Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002881.1 Hibiscus syriacus cultivar Beakdansim tig00005939_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1746118
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1520382 original size:23 final size:24
Alignment explanation
Indices: 1520349--1520396 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
1520339 TTTTAGTCCG
1520349 TTTTAATAACTAAAC-TTACAATTT
1 TTTTAATAACTAAACGTTA-AATTT
*
1520373 TTTTAA-AACTTAACGTTAAATTT
1 TTTTAATAACTAAACGTTAAATTT
1520396 T
1 T
1520397 GAACGAGTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTTAATAACTAAACGTTAAATTT
Found at i:1524507 original size:182 final size:183
Alignment explanation
Indices: 1524199--1524563 Score: 723
Period size: 182 Copynumber: 2.0 Consensus size: 183
1524189 AACCCATGCA
1524199 CAAAAATGCTCCCCAGGTTCCCCCTAAAACAACGTCGTTTGATGCCCCATATATAAGCTAGAAAT
1 CAAAAATGCTCCCCAGGTTCCCCCTAAAACAACGTCGTTTGATGCCCCATATATAAGCTAGAAAT
1524264 CACGCCAAAATCACCCTCAGCTTCATTTTTTTCTTTTCCTTCTTACACGAATGAGAGAGAAAGAG
66 CACGCCAAAATCACCCTCAGCTTCATTTTTTTCTTTTCCTTCTTACACGAATGAGAGAGAAAGAG
1524329 AGAGAAAGCTCTCAACCGGAGCTCAAGAGTTTCCAGAAACTGGGGAGCATCTG
131 AGAGAAAGCTCTCAACCGGAGCTCAAGAGTTTCCAGAAACTGGGGAGCATCTG
1524382 CAAAAATGCTCCCCAGGTTCCCCCTAAAACAACGTCGTTTGATGCCCC-TATATAAGCTAGAAAT
1 CAAAAATGCTCCCCAGGTTCCCCCTAAAACAACGTCGTTTGATGCCCCATATATAAGCTAGAAAT
1524446 CACGCCAAAATCACCCTCAGCTTCATTTTTTTCTTTTCCTTCTTACACGAATGAGAGAGAAAGAG
66 CACGCCAAAATCACCCTCAGCTTCATTTTTTTCTTTTCCTTCTTACACGAATGAGAGAGAAAGAG
1524511 AGAGAAAGCTCTCAACCGGAGCTCAAGAGTTTCCAGAAACTGGGGAGCATCTG
131 AGAGAAAGCTCTCAACCGGAGCTCAAGAGTTTCCAGAAACTGGGGAGCATCTG
1524564 TCGTGTCGGA
Statistics
Matches: 182, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
182 134 0.74
183 48 0.26
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (183 bp):
CAAAAATGCTCCCCAGGTTCCCCCTAAAACAACGTCGTTTGATGCCCCATATATAAGCTAGAAAT
CACGCCAAAATCACCCTCAGCTTCATTTTTTTCTTTTCCTTCTTACACGAATGAGAGAGAAAGAG
AGAGAAAGCTCTCAACCGGAGCTCAAGAGTTTCCAGAAACTGGGGAGCATCTG
Found at i:1524678 original size:9 final size:9
Alignment explanation
Indices: 1524664--1524708 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
1524654 GGGGTCAGAT
1524664 TTTCTTTTC
1 TTTCTTTTC
1524673 TTTCTTTTC
1 TTTCTTTTC
1524682 TTTC-TTTC
1 TTTCTTTTC
1524690 TTT-TTTT-
1 TTTCTTTTC
*
1524697 TTTTTTTTC
1 TTTCTTTTC
1524706 TTT
1 TTT
1524709 TTGATTCTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 3 0.09
8 14 0.42
9 16 0.48
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:1526163 original size:18 final size:17
Alignment explanation
Indices: 1526112--1526163 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
1526102 TTGTGTTTCG
* *
1526112 TTTTTTTTTTTGCAGGT
1 TTTTTTTTTTTGAAGCT
* *
1526129 TTTTTGTTCTTTAAAGCT
1 TTTTT-TTTTTTGAAGCT
1526147 TTTTTTCTTTTTGAAGC
1 TTTTTT-TTTTTGAAGC
1526164 CATCCATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.12, C:0.10, G:0.13, T:0.65
Consensus pattern (17 bp):
TTTTTTTTTTTGAAGCT
Found at i:1526407 original size:12 final size:12
Alignment explanation
Indices: 1526390--1526421 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1526380 ATAATGGATC
1526390 TTAATTGTTATA
1 TTAATTGTTATA
1526402 TTAATTGTTATA
1 TTAATTGTTATA
*
1526414 TTACTTGT
1 TTAATTGT
1526422 GTTACAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.03, G:0.09, T:0.59
Consensus pattern (12 bp):
TTAATTGTTATA
Found at i:1529606 original size:47 final size:46
Alignment explanation
Indices: 1529533--1529651 Score: 193
Period size: 47 Copynumber: 2.6 Consensus size: 46
1529523 TAAATCGAAC
* * *
1529533 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATT
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATG
*
1529579 CCATAATTAAAAATGCATGAAATGATGCATTAAGGCATAAAAGGATG
1 CCATAATT-AAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATG
1529626 CCATAATTAAAATGCATGAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATG
1529652 TCATAATTAA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
46 25 0.37
47 42 0.63
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.24
Consensus pattern (46 bp):
CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATG
Found at i:1529676 original size:26 final size:25
Alignment explanation
Indices: 1529618--1529678 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
1529608 TTAAGGCATA
* *
1529618 AAAGGATGCCATAATTAAAATGCAT
1 AAAGGATGTCATAATTAAAATACAT
*
1529643 GAAAGGATGTCATAATTAAAATACGT
1 -AAAGGATGTCATAATTAAAATACAT
1529669 AAATGGATGT
1 AAA-GGATGT
1529679 GTTAATGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 3 0.10
26 28 0.90
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (25 bp):
AAAGGATGTCATAATTAAAATACAT
Found at i:1531488 original size:117 final size:117
Alignment explanation
Indices: 1531313--1531604 Score: 503
Period size: 117 Copynumber: 2.5 Consensus size: 117
1531303 TTTCCTGAAA
* * ** *
1531313 CATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACAAAGCCGAGGATCCTGCAGTAAT
1 CATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAGCAAAGGAGCCTGCAGTAAT
1531378 AACTTCCCCATCCAGTCACTCCAATCACTACAATGTGTAGGTTCCCCAGAAC
66 AACTTCCCCATCCAGTCACTCCAATCACTACAATGTGTAGGTTCCCCAGAAC
* *
1531430 CATACACCCACCTGCACACCAGTAAGGTCTTACCCTGAGCACACAGCAAAGGAGCCTGCGGTAAT
1 CATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAGCAAAGGAGCCTGCAGTAAT
*
1531495 AACTTCCCCATCCAGTCACTCCAGTCACTACAATGTGTAGGTTCCCCAGAAC
66 AACTTCCCCATCCAGTCACTCCAATCACTACAATGTGTAGGTTCCCCAGAAC
*
1531547 CATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAGCAAAGGGGCCTG
1 CATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAGCAAAGGAGCCTG
1531605 AAATACTTCC
Statistics
Matches: 165, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 165 1.00
ACGTcount: A:0.30, C:0.35, G:0.17, T:0.17
Consensus pattern (117 bp):
CATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAGCAAAGGAGCCTGCAGTAAT
AACTTCCCCATCCAGTCACTCCAATCACTACAATGTGTAGGTTCCCCAGAAC
Found at i:1532585 original size:29 final size:28
Alignment explanation
Indices: 1532542--1532706 Score: 97
Period size: 29 Copynumber: 5.9 Consensus size: 28
1532532 GAAAAAACAC
* *
1532542 CATTTTGAAATTAATTACCAAAATAGCA
1 CATTTTCAAAATAATTACCAAAATAGCA
* *
1532570 TCATTTTCAAAATAATTACTAAAATAACA
1 -CATTTTCAAAATAATTACCAAAATAGCA
* * * ** *
1532599 CTTTTTTAAAA-ATTTTA-TTAAATTGC-
1 CATTTTCAAAATA-ATTACCAAAATAGCA
** * *
1532625 CACTTTTTTAAA-AA-TACAAAAATATCA
1 CA-TTTTCAAAATAATTACCAAAATAGCA
*
1532652 CCATTTTCAAAATAATTACCAGAATAGCA
1 -CATTTTCAAAATAATTACCAAAATAGCA
* *
1532681 CTATTTCCCAAATAATTACCAAAATA
1 C-ATTTTCAAAATAATTACCAAAATA
1532707 TCACCCGGTC
Statistics
Matches: 103, Mismatches: 25, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
25 2 0.02
26 6 0.06
27 23 0.22
28 17 0.17
29 55 0.53
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.35
Consensus pattern (28 bp):
CATTTTCAAAATAATTACCAAAATAGCA
Found at i:1539005 original size:117 final size:117
Alignment explanation
Indices: 1538800--1539089 Score: 485
Period size: 117 Copynumber: 2.5 Consensus size: 117
1538790 TTCCCGAAAT
* * **
1538800 ATACACCCACCTGCATACCAGTAAGGACTTACCCT-AACACA-AAGCCGAGGAGCCTGCAGTAAT
1 ATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAA-CAAAGGAGCCTGCAGTAAT
1538863 AACTTCCCCATCCAGTCACTCCAATCACTACAATGTGTAGGTTCCCCAGAACC
65 AACTTCCCCATCCAGTCACTCCAATCACTACAATGTGTAGGTTCCCCAGAACC
* * *
1538916 ATACACCCACCTGCACACCAATAAGGACTTACCCTGAGCACACAACAAAGGAGCTTGCGGTAATA
1 ATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAACAAAGGAGCCTGCAGTAATA
*
1538981 ACTTCCCTATCCAGTCACTCCAATCACTACAATGTGTAGGTTCCCCAGAACC
66 ACTTCCCCATCCAGTCACTCCAATCACTACAATGTGTAGGTTCCCCAGAACC
1539033 ATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAACAAAGGAGCCTG
1 ATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAACAAAGGAGCCTG
1539090 AAATACTTCC
Statistics
Matches: 162, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
116 33 0.20
117 127 0.78
118 2 0.01
ACGTcount: A:0.33, C:0.34, G:0.15, T:0.18
Consensus pattern (117 bp):
ATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAACAAAGGAGCCTGCAGTAATA
ACTTCCCCATCCAGTCACTCCAATCACTACAATGTGTAGGTTCCCCAGAACC
Found at i:1540045 original size:29 final size:29
Alignment explanation
Indices: 1540004--1540189 Score: 141
Period size: 29 Copynumber: 6.5 Consensus size: 29
1539994 ACATTTTTTT
* *
1540004 ATAATTACAAAAATAACACCATTTTGAAA
1 ATAATTACCAAAATAACACCATTTTCAAA
* *
1540033 TTAATTACCAAAATAGA-ATCATTTTCAAA
1 ATAATTACCAAAATA-ACACCATTTTCAAA
* *
1540062 ATAATTACTC-AAATATCACTC-TTTTAAAA
1 ATAATTAC-CAAAATAACAC-CATTTTCAAA
* *** *
1540091 AT-TTTA-CAAAATTGTTACC-TTTTTAAA
1 ATAATTACCAAAA-TAACACCATTTTCAAA
* * *
1540118 AAAATTACAAAAATAACACCTTTTTCAAA
1 ATAATTACCAAAATAACACCATTTTCAAA
* * *
1540147 ATAATTACCAGAATAACACCATTTCCCAA
1 ATAATTACCAAAATAACACCATTTTCAAA
1540176 ATAATTACCAAAAT
1 ATAATTACCAAAAT
1540190 GTCACCCGAT
Statistics
Matches: 122, Mismatches: 26, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
26 1 0.01
27 12 0.10
28 14 0.11
29 92 0.75
30 3 0.02
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.33
Consensus pattern (29 bp):
ATAATTACCAAAATAACACCATTTTCAAA
Found at i:1540254 original size:20 final size:20
Alignment explanation
Indices: 1540229--1540267 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1540219 GGTCGGGTCG
1540229 AAAACCGGTCAAACTGGTTC
1 AAAACCGGTCAAACTGGTTC
1540249 AAAACCGGTCAAACTGGTT
1 AAAACCGGTCAAACTGGTT
1540268 ATTTTAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (20 bp):
AAAACCGGTCAAACTGGTTC
Found at i:1542272 original size:20 final size:21
Alignment explanation
Indices: 1542229--1542278 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
1542219 TGGTCTTATA
*
1542229 GTATCGATATTTTTTTCTTAGG
1 GTATCGATA-TTTGTTCTTAGG
*
1542251 GTATCGATA-TTGTTCTTGGG
1 GTATCGATATTTGTTCTTAGG
1542271 GTATCGAT
1 GTATCGAT
1542279 CTCGAGGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 17 0.65
22 9 0.35
ACGTcount: A:0.18, C:0.10, G:0.24, T:0.48
Consensus pattern (21 bp):
GTATCGATATTTGTTCTTAGG
Found at i:1544064 original size:20 final size:20
Alignment explanation
Indices: 1544019--1544076 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
1544009 GCATGGGTAG
1544019 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
1544043 TGTATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
1544063 TGCATCGATGCACT
1 TGCATCGATGCACT
1544077 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:1544329 original size:20 final size:20
Alignment explanation
Indices: 1544304--1544343 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1544294 TTTATGGTGC
1544304 TAAATGGAAACAAGACTTGT
1 TAAATGGAAACAAGACTTGT
1544324 TAAATGGAAACAAGACTTGT
1 TAAATGGAAACAAGACTTGT
1544344 GACAAGTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (20 bp):
TAAATGGAAACAAGACTTGT
Found at i:1545119 original size:31 final size:31
Alignment explanation
Indices: 1545081--1545145 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1545071 AGAGTCGAGG
*
1545081 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTAGGTTC-TTCGAGACATATGGACA
* *
1545112 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGAGACATATGGACA
1545143 GTT
1 GTT
1545146 ACCGAGGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGACATATGGACA
Found at i:1545226 original size:29 final size:30
Alignment explanation
Indices: 1545131--1545232 Score: 143
Period size: 30 Copynumber: 3.4 Consensus size: 30
1545121 GGTTCTTCGG
* *
1545131 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
1545161 GACCTCTGGATAGTTACCGAGAATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* * *
1545191 GACCTCTGGATAGTTATCG-GGGTCTTTGT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1545220 GACCTCTGGATAG
1 GACCTCTGGATAG
1545233 GTCCTTCGGG
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
29 20 0.31
30 45 0.69
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:1546658 original size:25 final size:23
Alignment explanation
Indices: 1546629--1546681 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 23
1546619 CCACTAGGGG
1546629 CTATGAAATTTGTCCCGAAT-GACCA
1 CTATGAAA--TGTCCCG-ATGGACCA
*
1546654 CTATGTAATGTCCCGATGGACCA
1 CTATGAAATGTCCCGATGGACCA
1546677 CTATG
1 CTATG
1546682 TCCCGAAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 2 0.08
23 17 0.65
25 7 0.27
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (23 bp):
CTATGAAATGTCCCGATGGACCA
Found at i:1546666 original size:23 final size:23
Alignment explanation
Indices: 1546639--1546682 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1546629 CTATGAAATT
1546639 TGTCCCGAAT-GACCACTATGTAA
1 TGTCCCG-ATGGACCACTATGTAA
1546662 TGTCCCGATGGACCACTATGT
1 TGTCCCGATGGACCACTATGT
1546683 CCCGAAGGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (23 bp):
TGTCCCGATGGACCACTATGTAA
Found at i:1551275 original size:28 final size:28
Alignment explanation
Indices: 1551244--1551307 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
1551234 TTCATACAAG
*
1551244 TCATATCATACCTACAACAACATATAAT
1 TCATAACATACCTACAACAACATATAAT
1551272 TCATAACATACCTACAACAACATATAAT
1 TCATAACATACCTACAACAACATATAAT
1551300 TCATAACA
1 TCATAACA
1551308 AACACATGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (28 bp):
TCATAACATACCTACAACAACATATAAT
Found at i:1553008 original size:58 final size:59
Alignment explanation
Indices: 1552918--1553037 Score: 183
Period size: 58 Copynumber: 2.1 Consensus size: 59
1552908 AGAGGATTGG
*
1552918 TTAGAGTCATATTATCAATTGTTCCTTTTCATTGCGACTAGGA-GGTTCGATAGGACAC
1 TTAGAGCCATATTATCAATTGTTCCTTTTCATTGCGACTAGGAGGGTTCGATAGGACAC
*
1552976 TTAGAGCCATATTATCAAGTT-TGT-CTTTTCATTGTGACTAGGAGGGTTCGATAGGACAC
1 TTAGAGCCATATTATCAA-TTGT-TCCTTTTCATTGCGACTAGGAGGGTTCGATAGGACAC
1553035 TTA
1 TTA
1553038 TCCATATATT
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
58 36 0.63
59 21 0.37
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.37
Consensus pattern (59 bp):
TTAGAGCCATATTATCAATTGTTCCTTTTCATTGCGACTAGGAGGGTTCGATAGGACAC
Found at i:1554609 original size:37 final size:38
Alignment explanation
Indices: 1554529--1554609 Score: 89
Period size: 37 Copynumber: 2.2 Consensus size: 38
1554519 AACAAGTTGA
*
1554529 AAAATATTTATATATTTTCTTTAAAAAAATTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTAAAAAAATTAAAATCAT
*
1554568 -AAAATTTATATAATTTT-TTT-ACAAAATTAAAAAT-AT
1 AAAAATTTATAT-ATTTTCTTTAAAAAAATT-AAAATCAT
1554604 AAAAAT
1 AAAAAT
1554610 ATTTAATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
36 9 0.24
37 20 0.54
38 8 0.22
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (38 bp):
AAAAATTTATATATTTTCTTTAAAAAAATTAAAATCAT
Found at i:1557250 original size:60 final size:59
Alignment explanation
Indices: 1557198--1557314 Score: 141
Period size: 60 Copynumber: 1.9 Consensus size: 59
1557188 CGCAACTTAG
1557198 TTTCTACAATCGCAA-AGCGAATTTCT-TTCTCGCAACACGAATTTCTTTTTCGCAACAAGA
1 TTTCTA-AATCGCAACA-CGAATTT-TGTTCTCGCAACACGAATTTCTTTTTCGCAACAAGA
* * *
1557258 TTTTCTAAATTGCAACACGAATTTTGTTTTCGCAACACGAATTT-TAATTTCGCAACA
1 -TTTCTAAATCGCAACACGAATTTTGTTCTCGCAACACGAATTTCT-TTTTCGCAACA
1557315 TCTTTTATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
59 2 0.04
60 41 0.82
61 7 0.14
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (59 bp):
TTTCTAAATCGCAACACGAATTTTGTTCTCGCAACACGAATTTCTTTTTCGCAACAAGA
Found at i:1557302 original size:20 final size:19
Alignment explanation
Indices: 1557215--1557314 Score: 87
Period size: 20 Copynumber: 5.0 Consensus size: 19
1557205 AATCGCAAAG
*
1557215 CGAATTTCTTTCTCGCAACA
1 CGAATTT-TTTTTCGCAACA
1557235 CGAATTTCTTTTTCGCAACA
1 CGAATTT-TTTTTCGCAACA
* *
1557255 AG-ATTTTCTAAATT-GCAACA
1 CGAATTTT-T--TTTCGCAACA
1557275 CGAATTTTGTTTTCGCAACA
1 CGAATTTT-TTTTCGCAACA
*
1557295 CGAATTTTAATTTCGCAACA
1 CGAATTTT-TTTTCGCAACA
1557315 TCTTTTATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
18 1 0.01
19 7 0.10
20 51 0.76
21 8 0.12
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (19 bp):
CGAATTTTTTTTCGCAACA
Found at i:1557313 original size:40 final size:41
Alignment explanation
Indices: 1557227--1557314 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 41
1557217 AATTTCTTTC
*
1557227 TCGCAACACGAATTTCTTTTTCGCAACAAGATTTTCTAAAT
1 TCGCAACACGAATTTCTTTTTCGCAACAAGAATTTCTAAAT
* *
1557268 T-GCAACACGAATTT-TGTTTTCGCAACACGAATTT-TAATT
1 TCGCAACACGAATTTCT-TTTTCGCAACAAGAATTTCTAAAT
1557307 TCGCAACA
1 TCGCAACA
1557315 TCTTTTATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 6 0.14
40 35 0.83
41 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (41 bp):
TCGCAACACGAATTTCTTTTTCGCAACAAGAATTTCTAAAT
Found at i:1557326 original size:18 final size:18
Alignment explanation
Indices: 1557299--1557333 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1557289 GCAACACGAA
*
1557299 TTTTAATTTCGCAACATC
1 TTTTAATTTCGAAACATC
*
1557317 TTTTATTTTCGAAACAT
1 TTTTAATTTCGAAACAT
1557334 AAATGTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.49
Consensus pattern (18 bp):
TTTTAATTTCGAAACATC
Found at i:1557495 original size:16 final size:16
Alignment explanation
Indices: 1557474--1557507 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1557464 CCATCTCTAA
*
1557474 TTATTTTTACATAATT
1 TTATTTCTACATAATT
*
1557490 TTATTTCTATATAATT
1 TTATTTCTACATAATT
1557506 TT
1 TT
1557508 CAATGATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTTCTACATAATT
Found at i:1558123 original size:12 final size:12
Alignment explanation
Indices: 1558102--1558135 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1558092 ACCACATTTC
*
1558102 CAATACCAAACA
1 CAATATCAAACA
1558114 CAATATCAAACA
1 CAATATCAAACA
*
1558126 CAATCTCAAA
1 CAATATCAAA
1558136 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1560602 original size:18 final size:18
Alignment explanation
Indices: 1560579--1560614 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1560569 AAGCAAAAGG
1560579 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
1560597 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
1560615 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:1562325 original size:21 final size:21
Alignment explanation
Indices: 1562299--1562374 Score: 125
Period size: 21 Copynumber: 3.6 Consensus size: 21
1562289 GTGAATCGGG
*
1562299 CTCTTGAACGGTGGGAGAGGC
1 CTCTTGAACGATGGGAGAGGC
*
1562320 CTCTTGAACGATGAGAGAGGC
1 CTCTTGAACGATGGGAGAGGC
*
1562341 CTCTTGAACGATGGGAGGGGC
1 CTCTTGAACGATGGGAGAGGC
1562362 CTCTTGAACGATG
1 CTCTTGAACGATG
1562375 ACAGGTGAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.22, C:0.20, G:0.37, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGAGGC
Found at i:1562551 original size:4 final size:4
Alignment explanation
Indices: 1562519--1562564 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
1562509 AGGCCGCTAA
* * * *
1562519 AAAT AAAT TAAT ACAT AAAT CAGT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1562565 TGCCAAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:1562749 original size:21 final size:21
Alignment explanation
Indices: 1562725--1562770 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1562715 CCATTGTCAT
1562725 CACGTAAAACATC-TACCTCAC
1 CACGT-AAACATCGTACCTCAC
* *
1562746 CACGTAAAGATCGTACCTCAT
1 CACGTAAACATCGTACCTCAC
1562767 CACG
1 CACG
1562771 CCATTCATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.35, C:0.35, G:0.11, T:0.20
Consensus pattern (21 bp):
CACGTAAACATCGTACCTCAC
Found at i:1563007 original size:42 final size:42
Alignment explanation
Indices: 1562948--1563046 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
1562938 GTGATGGAAT
* * * *
1562948 AGGTGATGGCTCTCGGTGTGGAGGTGTATAATCGGCCCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCAGCCCGATC
**
1562990 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCAGTTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCAGCCCGATC
*
1563032 AGGTGATGGATCTCG
1 AGGTGATGGCTCTCG
1563047 AAGTGGGGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.18, C:0.18, G:0.36, T:0.27
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCAGCCCGATC
Found at i:1564618 original size:14 final size:14
Alignment explanation
Indices: 1564599--1564632 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1564589 TGCGATTTTC
1564599 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
*
1564613 ATTTTCGTGTTGCG
1 ATTTTCGCGTTGCG
*
1564627 AATTTC
1 ATTTTC
1564633 ATTTTCGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1564636 original size:20 final size:20
Alignment explanation
Indices: 1564613--1564651 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1564603 TCGCGTTGCG
1564613 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
1564633 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
1564652 AAGTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:1565186 original size:20 final size:20
Alignment explanation
Indices: 1565161--1565231 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
1565151 TAAACGTTCT
*
1565161 TTGCGAATTTGACTTCTGCG
1 TTGCGAATTTGAATTCTGCG
* ** *
1565181 TTGCGAATTTCAAAACTGAG
1 TTGCGAATTTGAATTCTGCG
* *
1565201 TTGCGAAATTGGAGTTC-GCG
1 TTGCG-AATTTGAATTCTGCG
1565221 TTGCGAATTTG
1 TTGCGAATTTG
1565232 TTGGCCATTT
Statistics
Matches: 38, Mismatches: 12, Indels: 3
0.72 0.23 0.06
Matches are distributed among these distances:
19 5 0.13
20 27 0.71
21 6 0.16
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (20 bp):
TTGCGAATTTGAATTCTGCG
Found at i:1565392 original size:21 final size:23
Alignment explanation
Indices: 1565368--1565417 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
1565358 CTTTGAATTG
* *
1565368 TCCTATAACTTTTTTTAAT-A-T
1 TCCTATAACTTATTTGAATGATT
1565389 TCCTATAACTTATTTGAATGATT
1 TCCTATAACTTATTTGAATGATT
1565412 TCCTAT
1 TCCTAT
1565418 GAAAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 17 0.68
22 1 0.04
23 7 0.28
ACGTcount: A:0.28, C:0.16, G:0.04, T:0.52
Consensus pattern (23 bp):
TCCTATAACTTATTTGAATGATT
Found at i:1566947 original size:21 final size:20
Alignment explanation
Indices: 1566909--1566948 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1566899 CAGATTGCCA
1566909 AAGGGGTACAGATTCCCCCC
1 AAGGGGTACAGATTCCCCCC
*
1566929 AAGGGGTACCGATTCCCCCC
1 AAGGGGTACAGATTCCCCCC
1566949 TATCTAACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.38, G:0.25, T:0.15
Consensus pattern (20 bp):
AAGGGGTACAGATTCCCCCC
Found at i:1567336 original size:34 final size:32
Alignment explanation
Indices: 1567296--1567365 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1567286 TTTTGTAAAG
* *
1567296 GGGAAATGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAATGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1567330 GGGAAATGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAATGTTCTAGCTTAGCCCGGAAAAACTA
1567362 GGGA
1 GGGA
1567366 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (32 bp):
GGGAAATGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1568252 original size:19 final size:20
Alignment explanation
Indices: 1568228--1568275 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1568218 AACGATTTTC
*
1568228 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
1568247 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1568267 TTTTGAAAA
1 TTTTGAAAA
1568276 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1569695 original size:20 final size:21
Alignment explanation
Indices: 1569670--1569733 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
1569660 AATCAGATTG
*
1569670 CCCAGGAGGTA-CAGATTCCC
1 CCCAGGGGGTACCAGATTCCC
1569690 CCCAGGGGGTACCA-ATTCCCC
1 CCCAGGGGGTACCAGATT-CCC
*
1569711 CCCAGGGGGTATC-GATTCCC
1 CCCAGGGGGTACCAGATTCCC
1569731 CCC
1 CCC
1569734 TGTCTAACGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 19 0.49
21 20 0.51
ACGTcount: A:0.19, C:0.41, G:0.25, T:0.16
Consensus pattern (21 bp):
CCCAGGGGGTACCAGATTCCC
Found at i:1570952 original size:19 final size:17
Alignment explanation
Indices: 1570928--1570977 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
1570918 TTAATTTTTT
1570928 AATAATTTGTTGTAAGAAA
1 AATAATTTGTT-TAA-AAA
* *
1570947 AATAATTTATTTAAACA
1 AATAATTTGTTTAAAAA
1570964 AATAATTTGTTTAA
1 AATAATTTGTTTAA
1570978 TTTTTTATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 15 0.54
18 3 0.11
19 10 0.36
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (17 bp):
AATAATTTGTTTAAAAA
Found at i:1572898 original size:2 final size:2
Alignment explanation
Indices: 1572891--1572932 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1572881 TTCGAACTTA
1572891 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1572933 TGAATATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1574878 original size:17 final size:16
Alignment explanation
Indices: 1574856--1574887 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
1574846 TATACAGAGA
1574856 TTTTTTCGCAGGGATTT
1 TTTTTTC-CAGGGATTT
1574873 TTTTTTCCAGGGATT
1 TTTTTTCCAGGGATT
1574888 ACTGCCCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.53
Consensus pattern (16 bp):
TTTTTTCCAGGGATTT
Found at i:1575504 original size:18 final size:18
Alignment explanation
Indices: 1575461--1575517 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
1575451 AAATTTTGGG
**
1575461 TAAACTACTAGTTTAATATA
1 TAAACTACTAGTTT--TAGC
1575481 TAAACTA-TAAGTTTTAGC
1 TAAACTACT-AGTTTTAGC
1575499 TAAACTACTAGTTTTAGC
1 TAAACTACTAGTTTTAGC
1575517 T
1 T
1575518 CATTTTAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 19 0.58
19 2 0.06
20 12 0.36
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (18 bp):
TAAACTACTAGTTTTAGC
Found at i:1581944 original size:2 final size:2
Alignment explanation
Indices: 1581937--1581961 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1581927 CTCTTTCAAG
1581937 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1581962 AAACAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1586519 original size:122 final size:121
Alignment explanation
Indices: 1586027--1586572 Score: 668
Period size: 121 Copynumber: 4.5 Consensus size: 121
1586017 TAACATTAAG
* * * * * * *
1586027 TTTTGAAAAGATAGAAAGTTTAGGTACTAAAA-GGGCCAAAATTGATAGTTTAGGTACTAAACAC
1 TTTTGAAAAAATTGAAAGTTTAGGTACTAAAACGGACTAAAACTGATAGCTTAGATACTAAACAC
* *
1586091 GTTAAGTTTTTAACTACGAGTACTAAAAAGAAACGAAAACTAAACTTTAGGTATGGA
66 GTTAAGTTTTTAACTACGTGTACTAAAACGAAACGAAAACTAAACTTTAGGTAT-GA
* * * * * *
1586148 -TTTGAAAACATTGACAGTTTAGGTACTAAAACAGA-TCAAAGCTGATATCTTAGATACTAAACG
1 TTTTGAAAAAATTGAAAGTTTAGGTACTAAAACGGACT-AAAACTGATAGCTTAGATACTAAACA
* * * * * *
1586211 TGTTAAGTTTTTAACTGCGGGTACTAAAACAAAATGAAAACTAAACTTTAGGTATGG
65 CGTTAAGTTTTTAACTACGTGTACTAAAACGAAACGAAAACTAAACTTTAGGTATGA
* * * *
1586268 TTCTAAAAAAATTAAAAGTTTAGGTACTAAAACGGAAC-AAAGCTGATAGCTTAGATACTAAACA
1 TTTTGAAAAAATTGAAAGTTTAGGTACTAAAACGG-ACTAAAACTGATAGCTTAGATACTAAACA
*
1586332 CGTTAAGTTTTTAACTACATGTACTAAAACGAAACGAAAACTAAACTTTAGGTATGA
65 CGTTAAGTTTTTAACTACGTGTACTAAAACGAAACGAAAACTAAACTTTAGGTATGA
* * * * **
1586389 TTCTGAAAAAATTGAAAGTTTAGGTACTAAAATGGACTAAAATTGATAGCTTAGATATTAAACGT
1 TTTTGAAAAAATTGAAAGTTTAGGTACTAAAACGGACTAAAACTGATAGCTTAGATACTAAACAC
*
1586454 GTTAAGTTTTTAACTGCGTGATACTAAAACGAAACGAAAACTAAACTTTAGGTATGA
66 GTTAAGTTTTTAACTACGTG-TACTAAAACGAAACGAAAACTAAACTTTAGGTATGA
* * * * * * *
1586511 TTTTGAAAATATTAAAAGTTTAGGTATTAAAACGGACCATAACTGATAGTTTATATACTAAA
1 TTTTGAAAAAATTGAAAGTTTAGGTACTAAAACGGACTAAAACTGATAGCTTAGATACTAAA
1586573 TGCGTATTTT
Statistics
Matches: 363, Mismatches: 55, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
120 31 0.09
121 244 0.67
122 88 0.24
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (121 bp):
TTTTGAAAAAATTGAAAGTTTAGGTACTAAAACGGACTAAAACTGATAGCTTAGATACTAAACAC
GTTAAGTTTTTAACTACGTGTACTAAAACGAAACGAAAACTAAACTTTAGGTATGA
Found at i:1593773 original size:40 final size:36
Alignment explanation
Indices: 1593704--1593784 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 36
1593694 AACTTAATGT
1593704 TAAATTTTGAATGGTGGTACTAAATGAAACAAAGAC
1 TAAATTTTGAATGGTGGTACTAAATGAAACAAAGAC
*
1593740 TAAAGTTTTTAATGGTGGGGTACTAAAATGAAACAAA-ATC
1 TAAA-TTTTGAATGGT--GGTACT-AAATGAAACAAAGA-C
1593780 TAAAT
1 TAAAT
1593785 GTTAGGTATG
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
36 4 0.10
37 10 0.26
39 8 0.21
40 17 0.44
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (36 bp):
TAAATTTTGAATGGTGGTACTAAATGAAACAAAGAC
Found at i:1598158 original size:32 final size:33
Alignment explanation
Indices: 1598109--1598192 Score: 77
Period size: 32 Copynumber: 2.6 Consensus size: 33
1598099 TCATATATCT
* * *
1598109 TATAACATATACA-ATAATCATTAACAC-ACACA
1 TATATCATAT-CATATAATCAATAACACAAAACA
* *
1598141 TATATCATATCATATAATTAATATCACAAAACA
1 TATATCATATCATATAATCAATAACACAAAACA
1598174 TATAT-ATAT-ATATATATCA
1 TATATCATATCATATA-ATCA
1598193 CATATATTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
31 7 0.16
32 27 0.63
33 9 0.21
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.33
Consensus pattern (33 bp):
TATATCATATCATATAATCAATAACACAAAACA
Found at i:1599223 original size:24 final size:20
Alignment explanation
Indices: 1599170--1599227 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
1599160 TTCCCCTTGG
*
1599170 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
1599190 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
1599213 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1599228 CTACCCTTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1602503 original size:2 final size:2
Alignment explanation
Indices: 1602496--1602533 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
1602486 ATCTCAAAAC
*
1602496 AT AT AT AT AT AT AT AT AT AT AT AT CAC AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
1602534 TCAATGTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.94
3 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1606846 original size:2 final size:2
Alignment explanation
Indices: 1606839--1606879 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
1606829 ATCTCAAAAC
*
1606839 AT AT AT AT AT AT AT AT AT AT AT AT CAC AT AT AT -T AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
1606880 TCAATGTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 31 0.91
3 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1609048 original size:16 final size:17
Alignment explanation
Indices: 1609016--1609049 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1609006 TTTAATTCGA
*
1609016 TCCATTCATTTCTTTAT
1 TCCATTCATTCCTTTAT
1609033 TCCATT-ATTCCTTTAT
1 TCCATTCATTCCTTTAT
1609049 T
1 T
1609050 TATTCCTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.59
Consensus pattern (17 bp):
TCCATTCATTCCTTTAT
Found at i:1612225 original size:19 final size:19
Alignment explanation
Indices: 1612201--1612238 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1612191 TTTAAGGGGG
*
1612201 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTACTTA
*
1612220 TGCATCGATTCACTACTTA
1 TGCATCGATGCACTACTTA
1612239 CATTCGATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.13, T:0.34
Consensus pattern (19 bp):
TGCATCGATGCACTACTTA
Found at i:1617658 original size:16 final size:17
Alignment explanation
Indices: 1617625--1617658 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1617615 ATCTTTTATT
*
1617625 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
1617642 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
1617658 T
1 T
1617659 AATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:1621116 original size:69 final size:69
Alignment explanation
Indices: 1621041--1621249 Score: 400
Period size: 69 Copynumber: 3.0 Consensus size: 69
1621031 GCTGAAAGAA
1621041 GTTTAAAGATATTTAAGTTTGGTTTAAAGATATTGTTAGTGATGTCTCGTGTGTCTTATATTTGT
1 GTTTAAAGATATTTAAGTTTGGTTTAAAGATATTGTTAGTGATGTCTCGTGTGTCTTATATTTGT
1621106 GTGT
66 GTGT
*
1621110 GTTTAAAGATATTTAAGTTTGATTTAAAGATATTGTTAGTGATGTCTCGTGTGTCTTATATTTGT
1 GTTTAAAGATATTTAAGTTTGGTTTAAAGATATTGTTAGTGATGTCTCGTGTGTCTTATATTTGT
1621175 GTGT
66 GTGT
*
1621179 GTTTAAAGATATTTAAGTTTGGTTTAAAGATATTGTTATTGATGTCTCGTGTGTCTTATATTTGT
1 GTTTAAAGATATTTAAGTTTGGTTTAAAGATATTGTTAGTGATGTCTCGTGTGTCTTATATTTGT
1621244 GTGT
66 GTGT
1621248 GT
1 GT
1621250 GTGTGTGATA
Statistics
Matches: 137, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 137 1.00
ACGTcount: A:0.23, C:0.04, G:0.22, T:0.50
Consensus pattern (69 bp):
GTTTAAAGATATTTAAGTTTGGTTTAAAGATATTGTTAGTGATGTCTCGTGTGTCTTATATTTGT
GTGT
Found at i:1621192 original size:20 final size:20
Alignment explanation
Indices: 1621167--1621212 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1621157 CGTGTGTCTT
1621167 ATATTT-GTGTGTGTTTAAAG
1 ATATTTAGTGTG-GTTTAAAG
*
1621187 ATATTTAAGTTTGGTTTAAAG
1 ATATTT-AGTGTGGTTTAAAG
1621208 ATATT
1 ATATT
1621213 GTTATTGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.26
21 13 0.57
22 4 0.17
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (20 bp):
ATATTTAGTGTGGTTTAAAG
Found at i:1627198 original size:2 final size:2
Alignment explanation
Indices: 1627191--1627244 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1627181 TTCTCATCAA
1627191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1627233 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1627245 TGCTGCTCTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1628128 original size:24 final size:25
Alignment explanation
Indices: 1628086--1628138 Score: 90
Period size: 24 Copynumber: 2.1 Consensus size: 25
1628076 CTAATGTGGC
1628086 CCTCATTCTTTTCTCTCTCAATGTGA
1 CCTCATTC-TTTCTCTCTCAATGTGA
1628112 CCTCATTC-TTCTCTCTCAATGTGA
1 CCTCATTCTTTCTCTCTCAATGTGA
1628136 CCT
1 CCT
1628139 TCCAACTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 19 0.70
26 8 0.30
ACGTcount: A:0.15, C:0.34, G:0.08, T:0.43
Consensus pattern (25 bp):
CCTCATTCTTTCTCTCTCAATGTGA
Found at i:1634210 original size:211 final size:213
Alignment explanation
Indices: 1633845--1634262 Score: 822
Period size: 211 Copynumber: 2.0 Consensus size: 213
1633835 TAGCTAATCT
1633845 TGAGAAGAATGACTCTTGCCAACAGTTTAATGGGGCTCCAATGAGGTCCATGGTGTAAAAAGTCA
1 TGAGAAGAATGACTCTTGCCAACAGTTTAATGGGGCTCCAATGAGGTCCATGGTGTAAAAAGTCA
1633910 TGAAAATTTTATCCTCCGATACTAAAAGATCCAGATAGTCAAACCAAAATGATAACTCAAACTTT
66 TGAAAATTTTATCCTCCGATACTAAAAGATCCAGATAGTCAAACCAAAATGATAACTCAAACTTT
1633975 CTATTCAACCAAGAGTTCTTCAAGATTTCCTCCGACAGGAATTGTAATACCCTGAAACCCAGGTC
131 CTATTCAACCAAGAGTTCTTCAAGATTTCCTCCGACAGGAATTGTAATACCCTGAAACCCAGGTC
1634040 AGTAG-TTGGTTAATGAG
196 AGTAGTTTGGTTAATGAG
1634057 TGAGAAGAATGACTCTTGCCAACAGTTTAAT-GGGCTCCAATGAGGTCCATGGTGTAAAAAGTCA
1 TGAGAAGAATGACTCTTGCCAACAGTTTAATGGGGCTCCAATGAGGTCCATGGTGTAAAAAGTCA
1634121 TGAAAATTTTATCCTCCGATACTAAAAGATCCAGATAGTCAAACCAAAATGATAACTCAAACTTT
66 TGAAAATTTTATCCTCCGATACTAAAAGATCCAGATAGTCAAACCAAAATGATAACTCAAACTTT
1634186 CTATTCAACCAAGAGTTCTTCAAGATTTCCTCCGACAGGAATTGTAATACCCTGAAACCCAGGTC
131 CTATTCAACCAAGAGTTCTTCAAGATTTCCTCCGACAGGAATTGTAATACCCTGAAACCCAGGTC
1634251 AGTAGTTTGGTT
196 AGTAGTTTGGTT
1634263 TAACCTGAGA
Statistics
Matches: 205, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
211 168 0.82
212 37 0.18
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (213 bp):
TGAGAAGAATGACTCTTGCCAACAGTTTAATGGGGCTCCAATGAGGTCCATGGTGTAAAAAGTCA
TGAAAATTTTATCCTCCGATACTAAAAGATCCAGATAGTCAAACCAAAATGATAACTCAAACTTT
CTATTCAACCAAGAGTTCTTCAAGATTTCCTCCGACAGGAATTGTAATACCCTGAAACCCAGGTC
AGTAGTTTGGTTAATGAG
Found at i:1635279 original size:20 final size:20
Alignment explanation
Indices: 1635230--1635282 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1635220 CTCTTCAAAG
*
1635230 AGTATCGAAACTTTAGGAAT
1 AGTATCGAAACTTCAGGAAT
* *
1635250 AGTTTTGAAACTCTCAGGAA-
1 AGTATCGAAACT-TCAGGAAT
1635270 AGTATCGAAACTT
1 AGTATCGAAACTT
1635283 GCCAGAACAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 1 0.04
20 20 0.74
21 6 0.22
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (20 bp):
AGTATCGAAACTTCAGGAAT
Found at i:1637753 original size:59 final size:59
Alignment explanation
Indices: 1637655--1637824 Score: 155
Period size: 60 Copynumber: 2.9 Consensus size: 59
1637645 AGTACGTCAT
* * *
1637655 TCATTTTAAATTGGTCCTTAAACTTTTAAATGCTCCAATTTAATCCCAAAACTATGATTA
1 TCATTTTAAATTAGTCCTTAAACATTTAAATACTCCAATTTAATCCC-AAACTATGATTA
* * * * **
1637715 TCATTTTAAATTAGT-CTTAAACATTTGAATATTTCAATTTCATCCCAAACTATG-GCA
1 TCATTTTAAATTAGTCCTTAAACATTTAAATACTCCAATTTAATCCCAAACTATGATTA
* ** * * * *
1637772 CTCATTCTAAATTAGTCCCCAAACGTTTTAAATATTCCAATTTTATCACAAAC
1 -TCATTTTAAATTAGTCCTTAAAC-ATTTAAATACTCCAATTTAATCCCAAAC
1637825 AATGCGTATA
Statistics
Matches: 90, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
57 1 0.01
58 22 0.24
59 30 0.33
60 37 0.41
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (59 bp):
TCATTTTAAATTAGTCCTTAAACATTTAAATACTCCAATTTAATCCCAAACTATGATTA
Found at i:1637982 original size:29 final size:29
Alignment explanation
Indices: 1637949--1638065 Score: 105
Period size: 29 Copynumber: 4.1 Consensus size: 29
1637939 TTTAGATGAA
*
1637949 TTTGGGGATGAAATTGGAATATTCAAAAG
1 TTTGGGGATGAAATTAGAATATTCAAAAG
* *****
1637978 TTTGGGGACT-AATTTAGAA-AGAGGGAA-
1 TTTGGGGA-TGAAATTAGAATATTCAAAAG
1638005 TTTGGGGATGAAATTAGAATATTCAAAAG
1 TTTGGGGATGAAATTAGAATATTCAAAAG
** * *
1638034 TTTATGGATAAAATTAGAATGTTCAAAAG
1 TTTGGGGATGAAATTAGAATATTCAAAAG
1638063 TTT
1 TTT
1638066 AAGGACTAAT
Statistics
Matches: 67, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
26 1 0.01
27 16 0.24
28 6 0.09
29 43 0.64
30 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.32
Consensus pattern (29 bp):
TTTGGGGATGAAATTAGAATATTCAAAAG
Found at i:1638051 original size:56 final size:56
Alignment explanation
Indices: 1637946--1638052 Score: 162
Period size: 56 Copynumber: 1.9 Consensus size: 56
1637936 ATATTTAGAT
* * *
1637946 GAATTTGGGGATGAAATTGGAATATTCAAAAGTTTGGGGACTAATTTAGAAAGAGG
1 GAATTTGGGGATGAAATTAGAATATTCAAAAGTTTAGGGACTAAATTAGAAAGAGG
*
1638002 GAATTTGGGGATGAAATTAGAATATTCAAAAGTTTATGGA-TAAAATTAGAA
1 GAATTTGGGGATGAAATTAGAATATTCAAAAGTTTAGGGACT-AAATTAGAA
1638053 TGTTCAAAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
55 1 0.02
56 45 0.98
ACGTcount: A:0.41, C:0.03, G:0.26, T:0.30
Consensus pattern (56 bp):
GAATTTGGGGATGAAATTAGAATATTCAAAAGTTTAGGGACTAAATTAGAAAGAGG
Found at i:1639298 original size:8 final size:8
Alignment explanation
Indices: 1639285--1639314 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1639275 TCTTCGTTCT
1639285 CAAAAAAA
1 CAAAAAAA
1639293 CAAAAAAA
1 CAAAAAAA
1639301 CAAAAAAA
1 CAAAAAAA
1639309 -AAAAAA
1 CAAAAAA
1639315 CCTTTCCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:1641898 original size:57 final size:57
Alignment explanation
Indices: 1641788--1641902 Score: 149
Period size: 57 Copynumber: 2.0 Consensus size: 57
1641778 CAATATCTTC
* * * *
1641788 TGCTTATACAAATGAACTTGAACCACACGAATTAAGGAGTTTATGCGGTAAAAGAAT
1 TGCTTATACAAATGAACTTGAACCACACGAATCAAAGAGTTTATGCAGCAAAAGAAT
* * * * *
1641845 TGCTTATACAAATGAATTTGATCCGCACGAATCAAAGAGTTTGTGTAGCAAAAGAAT
1 TGCTTATACAAATGAACTTGAACCACACGAATCAAAGAGTTTATGCAGCAAAAGAAT
1641902 T
1 T
1641903 ATTGTTATAG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (57 bp):
TGCTTATACAAATGAACTTGAACCACACGAATCAAAGAGTTTATGCAGCAAAAGAAT
Found at i:1643442 original size:108 final size:106
Alignment explanation
Indices: 1643251--1643445 Score: 252
Period size: 108 Copynumber: 1.8 Consensus size: 106
1643241 TAAATCACGT
*
1643251 TTTAAGTCCCCCAAACTTTCCCGTGTTTTACAAAATGGTCACTAGAAGGGACAATTTTTATAATT
1 TTTAAGTCCCCCAAACTTTCCCGTGTTTTACAAAA-GGTCACTAGAAGGGACAATTTTCATAATT
1643316 TTCCCTTTTCTGTTTATGCTTTATAATTTTTTGTATAATTTCG
65 TTCCCTTTTCTG-TTATGCTTTATAATTTTTTGTATAATTTCG
* * ** *
1643359 TTTAATTCCCCCAAACTTTCCTGTGTTTTTACAAAA-GTCACTA-ACAGGGACTGTTTTCCTAAT
1 TTTAAGTCCCCCAAACTTTCCCGTG-TTTTACAAAAGGTCACTAGA-AGGGACAATTTTCATAAT
1643422 TTTCCCATTTTACATG-TATGCTTT
64 TTTCCC-TTTT-C-TGTTATGCTTT
1643446 GTTTTTTGGT
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
106 1 0.01
107 27 0.36
108 35 0.46
109 11 0.14
110 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (106 bp):
TTTAAGTCCCCCAAACTTTCCCGTGTTTTACAAAAGGTCACTAGAAGGGACAATTTTCATAATTT
TCCCTTTTCTGTTATGCTTTATAATTTTTTGTATAATTTCG
Found at i:1643624 original size:51 final size:51
Alignment explanation
Indices: 1643569--1643669 Score: 125
Period size: 51 Copynumber: 2.0 Consensus size: 51
1643559 TTTTAATTTA
* *
1643569 GTCACTGTTAATTTCTGATTTAGCTACTATTA-TTTTAATTT-TTGCATTTTG
1 GTCACTATTAATTTCTGATTTAACTACTA--ACTTTTAATTTCTTGCATTTTG
* * *
1643620 GTCACTATTTATTTCTTATTTAACTACTAACTTTTATTTTCTTGCATTTT
1 GTCACTATTAATTTCTGATTTAACTACTAACTTTTAATTTCTTGCATTTT
1643670 AGTAGCTGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
49 1 0.02
50 8 0.19
51 34 0.79
ACGTcount: A:0.22, C:0.14, G:0.08, T:0.56
Consensus pattern (51 bp):
GTCACTATTAATTTCTGATTTAACTACTAACTTTTAATTTCTTGCATTTTG
Found at i:1643766 original size:19 final size:17
Alignment explanation
Indices: 1643724--1643772 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
1643714 GTTTATTTTA
*
1643724 TTTTAATTTTTTACTAT
1 TTTTTATTTTTTACTAT
*
1643741 TTTTTATTTTTTTCTAT
1 TTTTTATTTTTTACTAT
1643758 TATTGTTATTTTTTA
1 T-TT-TTATTTTTTA
1643773 TAATTAGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 16 0.59
18 2 0.07
19 9 0.33
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTTATTTTTTACTAT
Found at i:1649627 original size:16 final size:18
Alignment explanation
Indices: 1649606--1649640 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1649596 TAATCAATAA
1649606 AATATTA-AAAAT-TCGT
1 AATATTACAAAATCTCGT
1649622 AATATTACAAAATCTCGT
1 AATATTACAAAATCTCGT
1649640 A
1 A
1649641 TAAGAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 5 0.29
18 5 0.29
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (18 bp):
AATATTACAAAATCTCGT
Found at i:1652727 original size:2 final size:2
Alignment explanation
Indices: 1652720--1652755 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1652710 ATTTCCATAC
1652720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1652756 CAATATTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1653044 original size:19 final size:19
Alignment explanation
Indices: 1653020--1653068 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1653010 TCTATGCTAG
*
1653020 GGTACCGATACCCCACTTA
1 GGTACCGATACCCCACTCA
1653039 GGTACCGATACCCCACTCA
1 GGTACCGATACCCCACTCA
1653058 GGTACCGATAC
1 GGTACCGATAC
1653069 TAATATTAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.27, C:0.37, G:0.18, T:0.18
Consensus pattern (19 bp):
GGTACCGATACCCCACTCA
Found at i:1659232 original size:12 final size:12
Alignment explanation
Indices: 1659211--1659247 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1659201 TCAAAGGGGG
*
1659211 GAACAAGAACAA
1 GAACAGGAACAA
*
1659223 GAACAGGAACAG
1 GAACAGGAACAA
1659235 GAACAGGAACAA
1 GAACAGGAACAA
1659247 G
1 G
1659248 TTTTGGGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.57, C:0.16, G:0.27, T:0.00
Consensus pattern (12 bp):
GAACAGGAACAA
Found at i:1659233 original size:18 final size:18
Alignment explanation
Indices: 1659210--1659245 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1659200 ATCAAAGGGG
1659210 GGAACAAGAACAAGAACA
1 GGAACAAGAACAAGAACA
* *
1659228 GGAACAGGAACAGGAACA
1 GGAACAAGAACAAGAACA
1659246 AGTTTTGGGG
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:0.56, C:0.17, G:0.28, T:0.00
Consensus pattern (18 bp):
GGAACAAGAACAAGAACA
Found at i:1662352 original size:25 final size:25
Alignment explanation
Indices: 1662318--1662383 Score: 132
Period size: 25 Copynumber: 2.6 Consensus size: 25
1662308 GGATCCGTTC
1662318 ACACGCAGTGTAAAATTCTTAGTTT
1 ACACGCAGTGTAAAATTCTTAGTTT
1662343 ACACGCAGTGTAAAATTCTTAGTTT
1 ACACGCAGTGTAAAATTCTTAGTTT
1662368 ACACGCAGTGTAAAAT
1 ACACGCAGTGTAAAAT
1662384 CCTTGTGATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (25 bp):
ACACGCAGTGTAAAATTCTTAGTTT
Found at i:1662920 original size:16 final size:16
Alignment explanation
Indices: 1662899--1662960 Score: 56
Period size: 18 Copynumber: 3.8 Consensus size: 16
1662889 AGTTTTAATT
*
1662899 ATTAAAGTAAAACAAA
1 ATTAAAGTAAAAGAAA
*
1662915 ATTAAA-T-TAAGAAA
1 ATTAAAGTAAAAGAAA
1662929 ATATAAAGTAAAAGAAA
1 AT-TAAAGTAAAAGAAA
*
1662946 ACTTTAAATTAAAAG
1 A--TTAAAGTAAAAG
1662961 GGTTTAAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 7 0.19
15 5 0.14
16 7 0.19
17 7 0.19
18 10 0.27
19 1 0.03
ACGTcount: A:0.65, C:0.03, G:0.08, T:0.24
Consensus pattern (16 bp):
ATTAAAGTAAAAGAAA
Found at i:1663692 original size:20 final size:20
Alignment explanation
Indices: 1663663--1663715 Score: 90
Period size: 19 Copynumber: 2.7 Consensus size: 20
1663653 AGTGTTATTC
*
1663663 ATTTTCGTGATTTTTTTGGT
1 ATTTTTGTGATTTTTTTGGT
1663683 ATTTTTGTGA-TTTTTTGGT
1 ATTTTTGTGATTTTTTTGGT
1663702 ATTTTTGTGATTTT
1 ATTTTTGTGATTTT
1663716 CTTCGTATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 19 0.61
20 12 0.39
ACGTcount: A:0.11, C:0.02, G:0.19, T:0.68
Consensus pattern (20 bp):
ATTTTTGTGATTTTTTTGGT
Found at i:1664146 original size:16 final size:16
Alignment explanation
Indices: 1664124--1664164 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1664114 GACTTTGTCC
1664124 GAAAAAATATAAAAAT
1 GAAAAAATATAAAAAT
*
1664140 TAAAAAAT-TAAAAAT
1 GAAAAAATATAAAAAT
1664155 GAAATAAATA
1 GAAA-AAATA
1664165 AATAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (16 bp):
GAAAAAATATAAAAAT
Found at i:1664308 original size:35 final size:36
Alignment explanation
Indices: 1664264--1664456 Score: 166
Period size: 35 Copynumber: 5.4 Consensus size: 36
1664254 ACCCATATAC
* *
1664264 TATACGTTTTCAAAACCATTTCAAAAACTATATTA-
1 TATATGTTTTCAAAACAATTTCAAAAACTATATTAT
* *
1664299 TATATGTTTTCAAAACCATTTTC-AAAACTATA-CAT
1 TATATGTTTTCAAAA-CAATTTCAAAAACTATATTAT
* ** * *
1664334 TATACGTTTTCAAAATTATTTTAAAAACTATA-TAC
1 TATATGTTTTCAAAACAATTTCAAAAACTATATTAT
**
1664369 TATATGTTTTCAAAACAATTTTTAAAACTATA-TAT
1 TATATGTTTTCAAAACAATTTCAAAAACTATATTAT
* *
1664404 TATACAT-TTTTAAAAATAAGTTTCCAAAAACTAT-TTAT
1 TAT--ATGTTTTCAAAACAA-TTT-CAAAAACTATATTAT
*
1664442 TATATATTTTCAAAA
1 TATATGTTTTCAAAA
1664457 ACTATTTTTG
Statistics
Matches: 128, Mismatches: 21, Indels: 16
0.78 0.13 0.10
Matches are distributed among these distances:
34 4 0.03
35 80 0.62
36 17 0.13
37 13 0.10
38 14 0.11
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.42
Consensus pattern (36 bp):
TATATGTTTTCAAAACAATTTCAAAAACTATATTAT
Found at i:1664377 original size:70 final size:69
Alignment explanation
Indices: 1664264--1664456 Score: 233
Period size: 70 Copynumber: 2.7 Consensus size: 69
1664254 ACCCATATAC
** *
1664264 TATACGTTTTCAAAACCATTTCAAAAACTATATTATATATGTTTTCAAAACCATTTTCAAAACTA
1 TATACGTTTTCAAAATAATTTCAAAAACTATA-TATATATGTTTTCAAAACAATTTTCAAAACTA
1664329 TACAT
65 TACAT
* * *
1664334 TATACGTTTTCAAAATTATTTTAAAAACTATATACTATATGTTTTCAAAACAATTTTTAAAACTA
1 TATACGTTTTCAAAATAATTTCAAAAACTATATA-TATATGTTTTCAAAACAATTTTCAAAACTA
*
1664399 TATAT
65 TACAT
* * * *
1664404 TATACATTTTTAAAAATAAGTTTCCAAAAACTATTTATTATATATTTTCAAAA
1 TATAC-GTTTTCAAAATAA-TTT-CAAAAACTATATA-TATATGTTTTCAAAA
1664457 ACTATTTTTG
Statistics
Matches: 106, Mismatches: 13, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
69 2 0.02
70 66 0.62
71 10 0.09
72 3 0.03
73 25 0.24
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.42
Consensus pattern (69 bp):
TATACGTTTTCAAAATAATTTCAAAAACTATATATATATGTTTTCAAAACAATTTTCAAAACTAT
ACAT
Found at i:1672622 original size:24 final size:24
Alignment explanation
Indices: 1672595--1672642 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1672585 TACAGCAATC
**
1672595 GAGGCTTGTGGTTTTGTAGCGGAT
1 GAGGCTTGTACTTTTGTAGCGGAT
1672619 GAGGCTTGTACTTTTGTAGCGGAT
1 GAGGCTTGTACTTTTGTAGCGGAT
1672643 AAGTCCCCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (24 bp):
GAGGCTTGTACTTTTGTAGCGGAT
Found at i:1676042 original size:35 final size:35
Alignment explanation
Indices: 1675981--1676047 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
1675971 CGAAAATTAA
* *
1675981 TTTTAAAAATTATATACTATATGTTTTCAAAACCG
1 TTTTAAAAACTATATACTATAAGTTTTCAAAACCG
* * *
1676016 TTTTTAAAACTATATATTATAAGTTTTTAAAA
1 TTTTAAAAACTATATACTATAAGTTTTCAAAA
1676048 ATAAGTTTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.46
Consensus pattern (35 bp):
TTTTAAAAACTATATACTATAAGTTTTCAAAACCG
Found at i:1679014 original size:14 final size:14
Alignment explanation
Indices: 1678924--1679016 Score: 53
Period size: 14 Copynumber: 6.5 Consensus size: 14
1678914 TTTTTATTTA
*
1678924 TTTAATGTTAGTCC
1 TTTAATTTTAGTCC
* *
1678938 TTTAATTTCA-TAAC
1 TTTAATTTTAGT-CC
* *
1678952 TTTAATTTTTTGTCT
1 TTTAA-TTTTAGTCC
* * *
1678967 TTTTATTTTTGCCC
1 TTTAATTTTAGTCC
* * *
1678981 TTTATTTTTCAATAC
1 TTTAATTTT-AGTCC
1678996 TTTAATTTTAGTCC
1 TTTAATTTTAGTCC
1679010 TTTAATT
1 TTTAATT
1679017 ATTATGTTTT
Statistics
Matches: 56, Mismatches: 19, Indels: 8
0.67 0.23 0.10
Matches are distributed among these distances:
13 1 0.02
14 38 0.68
15 16 0.29
16 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.05, T:0.60
Consensus pattern (14 bp):
TTTAATTTTAGTCC
Found at i:1686286 original size:99 final size:98
Alignment explanation
Indices: 1686020--1686306 Score: 295
Period size: 99 Copynumber: 3.0 Consensus size: 98
1686010 ATTGTGACAA
* * ** **
1686020 CCAAATCTCTTCAATGCAGATGAGCAGTGTCGTCTCC-AGATTGAACTGGTGTCCTCAGAGAGAA
1 CCAAATCTCTTCAATGCAGATGAGCAGTGTCGTTTCCAAGATTGACCTGACGTCCTTGGAGAGAA
* *
1686084 AGAACAGTGTCA-A--C-ACTT--GAAAA-TGG
66 AGAACAGTGTCATATTCAATTTACCAAAAGTGG
* * * * * *
1686110 CCAAATCTCTTCAATGCGGATGAGCAATGTCATTTCCAAGATTGACCCGACGTCC-TGATAGAAA
1 CCAAATCTCTTCAATGCAGATGAGCAGTGTCGTTTCCAAGATTGACCTGACGTCCTTG-GAGAGA
*
1686174 AAGAACAATGTCATATTCAATTTAACCAAAAGTGG
65 AAGAACAGTGTCATATTCAATTT-ACCAAAAGTGG
* * *
1686209 CTATATCTCTTCAATGCAGATGAGCAGTGTTGTTTCCAAGATTGACCTGACGTCCTTGGAGAGAA
1 CCAAATCTCTTCAATGCAGATGAGCAGTGTCGTTTCCAAGATTGACCTGACGTCCTTGGAGAGAA
* * *
1686274 TGAACAGGGTCATATTCAATTCACCCAAAAGTG
66 AGAACAGTGTCATATTCAATTTA-CCAAAAGTG
1686307 AAAAAATCTA
Statistics
Matches: 157, Mismatches: 28, Indels: 15
0.79 0.14 0.08
Matches are distributed among these distances:
90 33 0.21
91 29 0.18
92 1 0.01
94 1 0.01
95 3 0.02
98 5 0.03
99 83 0.53
100 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (98 bp):
CCAAATCTCTTCAATGCAGATGAGCAGTGTCGTTTCCAAGATTGACCTGACGTCCTTGGAGAGAA
AGAACAGTGTCATATTCAATTTACCAAAAGTGG
Found at i:1686330 original size:99 final size:97
Alignment explanation
Indices: 1686112--1686338 Score: 222
Period size: 99 Copynumber: 2.3 Consensus size: 97
1686102 GAAAATGGCC
* *
1686112 AAATCTCTTCAATGCGGATGAGCAATGTCATTTCCAAGATTGACCCGACGTCCTGATAGAAAAAG
1 AAATCTATTCAAT--GGATGAGCAATGTCATTTCCAAGATTGACCCGACGTCCTGAGAGAAAAAG
* * ***
1686177 AACAATGTCATATTCAATTTAACCAAAAGTGGCT
64 AACAAGGTCATATTCAATTCAACCAAAAGTGAAA
* * * ** * * *
1686211 ATATCTCTTCAATGCAGATGAGCAGTGTTGTTTCCAAGATTGACCTGACGTCCTTG-GAGAGAAT
1 AAATCTATTCAATG--GATGAGCAATGTCATTTCCAAGATTGACCCGACGTCC-TGAGAGAAAAA
* *
1686275 GAACAGGGTCATATTCAATTCACCCAAAAGTGAAA
63 GAACAAGGTCATATTCAATTCAACCAAAAGTGAAA
*
1686310 AAATCTATTCAACATGGATGAGCATTGTC
1 AAATCTATTC-A-ATGGATGAGCAATGTC
1686339 GTCTTTAACA
Statistics
Matches: 104, Mismatches: 19, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
97 1 0.01
99 97 0.93
100 3 0.03
101 3 0.03
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (97 bp):
AAATCTATTCAATGGATGAGCAATGTCATTTCCAAGATTGACCCGACGTCCTGAGAGAAAAAGAA
CAAGGTCATATTCAATTCAACCAAAAGTGAAA
Found at i:1689458 original size:14 final size:14
Alignment explanation
Indices: 1689441--1689467 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1689431 TTTCCTAATC
1689441 TCTAACCACTAACT
1 TCTAACCACTAACT
1689455 TCTAACCACTAAC
1 TCTAACCACTAAC
1689468 AACTAACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.26
Consensus pattern (14 bp):
TCTAACCACTAACT
Found at i:1691426 original size:28 final size:29
Alignment explanation
Indices: 1691367--1691427 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
1691357 AAATTAAAAG
* * * *
1691367 TTTAGGGACTATATTTAAAGAAGTCTAAA
1 TTTAAGGACTAAATTAAAAGAAGACTAAA
*
1691396 TTTAAGGACTAAATTAAAAGAA-ACTAGA
1 TTTAAGGACTAAATTAAAAGAAGACTAAA
1691424 TTTA
1 TTTA
1691428 GAAATTTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.33
Consensus pattern (29 bp):
TTTAAGGACTAAATTAAAAGAAGACTAAA
Found at i:1693746 original size:20 final size:20
Alignment explanation
Indices: 1693717--1693755 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1693707 TTCCAAAGTG
1693717 ATGCACCGATGCAACAATTC
1 ATGCACCGATGCAACAATTC
* *
1693737 ATGCATCGATGCACCAATT
1 ATGCACCGATGCAACAATT
1693756 AATTTTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.23
Consensus pattern (20 bp):
ATGCACCGATGCAACAATTC
Found at i:1696897 original size:12 final size:12
Alignment explanation
Indices: 1696882--1696941 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
1696872 CAGAAATAAA
1696882 AACAGAATTCAG
1 AACAGAATTCAG
*
1696894 AACA-AATATCAT
1 AACAGAAT-TCAG
*
1696906 AACAGAATCCAG
1 AACAGAATTCAG
* *
1696918 ATCAGAAATCAG
1 AACAGAATTCAG
*
1696930 AACAAAATTCAG
1 AACAGAATTCAG
1696942 GTCATGTATC
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
11 3 0.08
12 31 0.84
13 3 0.08
ACGTcount: A:0.53, C:0.18, G:0.12, T:0.17
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:1696910 original size:24 final size:24
Alignment explanation
Indices: 1696872--1696941 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
1696862 ACGGAGATAT
* *
1696872 CAGAAATAAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * *
1696896 CA-AATATCATAACAGAATCCAGAT
1 CAGAA-ATCAGAACAGAATTCAGAA
*
1696920 CAGAAATCAGAACAAAATTCAG
1 CAGAAATCAGAACAGAATTCAG
1696942 GTCATGTATC
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 2 0.05
24 33 0.89
25 2 0.05
ACGTcount: A:0.56, C:0.17, G:0.11, T:0.16
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:1696976 original size:24 final size:25
Alignment explanation
Indices: 1696922--1696978 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
1696912 ATCCAGATCA
* *
1696922 GAAATCAGAACAAAATTCAGGTCAT
1 GAAATCAGAACAAAATTCAAGTCAG
* *
1696947 G-TATCAGAACATAATTCAAGTC-G
1 GAAATCAGAACAAAATTCAAGTCAG
1696970 GAAATCAGA
1 GAAATCAGA
1696979 TAAAATATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 1 0.04
24 24 0.92
25 1 0.04
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.21
Consensus pattern (25 bp):
GAAATCAGAACAAAATTCAAGTCAG
Found at i:1698776 original size:36 final size:36
Alignment explanation
Indices: 1698729--1698801 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
1698719 GATAAATTAT
1698729 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
*
1698765 AATCTACATATCGATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1698801 A
1 A
1698802 TTCCAAAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.41
Consensus pattern (36 bp):
AATCTACATATCCATGGCTGATTCTTTTATCACTTA
Found at i:1701604 original size:24 final size:24
Alignment explanation
Indices: 1701570--1701623 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1701560 ACGGAGATAT
* * *
1701570 CAGAATTCAGAACAGATATCATAA
1 CAGAATCCAGAACAGAAATCAGAA
*
1701594 CAGAATCCAGATCAGAAATCAGAA
1 CAGAATCCAGAACAGAAATCAGAA
1701618 CAGAAT
1 CAGAAT
1701624 TCAGGTCATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.17
Consensus pattern (24 bp):
CAGAATCCAGAACAGAAATCAGAA
Found at i:1701627 original size:12 final size:12
Alignment explanation
Indices: 1701570--1701627 Score: 64
Period size: 12 Copynumber: 4.8 Consensus size: 12
1701560 ACGGAGATAT
1701570 CAGAATTCAGAA
1 CAGAATTCAGAA
*
1701582 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* *
1701594 CAGAATCCAGAT
1 CAGAATTCAGAA
*
1701606 CAGAAATCAGAA
1 CAGAATTCAGAA
1701618 CAGAATTCAG
1 CAGAATTCAG
1701628 GTCATGTATC
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
11 2 0.06
12 32 0.89
13 2 0.06
ACGTcount: A:0.48, C:0.19, G:0.16, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1701662 original size:24 final size:25
Alignment explanation
Indices: 1701587--1701664 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 25
1701577 CAGAACAGAT
* *
1701587 ATCATAACAGAA-TCCAGATCA-GAA
1 ATCAGAACAGAATTCAAG-TCAGGAA
* * *
1701611 ATCAGAACAGAATTCAGGTCATG-T
1 ATCAGAACAGAATTCAAGTCAGGAA
*
1701635 ATCAGAACATAATTCAAGTC-GGAA
1 ATCAGAACAGAATTCAAGTCAGGAA
1701659 ATCAGA
1 ATCAGA
1701665 TAAAATATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
23 1 0.02
24 38 0.88
25 4 0.09
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.21
Consensus pattern (25 bp):
ATCAGAACAGAATTCAAGTCAGGAA
Found at i:1703465 original size:36 final size:36
Alignment explanation
Indices: 1703418--1703490 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
1703408 GATAAATTAT
1703418 AATCTACATATCCATGACTGATTCTTTTATCACTTA
1 AATCTACATATCCATGACTGATTCTTTTATCACTTA
* **
1703454 AATCTACATATCGATGGTTGATTCTTTTATCACTTA
1 AATCTACATATCCATGACTGATTCTTTTATCACTTA
1703490 A
1 A
1703491 TTCCAGAACT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.42
Consensus pattern (36 bp):
AATCTACATATCCATGACTGATTCTTTTATCACTTA
Found at i:1704166 original size:13 final size:13
Alignment explanation
Indices: 1704148--1704172 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1704138 AACGTCGGTT
1704148 AACGGGTCGGGTC
1 AACGGGTCGGGTC
1704161 AACGGGTCGGGT
1 AACGGGTCGGGT
1704173 TGGGTTGTAA
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:0.16, C:0.20, G:0.48, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTC
Found at i:1706972 original size:122 final size:122
Alignment explanation
Indices: 1706829--1707105 Score: 330
Period size: 122 Copynumber: 2.3 Consensus size: 122
1706819 AATTTAACGT
**
1706829 TATG-TTTTGAAAAAAAATTGAAAGTTTTGGTACTAAAAC-GATCAAAAACTGATAATTTAGATA
1 TATGATTTTG-AAAAAAATTGAAAGTTTAAGTACTAAAACAGATC-AAAACTGATAATTTAGATA
*
1706892 CTAAACACATTAAACTTTTAACAACA-AATATTAAAATGAAACAAAAACTAAATATTAGG
64 CTAAACACATTAAACTTTTAACAACAGAATACT-AAATGAAACAAAAACTAAATATTAGG
* * * *
1706951 TATGATTTTGAAAAAAATTGAAAGTTTAAGTACTAAAACAGATCGAAATTGATAGTTTAGGTACT
1 TATGATTTTGAAAAAAATTGAAAGTTTAAGTACTAAAACAGATCAAAACTGATAATTTAGATACT
** * ** * **
1707016 AAATGCGTTAAGGTTTTAACAATAGGGTACTAAATGAAACAAAAACTAAATATTAGG
66 AAACACATTAAACTTTTAACAACAGAATACTAAATGAAACAAAAACTAAATATTAGG
* * *
1707073 TAT-AATTT-AAAAAAAATAAAAGTTTAAGTACTA
1 TATGATTTTGAAAAAAATTGAAAGTTTAAGTACTA
1707106 TATCATACCA
Statistics
Matches: 134, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
120 23 0.17
121 4 0.03
122 95 0.71
123 12 0.09
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (122 bp):
TATGATTTTGAAAAAAATTGAAAGTTTAAGTACTAAAACAGATCAAAACTGATAATTTAGATACT
AAACACATTAAACTTTTAACAACAGAATACTAAATGAAACAAAAACTAAATATTAGG
Found at i:1717656 original size:34 final size:33
Alignment explanation
Indices: 1717618--1717684 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
1717608 GTAATAAACA
1717618 AAATTAAGCAAAATAAATTAACAA-AAAGTCCAAC
1 AAATTAAGCAAAATAAATTAA-AATAAA-TCCAAC
* *
1717652 AAATTTATCAAAATAAATTAAAATAAATCCAAC
1 AAATTAAGCAAAATAAATTAAAATAAATCCAAC
1717685 CATATTAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 8 0.27
34 22 0.73
ACGTcount: A:0.61, C:0.13, G:0.03, T:0.22
Consensus pattern (33 bp):
AAATTAAGCAAAATAAATTAAAATAAATCCAAC
Found at i:1717940 original size:12 final size:12
Alignment explanation
Indices: 1717922--1717953 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1717912 ATCATCATCA
1717922 TCATCGTCGTCG
1 TCATCGTCGTCG
*
1717934 TCCTCGTCGTCG
1 TCATCGTCGTCG
1717946 TCATCGTC
1 TCATCGTC
1717954 CTGATCAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.38, G:0.22, T:0.34
Consensus pattern (12 bp):
TCATCGTCGTCG
Found at i:1718277 original size:33 final size:33
Alignment explanation
Indices: 1718216--1718278 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
1718206 GCCTCCATGA
* **
1718216 GGGGTCATAAAACTCTGTGAAGGTGGCGGCGGC
1 GGGGTCATAAAACTCGGTGAAGACGGCGGCGGC
1718249 GGGGTCATAAAA-TCAGGTGAAGACGGCGGC
1 GGGGTCATAAAACTC-GGTGAAGACGGCGGC
1718279 AACATCTGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 2 0.08
33 24 0.92
ACGTcount: A:0.25, C:0.17, G:0.41, T:0.16
Consensus pattern (33 bp):
GGGGTCATAAAACTCGGTGAAGACGGCGGCGGC
Found at i:1720040 original size:21 final size:21
Alignment explanation
Indices: 1720011--1720091 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 21
1720001 ATCTGCAAAA
*
1720011 AAATTAATTAAATAAAATATT
1 AAATAAATTAAATAAAATATT
*
1720032 AAATAAATTAAAT---A-CTT
1 AAATAAATTAAATAAAATATT
1720049 AAATAAATTAAATACAAAATATT
1 AAATAAATTAAAT--AAAATATT
1720072 -AA-AAATATATAATAAAATAT
1 AAATAAAT-TA-AATAAAATAT
1720092 ACCTTAGACA
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
17 15 0.31
18 1 0.02
21 23 0.47
22 5 0.10
23 5 0.10
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATAAATTAAATAAAATATT
Found at i:1720041 original size:9 final size:9
Alignment explanation
Indices: 1720011--1720062 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
1720001 ATCTGCAAAA
*
1720011 AAATTAATT
1 AAATTAAAT
1720020 AAA-TAAA-
1 AAATTAAAT
*
1720027 ATATTAAAT
1 AAATTAAAT
1720036 AAATTAAAT
1 AAATTAAAT
*
1720045 -ACTTAAAT
1 AAATTAAAT
1720053 AAATTAAAT
1 AAATTAAAT
1720062 A
1 A
1720063 CAAAATATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 2 0.06
8 14 0.40
9 19 0.54
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
AAATTAAAT
Found at i:1720043 original size:17 final size:17
Alignment explanation
Indices: 1720008--1720060 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
1719998 TATATCTGCA
* *
1720008 AAAAAATTAATTAAA-T
1 AAAATATTAAATAAATT
1720024 AAAATATTAAATAAATT
1 AAAATATTAAATAAATT
1720041 -AAATACTTAAATAAATT
1 AAAATA-TTAAATAAATT
1720058 AAA
1 AAA
1720061 TACAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 18 0.56
17 12 0.38
18 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATATTAAATAAATT
Found at i:1720061 original size:17 final size:17
Alignment explanation
Indices: 1720014--1720063 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
1720004 TGCAAAAAAA
* *
1720014 TTAATTAAATAAAATA-
1 TTAAATAAATTAAATAC
1720030 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
1720047 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
1720064 AAAATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:1725585 original size:15 final size:15
Alignment explanation
Indices: 1725565--1725598 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1725555 TCATATAGTG
1725565 TCACCCTATCATGTA
1 TCACCCTATCATGTA
1725580 TCACCCTATCATGTA
1 TCACCCTATCATGTA
1725595 TCAC
1 TCAC
1725599 TTATGCAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.35, G:0.06, T:0.32
Consensus pattern (15 bp):
TCACCCTATCATGTA
Found at i:1727967 original size:28 final size:29
Alignment explanation
Indices: 1727927--1727986 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
1727917 TTGGGCATTT
*
1727927 TGAAGGCTCACATCAACATGAA-AAATGA
1 TGAAGGCTCACATCAACAAGAACAAATGA
*
1727955 TGAAGGCTCACATTAACAAGAAGCAAATGA
1 TGAAGGCTCACATCAACAAGAA-CAAATGA
1727985 TG
1 TG
1727987 GGGCATGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 20 0.71
30 8 0.29
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (29 bp):
TGAAGGCTCACATCAACAAGAACAAATGA
Found at i:1729313 original size:47 final size:48
Alignment explanation
Indices: 1729244--1729354 Score: 181
Period size: 47 Copynumber: 2.4 Consensus size: 48
1729234 TTTGATTTTC
*
1729244 ACGGAAGAGTAGTGGAACAAATTCTTCTTATTTCAGATTTAGTCTGT-
1 ACGGAAGAGTAGTGGAACAAATTCTTCTTATTTCAGATTTAGTCTCTG
* *
1729291 ACGGAAAAGTAGTGGAACAAATTCTTCTTATTTCAGATTTGGTCTCTG
1 ACGGAAGAGTAGTGGAACAAATTCTTCTTATTTCAGATTTAGTCTCTG
1729339 A-GGAAGAGTAGTGGAA
1 ACGGAAGAGTAGTGGAA
1729355 GTGAATCAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
47 58 0.98
48 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (48 bp):
ACGGAAGAGTAGTGGAACAAATTCTTCTTATTTCAGATTTAGTCTCTG
Found at i:1729490 original size:36 final size:36
Alignment explanation
Indices: 1729419--1729773 Score: 419
Period size: 36 Copynumber: 9.8 Consensus size: 36
1729409 TATTTCAAAT
* * *
1729419 TTAGCCTCCACGAAAGAGTAGTAAACCGAAA-TCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGC-AAAGTCATC
* * * *
1729455 CTATCCTTCACGGAAGAGTAGTGAAACAAAGTCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
* *
1729491 TTAGCCTTCACGAAAGAGTAGTGAAGCAAAGTCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
*
1729527 ATAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
*
1729563 TTAACCTCCACGGAAAGAGTAGTGAAGCAAAGTCATC
1 TTAGCCTCCACGG-AAGAGTAGTGAAGCAAAGTCATC
* *
1729600 TTAGCCTCCACGAAAGAGTAGTGAAACAAA-TCCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGT-CATC
* *
1729636 TTAGCCTTCACGGAAGAGTAGTGAAGCAAA-TCCATT
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGT-CATC
* *
1729672 TTAGCCTCCACGGAAGAGTAATGAAGCAAAGCCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
* **
1729708 TTAGTCTCCACGGAAGAGTAGTGAAGCAAAACCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
* * ***
1729744 ATAGCCTTCATAAAAAGAGTAGTGAAGCAA
1 TTAGCCTCCA-CGGAAGAGTAGTGAAGCAA
1729774 GAACAGATCA
Statistics
Matches: 279, Mismatches: 35, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
35 4 0.01
36 225 0.81
37 50 0.18
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (36 bp):
TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCATC
Found at i:1729697 original size:145 final size:144
Alignment explanation
Indices: 1729423--1729769 Score: 459
Period size: 145 Copynumber: 2.4 Consensus size: 144
1729413 TCAAATTTAG
* * * * *
1729423 CCTCCAC-GAAAGAGTAGTAAACCGAAATCATCCTATCCTTCACGGAAGAGTAGTGAAACAAAGT
1 CCTCCACGGAAAGAGTAGTGAAGC-AAATCATCATAGCCTTCACGAAAGAGTAGTGAAACAAAGT
*
1729487 CATCTTAGCCTTCACGAAAGAGTAGTGAAGCAAAGTCATCATAGCCTCCACGGAAGAGTAGTGAA
65 CATCTTAGCCTTCACGAAAGAGTAGTGAAGCAAAGTCATCATAGCCTCCACGGAAGAGTAATGAA
*
1729552 GCAAAGTCATCTTAA
130 GCAAAGCCATCTTAA
* *
1729567 CCTCCACGGAAAGAGTAGTGAAGCAAAGTCATCTTAGCCTCCACGAAAGAGTAGTGAAACAAA-T
1 CCTCCACGGAAAGAGTAGTGAAGCAAA-TCATCATAGCCTTCACGAAAGAGTAGTGAAACAAAGT
* **
1729631 CCATCTTAGCCTTCACGGAAGAGTAGTGAAGCAAA-TCCATTTTAGCCTCCACGGAAGAGTAATG
65 -CATCTTAGCCTTCACGAAAGAGTAGTGAAGCAAAGT-CATCATAGCCTCCACGGAAGAGTAATG
*
1729695 AAGCAAAGCCATCTTAG
128 AAGCAAAGCCATCTTAA
* * **
1729712 TCTCCACGG-AAGAGTAGTGAAGCAAAACCATCATAGCCTTCATAAAAAGAGTAGTGAA
1 CCTCCACGGAAAGAGTAGTGAAGC-AAATCATCATAGCCTTCA-CGAAAGAGTAGTGAA
1729770 GCAAGAACAG
Statistics
Matches: 179, Mismatches: 18, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
144 38 0.21
145 141 0.79
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (144 bp):
CCTCCACGGAAAGAGTAGTGAAGCAAATCATCATAGCCTTCACGAAAGAGTAGTGAAACAAAGTC
ATCTTAGCCTTCACGAAAGAGTAGTGAAGCAAAGTCATCATAGCCTCCACGGAAGAGTAATGAAG
CAAAGCCATCTTAA
Found at i:1729723 original size:181 final size:181
Alignment explanation
Indices: 1729419--1729773 Score: 500
Period size: 181 Copynumber: 2.0 Consensus size: 181
1729409 TATTTCAAAT
*
1729419 TTAGCCTCCACGAAAGAGTAGTAAACCGAAATCATCCTATCCTTCACGGAAGAGTAGTGAAACAA
1 TTAGCCTCCACGAAAGAGTAGTAAACCGAAATCATCCTAGCCTTCACGGAAGAGTAGTGAAACAA
* * *
1729484 AGTCATCTTAGCCTTCACGAAAGAGTAGTGAAGCAAAGTCATCATAGCCTCCACGGAAGAGTAGT
66 AGTCATCTTAGCCTCCACGAAAGAGTAATGAAGCAAAGCCATCATAGCCTCCACGGAAGAGTAGT
** * **
1729549 GAAGCAAAGTCATCTTAACCTCCACGGAAAGAGTAGTGAAGCAAAGTCATC
131 GAAGCAAAACCATCATAACCTCCACAAAAAGAGTAGTGAAGCAAAGTCATC
* *
1729600 TTAGCCTCCACGAAAGAGTAGTGAAA-C-AAATCCATCTTAGCCTTCACGGAAGAGTAGTGAAGC
1 TTAGCCTCCACGAAAGAGTAGT-AAACCGAAAT-CATCCTAGCCTTCACGGAAGAGTAGTGAAAC
* * * *
1729663 AAA-TCCATTTTAGCCTCCACGGAAGAGTAATGAAGCAAAGCCATCTTAGTCTCCACGGAAGAGT
64 AAAGT-CATCTTAGCCTCCACGAAAGAGTAATGAAGCAAAGCCATCATAGCCTCCACGGAAGAGT
* * *
1729727 AGTGAAGCAAAACCATCATAGCCTTCATAAAAAGAGTAGTGAAGCAA
128 AGTGAAGCAAAACCATCATAACCTCCACAAAAAGAGTAGTGAAGCAA
1729774 GAACAGATCA
Statistics
Matches: 153, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
180 5 0.03
181 145 0.95
182 3 0.02
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (181 bp):
TTAGCCTCCACGAAAGAGTAGTAAACCGAAATCATCCTAGCCTTCACGGAAGAGTAGTGAAACAA
AGTCATCTTAGCCTCCACGAAAGAGTAATGAAGCAAAGCCATCATAGCCTCCACGGAAGAGTAGT
GAAGCAAAACCATCATAACCTCCACAAAAAGAGTAGTGAAGCAAAGTCATC
Found at i:1735314 original size:30 final size:30
Alignment explanation
Indices: 1735241--1735336 Score: 104
Period size: 29 Copynumber: 3.2 Consensus size: 30
1735231 GATCAACGTG
*
1735241 AACTTGAAGGACTAAAATAGCCAAATA-AAA
1 AACTT-AAGGACTAAAATAGCCAAAAACAAA
** *
1735271 CCCTAAAGGACTAAAATAGCCAAAAACAAA
1 AACTTAAGGACTAAAATAGCCAAAAACAAA
* **
1735301 AACTTAGGGACTAAAATAGTAAAAAAACAAA
1 AACTTAAGGACTAAAATAG-CCAAAAACAAA
1735332 AACTT
1 AACTT
1735337 CATGGGCCAA
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
29 20 0.37
30 20 0.37
31 14 0.26
ACGTcount: A:0.57, C:0.16, G:0.11, T:0.16
Consensus pattern (30 bp):
AACTTAAGGACTAAAATAGCCAAAAACAAA
Found at i:1735330 original size:31 final size:30
Alignment explanation
Indices: 1735278--1735336 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
1735268 AAACCCTAAA
**
1735278 GGACTAAAATAGCCAAAAACAAAAACTTAG
1 GGACTAAAATAGAAAAAAACAAAAACTTAG
1735308 GGACTAAAATAGTAAAAAAACAAAAACTT
1 GGACTAAAATAG-AAAAAAACAAAAACTT
1735337 CATGGGCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.59, C:0.14, G:0.12, T:0.15
Consensus pattern (30 bp):
GGACTAAAATAGAAAAAAACAAAAACTTAG
Found at i:1737077 original size:43 final size:40
Alignment explanation
Indices: 1737027--1737122 Score: 113
Period size: 40 Copynumber: 2.3 Consensus size: 40
1737017 ATAACTCGGT
* *
1737027 TCCTACGTGATGAGGACGA-CTGGTTATCTAGGGGTGACACGAC
1 TCCTACGTGATGAGGA-GATCTGG---TCGAGGGATGACACGAC
*
1737070 TCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACGGC
1 TCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACGAC
*
1737110 TCATACGTGATGA
1 TCCTACGTGATGA
1737123 AGAGTTCTAG
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 26 0.54
42 2 0.04
43 20 0.42
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.23
Consensus pattern (40 bp):
TCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACGAC
Found at i:1737141 original size:134 final size:134
Alignment explanation
Indices: 1736924--1737256 Score: 492
Period size: 134 Copynumber: 2.5 Consensus size: 134
1736914 GGTCGTATAT
* * **
1736924 GGGTGACTCGGCTCCTACGTGATGAGGAGATCTGGTC-AGGGGATGACATTGCTCATACGTGATG
1 GGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGA-GGGATGACACGGCTCATACGTGATG
* * * * * * *
1736988 AAGAGTTCTGGCCATCTTTAGGAGGGGTGATAACTCGGTTCCTACGTGATGAGGACGACTGGTTA
65 AAGAGTTCTAGCCATCTTTAGGAAGGATGATAACTCAGTTCCTACGCGATAAGGACAACTGGTTA
1737053 TCTAG
130 TCTAG
1737058 GGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACGGCTCATACGTGATGA
1 GGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACGGCTCATACGTGATGA
1737123 AGAGTTCTAGCCATCTTTAGGAAGGATGATAACTCAGTTCCTACGCGATAAGGACAACTGGTTAT
66 AGAGTTCTAGCCATCTTTAGGAAGGATGATAACTCAGTTCCTACGCGATAAGGACAACTGGTTAT
1737188 CTAG
131 CTAG
* * *
1737192 GGGTGATAC-AGCTCCTACGTGATGAGGAGATCTGGTCG-GTGGATGACACGGTTCCTACGTGAT
1 GGGTGACACGA-CTCCTACGTGATGAGGAGATCTGGTCGAG-GGATGACACGGCTCATACGTGAT
1737255 GA
64 GA
1737257 GGACGGTAGG
Statistics
Matches: 182, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
133 2 0.01
134 179 0.98
135 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (134 bp):
GGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACGGCTCATACGTGATGA
AGAGTTCTAGCCATCTTTAGGAAGGATGATAACTCAGTTCCTACGCGATAAGGACAACTGGTTAT
CTAG
Found at i:1737227 original size:43 final size:43
Alignment explanation
Indices: 1737027--1737227 Score: 133
Period size: 43 Copynumber: 4.6 Consensus size: 43
1737017 ATAACTCGGT
1737027 TCCTACGTGATGAGGACGA-CTGGTTATCTAGGGGTGACAC-GAC
1 TCCTACGTGATGAGGA-GATCTGGTTATCTAGGGGTGACACAG-C
* * *
1737070 TCCTACGTGATGAGGAGATCTGG---TCGAGGGATGACACGGC
1 TCCTACGTGATGAGGAGATCTGGTTATCTAGGGGTGACACAGC
* * * * ** * *
1737110 TCATACGTGATGAAGAGTTCTAGCCATCTTTAGGAAGGATGATAACTCAGT
1 TCCTACGTGATGAGGAGATCTGGTTATC--TAGG--GG-TG---ACACAGC
* * * * *
1737161 TCCTACGCGATAAGGACAACTGGTTATCTAGGGGTGATACAGC
1 TCCTACGTGATGAGGAGATCTGGTTATCTAGGGGTGACACAGC
1737204 TCCTACGTGATGAGGAGATCTGGT
1 TCCTACGTGATGAGGAGATCTGGT
1737228 CGGTGGATGA
Statistics
Matches: 117, Mismatches: 28, Indels: 26
0.68 0.16 0.15
Matches are distributed among these distances:
40 32 0.27
41 1 0.01
42 2 0.02
43 46 0.39
45 3 0.03
46 2 0.02
47 3 0.03
48 2 0.02
49 4 0.03
51 22 0.19
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (43 bp):
TCCTACGTGATGAGGAGATCTGGTTATCTAGGGGTGACACAGC
Found at i:1737367 original size:35 final size:34
Alignment explanation
Indices: 1737286--1737416 Score: 92
Period size: 35 Copynumber: 3.8 Consensus size: 34
1737276 AGGATAATGA
* *
1737286 TTTCAAGGGAAACCGACTCAAAGATTGGATTTTG
1 TTTCAAGGGAAACAGAATCAAAGATTGGATTTTG
* *
1737320 TTTCCAA-AGAAACAGAATCAAAGATTTTTG-TTTTG
1 TTT-CAAGGGAAACAGAATCAAAGA--TTGGATTTTG
*
1737355 TTTCAAGGGAAACA-AACTCACAGA-TGGTAAATTTTG
1 TTTCAAGGGAAACAGAA-TCAAAGATTGG---ATTTTG
* *
1737391 TTTCCAA-AGAAACAGACTCAAAGATT
1 TTT-CAAGGGAAACAGAATCAAAGATT
1737417 TTTCTCAAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
32 2 0.03
34 22 0.29
35 23 0.31
36 23 0.31
37 5 0.07
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (34 bp):
TTTCAAGGGAAACAGAATCAAAGATTGGATTTTG
Found at i:1737403 original size:36 final size:35
Alignment explanation
Indices: 1737301--1737415 Score: 101
Period size: 36 Copynumber: 3.3 Consensus size: 35
1737291 AGGGAAACCG
**
1737301 ACTCAAAGAT-TGGATTTTGTTTCCAAAGAAACAGA
1 ACTCAAAGATGTAAATTTTGTTTCCAAAGAAACA-A
* *** *
1737336 A-TCAAAGATTTTTGTTTTGTTT-CAAGGGAAACAA
1 ACTCAAAGATGTAAATTTTGTTTCCAA-AGAAACAA
* *
1737370 ACTCACAGATGGTAAATTTTGTTTCCAAAGAAACAG
1 ACTCAAAGAT-GTAAATTTTGTTTCCAAAGAAACAA
1737406 ACTCAAAGAT
1 ACTCAAAGAT
1737416 TTTTCTCAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
34 13 0.21
35 23 0.37
36 24 0.38
37 3 0.05
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (35 bp):
ACTCAAAGATGTAAATTTTGTTTCCAAAGAAACAA
Found at i:1737981 original size:100 final size:99
Alignment explanation
Indices: 1737801--1737982 Score: 267
Period size: 100 Copynumber: 1.8 Consensus size: 99
1737791 GGAAAAACTG
* * *
1737801 TCTCAAGCGAGATGAATTTGTTTTGAAAGAGATAATCTCAAGTGAGATTAATTTTGTTTCAAGTA
1 TCTCAAGCGAGATGAATTTGCTTTGAAAGAAATAATCTCAAGTGAGATTAATTTTGTTTCAAATA
* **
1737866 AAACAACTTTGAAATTTTTGTTCCGAGGGTATTA
66 AAACAAATTCAAAATTTTTGTTCCGAGGGTATTA
1737900 TCTCAAGCGAGATGAAATTTGCTTT-AAGAGAAATAATCTCAAGTGAGATTAATTTTGTTTCAAA
1 TCTCAAGCGAGATG-AATTTGCTTTGAA-AGAAATAATCTCAAGTGAGATTAATTTTGTTTCAAA
* *
1737964 TGAAATAAATTCAAAATTT
64 TAAAACAAATTCAAAATTT
1737983 GCATCTCAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
99 16 0.22
100 57 0.78
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (99 bp):
TCTCAAGCGAGATGAATTTGCTTTGAAAGAAATAATCTCAAGTGAGATTAATTTTGTTTCAAATA
AAACAAATTCAAAATTTTTGTTCCGAGGGTATTA
Found at i:1739732 original size:25 final size:22
Alignment explanation
Indices: 1739704--1739759 Score: 58
Period size: 25 Copynumber: 2.4 Consensus size: 22
1739694 AATTTTGAAA
1739704 AAAAATATCAATTAAAAGAATTTTG
1 AAAAATATCAA-TAAAA-AA-TTTG
* *
1739729 AAAAATGTTTAATAAAAAATTTG
1 AAAAAT-ATCAATAAAAAATTTG
1739752 AAAAATAT
1 AAAAATAT
1739760 TACCCCTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 1 0.04
23 10 0.37
24 2 0.07
25 11 0.41
26 3 0.11
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (22 bp):
AAAAATATCAATAAAAAATTTG
Done.