Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008173.1 Hibiscus syriacus cultivar Beakdansim tig00110764_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: 490413
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:231244 original size:59 final size:59
Alignment explanation
Indices: 231117--231242 Score: 148
Period size: 59 Copynumber: 2.1 Consensus size: 59
231107 CAATCTGATG
* *
231117 ATCATTTTATAACTTCTAATAATTGAAAAACTCAACAAAATAATACCATATAATCAAAA
1 ATCATTTTATAACTTCTAATAATTCAAAAACTCAACAAAATAATACCATATAATAAAAA
* * ***
231176 ATTATTTTATAACTTAC-AATAA-TCAAAATACTTAACAAAATAATATTTTATAATAAAAAA
1 ATCATTTTATAACTT-CTAATAATTCAAAA-ACTCAACAAAATAATACCATATAAT-AAAAA
231236 ATCATTT
1 ATCATTT
231243 ATTTACTTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 5 0.09
59 40 0.71
60 11 0.20
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35
Consensus pattern (59 bp):
ATCATTTTATAACTTCTAATAATTCAAAAACTCAACAAAATAATACCATATAATAAAAA
Found at i:231939 original size:28 final size:27
Alignment explanation
Indices: 231890--231942 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
231880 TATGATTTTG
*
231890 AAAAAAATAAAGTTTGAATACTAAAAC
1 AAAAAAATAAAATTTGAATACTAAAAC
231917 AAAAAAATAATAATTT-AAGTACTAAA
1 AAAAAAATAA-AATTTGAA-TACTAAA
231943 GAGGCGTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.25
Consensus pattern (27 bp):
AAAAAAATAAAATTTGAATACTAAAAC
Found at i:233012 original size:21 final size:21
Alignment explanation
Indices: 232986--233030 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
232976 GATTTCTGGG
* *
232986 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
233007 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
233028 CAA
1 CAA
233031 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:234197 original size:14 final size:14
Alignment explanation
Indices: 234178--234205 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
234168 GAAAAGAAGC
234178 TATGTGATACGTGA
1 TATGTGATACGTGA
234192 TATGTGATACGTGA
1 TATGTGATACGTGA
234206 ATTACAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TATGTGATACGTGA
Found at i:234415 original size:63 final size:62
Alignment explanation
Indices: 234308--234429 Score: 183
Period size: 63 Copynumber: 2.0 Consensus size: 62
234298 GTCGAGGGTT
* *
234308 TACCTATGTTCTACGGAACATATGGACAGTTTTACCTATGTCTTTCGAGACATATGGACAATA
1 TACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGGTCTTT-GAGACATATGGACAATA
* *
234371 TACCTATGTTCTAAGGAACATATGGACAG-TTTACCTAGGTTCTTTGGGACCTATGGACA
1 TACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGG-TCTTTGAGACATATGGACA
234430 GTTGCCGAGG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
62 21 0.39
63 33 0.61
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (62 bp):
TACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGGTCTTTGAGACATATGGACAATA
Found at i:234426 original size:31 final size:31
Alignment explanation
Indices: 234305--234432 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
234295 AGAGTCGAGG
**
234305 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTTTGGAACATATGGACA
*
234336 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTTTGGA-ACATATGGACA
* * **
234368 ATATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTTTGGAACATATGGACA
* * *
234399 GTTTACCTAGGTTCTTTGGGACCTATGGACA
1 GTTTACCTATGTTCTTTGGAACATATGGACA
234430 GTT
1 GTT
234433 GCCGAGGTTC
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
31 53 0.67
32 26 0.33
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTTTGGAACATATGGACA
Found at i:234452 original size:30 final size:30
Alignment explanation
Indices: 234391--234466 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
234381 CTAAGGAACA
* *
234391 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTAGGACC
* *
234422 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
234452 TCTGGATAGTTACCG
1 TATGGACAGTTACCG
234467 GGGTCTGTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 29 0.76
31 9 0.24
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:234769 original size:2 final size:2
Alignment explanation
Indices: 234759--234820 Score: 106
Period size: 2 Copynumber: 31.0 Consensus size: 2
234749 GTATGTGTGG
*
234759 AT AT GT 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
*
234801 AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT
234821 GAAAGGTGCA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:237701 original size:21 final size:21
Alignment explanation
Indices: 237675--237719 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
237665 GATTTCTGGG
* *
237675 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
237696 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
237717 CAA
1 CAA
237720 ACGACATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:237789 original size:23 final size:22
Alignment explanation
Indices: 237745--237789 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
237735 AATGCCAGAG
*
237745 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
237767 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
237790 AAATGTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:238528 original size:15 final size:17
Alignment explanation
Indices: 238500--238534 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
238490 GATATAAGCA
238500 ATGTGACTATAAGT-AT
1 ATGTGACTATAAGTGAT
238516 ATGTG-CTATAAGTGAT
1 ATGTGACTATAAGTGAT
238532 ATG
1 ATG
238535 ACTTATAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (17 bp):
ATGTGACTATAAGTGAT
Found at i:238899 original size:14 final size:14
Alignment explanation
Indices: 238880--238907 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
238870 GAAAAGAAGC
238880 TATGTGATACGTGA
1 TATGTGATACGTGA
238894 TATGTGATACGTGA
1 TATGTGATACGTGA
238908 ATTACAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TATGTGATACGTGA
Found at i:239117 original size:63 final size:62
Alignment explanation
Indices: 239010--239131 Score: 183
Period size: 63 Copynumber: 2.0 Consensus size: 62
239000 GTCGAGGGTT
* *
239010 TACCTATGTTCTACGGAACATATGGACAGTTTTACCTATGTCTTTCGAGACATATGGACAATA
1 TACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGGTCTTT-GAGACATATGGACAATA
* *
239073 TACCTATGTTCTAAGGAACATATGGACAG-TTTACCTAGGTTCTTTGGGACCTATGGACA
1 TACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGG-TCTTTGAGACATATGGACA
239132 GTTGCCGAGG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
62 21 0.39
63 33 0.61
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (62 bp):
TACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGGTCTTTGAGACATATGGACAATA
Found at i:239128 original size:31 final size:31
Alignment explanation
Indices: 239007--239134 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
238997 ATAGTCGAGG
**
239007 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTTTGGAACATATGGACA
*
239038 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTTTGGA-ACATATGGACA
* * **
239070 ATATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTTTGGAACATATGGACA
* * *
239101 GTTTACCTAGGTTCTTTGGGACCTATGGACA
1 GTTTACCTATGTTCTTTGGAACATATGGACA
239132 GTT
1 GTT
239135 GCCGAGGTTC
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
31 53 0.67
32 26 0.33
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTTTGGAACATATGGACA
Found at i:239154 original size:30 final size:30
Alignment explanation
Indices: 239093--239166 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
239083 CTAAGGAACA
* *
239093 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTAGGACC
* *
239124 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
239154 TCTGGATAGTTAC
1 TATGGACAGTTAC
239167 TGGGGTCTGT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 27 0.75
31 9 0.25
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:239470 original size:2 final size:2
Alignment explanation
Indices: 239460--239521 Score: 106
Period size: 2 Copynumber: 31.0 Consensus size: 2
239450 GTATGTGTGG
*
239460 AT AT GT 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
*
239502 AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT
239522 GAAAGGTGCA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:241885 original size:24 final size:25
Alignment explanation
Indices: 241858--241906 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
241848 ACATTTTAAT
*
241858 ACTAT-AAATAAAGATAAATTGAAA
1 ACTATAAAAAAAAGATAAATTGAAA
*
241882 ACTATAAAAAAAAGATATATTGAAA
1 ACTATAAAAAAAAGATAAATTGAAA
241907 GGGTCACACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.63, C:0.04, G:0.08, T:0.24
Consensus pattern (25 bp):
ACTATAAAAAAAAGATAAATTGAAA
Found at i:242326 original size:15 final size:15
Alignment explanation
Indices: 242306--242336 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
242296 AATTCTTAAC
242306 AAATCGAAACAAACT
1 AAATCGAAACAAACT
242321 AAATCGAAACAAACT
1 AAATCGAAACAAACT
242336 A
1 A
242337 CATGATACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.19, G:0.06, T:0.13
Consensus pattern (15 bp):
AAATCGAAACAAACT
Found at i:246657 original size:6 final size:7
Alignment explanation
Indices: 246618--246655 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
246608 GAAGCAGAAG
*
246618 AAAAAGT
1 AAAAATT
*
246625 AAAAA-A
1 AAAAATT
246631 AAAAATT
1 AAAAATT
246638 AAAAATT
1 AAAAATT
246645 AAAAATT
1 AAAAATT
246652 AAAA
1 AAAA
246656 TTCACAGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (7 bp):
AAAAATT
Found at i:247444 original size:14 final size:14
Alignment explanation
Indices: 247427--247460 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
247417 AATAGGTATA
247427 GAGAAAAGAAAAAG
1 GAGAAAAGAAAAAG
* *
247441 GAGAAAAGAGAGAG
1 GAGAAAAGAAAAAG
247455 GAGAAA
1 GAGAAA
247461 GTGGGATTTT
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:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (14 bp):
GAGAAAAGAAAAAG
Found at i:254747 original size:25 final size:26
Alignment explanation
Indices: 254719--254784 Score: 71
Period size: 32 Copynumber: 2.3 Consensus size: 26
254709 TGAAATACTT
254719 AAATACTT-CCAAGTTCGATAAATTC
1 AAATACTTACCAAGTTCGATAAATTC
254744 AAATACTTAAAACTACCAAGTTCGATAAATTC
1 AAATAC-T-----TACCAAGTTCGATAAATTC
254776 AAATACTTA
1 AAATACTTA
254785 AAAACTTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
25 6 0.18
26 3 0.09
31 2 0.06
32 23 0.68
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.30
Consensus pattern (26 bp):
AAATACTTACCAAGTTCGATAAATTC
Found at i:254749 original size:33 final size:32
Alignment explanation
Indices: 254702--254804 Score: 154
Period size: 33 Copynumber: 3.2 Consensus size: 32
254692 ACAAAGTTTA
*
254702 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAA-ACTTCCAAGTT
*
254734 CGATAAATTCAAATACTTAAAACTACCAAGTT
1 CGATAAATTCAAATACTTAAAACTTCCAAGTT
*
254766 CGATAAATTCAAATACTTAAAAACTTACAAGTT
1 CGATAAATTCAAATACTT-AAAACTTCCAAGTT
254799 CGATAA
1 CGATAA
254805 GTGAAACAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
32 32 0.49
33 33 0.51
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.30
Consensus pattern (32 bp):
CGATAAATTCAAATACTTAAAACTTCCAAGTT
Found at i:254824 original size:21 final size:21
Alignment explanation
Indices: 254799--254840 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
254789 CTTACAAGTT
254799 CGATAAGTGAAACAAAGTTTA
1 CGATAAGTGAAACAAAGTTTA
* *
254820 CGATAATTGAAATAAAGTTTA
1 CGATAAGTGAAACAAAGTTTA
254841 AAAATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.29
Consensus pattern (21 bp):
CGATAAGTGAAACAAAGTTTA
Found at i:257141 original size:21 final size:22
Alignment explanation
Indices: 257117--257160 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
257107 TTAAACCCAG
* *
257117 ACCGGGTTTTT-TCGGGTAAAA
1 ACCGAGTTTTTATCCGGTAAAA
*
257138 ACCGATTTTTTATCCGGTAAAA
1 ACCGAGTTTTTATCCGGTAAAA
257160 A
1 A
257161 AACCGGTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (22 bp):
ACCGAGTTTTTATCCGGTAAAA
Found at i:266103 original size:16 final size:16
Alignment explanation
Indices: 266082--266113 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
266072 CTCAATGACA
266082 ACGCCAAATTTAGTCT
1 ACGCCAAATTTAGTCT
*
266098 ACGCCAAGTTTAGTCT
1 ACGCCAAATTTAGTCT
266114 TAGTTAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (16 bp):
ACGCCAAATTTAGTCT
Found at i:266679 original size:19 final size:20
Alignment explanation
Indices: 266633--266681 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
266623 TTGTATATGG
266633 AATTT-TTAATAAAAATATA
1 AATTTATTAATAAAAATATA
* * *
266652 TAGTTATTAATATAAAT-TA
1 AATTTATTAATAAAAATATA
266671 AATTTATTAAT
1 AATTTATTAAT
266682 TTTATATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AATTTATTAATAAAAATATA
Found at i:280167 original size:17 final size:18
Alignment explanation
Indices: 280145--280182 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
280135 ATATAATTGT
280145 TTAATTAAA-ATTTTAAA
1 TTAATTAAATATTTTAAA
*
280162 TTAATTAAATTTTTTAAA
1 TTAATTAAATATTTTAAA
280180 TTA
1 TTA
280183 TTATGAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAATTAAATATTTTAAA
Found at i:285216 original size:30 final size:30
Alignment explanation
Indices: 285182--285243 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
285172 AAAATAAAAT
285182 AATTAAAAAATAAGATAAGTAAAACTACCC
1 AATTAAAAAATAAGATAAGTAAAACTACCC
285212 AATTAAAAAATAAGATAAGTAAAACTACCC
1 AATTAAAAAATAAGATAAGTAAAACTACCC
285242 AA
1 AA
285244 ATCGGTATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (30 bp):
AATTAAAAAATAAGATAAGTAAAACTACCC
Found at i:285234 original size:16 final size:16
Alignment explanation
Indices: 285171--285235 Score: 53
Period size: 16 Copynumber: 4.2 Consensus size: 16
285161 TAAATGACAG
* *
285171 AAAAATAAAATAATTA
1 AAAAATAAGATAAGTA
285187 AAAAATAAGATAAGT-
1 AAAAATAAGATAAGTA
* *** *
285202 AAAACT-ACCCAATTA
1 AAAAATAAGATAAGTA
285217 AAAAATAAGATAAGTA
1 AAAAATAAGATAAGTA
285233 AAA
1 AAA
285236 CTACCCAAAT
Statistics
Matches: 35, Mismatches: 12, Indels: 4
0.69 0.24 0.08
Matches are distributed among these distances:
14 4 0.11
15 10 0.29
16 21 0.60
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.20
Consensus pattern (16 bp):
AAAAATAAGATAAGTA
Found at i:288144 original size:8 final size:8
Alignment explanation
Indices: 288131--288156 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
288121 TGTTAGAAGA
288131 TAAATTTT
1 TAAATTTT
288139 TAAATTTT
1 TAAATTTT
288147 TAAATTTT
1 TAAATTTT
288155 TA
1 TA
288157 GAAGAGGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TAAATTTT
Found at i:292203 original size:16 final size:16
Alignment explanation
Indices: 292182--292222 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
292172 CCAGATCCTA
*
292182 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
292198 TGAATCATTTAGCACT
1 TGAATCATTCAGCACT
292214 T-AATCATTC
1 TGAATCATTC
292223 TCAAGTAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:301728 original size:3 final size:3
Alignment explanation
Indices: 301695--301771 Score: 109
Period size: 3 Copynumber: 24.7 Consensus size: 3
301685 ACGGGTTTTG
* *
301695 TAA TAT TAA TAAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
301743 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
301772 TAAATAAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
3 58 0.85
4 10 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:302042 original size:20 final size:20
Alignment explanation
Indices: 302019--302079 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
302009 GAATAAGCTC
302019 TTCTTATTATGAACTTTCTT
1 TTCTTATTATGAACTTTCTT
* *
302039 TTCTTCA-AATG-A-GTTC--
1 TTCTT-ATTATGAACTTTCTT
*
302055 TTCTCATTATGAACTTTCTT
1 TTCTTATTATGAACTTTCTT
302075 TTCTT
1 TTCTT
302080 CAGATGAGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 12
0.62 0.13 0.26
Matches are distributed among these distances:
15 1 0.03
16 7 0.24
17 1 0.03
18 6 0.21
19 1 0.03
20 12 0.41
21 1 0.03
ACGTcount: A:0.20, C:0.18, G:0.07, T:0.56
Consensus pattern (20 bp):
TTCTTATTATGAACTTTCTT
Found at i:302064 original size:36 final size:36
Alignment explanation
Indices: 302017--302106 Score: 162
Period size: 36 Copynumber: 2.5 Consensus size: 36
302007 TTGAATAAGC
*
302017 TCTTCTTATTATGAACTTTCTTTTCTTCAAATGAGT
1 TCTTCTCATTATGAACTTTCTTTTCTTCAAATGAGT
*
302053 TCTTCTCATTATGAACTTTCTTTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTTCTTTTCTTCAAATGAGT
302089 TCTTCTCATTATGAACTT
1 TCTTCTCATTATGAACTT
302107 GAACTGGAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.21, C:0.19, G:0.09, T:0.51
Consensus pattern (36 bp):
TCTTCTCATTATGAACTTTCTTTTCTTCAAATGAGT
Found at i:302703 original size:113 final size:113
Alignment explanation
Indices: 302052--302709 Score: 868
Period size: 113 Copynumber: 5.8 Consensus size: 113
302042 TTCAAATGAG
*
302052 TTCTTCTCATTATGAAC-T-TTCTT--TTCTTCAGATGAGTTCTTCTCATTATGAACTTGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCAACTG
*
302113 GAAAAGTTGATCTATCAAGTGAT-GAGTTTGAGCAAAAGGTTGAACAAA
66 GAAAAGTTGATCCATCAAGTGATGGA-TTTGAGCAAAAGGTTGAACAAA
*
302161 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGACGAGTTCTTCTCATTATGAAC-TCTA
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTC-A
* * * * * ** * * *
302225 CCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAG
62 ACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
*
302277 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC-TCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCAACT
* * *
302341 GGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
65 GGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
* * **
302390 TTCTTCTCATTATGAACTTCTTCATCATTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCAACTG
** * *
302455 GAAAAGCGGATCCATCAAGTGATGTATTTGAGCAAAAGGTTGAATAAA
66 GAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
*
302503 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTA-T
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCAACT
* * * *
302567 GGAAAAGCTAATCCATC-TGATGATGGATTTGATCAAAAGGTTGAACAAA
65 GGAAAAGTTGATCCATCAAG-TGATGGATTTGAGCAAAAGGTTGAACAAA
* *
302616 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCAACTG
*
302681 GAAAAGTTGATCCATTGAA-TGATGGATTT
66 GAAAAGTTGATCCA-TCAAGTGATGGATTT
302710 AAATCTTTGC
Statistics
Matches: 480, Mismatches: 52, Indels: 30
0.85 0.09 0.05
Matches are distributed among these distances:
109 17 0.04
110 1 0.00
111 5 0.01
112 7 0.01
113 346 0.72
114 4 0.01
115 3 0.01
116 96 0.20
117 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCAACTG
GAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
Found at i:303591 original size:115 final size:115
Alignment explanation
Indices: 303390--303714 Score: 571
Period size: 115 Copynumber: 2.8 Consensus size: 115
303380 GATCATGAAG
* * * * *
303390 TTCATCTTTTAATTCCAATGATTGGTTCTGTAG-TTCCTACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACTAAACCAGATCAGATAACTCAAAG
303454 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAACAAA
66 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAACAAA
303504 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACTAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACTAAACCAGATCAGATAACTCAAAG
*
303569 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAACAAA
*
303619 TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACTAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACTAAACCAGATCAGATAACTCAAAG
*
303684 AACACTTCCAGAAGATGCTATTAAGTCTCCT
66 AACACTTCCAGAAGATGCTATTGAGTCTCCT
303715 CTTCTAAATT
Statistics
Matches: 202, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
114 30 0.15
115 172 0.85
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.33
Consensus pattern (115 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACTAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAACAAA
Found at i:303842 original size:83 final size:83
Alignment explanation
Indices: 303661--303873 Score: 342
Period size: 83 Copynumber: 2.6 Consensus size: 83
303651 GTTTCATACT
* * *
303661 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTA--AGTCTCCTCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAAGCAGTCTCATCTTCCAAAT
303724 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
* *
303742 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCA-TATTCATCTTCCAAA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAAGCAGT-CTCATCTTCCAAA
*
303806 TTTAATGATTGGTTCTGCC
65 TTCAATGATTGGTTCTGCC
303825 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAAGCA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAAGCA
303874 CATGGCATTT
Statistics
Matches: 123, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
81 45 0.37
82 1 0.01
83 77 0.63
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (83 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAAGCAGTCTCATCTTCCAAAT
TCAATGATTGGTTCTGCC
Found at i:305028 original size:1 final size:1
Alignment explanation
Indices: 305024--305072 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
305014 GACCCCCCCC
* * * * *
305024 TTTTTCTTTTTTTTTTTTTTTTTTTTCTTTTCTTTCTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
305073 CTTCAAGCAT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (1 bp):
T
Found at i:305073 original size:7 final size:7
Alignment explanation
Indices: 305024--305075 Score: 68
Period size: 7 Copynumber: 7.1 Consensus size: 7
305014 GACCCCCCCC
305024 TTTTTCT
1 TTTTTCT
*
305031 TTTTTTT
1 TTTTTCT
*
305038 TTTTTTT
1 TTTTTCT
305045 TTTTTCTT
1 TTTTTC-T
305053 TTCTTTCT
1 TT-TTTCT
305061 TTTTTCT
1 TTTTTCT
305068 TTTTTCT
1 TTTTTCT
305075 T
1 T
305076 CAAGCATAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
7 31 0.76
8 6 0.15
9 4 0.10
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:317829 original size:3 final size:3
Alignment explanation
Indices: 317796--317875 Score: 88
Period size: 3 Copynumber: 25.7 Consensus size: 3
317786 CCGGGTTTTG
* * * *
317796 TAA TAT TAA TAAA TAAA TAA TATA TAT TAA TAA TAA TTA TAA TTA TAA
1 TAA TAA TAA T-AA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
317844 TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
317876 TAAATAAAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
3 55 0.85
4 10 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:319406 original size:22 final size:22
Alignment explanation
Indices: 319380--319439 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
319370 TACATAAAAT
*
319380 ATAAATTAACACTAAATTAATG
1 ATAAATTAACACTAAATGAATG
** * *
319402 ATAAAAGAACATTAAATGAATT
1 ATAAATTAACACTAAATGAATG
319424 ATAAATTAACACTAAA
1 ATAAATTAACACTAAA
319440 CAAACGTTAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.28
Consensus pattern (22 bp):
ATAAATTAACACTAAATGAATG
Found at i:319708 original size:92 final size:99
Alignment explanation
Indices: 319528--319721 Score: 249
Period size: 101 Copynumber: 2.0 Consensus size: 99
319518 AACGAACAGG
** * *
319528 AACACCTTCACAAATTAATAAATGAACACGATATTAAAAATTTAAAAGAACACAAGTCAAACATG
1 AACACCTTCACAAAAAAATAAATGAACACAATATTAAAAATTTAAAACAACACAAGTCAAACA-G
319593 AACATTTTCAAAAGTAAACAAACGAACACCAACACA
65 AACA-TTTCAAAAGTAAACAAACGAACACCAACACA
* * *
319629 AACACCTTCACAAAAAAATAAATGAGCACAATATTAAAGATTT-AAACAA-AC-A-TGAAACA-A
1 AACACCTTCACAAAAAAATAAATGAACACAATATTAAAAATTTAAAACAACACAAGTCAAACAGA
*
319689 ACA-TT-AAAAGTAAACAAACGAACACGAACACA
66 ACATTTCAAAAGTAAACAAACGAACACCAACACA
319721 A
1 A
319722 CCTTGTTCGT
Statistics
Matches: 85, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
92 27 0.32
93 2 0.02
95 4 0.05
97 6 0.07
98 1 0.01
99 2 0.02
100 5 0.06
101 38 0.45
ACGTcount: A:0.57, C:0.19, G:0.07, T:0.17
Consensus pattern (99 bp):
AACACCTTCACAAAAAAATAAATGAACACAATATTAAAAATTTAAAACAACACAAGTCAAACAGA
ACATTTCAAAAGTAAACAAACGAACACCAACACA
Found at i:324065 original size:59 final size:59
Alignment explanation
Indices: 323973--324091 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
323963 TTAGAGAAAA
323973 TACATGGGGAAAATGGAATTGATGTATTGTTATTTTTATATAGTGGAGGCATGTGTGGC
1 TACATGGGGAAAATGGAATTGATGTATTGTTATTTTTATATAGTGGAGGCATGTGTGGC
*
324032 TACATGGGGAAAATGGAATTGATGTATTGTTATTTTTATATAGTGGAGGCCTGTGTGGC
1 TACATGGGGAAAATGGAATTGATGTATTGTTATTTTTATATAGTGGAGGCATGTGTGGC
324091 T
1 T
324092 CAAACTCTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.26, C:0.06, G:0.30, T:0.38
Consensus pattern (59 bp):
TACATGGGGAAAATGGAATTGATGTATTGTTATTTTTATATAGTGGAGGCATGTGTGGC
Found at i:327790 original size:60 final size:60
Alignment explanation
Indices: 327678--327793 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
327668 ATTATAAGTG
* *
327678 TCATTCTAAATTAATCCTCAAACTTTTAAACATTTCAATTTCATCCCTAAACTATATCCT
1 TCATTCTAAATTAATCCCCAAACTTTTAAACATTTCAATTCCATCCCTAAACTATATCCT
* * * * *
327738 TCATTCTAAATTACTCCCCAAACTTTATGACCTTTTTAATTCCATCCC-AAACTATA
1 TCATTCTAAATTAATCCCCAAACTTT-TAAACATTTCAATTCCATCCCTAAACTATA
327794 CATATATACT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 32 0.67
61 16 0.33
ACGTcount: A:0.34, C:0.27, G:0.01, T:0.39
Consensus pattern (60 bp):
TCATTCTAAATTAATCCCCAAACTTTTAAACATTTCAATTCCATCCCTAAACTATATCCT
Found at i:328781 original size:60 final size:60
Alignment explanation
Indices: 328717--328863 Score: 167
Period size: 60 Copynumber: 2.5 Consensus size: 60
328707 AATTGTTCCA
* *
328717 TAAACTTTTGAGTATTTCAATTTCATCCCAAAAATTATGG-C-TCTATTCTAAATT-AGTCTT
1 TAAACTTTTGAGTATTTCAATTTCATCCC-AAAACTATGGCCATCT-TTCTAAATTGA-TCTC
* * *
328777 TAAACTTTT-AGAAATTTTAATTTCATCCCTAAACTATGGCCATCTTTCTAAATTGATCTC
1 TAAACTTTTGAG-TATTTCAATTTCATCCCAAAACTATGGCCATCTTTCTAAATTGATCTC
* *
328837 TAAACTTTTGAATCTTTCAATTTCATC
1 TAAACTTTTGAGTATTTCAATTTCATC
328864 TTTAAATTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
59 10 0.14
60 58 0.79
61 5 0.07
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (60 bp):
TAAACTTTTGAGTATTTCAATTTCATCCCAAAACTATGGCCATCTTTCTAAATTGATCTC
Found at i:328869 original size:29 final size:30
Alignment explanation
Indices: 328777--328869 Score: 75
Period size: 29 Copynumber: 3.1 Consensus size: 30
328767 AATTAGTCTT
*
328777 TAAACTTTTAGAAAT-TTT-AATTTCATCCC
1 TAAACTTTT-GAAATCTTTCAATTTCATCTC
* * ** * *
328806 TAAACTATGGCCATCTTTCTAAATTGATCTC
1 TAAACTTTTGAAATCTTTC-AATTTCATCTC
*
328837 TAAACTTTTG-AATCTTTCAATTTCATCTT
1 TAAACTTTTGAAATCTTTCAATTTCATCTC
328866 TAAA
1 TAAA
328870 TTCATCCAAA
Statistics
Matches: 48, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
28 3 0.06
29 22 0.46
30 7 0.15
31 16 0.33
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.44
Consensus pattern (30 bp):
TAAACTTTTGAAATCTTTCAATTTCATCTC
Found at i:335775 original size:29 final size:29
Alignment explanation
Indices: 335742--335798 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
335732 ATTCGTGTAC
* *
335742 CCGAAACATGTTCGGGCGGGCATGAGTAT
1 CCGAAACATGTTCGGGCAGGCACGAGTAT
335771 CCGAAACATGTTCGGGCAGGCACGAGTA
1 CCGAAACATGTTCGGGCAGGCACGAGTA
335799 CGAGAATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.26, C:0.23, G:0.33, T:0.18
Consensus pattern (29 bp):
CCGAAACATGTTCGGGCAGGCACGAGTAT
Found at i:336089 original size:2 final size:2
Alignment explanation
Indices: 336082--336124 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
336072 ATCCTGCCCC
336082 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
336124 A
1 A
336125 CTCTTATCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:347346 original size:2 final size:2
Alignment explanation
Indices: 347341--347378 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
347331 ATATGTGTGC
*
347341 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
347379 TACAATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:352116 original size:172 final size:172
Alignment explanation
Indices: 351830--352176 Score: 694
Period size: 172 Copynumber: 2.0 Consensus size: 172
351820 CTATTTTATT
351830 TTTAATTATTCATTTTCAAAAATAGATTTATAATCACGTGAAAATTGAATTCATTATTCCGTCGA
1 TTTAATTATTCATTTTCAAAAATAGATTTATAATCACGTGAAAATTGAATTCATTATTCCGTCGA
351895 CGGTTAATGTAATGACAAAATAATAAATTAATAAAAATGATCGTATCGTTAAATTATTCAAACGG
66 CGGTTAATGTAATGACAAAATAATAAATTAATAAAAATGATCGTATCGTTAAATTATTCAAACGG
351960 TTATCAATAATTGGTTTGGTCCAAATTTAATGATTATATTGA
131 TTATCAATAATTGGTTTGGTCCAAATTTAATGATTATATTGA
352002 TTTAATTATTCATTTTCAAAAATAGATTTATAATCACGTGAAAATTGAATTCATTATTCCGTCGA
1 TTTAATTATTCATTTTCAAAAATAGATTTATAATCACGTGAAAATTGAATTCATTATTCCGTCGA
352067 CGGTTAATGTAATGACAAAATAATAAATTAATAAAAATGATCGTATCGTTAAATTATTCAAACGG
66 CGGTTAATGTAATGACAAAATAATAAATTAATAAAAATGATCGTATCGTTAAATTATTCAAACGG
352132 TTATCAATAATTGGTTTGGTCCAAATTTAATGATTATATTGA
131 TTATCAATAATTGGTTTGGTCCAAATTTAATGATTATATTGA
352174 TTT
1 TTT
352177 GAACTCATAA
Statistics
Matches: 175, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 175 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (172 bp):
TTTAATTATTCATTTTCAAAAATAGATTTATAATCACGTGAAAATTGAATTCATTATTCCGTCGA
CGGTTAATGTAATGACAAAATAATAAATTAATAAAAATGATCGTATCGTTAAATTATTCAAACGG
TTATCAATAATTGGTTTGGTCCAAATTTAATGATTATATTGA
Found at i:358712 original size:20 final size:20
Alignment explanation
Indices: 358668--358712 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
358658 CCCATGTAAA
*
358668 AACCCTATATCCCCTATAAT
1 AACCTTATATCCCCTATAAT
358688 AACCTTATATCCCCTATAAT
1 AACCTTATATCCCCTATAAT
358708 AACCT
1 AACCT
358713 ATCCCTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (20 bp):
AACCTTATATCCCCTATAAT
Found at i:358715 original size:17 final size:18
Alignment explanation
Indices: 358675--358717 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
358665 AAAAACCCTA
358675 TATCCCCTATAATAACCTT
1 TATCCCCTATAATAACC-T
358694 ATATCCCCTATAATAACC-
1 -TATCCCCTATAATAACCT
358712 TATCCC
1 TATCCC
358718 TTTTCCTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.26
20 17 0.74
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (18 bp):
TATCCCCTATAATAACCT
Found at i:363942 original size:152 final size:154
Alignment explanation
Indices: 363645--363954 Score: 588
Period size: 152 Copynumber: 2.0 Consensus size: 154
363635 TTTATTTATT
*
363645 TTTTAAAATTTAAACCTAACTATAAAACCCTCATTGATTGTAATTATTACTTTCCTCTCGAAATT
1 TTTTAAAATTTAAACCTAAC-ATAAAACCCTCATTGATTGTAACTATTACTTTCCTCTCGAAATT
363710 TCCTATCCAAACCCCTCTCTCTCTCTCTCTCTGAGTTCACCTACCGGTGTCGCTGTCGTTGGTGT
65 TCCTATCCAAACCCCTCTCTCTCTCTCTCTCTGAGTTCACCTACCGGTGTCGCTGTCGTTGGTGT
363775 CGCCGTCGCTTCAGCCACAGTGTTC
130 CGCCGTCGCTTCAGCCACAGTGTTC
363800 TTTTAAAATTTAAACCT-A-ATAAAACCCTCATTGATTGTAACTATTACTTTCCTCTCGAAATTT
1 TTTTAAAATTTAAACCTAACATAAAACCCTCATTGATTGTAACTATTACTTTCCTCTCGAAATTT
363863 CCTATCCAAACCCCTCTCTCTCTCTCTCTCTGAGTTCACCTACCGGTGTCGCTGTCGTTGGTGTC
66 CCTATCCAAACCCCTCTCTCTCTCTCTCTCTGAGTTCACCTACCGGTGTCGCTGTCGTTGGTGTC
363928 GCCGTCGCTTCAGCCACAGTGTTC
131 GCCGTCGCTTCAGCCACAGTGTTC
363952 TTT
1 TTT
363955 GTCTTTCCAA
Statistics
Matches: 154, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
152 136 0.88
154 1 0.01
155 17 0.11
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.36
Consensus pattern (154 bp):
TTTTAAAATTTAAACCTAACATAAAACCCTCATTGATTGTAACTATTACTTTCCTCTCGAAATTT
CCTATCCAAACCCCTCTCTCTCTCTCTCTCTGAGTTCACCTACCGGTGTCGCTGTCGTTGGTGTC
GCCGTCGCTTCAGCCACAGTGTTC
Found at i:365252 original size:22 final size:22
Alignment explanation
Indices: 365226--365267 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
365216 CTGGAGAAGG
*
365226 AGGAGAAGC-TTGCAAAGCAACA
1 AGGAGAAACTTTG-AAAGCAACA
365248 AGGAGAAACTTTGAAAGCAA
1 AGGAGAAACTTTGAAAGCAA
365268 ATTACAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.48, C:0.14, G:0.26, T:0.12
Consensus pattern (22 bp):
AGGAGAAACTTTGAAAGCAACA
Found at i:365897 original size:12 final size:12
Alignment explanation
Indices: 365880--365904 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
365870 TTTTTTGCTT
365880 TAATAAAAGGTC
1 TAATAAAAGGTC
365892 TAATAAAAGGTC
1 TAATAAAAGGTC
365904 T
1 T
365905 GATGTGGTGG
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:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (12 bp):
TAATAAAAGGTC
Found at i:366944 original size:28 final size:28
Alignment explanation
Indices: 366909--366962 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
366899 ATTTTAAAAT
*
366909 ATTTTTATA-ATTTTAAAATAAATTATGC
1 ATTTTTATATA-TTTAAAAAAAATTATGC
366937 ATTTTTATATATTTAAAAAAAATTAT
1 ATTTTTATATATTTAAAAAAAATTAT
366963 TATGCAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (28 bp):
ATTTTTATATATTTAAAAAAAATTATGC
Found at i:366968 original size:31 final size:28
Alignment explanation
Indices: 366909--366968 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 28
366899 ATTTTAAAAT
* *
366909 ATTTTTATAATTTTAAAATAAATTATGC
1 ATTTTTATAATTTAAAAAAAAATTATGC
366937 ATTTTTATATATTTAAAAAAAATTATTATGC
1 ATTTTTATA-ATTTAAAAAAAA--ATTATGC
366968 A
1 A
366969 ATTATAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 9 0.33
29 10 0.37
31 8 0.30
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (28 bp):
ATTTTTATAATTTAAAAAAAAATTATGC
Found at i:367472 original size:21 final size:21
Alignment explanation
Indices: 367444--367505 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
367434 TCCACAAACA
367444 TCCT-TTCCACCACTTCCTCC
1 TCCTCTTCCACCACTTCCTCC
*
367464 TCCTCTTCCACCACCTTCTCTCT
1 TCCTCTTCCACCA-CTTC-CTCC
367487 TCCTTCTTCCACCACTTCC
1 TCC-TCTTCCACCACTTCC
367506 ACCACCACTA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 4 0.11
21 8 0.22
22 5 0.14
23 10 0.27
24 10 0.27
ACGTcount: A:0.10, C:0.53, G:0.00, T:0.37
Consensus pattern (21 bp):
TCCTCTTCCACCACTTCCTCC
Found at i:368806 original size:34 final size:33
Alignment explanation
Indices: 368745--368829 Score: 138
Period size: 34 Copynumber: 2.6 Consensus size: 33
368735 TCCCGCCCCG
368745 ATTATATATATATATAAT-TTTTTTATTTTTTAT
1 ATTA-ATATATATATAATATTTTTTATTTTTTAT
368778 ATTAATCATATATATAATATTTTTTATTTTTTAT
1 ATTAAT-ATATATATAATATTTTTTATTTTTTAT
368812 ATTAAT-TATATATAATAT
1 ATTAATATATATATAATAT
368830 ATAATATTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
32 14 0.28
33 15 0.30
34 21 0.42
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (33 bp):
ATTAATATATATATAATATTTTTTATTTTTTAT
Found at i:368830 original size:39 final size:37
Alignment explanation
Indices: 368745--368859 Score: 141
Period size: 39 Copynumber: 3.2 Consensus size: 37
368735 TCCCGCCCCG
368745 ATTATATATATATATAAT-TTTTTTATTTTTTATATT
1 ATTATATATATATATAATATTTTTTATTTTTTATATT
*
368781 A--AT-CATATATATAATATTTTTTATTTTTTATATT
1 ATTATATATATATATAATATTTTTTATTTTTTATATT
* * *
368815 AATTATATATAATATATAATATTTTATATTCTATATATT
1 -ATTATATAT-ATATATAATATTTTTTATTTTTTATATT
368854 -TTATAT
1 ATTATAT
368860 TTTTTCTATT
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
33 11 0.16
34 20 0.29
35 1 0.01
36 1 0.01
37 8 0.12
38 2 0.03
39 25 0.37
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (37 bp):
ATTATATATATATATAATATTTTTTATTTTTTATATT
Found at i:369047 original size:11 final size:11
Alignment explanation
Indices: 369031--369063 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
369021 GGGGGAGCAA
369031 AACCCGCCCCG
1 AACCCGCCCCG
369042 AACCCGCCCCG
1 AACCCGCCCCG
369053 AACCCGCCCCG
1 AACCCGCCCCG
369064 TTTCCTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.18, C:0.64, G:0.18, T:0.00
Consensus pattern (11 bp):
AACCCGCCCCG
Found at i:383014 original size:70 final size:70
Alignment explanation
Indices: 382933--383077 Score: 263
Period size: 70 Copynumber: 2.1 Consensus size: 70
382923 AAATATCTAC
* * *
382933 CTACAAAGATAAAAATAATATTGTACCTTGGGTGGAGCAACACTTGCAGCTTTCTCACATCCCAT
1 CTACAAAGATAAAAAAAAGATTGTACCTTGGGTGGAGCAACAATTGCAGCTTTCTCACATCCCAT
382998 AGTGT
66 AGTGT
383003 CTACAAAGATAAAAAAAAGATTGTACCTTGGGTGGAGCAACAATTGCAGCTTTCTCACATCCCAT
1 CTACAAAGATAAAAAAAAGATTGTACCTTGGGTGGAGCAACAATTGCAGCTTTCTCACATCCCAT
383068 AGTGT
66 AGTGT
383073 CTACA
1 CTACA
383078 TGCGCATATT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (70 bp):
CTACAAAGATAAAAAAAAGATTGTACCTTGGGTGGAGCAACAATTGCAGCTTTCTCACATCCCAT
AGTGT
Found at i:385156 original size:189 final size:189
Alignment explanation
Indices: 384831--385201 Score: 512
Period size: 189 Copynumber: 2.0 Consensus size: 189
384821 TAGTTTTGGG
* **
384831 ATCAAATTTCATCACATATTAATCAACAGATTAACGACCAACCTTGACGACTATCAATTTTTTTT
1 ATCAAATTTCATCACATATCAATCAACAGATTAACGACCAACCTTGACGAC-ATCAATTTTTTAA
* * * *
384896 AAAAAATGACGAGTTTAAAACTATGAATAGTTGAGTGACAATTTTGTAACTTTTAATAGTTAAAA
65 AAAAAATGACGAGTTTAAAACTATGAATAGTTGAGTGACAATTTTATAAATTTTAATAATCAAAA
**
384961 ACTCAACAAAATAACACCCTATAATTAAAAGATTATTTTATAACTTTTAATAATTATGAT
130 ACTCAACAAAATAACACCCTATAATTAAAAGACCATTTTATAACTTTTAATAATTATGAT
* * * * * *
385021 ATCAAATTTTATCATATCTCAATCAACAGATTAACGTCCAACTTTGACGGC-TCAATTTTTTAAA
1 ATCAAATTTCATCACATATCAATCAACAGATTAACGACCAACCTTGACGACATCAATTTTTTAAA
* *
385085 GAAAAATGATGAGTTTAAAACTATGAATAGTTTGA-TGACCATTTTATAAATTTTAATAATCAAA
66 -AAAAATGACGAGTTTAAAACTATGAATAG-TTGAGTGACAATTTTATAAATTTTAATAATCAAA
* * **
385149 GACTCAACAAAGTAACGTCCTATAATTAAAAGACCATTTTATAACTTTTAATA
129 AACTCAACAAAATAACACCCTATAATTAAAAGACCATTTTATAACTTTTAATA
385202 GTCGGATGAC
Statistics
Matches: 158, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
188 11 0.07
189 99 0.63
190 48 0.30
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (189 bp):
ATCAAATTTCATCACATATCAATCAACAGATTAACGACCAACCTTGACGACATCAATTTTTTAAA
AAAAATGACGAGTTTAAAACTATGAATAGTTGAGTGACAATTTTATAAATTTTAATAATCAAAAA
CTCAACAAAATAACACCCTATAATTAAAAGACCATTTTATAACTTTTAATAATTATGAT
Found at i:385246 original size:59 final size:59
Alignment explanation
Indices: 385121--385234 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
385111 ATAGTTTGAT
** **
385121 GACCATTTTATAAATTTTAATAATCAAAGACTCAACAAAGTAACGTCCTATAATTAAAA
1 GACCATTTTATAAATTTTAATAATCAAAGACTCAACAAAACAACACCCTATAATTAAAA
* * * *
385180 GACCATTTTATAACTTTTAATAGTCGGATGACTCAACAAAACAACACCCTATAAT
1 GACCATTTTATAAATTTTAATAATC-AAAGACTCAACAAAACAACACCCTATAAT
385235 CGGAGACCAT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
59 23 0.50
60 23 0.50
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (59 bp):
GACCATTTTATAAATTTTAATAATCAAAGACTCAACAAAACAACACCCTATAATTAAAA
Found at i:389962 original size:20 final size:20
Alignment explanation
Indices: 389918--390405 Score: 465
Period size: 20 Copynumber: 24.2 Consensus size: 20
389908 AATGACCAAC
*
389918 AAAATCGCAACGCGA--AATA
1 AAAATCGCAACGCGATTAA-G
*
389937 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
389957 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
389977 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
389997 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
390018 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
390039 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
390060 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
390081 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
390103 --AATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
*
390121 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
390141 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
390161 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
390183 --AATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTAAG
*
390201 AAAATCGCAACACGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
390223 --AATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
390243 --AATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTAAG
*
390261 AAAATCGCAACACGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
390283 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
390301 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
390323 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
390341 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
390363 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
*
390381 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
390401 AAAAT
1 AAAAT
390406 GAGTAAATTC
Statistics
Matches: 401, Mismatches: 33, Indels: 69
0.80 0.07 0.14
Matches are distributed among these distances:
18 18 0.04
19 15 0.04
20 308 0.77
21 14 0.03
22 46 0.11
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:390512 original size:6 final size:6
Alignment explanation
Indices: 390501--390527 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
390491 GACACGTATT
390501 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
390528 CGAGACGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:391027 original size:6 final size:6
Alignment explanation
Indices: 391016--391042 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
391006 GTCTCGTCTC
391016 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
391043 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:391167 original size:20 final size:20
Alignment explanation
Indices: 391142--391301 Score: 218
Period size: 20 Copynumber: 7.8 Consensus size: 20
391132 CTCATTTTCT
391142 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
391162 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
391183 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
391202 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
391222 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
391242 GAAGATCGCGTTGCGATTCTCT-
1 G-A-ATCGCGTTGCGATTCT-TG
* *
391264 TAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
391284 GAATATCGCGTTGCGATT
1 G-A-ATCGCGTTGCGATT
391302 TTCTTTTGAC
Statistics
Matches: 126, Mismatches: 4, Indels: 18
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.04
19 1 0.01
20 82 0.65
21 3 0.02
22 34 0.27
23 1 0.01
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.36
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:391190 original size:40 final size:41
Alignment explanation
Indices: 391135--391380 Score: 257
Period size: 40 Copynumber: 6.1 Consensus size: 41
391125 GAATTTACTC
*
391135 ATTTTCTGAATCGCGTTGCGATTCTTGGA-ATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGATATCGCGTTGCG
391175 ATTTTCTTAATCGCGTTGCGATTCTTGGA-ATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGATATCGCGTTGCG
*
391215 A--TTCTTGGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGATTCTTGG-ATATCGCGTTGCG
* *
391257 ATTCTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-ATATCGCGTTGCG
* *
391299 ATTTTCTT--TTGACCGTTGCGATTTCTT---T-TCAACGTTGCG
1 ATTTTCTTAATCG--CGTTGCGA-TTCTTGGATATC-GCGTTGCG
* *
391338 ATTTTCTAAATCGCGTTGCGATT-TT--ATTTCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGATATCGCGTTGCG
391376 ATTTT
1 ATTTT
391381 GTTGGTCATT
Statistics
Matches: 181, Mismatches: 11, Indels: 30
0.82 0.05 0.14
Matches are distributed among these distances:
37 2 0.01
38 22 0.12
39 25 0.14
40 62 0.34
41 3 0.02
42 58 0.32
43 5 0.03
44 4 0.02
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.41
Consensus pattern (41 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGATATCGCGTTGCG
Found at i:391317 original size:20 final size:20
Alignment explanation
Indices: 391292--391344 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
391282 TGGAATATCG
* *
391292 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTCAA
391312 CGTTGCGA-TTTCTTTTCAA
1 CGTTGCGATTTTCTTTTCAA
391331 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
391345 AAATCGCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.11, C:0.21, G:0.19, T:0.49
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTCAA
Found at i:391354 original size:20 final size:20
Alignment explanation
Indices: 391135--391380 Score: 141
Period size: 20 Copynumber: 12.2 Consensus size: 20
391125 GAATTTACTC
*
391135 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
391155 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
391175 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
391195 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
**
391215 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
**
391235 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* * *
391257 ATTCTCTTAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
391277 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* *
391299 ATTTTCT--TTTGACCGTTGCG
1 ATTTTCTAAATCG--CGTTGCG
** *
391319 A-TTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
391338 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
391358 A-TTT-TATTTCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
391376 ATTTT
1 ATTTT
391381 GTTGGTCATT
Statistics
Matches: 185, Mismatches: 27, Indels: 29
0.77 0.11 0.12
Matches are distributed among these distances:
18 15 0.08
19 21 0.11
20 108 0.58
21 14 0.08
22 27 0.15
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.41
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:392317 original size:18 final size:19
Alignment explanation
Indices: 392294--392335 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
392284 CAGTAATCCT
392294 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
392312 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATCTTAC
392332 ATTC
1 ATTC
392336 TGTGAACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.14
19 3 0.14
20 16 0.73
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.38
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:395611 original size:218 final size:214
Alignment explanation
Indices: 395213--395644 Score: 828
Period size: 218 Copynumber: 2.0 Consensus size: 214
395203 GAAGCATAAC
395213 AAAGAAACTCCATTTTTCTAAAAGTCAGATTCTTGCACATAACATAGAGGGAATCAGTAATTAGA
1 AAAGAAACTCCATTTTTCTAAAAGTCAGATTCTTGCACATAACATAGAGGGAATCAGTAATTAGA
395278 GAAATCAACATACATAATATACCTACTGCTAAATATAGAATGATGAAAAAGTAACCATAAGAATC
66 GAAATCAACATACATAATATACCTACTGCTAAATATAGAATGATGAAAAAGTAACCATAAGAATC
395343 TTCTATTCCACTTATGAATGCAAGCTGAAACAAAGCCCCTGCATATCCTAATATCATTAACACTC
131 TTCTATTCCACTTATGAATGCAAGCTGAAACAAAGCCCCTGCATATCCTAATATCATTAACACTC
395408 AAAATAACAATGAATCTAT
196 AAAATAACAATGAATCTAT
395427 AAAGAAACTCCATTTTTCTAAAAGTCAGATTCTTGCACAATAACATAGAGGGGAATCAAGTAATT
1 AAAGAAACTCCATTTTTCTAAAAGTCAGATTCTTGCAC-ATAACATAGA-GGGAATC-AGTAATT
395492 AGAGAAATCAACATACATAATATACCTACTGCTAAATATAGAATGATGAAAAAGTATACCATAAG
63 AGAGAAATCAACATACATAATATACCTACTGCTAAATATAGAATGATGAAAAAGTA-ACCATAAG
395557 AATCTTCTATTCCACTTATGAATGCAAGCTGAAACAAAGCCCCTGCATATCCTAATATCATTAAC
127 AATCTTCTATTCCACTTATGAATGCAAGCTGAAACAAAGCCCCTGCATATCCTAATATCATTAAC
395622 ACTCAAAATAACAATGAATCTAT
192 ACTCAAAATAACAATGAATCTAT
395645 GCATAAAAAC
Statistics
Matches: 214, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
214 38 0.18
215 10 0.05
216 7 0.03
217 63 0.29
218 96 0.45
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.27
Consensus pattern (214 bp):
AAAGAAACTCCATTTTTCTAAAAGTCAGATTCTTGCACATAACATAGAGGGAATCAGTAATTAGA
GAAATCAACATACATAATATACCTACTGCTAAATATAGAATGATGAAAAAGTAACCATAAGAATC
TTCTATTCCACTTATGAATGCAAGCTGAAACAAAGCCCCTGCATATCCTAATATCATTAACACTC
AAAATAACAATGAATCTAT
Found at i:396672 original size:30 final size:30
Alignment explanation
Indices: 396636--396704 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
396626 ATAGAATAAT
* * *
396636 AATTTGACTTTAAACTTTAAATAAAGTATC
1 AATTTGACCTTAAACTATAAATAAAATATC
* *
396666 ATTTTGACCTTAAACTATAGATAAAATATC
1 AATTTGACCTTAAACTATAAATAAAATATC
396696 AATTTGACC
1 AATTTGACC
396705 CCTAATTCGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (30 bp):
AATTTGACCTTAAACTATAAATAAAATATC
Found at i:402150 original size:17 final size:19
Alignment explanation
Indices: 402113--402150 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
402103 TCTTTTTTTC
*
402113 TTTCGAACAGTCTCTCTTT
1 TTTCGAACAGTCTCGCTTT
402132 TTTCGAACAG-CT-GCTTT
1 TTTCGAACAGTCTCGCTTT
402149 TT
1 TT
402151 GTTTGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
19 10 0.56
ACGTcount: A:0.16, C:0.24, G:0.13, T:0.47
Consensus pattern (19 bp):
TTTCGAACAGTCTCGCTTT
Found at i:403034 original size:13 final size:12
Alignment explanation
Indices: 403014--403048 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
403004 GCTTAATCGG
403014 AAAAAAAAATAA
1 AAAAAAAAATAA
*
403026 AAGAAAAAATAA
1 AAAAAAAAATAA
*
403038 AAATAAAAATA
1 AAAAAAAAATA
403049 TAACAGAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (12 bp):
AAAAAAAAATAA
Found at i:409462 original size:2 final size:2
Alignment explanation
Indices: 409455--409484 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
409445 TTAAATTATC
409455 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
409485 CAGAATTTTC
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:412273 original size:23 final size:23
Alignment explanation
Indices: 412229--412273 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
412219 TTAAATAAAC
*
412229 GAGATAAAATTATAAATTTTTAA
1 GAGATAAAATTATAAAATTTTAA
412252 GAGATCAAAATTA-AAAATTTTA
1 GAGAT-AAAATTATAAAATTTTA
412274 TATTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (23 bp):
GAGATAAAATTATAAAATTTTAA
Found at i:412702 original size:16 final size:17
Alignment explanation
Indices: 412669--412706 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
412659 TCTCCTAAAA
412669 ATTTTAAATTTTTATAT
1 ATTTTAAATTTTTATAT
412686 ATTTTAAATTTTT-TAT
1 ATTTTAAATTTTTATAT
412702 ATTTT
1 ATTTT
412707 CTATTGAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTAAATTTTTATAT
Found at i:430362 original size:33 final size:33
Alignment explanation
Indices: 430325--430398 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
430315 CAGTCAAGTA
* *
430325 CTAATCCTTACAGCCAACTTGAACAGCCAGATG
1 CTAATCCATACAGCCAACCTGAACAGCCAGATG
** *
430358 CTAATCCATATGGCCAACCTGCACAGCCAGATG
1 CTAATCCATACAGCCAACCTGAACAGCCAGATG
430391 CTAATCCA
1 CTAATCCA
430399 CACGTCCTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.20
Consensus pattern (33 bp):
CTAATCCATACAGCCAACCTGAACAGCCAGATG
Found at i:430451 original size:99 final size:99
Alignment explanation
Indices: 430325--430707 Score: 480
Period size: 99 Copynumber: 3.9 Consensus size: 99
430315 CAGTCAAGTA
* * * * * * * * * * *
430325 CTAATCCTTACAGCCAACTTGAACAGCCAGATGCTAATCCATATGGCCAACCTGCACAGCCAGAT
1 CTAATCCTTACTGCCAGCCTGCACAGCCAAATGTTAATCCCTACGGCCAGCCTGCTCAGCCAAAT
* * * *
430390 GCTAATCCACACGTCCTGCCTGCAC-AGCCAAATG
66 GCTAATCCATACGGCCAGCCTGC-CGAGCCAAAAG
* * * * * * *
430424 TTAATCATTACAGGCAGCCTGCTCAGCCAAATGTTAATCCCTACGGGCAGCCTTCTCAGCCAAAT
1 CTAATCCTTACTGCCAGCCTGCACAGCCAAATGTTAATCCCTACGGCCAGCCTGCTCAGCCAAAT
* *
430489 GCTAATCCGTACGGCCAGCCTGCCGAGGCAAAAG
66 GCTAATCCATACGGCCAGCCTGCCGAGCCAAAAG
* *
430523 CTAATCCTTACTGCCAGCCTGCACAGCCAAATGTTAATCCCTACGGGCAGCCTGTTCAGCCAAAT
1 CTAATCCTTACTGCCAGCCTGCACAGCCAAATGTTAATCCCTACGGCCAGCCTGCTCAGCCAAAT
* *
430588 GCTAATCCGTACGGCCAGCCTGCCGAGGCAAAAG
66 GCTAATCCATACGGCCAGCCTGCCGAGCCAAAAG
*
430622 CTAATCCTTACTGCCAGCCTGCACAGCCAAATGTTAATCCCTACGGCCAGCCTGTTCAGCCAAAT
1 CTAATCCTTACTGCCAGCCTGCACAGCCAAATGTTAATCCCTACGGCCAGCCTGCTCAGCCAAAT
*
430687 GCTATTCCATACGGCCAGCCT
66 GCTAATCCATACGGCCAGCCT
430708 ACTCAGCCAA
Statistics
Matches: 251, Mismatches: 32, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
98 1 0.00
99 250 1.00
ACGTcount: A:0.27, C:0.34, G:0.19, T:0.20
Consensus pattern (99 bp):
CTAATCCTTACTGCCAGCCTGCACAGCCAAATGTTAATCCCTACGGCCAGCCTGCTCAGCCAAAT
GCTAATCCATACGGCCAGCCTGCCGAGCCAAAAG
Found at i:430704 original size:33 final size:33
Alignment explanation
Indices: 430348--430718 Score: 363
Period size: 33 Copynumber: 11.2 Consensus size: 33
430338 CCAACTTGAA
* * * *
430348 CAGCCAGATGCTAATCCATATGGCCAACCTGCA
1 CAGCCAAATGCTAATCCATACGGCCAGCCTGCT
* * * * *
430381 CAGCCAGATGCTAATCCACACGTCCTGCCTGCA
1 CAGCCAAATGCTAATCCATACGGCCAGCCTGCT
*
430414 CAGCCAAATGTTAAT-CATTACAGG-CAGCCTGCT
1 CAGCCAAATGCTAATCCA-TAC-GGCCAGCCTGCT
* * * *
430447 CAGCCAAATGTTAATCCCTACGGGCAGCCTTCT
1 CAGCCAAATGCTAATCCATACGGCCAGCCTGCT
*
430480 CAGCCAAATGCTAATCCGTACGGCCAGCCTGC-
1 CAGCCAAATGCTAATCCATACGGCCAGCCTGCT
* * * * *
430512 CGAGGCAAAAGCTAATCCTTACTGCCAGCCTGCA
1 C-AGCCAAATGCTAATCCATACGGCCAGCCTGCT
* * * *
430546 CAGCCAAATGTTAATCCCTACGGGCAGCCTGTT
1 CAGCCAAATGCTAATCCATACGGCCAGCCTGCT
*
430579 CAGCCAAATGCTAATCCGTACGGCCAGCCTGC-
1 CAGCCAAATGCTAATCCATACGGCCAGCCTGCT
* * * * *
430611 CGAGGCAAAAGCTAATCCTTACTGCCAGCCTGCA
1 C-AGCCAAATGCTAATCCATACGGCCAGCCTGCT
* * *
430645 CAGCCAAATGTTAATCCCTACGGCCAGCCTGTT
1 CAGCCAAATGCTAATCCATACGGCCAGCCTGCT
* *
430678 CAGCCAAATGCTATTCCATACGGCCAGCCTACT
1 CAGCCAAATGCTAATCCATACGGCCAGCCTGCT
430711 CAGCCAAA
1 CAGCCAAA
430719 CCAGCGTACA
Statistics
Matches: 281, Mismatches: 49, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
32 6 0.02
33 271 0.96
34 4 0.01
ACGTcount: A:0.27, C:0.34, G:0.19, T:0.20
Consensus pattern (33 bp):
CAGCCAAATGCTAATCCATACGGCCAGCCTGCT
Found at i:430797 original size:33 final size:32
Alignment explanation
Indices: 430728--430803 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
430718 ACCAGCGTAC
* **
430728 ACAGCCCAGTGCTAATATATACTACCAGCCTGT
1 ACAGCCAAGTGCTAATATATACTA-CAGCCCAT
*
430761 ACAGCTAAGTGCTAATCCATATACT-CAGCCCAT
1 ACAGCCAAGTGCTAAT--ATATACTACAGCCCAT
430794 ACAGCCAAGT
1 ACAGCCAAGT
430804 TCAAATAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
33 29 0.81
35 7 0.19
ACGTcount: A:0.33, C:0.30, G:0.14, T:0.22
Consensus pattern (32 bp):
ACAGCCAAGTGCTAATATATACTACAGCCCAT
Found at i:431665 original size:33 final size:33
Alignment explanation
Indices: 431628--431833 Score: 268
Period size: 33 Copynumber: 6.2 Consensus size: 33
431618 CATGGGAATC
* *
431628 GGGATGAACAACACGGGCATGAATCCAGGCATG
1 GGGATGAACAACATGGGCATGAACCCAGGCATG
* * *
431661 GGGATGAACAATACGGGCATGAACCAAGGCATG
1 GGGATGAACAACATGGGCATGAACCCAGGCATG
* *
431694 GGGATGAACAATATGGGCATGAACCCTGGCATG
1 GGGATGAACAACATGGGCATGAACCCAGGCATG
* *
431727 GGGATGAATAACATGGGCATGAACCCTGGCATG
1 GGGATGAACAACATGGGCATGAACCCAGGCATG
* **
431760 GGGATGAATAACATGGAAATGAACCCAGGCATG
1 GGGATGAACAACATGGGCATGAACCCAGGCATG
* * * *
431793 AGGATGAACAACATGGGTATGAGCTCAGGCATG
1 GGGATGAACAACATGGGCATGAACCCAGGCATG
431826 GGGATGAA
1 GGGATGAA
431834 TATGGGAATG
Statistics
Matches: 155, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 155 1.00
ACGTcount: A:0.34, C:0.17, G:0.33, T:0.16
Consensus pattern (33 bp):
GGGATGAACAACATGGGCATGAACCCAGGCATG
Found at i:431684 original size:15 final size:15
Alignment explanation
Indices: 431658--431717 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
431648 GAATCCAGGC
*
431658 ATGGGGATGAACAAT
1 ATGGGCATGAACAAT
* *
431673 ACGGGCATGAACCAAGGC
1 ATGGGCATGAA-CAA--T
*
431691 ATGGGGATGAACAAT
1 ATGGGCATGAACAAT
431706 ATGGGCATGAAC
1 ATGGGCATGAAC
431718 CCTGGCATGG
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
15 20 0.57
16 3 0.09
17 3 0.09
18 9 0.26
ACGTcount: A:0.37, C:0.15, G:0.33, T:0.15
Consensus pattern (15 bp):
ATGGGCATGAACAAT
Found at i:431743 original size:15 final size:15
Alignment explanation
Indices: 431723--431775 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
431713 TGAACCCTGG
431723 CATGGGGATGAATAA
1 CATGGGGATGAATAA
* **
431738 CATGGGCATGAACCCTGG
1 CATGGGGATGAA---TAA
431756 CATGGGGATGAATAA
1 CATGGGGATGAATAA
431771 CATGG
1 CATGG
431776 AAATGAACCC
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
15 17 0.59
18 12 0.41
ACGTcount: A:0.32, C:0.15, G:0.34, T:0.19
Consensus pattern (15 bp):
CATGGGGATGAATAA
Found at i:445855 original size:22 final size:22
Alignment explanation
Indices: 445803--445845 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
445793 AATTTATTAG
* *
445803 TATGAATTGATTTATTTTAAAA
1 TATGGATTAATTTATTTTAAAA
445825 TATGGATTAATTTATTTTAAA
1 TATGGATTAATTTATTTTAAA
445846 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TATGGATTAATTTATTTTAAAA
Found at i:445861 original size:54 final size:55
Alignment explanation
Indices: 445771--445894 Score: 223
Period size: 54 Copynumber: 2.3 Consensus size: 55
445761 TGGTGCAGAC
445771 ATGGATTGATTTATTTTAAAATAATTTATTAGTATGAATTGATTTATTTTAAAAT
1 ATGGATTGATTTATTTTAAAATAATTTATTAGTATGAATTGATTTATTTTAAAAT
*
445826 ATGGATTAATTTATTTT-AAATAATTTATTAGTATGAATTGATTTATTTTAAAAT
1 ATGGATTGATTTATTTTAAAATAATTTATTAGTATGAATTGATTTATTTTAAAAT
*
445880 ATGAATTGATTTATT
1 ATGGATTGATTTATT
445895 ATTGTAGTTG
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
54 50 0.76
55 16 0.24
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (55 bp):
ATGGATTGATTTATTTTAAAATAATTTATTAGTATGAATTGATTTATTTTAAAAT
Found at i:445871 original size:18 final size:18
Alignment explanation
Indices: 445848--445895 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
445838 ATTTTAAATA
*
445848 ATTTATTAGTATGAATTG
1 ATTTATTAATATGAATTG
445866 ATTTATTTTAAAATATGAATTG
1 ATTTA--TT--AATATGAATTG
445888 ATTTATTA
1 ATTTATTA
445896 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGAATTG
Found at i:445932 original size:80 final size:78
Alignment explanation
Indices: 445825--445972 Score: 260
Period size: 80 Copynumber: 1.9 Consensus size: 78
445815 TATTTTAAAA
445825 TATGGATTAATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGAATTGAT
1 TATGGATTAATTTATTTTAAATAATTTATTAGTAT--ATTGATTTATTTTAAAATATGAATTGAT
445890 TTATTATTGTAGTTG
64 TTATTATTGTAGTTG
* *
445905 TATGGATTGATTTATTTTAAATAATTTATTAGTATATTGATTTATTTTAAAATATGGATTGATTT
1 TATGGATTAATTTATTTTAAATAATTTATTAGTATATTGATTTATTTTAAAATATGAATTGATTT
445970 ATT
66 ATT
445973 TTAAATAATT
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
78 32 0.48
80 34 0.52
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (78 bp):
TATGGATTAATTTATTTTAAATAATTTATTAGTATATTGATTTATTTTAAAATATGAATTGATTT
ATTATTGTAGTTG
Found at i:446067 original size:23 final size:24
Alignment explanation
Indices: 446041--446085 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
446031 AATTTATTAG
446041 TATGGATTGA-TTTATTTTAAAAA
1 TATGGATTGATTTTATTTTAAAAA
446064 TATGGATTGATTTTATTTTAAA
1 TATGGATTGATTTTATTTTAAA
446086 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (24 bp):
TATGGATTGATTTTATTTTAAAAA
Found at i:446161 original size:32 final size:32
Alignment explanation
Indices: 446064--446317 Score: 295
Period size: 32 Copynumber: 8.7 Consensus size: 32
446054 ATTTTAAAAA
446064 TATGGATTGATTTTATTTTAAATAATTTATTAG
1 TATGGATTGA-TTTATTTTAAATAATTTATTAG
446097 TATGGATTGATTTA-TTTAAATAA---ATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
446125 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
446157 TATGGATTGATTTATTTT-AA-AA--TA-T-G
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
446183 -A---ATTGATTTATTTTAAATAATTTATTAA
1 TATGGATTGATTTATTTTAAATAATTTATTAG
446211 TATGGATTGATTTA-TTT---TAA---A--A-
1 TATGGATTGATTTATTTTAAATAATTTATTAG
446233 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
* *
446265 TATCGATTGATTTATTTTAAGTAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
446297 TATAGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
446318 ATATGGATTG
Statistics
Matches: 192, Mismatches: 5, Indels: 49
0.78 0.02 0.20
Matches are distributed among these distances:
22 27 0.14
23 6 0.03
24 2 0.01
25 2 0.01
26 6 0.03
27 2 0.01
28 24 0.12
29 11 0.06
30 2 0.01
31 15 0.08
32 85 0.44
33 10 0.05
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:446171 original size:18 final size:18
Alignment explanation
Indices: 446120--446172 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 18
446110 ATTTAAATAA
446120 ATTAGTATGGATTGATTT
1 ATTAGTATGGATTGATTT
* * *
446138 ATT--T-T-AAATAATTT
1 ATTAGTATGGATTGATTT
446152 ATTAGTATGGATTGATTT
1 ATTAGTATGGATTGATTT
446170 ATT
1 ATT
446173 TTAAAATATG
Statistics
Matches: 25, Mismatches: 6, Indels: 8
0.64 0.15 0.21
Matches are distributed among these distances:
14 9 0.36
15 1 0.04
16 2 0.08
17 1 0.04
18 12 0.48
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (18 bp):
ATTAGTATGGATTGATTT
Found at i:446182 original size:22 final size:22
Alignment explanation
Indices: 446157--446253 Score: 77
Period size: 22 Copynumber: 4.0 Consensus size: 22
446147 AATTTATTAG
*
446157 TATGGATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
446179 TATGAATTGATTTATTTTAAATAA
1 TATGAATTGATTTATTTT-AA-AA
*
446203 TTTATTAATATGGATTGATTTATTTTAAAA
1 --TATGAAT-T-GA-T---TTATTTTAAAA
*
446233 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
446254 TAATTTATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
22 27 0.44
23 2 0.03
24 2 0.03
25 1 0.02
26 8 0.13
27 2 0.03
28 7 0.11
29 1 0.02
30 2 0.03
31 2 0.03
32 7 0.11
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:446215 original size:54 final size:54
Alignment explanation
Indices: 445905--446428 Score: 665
Period size: 54 Copynumber: 9.6 Consensus size: 54
445895 ATTGTAGTTG
445905 TATGGATTGATTTATTTTAAATAATTTATTAGTAT--ATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
445957 TATGGATTGATTTATTTTAAATAATTTATTAGTA-GGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
446010 TATAGATTGATTTA-TTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAAA
446064 TATGGATTGATTTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTAAATAAATTA
1 TATGGATTGA-TTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT---TAAA--A
446124 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 -TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
446179 TATGAATTGATTTATTTTAAATAATTTATTAATATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
446233 TATGGATTGATTTATTTTAAATAATTTATTAGTATCGATTGATTTATTTTAAGTAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAA--AA
* * * * * ***
446289 TTTATTAGTATAGATTGA-TTT--AT--TTTA-AAATATGGATTGATTTATTATTGTAGTTG
1 --TA-T-GGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAA
* * *
446345 TATGAATTGATTTA-TTTAAATAATTTATTAGTATGAATTTATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
446398 TATGAATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
446429 TGTAGTTGTA
Statistics
Matches: 418, Mismatches: 26, Indels: 54
0.84 0.05 0.11
Matches are distributed among these distances:
52 64 0.15
53 60 0.14
54 150 0.36
55 12 0.03
56 43 0.10
57 21 0.05
58 5 0.01
59 5 0.01
60 48 0.11
61 10 0.02
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:446311 original size:18 final size:18
Alignment explanation
Indices: 446256--446312 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
446246 ATTTTAAATA
*
446256 ATTTATTAGTATCGATTG
1 ATTTATTAGTATAGATTG
* *
446274 ATTTATT--T-TA-AGTA
1 ATTTATTAGTATAGATTG
446288 ATTTATTAGTATAGATTG
1 ATTTATTAGTATAGATTG
446306 ATTTATT
1 ATTTATT
446313 TTAAAATATG
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 9 0.30
15 1 0.03
16 2 0.07
17 2 0.07
18 16 0.53
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATAGATTG
Found at i:446379 original size:31 final size:31
Alignment explanation
Indices: 446344--446428 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
446334 TATTGTAGTT
446344 GTATGAATTGATTTATTTAAATAATTTATTA
1 GTATGAATTGATTTATTTAAATAATTTATTA
*
446375 GTATGAATTTATTTATTT---TAA---A--A
1 GTATGAATTGATTTATTTAAATAATTTATTA
446398 -TATGAATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTA-TTTAAATAATTTATTA
446429 TGTAGTTGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 18
0.68 0.03 0.29
Matches are distributed among these distances:
22 13 0.30
23 4 0.09
25 1 0.02
26 3 0.07
28 3 0.07
29 1 0.02
31 18 0.42
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (31 bp):
GTATGAATTGATTTATTTAAATAATTTATTA
Found at i:446401 original size:22 final size:22
Alignment explanation
Indices: 446376--446418 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
446366 AATTTATTAG
*
446376 TATGAATTTATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
446398 TATGAATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
446419 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:451277 original size:160 final size:160
Alignment explanation
Indices: 451002--451322 Score: 594
Period size: 160 Copynumber: 2.0 Consensus size: 160
450992 ACAACCATGT
451002 ATCCCGAATTCTGCAAGGAAATGATAAGTAGATGATGCTATCCAAACATTGCATCTCTACAAGAA
1 ATCCCGAATTCTGCAAGGAAATGATAAGTAGATGATGCTATCCAAACATTGCATCTCTACAAGAA
451067 GGTTGTCGACCAAAATTACAAAGGTGTATACACCTAATCCCTAACACCATATTTCTAAGCTAACA
66 GGTTGTCGACCAAAATTACAAAGGTGTATACACCTAATCCCTAACACCATATTTCTAAGCTAACA
451132 TGAGTGA-AGAGTC-AAAACGTAGAGAGAG
131 TGAGTGAGAGAGTCAAAAACGTAGAGAGAG
451160 ATCCCGGAATTCTGCAAGGAAATGATAAGTAGATGATATGCTATCCAAACATTGCATCTCTACAA
1 ATCCC-GAATTCTGCAAGGAAATGATAAGTAGATG--ATGCTATCCAAACATTGCATCTCTACAA
451225 GAAGGTTGTCGA-CAAAATTACAAAGGTGTATACACCTAATCCCTAACACCATATTTCTAAGCTA
63 GAAGGTTGTCGACCAAAATTACAAAGGTGTATACACCTAATCCCTAACACCATATTTCTAAGCTA
451289 ACATGAGTGAGAGAGTCAAAAACGTAGAGAGAG
128 ACATGAGTGAGAGAGTCAAAAACGTAGAGAGAG
451322 A
1 A
451323 AAGAGTGTTA
Statistics
Matches: 158, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
158 5 0.03
159 29 0.18
160 62 0.39
161 46 0.29
162 16 0.10
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (160 bp):
ATCCCGAATTCTGCAAGGAAATGATAAGTAGATGATGCTATCCAAACATTGCATCTCTACAAGAA
GGTTGTCGACCAAAATTACAAAGGTGTATACACCTAATCCCTAACACCATATTTCTAAGCTAACA
TGAGTGAGAGAGTCAAAAACGTAGAGAGAG
Found at i:453299 original size:12 final size:12
Alignment explanation
Indices: 453282--453314 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
453272 GCAGGGAAAC
453282 AGAGAAGGAGAA
1 AGAGAAGGAGAA
*
453294 AGAGAAGGAGAG
1 AGAGAAGGAGAA
453306 AGAGAAGGA
1 AGAGAAGGA
453315 TTTTAATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (12 bp):
AGAGAAGGAGAA
Found at i:471227 original size:35 final size:35
Alignment explanation
Indices: 471181--471292 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
471171 AAAATAGTCC
* * *
471181 TCAATTTCATTCTAAACCCCAATTTTTAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
* *
471216 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
** * *
471251 TCAATTAAATTTTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
471286 TCAATTT
1 TCAATTT
471293 AAGGTTTAGA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
Found at i:471356 original size:35 final size:35
Alignment explanation
Indices: 471288--471362 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
471278 AAAATACTTC
* * *
471288 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
* *
471323 AATTTAGGGTTTAGAATGAAATT-AAGGTGTTTTGA
1 AATTTAAGGTTTAGAATGAAATTGAA-GTATTTTGA
471358 AATTT
1 AATTT
471363 TGAACATGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
Found at i:473707 original size:22 final size:22
Alignment explanation
Indices: 473679--473720 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
473669 AAAATATCTT
*
473679 AAAAATAACAAAATCGATAGAA
1 AAAAATAACAAAATAGATAGAA
473701 AAAAATAACAAAATAGATAG
1 AAAAATAACAAAATAGATAG
473721 TGCATTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.69, C:0.07, G:0.10, T:0.14
Consensus pattern (22 bp):
AAAAATAACAAAATAGATAGAA
Found at i:474742 original size:26 final size:25
Alignment explanation
Indices: 474713--474768 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
474703 CTTCTCATAT
*
474713 TTTAAAATTTAAAATTTAATCTTTA
1 TTTAAAATGTAAAATTTAATCTTTA
* * *
474738 GTTTAAAATGTAAACTTTTATTTTTA
1 -TTTAAAATGTAAAATTTAATCTTTA
474764 TTTAA
1 TTTAA
474769 TTTAGTTCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (25 bp):
TTTAAAATGTAAAATTTAATCTTTA
Found at i:474968 original size:23 final size:23
Alignment explanation
Indices: 474942--474997 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 23
474932 TAACATTTGA
474942 TTAATTAACATTGTTT-TTGGATT
1 TTAATTAACATTGTTTATTGG-TT
* *
474965 TTAATTTACTTTGTTTGATTGGTT
1 TTAATTAACATTGTTT-ATTGGTT
474989 TTAAATTAA
1 TT-AATTAA
474998 AAGAGAGACA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 14 0.52
24 4 0.15
25 9 0.33
ACGTcount: A:0.27, C:0.04, G:0.12, T:0.57
Consensus pattern (23 bp):
TTAATTAACATTGTTTATTGGTT
Done.