score: 395
Period size: 138 Copynumber: 2.0 Consensus size: 137
2962326 AATCACCCCA
2962336 AATTCATTTGGTATCGAAAAATTACAAACTATACATTTCCAGAAAACTAATTTCATGACGTTTTT
1 AATTCATTTGGTATCGAAAAATTACAAACTATACATTTCCAGAAAACTAATTTCATGACGTTTTT
* *** *
2962401 AGCAAAAATGTTTGGAAAATTTATAAAAATCATCTATTTGGCCAAAGCGGCCCGACTAGAATGCG
66 AGCAAAAATGTTTGGAAAATTTAGAAAAATCATCTAGCAGGCCAAAGCGGCCCGACCAGAATGCG
*
2962466 AATCTCT
131 AATCGCT
* * * *
2962473 GAATTCATTTGGTATCGAAAAATTATAAAGTATACCTTTCTAGAAAGA-TAATTTCATGACGTTT
1 -AATTCATTTGGTATCGAAAAATTACAAACTATACATTTCCAGAAA-ACTAATTTCATGACGTTT
*
2962537 TTATG-AAAAATGTTTGGAAAATTTGGAAAAATCATCTAGCAGGCCTAAA-CGGCCCGACCAGAA
64 TTA-GCAAAAATGTTTGGAAAATTTAGAAAAATCATCTAGCAGGCC-AAAGCGGCCCGACCAGAA
*
2962600 TGTGAATCGCT
127 TGCGAATCGCT
2962611 AATTC
1 AATTC
2962616 CAGGGGTTCT
Statistics
Matches: 127, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
137 5 0.04
138 117 0.92
139 5 0.04
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (137 bp):
AATTCATTTGGTATCGAAAAATTACAAACTATACATTTCCAGAAAACTAATTTCATGACGTTTTT
AGCAAAAATGTTTGGAAAATTTAGAAAAATCATCTAGCAGGCCAAAGCGGCCCGACCAGAATGCG
AATCGCT
Found at i:2964225 original size:20 final size:19
Alignment explanation
Indices: 2964195--2964271 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 19
2964185 GTAAAAGGAC
*
2964195 AAAACGTATCGATACATTG
1 AAAATGTATCGATACATTG
*
2964214 AAGAATGTATCGATACATTC
1 AA-AATGTATCGATACATTG
* *
2964234 ATACATGTATCGATATATTG
1 A-AAATGTATCGATACATTG
*
2964254 AAAAATGTATCAATACAT
1 -AAAATGTATCGATACAT
2964272 CTAGGTAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
19 2 0.04
20 43 0.91
21 2 0.04
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (19 bp):
AAAATGTATCGATACATTG
Found at i:2969536 original size:49 final size:49
Alignment explanation
Indices: 2969480--2969599 Score: 186
Period size: 49 Copynumber: 2.4 Consensus size: 49
2969470 GTGCCAATTT
* *
2969480 AAGGCCAGCGACATTGGGCTAAAAGAAAAGTGGACCAAAGTGTTGATTC
1 AAGGCCAGCGACATTGGGCTAAAAGAAAAGTAGACCAAAGTGCTGATTC
* * *
2969529 AAGGCCAGCGACATTGGGCTAAAGGAAAAGTAGACTAATGTGCTGATTC
1 AAGGCCAGCGACATTGGGCTAAAAGAAAAGTAGACCAAAGTGCTGATTC
*
2969578 AAGGCCAGCGACATTTGGCTAA
1 AAGGCCAGCGACATTGGGCTAA
2969600 TAAAGGTGCC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.19
Consensus pattern (49 bp):
AAGGCCAGCGACATTGGGCTAAAAGAAAAGTAGACCAAAGTGCTGATTC
Found at i:2969861 original size:28 final size:28
Alignment explanation
Indices: 2969715--2970425 Score: 767
Period size: 28 Copynumber: 24.5 Consensus size: 28
2969705 CATTAACTTG
* *
2969715 TGTGGGCTGTGAAAAGAGTCGCCACTGACT
1 TGTGGGCTTTG-AAAGGGT-GCCACTGACT
* * *
2969745 CGTGTGGGCTTTGAAAAGAGTTACCACTGGCT
1 --TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* *
2969777 TGTGGGCTTTGAAAAGAGTGCCACTGGCT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
**
2969806 TGTGGGCTTTGAAAAGAATGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
2969835 TGTGGGCTTTAAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
2969863 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
2969891 TGTGGGCTTTGAAAGGATGCC-CTTGACT
1 TGTGGGCTTTGAAAGGGTGCCAC-TGACT
*
2969919 TGTGGGCATTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
2969947 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
2969975 TATGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2970003 TATGGGCTTTGAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
2970031 TGTGGGCTTTAAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
2970059 TGTGGGCTTTGAAAAGAGTTACCACCGACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
*
2970089 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2970117 TGTGGGCTTTGAAAGGGTGCCATTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
2970145 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * **
2970173 TGTGGGCTTTGAAAAGATGCCACCAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2970201 TGTGGACTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
2970229 TGTGGGCTTTGAAAGGGTGCCACTAACTT
1 TGTGGGCTTTGAAAGGGTGCCACTGAC-T
**
2970258 GTGTGGGCTTTGAAATGGGTTGCCACCAACTT
1 -TGTGGGCTTTGAAA-GGG-TGCCACTGAC-T
* *
2970290 GTGTGGGCTTTGAAATGAGTTGCCACCGACTT
1 -TGTGGGCTTTGAAA-G-GGTGCCACTGAC-T
* * *
2970322 GTGTGGGCTTTGAAATGATGCGACTGACTT
1 -TGTGGGCTTTGAAAGGGTGCCACTGAC-T
* *
2970352 GTGTGGGCTTTCAAATGAGTTGCCACTGACTT
1 -TGTGGGCTTTGAAA-G-GGTGCCACTGAC-T
* *
2970384 ATGTGGGCTTTGAAATGATGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
2970413 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
2970426 GAGATGAACG
Statistics
Matches: 598, Mismatches: 69, Indels: 28
0.86 0.10 0.04
Matches are distributed among these distances:
27 1 0.00
28 346 0.58
29 58 0.10
30 86 0.14
31 3 0.01
32 102 0.17
33 2 0.00
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:2971648 original size:1 final size:1
Alignment explanation
Indices: 2971642--2971740 Score: 54
Period size: 1 Copynumber: 99.0 Consensus size: 1
2971632 CCCCTTTCTG
** * * ** * * ** *
2971642 TTTTTTTTTTTTTGCTATTTTTTCTTGGTTTTTTGTTTTTTTTTTGTTTTTTTAATTTTTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
2971707 GTTTCTTTATTTTTTTTGTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2971741 GGGTATAGAG
Statistics
Matches: 72, Mismatches: 26, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.04, C:0.04, G:0.08, T:0.84
Consensus pattern (1 bp):
T
Found at i:2971681 original size:8 final size:8
Alignment explanation
Indices: 2971660--2971739 Score: 60
Period size: 8 Copynumber: 9.9 Consensus size: 8
2971650 TTTTTGCTAT
2971660 TTTTTCTTG
1 TTTTT-TTG
*
2971669 GTTTTTTG
1 TTTTTTTG
2971677 TTTTTTT-
1 TTTTTTTG
2971684 TTTGTTTT-
1 TTT-TTTTG
*
2971692 TTTAATTT-
1 TTT-TTTTG
*
2971700 TTTTTTCG
1 TTTTTTTG
2971708 TTTCTTTAT-
1 TTT-TTT-TG
2971717 TTTTTTTG
1 TTTTTTTG
2971725 TTTTTTTG
1 TTTTTTTG
2971733 TTTTTTT
1 TTTTTTT
2971740 TGGGTATAGA
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
7 6 0.10
8 43 0.73
9 10 0.17
ACGTcount: A:0.04, C:0.04, G:0.09, T:0.84
Consensus pattern (8 bp):
TTTTTTTG
Found at i:2971681 original size:19 final size:18
Alignment explanation
Indices: 2971649--2971740 Score: 78
Period size: 19 Copynumber: 4.8 Consensus size: 18
2971639 CTGTTTTTTT
2971649 TTTTTTGCTATTTTTTCTTGG
1 TTTTTTG-T-TTTTTT-TTGG
*
2971670 TTTTTTGTTTTTTTTTTGT
1 TTTTTTG-TTTTTTTTTGG
* *
2971689 TTTTTTAATTTTTTTTTCG
1 TTTTTT-GTTTTTTTTTGG
* *
2971708 TTTCTTT-ATTTTTTTTGT
1 TTT-TTTGTTTTTTTTTGG
2971726 TTTTTTGTTTTTTTT
1 TTTTTTGTTTTTTTT
2971741 GGGTATAGAG
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
17 3 0.05
18 18 0.31
19 21 0.36
20 9 0.15
21 8 0.14
ACGTcount: A:0.04, C:0.04, G:0.09, T:0.83
Consensus pattern (18 bp):
TTTTTTGTTTTTTTTTGG
Found at i:2971684 original size:38 final size:38
Alignment explanation
Indices: 2971642--2971740 Score: 112
Period size: 38 Copynumber: 2.6 Consensus size: 38
2971632 CCCCTTTCTG
* *
2971642 TTTTTTTTTTTTTGCTATTTTTTCTTGGTTT-TTTGTTT
1 TTTTTTTTTTTTTG-TATTTTTTCTTCGTTTCTTTATTT
*
2971680 TTTTTTTGTTTTTT-TAATTTTTTTTTCGTTTCTTTATTT
1 TTTTTTT-TTTTTTGT-ATTTTTTCTTCGTTTCTTTATTT
* *
2971719 TTTTTGTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTGTATTTTTT
2971741 GGGTATAGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
37 1 0.02
38 32 0.62
39 19 0.37
ACGTcount: A:0.04, C:0.04, G:0.08, T:0.84
Consensus pattern (38 bp):
TTTTTTTTTTTTTGTATTTTTTCTTCGTTTCTTTATTT
Found at i:2981497 original size:13 final size:13
Alignment explanation
Indices: 2981479--2981506 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2981469 ATACAAAGAT
2981479 CAATGTATCGATA
1 CAATGTATCGATA
2981492 CAATGTATCGATA
1 CAATGTATCGATA
2981505 CA
1 CA
2981507 TTGAATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2981503 original size:33 final size:33
Alignment explanation
Indices: 2981461--2981524 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
2981451 AAATTCCTAG
2981461 ATGTATCGATACAAAG-ATCAATGTATCGATACA
1 ATGTATCGATACAAAGAAT-AATGTATCGATACA
**
2981494 ATGTATCGATACATTGAATAATGTATCGATA
1 ATGTATCGATACAAAGAATAATGTATCGATA
2981525 TATTTCCTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCGATACA
Found at i:2981617 original size:19 final size:19
Alignment explanation
Indices: 2981558--2981623 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
2981548 AGCGATACAT
2981558 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
* * *
2981577 TGTATTGAT--GATA--TA
1 TGTATCGATACAACACTTA
2981592 TTGTATCGATACAACACTTA
1 -TGTATCGATACAACACTTA
*
2981612 TGTATCGGTACA
1 TGTATCGATACA
2981624 TTTACTGTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
15 2 0.06
16 8 0.23
17 2 0.06
18 2 0.06
19 19 0.54
20 2 0.06
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:2982534 original size:52 final size:49
Alignment explanation
Indices: 2982478--2983143 Score: 329
Period size: 52 Copynumber: 13.4 Consensus size: 49
2982468 TGTGTTGAGA
* *
2982478 CAAGGCTAGCGACATTGGGCTT-AGGAATGTTAAAGATGCCAATATGATAATT
1 CAAGGCCAGCGACATTGGACTTAAGG-ATG---AAGATGCCAATATGATAATT
* * * * * *
2982530 CAAGGCCAACGATATCGGACTTAAGGATGAAGGTGCCAATGTGCTAATT
1 CAAGGCCAGCGACATTGGACTTAAGGATGAAGATGCCAATATGATAATT
* * * * *
2982579 CAAGGCCAGCGACATTGGTA-TTAAAGATGACAAAAGCGCCAATATGCTGATT
1 CAAGGCCAGCGACATTGG-ACTTAAGGATG--AAGA-TGCCAATATGATAATT
* * * * * *
2982631 CAAGGCCAGCGATATTGGA-TTAAAAGATGAAGGTGCCAATGTGCTGATT
1 CAAGGCCAGCGACATTGGACTT-AAGGATGAAGATGCCAATATGATAATT
* * * * * * * *
2982680 CAAGGCTAGCAACATTGGTCTTAAAGATGACGAAAGCACCAATATGCTGATT
1 CAAGGCCAGCGACATTGGACTTAAGGATGAAG-ATG--CCAATATGATAATT
* * * * * *
2982732 CAAGGCCAGCGATATTGGA-TTAAAAGATGAAGGTGCCAATGTGCTGATT
1 CAAGGCCAGCGACATTGGACTT-AAGGATGAAGATGCCAATATGATAATT
* * * * *
2982781 CAAGGCCAGCGACATTGGACTTAAAGATGACGAAGGTACCAATATGCTGATT
1 CAAGGCCAGCGACATTGGACTT-AAG--GATGAAGATGCCAATATGATAATT
* * * * *
2982833 CAAGGCCAGCGATATTGGGC-T-----T---G-TGCCAATGTGCTGATT
1 CAAGGCCAGCGACATTGGACTTAAGGATGAAGATGCCAATATGATAATT
* * * *
2982872 CAAAGCCAGCGACATTGGTCTT-AGGAATGTTAAAGATGCCAATATAATGATT
1 CAAGGCCAGCGACATTGGACTTAAGG-ATG---AAGATGCCAATATGATAATT
* * * * * *
2982924 CAAGGCCAACGATATCGGACTTAAGGATGAAGATGCCAATGTGCTGATT
1 CAAGGCCAGCGACATTGGACTTAAGGATGAAGATGCCAATATGATAATT
* * * * * * *
2982973 CAAGGCCATCGACATTGGTCTTAAAGATGACGAAAGCGCCAATATGCTGATT
1 CAAGGCCAGCGACATTGGACTTAAGGATGA--AGA-TGCCAATATGATAATT
* * * * * *
2983025 CAAGGCCAGCAATATTGGA-TTAAAAGATGAAGGTGCCAATATGCTGATT
1 CAAGGCCAGCGACATTGGACTT-AAGGATGAAGATGCCAATATGATAATT
* * * * *
2983074 CAAGGCCAGCGACATTGGACTTAAAGATGACGAAGGTACCAATATGCTGATT
1 CAAGGCCAGCGACATTGGACTT-AAG--GATGAAGATGCCAATATGATAATT
*
2983126 CAAGGCCAGCGATATTGG
1 CAAGGCCAGCGACATTGG
2983144 GCTTGTGCCA
Statistics
Matches: 496, Mismatches: 83, Indels: 70
0.76 0.13 0.11
Matches are distributed among these distances:
39 31 0.06
40 2 0.00
45 1 0.00
49 183 0.37
50 17 0.03
51 14 0.03
52 242 0.49
53 6 0.01
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (49 bp):
CAAGGCCAGCGACATTGGACTTAAGGATGAAGATGCCAATATGATAATT
Found at i:2982620 original size:101 final size:101
Alignment explanation
Indices: 2982515--2983324 Score: 817
Period size: 101 Copynumber: 8.4 Consensus size: 101
2982505 TGTTAAAGAT
* * * * * *
2982515 GCCAATATGATAATTCAAGGCCAACGATATCGGACTT-AAGGATGAAGGTGCCAATGTGCTAATT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGA-TTAAAAGATGAAGGTGCCAATGTGCTGATT
*
2982579 CAAGGCCAGCGACATTGGTATTAAAGATGACAAAAGC
65 CAAGGCCAGCGACATTGGTATTAAAGATGACGAAAGC
2982616 GCCAATATGCTGATTCAAGGCCAGCGATATTGGATTAAAAGATGAAGGTGCCAATGTGCTGATTC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGATTAAAAGATGAAGGTGCCAATGTGCTGATTC
* * *
2982681 AAGGCTAGCAACATTGGTCTTAAAGATGACGAAAGC
66 AAGGCCAGCGACATTGGTATTAAAGATGACGAAAGC
*
2982717 ACCAATATGCTGATTCAAGGCCAGCGATATTGGATTAAAAGATGAAGGTGCCAATGTGCTGATTC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGATTAAAAGATGAAGGTGCCAATGTGCTGATTC
* *
2982782 AAGGCCAGCGACATTGG-ACTTAAAGATGACGAAGGT
66 AAGGCCAGCGACATTGGTA-TTAAAGATGACGAAAGC
* * *
2982818 ACCAATATGCTGATTCAAGGCCAGCGATATTGG-------GCT---TGTGCCAATGTGCTGATTC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGATTAAAAGATGAAGGTGCCAATGTGCTGATTC
* * * ** *
2982873 AAAGCCAGCGACATTGGTCTT-AGGAATG-TTAAAGAT
66 AAGGCCAGCGACATTGGTATTAAAG-ATGACGAAAG-C
** * * * *
2982909 GCCAATATAATGATTCAAGGCCAACGATATCGGACTT-AAGGATGAAGATGCCAATGTGCTGATT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGA-TTAAAAGATGAAGGTGCCAATGTGCTGATT
* *
2982973 CAAGGCCATCGACATTGGTCTTAAAGATGACGAAAGC
65 CAAGGCCAGCGACATTGGTATTAAAGATGACGAAAGC
* *
2983010 GCCAATATGCTGATTCAAGGCCAGCAATATTGGATTAAAAGATGAAGGTGCCAATATGCTGATTC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGATTAAAAGATGAAGGTGCCAATGTGCTGATTC
* *
2983075 AAGGCCAGCGACATTGG-ACTTAAAGATGACGAAGGT
66 AAGGCCAGCGACATTGGTA-TTAAAGATGACGAAAGC
* * *
2983111 ACCAATATGCTGATTCAAGGCCAGCGATATTGG-------GCT---TGTGCCAATGTGCTGATTC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGATTAAAAGATGAAGGTGCCAATGTGCTGATTC
* * *
2983166 AAGGCCAGCGACATTGGTCTT-AA-A-GAC-AAGGT
66 AAGGCCAGCGACATTGGTATTAAAGATGACGAAAGC
* * *
2983198 GCCAATATGCTGATTCAAGGCCAGCGATATTGG-------GCT-TA--TGCCAATGTGTTGATTC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGATTAAAAGATGAAGGTGCCAATGTGCTGATTC
* * *
2983253 AAGGCCAGCGACATTGGTCTTAAA-A--AC-AAGGT
66 AAGGCCAGCGACATTGGTATTAAAGATGACGAAAGC
* *
2983285 GCCAATATGCCGATTCAAGGCCAACGATATTGGGATTAAA
1 GCCAATATGCTGATTCAAGGCCAGCGATATT-GGATTAAA
2983325 GGTGCCACGG
Statistics
Matches: 619, Mismatches: 60, Indels: 67
0.83 0.08 0.09
Matches are distributed among these distances:
87 113 0.18
88 8 0.01
89 1 0.00
90 7 0.01
91 104 0.17
94 4 0.01
98 2 0.00
100 4 0.01
101 370 0.60
102 6 0.01
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (101 bp):
GCCAATATGCTGATTCAAGGCCAGCGATATTGGATTAAAAGATGAAGGTGCCAATGTGCTGATTC
AAGGCCAGCGACATTGGTATTAAAGATGACGAAAGC
Found at i:2982925 original size:293 final size:289
Alignment explanation
Indices: 2982562--2983235 Score: 1073
Period size: 293 Copynumber: 2.3 Consensus size: 289
2982552 AAGGATGAAG
* * * *
2982562 GTGCCAATGTGCTAATTCAAGGCCAGCGACATTGGTATTAAAGATGACAAAAGCGCCAATATGCT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AA-ATGA-AAGA-TGCCAATATGCT
* *
2982627 GATTCAAGGCCAGCGATATTGGA-TTAAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCTAGCA
62 GATTCAAGGCCAGCGATATTGGACTT-AAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCA
*
2982691 ACATTGGTCTTAAAGATGACGAAAGCACCAATATGCTGATTCAAGGCCAGCGATATTGGATTAAA
126 ACATTGGTCTTAAAGATGACGAAAGCACCAATATGCTGATTCAAGGCCAGCAATATTGGATTAAA
*
2982756 AGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGGTACC
191 AGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGGTACC
2982821 AATATGCTGATTCAAGGCCAGCGATATTGGGCTT
256 AATATGCTGATTCAAGGCCAGCGATATTGGGCTT
* **
2982855 GTGCCAATGTGCTGATTCAAAGCCAGCGACATTGGTCTTAGGAATGTTAAAGATGCCAATATAAT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA--AATG--AAAGATGCCAATATGCT
* * * * *
2982920 GATTCAAGGCCAACGATATCGGACTTAAGGATGAAGATGCCAATGTGCTGATTCAAGGCCATCGA
62 GATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCAA
*
2982985 CATTGGTCTTAAAGATGACGAAAGCGCCAATATGCTGATTCAAGGCCAGCAATATTGGATTAAAA
127 CATTGGTCTTAAAGATGACGAAAGCACCAATATGCTGATTCAAGGCCAGCAATATTGGATTAAAA
2983050 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGGTACCA
192 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGGTACCA
2983115 ATATGCTGATTCAAGGCCAGCGATATTGGGCTT
257 ATATGCTGATTCAAGGCCAGCGATATTGGGCTT
*
2983148 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAA-GACAAGGTGCCAATATGCTGAT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAATGA-AAGATGCCAATATGCTGAT
*
2983212 TCAAGGCCAGCGATATTGGGCTTA
65 TCAAGGCCAGCGATATTGGACTTA
2983236 TGCCAATGTG
Statistics
Matches: 351, Mismatches: 24, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
288 1 0.00
289 37 0.11
290 1 0.00
291 2 0.01
292 1 0.00
293 302 0.86
294 6 0.02
295 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (289 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAATGAAAGATGCCAATATGCTGATT
CAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCAACATT
GGTCTTAAAGATGACGAAAGCACCAATATGCTGATTCAAGGCCAGCAATATTGGATTAAAAGATG
AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGGTACCAATAT
GCTGATTCAAGGCCAGCGATATTGGGCTT
Found at i:2983166 original size:39 final size:39
Alignment explanation
Indices: 2983112--2983269 Score: 172
Period size: 39 Copynumber: 3.8 Consensus size: 39
2983102 GACGAAGGTA
*
2983112 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTGTG
* *
2983151 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGGCTT---------GTG
* *
2983199 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTATG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTGTG
* *
2983238 CCAATGTGTTGATTCAAGGCCAGCGACATTGG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGG
2983270 TCTTAAAAAC
Statistics
Matches: 100, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
39 64 0.64
48 36 0.36
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (39 bp):
CCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTGTG
Found at i:2983219 original size:48 final size:47
Alignment explanation
Indices: 2983148--2983317 Score: 194
Period size: 48 Copynumber: 3.7 Consensus size: 47
2983138 TATTGGGCTT
*
2983148 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAA-ACAAG
* *
2983196 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT------A-
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAACAAG
* *
2983236 -TGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAAACAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT-AAAACAAG
* * *
2983283 GTGCCAATATGCCGATTCAAGGCCAACGATATTGG
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGG
2983318 GATTAAAGGT
Statistics
Matches: 101, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
39 34 0.34
41 1 0.01
46 1 0.01
48 65 0.64
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.25
Consensus pattern (47 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAACAAG
Found at i:2983240 original size:87 final size:87
Alignment explanation
Indices: 2983058--2983318 Score: 414
Period size: 87 Copynumber: 3.0 Consensus size: 87
2983048 AAGATGAAGG
* * *
2983058 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGGTACCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AA-A-GAC-AAGGTGCCAATATGCTG
*
2983123 ATTCAAGGCCAGCGATATTGGGCTTG
62 ATTCAAGGCCAGCGATATTGGGCTTA
2983149 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
2983214 AAGGCCAGCGATATTGGGCTTA
66 AAGGCCAGCGATATTGGGCTTA
* * *
2983236 TGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAAACAAGGTGCCAATATGCCGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
*
2983301 AAGGCCAACGATATTGGG
66 AAGGCCAGCGATATTGGG
2983319 ATTAAAGGTG
Statistics
Matches: 162, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
87 120 0.74
88 3 0.02
89 1 0.01
90 2 0.01
91 36 0.22
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (87 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
AAGGCCAGCGATATTGGGCTTA
Found at i:2983396 original size:33 final size:32
Alignment explanation
Indices: 2983322--2983411 Score: 117
Period size: 32 Copynumber: 2.8 Consensus size: 32
2983312 TATTGGGATT
*
2983322 AAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGA
*
2983354 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAG-A
* * * *
2983387 AAAGATGCCATGGACTTATGGGCTT
1 AAAGGTGCCACGGAGTTGTGGGCTT
2983412 TTGAAGGTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 29 0.57
33 22 0.43
ACGTcount: A:0.33, C:0.13, G:0.32, T:0.21
Consensus pattern (32 bp):
AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGA
Found at i:2984921 original size:1 final size:1
Alignment explanation
Indices: 2984917--2984995 Score: 59
Period size: 1 Copynumber: 79.0 Consensus size: 1
2984907 TTGTTGTTTG
* * * ** * * * * *
2984917 TTTTTCTTTGTTTGTTTTTTTTTTTGGTTTTTTTTTTGTTTTTTTTGTTTGTTTTGTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
2984982 TGTTTTTTTTTTTT
1 TTTTTTTTTTTTTT
2984996 GCGGAGGACG
Statistics
Matches: 58, Mismatches: 20, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.00, C:0.01, G:0.13, T:0.86
Consensus pattern (1 bp):
T
Found at i:2984930 original size:21 final size:19
Alignment explanation
Indices: 2984906--2984995 Score: 100
Period size: 19 Copynumber: 4.7 Consensus size: 19
2984896 TCGGACCCTT
2984906 TTTGTTGTTTGTTTTTCTTTG
1 TTTGTT-TTTGTTTTT-TTTG
2984927 TTTGTTTTT-TTTTTTGGTT-
1 TTTGTTTTTGTTTTTT--TTG
2984946 TTT-TTTTTGTTTTTTTTG
1 TTTGTTTTTGTTTTTTTTG
2984964 TTTGTTTTGTGTTTTTTTTG
1 TTTGTTTT-TGTTTTTTTTG
2984984 TTT-TTTTT-TTTT
1 TTTGTTTTTGTTTT
2984996 GCGGAGGACG
Statistics
Matches: 63, Mismatches: 0, Indels: 16
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.10
18 10 0.16
19 22 0.35
20 19 0.30
21 6 0.10
ACGTcount: A:0.00, C:0.01, G:0.14, T:0.84
Consensus pattern (19 bp):
TTTGTTTTTGTTTTTTTTG
Found at i:2984934 original size:13 final size:12
Alignment explanation
Indices: 2984904--2984996 Score: 79
Period size: 11 Copynumber: 7.7 Consensus size: 12
2984894 ATTCGGACCC
2984904 TTTTTGTTGTTTG
1 TTTTT-TTGTTTG
2984917 TTTTTCTTTGTTTG
1 -TTTT-TTTGTTTG
*
2984931 TTTTTTTTTTTGG
1 TTTTTTTGTTT-G
2984944 TTTTTTT-TTTG
1 TTTTTTTGTTTG
2984955 TTTTTTTTGTTTG
1 -TTTTTTTGTTTG
*
2984968 -TTTTGTGTTT-
1 TTTTTTTGTTTG
2984978 TTTTTGTT-TTT-
1 TTTTT-TTGTTTG
2984989 TTTTTTTG
1 TTTTTTTG
2984997 CGGAGGACGT
Statistics
Matches: 69, Mismatches: 3, Indels: 17
0.78 0.03 0.19
Matches are distributed among these distances:
10 2 0.03
11 22 0.32
12 17 0.25
13 16 0.23
14 11 0.16
15 1 0.01
ACGTcount: A:0.00, C:0.01, G:0.15, T:0.84
Consensus pattern (12 bp):
TTTTTTTGTTTG
Found at i:2984949 original size:9 final size:9
Alignment explanation
Indices: 2984913--2984995 Score: 91
Period size: 10 Copynumber: 8.9 Consensus size: 9
2984903 CTTTTTGTTG
2984913 TTTGTTTTT
1 TTTGTTTTT
2984922 CTTTGTTTGTT
1 -TTTGTTT-TT
2984933 TTT-TTTTT
1 TTTGTTTTT
2984941 TGGTT-TTTTT
1 T--TTGTTTTT
2984951 TTTGTTTTT
1 TTTGTTTTT
2984960 TTTGTTTGTT
1 TTTGTTT-TT
2984970 TTGTGTTTTT
1 TT-TGTTTTT
2984980 TTTGTTTTT
1 TTTGTTTTT
2984989 TTT-TTTT
1 TTTGTTTT
2984996 GCGGAGGACG
Statistics
Matches: 67, Mismatches: 0, Indels: 14
0.83 0.00 0.17
Matches are distributed among these distances:
8 9 0.13
9 25 0.37
10 26 0.39
11 7 0.10
ACGTcount: A:0.00, C:0.01, G:0.13, T:0.86
Consensus pattern (9 bp):
TTTGTTTTT
Found at i:2984949 original size:11 final size:10
Alignment explanation
Indices: 2984913--2984992 Score: 78
Period size: 9 Copynumber: 8.3 Consensus size: 10
2984903 CTTTTTGTTG
*
2984913 TTTGTTTTTC
1 TTTGTTTTTT
*
2984923 TTTGTTTGTT
1 TTTGTTTTTT
2984933 TTT-TTTTTT
1 TTTGTTTTTT
**
2984942 GGT-TTTTTT
1 TTTGTTTTTT
2984951 TTTG-TTTTT
1 TTTGTTTTTT
*
2984960 TTTG-TTTGT
1 TTTGTTTTTT
2984969 TTTGTGTTTTT
1 TTTGT-TTTTT
2984980 TTTGTTTTTT
1 TTTGTTTTTT
2984990 TTT
1 TTT
2984993 TTTGCGGAGG
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
9 30 0.52
10 19 0.33
11 9 0.16
ACGTcount: A:0.00, C:0.01, G:0.14, T:0.85
Consensus pattern (10 bp):
TTTGTTTTTT
Found at i:2984949 original size:41 final size:40
Alignment explanation
Indices: 2984905--2984993 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
2984895 TTCGGACCCT
* * * *
2984905 TTTTGTTGTTTGTTTTTCTTTGTTTGTTTTTTTTTTTGGTTT
1 TTTTTTTGTTT-TTTTTGTTTGTTT-TGTGTTTTTTTGGTTT
*
2984947 TTTTTTTGTTTTTTTTGTTTGTTTTGTGTTTTTTTTGTTT
1 TTTTTTTGTTTTTTTTGTTTGTTTTGTGTTTTTTTGGTTT
2984987 TTTTTTT
1 TTTTTTT
2984994 TTGCGGAGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 20 0.48
41 12 0.29
42 10 0.24
ACGTcount: A:0.00, C:0.01, G:0.15, T:0.84
Consensus pattern (40 bp):
TTTTTTTGTTTTTTTTGTTTGTTTTGTGTTTTTTTGGTTT
Found at i:2984958 original size:20 final size:20
Alignment explanation
Indices: 2984904--2984993 Score: 101
Period size: 20 Copynumber: 4.4 Consensus size: 20
2984894 ATTCGGACCC
* *
2984904 TTTTTGTTGTTTGTTTTTCTT
1 TTTTTTTTGTTT-TTTTTGTT
*
2984925 TGTTTGTTTT-TTTTTTTGGTT
1 T-TTT-TTTTGTTTTTTTTGTT
2984946 TTTTTTTTGTTTTTTTTGTT
1 TTTTTTTTGTTTTTTTTGTT
* *
2984966 TGTTTTGTGTTTTTTTTGTT
1 TTTTTTTTGTTTTTTTTGTT
2984986 TTTTTTTT
1 TTTTTTTT
2984994 TTGCGGAGGA
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
19 4 0.07
20 37 0.64
21 8 0.14
22 6 0.10
23 3 0.05
ACGTcount: A:0.00, C:0.01, G:0.14, T:0.84
Consensus pattern (20 bp):
TTTTTTTTGTTTTTTTTGTT
Found at i:2984996 original size:42 final size:41
Alignment explanation
Indices: 2984904--2984993 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
2984894 ATTCGGACCC
*
2984904 TTTTTGTTGTTTGTTTTTCTTTGTTTGTTTTTTTTTTTGGTT
1 TTTTTTTTGTTTGTTTTTCTTTGTTTGTTTTTTTTTTT-GTT
* *
2984946 TTTTTTTTGTTT-TTTTTGTTTGTTT-TGTGTTTTTTTTGTT
1 TTTTTTTTGTTTGTTTTTCTTTGTTTGT-TTTTTTTTTTGTT
2984986 TTTTTTTT
1 TTTTTTTT
2984994 TTGCGGAGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 12 0.27
41 21 0.48
42 11 0.25
ACGTcount: A:0.00, C:0.01, G:0.14, T:0.84
Consensus pattern (41 bp):
TTTTTTTTGTTTGTTTTTCTTTGTTTGTTTTTTTTTTTGTT
Found at i:3003855 original size:20 final size:20
Alignment explanation
Indices: 3003830--3003883 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
3003820 TTTTAACTAG
3003830 ATGTATCGATACATTAAAAA
1 ATGTATCGATACATTAAAAA
*
3003850 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTAAAAA
*
3003870 ATGTATCAATACAT
1 ATGTATCGATACAT
3003884 CTGGGTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTAAAAA
Found at i:3003926 original size:20 final size:20
Alignment explanation
Indices: 3003900--3003955 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
3003890 AAAAAGATAG
*
3003900 AATGTATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* *
3003920 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
*
3003940 AATGTATCAATACATT
1 AATGTATCGATACATT
3003956 TGGGTGCTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:3008596 original size:25 final size:22
Alignment explanation
Indices: 3008564--3008615 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 22
3008554 GTAAATTTAA
3008564 AAATTAATGATAAAATATATATTT
1 AAATTAAT-ATAAAA-ATATATTT
*
3008588 AAATGTAATATATAAATATATTT
1 AAAT-TAATATAAAAATATATTT
3008611 AAATT
1 AAATT
3008616 TAACATGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 1 0.04
23 12 0.46
24 9 0.35
25 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
AAATTAATATAAAAATATATTT
Found at i:3008628 original size:23 final size:23
Alignment explanation
Indices: 3008580--3008630 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
3008570 ATGATAAAAT
*
3008580 ATATATTTAAATGTAATATATAA
1 ATATATTTAAATGTAACATATAA
* * *
3008603 ATATATTTAAATTTAACATGTGA
1 ATATATTTAAATGTAACATATAA
3008626 ATATA
1 ATATA
3008631 GTATGAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (23 bp):
ATATATTTAAATGTAACATATAA
Found at i:3008969 original size:4 final size:4
Alignment explanation
Indices: 3008949--3008981 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
3008939 GGAAGAACTG
3008949 TAAA -AAA TAAA -AAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
3008982 GAATTTGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 6 0.22
4 21 0.78
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
TAAA
Found at i:3009687 original size:2 final size:2
Alignment explanation
Indices: 3009680--3009720 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
3009670 TTATTAACCT
* * *
3009680 TC TC TC TC TC TC TC TC TC TC TC TC GC TG GC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3009721 TTGTTGCCCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.46, G:0.07, T:0.46
Consensus pattern (2 bp):
TC
Found at i:3014632 original size:12 final size:12
Alignment explanation
Indices: 3014615--3014639 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3014605 AATAAAAAAT
3014615 AATTTAATTTTA
1 AATTTAATTTTA
3014627 AATTTAATTTTA
1 AATTTAATTTTA
3014639 A
1 A
3014640 TCTTATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AATTTAATTTTA
Found at i:3015227 original size:13 final size:13
Alignment explanation
Indices: 3015209--3015233 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3015199 GGAGAGACAG
3015209 AAAGAGAGGAAAA
1 AAAGAGAGGAAAA
3015222 AAAGAGAGGAAA
1 AAAGAGAGGAAA
3015234 TGAAAGAAAA
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (13 bp):
AAAGAGAGGAAAA
Found at i:3015325 original size:17 final size:18
Alignment explanation
Indices: 3015303--3015365 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 18
3015293 ATTTATATAA
3015303 ATTTTA-ATATATTATTT
1 ATTTTACATATATTATTT
*
3015320 ATTTTACGTATATT-TTT
1 ATTTTACATATATTATTT
* **
3015337 ATTATATTTATATTA-TT
1 ATTTTACATATATTATTT
3015354 -TTTTA-ATATATT
1 ATTTTACATATATT
3015366 TTAATAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 6 0.16
16 4 0.11
17 22 0.58
18 6 0.16
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTTACATATATTATTT
Found at i:3015342 original size:11 final size:11
Alignment explanation
Indices: 3015328--3015367 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
3015318 TTATTTTACG
3015328 TATATTTTTAT
1 TATATTTTTAT
*
3015339 TATATTTATAT
1 TATATTTTTAT
*
3015350 TAT-TTTTTAA
1 TATATTTTTAT
3015360 TATATTTT
1 TATATTTT
3015368 AATAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATATTTTTAT
Found at i:3015375 original size:21 final size:21
Alignment explanation
Indices: 3015332--3015378 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3015322 TTTACGTATA
* *
3015332 TTTTTATTATATTTATATTAT
1 TTTTTAATATATTTATATAAT
3015353 TTTTTAATATATTT-TAATAAT
1 TTTTTAATATATTTAT-ATAAT
3015374 TTTTT
1 TTTTT
3015379 GAGATAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTAATATATTTATATAAT
Found at i:3016148 original size:18 final size:18
Alignment explanation
Indices: 3016086--3016148 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
3016076 AATTTATTTA
*
3016086 ATTAAAATATTAAAATAT
1 ATTAAAAAATTAAAATAT
* * *
3016104 TTTAAAATATATAGAATAT
1 ATTAAAAAAT-TAAAATAT
3016123 AATT-AAAAATTAAAATAT
1 -ATTAAAAAATTAAAATAT
3016141 ATTAAAAA
1 ATTAAAAA
3016149 GATCTCCATG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
17 3 0.08
18 20 0.54
19 12 0.32
20 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
ATTAAAAAATTAAAATAT
Found at i:3016580 original size:17 final size:17
Alignment explanation
Indices: 3016554--3016589 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3016544 TACTCACAAC
3016554 ACTTAAATACAAACATT
1 ACTTAAATACAAACATT
* *
3016571 ACTTACATACAAATATT
1 ACTTAAATACAAACATT
3016588 AC
1 AC
3016590 CAAAATTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (17 bp):
ACTTAAATACAAACATT
Found at i:3017255 original size:14 final size:15
Alignment explanation
Indices: 3017236--3017265 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3017226 AATAAAAAAT
3017236 AAAAAATTAT-TTTA
1 AAAAAATTATATTTA
3017250 AAAAAATTATATTTA
1 AAAAAATTATATTTA
3017265 A
1 A
3017266 TTTTTTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAAAATTATATTTA
Found at i:3017340 original size:21 final size:21
Alignment explanation
Indices: 3017298--3017337 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3017288 ATAAATGCAT
3017298 TATAGTTTCAGTAATATTTTA
1 TATAGTTTCAGTAATATTTTA
*
3017319 TATAG-TTCTGTAATATTTT
1 TATAGTTTCAGTAATATTTT
3017338 TATGTAACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (21 bp):
TATAGTTTCAGTAATATTTTA
Found at i:3017742 original size:16 final size:15
Alignment explanation
Indices: 3017721--3017784 Score: 74
Period size: 16 Copynumber: 4.1 Consensus size: 15
3017711 TTTGAGTTAG
*
3017721 GTCATTTTAGATTTAA
1 GTCATTTTAAATTT-A
*
3017737 GTCATTTTAAATTTT
1 GTCATTTTAAATTTA
3017752 GATCATTTTAAATTTGA
1 G-TCATTTTAAATTT-A
*
3017769 GTCATTTCAAATTTA
1 GTCATTTTAAATTTA
3017784 G
1 G
3017785 GTTGATTGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
15 3 0.07
16 38 0.90
17 1 0.02
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.50
Consensus pattern (15 bp):
GTCATTTTAAATTTA
Found at i:3017772 original size:32 final size:32
Alignment explanation
Indices: 3017722--3017782 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
3017712 TTGAGTTAGG
* *
3017722 TCATTTTAGATTTAAGTCATTTTAAATTTTGA
1 TCATTTTAAATTTAAGTCATTTCAAATTTTGA
*
3017754 TCATTTTAAATTTGAGTCATTTCAAATTT
1 TCATTTTAAATTTAAGTCATTTCAAATTT
3017783 AGGTTGATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.52
Consensus pattern (32 bp):
TCATTTTAAATTTAAGTCATTTCAAATTTTGA
Found at i:3018295 original size:19 final size:20
Alignment explanation
Indices: 3018253--3018291 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
3018243 CATAAAAATA
3018253 TATGTAACTTATAATATATT
1 TATGTAACTTATAATATATT
3018273 TATGTAA-TTATAATA-ATT
1 TATGTAACTTATAATATATT
3018291 T
1 T
3018292 TATGCATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 8 0.42
20 7 0.37
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (20 bp):
TATGTAACTTATAATATATT
Found at i:3019877 original size:50 final size:50
Alignment explanation
Indices: 3019813--3020072 Score: 360
Period size: 50 Copynumber: 5.2 Consensus size: 50
3019803 AAGTGTTACC
* * *
3019813 ATTGTTGACTATTCTTCACCAACCTTTGATAATCGAGAGAAGTGGTTATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCATA
*
3019863 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGAT-AGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCA-TA
* *
3019913 ATTGTTGATTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCATA
* * * *
3019963 ATTGTTGACGATTCTTTACCAACCTTTGACAATTGAGAGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCATA
* * * * * *
3020013 ATTGTTCACTATTCTTCACTAACCTTTAATAATAGAGAGAGGTGGTCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCATA
3020063 ATTGTTGACT
1 ATTGTTGACT
3020073 CTAAACAACT
Statistics
Matches: 186, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 1 0.01
50 185 0.99
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCATA
Found at i:3021672 original size:14 final size:14
Alignment explanation
Indices: 3021649--3021696 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
3021639 GTGATGTATC
*
3021649 GATACATGAATAGT
1 GATACGTGAATAGT
3021663 GATACGTGAATAGT
1 GATACGTGAATAGT
*
3021677 TATGAACAGTGAATAGT
1 GAT--AC-GTGAATAGT
3021694 GAT
1 GAT
3021697 GAACAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 15 0.54
16 2 0.07
17 11 0.39
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.29
Consensus pattern (14 bp):
GATACGTGAATAGT
Found at i:3021690 original size:17 final size:17
Alignment explanation
Indices: 3021626--3021705 Score: 77
Period size: 17 Copynumber: 5.1 Consensus size: 17
3021616 GCTTTTATTA
3021626 AATAGTG-TGAACAGTG
1 AATAGTGATGAACAGTG
3021642 -AT-GT-ATCGATACA-TG
1 AATAGTGAT-GA-ACAGTG
3021657 AATAGTGAT--AC-GTG
1 AATAGTGATGAACAGTG
*
3021671 AATAGTTATGAACAGTG
1 AATAGTGATGAACAGTG
3021688 AATAGTGATGAACAGTG
1 AATAGTGATGAACAGTG
3021705 A
1 A
3021706 TGTATCGATA
Statistics
Matches: 52, Mismatches: 2, Indels: 19
0.71 0.03 0.26
Matches are distributed among these distances:
14 15 0.29
15 6 0.12
16 7 0.13
17 22 0.42
18 2 0.04
ACGTcount: A:0.39, C:0.07, G:0.26, T:0.28
Consensus pattern (17 bp):
AATAGTGATGAACAGTG
Found at i:3024083 original size:23 final size:24
Alignment explanation
Indices: 3024038--3024084 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
3024028 AAAAGAATTG
*
3024038 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
3024062 AACAC-AATTCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
3024085 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.60, C:0.19, G:0.04, T:0.17
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:3027912 original size:49 final size:52
Alignment explanation
Indices: 3027805--3027930 Score: 195
Period size: 49 Copynumber: 2.5 Consensus size: 52
3027795 CGAAATATGA
* *
3027805 AAATTTACCTGCATGTATTGATACATGTAATAGTATATCGATATATCTGGGC
1 AAATTTGCCTGCATGTATTGATACATGTAATAGTATATCGATACATCTGGGC
* *
3027857 AAATTTGCCTGCATGTATCGATACAT-TAA-A-TGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATTGATACATGTAATAGTATATCGATACATCTGGGC
3027906 AAATTTGCCTGCATGTATTGATACA
1 AAATTTGCCTGCATGTATTGATACA
3027931 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
49 41 0.59
50 1 0.01
51 3 0.04
52 24 0.35
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATTGATACATGTAATAGTATATCGATACATCTGGGC
Found at i:3027957 original size:13 final size:13
Alignment explanation
Indices: 3027939--3027963 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3027929 CAAAGATCAG
3027939 TGTATCGATACAA
1 TGTATCGATACAA
3027952 TGTATCGATACA
1 TGTATCGATACA
3027964 TTTGAGTAAT
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:3028011 original size:13 final size:13
Alignment explanation
Indices: 3027993--3028017 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3027983 CAAAAAAATA
3027993 TGTATCGATACAT
1 TGTATCGATACAT
3028006 TGTATCGATACA
1 TGTATCGATACA
3028018 ACACTTTATG
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:3028015 original size:33 final size:33
Alignment explanation
Indices: 3027973--3028037 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
3027963 ATTTGAGTAA
3027973 TGTATCGATACAAAAAAATATGTATCGATACAT
1 TGTATCGATACAAAAAAATATGTATCGATACAT
* ***
3028006 TGTATCGATACAACACTTTATGTATCGATACA
1 TGTATCGATACAAAAAAATATGTATCGATACA
3028038 AATCGTTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAAAAAAATATGTATCGATACAT
Found at i:3029003 original size:13 final size:13
Alignment explanation
Indices: 3028985--3029010 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3028975 TACAGCAAGT
3028985 ATGTATCGATACA
1 ATGTATCGATACA
3028998 ATGTATCGATACA
1 ATGTATCGATACA
3029011 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3031259 original size:21 final size:21
Alignment explanation
Indices: 3031226--3031270 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3031216 TTGCAAGTTG
*
3031226 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3031248 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3031268 AAA
1 AAA
3031271 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3033094 original size:15 final size:15
Alignment explanation
Indices: 3033074--3033104 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3033064 TAAAAATGTC
*
3033074 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3033089 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3033104 C
1 C
3033105 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3035197 original size:20 final size:21
Alignment explanation
Indices: 3035118--3035196 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
3035108 AATGTCCAAA
*
3035118 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
3035138 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
3035163 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
3035183 TTGTATCGATACAT
1 ATGTATCGATACAT
3035197 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:3035201 original size:13 final size:13
Alignment explanation
Indices: 3035183--3035221 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3035173 ACATTTTTCT
3035183 TTGTATCGATACA
1 TTGTATCGATACA
3035196 TTGTATCGATACA
1 TTGTATCGATACA
*
3035209 CTGTATCGATACA
1 TTGTATCGATACA
3035222 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3037124 original size:1 final size:1
Alignment explanation
Indices: 3037118--3037144 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
3037108 ATTCGTAAAA
3037118 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
3037145 AAGGGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3037789 original size:13 final size:13
Alignment explanation
Indices: 3037771--3037796 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3037761 TACAGCAAGT
3037771 ATGTATCGATACA
1 ATGTATCGATACA
3037784 ATGTATCGATACA
1 ATGTATCGATACA
3037797 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3038955 original size:55 final size:52
Alignment explanation
Indices: 3038895--3039273 Score: 204
Period size: 49 Copynumber: 8.0 Consensus size: 52
3038885 CGATATTGGG
* *
3038895 CTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAA
1 CTTAAAGATG-G-AAAAGG-TGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * *
3038950 CTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** *
3039002 C-T-----T----AA-GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * * * **
3039043 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCGATATCGGG
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** *
3039092 C-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * * * *
3039135 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** *
3039184 C-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* *
3039227 CTTAAAGAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTG
3039274 GGCTTAGAAG
Statistics
Matches: 270, Mismatches: 31, Indels: 52
0.76 0.09 0.15
Matches are distributed among these distances:
41 35 0.13
42 3 0.01
43 71 0.26
44 2 0.01
46 1 0.00
47 1 0.00
48 4 0.01
49 104 0.39
51 1 0.00
52 31 0.11
53 6 0.02
54 1 0.00
55 10 0.04
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (52 bp):
CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
Found at i:3039080 original size:49 final size:48
Alignment explanation
Indices: 3039005--3039279 Score: 336
Period size: 49 Copynumber: 5.9 Consensus size: 48
3038995 TATTGGACTT
*
3039005 AAGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* * * *
3039053 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATCGGGCTT-AA-A-G
1 AAG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
*
3039099 --GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* * *
3039145 AAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGACTT-AA-A-G
1 AAG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* *
3039191 --GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA
1 AAGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* *
3039237 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 AA-GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
3039280 GAAGGGTTGC
Statistics
Matches: 192, Mismatches: 22, Indels: 25
0.80 0.09 0.10
Matches are distributed among these distances:
43 67 0.35
44 6 0.03
45 2 0.01
46 3 0.02
47 2 0.01
48 8 0.04
49 104 0.54
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (48 bp):
AAGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
Found at i:3039133 original size:92 final size:92
Alignment explanation
Indices: 3038922--3039284 Score: 586
Period size: 92 Copynumber: 3.9 Consensus size: 92
3038912 GGATGTCAAC
* *
3038922 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAG
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAG
*
3038987 GCCAGCTATATTGGACTT-AA-GTGCCAAT
63 GCCAGCGATATTGGACTTAAAGGTGCCAAT
3039015 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
* *
3039080 AGCGATATCGGGCTTAAAGGTGCCAAT
66 AGCGATATTGGACTTAAAGGTGCCAAT
3039107 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
*
3039172 AACGATATTGGACTTAAAGGTGCCAAT
66 AGCGATATTGGACTTAAAGGTGCCAAT
* *
3039199 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
* *
3039264 AGCTATATTGGGCTTAGAAGG
66 AGCGATATTGGACTTA-AAGG
3039285 GTTGCCACCG
Statistics
Matches: 254, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
90 38 0.15
91 2 0.01
92 174 0.69
93 40 0.16
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (92 bp):
GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
AGCGATATTGGACTTAAAGGTGCCAAT
Found at i:3039323 original size:33 final size:35
Alignment explanation
Indices: 3039279--3039348 Score: 117
Period size: 33 Copynumber: 2.1 Consensus size: 35
3039269 TATTGGGCTT
3039279 AGAAGGGTTGCCACCGACTTGTATGGGCTTT-GGA
1 AGAAGGGTTGCCACCGACTTGTATGGGCTTTAGGA
*
3039313 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AGAAGGGTTGCCACCGACTTGTATGGGCTTTAGGA
3039347 AG
1 AG
3039349 GGAGAAAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 25 0.74
34 9 0.26
ACGTcount: A:0.21, C:0.17, G:0.36, T:0.26
Consensus pattern (35 bp):
AGAAGGGTTGCCACCGACTTGTATGGGCTTTAGGA
Found at i:3039391 original size:34 final size:33
Alignment explanation
Indices: 3039353--3039898 Score: 414
Period size: 34 Copynumber: 16.6 Consensus size: 33
3039343 AGGAAGGGAG
*
3039353 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAA-GGAA
*
3039387 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAA
1 AAAGA-TGCCACGGAGTTGTGGGC-TTAAAAGGAA
3039422 AAAG-TGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGC-TT-AAAA-GGAA
* *
3039457 AAAGAGTGCCACAGAGTTGTGGGCTTTAAACAGAAA
1 AAAGA-TGCCACGGAGTTGTGGGC-TTAAA-AGGAA
* *
3039493 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGATGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * *
3039527 AAAGGTGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAA-AGGAA
*
3039561 AAA-AGTGCCACAGAGTTGTGGGCTTAAAAGG--
1 AAAGA-TGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
3039592 ---G-TGCCATGGAGTTGTGGGCTTAGAAGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
** *
3039621 AAAGAGTGCCACAAAGTTGTGGGCTTAGAAGGAA
1 AAAGA-TGCCACGGAGTTGTGGGCTTAAAAGGAA
*
3039655 AAAGAGTGCCACGGAGTTGTGGGCTT-TAA--AA
1 AAAGA-TGCCACGGAGTTGTGGGCTTAAAAGGAA
*
3039686 AGAG-TGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 AAAGATGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* * *
3039719 AAAGGTGCCATGGAGTTGTAGGCTTTGAAAA-GAA
1 AAAGATGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* * * *
3039753 GAAGGTGCCACGAAGTTGTGGGCTTTAAAGG-A
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* * **
3039785 AAAGGTGCCATGGAGTTGTGGGCTTTGAA-GAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* * * * ** *
3039817 AAA-AAGCCACTGAGTCGTGGACTT-TGA-GAC
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* * * *
3039847 AAA-ATGCCACTGAGTCGTGGACTTTAAA-GAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
3039878 AAAGATGCCACTGAGTCGTGG
1 AAAGATGCCACGGAGTTGTGG
3039899 ACTTTGAGAA
Statistics
Matches: 435, Mismatches: 51, Indels: 54
0.81 0.09 0.10
Matches are distributed among these distances:
27 23 0.05
29 18 0.04
30 28 0.06
31 27 0.06
32 53 0.12
33 38 0.09
34 157 0.36
35 54 0.12
36 16 0.04
37 21 0.05
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.21
Consensus pattern (33 bp):
AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:3039403 original size:35 final size:34
Alignment explanation
Indices: 3039353--3039809 Score: 458
Period size: 34 Copynumber: 13.8 Consensus size: 34
3039343 AGGAAGGGAG
*
3039353 AAAGA-TGCCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAA-GGAA
3039387 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAA-GAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
3039421 AAA-AGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AAAA-GGAA
* *
3039457 AAAGAGTGCCACAGAGTTGTGGGCTTTAAACAGAAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAA-AGGAA
*
3039493 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
3039527 AAAG-GTGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAA-AGGAA
*
3039561 AAA-AGTGCCACAGAGTTGTGGGCTTAAAA-G--
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
3039591 ---G-GTGCCATGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
** *
3039621 AAAGAGTGCCACAAAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
3039655 AAAGAGTGCCACGGAGTTGTGGGCTT-----TAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
3039684 AAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* *
3039719 AAAG-GTGCCATGGAGTTGTAGGCTTTGAAAA-GAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* * *
3039753 GAAG-GTGCCACGAAGTTGTGGGCTTTAAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
3039785 AAAG-GTGCCATGGAGTTGTGGGCTT
1 AAAGAGTGCCACGGAGTTGTGGGCTT
3039810 TGAAGAAAAA
Statistics
Matches: 369, Mismatches: 30, Indels: 50
0.82 0.07 0.11
Matches are distributed among these distances:
27 22 0.06
28 1 0.00
29 26 0.07
30 2 0.01
32 27 0.07
33 33 0.09
34 166 0.45
35 47 0.13
36 22 0.06
37 23 0.06
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (34 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:3039597 original size:27 final size:27
Alignment explanation
Indices: 3039565--3039618 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
3039555 GATGAAAAAA
3039565 GTGCCACAGAGTTGTGGGCTTAAAAGG
1 GTGCCACAGAGTTGTGGGCTTAAAAGG
** *
3039592 GTGCCATGGAGTTGTGGGCTTAGAAGG
1 GTGCCACAGAGTTGTGGGCTTAAAAGG
3039619 AAAAAGAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.22, C:0.13, G:0.41, T:0.24
Consensus pattern (27 bp):
GTGCCACAGAGTTGTGGGCTTAAAAGG
Found at i:3039605 original size:95 final size:94
Alignment explanation
Indices: 3039385--3039810 Score: 425
Period size: 95 Copynumber: 4.3 Consensus size: 94
3039375 CTTAAAAGGG
*
3039385 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGA
1 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGT-GGC-TT--
*
3039449 AAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAACAGA
61 AAAGAGAAAAA-AGTGCCAC-GAGTTGTGGGCTTT------A
3039491 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGG-CTTAAAG
3039556 ATGAAAAAAGTGCCACAGAGTTGTGGGC-TT-
65 A-GAAAAAAGTGCCAC-GAGTTGTGGGCTTTA
* * * * **
3039586 AAAAGGGTGCCATGGAGTTGTGGGC-TTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTAGA
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGTTGT-GGCTTA-A
3039650 AG-GAAAAAGAGTGCCACGGAGTTGTGGGCTTT-
63 AGAGAAAAA-AGTGCCAC-GAGTTGTGGGCTTTA
* *
3039682 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCATGGAGTTGTAGGCTTTGA
1 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGT-GGC-TT-A
* *
3039747 AA-AGAAGAAGGTGCCACGAAGTTGTGGGCTTTAA
62 AAGAGAAAAAAGTGCCACG-AGTTGTGGGCTTT-A
*
3039781 AGGAAAAGGTGCCATGGAGTTGTGGGCTTT
1 A--AAAAGGTGCCACGGAGTTGTGGGCTTT
3039811 GAAGAAAAAA
Statistics
Matches: 281, Mismatches: 21, Indels: 42
0.82 0.06 0.12
Matches are distributed among these distances:
94 18 0.06
95 59 0.21
96 13 0.05
97 53 0.19
98 20 0.07
99 2 0.01
100 21 0.07
101 5 0.02
102 2 0.01
103 24 0.09
104 6 0.02
105 26 0.09
106 32 0.11
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (94 bp):
AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGCTTAAAGA
GAAAAAAGTGCCACGAGTTGTGGGCTTTA
Found at i:3039727 original size:97 final size:97
Alignment explanation
Indices: 3039385--3039822 Score: 480
Period size: 97 Copynumber: 4.4 Consensus size: 97
3039375 CTTAAAAGGG
*
3039385 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGC-TT-A
*
3039449 AAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
64 GAA-GGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
* * *
3039484 AAACAGAAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGA
1 ----A-AAAAGA-GTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGG
3039549 CTTA-AAGATGAAAAA-AGTGCCACAGAGTTGTGGGC-TT
60 CTTAGAAG--GAAAAAGAGTGCCACAGAGTTGTGGGCTTT
* * * * **
3039586 -AAAAGGGTGCCATGGAGTTGTGGGCTTAG-AAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTAG
*
3039649 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
65 AAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
* * *
3039682 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCATGGAGTTGTAGGCTTTGA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTAG-
* *
3039747 AAAGAAGAAG-GTGCCAC-GAAGTTGTGGGCTTT
65 AAGGAAAAAGAGTGCCACAG-AGTTGTGGGCTTT
* *
3039779 AAAGGAAAAGGTGCCATGGAGTTGTGGGCTTTGAAGAA-AAAAAG
1 AAA--AAGA-GTGCCACGGAGTTGTGGGCTTTGAA-AAGAAAAAG
3039823 CCACTGAGTC
Statistics
Matches: 292, Mismatches: 26, Indels: 37
0.82 0.07 0.10
Matches are distributed among these distances:
94 15 0.05
95 58 0.20
96 10 0.03
97 67 0.23
98 17 0.06
99 3 0.01
100 30 0.10
101 2 0.01
102 3 0.01
103 23 0.08
104 12 0.04
105 24 0.08
106 28 0.10
ACGTcount: A:0.34, C:0.11, G:0.34, T:0.21
Consensus pattern (97 bp):
AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTAGA
AGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
Found at i:3039763 original size:192 final size:199
Alignment explanation
Indices: 3039385--3039822 Score: 542
Period size: 192 Copynumber: 2.2 Consensus size: 199
3039375 CTTAAAAGGG
* * * **
3039385 AAAAAGAGTGCCACGGAGTTGTGGGCTTTA-AAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGA
1 AAAAAGGGTGCCATGGAGTTGTGGGC-TTAGAAGGAAAAAAGTGCCACAAAGTTGTGGGCTTTGA
3039449 AAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAACAGAAAAAAGGTGCCACGGAGTTGTGG
65 AAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT--A-AGAAAAAAGGTGCCACGGAGTTGTGG
3039514 GCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCAC-AGAGTT
127 GCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGA-AGTT
3039578 GTGGGC-TT
191 GTGGGCTTT
3039586 -AAAAGGGTGCCATGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGC-TT-A
1 AAAAAGGGTGCCATGGAGTTGTGGGCTTAGAAGGAAAAA-AGTGCCACAAAGTTGTGGGCTTTGA
* * *
3039648 GAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-A-AAAAGA-GTGCCACGGAGTTGTGGGCT
65 AAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAGAAAAAAGGTGCCACGGAGTTGTGGGCT
* * * *
3039709 TTGAAAAGAAAAAGGTGCCATGGAGTTGTAGG-CTTTGAAA-A-GAAGAAGGTGCCACGAAGTTG
130 TTAAAAAGAAAAAGGTGCCACGGAGTTGT-GGAC-TT-AAAGATGAAAAAAGTGCCACGAAGTTG
3039771 TGGGCTTT
192 TGGGCTTT
* * *
3039779 AAAGGAAAAGGTGCCATGGAGTTGTGGGCTTTGAAGAAAAAAAG
1 -AA--AAAGGGTGCCATGGAGTTGTGGGCTTAGAAGGAAAAAAG
3039823 CCACTGAGTC
Statistics
Matches: 211, Mismatches: 15, Indels: 27
0.83 0.06 0.11
Matches are distributed among these distances:
192 70 0.33
193 13 0.06
194 4 0.02
195 1 0.00
196 2 0.01
197 34 0.16
198 30 0.14
199 6 0.03
200 33 0.16
201 18 0.09
ACGTcount: A:0.34, C:0.11, G:0.34, T:0.21
Consensus pattern (199 bp):
AAAAAGGGTGCCATGGAGTTGTGGGCTTAGAAGGAAAAAAGTGCCACAAAGTTGTGGGCTTTGAA
AAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAGAAAAAAGGTGCCACGGAGTTGTGGGCTT
TAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGAAGTTGTGGG
CTTT
Found at i:3039843 original size:97 final size:98
Alignment explanation
Indices: 3039353--3039843 Score: 399
Period size: 97 Copynumber: 4.9 Consensus size: 98
3039343 AGGAAGGGAG
* * * *
3039353 AAAGA-TGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAGAGTGCCACGAAGTTGTGGGCTTTAAA--G-AAAAG-GTGCCACGGAGTTGTGGGCTTT-GA
* *
3039417 AGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
61 AGAAAAAA-AGCCACGGAGTTGTGGACTTTGAAAA-GGAA
3039457 AAAGAGTGCCAC-AGAGTTGTGGGCTTTAAACAGAAAAAAGGTGCCACGGAGTTGTGGGCTTT-A
1 AAAGAGTGCCACGA-AGTTGTGGGCTTT-AA-AG--AAAAGGTGCCACGGAGTTGTGGGCTTTGA
* *
3039520 AAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TT-AAAGATGAA
61 AGAA-AAAAA---GCCACGGAGTTGTGGACTTTGAAA-AGGAA
* * *
3039561 AAA-AGTGCCAC-AGAGTTGTGGGC-TT--A-AAAGGGTGCCATGGAGTTGTGGGCTTAGAAGGA
1 AAAGAGTGCCACGA-AGTTGTGGGCTTTAAAGAAAAGGTGCCACGGAGTTGTGGGCTTTGAA-GA
* ** * *
3039620 AAAAGAGTGCCACAAAGTTGTGGGC-TT-AGAAGGAA
64 AAAA-A-AGCCACGGAGTTGTGGACTTTGAAAAGGAA
* *
3039655 AAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AAGA-GTGCCACGGAGTTGTGGGCTTTGAA-AAG
1 AAAGAGTGCCACGAAGTTGTGGGCTTTAAAGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAGAA-
*
3039717 AAAAAGGTGCCATGGAGTTGTAGG-CTTTGAAAA-GAA
65 AAAAA---GCCACGGAGTTGT-GGACTTTGAAAAGGAA
* *
3039753 GAAG-GTGCCACGAAGTTGTGGGCTTTAAAGGAAAAGGTGCCATGGAGTTGTGGGCTTTGAAGAA
1 AAAGAGTGCCACGAAGTTGTGGGCTTTAAA-GAAAAGGTGCCACGGAGTTGTGGGCTTTGAAGAA
* *
3039817 AAAAAGCCACTGAGTCGTGGACTTTGA
65 AAAAAGCCACGGAGTTGTGGACTTTGA
3039844 GACAAAATGC
Statistics
Matches: 322, Mismatches: 34, Indels: 69
0.76 0.08 0.16
Matches are distributed among these distances:
94 7 0.02
95 63 0.20
96 12 0.04
97 77 0.24
98 14 0.04
99 6 0.02
100 29 0.09
101 2 0.01
102 2 0.01
103 24 0.07
104 18 0.06
105 43 0.13
106 24 0.07
107 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.21
Consensus pattern (98 bp):
AAAGAGTGCCACGAAGTTGTGGGCTTTAAAGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAGAAA
AAAAGCCACGGAGTTGTGGACTTTGAAAAGGAA
Found at i:3039857 original size:30 final size:30
Alignment explanation
Indices: 3039797--3039922 Score: 153
Period size: 31 Copynumber: 4.1 Consensus size: 30
3039787 AGGTGCCATG
* * *
3039797 GAGTTGTGGGCTTTGAAGAAAAAAAGCCACT
1 GAGTCGTGGACTTTG-AGAAAAAATGCCACT
*
3039828 GAGTCGTGGACTTTGAGACAAAATGCCACT
1 GAGTCGTGGACTTTGAGAAAAAATGCCACT
*
3039858 GAGTCGTGGACTTTAAAGAAAAAGATGCCACT
1 GAGTCGTGGACTTT-GAGAAAAA-ATGCCACT
* *
3039890 GAGTCGTGGACTTTGAGAAGAGATTGCCACT
1 GAGTCGTGGACTTTGAGAA-AAAATGCCACT
3039921 GA
1 GA
3039923 ATTTTGGACT
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
30 27 0.33
31 32 0.39
32 24 0.29
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (30 bp):
GAGTCGTGGACTTTGAGAAAAAATGCCACT
Found at i:3048192 original size:50 final size:52
Alignment explanation
Indices: 3048084--3048210 Score: 204
Period size: 50 Copynumber: 2.5 Consensus size: 52
3048074 CGAAATATGA
* * * *
3048084 AAATTTACCTGCATGTATCGATACATGTAATAGTGTATCGATATATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATGTAATAATGTATCGATACATCCGGGC
3048136 AAATTTGCCTGCATGTATCGATACAT-TAA-AATGTATCGATACATCCGGGC
1 AAATTTGCCTGCATGTATCGATACATGTAATAATGTATCGATACATCCGGGC
3048186 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
3048211 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 43 0.61
51 3 0.04
52 25 0.35
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATGTAATAATGTATCGATACATCCGGGC
Found at i:3048237 original size:13 final size:13
Alignment explanation
Indices: 3048219--3048243 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3048209 CAAAGATCAG
3048219 TGTATCGATACAA
1 TGTATCGATACAA
3048232 TGTATCGATACA
1 TGTATCGATACA
3048244 TTTGAGTAAT
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:3048321 original size:33 final size:33
Alignment explanation
Indices: 3048284--3048350 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3048274 AGTAGCTTAA
3048284 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3048317 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3048350 A
1 A
3048351 AATCGTTGAA
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:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3048324 original size:13 final size:13
Alignment explanation
Indices: 3048306--3048330 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3048296 CAAAAAAATA
3048306 TGTATCGATACAT
1 TGTATCGATACAT
3048319 TGTATCGATACA
1 TGTATCGATACA
3048331 ACACTTTATG
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:3049320 original size:55 final size:52
Alignment explanation
Indices: 3049260--3049638 Score: 204
Period size: 49 Copynumber: 8.0 Consensus size: 52
3049250 CGATATTGGG
* *
3049260 CTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAA
1 CTTAAAGATG-G-AAAAGG-TGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * *
3049315 CTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** * *
3049367 C-T-----T----AA-GTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * * * **
3049408 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCGATATCGGG
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** *
3049457 C-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * * *
3049500 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** *
3049549 C-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* *
3049592 CTTAAAGAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTG
3049639 GGCTTAGAAG
Statistics
Matches: 270, Mismatches: 31, Indels: 52
0.76 0.09 0.15
Matches are distributed among these distances:
41 34 0.13
42 3 0.01
43 72 0.27
44 2 0.01
46 1 0.00
47 1 0.00
48 4 0.01
49 104 0.39
51 1 0.00
52 31 0.11
53 6 0.02
54 1 0.00
55 10 0.04
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (52 bp):
CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
Found at i:3049483 original size:43 final size:43
Alignment explanation
Indices: 3049327--3049649 Score: 353
Period size: 49 Copynumber: 7.1 Consensus size: 43
3049317 TAAAGATGGA
3049327 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
3049370 -AA-GTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
3049411 AAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATCGGGCTT
1 -AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
3049460 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
3049503 AAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 -AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
3049552 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
*
3049601 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
3049644 AGAAGG
1 A-AAGG
3049650 GTTGCCACCG
Statistics
Matches: 236, Mismatches: 23, Indels: 41
0.79 0.08 0.14
Matches are distributed among these distances:
41 36 0.15
42 2 0.01
43 69 0.29
44 10 0.04
45 1 0.00
46 3 0.01
47 2 0.01
48 7 0.03
49 106 0.45
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:3049495 original size:92 final size:92
Alignment explanation
Indices: 3049287--3049649 Score: 586
Period size: 92 Copynumber: 3.9 Consensus size: 92
3049277 GGATGTCAAC
* *
3049287 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAG
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAG
*
3049352 GCCAGCTATATTGGACTT-AA-GTGCCAAT
63 GCCAGCGATATTGGACTTAAAGGTGCCAAT
*
3049380 GTGCTGATTCAAGGTCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
* *
3049445 AGCGATATCGGGCTTAAAGGTGCCAAT
66 AGCGATATTGGACTTAAAGGTGCCAAT
3049472 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
3049537 AGCGATATTGGACTTAAAGGTGCCAAT
66 AGCGATATTGGACTTAAAGGTGCCAAT
* *
3049564 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
* *
3049629 AGCTATATTGGGCTTAGAAGG
66 AGCGATATTGGACTTA-AAGG
3049650 GTTGCCACCG
Statistics
Matches: 254, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
90 38 0.15
91 2 0.01
92 175 0.69
93 39 0.15
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (92 bp):
GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
AGCGATATTGGACTTAAAGGTGCCAAT
Found at i:3049688 original size:33 final size:35
Alignment explanation
Indices: 3049644--3049713 Score: 117
Period size: 33 Copynumber: 2.1 Consensus size: 35
3049634 TATTGGGCTT
3049644 AGAAGGGTTGCCACCGACTTGTATGGGCTTT-GGA
1 AGAAGGGTTGCCACCGACTTGTATGGGCTTTAGGA
*
3049678 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AGAAGGGTTGCCACCGACTTGTATGGGCTTTAGGA
3049712 AG
1 AG
3049714 GGAGAAAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 25 0.74
34 9 0.26
ACGTcount: A:0.21, C:0.17, G:0.36, T:0.26
Consensus pattern (35 bp):
AGAAGGGTTGCCACCGACTTGTATGGGCTTTAGGA
Found at i:3049756 original size:34 final size:33
Alignment explanation
Indices: 3049718--3050263 Score: 405
Period size: 34 Copynumber: 16.6 Consensus size: 33
3049708 AGGAAGGGAG
*
3049718 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAA-GGAA
*
3049752 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAA
1 AAAGA-TGCCACGGAGTTGTGGGC-TTAAAAGGAA
3049787 AAAG-TGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGC-TT-AAAA-GGAA
* *
3049822 AAAGAGTGCCACAGAGTTGTGGGCTTTAAACAGAAA
1 AAAGA-TGCCACGGAGTTGTGGGC-TTAAA-AGGAA
* *
3049858 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGATGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * *
3049892 AAAGGTGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAA-AGGAA
*
3049926 AAA-AGTGCCACAGAGTTGTGGGCTTAAAAGG--
1 AAAGA-TGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
3049957 ---G-TGCCATGGAGTTGTGGGCTTAGAAGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
** *
3049986 AAAGAGTGCCACAAAGTTGTGGGCTTAGAAGGAA
1 AAAGA-TGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
3050020 AAAGAGTACCACGGAGTTGTGGGCTT-TAA--AA
1 AAAGA-TGCCACGGAGTTGTGGGCTTAAAAGGAA
*
3050051 AGAG-TGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 AAAGATGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* * *
3050084 AAAGGTGCCATGGAGTTGTAGGCTTTGAAAA-GAA
1 AAAGATGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* * * *
3050118 GAAGGTGCCACGAAGTTGTGGGCTTTAAAGG-A
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* * **
3050150 AAAGGTGCCATGGAGTTGTGGGCTTTGAA-GAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* * * * ** *
3050182 AAA-AAGCCACTGAGTCGTGGACTT-TGA-GAC
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* * * *
3050212 AAA-ATGCCACTGAGTCGTGGACTTTAAA-GAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
3050243 AAAGATGCCACTGAGTCGTGG
1 AAAGATGCCACGGAGTTGTGG
3050264 ACTTTGAGAA
Statistics
Matches: 433, Mismatches: 53, Indels: 54
0.80 0.10 0.10
Matches are distributed among these distances:
27 23 0.05
29 17 0.04
30 28 0.06
31 27 0.06
32 53 0.12
33 38 0.09
34 156 0.36
35 54 0.12
36 16 0.04
37 21 0.05
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.21
Consensus pattern (33 bp):
AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:3049768 original size:35 final size:34
Alignment explanation
Indices: 3049718--3050174 Score: 449
Period size: 34 Copynumber: 13.8 Consensus size: 34
3049708 AGGAAGGGAG
*
3049718 AAAGA-TGCCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAA-GGAA
3049752 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAA-GAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
3049786 AAA-AGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AAAA-GGAA
* *
3049822 AAAGAGTGCCACAGAGTTGTGGGCTTTAAACAGAAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAA-AGGAA
*
3049858 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
3049892 AAAG-GTGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAA-AGGAA
*
3049926 AAA-AGTGCCACAGAGTTGTGGGCTTAAAA-G--
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
3049956 ---G-GTGCCATGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
** *
3049986 AAAGAGTGCCACAAAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
3050020 AAAGAGTACCACGGAGTTGTGGGCTT-----TAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
3050049 AAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* *
3050084 AAAG-GTGCCATGGAGTTGTAGGCTTTGAAAA-GAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* * *
3050118 GAAG-GTGCCACGAAGTTGTGGGCTTTAAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
3050150 AAAG-GTGCCATGGAGTTGTGGGCTT
1 AAAGAGTGCCACGGAGTTGTGGGCTT
3050175 TGAAGAAAAA
Statistics
Matches: 367, Mismatches: 32, Indels: 50
0.82 0.07 0.11
Matches are distributed among these distances:
27 22 0.06
28 1 0.00
29 25 0.07
30 2 0.01
32 27 0.07
33 33 0.09
34 165 0.45
35 47 0.13
36 22 0.06
37 23 0.06
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (34 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:3049962 original size:27 final size:27
Alignment explanation
Indices: 3049930--3049983 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
3049920 GATGAAAAAA
3049930 GTGCCACAGAGTTGTGGGCTTAAAAGG
1 GTGCCACAGAGTTGTGGGCTTAAAAGG
** *
3049957 GTGCCATGGAGTTGTGGGCTTAGAAGG
1 GTGCCACAGAGTTGTGGGCTTAAAAGG
3049984 AAAAAGAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.22, C:0.13, G:0.41, T:0.24
Consensus pattern (27 bp):
GTGCCACAGAGTTGTGGGCTTAAAAGG
Found at i:3049970 original size:95 final size:94
Alignment explanation
Indices: 3049750--3050175 Score: 416
Period size: 95 Copynumber: 4.3 Consensus size: 94
3049740 CTTAAAAGGG
*
3049750 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGA
1 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGT-GGC-TT--
*
3049814 AAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAACAGA
61 AAAGAGAAAAA-AGTGCCAC-GAGTTGTGGGCTTT------A
3049856 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGG-CTTAAAG
3049921 ATGAAAAAAGTGCCACAGAGTTGTGGGC-TT-
65 A-GAAAAAAGTGCCAC-GAGTTGTGGGCTTTA
* * * * **
3049951 AAAAGGGTGCCATGGAGTTGTGGGC-TTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTAGA
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGTTGT-GGCTTA-A
*
3050015 AG-GAAAAAGAGTACCACGGAGTTGTGGGCTTT-
63 AGAGAAAAA-AGTGCCAC-GAGTTGTGGGCTTTA
* *
3050047 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCATGGAGTTGTAGGCTTTGA
1 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGT-GGC-TT-A
* *
3050112 AA-AGAAGAAGGTGCCACGAAGTTGTGGGCTTTAA
62 AAGAGAAAAAAGTGCCACG-AGTTGTGGGCTTT-A
*
3050146 AGGAAAAGGTGCCATGGAGTTGTGGGCTTT
1 A--AAAAGGTGCCACGGAGTTGTGGGCTTT
3050176 GAAGAAAAAA
Statistics
Matches: 279, Mismatches: 23, Indels: 42
0.81 0.07 0.12
Matches are distributed among these distances:
94 18 0.06
95 58 0.21
96 13 0.05
97 52 0.19
98 20 0.07
99 2 0.01
100 21 0.08
101 5 0.02
102 2 0.01
103 24 0.09
104 6 0.02
105 26 0.09
106 32 0.11
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (94 bp):
AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGCTTAAAGA
GAAAAAAGTGCCACGAGTTGTGGGCTTTA
Found at i:3049994 original size:61 final size:60
Alignment explanation
Indices: 3049890--3050017 Score: 177
Period size: 61 Copynumber: 2.1 Consensus size: 60
3049880 CTTTAAAAAG
* *
3049890 AAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACAGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAGA-GAAAAAAGTGCCACAAAGTTGTGGGCTT
* *
3049951 AAAAGGGTGCCATGGAGTTGTGGGCTTAGAAG-GAAAAAGAGTGCCACAAAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTA-AAGAGAAAAA-AGTGCCACAAAGTTGTGGGCTT
*
3050012 AGAAGG
1 AAAAGG
3050018 AAAAAGAGTA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
60 6 0.10
61 51 0.85
62 3 0.05
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (60 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAAAGAGAAAAAAGTGCCACAAAGTTGTGGGCTT
Found at i:3050059 original size:63 final size:63
Alignment explanation
Indices: 3049951--3050175 Score: 249
Period size: 63 Copynumber: 3.4 Consensus size: 63
3049941 TTGTGGGCTT
* * *
3049951 AAAAGGGTGCCATGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTAGAA
1 AAAAAGGTGCCATGGAGTTGTGGGCTT--TA--AAAAAGAGTGCCACGAAGTTGTGGGCTTAGAA
3050016 GG
62 GG
* * * * *
3050018 AAAAAGAGTACCACGGAGTTGTGGGCTTT-AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAG
1 AAAAAG-GTGCCATGGAGTTGTGGGCTTTAAAAAAGAGTGCCACGAAGTTGTGGGCTTAG-AAGG
*
3050082 AAAAAGGTGCCATGGAGTTGTAGGCTTTGAAAAGAAGAAGGTGCCACGAAGTTGTGGGCTTTA-A
1 AAAAAGGTGCCATGGAGTTGTGGGCTTT-AAAA-AAG-A-GTGCCACGAAGTTGTGGGC-TTAGA
3050146 AGG
61 AGG
3050149 -AAAAGGTGCCATGGAGTTGTGGGCTTT
1 AAAAAGGTGCCATGGAGTTGTGGGCTTT
3050176 GAAGAAAAAA
Statistics
Matches: 135, Mismatches: 15, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
63 46 0.34
64 9 0.07
65 3 0.02
66 29 0.21
67 9 0.07
68 37 0.27
69 2 0.01
ACGTcount: A:0.32, C:0.11, G:0.35, T:0.22
Consensus pattern (63 bp):
AAAAAGGTGCCATGGAGTTGTGGGCTTTAAAAAAGAGTGCCACGAAGTTGTGGGCTTAGAAGG
Found at i:3050092 original size:97 final size:97
Alignment explanation
Indices: 3049750--3050187 Score: 471
Period size: 97 Copynumber: 4.4 Consensus size: 97
3049740 CTTAAAAGGG
*
3049750 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGC-TT-A
*
3049814 AAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
64 GAA-GGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
* * *
3049849 AAACAGAAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGA
1 ----A-AAAAGA-GTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGG
3049914 CTTA-AAGATGAAAAA-AGTGCCACAGAGTTGTGGGC-TT
60 CTTAGAAG--GAAAAAGAGTGCCACAGAGTTGTGGGCTTT
* * * * **
3049951 -AAAAGGGTGCCATGGAGTTGTGGGCTTAG-AAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTAG
* *
3050014 AAGGAAAAAGAGTACCACGGAGTTGTGGGCTTT
65 AAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
* * *
3050047 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCATGGAGTTGTAGGCTTTGA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTAG-
* *
3050112 AAAGAAGAAG-GTGCCAC-GAAGTTGTGGGCTTT
65 AAGGAAAAAGAGTGCCACAG-AGTTGTGGGCTTT
* *
3050144 AAAGGAAAAGGTGCCATGGAGTTGTGGGCTTTGAAGAA-AAAAAG
1 AAA--AAGA-GTGCCACGGAGTTGTGGGCTTTGAA-AAGAAAAAG
3050188 CCACTGAGTC
Statistics
Matches: 290, Mismatches: 28, Indels: 37
0.82 0.08 0.10
Matches are distributed among these distances:
94 15 0.05
95 57 0.20
96 10 0.03
97 66 0.23
98 17 0.06
99 3 0.01
100 30 0.10
101 2 0.01
102 3 0.01
103 23 0.08
104 12 0.04
105 24 0.08
106 28 0.10
ACGTcount: A:0.34, C:0.11, G:0.33, T:0.21
Consensus pattern (97 bp):
AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTAGA
AGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
Found at i:3050128 original size:192 final size:199
Alignment explanation
Indices: 3049750--3050187 Score: 533
Period size: 192 Copynumber: 2.2 Consensus size: 199
3049740 CTTAAAAGGG
* * * **
3049750 AAAAAGAGTGCCACGGAGTTGTGGGCTTTA-AAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGA
1 AAAAAGGGTGCCATGGAGTTGTGGGC-TTAGAAGGAAAAAAGTGCCACAAAGTTGTGGGCTTTGA
*
3049814 AAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAACAGAAAAAAGGTGCCACGGAGTTGTGG
65 AAAGGGAAAAAGAGTACCACAGAGTTGTGGGCTTT--A-AGAAAAAAGGTGCCACGGAGTTGTGG
3049879 GCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCAC-AGAGTT
127 GCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGA-AGTT
3049943 GTGGGC-TT
191 GTGGGCTTT
3049951 -AAAAGGGTGCCATGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGC-TT-A
1 AAAAAGGGTGCCATGGAGTTGTGGGCTTAGAAGGAAAAA-AGTGCCACAAAGTTGTGGGCTTTGA
* * *
3050013 GAA-GGAAAAAGAGTACCACGGAGTTGTGGGCTTT-A-AAAAGA-GTGCCACGGAGTTGTGGGCT
65 AAAGGGAAAAAGAGTACCACAGAGTTGTGGGCTTTAAGAAAAAAGGTGCCACGGAGTTGTGGGCT
* * * *
3050074 TTGAAAAGAAAAAGGTGCCATGGAGTTGTAGG-CTTTGAAA-A-GAAGAAGGTGCCACGAAGTTG
130 TTAAAAAGAAAAAGGTGCCACGGAGTTGT-GGAC-TT-AAAGATGAAAAAAGTGCCACGAAGTTG
3050136 TGGGCTTT
192 TGGGCTTT
* * *
3050144 AAAGGAAAAGGTGCCATGGAGTTGTGGGCTTTGAAGAAAAAAAG
1 -AA--AAAGGGTGCCATGGAGTTGTGGGCTTAGAAGGAAAAAAG
3050188 CCACTGAGTC
Statistics
Matches: 210, Mismatches: 16, Indels: 27
0.83 0.06 0.11
Matches are distributed among these distances:
192 70 0.33
193 13 0.06
194 4 0.02
195 1 0.00
196 2 0.01
197 34 0.16
198 29 0.14
199 6 0.03
200 33 0.16
201 18 0.09
ACGTcount: A:0.34, C:0.11, G:0.33, T:0.21
Consensus pattern (199 bp):
AAAAAGGGTGCCATGGAGTTGTGGGCTTAGAAGGAAAAAAGTGCCACAAAGTTGTGGGCTTTGAA
AAGGGAAAAAGAGTACCACAGAGTTGTGGGCTTTAAGAAAAAAGGTGCCACGGAGTTGTGGGCTT
TAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGAAGTTGTGGG
CTTT
Found at i:3050222 original size:30 final size:30
Alignment explanation
Indices: 3050162--3050287 Score: 153
Period size: 31 Copynumber: 4.1 Consensus size: 30
3050152 AGGTGCCATG
* * *
3050162 GAGTTGTGGGCTTTGAAGAAAAAAAGCCACT
1 GAGTCGTGGACTTTG-AGAAAAAATGCCACT
*
3050193 GAGTCGTGGACTTTGAGACAAAATGCCACT
1 GAGTCGTGGACTTTGAGAAAAAATGCCACT
*
3050223 GAGTCGTGGACTTTAAAGAAAAAGATGCCACT
1 GAGTCGTGGACTTT-GAGAAAAA-ATGCCACT
* *
3050255 GAGTCGTGGACTTTGAGAAGAGATTGCCACT
1 GAGTCGTGGACTTTGAGAA-AAAATGCCACT
3050286 GA
1 GA
3050288 ATTTTGGACT
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
30 27 0.33
31 32 0.39
32 24 0.29
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (30 bp):
GAGTCGTGGACTTTGAGAAAAAATGCCACT
Done.