Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 5 of 150
Found at i:1383794 original size:24 final size:24
Alignment explanation
Indices: 1383725--1383794 Score: 59
Period size: 29 Copynumber: 2.7 Consensus size: 24
1383715 CGACCTTTCA
*
1383725 AAATTTTTAACCGTTAACCGAACCG
1 AAATTTTT-TCCGTTAACCGAACCG
**
1383750 AAATTTTTTCAAAAAAATTAACCGAACCG
1 AAATTTTTTC-----CGTTAACCGAACCG
1383779 AAATTTTTTCCGTTAA
1 AAATTTTTTCCGTTAA
1383795 TTCGGTCGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 11
0.69 0.10 0.22
Matches are distributed among these distances:
24 5 0.14
25 8 0.23
29 22 0.63
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.33
Consensus pattern (24 bp):
AAATTTTTTCCGTTAACCGAACCG
Found at i:1383872 original size:9 final size:9
Alignment explanation
Indices: 1383851--1383917 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
1383841 TTTGGTTAAA
*
1383851 AATTAGCCG
1 AATTAACCG
*
1383860 AATTAACCA
1 AATTAACCG
1383869 AATTAACCG
1 AATTAACCG
*
1383878 AATTACCCG
1 AATTAACCG
*
1383887 AATTACCCG
1 AATTAACCG
*
1383896 AATTACCCG
1 AATTAACCG
*
1383905 AATTAACCT
1 AATTAACCG
1383914 AATT
1 AATT
1383918 GAATCATACA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 52 1.00
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:1387919 original size:13 final size:13
Alignment explanation
Indices: 1387903--1387968 Score: 80
Period size: 13 Copynumber: 5.1 Consensus size: 13
1387893 TTTAAACCAA
1387903 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
1387916 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
1387929 ACTTTTTC-ACAGC
1 AC-TTTTCAAAAGC
* *
1387942 ACTTTTCGAAAGT
1 ACTTTTCAAAAGC
*
1387955 ATTTTTCAAAAGC
1 ACTTTTCAAAAGC
1387968 A
1 A
1387969 ATGAAGAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
12 5 0.11
13 35 0.78
14 5 0.11
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:1390333 original size:26 final size:26
Alignment explanation
Indices: 1390297--1390351 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
1390287 TCTCCGACAG
1390297 CAGGTACGACGCTGTAGACCTCGTAT
1 CAGGTACGACGCTGTAGACCTCGTAT
1390323 CAGGTACGACGCTGTAGACCTCGTAT
1 CAGGTACGACGCTGTAGACCTCGTAT
1390349 CAG
1 CAG
1390352 ACTCGGACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (26 bp):
CAGGTACGACGCTGTAGACCTCGTAT
Found at i:1403375 original size:48 final size:48
Alignment explanation
Indices: 1403323--1403416 Score: 179
Period size: 48 Copynumber: 2.0 Consensus size: 48
1403313 GCAAAATTTG
*
1403323 ATTAAGGGAATTTTAGAATTTTATTTTGTTATATCAAAACATTTAATT
1 ATTAAGGGAATTTTAAAATTTTATTTTGTTATATCAAAACATTTAATT
1403371 ATTAAGGGAATTTTAAAATTTTATTTTGTTATATCAAAACATTTAA
1 ATTAAGGGAATTTTAAAATTTTATTTTGTTATATCAAAACATTTAA
1403417 AAATCAAAGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (48 bp):
ATTAAGGGAATTTTAAAATTTTATTTTGTTATATCAAAACATTTAATT
Found at i:1404429 original size:34 final size:34
Alignment explanation
Indices: 1404386--1404476 Score: 164
Period size: 34 Copynumber: 2.7 Consensus size: 34
1404376 GAATTTTTTT
*
1404386 TAAATTAATTAAATTAGGCTTTAAGGGTTTTAAA
1 TAAATTAATTAAATTAGGGTTTAAGGGTTTTAAA
*
1404420 TAAATTAATTAAATTAGGGTTTAGGGGTTTTAAA
1 TAAATTAATTAAATTAGGGTTTAAGGGTTTTAAA
1404454 TAAATTAATTAAATTAGGGTTTA
1 TAAATTAATTAAATTAGGGTTTA
1404477 TTTTTTAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.41, C:0.01, G:0.16, T:0.42
Consensus pattern (34 bp):
TAAATTAATTAAATTAGGGTTTAAGGGTTTTAAA
Found at i:1404826 original size:51 final size:49
Alignment explanation
Indices: 1404720--1404827 Score: 171
Period size: 49 Copynumber: 2.2 Consensus size: 49
1404710 CCGAATGGTA
*
1404720 TATTTTTTTAATCGCGCCTATCTGACAAGCGCGAATCAATTTTTTATAT
1 TATTTTTTTAATAGCGCCTATCTGACAAGCGCGAATCAATTTTTTATAT
* * *
1404769 TATTTTTTTAATATCGCCTATCTGATAGGCGCGAATCAATTTTTTATAT
1 TATTTTTTTAATAGCGCCTATCTGACAAGCGCGAATCAATTTTTTATAT
1404818 TAATTTTTTT
1 T-ATTTTTTT
1404828 TGTTTAATAA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
49 46 0.85
50 8 0.15
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (49 bp):
TATTTTTTTAATAGCGCCTATCTGACAAGCGCGAATCAATTTTTTATAT
Found at i:1404926 original size:27 final size:27
Alignment explanation
Indices: 1404888--1404977 Score: 119
Period size: 27 Copynumber: 3.3 Consensus size: 27
1404878 ATATAGATAC
*
1404888 GAGGCGCGACTAGTTGAGCCTATTTCA
1 GAGGCGCGACTAGTTGAGCCTATCTCA
*
1404915 GAGGCGCGACTAGTTGAGCCTATCT-G
1 GAGGCGCGACTAGTTGAGCCTATCTCA
* * *
1404941 GCAGGCACGACTAGTTGTGCCTAACTCA
1 G-AGGCGCGACTAGTTGAGCCTATCTCA
1404969 GAGGCGCGA
1 GAGGCGCGA
1404978 ATGGTGGGGC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.02
27 52 0.96
28 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.32, T:0.21
Consensus pattern (27 bp):
GAGGCGCGACTAGTTGAGCCTATCTCA
Found at i:1410083 original size:3 final size:3
Alignment explanation
Indices: 1410075--1410123 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1410065 TTGATATGTG
1410075 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1410123 A
1 A
1410124 ATAAAAGAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1410492 original size:15 final size:15
Alignment explanation
Indices: 1410472--1410523 Score: 95
Period size: 15 Copynumber: 3.4 Consensus size: 15
1410462 AAAAAATCAA
1410472 ATAAAATTACATTAT
1 ATAAAATTACATTAT
1410487 ATAAAAATTACATTAT
1 AT-AAAATTACATTAT
1410503 ATAAAATTACATTAT
1 ATAAAATTACATTAT
1410518 ATAAAA
1 ATAAAA
1410524 ATATTCATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 21 0.58
16 15 0.42
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAAAATTACATTAT
Found at i:1410493 original size:16 final size:16
Alignment explanation
Indices: 1410474--1410525 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
1410464 AAAATCAAAT
1410474 AAAATTACATTATATA
1 AAAATTACATTATATA
1410490 AAAATTACATTATAT-
1 AAAATTACATTATATA
1410505 AAAATTACATTATATA
1 AAAATTACATTATATA
1410521 AAAAT
1 AAAAT
1410526 ATTCATATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.43
16 20 0.57
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATTACATTATATA
Found at i:1411286 original size:20 final size:20
Alignment explanation
Indices: 1411261--1411301 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1411251 TTTTCCCATT
*
1411261 GAAGGGACAGCAGCCTGGTG
1 GAAGGGACAGCAGCATGGTG
*
1411281 GAAGGGATAGCAGCATGGTG
1 GAAGGGACAGCAGCATGGTG
1411301 G
1 G
1411302 TGCAGCAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.46, T:0.12
Consensus pattern (20 bp):
GAAGGGACAGCAGCATGGTG
Found at i:1411761 original size:125 final size:126
Alignment explanation
Indices: 1411629--1411962 Score: 492
Period size: 125 Copynumber: 2.7 Consensus size: 126
1411619 AAAAACCCTA
* *
1411629 TCAAAAACGCTTTAAGTAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACATGGACGC
1 TCAAAAACGCTTTAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGC
*
1411694 TCTTTTTCTACAGTAGTTCCT-AAAAAATAATTTTGAGAAAATGGTTCTAAAAAAATAGTG
66 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAAACGGTTCTAAAAAAATAGTG
* * * * *
1411754 TCAAAAACGCTTTAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGGTCTCACGTGAACAC
1 TCAAAAACGCTTTAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGC
* * * *
1411819 T-TTTTTCTATAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTG
66 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAAACGGTTCTAAAAAAATAGTG
* * * * *
1411879 TCAAAAACGCTTTAAGCAAGATGCACTGTCAGTAAAATTACTTAAAAAAACTCCCACGTGGATGC
1 TCAAAAACGCTTTAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGC
*
1411944 TCTTTTTCTACATTAGTTC
66 TCTTTTTCTACAGTAGTTC
1411963 TTGCTTGGCC
Statistics
Matches: 183, Mismatches: 24, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
124 17 0.09
125 151 0.83
126 15 0.08
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (126 bp):
TCAAAAACGCTTTAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGC
TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAAACGGTTCTAAAAAAATAGTG
Found at i:1423198 original size:2 final size:2
Alignment explanation
Indices: 1423185--1423214 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1423175 TTAGGAAATT
*
1423185 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1423215 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1423219 original size:2 final size:2
Alignment explanation
Indices: 1423214--1423246 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1423204 ATATATATAT
1423214 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1423247 ATATAGATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1427215 original size:15 final size:15
Alignment explanation
Indices: 1427181--1427222 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
1427171 TATTAACAAG
*
1427181 TAAAAGAATCAAACTA
1 TAAAA-AATTAAACTA
*
1427197 TAAAAAATTAAAGTA
1 TAAAAAATTAAACTA
1427212 T-AAAAATTAAA
1 TAAAAAATTAAA
1427223 TCTCAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 10 0.42
15 9 0.38
16 5 0.21
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.24
Consensus pattern (15 bp):
TAAAAAATTAAACTA
Found at i:1428440 original size:2 final size:2
Alignment explanation
Indices: 1428433--1428469 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1428423 TAATCAGAAC
1428433 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1428470 ACATGATCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1434469 original size:2 final size:2
Alignment explanation
Indices: 1434462--1434491 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1434452 ATATTTGACT
1434462 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1434492 AATCTAGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1441194 original size:6 final size:6
Alignment explanation
Indices: 1441174--1441208 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1441164 AATTGTGTAA
**
1441174 TTTAAT TTTCTT TTTAAT TTTAAT TTTAAT TTTAA
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAA
1441209 AATCAAGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTAAT
Found at i:1443202 original size:17 final size:17
Alignment explanation
Indices: 1443161--1443214 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
1443151 TACAACACCA
*
1443161 AAAAAGTATATAT--TT
1 AAAAAGTATATTTGATT
1443176 AATAAA-TATATTTGATT
1 AA-AAAGTATATTTGATT
1443193 AAAAAGTATATTTGATT
1 AAAAAGTATATTTGATT
1443210 AAAAA
1 AAAAA
1443215 TAAAATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 8 0.24
16 6 0.18
17 20 0.59
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (17 bp):
AAAAAGTATATTTGATT
Found at i:1443222 original size:19 final size:19
Alignment explanation
Indices: 1443176--1443222 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 19
1443166 GTATATATTT
1443176 AATAAATATATTTGATTAAA
1 AATAAA-ATATTTGATTAAA
1443196 AAGT---ATATTTGATTAAA
1 AA-TAAAATATTTGATTAAA
1443213 AATAAAATAT
1 AATAAAATAT
1443223 ATATTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 9
0.72 0.00 0.28
Matches are distributed among these distances:
16 1 0.04
17 15 0.65
19 4 0.17
20 2 0.09
21 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (19 bp):
AATAAAATATTTGATTAAA
Found at i:1444014 original size:9 final size:9
Alignment explanation
Indices: 1444000--1444030 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1443990 GTTAAACGAA
1444000 TCGAGTTAT
1 TCGAGTTAT
*
1444009 TCGAGTTAA
1 TCGAGTTAT
1444018 TCGAGTTAT
1 TCGAGTTAT
1444027 TCGA
1 TCGA
1444031 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:1445028 original size:27 final size:27
Alignment explanation
Indices: 1444998--1445064 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
1444988 CTCTAATATT
1444998 TAAATCTCAAA-CCCAAACCCTGAACCC
1 TAAATCTCAAATCCCAAACCC-GAACCC
* * * *
1445025 TAAACCTTAAATCTCAAACTCGAACCC
1 TAAATCTCAAATCCCAAACCCGAACCC
*
1445052 TAAATCTTAAATC
1 TAAATCTCAAATC
1445065 TCGAACCCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 27 0.79
28 7 0.21
ACGTcount: A:0.42, C:0.33, G:0.03, T:0.22
Consensus pattern (27 bp):
TAAATCTCAAATCCCAAACCCGAACCC
Found at i:1445055 original size:20 final size:21
Alignment explanation
Indices: 1445027--1445072 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
1445017 CTGAACCCTA
*
1445027 AACCTTAAATCTCAAA-CTCG
1 AACCCTAAATCTCAAATCTCG
*
1445047 AACCCTAAATCTTAAATCTCG
1 AACCCTAAATCTCAAATCTCG
1445068 AACCC
1 AACCC
1445073 CAAACCTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.39, C:0.33, G:0.04, T:0.24
Consensus pattern (21 bp):
AACCCTAAATCTCAAATCTCG
Found at i:1445187 original size:21 final size:21
Alignment explanation
Indices: 1445163--1445202 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1445153 AATGGTCAAT
*
1445163 GTTCAATGTTCAAGGTTTAAG
1 GTTCAAGGTTCAAGGTTTAAG
* *
1445184 GTTCGAGGTTCAATGTTTA
1 GTTCAAGGTTCAAGGTTTA
1445203 TGTTTATGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (21 bp):
GTTCAAGGTTCAAGGTTTAAG
Found at i:1451811 original size:59 final size:59
Alignment explanation
Indices: 1451716--1451886 Score: 229
Period size: 59 Copynumber: 2.9 Consensus size: 59
1451706 TTTGAACTTG
* * * * * *
1451716 AACTTGGCAACTATTCTCACATTGAGGCCTGAACTTTTTTTTGTCTAAGTTAGTCCCTA
1 AACTTGGCAATTGTTCCCACATTAAGGCCTAAACTTTTTTTTGTCCAAGTTAGTCCCTA
*
1451775 AATTTGGCAATTGTTCCCACATTAAGGCCTAAACTTTTTTTTGTCCAAGTTAGTCCCTA
1 AACTTGGCAATTGTTCCCACATTAAGGCCTAAACTTTTTTTTGTCCAAGTTAGTCCCTA
* *
1451834 AACTTGGCAATTGTTCCCACTTTCGAA--CCTAAACTTTTTTTGGTCCAAGTTAG
1 AACTTGGCAATTGTTCCCACATT--AAGGCCTAAACTTTTTTTTGTCCAAGTTAG
1451887 ATCCTGATAT
Statistics
Matches: 100, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
59 98 0.98
61 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.39
Consensus pattern (59 bp):
AACTTGGCAATTGTTCCCACATTAAGGCCTAAACTTTTTTTTGTCCAAGTTAGTCCCTA
Found at i:1453629 original size:10 final size:11
Alignment explanation
Indices: 1453610--1453672 Score: 55
Period size: 11 Copynumber: 6.1 Consensus size: 11
1453600 AAAATTATTA
1453610 TTTTAGAAATT
1 TTTTAGAAATT
1453621 TTTTA-AAA-T
1 TTTTAGAAATT
1453630 TTTT--AAATT
1 TTTTAGAAATT
* *
1453639 TATTTACATATT
1 T-TTTAGAAATT
*
1453651 CTTTAGAAATT
1 TTTTAGAAATT
1453662 TTTTA-AAATT
1 TTTTAGAAATT
1453672 T
1 T
1453673 ATAAATTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
8 3 0.07
9 7 0.16
10 12 0.28
11 17 0.40
12 4 0.09
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (11 bp):
TTTTAGAAATT
Found at i:1453632 original size:9 final size:9
Alignment explanation
Indices: 1453610--1453716 Score: 58
Period size: 9 Copynumber: 11.1 Consensus size: 9
1453600 AAAATTATTA
1453610 TTTTAGAAATT
1 TTTTA-AAA-T
1453621 TTTTAAAAT
1 TTTTAAAAT
*
1453630 TTTTAAATT
1 TTTTAAAAT
*
1453639 TATTTACATAT
1 T-TTTA-AAAT
1453650 TCTTTAGAAATT
1 T-TTTA-AAA-T
1453662 TTTTAAAAT
1 TTTTAAAAT
*
1453671 TTAT-AAA-
1 TTTTAAAAT
*
1453678 TTTTAGAAT
1 TTTTAAAAT
*
1453687 TCTTATAAAT
1 TTTTA-AAAT
1453697 ATTTT-AAAT
1 -TTTTAAAAT
1453706 TTTTGAAAAT
1 TTTT-AAAAT
1453716 T
1 T
1453717 ATTTTGTATT
Statistics
Matches: 75, Mismatches: 12, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
7 3 0.04
8 9 0.12
9 22 0.29
10 18 0.24
11 21 0.28
12 2 0.03
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:1453683 original size:27 final size:28
Alignment explanation
Indices: 1453652--1453713 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
1453642 TTACATATTC
*
1453652 TTTAGAAATT-TTTTAAA-ATTTATAAAT
1 TTTAGAAATTCTTATAAATATTT-TAAAT
1453679 TTTAG-AATTCTTATAAATATTTTAAAT
1 TTTAGAAATTCTTATAAATATTTTAAAT
*
1453706 TTTTGAAA
1 TTTAGAAA
1453714 ATTATTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 4 0.13
27 20 0.67
28 6 0.20
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (28 bp):
TTTAGAAATTCTTATAAATATTTTAAAT
Found at i:1454512 original size:24 final size:23
Alignment explanation
Indices: 1454463--1454513 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
1454453 AATCAAAGTC
*
1454463 AAATATATATGCTAATAAATACT
1 AAATATATATACTAATAAATACT
* *
1454486 AAATATATTATACTCATAAATATT
1 AAATATA-TATACTAATAAATACT
1454510 AAAT
1 AAAT
1454514 CTTCTAGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (23 bp):
AAATATATATACTAATAAATACT
Found at i:1454533 original size:2 final size:2
Alignment explanation
Indices: 1454526--1454559 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1454516 TCTAGATTGA
1454526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1454560 GTAACTTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1457793 original size:2 final size:2
Alignment explanation
Indices: 1457786--1457815 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1457776 CCTTATTTAA
1457786 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1457816 TGCATTTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1461629 original size:22 final size:21
Alignment explanation
Indices: 1461580--1461629 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1461570 TTCGGATCAA
*
1461580 AATTCTTTTTCCCACATTTTG
1 AATTTTTTTTCCCACATTTTG
** *
1461601 GGTTTTTTTTCCCACATTTTT
1 AATTTTTTTTCCCACATTTTG
*
1461622 AATGTTTT
1 AATTTTTT
1461630 GCAATTTAAT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.18, G:0.08, T:0.58
Consensus pattern (21 bp):
AATTTTTTTTCCCACATTTTG
Found at i:1464426 original size:20 final size:20
Alignment explanation
Indices: 1464390--1464427 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1464380 ATTATAATCT
*
1464390 TTTTAGTGATGTTTTAATAA
1 TTTTAGTGATGTGTTAATAA
1464410 TTTTAGT-ATTGTGTTAAT
1 TTTTAGTGA-TGTGTTAAT
1464428 GTAAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (20 bp):
TTTTAGTGATGTGTTAATAA
Found at i:1465491 original size:2 final size:2
Alignment explanation
Indices: 1465484--1465509 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1465474 GTTTAGTGTG
1465484 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1465510 GACAATAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1466181 original size:38 final size:38
Alignment explanation
Indices: 1466120--1466200 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 38
1466110 GACCTATCCA
* * *
1466120 TATTATTTTTAATATTTTAAATTTTTTATA-TTATATT
1 TATTATTTTTAATATTTAAAATTTTATACATTTATATT
1466157 CTATTA-TTTTAATATTTAATAATTTTATACATTTATATT
1 -TATTATTTTTAATATTTAA-AATTTTATACATTTATATT
1466196 TATTA
1 TATTA
1466201 AATTTTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 12 0.32
38 19 0.50
39 7 0.18
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (38 bp):
TATTATTTTTAATATTTAAAATTTTATACATTTATATT
Found at i:1466444 original size:22 final size:22
Alignment explanation
Indices: 1466419--1466464 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1466409 TTTATCTAAA
1466419 CTCTCCCAAATTTCAAAAAAAT
1 CTCTCCCAAATTTCAAAAAAAT
** * *
1466441 CTCTCTTAAATTTCGATAAAAT
1 CTCTCCCAAATTTCAAAAAAAT
1466463 CT
1 CT
1466465 TCAAGCCTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (22 bp):
CTCTCCCAAATTTCAAAAAAAT
Found at i:1468779 original size:29 final size:29
Alignment explanation
Indices: 1468745--1468800 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
1468735 ATGATTTAAT
*
1468745 ATGTAATT-TCATACGTAAATTTTAATTTG
1 ATGTAATTAT-ATACGTAAATTTGAATTTG
1468774 ATGTAATTATATACGTAAATTTGAATT
1 ATGTAATTATATACGTAAATTTGAATT
1468801 ACGATTCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (29 bp):
ATGTAATTATATACGTAAATTTGAATTTG
Found at i:1469023 original size:29 final size:30
Alignment explanation
Indices: 1468977--1469049 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
1468967 TTTTGAATCA
* *
1468977 AATCACAATTTCATGTATAACATTGCACA-G
1 AATCA-AAATTCACGTATAACATTGCACATG
* * *
1469007 AATCAAAATTCACGTATGACATTGTACATT
1 AATCAAAATTCACGTATAACATTGCACATG
1469037 AGATCAAAATTCA
1 A-ATCAAAATTCA
1469050 TGTACAGTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 19 0.53
30 6 0.17
31 11 0.31
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (30 bp):
AATCAAAATTCACGTATAACATTGCACATG
Found at i:1469916 original size:20 final size:20
Alignment explanation
Indices: 1469878--1469917 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1469868 TTATACTGAT
* * *
1469878 TTTAAAGTGTCTAACATAAA
1 TTTAAAGTGACCAAAATAAA
1469898 TTTAAAGTGACCAAAATAAA
1 TTTAAAGTGACCAAAATAAA
1469918 ACAAAATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
TTTAAAGTGACCAAAATAAA
Found at i:1476967 original size:30 final size:29
Alignment explanation
Indices: 1476933--1476991 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
1476923 GTAATTTTTG
*
1476933 AAAATTGAACCAAATCAAGAATTCATGTAT
1 AAAATTGAACAAAATCAA-AATTCATGTAT
* * *
1476963 AAAATTGCACAAAATTAAAGTTCATGTAT
1 AAAATTGAACAAAATCAAAATTCATGTAT
1476992 GACATTACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (29 bp):
AAAATTGAACAAAATCAAAATTCATGTAT
Found at i:1489764 original size:11 final size:11
Alignment explanation
Indices: 1489748--1489772 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1489738 ATTCGTAATT
1489748 TTTTAATTTAA
1 TTTTAATTTAA
1489759 TTTTAATTTAA
1 TTTTAATTTAA
1489770 TTT
1 TTT
1489773 ATTGATTTGA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTAATTTAA
Found at i:1490690 original size:18 final size:18
Alignment explanation
Indices: 1490656--1490691 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1490646 AAAAAGCTAG
*
1490656 TGATGAAGAAGAGTTGCT
1 TGATGAAGAAGAATTGCT
*
1490674 TGATGAAGATGAATTGCT
1 TGATGAAGAAGAATTGCT
1490692 GAGAAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.31, T:0.31
Consensus pattern (18 bp):
TGATGAAGAAGAATTGCT
Found at i:1492152 original size:29 final size:31
Alignment explanation
Indices: 1492105--1492173 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
1492095 AAATTAATAC
1492105 ATGATAAAATTACATTTTAA-CTTCTT-AAA
1 ATGATAAAATTACATTTTAATCTTCTTAAAA
* *
1492134 ATGATAAAATTCCGA-TTTAATCTTTTTAAAA
1 ATGATAAAATTAC-ATTTTAATCTTCTTAAAA
*
1492165 ATTATAAAA
1 ATGATAAAA
1492174 AAAATTAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 17 0.50
30 6 0.18
31 11 0.32
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (31 bp):
ATGATAAAATTACATTTTAATCTTCTTAAAA
Found at i:1493237 original size:6 final size:6
Alignment explanation
Indices: 1493226--1493261 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1493216 GATAATAATA
* *
1493226 TTAAAT TTAAAT TTAAAT TTAGAT TTAGAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
1493262 ATAGACAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (6 bp):
TTAAAT
Found at i:1493257 original size:18 final size:18
Alignment explanation
Indices: 1493230--1493266 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1493220 ATAATATTAA
*
1493230 ATTTAAATTTAAATTTAG
1 ATTTAAATTTAAATATAG
*
1493248 ATTTAGATTTAAATATAG
1 ATTTAAATTTAAATATAG
1493266 A
1 A
1493267 CAATAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (18 bp):
ATTTAAATTTAAATATAG
Found at i:1495805 original size:20 final size:20
Alignment explanation
Indices: 1495782--1495819 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1495772 ATTAAAAATC
1495782 TTTTGAAAAA-TATAATTTAG
1 TTTT-AAAAAGTATAATTTAG
1495802 TTTTAAAAAGTATAATTT
1 TTTTAAAAAGTATAATTT
1495820 TTTAGACAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (20 bp):
TTTTAAAAAGTATAATTTAG
Found at i:1495862 original size:31 final size:31
Alignment explanation
Indices: 1495824--1495897 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
1495814 TAATTTTTTA
*
1495824 GACAAGTTCAGGTACCAATTAGGTACTCCCG
1 GACAAGTTCAGGTACCAAGTAGGTACTCCCG
* * * *
1495855 GACAAGTTCAAGTATCAAGTAGGTACTTCTG
1 GACAAGTTCAGGTACCAAGTAGGTACTCCCG
1495886 GACAAGTTCAGG
1 GACAAGTTCAGG
1495898 GGACAAACTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (31 bp):
GACAAGTTCAGGTACCAAGTAGGTACTCCCG
Found at i:1499616 original size:3 final size:3
Alignment explanation
Indices: 1499608--1499645 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1499598 CATTGTCTAA
1499608 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1499646 GAAAATAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1516388 original size:56 final size:56
Alignment explanation
Indices: 1516302--1516413 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
1516292 CAACTGGTAA
1516302 ACAAAAGAGTGTGAGATAAATTACAAAAGTTTAAGGCATGATGTGCTTTGTCAATT
1 ACAAAAGAGTGTGAGATAAATTACAAAAGTTTAAGGCATGATGTGCTTTGTCAATT
1516358 ACAAAAGAGTGTGAGATAAATTACAAAAGTTTAAGGCATGATGTGCTTTGTCAATT
1 ACAAAAGAGTGTGAGATAAATTACAAAAGTTTAAGGCATGATGTGCTTTGTCAATT
1516414 GCCATAGCCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (56 bp):
ACAAAAGAGTGTGAGATAAATTACAAAAGTTTAAGGCATGATGTGCTTTGTCAATT
Found at i:1524707 original size:18 final size:17
Alignment explanation
Indices: 1524683--1524727 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
1524673 ATTTTACTTG
1524683 AATTTTTATATTTTTAA
1 AATTTTTATATTTTTAA
*
1524700 ATATTTTTGA-ATTTTTAC
1 A-ATTTTT-ATATTTTTAA
1524718 AATTTTTATA
1 AATTTTTATA
1524728 CAAAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 1 0.04
17 8 0.33
18 14 0.58
19 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
AATTTTTATATTTTTAA
Found at i:1526496 original size:21 final size:22
Alignment explanation
Indices: 1526472--1526527 Score: 98
Period size: 21 Copynumber: 2.6 Consensus size: 22
1526462 CACCATTGTT
1526472 TCTAATCTCACCGCTACAGT-A
1 TCTAATCTCACCGCTACAGTGA
1526493 TCTAATCTCACCGCTACAGTGA
1 TCTAATCTCACCGCTACAGTGA
1526515 T-TAATCTCACCGC
1 TCTAATCTCACCGC
1526528 CACCGCTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 32 0.94
22 2 0.06
ACGTcount: A:0.27, C:0.34, G:0.11, T:0.29
Consensus pattern (22 bp):
TCTAATCTCACCGCTACAGTGA
Found at i:1528700 original size:14 final size:14
Alignment explanation
Indices: 1528676--1528710 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
1528666 GACATCTACC
1528676 ACATG-TAAATCAT
1 ACATGATAAATCAT
1528689 ACATGATAAATCAT
1 ACATGATAAATCAT
1528703 ACAATGAT
1 AC-ATGAT
1528711 TATTTTTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.25
14 10 0.50
15 5 0.25
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.29
Consensus pattern (14 bp):
ACATGATAAATCAT
Found at i:1537724 original size:98 final size:98
Alignment explanation
Indices: 1537550--1537746 Score: 351
Period size: 98 Copynumber: 2.0 Consensus size: 98
1537540 ATATAATAAA
*
1537550 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
1537615 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
*
1537648 ACTTTAAAAGAA-AGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAAT
1 ACTTTAAAAGAACA-TCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAAT
1537712 TCCTTTAAAATCCCAAACTCGGAATATTTCCTTT
65 TCCTTTAAAATCCCAAACTCGGAATATTTCCTTT
1537746 A
1 A
1537747 TGATTTTTAA
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
97 1 0.01
98 94 0.99
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.29
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:1538112 original size:2 final size:2
Alignment explanation
Indices: 1538100--1538135 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1538090 GACATGCAAA
1538100 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1538136 AATGTAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1538535 original size:2 final size:2
Alignment explanation
Indices: 1538530--1538568 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1538520 ATGAAGAGTA
1538530 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1538569 ACATGTATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1538666 original size:3 final size:3
Alignment explanation
Indices: 1538658--1538719 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
1538648 TATATACATT
1538658 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1538706 ATA ATA ATA ATA AT
1 ATA ATA ATA ATA AT
1538720 GAGAAAATAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1544401 original size:20 final size:20
Alignment explanation
Indices: 1544375--1544431 Score: 96
Period size: 20 Copynumber: 2.8 Consensus size: 20
1544365 TTCCTTAAAC
1544375 AATATATATTTTTTAGATTTTA
1 AATATATA-TTTTTA-ATTTTA
1544397 AATATATATTTTTAATTTTA
1 AATATATATTTTTAATTTTA
1544417 AATATATATTTTTAA
1 AATATATATTTTTAA
1544432 ATTATAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 21 0.60
21 6 0.17
22 8 0.23
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
AATATATATTTTTAATTTTA
Found at i:1544427 original size:13 final size:13
Alignment explanation
Indices: 1544409--1544442 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1544399 TATATATTTT
1544409 TAATTTTAAATATA
1 TAATTTTAAAT-TA
*
1544423 TATTTTTAAATTA
1 TAATTTTAAATTA
1544436 TAATTTT
1 TAATTTT
1544443 TTAACATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAATTTTAAATTA
Found at i:1544522 original size:10 final size:12
Alignment explanation
Indices: 1544497--1544551 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
1544487 AATATATACA
1544497 TTAAAATTATAT
1 TTAAAATTATAT
1544509 TTAAAA-TA-AT
1 TTAAAATTATAT
*
1544519 TTAAAAATATAAT
1 TTAAAATTAT-AT
* *
1544532 TTTAAATTCTAT
1 TTAAAATTATAT
1544544 TTAAAATT
1 TTAAAATT
1544552 TTAAAAAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 8 0.22
11 4 0.11
12 15 0.42
13 9 0.25
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
TTAAAATTATAT
Found at i:1544524 original size:37 final size:36
Alignment explanation
Indices: 1544481--1544608 Score: 115
Period size: 36 Copynumber: 3.6 Consensus size: 36
1544471 TTTGAATATC
1544481 TTTAAAAATATATACATTAAAATTATATTTAAAATAA
1 TTTAAAAATATATA-ATTAAAATTATATTTAAAATAA
* * *
1544518 TTTAAAAATATA-ATTTTAAATTCTATTTAAAAT--
1 TTTAAAAATATATAATTAAAATTATATTTAAAATAA
*
1544551 TTTAAAAA-ATCATAATTAAAAAAATATATTT-AAA-AA
1 TTTAAAAATAT-ATAATT--AAAATTATATTTAAAATAA
* * *
1544587 TTTTAAAATATACATTTAAAAT
1 TTTAAAAATATATAATTAAAAT
1544609 ATTATAAAAC
Statistics
Matches: 73, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
32 2 0.03
33 9 0.12
34 7 0.10
35 20 0.27
36 21 0.29
37 14 0.19
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (36 bp):
TTTAAAAATATATAATTAAAATTATATTTAAAATAA
Found at i:1544527 original size:11 final size:12
Alignment explanation
Indices: 1544475--1544607 Score: 66
Period size: 11 Copynumber: 11.1 Consensus size: 12
1544465 AAAATGTTTG
*
1544475 AATATCTTTAAA
1 AATATATTTAAA
1544487 AATATATACATTAAA
1 AATATAT---TTAAA
*
1544502 ATTATATTT-AA
1 AATATATTTAAA
1544513 AATA-ATTTAAA
1 AATATATTTAAA
*
1544524 AATATAATTTTAA
1 AATAT-ATTTAAA
* *
1544537 ATTCTATTT-AA
1 AATATATTTAAA
*
1544548 AAT-T-TTAAAA
1 AATATATTTAAA
*
1544558 AATCATAATTAAAAA
1 AAT-AT-ATT-TAAA
1544573 AATATATTT-AA
1 AATATATTTAAA
1544584 AA-AT-TTTAAA
1 AATATATTTAAA
*
1544594 ATATACATTTAAA
1 A-ATATATTTAAA
1544607 A
1 A
1544608 TATTATAAAA
Statistics
Matches: 95, Mismatches: 10, Indels: 31
0.70 0.07 0.23
Matches are distributed among these distances:
9 5 0.05
10 15 0.16
11 20 0.21
12 14 0.15
13 19 0.20
14 4 0.04
15 18 0.19
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (12 bp):
AATATATTTAAA
Found at i:1544539 original size:35 final size:36
Alignment explanation
Indices: 1544485--1544608 Score: 118
Period size: 35 Copynumber: 3.5 Consensus size: 36
1544475 AATATCTTTA
1544485 AAAATATATACA-TTAAAATTATATTTAAAATAATTT
1 AAAA-ATATACATTTAAAATTATATTTAAAATAATTT
* *
1544521 AAAAATATA-ATTTTAAATTCTATTTAAAAT--TTT
1 AAAAATATACATTTAAAATTATATTTAAAATAATTT
* *
1544554 AAAAAATCATA-ATTAAAAAAATATATTT-AAA-AATTT
1 -AAAAAT-ATACATT-TAAAATTATATTTAAAATAATTT
*
1544590 TAAAATATACATTTAAAAT
1 AAAAATATACATTTAAAAT
1544609 ATTATAAAAC
Statistics
Matches: 72, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
33 3 0.04
34 14 0.19
35 39 0.54
36 16 0.22
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (36 bp):
AAAAATATACATTTAAAATTATATTTAAAATAATTT
Found at i:1544710 original size:20 final size:19
Alignment explanation
Indices: 1544673--1544783 Score: 59
Period size: 18 Copynumber: 5.6 Consensus size: 19
1544663 TAAATGTTTT
*
1544673 ATAATA-TT-AATATAAAA
1 ATAATATTTAAATTTAAAA
*
1544690 AT-ATTTTTAAAATTTTAAAA
1 ATAATATTT-AAA-TTTAAAA
1544710 ATAATATTTAAATTTAAAA
1 ATAATATTTAAATTTAAAA
* ** *
1544729 A-AAAAACTAATTTTAAAA
1 ATAATATTTAAATTTAAAA
*
1544747 AAATATATTTAAAATTTTTAAAAA
1 ATA-ATATTT-AAA--TTT-AAAA
1544771 ATAATATTATAAA
1 ATAATATT-TAAA
1544784 ACATTTCAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
16 2 0.03
17 4 0.06
18 14 0.20
19 11 0.16
20 14 0.20
21 7 0.10
23 11 0.16
24 7 0.10
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAATATTTAAATTTAAAA
Found at i:1544767 original size:23 final size:24
Alignment explanation
Indices: 1544737--1544784 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
1544727 AAAAAAAACT
*
1544737 AATTTTAAAAAAAT-ATATT-TAA
1 AATTTTTAAAAAATAATATTATAA
1544759 AATTTTTAAAAAATAATATTATAA
1 AATTTTTAAAAAATAATATTATAA
1544783 AA
1 AA
1544785 CATTTCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.57
23 5 0.22
24 5 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AATTTTTAAAAAATAATATTATAA
Found at i:1544784 original size:38 final size:39
Alignment explanation
Indices: 1544706--1544784 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 39
1544696 TTAAAATTTT
*
1544706 AAAAATAATATTTAAATTTAAAAAAAAAACTAATTTTAA
1 AAAAATAATATTTAAATTTAAAAAAAAAACTAATTATAA
* *
1544745 AAAAAT-ATATTTAAAATTTTTAAAAAATAA-T-ATTATAA
1 AAAAATAATATTT-AAA-TTTAAAAAAAAAACTAATTATAA
1544783 AA
1 AA
1544785 CATTTCAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
38 14 0.40
39 10 0.29
40 11 0.31
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (39 bp):
AAAAATAATATTTAAATTTAAAAAAAAAACTAATTATAA
Found at i:1558213 original size:28 final size:29
Alignment explanation
Indices: 1558173--1558235 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
1558163 AAAAACATAG
* *
1558173 AAAAATTACGTTAAAAGAAA-AT-AAAGAA
1 AAAAATAAAGTTAAAA-AAATATAAAAGAA
1558201 AAAAATAAAGTTAAAAAAATATAAAAGAA
1 AAAAATAAAGTTAAAAAAATATAAAAGAA
1558230 AAAAAT
1 AAAAAT
1558236 TAAATTACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 3 0.10
28 16 0.52
29 12 0.39
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (29 bp):
AAAAATAAAGTTAAAAAAATATAAAAGAA
Found at i:1560576 original size:8 final size:8
Alignment explanation
Indices: 1560563--1560587 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1560553 AAAACTATAT
1560563 TTTAAATA
1 TTTAAATA
1560571 TTTAAATA
1 TTTAAATA
1560579 TTTAAATA
1 TTTAAATA
1560587 T
1 T
1560588 AACCATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTAAATA
Found at i:1566482 original size:21 final size:21
Alignment explanation
Indices: 1566456--1566497 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1566446 TATTTTTTAC
1566456 ATTATAAA-AAATTTAAAAATA
1 ATTATAAATAAA-TTAAAAATA
1566477 ATTATAAATTAAATTAAAAAT
1 ATTATAAA-TAAATTAAAAAT
1566498 TTTAGTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 8 0.42
23 3 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATTATAAATAAATTAAAAATA
Found at i:1568089 original size:20 final size:20
Alignment explanation
Indices: 1568052--1568089 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1568042 CTAATTCTAC
*
1568052 AAAATCCAAAAACTAAAAAA
1 AAAATCCAAAAACAAAAAAA
*
1568072 AAAATCCAAAATCAAAAA
1 AAAATCCAAAAACAAAAA
1568090 GCTAACAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.16, G:0.00, T:0.11
Consensus pattern (20 bp):
AAAATCCAAAAACAAAAAAA
Found at i:1575447 original size:15 final size:16
Alignment explanation
Indices: 1575427--1575465 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1575417 AACTACCTTG
1575427 AATTAATATT-TAAAA
1 AATTAATATTCTAAAA
1575442 AATTAAT-TTCTAAAA
1 AATTAATATTCTAAAA
*
1575457 TATTAATAT
1 AATTAATAT
1575466 ATTGTGGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 18 0.86
16 1 0.05
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTAATATTCTAAAA
Found at i:1575526 original size:3 final size:3
Alignment explanation
Indices: 1575518--1575565 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
1575508 TTTTTAAAAT
1575518 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1575566 GATTTATGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1588880 original size:18 final size:18
Alignment explanation
Indices: 1588840--1588881 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1588830 GTATTACTTC
*
1588840 TAAAAAATACTTTTGGGA
1 TAAAAAATACTTTTGAGA
* *
1588858 CAAAAAGTACTTTTGAGA
1 TAAAAAATACTTTTGAGA
1588876 TAAAAA
1 TAAAAA
1588882 TATTCTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (18 bp):
TAAAAAATACTTTTGAGA
Found at i:1589895 original size:23 final size:22
Alignment explanation
Indices: 1589878--1589920 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1589868 AATTAAGAGA
1589878 AATTAGGAAAAAGGATTAAATTG
1 AATTAGGAAAAAGGATTAAA-TG
*
1589901 AATTAGGGAAAAGGATTAAA
1 AATTAGGAAAAAGGATTAAA
1589921 ATGGCAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.23
Consensus pattern (22 bp):
AATTAGGAAAAAGGATTAAATG
Found at i:1590013 original size:5 final size:5
Alignment explanation
Indices: 1589990--1590047 Score: 66
Period size: 5 Copynumber: 11.4 Consensus size: 5
1589980 TTATGTTATG
*
1589990 TATAT TATTT TAT-T ATATAT TATAT TA-AT TATAT TATAT TATAT TATTAT
1 TATAT TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT
1590040 ATATAT TA
1 -TATAT TA
1590048 AATAAAGTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
4 5 0.11
5 33 0.70
6 7 0.15
7 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:1590021 original size:19 final size:17
Alignment explanation
Indices: 1589985--1590047 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 17
1589975 GATTTTTATG
* *
1589985 TTATGTATATTATTTTA
1 TTATATATATTATATTA
1590002 -T-TATATATTATATTAA
1 TTATATATATTATATT-A
1590018 TTATATTATATTATATTA
1 TTATA-TATATTATATTA
1590036 TTATATATATTA
1 TTATATATATTA
1590048 AATAAAGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 11 0.28
16 2 0.05
17 8 0.20
18 8 0.20
19 11 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTATATATATTATATTA
Found at i:1590045 original size:31 final size:29
Alignment explanation
Indices: 1589990--1590048 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
1589980 TTATGTTATG
1589990 TATATTATTTTATTATATATTATATTAAT
1 TATATTATTTTATTATATATTATATTAAT
1590019 TATATTATATTATATTAT-TATATATATTAA
1 TATATTAT-TT-TATTATATAT-TATATTAA
1590049 ATAAAGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 8 0.30
30 5 0.19
31 14 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
TATATTATTTTATTATATATTATATTAAT
Found at i:1593321 original size:130 final size:130
Alignment explanation
Indices: 1593141--1593427 Score: 380
Period size: 130 Copynumber: 2.2 Consensus size: 130
1593131 TAAAAATGAC
* * *
1593141 AGTTGTAATCGTAAATCAGCGAACCTTAATAATATCAGCTGTGATCGTAAATCAATGGGTTGTTT
1 AGTTGTGATCGTAAATCAGCGAACCTTAATAATATCAGCTGTGATCGTAAATCAACGAGTTGTTT
* *
1593206 GGACTAGCCATAGTAAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATAAACTTA
66 GGACTAGCCATAGTAAATCAACTAACTCAGAAAAGATTGTTCATGATAGTAAATCAATAAACTTA
* ** * *
1593271 AGTTGTGATTGTAAATCAGC-AAGCCTTAATGGTATCAG-TAGTGATTGTAAATCGACGAGTTGT
1 AGTTGTGATCGTAAATCAGCGAA-CCTTAATAATATCAGCT-GTGATCGTAAATCAACGAGTTGT
* * * *
1593334 TTGGAGTAGCGATAGTAAATCAACTAACTCAGAAAATATTGTTCATGATAGTAAATCAATGAACT
64 TTGGACTAGCCATAGTAAATCAACTAACTCAGAAAAGATTGTTCATGATAGTAAATCAATAAACT
1593399 TA
129 TA
* * **
1593401 GGTTGTGATCATAAATCAATGAACCTT
1 AGTTGTGATCGTAAATCAGCGAACCTT
1593428 TGTGATCATA
Statistics
Matches: 135, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
129 3 0.02
130 130 0.96
131 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (130 bp):
AGTTGTGATCGTAAATCAGCGAACCTTAATAATATCAGCTGTGATCGTAAATCAACGAGTTGTTT
GGACTAGCCATAGTAAATCAACTAACTCAGAAAAGATTGTTCATGATAGTAAATCAATAAACTTA
Found at i:1593435 original size:24 final size:24
Alignment explanation
Indices: 1593385--1593451 Score: 98
Period size: 24 Copynumber: 2.7 Consensus size: 24
1593375 TTCATGATAG
*
1593385 TAAATCAATGAACTTAGGTTGTGATCA
1 TAAATCAATGAACCT---TTGTGATCA
1593412 TAAATCAATGAACCTTTGTGATCA
1 TAAATCAATGAACCTTTGTGATCA
1593436 TAAATCAATGAACCTT
1 TAAATCAATGAACCTT
1593452 AATAATATCA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
24 25 0.64
27 14 0.36
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (24 bp):
TAAATCAATGAACCTTTGTGATCA
Found at i:1593553 original size:154 final size:154
Alignment explanation
Indices: 1593294--1593581 Score: 445
Period size: 154 Copynumber: 1.9 Consensus size: 154
1593284 AATCAGCAAG
** * * * *
1593294 CCTTAATGGTATCAGTAGTGATTGTAAATCGACGAGTTGTTTGGAGTAGCGATAGTAAATCAACT
1 CCTTAATAATATCAGTAGTGATCGTAAATCGACAAGTTGTTTGGAATAGAGATAGTAAATCAACT
*
1593359 AACTCAGAAAATATTGTTCATGATAGTAAATCAATGAACTTAGGTTGTGATCATAAATCAATGAA
66 AACTCAGAAAAGATTGTTCATGATAGTAAATCAATGAACTTAGGTTGTGATCATAAATCAATGAA
1593424 CCTTTGTGATCATAAATCAATGAA
131 CCTTTGTGATCATAAATCAATGAA
*
1593448 CCTTAATAATATCAGCT-GTGATCGTAAATC-AGCAAGTTTTTTGGAATAGAGATAGTAAATCAA
1 CCTTAATAATATCAG-TAGTGATCGTAAATCGA-CAAGTTGTTTGGAATAGAGATAGTAAATCAA
* * *
1593511 CTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATGAACTTAGGTTGTGATCATAAATTAGTG
64 CTAACTCAGAAAAGATTGTTCATGATAGTAAATCAATGAACTTAGGTTGTGATCATAAATCAATG
1593576 AACCTT
129 AACCTT
1593582 AATAATATCA
Statistics
Matches: 121, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
153 1 0.01
154 119 0.98
155 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (154 bp):
CCTTAATAATATCAGTAGTGATCGTAAATCGACAAGTTGTTTGGAATAGAGATAGTAAATCAACT
AACTCAGAAAAGATTGTTCATGATAGTAAATCAATGAACTTAGGTTGTGATCATAAATCAATGAA
CCTTTGTGATCATAAATCAATGAA
Found at i:1593662 original size:284 final size:282
Alignment explanation
Indices: 1593143--1593851 Score: 868
Period size: 284 Copynumber: 2.6 Consensus size: 282
1593133 AAAATGACAG
* ** ** *
1593143 TTGTAATCGTAAATCAGCGAACCTTAATAATATCAGCTGTGATCGTAAATCAATGGGTTGTTTGG
1 TTGT-ATCATAAATCAATGAACCTTAATAATATCAGCTGTGATCGTAAATCAGCGAGTTGTTTGG
* * * *
1593208 ACTAGCCATAGTAAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATAAACTTAAG
65 AATAGCGATAGTAAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATGAACTTAGG
* * * * ** * * *
1593273 TTGTGATTGTAAATCAGCAAGCCTTAATGGTATCAGTAGTGATTGTAAATCGACGAGTTGTTTGG
130 TTGTGATCGTAAATTAGTAAACCTTAATAATATCAGTAGTGATCGTAAATCGACGAGCTATTTGG
* * *
1593338 AGTAGCGATAGTAAATCAACTAACTCAGAAAATATTGTTCATGATAGTAAATCAATGAACTTAGG
195 AATAGAGATAGTAAATCAACTAACTCAGAAAAGATTGTTCATGATAGTAAATCAATGAACTTAGG
*
1593403 TTGTGATCATAAATCAATGAACC
260 TTCTGATCATAAATCAATGAACC
* *
1593426 TTTGTGATCATAAATCAATGAACCTTAATAATATCAGCTGTGATCGTAAATCAGCAAGTTTTTTG
1 -TTGT-ATCATAAATCAATGAACCTTAATAATATCAGCTGTGATCGTAAATCAGCGAGTTGTTTG
* *
1593491 GAATAGAGATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATGAACTTAG
64 GAATAGCGATAGTAAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATGAACTTAG
* * * **
1593556 GTTGTGATCATAAATTAGTGAACCTTAATAATATCAGTTGTGATCGTAAATCGGTGAGCTATTTG
129 GTTGTGATCGTAAATTAGTAAACCTTAATAATATCAGTAGTGATCGTAAATCGACGAGCTATTTG
** *
1593621 GAATAGAGATAGTAAATCAACTAACTCAGAGGAGATTGTTCATGATAGTAAATCAATTAACTTAG
194 GAATAGAGATAGTAAATCAACTAACTCAGAAAAGATTGTTCATGATAGTAAATCAATGAACTTAG
1593686 GTTCTGATCATAAATCAATGAACC
259 GTTCTGATCATAAATCAATGAACC
**
1593710 -T-TA--AT-AAT--AT----C------A-AT----TGTGATCGTAAATTGGCGAGTTGTTTGGA
1 TTGTATCATAAATCAATGAACCTTAATAATATCAGCTGTGATCGTAAATCAGCGAGTTGTTTGGA
* * *
1593753 GTAGCGATAGTAAATCAGCTAACTCAGAGAAGATTGCTCATGATAGTAAATCAATGAAATTAGGT
66 ATAGCGATAGTAAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATGAACTTAGGT
*
1593818 TGTGACCGTAAATTAGTAAACCTTAATAATATCA
131 TGTGATCGTAAATTAGTAAACCTTAATAATATCA
1593852 ACTCTGATTG
Statistics
Matches: 377, Mismatches: 48, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
260 116 0.31
264 2 0.01
265 1 0.00
271 1 0.00
275 2 0.01
277 3 0.01
278 2 0.01
280 1 0.00
281 1 0.00
282 1 0.00
284 247 0.66
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (282 bp):
TTGTATCATAAATCAATGAACCTTAATAATATCAGCTGTGATCGTAAATCAGCGAGTTGTTTGGA
ATAGCGATAGTAAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATGAACTTAGGT
TGTGATCGTAAATTAGTAAACCTTAATAATATCAGTAGTGATCGTAAATCGACGAGCTATTTGGA
ATAGAGATAGTAAATCAACTAACTCAGAAAAGATTGTTCATGATAGTAAATCAATGAACTTAGGT
TCTGATCATAAATCAATGAACC
Found at i:1593876 original size:130 final size:130
Alignment explanation
Indices: 1593412--1593879 Score: 636
Period size: 130 Copynumber: 3.6 Consensus size: 130
1593402 GTTGTGATCA
* * * *
1593412 TAAATCAATGAACCT---TTGTGATCATAAATCAATGAACCTTAATAATATCAGCTGTGATCGTA
1 TAAATCAATGAACTTAGGTTGTGATCATAAATTAGTGAACCTTAATAATATCAACTGTGATCGTA
*
1593474 AATCAGCAAGTTTTTTGGAATAGAGATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGATAG
66 AATCAGCAAGTTGTTTGGAATAGAGATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGATAG
**
1593539 TAAATCAATGAACTTAGGTTGTGATCATAAATTAGTGAACCTTAATAATATCAGTTGTGATCGTA
1 TAAATCAATGAACTTAGGTTGTGATCATAAATTAGTGAACCTTAATAATATCAACTGTGATCGTA
* ** * * *
1593604 AATCGGTGAGCTATTTGGAATAGAGATAGTAAATCAACTAACTCAGAGGAGATTGTTCATGATAG
66 AATCAGCAAGTTGTTTGGAATAGAGATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGATAG
* * * * *
1593669 TAAATCAATTAACTTAGGTTCTGATCATAAATCAATGAACCTTAATAATATCAATTGTGATCGTA
1 TAAATCAATGAACTTAGGTTGTGATCATAAATTAGTGAACCTTAATAATATCAACTGTGATCGTA
** * * * * *
1593734 AATTGGCGAGTTGTTTGGAGTAGCGATAGTAAATCAGCTAACTCAGAGAAGATTGCTCATGATAG
66 AATCAGCAAGTTGTTTGGAATAGAGATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGATAG
* * * * * *
1593799 TAAATCAATGAAATTAGGTTGTGACCGTAAATTAGTAAACCTTAATAATATCAACTCTGATTGTA
1 TAAATCAATGAACTTAGGTTGTGATCATAAATTAGTGAACCTTAATAATATCAACTGTGATCGTA
1593864 AATCAGCAAGTTGTTT
66 AATCAGCAAGTTGTTT
1593880 CATATATTTT
Statistics
Matches: 300, Mismatches: 38, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
127 14 0.05
130 286 0.95
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (130 bp):
TAAATCAATGAACTTAGGTTGTGATCATAAATTAGTGAACCTTAATAATATCAACTGTGATCGTA
AATCAGCAAGTTGTTTGGAATAGAGATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGATAG
Found at i:1600654 original size:26 final size:27
Alignment explanation
Indices: 1600603--1600654 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
1600593 TCTGTTAAGA
*
1600603 ATTTGGGGGCTCAAAATGAAATTTTAT
1 ATTTGGGGGCTCAAAATGAAACTTTAT
*
1600630 ATTTTGGGG-TCAAAA-GATAACTTTA
1 ATTTGGGGGCTCAAAATGA-AACTTTA
1600655 CCGTTATACC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 2 0.09
26 12 0.55
27 8 0.36
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.37
Consensus pattern (27 bp):
ATTTGGGGGCTCAAAATGAAACTTTAT
Found at i:1605693 original size:21 final size:23
Alignment explanation
Indices: 1605654--1605695 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1605644 CAAGTCAACA
*
1605654 AAATATAATAAATTCATTTTTTT
1 AAATATAAAAAATTCATTTTTTT
1605677 AAATA-AAAAAATT-ATTTTT
1 AAATATAAAAAATTCATTTTT
1605696 ATTGGAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 7 0.39
23 5 0.28
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATATAAAAAATTCATTTTTTT
Found at i:1605791 original size:29 final size:31
Alignment explanation
Indices: 1605746--1605807 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
1605736 CTTTCAAAGC
*
1605746 TTAATTTCTTTTAAAATTT-ATATGTTTTAAA
1 TTAATTTCTTTTAAAATTTCATAT-TTTAAAA
1605777 TTAATTT-TTTT-AAATTTCATATTTTAAAA
1 TTAATTTCTTTTAAAATTTCATATTTTAAAA
1605806 TT
1 TT
1605808 TATAAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 14 0.48
30 8 0.28
31 7 0.24
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (31 bp):
TTAATTTCTTTTAAAATTTCATATTTTAAAA
Found at i:1605806 original size:15 final size:14
Alignment explanation
Indices: 1605754--1605811 Score: 62
Period size: 15 Copynumber: 4.0 Consensus size: 14
1605744 GCTTAATTTC
1605754 TTTTAAAATTTATA
1 TTTTAAAATTTATA
* * *
1605768 TGTTTTAAATTAATT
1 T-TTTAAAATTTATA
*
1605783 TTTTTAAATTTCATA
1 TTTTAAAATTT-ATA
1605798 TTTTAAAATTTATA
1 TTTTAAAATTTATA
1605812 AAAAATTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 13 0.36
15 23 0.64
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (14 bp):
TTTTAAAATTTATA
Found at i:1608114 original size:137 final size:141
Alignment explanation
Indices: 1607939--1608218 Score: 442
Period size: 141 Copynumber: 2.0 Consensus size: 141
1607929 AGAGAGGTTA
* * * *
1607939 AACCAAAATAGAAACTCTAGCAGAGAAGAGGGAGGAAATTTTAGTAGCAATTGAATGGAAAATAT
1 AACCAAAACAGAAACTCTACCACAGAAGAGGGAGGAAATTTTAGTAGCAATCGAATGGAAAATAT
* *
1608004 GC-AAAAA-AAAAAAAGGAAGAATTTTGCACTAACAAAGGAACTAATGTGAAAAGAAAGATAGTG
66 GCAAAAAATAAAAAAAGGAAGAATTTTGCAATAACAAAGGAACTAATGTCAAAAGAAAGATAGTG
1608067 GGATGT-GATT
131 GGATGTAGATT
* *
1608077 AACCAAAACAGAAACTC-ACCACAGAAGAGGGAGGAAATTTTAGTAGTAATCGAATGGAAAATTT
1 AACCAAAACAGAAACTCTACCACAGAAGAGGGAGGAAATTTTAGTAGCAATCGAATGGAAAATAT
1608141 GCAAAAAAAATAAAAAAAGGAAGAATTTTGCAATAACAAAGGAACTAATGTCAAAAGAAAGATAG
66 GC--AAAAAATAAAAAAAGGAAGAATTTTGCAATAACAAAGGAACTAATGTCAAAAGAAAGATAG
1608206 TGGGATGTAGATT
129 TGGGATGTAGATT
1608219 GCAGTTTGGA
Statistics
Matches: 129, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
137 44 0.34
138 16 0.12
140 5 0.04
141 60 0.47
142 4 0.03
ACGTcount: A:0.50, C:0.09, G:0.22, T:0.19
Consensus pattern (141 bp):
AACCAAAACAGAAACTCTACCACAGAAGAGGGAGGAAATTTTAGTAGCAATCGAATGGAAAATAT
GCAAAAAATAAAAAAAGGAAGAATTTTGCAATAACAAAGGAACTAATGTCAAAAGAAAGATAGTG
GGATGTAGATT
Found at i:1609761 original size:14 final size:14
Alignment explanation
Indices: 1609721--1609763 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1609711 TTTTAATCTT
1609721 ATAAAAAATATTAAA
1 ATAAAAAATATT-AA
* * *
1609736 ATATAAATTATTAG
1 ATAAAAAATATTAA
1609750 ATAAAAAATATTAA
1 ATAAAAAATATTAA
1609764 TTTCAACACT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
ATAAAAAATATTAA
Found at i:1612437 original size:28 final size:28
Alignment explanation
Indices: 1612338--1612435 Score: 180
Period size: 28 Copynumber: 3.5 Consensus size: 28
1612328 AATAATAAAA
1612338 ATTTACCAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
1612366 ATTTACCAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
1612394 ATTTACCAAAATATATA-AACTTTTTTTT
1 ATTTACCAAAATAT-TACAACTTTTTTTT
1612422 ATTTACCAAAATAT
1 ATTTACCAAAATAT
1612436 ATCAAAAAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
28 67 0.97
29 2 0.03
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTTACCAAAATATTACAACTTTTTTTT
Found at i:1612791 original size:3 final size:3
Alignment explanation
Indices: 1612785--1612834 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
1612775 ATTATTATTA
1612785 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1612833 TT
1 TT
1612835 AGTATGAAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:1613089 original size:12 final size:12
Alignment explanation
Indices: 1613072--1613102 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1613062 ATAATTTTAG
1613072 TGTGTATTATTT
1 TGTGTATTATTT
1613084 TGTGTATTATTT
1 TGTGTATTATTT
*
1613096 TGAGTAT
1 TGTGTAT
1613103 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (12 bp):
TGTGTATTATTT
Found at i:1618773 original size:12 final size:11
Alignment explanation
Indices: 1618736--1618770 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1618726 AAAACTTTAG
1618736 AATATTTTGGT
1 AATATTTTGGT
* *
1618747 AATTTTTTTGT
1 AATATTTTGGT
1618758 AATATTTTGGT
1 AATATTTTGGT
1618769 AA
1 AA
1618771 ATAACCCGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (11 bp):
AATATTTTGGT
Found at i:1619400 original size:19 final size:19
Alignment explanation
Indices: 1619365--1619402 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1619355 TTTAAACACA
1619365 CAAATATTACAAAAAAATT
1 CAAATATTACAAAAAAATT
*
1619384 CAAAT-TTATAAATAAAATT
1 CAAATATTACAAA-AAAATT
1619403 ACCTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
CAAATATTACAAAAAAATT
Found at i:1619468 original size:44 final size:44
Alignment explanation
Indices: 1619423--1619510 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
1619413 CCTTTTTTTT
* *
1619423 CCTTTC-TTCCCTC-TTCTTCTTCTTTTTTTTTTCTCTTCTCCTTTC
1 CCTTTCATTCCCTCTTTC-T-TTC-TTTTTTCTTCCCTTCTCCTTTC
*
1619468 CCTTTCATTCCTTCTTTCTTTCTTTTTTCTTCCCTTCTCCTTT
1 CCTTTCATTCCCTCTTTCTTTCTTTTTTCTTCCCTTCTCCTTT
1619511 TCTTCTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
44 19 0.50
45 9 0.24
46 7 0.18
47 3 0.08
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64
Consensus pattern (44 bp):
CCTTTCATTCCCTCTTTCTTTCTTTTTTCTTCCCTTCTCCTTTC
Found at i:1619531 original size:25 final size:26
Alignment explanation
Indices: 1619481--1619544 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
1619471 TTCATTCCTT
1619481 CTTTCTTTCTTTTTTCTTCCCTTCTC
1 CTTTCTTTCTTTTTTCTTCCCTTCTC
*
1619507 CTTT-TCTTCTTTTTTCTTTCC-TCTC
1 CTTTCT-TTCTTTTTTCTTCCCTTCTC
1619532 CTTTCTTTCTTTT
1 CTTTCTTTCTTTT
1619545 CCTCCTTCTG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
25 16 0.46
26 19 0.54
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (26 bp):
CTTTCTTTCTTTTTTCTTCCCTTCTC
Found at i:1619733 original size:27 final size:27
Alignment explanation
Indices: 1619705--1619799 Score: 140
Period size: 27 Copynumber: 3.5 Consensus size: 27
1619695 TTTTTTTGAT
1619705 ATATTTTGATAAATAAAAAAAGTT-TA
1 ATATTTTGATAAATAAAAAAAGTTGTA
*
1619731 TATATTTT-AGTTAATAAAAAAAGTTGTA
1 -ATATTTTGA-TAAATAAAAAAAGTTGTA
*
1619759 ATATTTTGATAAATAAAAAAAATTGTA
1 ATATTTTGATAAATAAAAAAAGTTGTA
1619786 ATATTTTGATAAAT
1 ATATTTTGATAAAT
1619800 TTTTATTATT
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
26 1 0.02
27 58 0.94
28 3 0.05
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (27 bp):
ATATTTTGATAAATAAAAAAAGTTGTA
Found at i:1619820 original size:11 final size:11
Alignment explanation
Indices: 1619784--1619823 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
1619774 AAAAAAATTG
*
1619784 TAATATTTTGA
1 TAATATTTTTA
1619795 TAA-ATTTTTA
1 TAATATTTTTA
1619805 T--TATTTTTA
1 TAATATTTTTA
1619814 TAATATTTTT
1 TAATATTTTT
1619824 GTAAAAAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
9 8 0.32
10 7 0.28
11 10 0.40
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (11 bp):
TAATATTTTTA
Found at i:1630326 original size:45 final size:44
Alignment explanation
Indices: 1630253--1630384 Score: 140
Period size: 45 Copynumber: 3.0 Consensus size: 44
1630243 CAGATACACG
* * * *
1630253 GTGG-ATCAGCACACAGCACCACCCTTATAGTCATTGATACTCA
1 GTGGAATCAGCACATAGAACCACCCTTATAATCAATGATACTCA
* * * *
1630296 GTGGAATCAGCACATAGTAACCACCTTTATAATCAATGGTACCCG
1 GTGGAATCAGCACATAG-AACCACCCTTATAATCAATGATACTCA
* * *
1630341 GCGGAATCAGCACATAGCAACCACCGTTACAATCAATGATACTC
1 GTGGAATCAGCACATAG-AACCACCCTTATAATCAATGATACTC
1630385 GATACACGTA
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
43 4 0.05
44 11 0.15
45 58 0.79
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (44 bp):
GTGGAATCAGCACATAGAACCACCCTTATAATCAATGATACTCA
Found at i:1635972 original size:46 final size:46
Alignment explanation
Indices: 1635920--1636012 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
1635910 TGCATTTGGT
1635920 CCATCCAGTTCCTACCACAATAATCAACTCAAAAAATATAAATTAA
1 CCATCCAGTTCCTACCACAATAATCAACTCAAAAAATATAAATTAA
1635966 CCATCCAGTTCCTACCACAATAATCAACTCAAAAAATATAAATTAA
1 CCATCCAGTTCCTACCACAATAATCAACTCAAAAAATATAAATTAA
1636012 C
1 C
1636013 GGATAAATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.47, C:0.27, G:0.02, T:0.24
Consensus pattern (46 bp):
CCATCCAGTTCCTACCACAATAATCAACTCAAAAAATATAAATTAA
Found at i:1640890 original size:31 final size:28
Alignment explanation
Indices: 1640854--1640933 Score: 72
Period size: 31 Copynumber: 2.7 Consensus size: 28
1640844 GATTAAATCA
1640854 AAATTAAAGTTTCAAGTATATATTTGAACC
1 AAATTAAAGTTTCAAGTATA-A-TTGAACC
* * *
1640884 ACAATTAAAATTTTATATGTATAATTGTACC
1 A-AATTAAAGTTTCA-A-GTATAATTGAACC
*
1640915 AAATTAAAG-TTCATGTATA
1 AAATTAAAGTTTCAAGTATA
1640934 CAATCATATA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
27 5 0.12
29 3 0.07
30 8 0.20
31 18 0.44
32 2 0.05
33 5 0.12
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.39
Consensus pattern (28 bp):
AAATTAAAGTTTCAAGTATAATTGAACC
Found at i:1645703 original size:12 final size:12
Alignment explanation
Indices: 1645686--1645710 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1645676 GATATCAAAA
1645686 TTCAGGTTCAGC
1 TTCAGGTTCAGC
1645698 TTCAGGTTCAGC
1 TTCAGGTTCAGC
1645710 T
1 T
1645711 GTTAGTATTA
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:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (12 bp):
TTCAGGTTCAGC
Found at i:1646183 original size:18 final size:18
Alignment explanation
Indices: 1646160--1646214 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
1646150 TGAAAATTAT
1646160 AATATTTTAATAATTTTA
1 AATATTTTAATAATTTTA
*
1646178 AATATTTTAAAAATATTT-
1 AATATTTTAATAAT-TTTA
* * *
1646196 ATTATTATAATAATATTA
1 AATATTTTAATAATTTTA
1646214 A
1 A
1646215 GCTTGACTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 2 0.07
18 25 0.83
19 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATATTTTAATAATTTTA
Found at i:1655467 original size:31 final size:31
Alignment explanation
Indices: 1655424--1655482 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1655414 AATAACCCAA
*
1655424 TGACTTAAATAAAAACTTTCGAATAGTTTAG
1 TGACATAAATAAAAACTTTCGAATAGTTTAG
** *
1655455 TGACATAAATAAAATTTTTTGAATAGTT
1 TGACATAAATAAAAACTTTCGAATAGTT
1655483 CACTGATCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (31 bp):
TGACATAAATAAAAACTTTCGAATAGTTTAG
Found at i:1658302 original size:16 final size:16
Alignment explanation
Indices: 1658281--1658311 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1658271 ACTGATTTGA
*
1658281 ATCTCATTACTACAAT
1 ATCTCATCACTACAAT
1658297 ATCTCATCACTACAA
1 ATCTCATCACTACAA
1658312 CAACTAGTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (16 bp):
ATCTCATCACTACAAT
Found at i:1666880 original size:9 final size:9
Alignment explanation
Indices: 1666851--1667144 Score: 263
Period size: 9 Copynumber: 33.3 Consensus size: 9
1666841 TACAAGGGTA
1666851 TAAGTTATG
1 TAAGTTATG
*
1666860 TACGTGTATG
1 TAAGT-TATG
1666870 TAAGTTATG
1 TAAGTTATG
*
1666879 TACGTGTA--
1 TAAGT-TATG
*
1666887 TAAATTATG
1 TAAGTTATG
1666896 TAAGTTATG
1 TAAGTTATG
*
1666905 TACGTGTA--
1 TAAGT-TATG
1666913 TAAGTTATG
1 TAAGTTATG
1666922 TAAGTTATG
1 TAAGTTATG
*
1666931 T-A-TTAAG
1 TAAGTTATG
1666938 TAAGTTATG
1 TAAGTTATG
*
1666947 TAAGTTTTG
1 TAAGTTATG
1666956 T-A-TTATG
1 TAAGTTATG
1666963 TAAGTTATG
1 TAAGTTATG
*
1666972 TAAGTTATC
1 TAAGTTATG
* *
1666981 AAAGTAATG
1 TAAGTTATG
*
1666990 TATGTTATG
1 TAAGTTATG
1666999 TAAG-T-TG
1 TAAGTTATG
1667006 TAAGTTAT-
1 TAAGTTATG
*
1667014 TATGTATTATG
1 TAAG--TTATG
1667025 TAAGTTATG
1 TAAGTTATG
1667034 TAAGTTATG
1 TAAGTTATG
1667043 TAAGTTAAATG
1 TAAGTT--ATG
1667054 T-A-TTATG
1 TAAGTTATG
*
1667061 TAGGTTATG
1 TAAGTTATG
*
1667070 TAAGTTGTG
1 TAAGTTATG
* *
1667079 TAAGATATT
1 TAAGTTATG
1667088 TAAGTTATG
1 TAAGTTATG
* *
1667097 TGAGTTTTG
1 TAAGTTATG
1667106 TAAGTTATG
1 TAAGTTATG
1667115 TAAGTTATG
1 TAAGTTATG
*
1667124 TAGGTTATG
1 TAAGTTATG
*
1667133 TAAGTTTTG
1 TAAGTTATG
1667142 TAA
1 TAA
1667145 TGTACAAGTG
Statistics
Matches: 228, Mismatches: 37, Indels: 40
0.75 0.12 0.13
Matches are distributed among these distances:
7 24 0.11
8 16 0.07
9 164 0.72
10 17 0.07
11 7 0.03
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:1666895 original size:26 final size:26
Alignment explanation
Indices: 1666866--1666932 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
1666856 TATGTACGTG
1666866 TATGTAAGTTATGTACGTGTATAAAT
1 TATGTAAGTTATGTACGTGTATAAAT
*
1666892 TATGTAAGTTATGTACGTGTATAAGT
1 TATGTAAGTTATGTACGTGTATAAAT
1666918 TATGTAAGTTATGTA
1 TATGTAAGTTATGTA
1666933 TTAAGTAAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.43
Consensus pattern (26 bp):
TATGTAAGTTATGTACGTGTATAAAT
Found at i:1666896 original size:17 final size:17
Alignment explanation
Indices: 1666848--1666923 Score: 78
Period size: 17 Copynumber: 4.8 Consensus size: 17
1666838 AATTACAAGG
1666848 GTATAAGTTATGTACGT
1 GTATAAGTTATGTACGT
1666865 GTATGTAAGTTATGTACGT
1 GTA--TAAGTTATGTACGT
1666884 GTATAA---AT-TA--T
1 GTATAAGTTATGTACGT
1666895 G--TAAGTTATGTACGT
1 GTATAAGTTATGTACGT
1666910 GTATAAGTTATGTA
1 GTATAAGTTATGTA
1666924 AGTTATGTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 20
0.71 0.00 0.29
Matches are distributed among these distances:
9 3 0.06
11 2 0.04
12 2 0.04
13 4 0.08
14 2 0.04
15 2 0.04
17 17 0.35
19 17 0.35
ACGTcount: A:0.32, C:0.04, G:0.22, T:0.42
Consensus pattern (17 bp):
GTATAAGTTATGTACGT
Found at i:1667216 original size:9 final size:9
Alignment explanation
Indices: 1667202--1667240 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
1667192 TAAATATATT
1667202 TAAGTTATG
1 TAAGTTATG
1667211 TAAGTTATG
1 TAAGTTATG
*
1667220 TAGGTTATG
1 TAAGTTATG
*
1667229 TAAGTTTTG
1 TAAGTTATG
1667238 TAA
1 TAA
1667241 TGTACAAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:1667224 original size:96 final size:96
Alignment explanation
Indices: 1667106--1667298 Score: 377
Period size: 96 Copynumber: 2.0 Consensus size: 96
1667096 GTGAGTTTTG
1667106 TAAGTTATGTAAGTTATGTAGGTTATGTAAGTTTTGTAATGTACAAGTGTCAGGTAATTGTTATT
1 TAAGTTATGTAAGTTATGTAGGTTATGTAAGTTTTGTAATGTACAAGTGTCAGGTAATTGTTATT
*
1667171 AAATTTTAATAAGATTATTGTTAAATATATT
66 AAATTTTAATAAGATTATTGCTAAATATATT
1667202 TAAGTTATGTAAGTTATGTAGGTTATGTAAGTTTTGTAATGTACAAGTGTCAGGTAATTGTTATT
1 TAAGTTATGTAAGTTATGTAGGTTATGTAAGTTTTGTAATGTACAAGTGTCAGGTAATTGTTATT
1667267 AAATTTTAATAAGATTATTGCTAAATATATT
66 AAATTTTAATAAGATTATTGCTAAATATATT
1667298 T
1 T
1667299 TAATAAAAAA
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.46
Consensus pattern (96 bp):
TAAGTTATGTAAGTTATGTAGGTTATGTAAGTTTTGTAATGTACAAGTGTCAGGTAATTGTTATT
AAATTTTAATAAGATTATTGCTAAATATATT
Found at i:1667413 original size:13 final size:13
Alignment explanation
Indices: 1667395--1667428 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
1667385 ATATAATTAT
1667395 TAATAATATTTAA
1 TAATAATATTTAA
1667408 TAATAAT-TTTAA
1 TAATAATATTTAA
1667420 T-ATAATATT
1 TAATAATATT
1667429 ATTATTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.25
12 8 0.40
13 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATAATATTTAA
Found at i:1670334 original size:39 final size:40
Alignment explanation
Indices: 1670248--1670336 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 40
1670238 CCCAAATTCC
* *
1670248 TAACCCAT-AACCCCTAAATCCCCCTTAACCCTTAAAGCA
1 TAACCCCTAAACCCCTAAATCCCCCTTAACCCCTAAAGCA
* * *
1670287 AAAACCCTAAACCCCTAAATCTCCC-TAACCCCTAAAGCA
1 TAACCCCTAAACCCCTAAATCCCCCTTAACCCCTAAAGCA
1670326 TAACCCCTAAA
1 TAACCCCTAAA
1670337 AAATTTTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 27 0.64
40 15 0.36
ACGTcount: A:0.39, C:0.40, G:0.02, T:0.18
Consensus pattern (40 bp):
TAACCCCTAAACCCCTAAATCCCCCTTAACCCCTAAAGCA
Found at i:1670625 original size:7 final size:7
Alignment explanation
Indices: 1670613--1670703 Score: 51
Period size: 7 Copynumber: 12.4 Consensus size: 7
1670603 CTTACCGTTC
1670613 AAACCCT
1 AAACCCT
*
1670620 AAACCCC
1 AAACCCT
1670627 AAATCCCT
1 AAA-CCCT
*
1670635 AACCCCT
1 AAACCCT
1670642 AAATCTCCTT
1 AAA-C-CC-T
*
1670652 AACCCCT
1 AAACCCT
* *
1670659 AAAGCAT
1 AAACCCT
1670666 AATA-CCT
1 AA-ACCCT
*
1670673 AACCCCT
1 AAACCCT
*
1670680 AAACCTT
1 AAACCCT
1670687 AAATCCC-
1 AAA-CCCT
1670694 AAACCCT
1 AAACCCT
1670701 AAA
1 AAA
1670704 TCCATACCCT
Statistics
Matches: 63, Mismatches: 13, Indels: 16
0.68 0.14 0.17
Matches are distributed among these distances:
6 3 0.05
7 43 0.68
8 11 0.17
9 3 0.05
10 3 0.05
ACGTcount: A:0.41, C:0.40, G:0.01, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:1670656 original size:17 final size:15
Alignment explanation
Indices: 1670616--1670661 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 15
1670606 ACCGTTCAAA
1670616 CCCTAAACCCC-AAAT
1 CCCT-AACCCCTAAAT
1670631 CCCTAACCCCTAAAT
1 CCCTAACCCCTAAAT
1670646 CTCCTTAACCCCTAAA
1 C-CC-TAACCCCTAAA
1670662 GCATAATACC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.21
15 9 0.32
16 2 0.07
17 11 0.39
ACGTcount: A:0.35, C:0.46, G:0.00, T:0.20
Consensus pattern (15 bp):
CCCTAACCCCTAAAT
Found at i:1671119 original size:114 final size:110
Alignment explanation
Indices: 1670918--1671374 Score: 449
Period size: 114 Copynumber: 4.0 Consensus size: 110
1670908 TAAATTATTT
* * *
1670918 TAAATCCCTGAGCATTAGCGACGCTTTTCTAAAAACGCCGCTAAATCCCTGAAAGCACAGAAAAC
1 TAAATCCCTGAGCATTAGCGGCGC-TTTCTAAAAACGCCACTAAATCCC-GAAAGCTCAGAAAAC
* * * * * *
1670983 GACGACGTTGGGCTTAGTTTTTTTTGCGGTGCTACTCCAAAAACGCTGC
64 GACGTCGTTGGACTTAG-GTTTTTTGCGGCGCT-TTCCAAAAACGCCGC
* * *
1671032 TAAATCCCTGAGCATTAGCGGCGCTTCTCTAGAAATGCCACTAAATTCCCGAAAAGGTCAG-AAA
1 TAAATCCCTGAGCATTAGCGGCGCTT-TCTAAAAACGCCACTAAA-TCCCG-AAAGCTCAGAAAA
* * * *
1671096 CG-CTGTCGTTGTACTTAGGTTTTTTGTGGCGCTTTTTCGAAAACGCCGC
63 CGAC-GTCGTTGGACTTAGGTTTTTTGCGGCGC-TTTCCAAAAACGCCGC
* *
1671145 TAAATCCCTAAGAATTAGCGGCGCTTAAT-TAAAAACGCCACT-AATCACTCGAAAGCTCAGAAA
1 TAAATCCCTGAGCATTAGCGGCGCTT--TCTAAAAACGCCACTAAATC-C-CGAAAGCTCAG-AA
*
1671208 AACGACGTCGTTGGGA-TTAGGCTTTTTGCGGCGCTTTCTCAAAAACGCCGC
61 AACGACGTCGTT-GGACTTAGGTTTTTTGCGGCGCTTTC-CAAAAACGCCGC
* * * * * *
1671259 TAAATCCCTGAGCATTAACGGCGCTTTATTAGAAACGCCGCTAAATCCCCGAAAGCTCGGCAAAC
1 TAAATCCCTGAGCATTAGCGGCGCTTT-CTAAAAACGCCACTAAAT-CCCGAAAGCTCAGAAAAC
* *
1671324 GACGTCGTTCGGA-TTAGGTTTTTTGCGGCGATTTCTATAAAACGCCGC
64 GACGTCGTT-GGACTTAGGTTTTTTGCGGCGCTTTCCA-AAAACGCCGC
1671372 TAA
1 TAA
1671375 TTCTTATTCT
Statistics
Matches: 287, Mismatches: 38, Indels: 37
0.79 0.10 0.10
Matches are distributed among these distances:
111 2 0.01
112 13 0.05
113 114 0.40
114 139 0.48
115 18 0.06
116 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (110 bp):
TAAATCCCTGAGCATTAGCGGCGCTTTCTAAAAACGCCACTAAATCCCGAAAGCTCAGAAAACGA
CGTCGTTGGACTTAGGTTTTTTGCGGCGCTTTCCAAAAACGCCGC
Found at i:1671343 original size:227 final size:227
Alignment explanation
Indices: 1670918--1671374 Score: 543
Period size: 227 Copynumber: 2.0 Consensus size: 227
1670908 TAAATTATTT
* * * * *
1670918 TAAATCCCTGAGCATTAGCGACGCTTTTCTAAAAACGCCGCTAAATCCCTGAAAGCACAGAAAAC
1 TAAATCCCTAAGAATTAGCGACGCTTATCTAAAAACGCCACTAAATCACTGAAAGCACAGAAAAC
* ** * *
1670983 GACGACGTTGGGCTTAGTTTTTTTTGCGGTGCTACTCCAAAAACGCTGCTAAATCCCTGAGCATT
66 GACGACGTTGGGATTAGTGCTTTTTGCGGCGCTACTCCAAAAACGCCGCTAAATCCCTGAGCATT
* * * * *
1671048 AGCGGCGCTTCTCTAGAAATGCCACTAAATTCCCGAAAAGGTCAGAAACGCTGTCGTTGTACTTA
131 AACGGCGCTTCTCTAGAAACGCCACTAAATCCCCGAAAAGCTCAGAAACGCTGTCGTTGGACTTA
* * * *
1671113 GGTTTTTTGTGGCGCTTTTTCGAAAACGCCGC
196 GGTTTTTTGCGGCGATTTCTAGAAAACGCCGC
* *
1671145 TAAATCCCTAAGAATTAGCGGCGCTTAAT-TAAAAACGCCACT-AATCACTCGAAAGCTCAGAAA
1 TAAATCCCTAAGAATTAGCGACGCTT-ATCTAAAAACGCCACTAAATCACT-GAAAGCACAG-AA
* *
1671208 AACGACGTCGTTGGGATTAG-GCTTTTTGCGGCGCT-TTCTCAAAAACGCCGCTAAATCCCTGAG
63 AACGACGACGTTGGGATTAGTGCTTTTTGCGGCGCTACTC-CAAAAACGCCGCTAAATCCCTGAG
* * *
1671271 CATTAACGGCGCTT-TATTAGAAACGCCGCTAAATCCCCG-AAAGCTCGGCAAACGAC-GTCGTT
127 CATTAACGGCGCTTCT-CTAGAAACGCCACTAAATCCCCGAAAAGCTCAG-AAACG-CTGTCGTT
*
1671333 CGGA-TTAGGTTTTTTGCGGCGATTTCTATAAAACGCCGC
189 -GGACTTAGGTTTTTTGCGGCGATTTCTAGAAAACGCCGC
1671372 TAA
1 TAA
1671375 TTCTTATTCT
Statistics
Matches: 195, Mismatches: 27, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
226 16 0.08
227 155 0.79
228 24 0.12
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (227 bp):
TAAATCCCTAAGAATTAGCGACGCTTATCTAAAAACGCCACTAAATCACTGAAAGCACAGAAAAC
GACGACGTTGGGATTAGTGCTTTTTGCGGCGCTACTCCAAAAACGCCGCTAAATCCCTGAGCATT
AACGGCGCTTCTCTAGAAACGCCACTAAATCCCCGAAAAGCTCAGAAACGCTGTCGTTGGACTTA
GGTTTTTTGCGGCGATTTCTAGAAAACGCCGC
Found at i:1677497 original size:20 final size:20
Alignment explanation
Indices: 1677470--1677518 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1677460 GAACTGTTTG
*
1677470 TAGTTTTGAGACTTTATTAT
1 TAGTTTTGAGACTTTATTAA
* *
1677490 TGGTTTTGGGACTTTATTAA
1 TAGTTTTGAGACTTTATTAA
1677510 TAGTTTTGA
1 TAGTTTTGA
1677519 ACTCTTGATG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.04, G:0.20, T:0.53
Consensus pattern (20 bp):
TAGTTTTGAGACTTTATTAA
Found at i:1680275 original size:31 final size:31
Alignment explanation
Indices: 1680235--1680293 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1680225 AACAACCCAA
*
1680235 TGACTTAAATAAAAACTTTCGAATAGTTTAG
1 TGACATAAATAAAAACTTTCGAATAGTTTAG
* *
1680266 TGACATAAATAAAAATTTTTGAATAGTT
1 TGACATAAATAAAAACTTTCGAATAGTT
1680294 CACTAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (31 bp):
TGACATAAATAAAAACTTTCGAATAGTTTAG
Found at i:1688133 original size:44 final size:44
Alignment explanation
Indices: 1688084--1688562 Score: 266
Period size: 44 Copynumber: 10.6 Consensus size: 44
1688074 ATGGCAAATA
* * * **
1688084 TTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCCACTAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACTAGTC
* * * * *
1688128 TTATCTCCCTAAAGTTGCAGTAGAGTAGACTGAAGATAACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-ACTAGTC
* * ** * *
1688173 TTATTTCTC-GAAGTTGCAGTGGAATAGATTGAAGTTATAAATTACAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG--AT--ACT--AG-TC
* **
1688223 TTATC-CCCTTGAAGTTACAGTGGAGCAGACTGAAGCCACTAGTC
1 TTATCTCCC-TGAAGTTGCAGTGGAGCAGACTGAAGATACTAGTC
* * * * *
1688267 TTATCTCCCTGAAGTTGTAATAGAGCAGACTGAAGATAGCAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATA-CTAGTC
* * * *
1688312 TTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAGTTACAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG--AT-A-CT--AG-TC
* * * * * * **
1688363 TTATCTCTCTGAAGTTGCAGTAGAGCA-AAT-CATAT-CAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACTAGTC
** * * ** *
1688404 TTATCTTTCTGAAGTTGCTGTAGAGCAGGTTGAAGATACAAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACTAGTC
* * * * * *
1688448 TTATCTCCCAGAAATTACAATGGAGCAGACTGAAGATATCAAGTA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATA-CTAGTC
* * * * *
1688493 TTATCTTCCTGAAGATACAGTGGAGCAGACTGAAGCTACTAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACTAGTC
*
1688537 TTATCTCCCTGAAGCTGCAGTGGAGC
1 TTATCTCCCTGAAGTTGCAGTGGAGC
1688563 GAATTAAAAC
Statistics
Matches: 329, Mismatches: 85, Indels: 42
0.72 0.19 0.09
Matches are distributed among these distances:
41 26 0.08
42 2 0.01
43 3 0.01
44 140 0.43
45 87 0.26
46 2 0.01
47 8 0.02
48 2 0.01
49 4 0.01
50 9 0.03
51 46 0.14
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACTAGTC
Found at i:1688282 original size:139 final size:140
Alignment explanation
Indices: 1688084--1688389 Score: 463
Period size: 139 Copynumber: 2.2 Consensus size: 140
1688074 ATGGCAAATA
* * *
1688084 TTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCCACTAGTCTTATCTCCCTAAAGTTGCAGT
1 TTATCCCTCTGAAGTTGCAGTAGAGCAGACTGAAGCCACTAGTCTTATCTCCCTAAAGTTGCAAT
* * * *
1688149 AGAGTAGACTGAAGATAACAAATCTTATTTCTC-GAAGTTGCAGTGGAATAGATTGAAGTTATAA
66 AGAGCAGACTGAAGATAACAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAA
1688213 ATTACAGATC
131 ATTACAGATC
* * * *
1688223 TTATCCC-CTTGAAGTTACAGTGGAGCAGACTGAAGCCACTAGTCTTATCTCCCTGAAGTTGTAA
1 TTATCCCTC-TGAAGTTGCAGTAGAGCAGACTGAAGCCACTAGTCTTATCTCCCTAAAGTTGCAA
*
1688287 TAGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATA
65 TAGAGCAGACTGAAGATAACAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATA
*
1688352 AGTTACAGATC
130 AATTACAGATC
*
1688363 TTATCTCTCTGAAGTTGCAGTAGAGCA
1 TTATCCCTCTGAAGTTGCAGTAGAGCA
1688390 AATCATATCA
Statistics
Matches: 148, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
138 1 0.01
139 86 0.58
140 60 0.41
141 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (140 bp):
TTATCCCTCTGAAGTTGCAGTAGAGCAGACTGAAGCCACTAGTCTTATCTCCCTAAAGTTGCAAT
AGAGCAGACTGAAGATAACAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAA
ATTACAGATC
Found at i:1688335 original size:89 final size:89
Alignment explanation
Indices: 1688232--1688555 Score: 280
Period size: 89 Copynumber: 3.6 Consensus size: 89
1688222 CTTATCCCCT
* *
1688232 TGAAGTTACAGTGGAGCAGACTGAAGCCACTAGTCTTATCTCCCTGAAGTTGTAATAGAGCAGAC
1 TGAAGTTACAGTGGAGCAGACTGAAGCTACTAGTCTTATCTCCCTGAAGTTGCAATAGAGCAGAC
*
1688297 TGAAGATAGCAAATCTTAT-TTCCC
66 TGAAGATATCAAATCTTATCTT-CC
* * * * * *
1688321 TGAAGTTGCAGTGGAACAGATTGAAGCTATAAGTTACAGATCTTATCTCTCTGAAGTTGCAGTAG
1 TGAAGTTACAGTGGAGCAGACTGAAGC--T-A-CT--AG-TCTTATCTCCCTGAAGTTGCAATAG
** * *
1688386 AGCA-A---ATCATATCAAACCTTATCTTTC
59 AGCAGACTGAAGATATCAAATCTTATCTTCC
* * * ** * * * * * *
1688413 TGAAGTTGCTGTAGAGCAGGTTGAAGATACAAGTCTTATCTCCCAGAAATTACAATGGAGCAGAC
1 TGAAGTTACAGTGGAGCAGACTGAAGCTACTAGTCTTATCTCCCTGAAGTTGCAATAGAGCAGAC
* *
1688478 TGAAGATATCAAGTATTATCTTCC
66 TGAAGATATCAAATCTTATCTTCC
* * *
1688502 TGAAGATACAGTGGAGCAGACTGAAGCTACTAATCTTATCTCCCTGAAGCTGCA
1 TGAAGTTACAGTGGAGCAGACTGAAGCTACTAGTCTTATCTCCCTGAAGTTGCA
1688556 GTGGAGCGAA
Statistics
Matches: 178, Mismatches: 45, Indels: 24
0.72 0.18 0.10
Matches are distributed among these distances:
85 23 0.13
86 3 0.02
89 82 0.46
90 1 0.01
92 37 0.21
93 3 0.02
95 3 0.02
96 26 0.15
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (89 bp):
TGAAGTTACAGTGGAGCAGACTGAAGCTACTAGTCTTATCTCCCTGAAGTTGCAATAGAGCAGAC
TGAAGATATCAAATCTTATCTTCC
Done.