Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008668.1 Hibiscus syriacus cultivar Beakdansim tig00111671_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: 2122653
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1428191 original size:30 final size:30
Alignment explanation
Indices: 1428157--1428236 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
1428147 CATATCTCTT
*
1428157 GTTTTATTTATTTCTGATTTT-GACATTTAA
1 GTTTTATTTATTTCT-ATTTTAGACACTTAA
*
1428187 GTTTT-TGTTATTT-TATTTTAGTCACTTAA
1 GTTTTAT-TTATTTCTATTTTAGACACTTAA
1428216 GTTTCTATTT-TTTCTATTTTA
1 GTTT-TATTTATTTCTATTTTA
1428237 ATCCTTTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
28 5 0.12
29 16 0.37
30 21 0.49
31 1 0.02
ACGTcount: A:0.20, C:0.07, G:0.09, T:0.64
Consensus pattern (30 bp):
GTTTTATTTATTTCTATTTTAGACACTTAA
Found at i:1428246 original size:30 final size:29
Alignment explanation
Indices: 1428157--1428248 Score: 75
Period size: 30 Copynumber: 3.1 Consensus size: 29
1428147 CATATCTCTT
* *
1428157 GTTTTATTTATTTCTGATTTTGA-CATTTAA
1 GTTTTATTT-TTTCT-ATTTTAATCCTTTAA
*
1428187 GTTTT-TGTTATTT-TATTTTAGTCAC-TTAA
1 GTTTTAT-TT-TTTCTATTTTAATC-CTTTAA
1428216 GTTTCTATTTTTTCTATTTTAATCCTTTAA
1 GTTT-TATTTTTTCTATTTTAATCCTTTAA
1428246 GTT
1 GTT
1428249 AATGTTTTCA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
28 5 0.10
29 15 0.29
30 30 0.59
31 1 0.02
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.62
Consensus pattern (29 bp):
GTTTTATTTTTTCTATTTTAATCCTTTAA
Found at i:1431375 original size:19 final size:18
Alignment explanation
Indices: 1431353--1431399 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
1431343 AAAGAAGTAA
1431353 AAAAACAAAGA-AAAAAAG
1 AAAAACAAA-ATAAAAAAG
*
1431371 CAAAAAGAAAATAAAAAAG
1 -AAAAACAAAATAAAAAAG
*
1431390 AGAAACAAAA
1 AAAAACAAAA
1431400 ACAACGGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.81, C:0.06, G:0.11, T:0.02
Consensus pattern (18 bp):
AAAAACAAAATAAAAAAG
Found at i:1435579 original size:21 final size:21
Alignment explanation
Indices: 1435498--1435581 Score: 71
Period size: 21 Copynumber: 3.9 Consensus size: 21
1435488 TTGGTGCAGA
* *
1435498 GGGAATCGATACCCCTTGAAG
1 GGGAATCGATACCCCCTGTAG
* *
1435519 GGGAA-CTGAGTCCCCCCTTTAAAG
1 GGGAATC-GA-TACCCCCTGT--AG
* *
1435543 GGGAACCGATTCCCCCTGTAG
1 GGGAATCGATACCCCCTGTAG
1435564 GGGAATCGATACCCCCTG
1 GGGAATCGATACCCCCTG
1435582 GAGGTTCTGT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
20 1 0.02
21 25 0.50
22 6 0.12
23 8 0.16
24 9 0.18
25 1 0.02
ACGTcount: A:0.24, C:0.30, G:0.27, T:0.19
Consensus pattern (21 bp):
GGGAATCGATACCCCCTGTAG
Found at i:1437177 original size:18 final size:18
Alignment explanation
Indices: 1437154--1437194 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1437144 AGAACAGCAT
1437154 GAGGAACAAGCACGAAC-A
1 GAGGAACAAGCAC-AACTA
1437172 GAGGAACAAGCACAACTA
1 GAGGAACAAGCACAACTA
1437190 GAGGA
1 GAGGA
1437195 TCAAATGCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.49, C:0.20, G:0.29, T:0.02
Consensus pattern (18 bp):
GAGGAACAAGCACAACTA
Found at i:1445971 original size:21 final size:21
Alignment explanation
Indices: 1445945--1446005 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
1445935 CCCCCTTTGA
* *
1445945 AGGGGAACCGATTCCCCCCAC
1 AGGGGAATCGATACCCCCCAC
1445966 AGGGGAATCGATACCCCCCAC
1 AGGGGAATCGATACCCCCCAC
1445987 AGGGGAATCGATACCCCCC
1 AGGGGAATCGATACCCCCC
1446006 TGGGGTTCTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.26, C:0.39, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAATCGATACCCCCCAC
Found at i:1450677 original size:21 final size:21
Alignment explanation
Indices: 1450651--1450702 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1450641 GGAGTGTGGG
*
1450651 GGGAATTGGTACCCCCTCATA
1 GGGAATCGGTACCCCCTCATA
1450672 GGGAATCGGTACCCCCTCATA
1 GGGAATCGGTACCCCCTCATA
1450693 GGGAATCGGT
1 GGGAATCGGT
1450703 TCTTGCAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.27, G:0.29, T:0.21
Consensus pattern (21 bp):
GGGAATCGGTACCCCCTCATA
Found at i:1450851 original size:34 final size:35
Alignment explanation
Indices: 1450786--1450851 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
1450776 AAACCTGGGC
*
1450786 GAATCGGTACCCCCTGGGGGGAATCTATTCCCGGG
1 GAATCGGTACCCCCTGGGGGGAATATATTCCCGGG
*
1450821 GAATCGGTACCCCCTGGGGGG-ATATGTTCCC
1 GAATCGGTACCCCCTGGGGGGAATATATTCCC
1450852 TCTGGCAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 8 0.28
35 21 0.72
ACGTcount: A:0.17, C:0.29, G:0.33, T:0.21
Consensus pattern (35 bp):
GAATCGGTACCCCCTGGGGGGAATATATTCCCGGG
Found at i:1451068 original size:19 final size:20
Alignment explanation
Indices: 1451044--1451083 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1451034 AATTTAATCG
*
1451044 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
1451063 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
1451083 A
1 A
1451084 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:1454587 original size:19 final size:20
Alignment explanation
Indices: 1454563--1454602 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1454553 AATTTAATCG
*
1454563 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
1454582 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
1454602 A
1 A
1454603 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:1456577 original size:34 final size:34
Alignment explanation
Indices: 1456537--1456605 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
1456527 CGTTCTAAGT
1456537 CCACCGGTGTCCTCCTTGTCTCCGTCGTCACCGA
1 CCACCGGTGTCCTCCTTGTCTCCGTCGTCACCGA
1456571 CCACCGGTGTCCTCCTTGTCTCCGTCGTCACCGA
1 CCACCGGTGTCCTCCTTGTCTCCGTCGTCACCGA
1456605 C
1 C
1456606 GCGTGAGGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.09, C:0.45, G:0.20, T:0.26
Consensus pattern (34 bp):
CCACCGGTGTCCTCCTTGTCTCCGTCGTCACCGA
Found at i:1456713 original size:10 final size:10
Alignment explanation
Indices: 1456698--1456722 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1456688 TAAGTGTCTC
1456698 AAAATTTTAG
1 AAAATTTTAG
1456708 AAAATTTTAG
1 AAAATTTTAG
1456718 AAAAT
1 AAAAT
1456723 CCCATTAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (10 bp):
AAAATTTTAG
Found at i:1456922 original size:134 final size:134
Alignment explanation
Indices: 1456758--1457016 Score: 332
Period size: 134 Copynumber: 1.9 Consensus size: 134
1456748 TTAACTATTG
1456758 ACTTTGACCAAAAAGTCAAAATTTTTG-AAAAGTTATA-TTTTATGT-TTTCAACGTCCTGAGTC
1 ACTTTGACCAAAAAGTCAAAATTTTTGAAAAAGTTATATTTTTATGTATTTCAAC-T--TGAGTC
* *
1456820 CGAATCT-GAAGTCAGTTTTGCCAAATTCGAAC-CTGAAAGCCTCGAAATTGTCAGTCAAACCCG
63 CG-ATCTCGAAGTCAGTTTTGCCAAATTCGAACTC-AAAAGCCTCGAAATTATCAGTCAAACCCG
1456883 TTGACTTTA
126 TTGACTTTA
* * *
1456892 ACTTTGACCAAAAAGT-TAAATTTTTCGAAAAAGTTATATTTTTATGTATTTCGACTTGAGTTCG
1 ACTTTGACCAAAAAGTCAAAATTTTT-GAAAAAGTTATATTTTTATGTATTTCAACTTGAGTCCG
* * * * *
1456956 ATTTCGAAGTCCGTTTTTCCAATTTCGTACTCAAAAGCCTCGAAATTATCAGTCAAACCCG
65 ATCTCGAAGTCAGTTTTGCCAAATTCGAACTCAAAAGCCTCGAAATTATCAGTCAAACCCG
1457017 AACATGTATA
Statistics
Matches: 109, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
133 11 0.10
134 72 0.66
135 11 0.10
136 9 0.08
137 6 0.06
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.35
Consensus pattern (134 bp):
ACTTTGACCAAAAAGTCAAAATTTTTGAAAAAGTTATATTTTTATGTATTTCAACTTGAGTCCGA
TCTCGAAGTCAGTTTTGCCAAATTCGAACTCAAAAGCCTCGAAATTATCAGTCAAACCCGTTGAC
TTTA
Found at i:1466264 original size:32 final size:31
Alignment explanation
Indices: 1466188--1466264 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
1466178 ATAATGTGAC
* *
1466188 TCTTAGGTAGGCCCTGCGGCCCTTAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTGAGATCAT
* **
1466219 TC-TCGGTTAGGCCCTACGGCCCTGAGATGTGT
1 TCTTAGG-TAGGCCCTACGGCCCTGAGAT-CAT
1466251 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
1466265 CGTGGCCCTG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
30 3 0.08
31 21 0.57
32 10 0.27
33 3 0.08
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTGAGATCAT
Found at i:1467695 original size:64 final size:63
Alignment explanation
Indices: 1467519--1467725 Score: 195
Period size: 64 Copynumber: 3.2 Consensus size: 63
1467509 GCACTAAGTA
* * * ** * ***
1467519 TGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGGCTTG
1 TGCATCGGTGCATGAAATGCATTCGATG-TTCAAAAATATTCAGGTGCATCGATGCATGGAGAG
* * ** *
1467583 TGCATCGTTGCATCAAATGCATTCGATGTTTGAAAATATTCAGAGTGCATTGATGCATGGAGAG
1 TGCATCGGTGCATGAAATGCATTCGATGTTCAAAAATATTCAG-GTGCATCGATGCATGGAGAG
*
1467647 TGAATCGGTGCATGAAATGCATTCGATGTTCAATTAAATCA-T-AGGTGCATCGATGCATGGACT
1 TGCATCGGTGCATGAAATGCATTCGATGTTCAA--AAAT-ATTCAGGTGCATCGATGCATGGA--
1467710 GA-
61 GAG
1467712 TGCATCGGTGCATG
1 TGCATCGGTGCATG
1467726 CCTTTGAAAA
Statistics
Matches: 119, Mismatches: 18, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
63 10 0.08
64 86 0.72
65 15 0.13
66 7 0.06
67 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.30
Consensus pattern (63 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTCAAAAATATTCAGGTGCATCGATGCATGGAGAG
Found at i:1468376 original size:18 final size:19
Alignment explanation
Indices: 1468345--1468384 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1468335 CAAGCATCCA
*
1468345 AAACAAAAATATCCAAA-C
1 AAACAAAAACATCCAAATC
*
1468363 AAACATAAACATCCAAATC
1 AAACAAAAACATCCAAATC
1468382 AAA
1 AAA
1468385 ATGTTTAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.65, C:0.23, G:0.00, T:0.12
Consensus pattern (19 bp):
AAACAAAAACATCCAAATC
Found at i:1474227 original size:22 final size:21
Alignment explanation
Indices: 1474185--1474224 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1474175 GAGTTTGTTT
*
1474185 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1474206 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1474225 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1476178 original size:64 final size:63
Alignment explanation
Indices: 1476110--1476287 Score: 182
Period size: 64 Copynumber: 2.8 Consensus size: 63
1476100 GGGACACTTA
*
1476110 GTGCATCGGTGCACTAAG-TATGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTG
1 GTGCATCGATGCA-T-AGCTATGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTG
* * * ** *
1476174 GTGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTG-AAAATATTCAG
1 GTGCATCGATGCATAGC-TATGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTG
* ** *
1476237 AGTGCATCGATGCATGGAGAGTGCATC-AGTGCATGAAATGCATTCGATGTT
1 -GTGCATCGATGCATAGCTA-TGCATCGA-TGCATAAAATGCATTCGATGTT
1476288 CAATTAAATC
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
62 1 0.01
63 10 0.10
64 87 0.89
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (63 bp):
GTGCATCGATGCATAGCTATGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTG
Found at i:1476306 original size:64 final size:62
Alignment explanation
Indices: 1476130--1476336 Score: 195
Period size: 64 Copynumber: 3.2 Consensus size: 62
1476120 GCACTAAGTA
* * ** * ***
1476130 TGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGGCTTG
1 TGCATCG-TGCATGAAATGCATTCGATG-TTCAAAAATATTCAGGTGCATCGATGCATGGAGAG
* **
1476194 TGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTCAGAGTGCATCGATGCATGGAGAG
1 TGCATCG-TGCATGAAATGCATTCGATGTTCAAAAATATTCAG-GTGCATCGATGCATGGAGAG
1476258 TGCATCAGTGCATGAAATGCATTCGATGTTCAATTAAATCA-T-AGGTGCATCGATGCATGGACT
1 TGCATC-GTGCATGAAATGCATTCGATGTTCAA--AAAT-ATTCAGGTGCATCGATGCATGGA--
1476321 GA-
60 GAG
1476323 TGCATCGGTGCATG
1 TGCATC-GTGCATG
1476337 CCTTTGAAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
63 10 0.08
64 89 0.72
65 16 0.13
66 7 0.06
67 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (62 bp):
TGCATCGTGCATGAAATGCATTCGATGTTCAAAAATATTCAGGTGCATCGATGCATGGAGAG
Found at i:1482160 original size:20 final size:20
Alignment explanation
Indices: 1482097--1482160 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 20
1482087 AATATAAGTT
1482097 TATATA-AATTATATATAAAC
1 TATATATAATTAT-TATAAAC
*
1482117 TATAT-TTA-TATTATAAAC
1 TATATATAATTATTATAAAC
*
1482135 --TATATAATTATTATAAGC
1 TATATATAATTATTATAAAC
1482153 TATATATA
1 TATATATA
1482161 TAATTGTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 3 0.08
17 2 0.06
18 16 0.44
19 3 0.08
20 12 0.33
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (20 bp):
TATATATAATTATTATAAAC
Found at i:1482249 original size:2 final size:2
Alignment explanation
Indices: 1482242--1482296 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
1482232 ATTTATATTA
1482242 AT AT AT AT AT AT A- 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
1482283 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1482297 TCAAAGTGAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1482429 original size:19 final size:19
Alignment explanation
Indices: 1482394--1482448 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
1482384 TTGATAAATT
*
1482394 TTGAGAATATAGA--GAAA
1 TTGAGAATTTAGAGGGAAA
1482411 TTGAGAATTTAGAGGGAAA
1 TTGAGAATTTAGAGGGAAA
* *
1482430 TTGGGAAAATTAGAGGGAA
1 TTGAG-AATTTAGAGGGAA
1482449 TAGAAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 12 0.38
19 8 0.25
20 12 0.38
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (19 bp):
TTGAGAATTTAGAGGGAAA
Found at i:1482452 original size:46 final size:45
Alignment explanation
Indices: 1482369--1482457 Score: 108
Period size: 46 Copynumber: 2.0 Consensus size: 45
1482359 TTTTATTTGG
* * *
1482369 GAATTTAGAGGGAAATTGATAAATTTTGAGAATATAGAGAAATTGA
1 GAATTTAGAGGGAAATTGAGAAAATTAGAGAATATAGA-AAATTGA
* *
1482415 GAATTTAGAGGGAAATTGGGAAAATTAGAGGGA-ATAGAAAATT
1 GAATTTAGAGGGAAATTGAGAAAATTAGA-GAATATAGAAAATT
1482458 TTGGGAAGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
45 5 0.14
46 30 0.81
47 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.27, T:0.27
Consensus pattern (45 bp):
GAATTTAGAGGGAAATTGAGAAAATTAGAGAATATAGAAAATTGA
Found at i:1482679 original size:8 final size:8
Alignment explanation
Indices: 1482666--1482719 Score: 108
Period size: 8 Copynumber: 6.8 Consensus size: 8
1482656 TTTCTATATA
1482666 TATGTACG
1 TATGTACG
1482674 TATGTACG
1 TATGTACG
1482682 TATGTACG
1 TATGTACG
1482690 TATGTACG
1 TATGTACG
1482698 TATGTACG
1 TATGTACG
1482706 TATGTACG
1 TATGTACG
1482714 TATGTA
1 TATGTA
1482720 TAAACTATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 46 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (8 bp):
TATGTACG
Found at i:1482900 original size:7 final size:7
Alignment explanation
Indices: 1482888--1482962 Score: 73
Period size: 7 Copynumber: 10.7 Consensus size: 7
1482878 AAAAAAATCC
*
1482888 TAAACCT
1 TAAACCA
*
1482895 TAAACCC
1 TAAACCA
1482902 TAAA-CA
1 TAAACCA
1482908 TTAAACCA
1 -TAAACCA
*
1482916 TACA-CA
1 TAAACCA
*
1482922 CTAAGCCA
1 -TAAACCA
1482930 TAAACCA
1 TAAACCA
1482937 TAAACCA
1 TAAACCA
*
1482944 TAAACCT
1 TAAACCA
1482951 TAAACCA
1 TAAACCA
1482958 TAAAC
1 TAAAC
1482963 TCTAATGTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
6 3 0.05
7 49 0.88
8 4 0.07
ACGTcount: A:0.51, C:0.29, G:0.01, T:0.19
Consensus pattern (7 bp):
TAAACCA
Found at i:1482905 original size:14 final size:14
Alignment explanation
Indices: 1482888--1482962 Score: 89
Period size: 14 Copynumber: 5.4 Consensus size: 14
1482878 AAAAAAATCC
*
1482888 TAAACCTTAAACCC
1 TAAACCTTAAACCA
*
1482902 TAAACATTAAACCA
1 TAAACCTTAAACCA
* *
1482916 TACACAC-TAAGCCA
1 TAAAC-CTTAAACCA
*
1482930 TAAACCATAAACCA
1 TAAACCTTAAACCA
1482944 TAAACCTTAAACCA
1 TAAACCTTAAACCA
1482958 TAAAC
1 TAAAC
1482963 TCTAATGTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
13 1 0.02
14 50 0.98
ACGTcount: A:0.51, C:0.29, G:0.01, T:0.19
Consensus pattern (14 bp):
TAAACCTTAAACCA
Found at i:1482913 original size:21 final size:21
Alignment explanation
Indices: 1482888--1482967 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
1482878 AAAAAAATCC
*
1482888 TAAACCTTAAACCCTAAACAT
1 TAAACCATAAACCCTAAACAT
* * *
1482909 TAAACCATACACACTAAGCCA-
1 TAAACCATAAACCCTAA-ACAT
* *
1482930 TAAACCATAAACCATAAACCT
1 TAAACCATAAACCCTAAACAT
*
1482951 TAAACCATAAACTCTAA
1 TAAACCATAAACCCTAA
1482968 TGTAAATAGA
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 1 0.02
21 43 0.93
22 2 0.04
ACGTcount: A:0.50, C:0.29, G:0.01, T:0.20
Consensus pattern (21 bp):
TAAACCATAAACCCTAAACAT
Found at i:1483621 original size:21 final size:21
Alignment explanation
Indices: 1483597--1483638 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1483587 AAAAATGCAC
1483597 TTAAGTGGGAAAAAAGCAAAA
1 TTAAGTGGGAAAAAAGCAAAA
* * *
1483618 TTAATTGGGGAAAAAGTAAAA
1 TTAAGTGGGAAAAAAGCAAAA
1483639 CCATTCAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.24, T:0.19
Consensus pattern (21 bp):
TTAAGTGGGAAAAAAGCAAAA
Found at i:1483819 original size:13 final size:13
Alignment explanation
Indices: 1483801--1483845 Score: 72
Period size: 13 Copynumber: 3.3 Consensus size: 13
1483791 CCATGTACAG
1483801 TATATATAAACTA
1 TATATATAAACTA
1483814 TATATATATAACCTA
1 TATATATA-AA-CTA
1483829 TATATATAAACTA
1 TATATATAAACTA
1483842 TATA
1 TATA
1483846 AAGTAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 15 0.50
14 4 0.13
15 11 0.37
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:1483821 original size:15 final size:15
Alignment explanation
Indices: 1483801--1483845 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
1483791 CCATGTACAG
1483801 TATATATAAACTATA
1 TATATATAAACTATA
*
1483816 TATATAT-AAC-CTA
1 TATATATAAACTATA
1483829 TATATATAAACTATA
1 TATATATAAACTATA
1483844 TA
1 TA
1483846 AAGTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 9 0.35
14 6 0.23
15 11 0.42
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (15 bp):
TATATATAAACTATA
Found at i:1483948 original size:7 final size:7
Alignment explanation
Indices: 1483932--1483983 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
1483922 ACCCTAATCA
*
1483932 TAAACTC
1 TAAACCC
1483939 TAAACCC
1 TAAACCC
**
1483946 TAAACTT
1 TAAACCC
1483953 TAAACCC
1 TAAACCC
*
1483960 TAAACAC
1 TAAACCC
1483967 TAAACCC
1 TAAACCC
*
1483974 TAAACTC
1 TAAACCC
1483981 TAA
1 TAA
1483984 TGTAAATGGA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAACCC
Found at i:1483951 original size:14 final size:14
Alignment explanation
Indices: 1483932--1483983 Score: 86
Period size: 14 Copynumber: 3.7 Consensus size: 14
1483922 ACCCTAATCA
1483932 TAAACTCTAAACCC
1 TAAACTCTAAACCC
*
1483946 TAAACTTTAAACCC
1 TAAACTCTAAACCC
*
1483960 TAAACACTAAACCC
1 TAAACTCTAAACCC
1483974 TAAACTCTAA
1 TAAACTCTAA
1483984 TGTAAATGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACTCTAAACCC
Found at i:1483977 original size:21 final size:21
Alignment explanation
Indices: 1483932--1483983 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1483922 ACCCTAATCA
* **
1483932 TAAACTCTAAACCCTAAACTT
1 TAAACTCTAAACACTAAACCC
*
1483953 TAAACCCTAAACACTAAACCC
1 TAAACTCTAAACACTAAACCC
1483974 TAAACTCTAA
1 TAAACTCTAA
1483984 TGTAAATGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACTCTAAACACTAAACCC
Found at i:1484069 original size:29 final size:27
Alignment explanation
Indices: 1484005--1484068 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
1483995 TAACACTAAT
1484005 GCATATATATTTGTAATAAAAGAGTGG
1 GCATATATATTTGTAATAAAAGAGTGG
1484032 GCATATATATTTGTAATAAAAGAGTGG
1 GCATATATATTTGTAATAAAAGAGTGG
1484059 GCATATATAT
1 GCATATATAT
1484069 ATTGGGTCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (27 bp):
GCATATATATTTGTAATAAAAGAGTGG
Found at i:1484215 original size:22 final size:22
Alignment explanation
Indices: 1484176--1484222 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
1484166 TTATTTTTTC
1484176 TTTATATAAATTAAACTATATAA
1 TTTATATAAATTAAACTATA-AA
1484199 TTTATATAAA-TAAACTATAAA
1 TTTATATAAATTAAACTATAAA
1484220 TTT
1 TTT
1484223 TCCTTTGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 5 0.21
22 9 0.38
23 10 0.42
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTATATAAATTAAACTATAAA
Found at i:1484272 original size:25 final size:22
Alignment explanation
Indices: 1484244--1484296 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
1484234 ATTAATCATG
1484244 TTTTATCTATTATACATTTAAATAA
1 TTTTATCTATT-T-CA-TTAAATAA
* *
1484269 TTTTATTTATTTTATTAAATAA
1 TTTTATCTATTTCATTAAATAA
1484291 TTTTAT
1 TTTTAT
1484297 ATAATATGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 14 0.54
23 1 0.04
24 1 0.04
25 10 0.38
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTATCTATTTCATTAAATAA
Found at i:1484494 original size:16 final size:16
Alignment explanation
Indices: 1484473--1484514 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1484463 GATCAGGTTA
*
1484473 AAAACATGTCAAGTTG
1 AAAACAGGTCAAGTTG
* *
1484489 AAAACAGGTTAGGTTG
1 AAAACAGGTCAAGTTG
1484505 AAAACAGGTC
1 AAAACAGGTC
1484515 GGGTAATACC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.21
Consensus pattern (16 bp):
AAAACAGGTCAAGTTG
Found at i:1485710 original size:33 final size:33
Alignment explanation
Indices: 1485668--1485790 Score: 237
Period size: 33 Copynumber: 3.7 Consensus size: 33
1485658 TGAGGATAAC
1485668 ATACGGGTAAACATCTGGGTTCCCAAATAGGAA
1 ATACGGGTAAACATCTGGGTTCCCAAATAGGAA
1485701 ATACGGGTAAACATCTGGGTTCCCAAATAGGAA
1 ATACGGGTAAACATCTGGGTTCCCAAATAGGAA
1485734 ATACGGGTAAACATCTGGGTTCCCAAATAGGAA
1 ATACGGGTAAACATCTGGGTTCCCAAATAGGAA
*
1485767 ATACGAGTAAACATCTGGGTTCCC
1 ATACGGGTAAACATCTGGGTTCCC
1485791 GTAAAAGTAT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22
Consensus pattern (33 bp):
ATACGGGTAAACATCTGGGTTCCCAAATAGGAA
Found at i:1487750 original size:28 final size:28
Alignment explanation
Indices: 1487719--1487788 Score: 140
Period size: 28 Copynumber: 2.5 Consensus size: 28
1487709 AATTGGTCCC
1487719 CAAACTTTTGAATGTTTCAATTTCATCT
1 CAAACTTTTGAATGTTTCAATTTCATCT
1487747 CAAACTTTTGAATGTTTCAATTTCATCT
1 CAAACTTTTGAATGTTTCAATTTCATCT
1487775 CAAACTTTTGAATG
1 CAAACTTTTGAATG
1487789 ATTTTGGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.44
Consensus pattern (28 bp):
CAAACTTTTGAATGTTTCAATTTCATCT
Found at i:1490204 original size:18 final size:18
Alignment explanation
Indices: 1490132--1490205 Score: 71
Period size: 18 Copynumber: 3.9 Consensus size: 18
1490122 TCTTATGTAA
*
1490132 ATTTTTAAATTCTTTTAT
1 ATTTTTAAATTTTTTTAT
*
1490150 ATTTTAAAAAATTTTCTTTAT
1 ATTTT--TAAATTTT-TTTAT
1490171 ATTTTT-AATTTGTTTT-T
1 ATTTTTAAATTT-TTTTAT
1490188 ATTTTTGAAATTTTTTTA
1 ATTTTT-AAATTTTTTTA
1490206 AGTTCGTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
17 7 0.15
18 17 0.37
19 6 0.13
20 6 0.13
21 10 0.22
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (18 bp):
ATTTTTAAATTTTTTTAT
Found at i:1495610 original size:17 final size:18
Alignment explanation
Indices: 1495588--1495623 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1495578 CCGGTCCGAT
1495588 CCGACCCG-ACCGTTGAC
1 CCGACCCGAACCGTTGAC
1495605 CCGACCCGAACCGTTGAC
1 CCGACCCGAACCGTTGAC
1495623 C
1 C
1495624 GTTGACTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.19, C:0.47, G:0.22, T:0.11
Consensus pattern (18 bp):
CCGACCCGAACCGTTGAC
Found at i:1497195 original size:32 final size:31
Alignment explanation
Indices: 1497159--1497236 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 31
1497149 ATATATTTAA
*
1497159 AAATAGAATTATAAAATTATATTTGATTTATC
1 AAATA-AATTATAAAACTATATTTGATTTATC
1497191 AAATAAAATTATAAAACTATATTTGATTTATC
1 AAAT-AAATTATAAAACTATATTTGATTTATC
1497223 AAATAACATTATAA
1 AAATAA-ATTATAA
1497237 TATGAAAAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
31 2 0.05
32 40 0.93
33 1 0.02
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (31 bp):
AAATAAATTATAAAACTATATTTGATTTATC
Found at i:1497559 original size:4 final size:4
Alignment explanation
Indices: 1497550--1497584 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
1497540 ATTAAATATA
1497550 TAAT TAAT TAAT TAAT T-AT ATAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT -TAAT TAAT TAAT TAA
1497585 AAAATAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 2 0.07
4 25 0.86
5 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
TAAT
Found at i:1497569 original size:20 final size:20
Alignment explanation
Indices: 1497540--1497585 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1497530 TAAACTATTC
1497540 ATTAAATATATAATTAATTA
1 ATTAAATATATAATTAATTA
*
1497560 ATTAATTATATAATTAATTA
1 ATTAAATATATAATTAATTA
1497580 ATTAAA
1 ATTAAA
1497586 AAATAAGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTAAATATATAATTAATTA
Found at i:1502090 original size:29 final size:29
Alignment explanation
Indices: 1502035--1502090 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1502025 ATTCAATTTT
* *
1502035 TGTATTTGCTATTTAGTCCCTTAAATTCC
1 TGTATTTGCTATTTAGTCACATAAATTCC
*
1502064 TGTATTTGCTATTTTAGT-ACATCAATT
1 TGTATTTGCTA-TTTAGTCACATAAATT
1502091 TTATGTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 17 0.74
30 6 0.26
ACGTcount: A:0.23, C:0.16, G:0.11, T:0.50
Consensus pattern (29 bp):
TGTATTTGCTATTTAGTCACATAAATTCC
Found at i:1506941 original size:82 final size:82
Alignment explanation
Indices: 1506804--1506968 Score: 330
Period size: 82 Copynumber: 2.0 Consensus size: 82
1506794 ATGATAACAA
1506804 CGATTCAATATTGTTTCCACCTAAAAGCTTATGATTACAATTATTTAAATATCATCGTAAACATA
1 CGATTCAATATTGTTTCCACCTAAAAGCTTATGATTACAATTATTTAAATATCATCGTAAACATA
1506869 TTCAGGCTGCATGATAC
66 TTCAGGCTGCATGATAC
1506886 CGATTCAATATTGTTTCCACCTAAAAGCTTATGATTACAATTATTTAAATATCATCGTAAACATA
1 CGATTCAATATTGTTTCCACCTAAAAGCTTATGATTACAATTATTTAAATATCATCGTAAACATA
1506951 TTCAGGCTGCATGATAC
66 TTCAGGCTGCATGATAC
1506968 C
1 C
1506969 TGAAAAGGCT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (82 bp):
CGATTCAATATTGTTTCCACCTAAAAGCTTATGATTACAATTATTTAAATATCATCGTAAACATA
TTCAGGCTGCATGATAC
Found at i:1508242 original size:58 final size:58
Alignment explanation
Indices: 1508147--1508547 Score: 630
Period size: 57 Copynumber: 7.0 Consensus size: 58
1508137 AAAAAACTCG
*
1508147 GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACATAATTAATTTCTGTTC
1 GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTC
* *
1508205 GGTGCTATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTTTGTTC
1 GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTC
* *
1508263 GGTGATA-TTTTGTAAATATTTTTAAAAGGGTGCCTAATATGTAATTAATTTTTGTTC
1 GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTC
* *
1508320 GTTGATA-TTTTGTAAATATTTTTAAAAGGGTGTCTAATACGTAATTAATTTCTGTTC
1 GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTC
*
1508377 GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCTTAATACGTAATTAATTTCT-TTCC
1 GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTT-C
* *
1508435 GGTGATA-TTTTGTAAATATTTTTAAAATGGTGCCTAATACATAATTAATTTCTGTTC
1 GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTC
* * * * *
1508492 GGTGCTTTTTTTGTAAATATTTTTAAAAGAGTGCCTAGTACGTAAATAATTTCTGT
1 GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGT
1508548 AAGGGTGAAG
Statistics
Matches: 317, Mismatches: 22, Indels: 8
0.91 0.06 0.02
Matches are distributed among these distances:
57 159 0.50
58 158 0.50
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (58 bp):
GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTC
Found at i:1508249 original size:29 final size:30
Alignment explanation
Indices: 1508216--1508315 Score: 82
Period size: 29 Copynumber: 3.5 Consensus size: 30
1508206 GTGCTATTTT
1508216 TGTAAAT-ATTTTTAAAAGGGTGCCTAATA
1 TGTAAATAATTTTTAAAAGGGTGCCTAATA
* * **** * * *
1508245 CGTAATTAATTTTT-GTTCGGTG-ATATTT
1 TGTAAATAATTTTTAAAAGGGTGCCTAATA
1508273 TGTAAAT-ATTTTTAAAAGGGTGCCTAATA
1 TGTAAATAATTTTTAAAAGGGTGCCTAATA
*
1508302 TGTAATTAATTTTT
1 TGTAAATAATTTTT
1508316 GTTCGTTGAT
Statistics
Matches: 48, Mismatches: 19, Indels: 7
0.65 0.26 0.09
Matches are distributed among these distances:
27 6 0.12
28 12 0.25
29 18 0.38
30 12 0.25
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.46
Consensus pattern (30 bp):
TGTAAATAATTTTTAAAAGGGTGCCTAATA
Found at i:1508285 original size:28 final size:28
Alignment explanation
Indices: 1508254--1508342 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 28
1508244 ACGTAATTAA
1508254 TTTTTGTTCGGTGATATTTTGTAAATAT
1 TTTTTGTTCGGTGATATTTTGTAAATAT
***** * * * * *
1508282 TTTTAAAAGGGTGCCTAATATGTAATTAA
1 TTTTTGTTCGGTG-ATATTTTGTAAATAT
*
1508311 TTTTTGTTCGTTGATATTTTGTAAATAT
1 TTTTTGTTCGGTGATATTTTGTAAATAT
1508339 TTTT
1 TTTT
1508343 AAAAGGGTGT
Statistics
Matches: 39, Mismatches: 21, Indels: 2
0.63 0.34 0.03
Matches are distributed among these distances:
28 22 0.56
29 17 0.44
ACGTcount: A:0.26, C:0.04, G:0.16, T:0.54
Consensus pattern (28 bp):
TTTTTGTTCGGTGATATTTTGTAAATAT
Found at i:1508301 original size:57 final size:57
Alignment explanation
Indices: 1508147--1508547 Score: 615
Period size: 58 Copynumber: 7.0 Consensus size: 57
1508137 AAAAAACTCG
*
1508147 GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACATAATTAATTTCTGTTC
1 GGTGATA-TTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTC
* *
1508205 GGTGCTATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTTTGTTC
1 GGTGATA-TTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTC
* *
1508263 GGTGATATTTTGTAAATATTTTTAAAAGGGTGCCTAATATGTAATTAATTTTTGTTC
1 GGTGATATTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTC
* *
1508320 GTTGATATTTTGTAAATATTTTTAAAAGGGTGTCTAATACGTAATTAATTTCTGTTC
1 GGTGATATTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTC
*
1508377 GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCTTAATACGTAATTAATTTCT-TTCC
1 GGTGATA-TTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTT-C
* *
1508435 GGTGATATTTTGTAAATATTTTTAAAATGGTGCCTAATACATAATTAATTTCTGTTC
1 GGTGATATTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTC
* * * * *
1508492 GGTGCTTTTTTTGTAAATATTTTTAAAAGAGTGCCTAGTACGTAAATAATTTCTGT
1 GGTG-ATATTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGT
1508548 AAGGGTGAAG
Statistics
Matches: 317, Mismatches: 22, Indels: 8
0.91 0.06 0.02
Matches are distributed among these distances:
57 158 0.50
58 159 0.50
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (57 bp):
GGTGATATTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTC
Found at i:1508389 original size:115 final size:115
Alignment explanation
Indices: 1508147--1508543 Score: 618
Period size: 115 Copynumber: 3.5 Consensus size: 115
1508137 AAAAAACTCG
* * *
1508147 GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACATAATTAATTTCTGTTCGGTGCTA
1 GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTTTGTTCGGTGATA
*
1508212 TTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTTTGTTC
66 -TTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTC
* *
1508263 GGTGATA-TTTTGTAAATATTTTTAAAAGGGTGCCTAATATGTAATTAATTTTTGTTCGTTGATA
1 GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTTTGTTCGGTGATA
*
1508327 TTTTGTAAATATTTTTAAAAGGGTGTCTAATACGTAATTAATTTCTGTTC
66 TTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTC
* *
1508377 GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCTTAATACGTAATTAATTTCTT-TCCGGTGAT
1 GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTT-TTGTTCGGTGAT
* *
1508441 ATTTTGTAAATATTTTTAAAATGGTGCCTAATACATAATTAATTTCTGTTC
65 ATTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTC
* * * * *
1508492 GGTGCTTTTTTTGTAAATATTTTTAAAAGAGTGCCTAGTACGTAAATAATTT
1 GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTT
1508544 CTGTAAGGGT
Statistics
Matches: 259, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
114 55 0.21
115 195 0.75
116 9 0.03
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (115 bp):
GGTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTTTGTTCGGTGATA
TTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTC
Found at i:1512054 original size:54 final size:54
Alignment explanation
Indices: 1511972--1512095 Score: 239
Period size: 54 Copynumber: 2.3 Consensus size: 54
1511962 TAACATGAAC
1511972 AGTGCATCGATGCATAAAACATCGAATACTAAATGTGTATCGATGCACTGCTAT
1 AGTGCATCGATGCATAAAACATCGAATACTAAATGTGTATCGATGCACTGCTAT
1512026 AGTGCATCGATGCATAAAACATCGAATACTAAATGTGTATCGATGCACTGCTAT
1 AGTGCATCGATGCATAAAACATCGAATACTAAATGTGTATCGATGCACTGCTAT
*
1512080 TGTGCATCGATGCATA
1 AGTGCATCGATGCATA
1512096 GCTACAGTAC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (54 bp):
AGTGCATCGATGCATAAAACATCGAATACTAAATGTGTATCGATGCACTGCTAT
Found at i:1512114 original size:11 final size:11
Alignment explanation
Indices: 1512098--1512137 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
1512088 GATGCATAGC
1512098 TACAGTACTGT
1 TACAGTACTGT
* *
1512109 TACAGTAATGC
1 TACAGTACTGT
1512120 TACAGTACTGT
1 TACAGTACTGT
1512131 TACAGTA
1 TACAGTA
1512138 TTTCCAGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (11 bp):
TACAGTACTGT
Found at i:1512124 original size:22 final size:22
Alignment explanation
Indices: 1512096--1512137 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1512086 TCGATGCATA
1512096 GCTACAGTACTGTTACAGTAAT
1 GCTACAGTACTGTTACAGTAAT
1512118 GCTACAGTACTGTTACAGTA
1 GCTACAGTACTGTTACAGTA
1512138 TTTCCAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (22 bp):
GCTACAGTACTGTTACAGTAAT
Found at i:1512637 original size:59 final size:59
Alignment explanation
Indices: 1512574--1512686 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 59
1512564 CTTCCCCTTT
* * *
1512574 CATTTTAGCACACGAAGTGCCCTAT-TCAAAAATCCATACCCTTAGTATGATTTTGTTAC
1 CATTTTAGCACACAAAATGCCCTATGT-AAAAATCCATACCATTAGTATGATTTTGTTAC
* *
1512633 CATTTTAGCACATAAAATGCCCTATGTGAAAATCCATACCATTAGTATGATTTT
1 CATTTTAGCACACAAAATGCCCTATGTAAAAATCCATACCATTAGTATGATTTT
1512687 CTTATCCTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 47 0.98
60 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.35
Consensus pattern (59 bp):
CATTTTAGCACACAAAATGCCCTATGTAAAAATCCATACCATTAGTATGATTTTGTTAC
Found at i:1512784 original size:118 final size:118
Alignment explanation
Indices: 1512603--1512820 Score: 255
Period size: 118 Copynumber: 1.8 Consensus size: 118
1512593 CCCTATTCAA
* * **
1512603 AAATCCATACCCTTAGTATGATTTTGTTACCATTTTAGCACATAAAATGCCCTATGTGAAAATCC
1 AAATCCATACACTCAGTATGATTTCCTTACCATTTTAGCACATAAAATGCCCTATGTGAAAATCC
* * * *
1512668 ATAC-CATTAGTATGATTTTCTTATCCTTGTAGCACCCTTAGTGCTTTATCTGG
66 ATACAC-TCAGTATAATTTCCTTATCATTGTAGCACCCTTAGTGCTTTATCTGG
* * *
1512721 AAATCTATACACTCAGTATGATTTCCTTACCATTTTAGCACA-ATCAGTGCTCCATATG-G-AAA
1 AAATCCATACACTCAGTATGATTTCCTTACCATTTTAGCACATA-AAATGC-CC-TATGTGAAAA
* *
1512783 TCTATACACTCAGTATAATTTCCTTATCATTTTAGCAC
63 TCCATACACTCAGTATAATTTCCTTATCATTGTAGCAC
1512821 ACAAAGTGCC
Statistics
Matches: 83, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
117 1 0.01
118 74 0.89
119 4 0.05
120 4 0.05
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (118 bp):
AAATCCATACACTCAGTATGATTTCCTTACCATTTTAGCACATAAAATGCCCTATGTGAAAATCC
ATACACTCAGTATAATTTCCTTATCATTGTAGCACCCTTAGTGCTTTATCTGG
Found at i:1512829 original size:59 final size:59
Alignment explanation
Indices: 1512718--1512829 Score: 181
Period size: 59 Copynumber: 1.9 Consensus size: 59
1512708 GTGCTTTATC
* *
1512718 TGGAAATCTATACACTCAGTATGATTTCCTTACCATTTTAGCACAATCAGTGCTCCATA
1 TGGAAATCTATACACTCAGTATAATTTCCTTACCATTTTAGCACAATAAGTGCTCCATA
*
1512777 TGGAAATCTATACACTCAGTATAATTTCCTTATCATTTTAGCACACA-AAGTGC
1 TGGAAATCTATACACTCAGTATAATTTCCTTACCATTTTAGCACA-ATAAGTGC
1512830 CATTCGGTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
59 48 0.98
60 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (59 bp):
TGGAAATCTATACACTCAGTATAATTTCCTTACCATTTTAGCACAATAAGTGCTCCATA
Found at i:1512829 original size:118 final size:118
Alignment explanation
Indices: 1512569--1512830 Score: 248
Period size: 118 Copynumber: 2.2 Consensus size: 118
1512559 GTATGCTTCC
* * * **
1512569 CCTT-TCATTTTAGCACACGAAGTGCCCTATTCAAAAATCCATACCCTTAGTATGATTTTGTTAC
1 CCTTATCATTTTAGCACACAAAGTGCCCTATTCAAAAATCCATACACTCAGTATGATTTCCTTAC
* *
1512633 CATTTTAGCACATAAAATGCCCTATGTGAAAATCCATACCATTAGTATGATTT
66 CATTTTAGCACATAAAATGCCCTATGTGAAAATCCATACCATCAGTATAATTT
* * * * ** ** ** *
1512686 TCTTATCCTTGTAGCACCCTTAGTGCTTTA-TCTGGAAATCTATACACTCAGTATGATTTCCTTA
1 CCTTATCATTTTAGCACACAAAGTGCCCTATTC-AAAAATCCATACACTCAGTATGATTTCCTTA
* * *
1512750 CCATTTTAGCACA-ATCAGTGCTCCATATG-G-AAATCTATA-CACTCAGTATAATTT
65 CCATTTTAGCACATA-AAATGC-CC-TATGTGAAAATCCATACCA-TCAGTATAATTT
1512804 CCTTATCATTTTAGCACACAAAGTGCC
1 CCTTATCATTTTAGCACACAAAGTGCC
1512831 ATTCGGTAAT
Statistics
Matches: 112, Mismatches: 27, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
117 8 0.07
118 97 0.87
119 3 0.03
120 4 0.04
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.35
Consensus pattern (118 bp):
CCTTATCATTTTAGCACACAAAGTGCCCTATTCAAAAATCCATACACTCAGTATGATTTCCTTAC
CATTTTAGCACATAAAATGCCCTATGTGAAAATCCATACCATCAGTATAATTT
Found at i:1513270 original size:63 final size:64
Alignment explanation
Indices: 1513161--1513321 Score: 179
Period size: 63 Copynumber: 2.5 Consensus size: 64
1513151 TTCTTTCACA
* *
1513161 GATGCATCGGTACACAACCTATGCATCAATGCA-TATATTACATTCGATGTTT-TCATCTTAAGG
1 GATGCATCGGTACACTACCTATGCATCGATGCATTATATTACATTCGATGTTTATCAT-TTAAGG
* * *
1513224 GATGCATCGATACACTACCTATGCATCGATGCATTA-ACTT-CCTTCGATGTTTAATTATTTAAG
1 GATGCATCGGTACACTACCTATGCATCGATGCATTATA-TTACATTCGATGTTT-ATCATTTAAG
*
1513287 T
64 G
* *
1513288 G-TGCATCGGTGCACTCACTTATGCATCGATGCAT
1 GATGCATCGGTACACT-ACCTATGCATCGATGCAT
1513322 CTTGCCCATA
Statistics
Matches: 84, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
63 54 0.64
64 27 0.32
65 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (64 bp):
GATGCATCGGTACACTACCTATGCATCGATGCATTATATTACATTCGATGTTTATCATTTAAGG
Found at i:1517162 original size:28 final size:28
Alignment explanation
Indices: 1517104--1517292 Score: 234
Period size: 29 Copynumber: 6.5 Consensus size: 28
1517094 CGTTGACCGA
1517104 GTGCTATTTTCGTAATTATTTTTAAAAGG
1 GTGCTATTTTCGTAATT-TTTTTAAAAGG
*
1517133 GTGTTATTTTCGTAATTTTTTTAAAAGG
1 GTGCTATTTTCGTAATTTTTTTAAAAGG
*
1517161 GTGCTATTTTCGTAATTTTTTTAAAAATATG
1 GTGCTATTTTCGTAATTTTTTT--AAA-AGG
1517192 GTGCTATTTTCGTAATTTTTTTAAAAGG
1 GTGCTATTTTCGTAATTTTTTTAAAAGG
* *
1517220 GTGCTATTTTCGTAAATATTTTTGAAAGG
1 GTGCTATTTTCGT-AATTTTTTTAAAAGG
* * * *
1517249 GTGTTATTTACGTAAATATTTTAAAAAGG
1 GTGCTATTTTCGT-AATTTTTTTAAAAGG
* *
1517278 GTGATAGTTTCGTAA
1 GTGCTATTTTCGTAA
1517293 ATATTTCCAA
Statistics
Matches: 143, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
28 49 0.34
29 67 0.47
30 3 0.02
31 24 0.17
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.48
Consensus pattern (28 bp):
GTGCTATTTTCGTAATTTTTTTAAAAGG
Found at i:1517217 original size:59 final size:57
Alignment explanation
Indices: 1517104--1517298 Score: 248
Period size: 59 Copynumber: 3.4 Consensus size: 57
1517094 CGTTGACCGA
*
1517104 GTGCTATTTTCGTAATTATTTTTAAAAGGGTGTTATTTTCGTAATTTTTTTAAAAGG
1 GTGCTATTTTCGTAATTATTTTTAAAAGGGTGCTATTTTCGTAATTTTTTTAAAAGG
*
1517161 GTGCTATTTTCGTAATT-TTTTTAAAAATATGGTGCTATTTTCGTAATTTTTTTAAAAGG
1 GTGCTATTTTCGTAATTATTTTT--AAA-AGGGTGCTATTTTCGTAATTTTTTTAAAAGG
* * * * * *
1517220 GTGCTATTTTCGTAAATATTTTTGAAAGGGTGTTATTTACGTAAATATTTTAAAAAGG
1 GTGCTATTTTCGTAATTATTTTTAAAAGGGTGCTATTTTCGT-AATTTTTTTAAAAGG
* * *
1517278 GTGATAGTTTCGTAAATATTT
1 GTGCTATTTTCGTAATTATTT
1517299 CCAAAAAAGG
Statistics
Matches: 122, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
56 5 0.04
57 30 0.25
58 37 0.30
59 45 0.37
60 5 0.04
ACGTcount: A:0.29, C:0.06, G:0.17, T:0.48
Consensus pattern (57 bp):
GTGCTATTTTCGTAATTATTTTTAAAAGGGTGCTATTTTCGTAATTTTTTTAAAAGG
Found at i:1517257 original size:88 final size:88
Alignment explanation
Indices: 1517104--1517275 Score: 265
Period size: 88 Copynumber: 2.0 Consensus size: 88
1517094 CGTTGACCGA
* *
1517104 GTGCTATTTTCGTAATTATTTTTAAAAGGGTGTTATTTTCGTAATTTTTTTAAAAGGGTGCTATT
1 GTGCTATTTTCGTAATTATTTTTAAAAGGGTGCTATTTTCGTAATATTTTTAAAAGGGTGCTATT
* * *
1517169 TTCGTAATTTTTTTAAAAATATG
66 TACGTAAATATTTTAAAAATATG
* *
1517192 GTGCTATTTTCGTAATT-TTTTTAAAAGGGTGCTATTTTCGTAAATATTTTTGAAAGGGTGTTAT
1 GTGCTATTTTCGTAATTATTTTTAAAAGGGTGCTATTTTCGT-AATATTTTTAAAAGGGTGCTAT
1517256 TTACGTAAATATTTTAAAAA
65 TTACGTAAATATTTTAAAAA
1517276 GGGTGATAGT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
87 23 0.30
88 53 0.70
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.49
Consensus pattern (88 bp):
GTGCTATTTTCGTAATTATTTTTAAAAGGGTGCTATTTTCGTAATATTTTTAAAAGGGTGCTATT
TACGTAAATATTTTAAAAATATG
Found at i:1517304 original size:29 final size:28
Alignment explanation
Indices: 1517111--1517313 Score: 149
Period size: 29 Copynumber: 7.0 Consensus size: 28
1517101 CGAGTGCTAT
* * *
1517111 TTTCGTAATTATTTTTAAAAGGGTGTTA
1 TTTCGTAAATATTTTAAAAAGGGTGATA
* * *
1517139 TTTTCGT-AATTTTTTTAAAAGGGTGCTA
1 -TTTCGTAAATATTTTAAAAAGGGTGATA
* * * *
1517167 TTTTCGTAATTTTTTTAAAAATATGGTGCTA
1 -TTTCGTAAATATTTT-AAAA-AGGGTGATA
* * *
1517198 TTTTCGT-AATTTTTTTAAAAGGGTGCTA
1 -TTTCGTAAATATTTTAAAAAGGGTGATA
** *
1517226 TTTTCGTAAATATTTTTGAAAGGGTGTTA
1 -TTTCGTAAATATTTTAAAAAGGGTGATA
1517255 TTTACGTAAATATTTTAAAAAGGGTGATA
1 TTT-CGTAAATATTTTAAAAAGGGTGATA
* *
1517284 GTTTCGTAAATATTTCCAAAAAAGGTGATA
1 -TTTCGTAAATATTT-TAAAAAGGGTGATA
1517314 ATTGTGTAAA
Statistics
Matches: 150, Mismatches: 17, Indels: 13
0.83 0.09 0.07
Matches are distributed among these distances:
28 43 0.29
29 67 0.45
30 25 0.17
31 15 0.10
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (28 bp):
TTTCGTAAATATTTTAAAAAGGGTGATA
Found at i:1520562 original size:29 final size:29
Alignment explanation
Indices: 1520530--1520620 Score: 69
Period size: 29 Copynumber: 3.1 Consensus size: 29
1520520 TGATGTTTTT
1520530 GTAAATATTTTTAAAAGGGTGCCTAATAC
1 GTAAATATTTTTAAAAGGGTGCCTAATAC
* * **** * **
1520559 GTAATTAATTTCT-GTTCGGTG-CTATTTTT
1 GTAAAT-ATTTTTAAAAGGGTGCCTA-ATAC
1520588 GTAAATATTTTTAAAAGGGTGCCTAATAC
1 GTAAATATTTTTAAAAGGGTGCCTAATAC
1520617 GTAA
1 GTAA
1520621 TTAATTTCTG
Statistics
Matches: 40, Mismatches: 18, Indels: 8
0.61 0.27 0.12
Matches are distributed among these distances:
28 8 0.20
29 24 0.60
30 8 0.20
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.41
Consensus pattern (29 bp):
GTAAATATTTTTAAAAGGGTGCCTAATAC
Found at i:1520615 original size:58 final size:58
Alignment explanation
Indices: 1520525--1520653 Score: 249
Period size: 58 Copynumber: 2.2 Consensus size: 58
1520515 ACGGGTGATG
1520525 TTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTCGGTGCTA
1 TTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTCGGTGCTA
*
1520583 TTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTCGGTGTTA
1 TTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTCGGTGCTA
1520641 TTTTTGTAAATAT
1 TTTTTGTAAATAT
1520654 CTTAAAGTAC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
58 70 1.00
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (58 bp):
TTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTCGGTGCTA
Found at i:1520637 original size:29 final size:29
Alignment explanation
Indices: 1520547--1520637 Score: 69
Period size: 29 Copynumber: 3.1 Consensus size: 29
1520537 TTTTTAAAAG
1520547 GGTGCCTAATACGTAATTAATTTCTGTTC
1 GGTGCCTAATACGTAATTAATTTCTGTTC
* ** * * ****
1520576 GGTG-CTATTTTTGTAAAT-ATTTTTAAAAG
1 GGTGCCTA-ATACGTAATTAATTTCT-GTTC
1520605 GGTGCCTAATACGTAATTAATTTCTGTTC
1 GGTGCCTAATACGTAATTAATTTCTGTTC
1520634 GGTG
1 GGTG
1520638 TTATTTTTGT
Statistics
Matches: 40, Mismatches: 18, Indels: 8
0.61 0.27 0.12
Matches are distributed among these distances:
28 8 0.20
29 24 0.60
30 8 0.20
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (29 bp):
GGTGCCTAATACGTAATTAATTTCTGTTC
Found at i:1525347 original size:82 final size:82
Alignment explanation
Indices: 1525210--1525373 Score: 249
Period size: 82 Copynumber: 2.0 Consensus size: 82
1525200 TTGACCGTTG
* * * *
1525210 ACTCGGGTGTTAGTTTTGTAAATATTTTTAAAAGGGTGCCTCATTTGTAATTAATTTCTGTTAGG
1 ACTCGGGTGATAGTTTTGTAAATATTTATAAAAGGGTGCCTAATCTGTAATTAATTTCTGTTAGG
*
1525275 GTGA-GATTTATGTAAAA
66 GTGATAATTT-TGTAAAA
**
1525292 ACTCGGGTGATAGTTTTGTAAATATTTATAAAAGGGTGTTTAATCTGTAATTAATTTCTGTTAGG
1 ACTCGGGTGATAGTTTTGTAAATATTTATAAAAGGGTGCCTAATCTGTAATTAATTTCTGTTAGG
1525357 GTGATAATTTTGTAAAA
66 GTGATAATTTTGTAAAA
1525374 CAGTTTACCG
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
82 70 0.95
83 4 0.05
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (82 bp):
ACTCGGGTGATAGTTTTGTAAATATTTATAAAAGGGTGCCTAATCTGTAATTAATTTCTGTTAGG
GTGATAATTTTGTAAAA
Found at i:1527628 original size:10 final size:9
Alignment explanation
Indices: 1527613--1527664 Score: 59
Period size: 10 Copynumber: 5.4 Consensus size: 9
1527603 AACCGGCTTA
1527613 ACCGGTTCTG
1 ACCGGTT-TG
1527623 ACCGGTTTG
1 ACCGGTTTG
*
1527632 ACAGGTTTTG
1 ACCGG-TTTG
*
1527642 ACCGGTTCG
1 ACCGGTTTG
1527651 AACCGGTTTG
1 -ACCGGTTTG
1527661 ACCG
1 ACCG
1527665 ATCTGACCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 13 0.36
10 23 0.64
ACGTcount: A:0.15, C:0.25, G:0.31, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1527660 original size:19 final size:19
Alignment explanation
Indices: 1527612--1527664 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
1527602 AAACCGGCTT
*
1527612 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTTCG
*
1527632 -ACAGGTTTTGACCGGTTCG
1 AACCGG-TTTGACCGGTTCG
1527651 AACCGGTTTGACCG
1 AACCGGTTTGACCG
1527665 ATCTGACCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:1527721 original size:22 final size:21
Alignment explanation
Indices: 1527677--1527729 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
1527667 CTGACCCAAC
* *
1527677 CCGTGTGACCCGACTGACTCGA
1 CCGT-TGACCCGACCGACCCGA
1527699 CCGTTGACCCGACCCGACCCGA
1 CCGTTGACCCGA-CCGACCCGA
1527721 CCGTTGACC
1 CCGTTGACC
1527730 GTTGACCGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.17, C:0.43, G:0.25, T:0.15
Consensus pattern (21 bp):
CCGTTGACCCGACCGACCCGA
Found at i:1535032 original size:14 final size:14
Alignment explanation
Indices: 1535010--1535069 Score: 88
Period size: 14 Copynumber: 4.4 Consensus size: 14
1535000 AACCGGTTCT
*
1535010 GACCGGTCTGACCC
1 GACCCGTCTGACCC
1535024 GACCCGTCTGACCC
1 GACCCGTCTGACCC
*
1535038 GACCCGACTGACCC
1 GACCCGTCTGACCC
1535052 GA-CCGT-TGACCC
1 GACCCGTCTGACCC
1535064 GACCCG
1 GACCCG
1535070 ACCGTTGACC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
12 8 0.19
13 6 0.14
14 28 0.67
ACGTcount: A:0.17, C:0.47, G:0.25, T:0.12
Consensus pattern (14 bp):
GACCCGTCTGACCC
Found at i:1535068 original size:26 final size:28
Alignment explanation
Indices: 1535017--1535071 Score: 96
Period size: 26 Copynumber: 2.0 Consensus size: 28
1535007 TCTGACCGGT
1535017 CTGACCCGACCCGTCTGACCCGACCCGA
1 CTGACCCGACCCGTCTGACCCGACCCGA
1535045 CTGACCCGA-CCGT-TGACCCGACCCGA
1 CTGACCCGACCCGTCTGACCCGACCCGA
1535071 C
1 C
1535072 CGTTGACCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 14 0.52
27 4 0.15
28 9 0.33
ACGTcount: A:0.18, C:0.49, G:0.22, T:0.11
Consensus pattern (28 bp):
CTGACCCGACCCGTCTGACCCGACCCGA
Found at i:1535069 original size:17 final size:17
Alignment explanation
Indices: 1535047--1535079 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1535037 CGACCCGACT
1535047 GACCCGACCGTTGACCC
1 GACCCGACCGTTGACCC
1535064 GACCCGACCGTTGACC
1 GACCCGACCGTTGACC
1535080 GTTGACTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.12
Consensus pattern (17 bp):
GACCCGACCGTTGACCC
Found at i:1555130 original size:30 final size:30
Alignment explanation
Indices: 1555057--1555130 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
1555047 GCTTTTAGTG
* *
1555057 AAGACGCAATGTCTTCCGGCGACTTTTCCG
1 AAGACGCAATGTGTTCCGGCGACTTTTCCA
* *
1555087 AAGACACACTGTGTTCTCGGCGAC-TTTCCA
1 AAGACGCAATGTGTTC-CGGCGACTTTTCCA
*
1555117 AAGACGCATTGTGT
1 AAGACGCAATGTGT
1555131 CCCAACGACT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 30 0.81
31 7 0.19
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (30 bp):
AAGACGCAATGTGTTCCGGCGACTTTTCCA
Found at i:1558449 original size:18 final size:18
Alignment explanation
Indices: 1558426--1558461 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1558416 GACTATTCTG
1558426 GTTGATCATTGTCCACTC
1 GTTGATCATTGTCCACTC
1558444 GTTGATCATTGTCCACTC
1 GTTGATCATTGTCCACTC
1558462 TCACGAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.39
Consensus pattern (18 bp):
GTTGATCATTGTCCACTC
Found at i:1559592 original size:26 final size:27
Alignment explanation
Indices: 1559560--1559620 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
1559550 CAAACTATAC
* *
1559560 ATTTTTTCCCGAATAGGTGCATACAGT
1 ATTTTTTCCAGAATAGGTGCATACAAT
* *
1559587 ATTTTTTCCATAATAGGTGCCTACAAT
1 ATTTTTTCCAGAATAGGTGCATACAAT
1559614 ATTTTTT
1 ATTTTTT
1559621 GACCATCCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.44
Consensus pattern (27 bp):
ATTTTTTCCAGAATAGGTGCATACAAT
Found at i:1560748 original size:20 final size:18
Alignment explanation
Indices: 1560708--1560764 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
1560698 TAATTTACTA
*
1560708 TTAAAAATTATTACTTAT
1 TTAAAAATTATTACATAT
1560726 TTAAAAATTATTACACATAT
1 TTAAAAATTATT--ACATAT
*
1560746 TTAAATAATAATT-CATAT
1 TTAAA-AATTATTACATAT
1560764 T
1 T
1560765 GAATATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 18 0.53
20 10 0.29
21 6 0.18
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAAAAATTATTACATAT
Found at i:1561591 original size:134 final size:134
Alignment explanation
Indices: 1561350--1561750 Score: 748
Period size: 134 Copynumber: 3.0 Consensus size: 134
1561340 GATTCAGCTC
* *
1561350 GTGTTCTGTCCAAGTAAAGCAAAGATTCCGTTCGCGGTGGCAGAATTGGAGGAAAGCAAAGCATG
1 GTGTTCTGTCCGAGTAAAGCAAAGATTCCGTTCGTGGTGGCAGAATTGGAGGAAAGCAAAGCATG
1561415 TCTGCTTTCTTGTTCTCAGATGCTACATAACGGCCGGGTTTTCACTCTGTCTCCTCTTTGAACGA
66 TCTGCTTTCTTGTTCTCAGATGCTACATAACGGCCGGGTTTTCACTCTGTCTCCTCTTTGAACGA
1561480 TTTT
131 TTTT
*
1561484 GTGTTCTGTCCGGGTAAAGCAAAGATTCCGTTCGTGGTGGCAGAATTGGAGGAAAGCAAAGCATG
1 GTGTTCTGTCCGAGTAAAGCAAAGATTCCGTTCGTGGTGGCAGAATTGGAGGAAAGCAAAGCATG
* *
1561549 TCTGCTTTCTTGTTCTCAGATGCTACATAACGGCCGGCTTTTCACCCTGTCTCCTCTTTGAACGA
66 TCTGCTTTCTTGTTCTCAGATGCTACATAACGGCCGGGTTTTCACTCTGTCTCCTCTTTGAACGA
1561614 TTTT
131 TTTT
1561618 GTGTTCTGTCCGAGTAAAGCAAAGATTCCGTTCGTGGTGGCAGAATTGGAGGAAAGCAAAGCATG
1 GTGTTCTGTCCGAGTAAAGCAAAGATTCCGTTCGTGGTGGCAGAATTGGAGGAAAGCAAAGCATG
*
1561683 TCTGCTTTCTTGTTCTCAGATGCTACATAACGGCCGGGTTTTCACTCTGTCTCCTCTTTAAACGA
66 TCTGCTTTCTTGTTCTCAGATGCTACATAACGGCCGGGTTTTCACTCTGTCTCCTCTTTGAACGA
1561748 TTT
131 TTT
1561751 ATTTGGCTTG
Statistics
Matches: 258, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
134 258 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (134 bp):
GTGTTCTGTCCGAGTAAAGCAAAGATTCCGTTCGTGGTGGCAGAATTGGAGGAAAGCAAAGCATG
TCTGCTTTCTTGTTCTCAGATGCTACATAACGGCCGGGTTTTCACTCTGTCTCCTCTTTGAACGA
TTTT
Found at i:1568669 original size:24 final size:24
Alignment explanation
Indices: 1568637--1568686 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1568627 TTAGAATAGC
1568637 TAATATTTTGCATTGTTAACCATG
1 TAATATTTTGCATTGTTAACCATG
1568661 TAATATTTTGCATTGTTAACCATG
1 TAATATTTTGCATTGTTAACCATG
1568685 TA
1 TA
1568687 TAATATAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (24 bp):
TAATATTTTGCATTGTTAACCATG
Found at i:1574297 original size:13 final size:13
Alignment explanation
Indices: 1574279--1574303 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1574269 TTGTTCCTCA
1574279 ATGATAGTTGATC
1 ATGATAGTTGATC
1574292 ATGATAGTTGAT
1 ATGATAGTTGAT
1574304 AGTGAGCTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
ATGATAGTTGATC
Found at i:1578469 original size:18 final size:18
Alignment explanation
Indices: 1578446--1578481 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1578436 GACTATTCTG
1578446 GTTGATCATTGTCCACTC
1 GTTGATCATTGTCCACTC
1578464 GTTGATCATTGTCCACTC
1 GTTGATCATTGTCCACTC
1578482 TCACGAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.39
Consensus pattern (18 bp):
GTTGATCATTGTCCACTC
Found at i:1579472 original size:22 final size:22
Alignment explanation
Indices: 1579447--1579490 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1579437 TTTTTTGTAA
*
1579447 TTTA-AAAGAAATTATGATTTTT
1 TTTATAAAGAAATAAT-ATTTTT
*
1579469 TTTATAAATAAATAATATTTTT
1 TTTATAAAGAAATAATATTTTT
1579491 AATATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
TTTATAAAGAAATAATATTTTT
Found at i:1579521 original size:26 final size:28
Alignment explanation
Indices: 1579467--1579517 Score: 72
Period size: 25 Copynumber: 1.9 Consensus size: 28
1579457 ATTATGATTT
*
1579467 TTTTTATAAATAAATAATATTTTTAATA
1 TTTTTATAAATAAATAATATTTTAAATA
1579495 TTTTT-TAAA-AAATAA-ATTTTAAA
1 TTTTTATAAATAAATAATATTTTAAA
1579518 ATATCATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 6 0.27
27 4 0.18
28 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTTTATAAATAAATAATATTTTAAATA
Found at i:1580500 original size:28 final size:28
Alignment explanation
Indices: 1580469--1580524 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
1580459 GATGATTATT
1580469 TTATAACTTTTAATAGCCGAGAGATTCA
1 TTATAACTTTTAATAGCCGAGAGATTCA
**
1580497 TTATAACTTTTAATAGTTGAGAGATTCA
1 TTATAACTTTTAATAGCCGAGAGATTCA
1580525 ACAAAACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (28 bp):
TTATAACTTTTAATAGCCGAGAGATTCA
Found at i:1580773 original size:31 final size:31
Alignment explanation
Indices: 1580735--1580794 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1580725 ATTTGTTTTC
* *
1580735 GGTTGATGCTCGAAGTTATCATTACCTCAAG
1 GGTTGATGCTCGAAGATATCATTAACTCAAG
1580766 GGTTGATGCTCGAAGATATCATTAACTCA
1 GGTTGATGCTCGAAGATATCATTAACTCA
1580795 CCCATTTACG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (31 bp):
GGTTGATGCTCGAAGATATCATTAACTCAAG
Found at i:1582342 original size:30 final size:29
Alignment explanation
Indices: 1582308--1582385 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 29
1582298 GCTTTTAGTT
*
1582308 GAAGAAGCATTGTCTTCCGGCGACTTTTCC
1 GAAGAAGCATTGTGTTCCGGCGAC-TTTCC
*
1582338 GAAGACA-CACTGTGTTCTCGGCGACTTTCC
1 GAAGA-AGCATTGTGTTC-CGGCGACTTTCC
* *
1582368 AAAGACGCATTGTGTTCC
1 GAAGAAGCATTGTGTTCC
1582386 CAACGACTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
29 1 0.03
30 31 0.77
31 8 0.20
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (29 bp):
GAAGAAGCATTGTGTTCCGGCGACTTTCC
Found at i:1583915 original size:2 final size:2
Alignment explanation
Indices: 1583908--1583936 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1583898 TGTTAAGTAT
1583908 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1583937 TGCATGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1585556 original size:18 final size:18
Alignment explanation
Indices: 1585529--1585564 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1585519 GACTATTCTG
*
1585529 GTTGATCATTGTCCACTC
1 GTTGACCATTGTCCACTC
1585547 GTTGACCATTGTCCACTC
1 GTTGACCATTGTCCACTC
1585565 TCACGAAGTA
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:0.17, C:0.31, G:0.17, T:0.36
Consensus pattern (18 bp):
GTTGACCATTGTCCACTC
Found at i:1589311 original size:90 final size:91
Alignment explanation
Indices: 1589152--1589363 Score: 257
Period size: 90 Copynumber: 2.3 Consensus size: 91
1589142 TGGTGGGGAC
* * * * ** *
1589152 GACACTGCTCATACGTGATGAAGAGGTCTGGTCGTCTAAGGGTGGATGATAACTCGGTTCCTACG
1 GACACGGCTCATACGTGATGAAGAGATCTGGCCATCTAAGGAAGGATGATAACACGGTTCCTACG
*
1589217 TGATGAGGACAACTGGTT-GGT-GGAT
66 TGATGAGGACAACTGGTTAGCTAGG-T
* * * * *
1589242 GACATGGCTCATACATGATGAAGAGTTCTGGCCATCTTAGGAAGGGTGATAACACGGTTCCTACG
1 GACACGGCTCATACGTGATGAAGAGATCTGGCCATCTAAGGAAGGATGATAACACGGTTCCTACG
** *
1589307 TGATGAGGACGGCTGGTTATCTAGGT
66 TGATGAGGACAACTGGTTAGCTAGGT
1589333 GACACGGCTCATACGTGATGAAGAGATCTGG
1 GACACGGCTCATACGTGATGAAGAGATCTGG
1589364 TCGGGGTGAC
Statistics
Matches: 102, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
90 70 0.69
91 30 0.29
92 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.25
Consensus pattern (91 bp):
GACACGGCTCATACGTGATGAAGAGATCTGGCCATCTAAGGAAGGATGATAACACGGTTCCTACG
TGATGAGGACAACTGGTTAGCTAGGT
Found at i:1589348 original size:41 final size:41
Alignment explanation
Indices: 1589293--1589489 Score: 138
Period size: 41 Copynumber: 4.8 Consensus size: 41
1589283 AAGGGTGATA
* * *
1589293 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAGGTG
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGTTATCTAGGTG
* **
1589334 ACACGGCTCATACGTGATGAAGAGATCTGG---TCGGGGTG
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAGGTG
** **
1589372 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTG
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCT--AGGTG
* * *
1589415 ATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ---ACACGGCTCATACGTGATGAAGA-GAGCTGGTTATCTA-GG-TG
*
1589461 ACACGG--CATACGTGATGAAGAGATCTGGT
1 ACACGGCTCATACGTGATGAAGAGAGCTGGT
1589490 CTGGGGATGA
Statistics
Matches: 125, Mismatches: 18, Indels: 26
0.74 0.11 0.15
Matches are distributed among these distances:
38 35 0.28
40 2 0.02
41 44 0.35
43 10 0.08
44 1 0.01
45 2 0.02
46 30 0.24
47 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (41 bp):
ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAGGTG
Found at i:1589446 original size:125 final size:129
Alignment explanation
Indices: 1589213--1589535 Score: 453
Period size: 125 Copynumber: 2.5 Consensus size: 129
1589203 ACTCGGTTCC
* * * * *
1589213 TACGTGATGAGGACAACTGGTTGGTGGATGACATGGCTCATACATGATGAAGAGTTCTGGCCATC
1 TACGTGATGAAGAGATCTGGTCGG-GGATGACACGGCTCATACATGATGAAGAGTTCTGGCCATC
1589278 TTAGGAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA-GG-TGACACGGC
65 TTA-GAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGG-
1589341 TCA
128 -CA
*
1589344 TACGTGATGAAGAGATCTGGTCGGGG-TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATC-
1 TACGTGATGAAGAGATCTGGTCGGGGATGACACGGCTCATACATGATGAAGAGTTCTGGCCATCT
1589407 TA-AA-GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCA
66 TAGAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCA
* * * *
1589469 TACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGACG-GCTGGCCAT
1 TACGTGATGAAGAGATCTGGTC-GGGGATGACACGGCTCATACATGATGAAGA-GTTCTGGCCAT
1589533 CTT
64 CTT
1589536 TAGGAGTTAT
Statistics
Matches: 175, Mismatches: 11, Indels: 15
0.87 0.05 0.07
Matches are distributed among these distances:
125 68 0.39
126 8 0.05
127 38 0.22
128 4 0.02
129 35 0.20
130 2 0.01
131 20 0.11
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.25
Consensus pattern (129 bp):
TACGTGATGAAGAGATCTGGTCGGGGATGACACGGCTCATACATGATGAAGAGTTCTGGCCATCT
TAGAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCA
Found at i:1589598 original size:28 final size:28
Alignment explanation
Indices: 1589567--1589628 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
1589557 AAACCAAATT
1589567 AAAGATTTGTTTCAA-AAGAAACAAACCC
1 AAAGATTTGTTTCAAGAA-AAACAAACCC
* * *
1589595 AAAGCTTTGTTTCAAGAAAAATAAACTC
1 AAAGATTTGTTTCAAGAAAAACAAACCC
1589623 AAAGAT
1 AAAGAT
1589629 GATATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 27 0.93
29 2 0.07
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.24
Consensus pattern (28 bp):
AAAGATTTGTTTCAAGAAAAACAAACCC
Found at i:1590148 original size:15 final size:16
Alignment explanation
Indices: 1590123--1590169 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
1590113 AAAGATGATC
*
1590123 TTGTTTTAAGAGAAAA
1 TTGTTTCAAGAGAAAA
*
1590139 -TGTTTCAAGACAAAA
1 TTGTTTCAAGAGAAAA
*
1590154 TTCGTTTCAAGGGAAA
1 TT-GTTTCAAGAGAAA
1590170 CGACTCAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 13 0.52
16 1 0.04
17 11 0.44
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (16 bp):
TTGTTTCAAGAGAAAA
Found at i:1590642 original size:66 final size:66
Alignment explanation
Indices: 1590572--1590697 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 66
1590562 AAACGGTCTC
* * *
1590572 AAGAGATACAAAATTCAT-TTT-AAGAGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAATTAT
1 AAGAGAGACAAAATT-ATGTTTCAA-AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTAT
1590635 CTT
64 CTT
*
1590638 AAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
1 AAGAGAGACAAAATTATGTTT-CAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
1590698 CAATCTCAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
65 1 0.02
66 17 0.32
67 33 0.62
68 2 0.04
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (66 bp):
AAGAGAGACAAAATTATGTTTCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCT
T
Found at i:1590685 original size:30 final size:30
Alignment explanation
Indices: 1590651--1590711 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1590641 AGAGACAAAA
*
1590651 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
*
1590681 TTTTGTTTCAAAAGAAACAATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
1590711 T
1 T
1590712 GTTTTACAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.33
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:1591045 original size:36 final size:35
Alignment explanation
Indices: 1590961--1591058 Score: 117
Period size: 36 Copynumber: 2.8 Consensus size: 35
1590951 GAGAAAATGA
* * *
1590961 TGTCTCAAGCGAGACGAAATTTG-CTTTAAGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
* **
1590995 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTA-AGAAAT
*
1591031 TGTCTCAAGCGAGACAAAGTTTGTTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT
1591059 GAGGAAACGA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 19 0.37
35 4 0.08
36 29 0.56
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
Found at i:1591073 original size:36 final size:36
Alignment explanation
Indices: 1590962--1591080 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
1590952 AGAAAATGAT
* * * *
1590962 GTCTCAAGCGAGACGAAATTTG-CTTTA-AGATATA
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATC
** *
1590996 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATC
*
1591032 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGGAAA-C
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGA-GAAATC
*
1591067 GATCTCAAGTGAGA
1 G-TCTCAAGCGAGA
1591081 TCAACTTTGT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
34 19 0.27
35 7 0.10
36 44 0.63
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATC
Found at i:1591219 original size:105 final size:105
Alignment explanation
Indices: 1591075--1591264 Score: 292
Period size: 105 Copynumber: 1.8 Consensus size: 105
1591065 ACGATCTCAA
* *
1591075 GTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAGGTCTCA
1 GTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAGGTCTCA
1591140 AGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCTAAG
66 AGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCTAAG
* * * * *
1591180 GTGAGATTAATTTTGTTTTAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTC
1 GTGAGATCAACTTTG-TTTAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAGGTCTC
*
1591244 AAGCGAGACGAAGTTTGTTTT
65 AAGCGAGACGAAATTTGTTTT
1591265 AAGAGAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
105 71 0.93
106 5 0.07
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (105 bp):
GTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAGGTCTCA
AGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCTAAG
Found at i:1591278 original size:36 final size:36
Alignment explanation
Indices: 1591238--1591374 Score: 170
Period size: 36 Copynumber: 3.8 Consensus size: 36
1591228 AAAGGAAAAA
* * *
1591238 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
* * **
1591274 TGTCTCAAACGAGACAAAATTTGTTTTTAGA-AAGC
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
*
1591309 TGTCTCAAGCGAGACAAAATTTGCTTTGAA-AGAAAT
1 TGTCTCAAGCGAGACAAAATTTG-TTTTAAGAGAAAT
1591345 TGTCTCAAGCGAGACAAAAATTTGTTTTAA
1 TGTCTCAAGCGAGAC-AAAATTTGTTTTAA
1591375 AATTCTCAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
35 25 0.29
36 53 0.62
37 8 0.09
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
Found at i:1591348 original size:71 final size:72
Alignment explanation
Indices: 1591238--1591372 Score: 202
Period size: 71 Copynumber: 1.9 Consensus size: 72
1591228 AAAGGAAAAA
* * * *
1591238 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATTTGTCTCAAACGAGAC-AAAATTTGTTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTTT
1591302 AGAAAGC
66 AGAAAGC
*
1591309 TGTCTCAAGCGAGACAAAATTTGCTTTGAA-AGAAATTGTCTCAAGCGAGACAAAAATTTGTTTT
1 TGTCTCAAGCGAGACAAAATTTG-TTTGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTT
1591373 AAAATTCTCA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
71 40 0.70
72 17 0.30
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (72 bp):
TGTCTCAAGCGAGACAAAATTTGTTTGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTTT
AGAAAGC
Found at i:1591730 original size:4 final size:4
Alignment explanation
Indices: 1591714--1591753 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
1591704 ATGCAAATTT
*
1591714 TATG TAT- TATG TATG TATG --TG TATA TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1591754 ATGTTTTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
2 2 0.06
3 3 0.10
4 26 0.84
ACGTcount: A:0.28, C:0.00, G:0.20, T:0.53
Consensus pattern (4 bp):
TATG
Found at i:1591744 original size:14 final size:14
Alignment explanation
Indices: 1591714--1591757 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1591704 ATGCAAATTT
*
1591714 TATGTATTATGTATG
1 TATGTA-TATATATG
*
1591729 TATGTGTATATATG
1 TATGTATATATATG
*
1591743 TATGTATGTATATG
1 TATGTATATATATG
1591757 T
1 T
1591758 TTTTTCTCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.52
Consensus pattern (14 bp):
TATGTATATATATG
Found at i:1591744 original size:18 final size:17
Alignment explanation
Indices: 1591716--1591751 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
1591706 GCAAATTTTA
1591716 TGTATTATGTATGTATG
1 TGTATTATGTATGTATG
1591733 TGTATATATGTATGTATG
1 TGTAT-TATGTATGTATG
1591751 T
1 T
1591752 ATATGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (17 bp):
TGTATTATGTATGTATG
Found at i:1592937 original size:14 final size:14
Alignment explanation
Indices: 1592920--1592946 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1592910 TCTTCTTTTT
1592920 TTTCACTTTGTTTC
1 TTTCACTTTGTTTC
1592934 TTTCACTTTGTTT
1 TTTCACTTTGTTT
1592947 TTCTTTTCTC
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:0.07, C:0.19, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTCACTTTGTTTC
Found at i:1593598 original size:24 final size:23
Alignment explanation
Indices: 1593571--1593637 Score: 86
Period size: 24 Copynumber: 3.0 Consensus size: 23
1593561 AAGGTGGAAA
1593571 GAATGTTTCAAGGTCTCAAAGAGG
1 GAATGTTTCAAGGTCTCAAAGA-G
*
1593595 GAATGTTTCAAGGTC-GAAA-A-
1 GAATGTTTCAAGGTCTCAAAGAG
*
1593615 GAATATTTCAAGGTCTCAAAGAG
1 GAATGTTTCAAGGTCTCAAAGAG
1593638 ATAGAATGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 14 0.38
21 3 0.08
22 2 0.05
23 3 0.08
24 15 0.41
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.25
Consensus pattern (23 bp):
GAATGTTTCAAGGTCTCAAAGAG
Found at i:1593623 original size:20 final size:20
Alignment explanation
Indices: 1593555--1593629 Score: 80
Period size: 24 Copynumber: 3.6 Consensus size: 20
1593545 ATAAATACAG
*
1593555 TGTTTCAAGGT-GGAAAGAA
1 TGTTTCAAGGTCGAAAAGAA
*
1593574 TGTTTCAAGGTCTCAAAGAGGGAA
1 TGTTTCAAGGTC-GAAA-A--GAA
1593598 TGTTTCAAGGTCGAAAAGAA
1 TGTTTCAAGGTCGAAAAGAA
*
1593618 TATTTCAAGGTC
1 TGTTTCAAGGTC
1593630 TCAAAGAGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
19 11 0.23
20 14 0.30
21 2 0.04
22 2 0.04
23 3 0.06
24 15 0.32
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.28
Consensus pattern (20 bp):
TGTTTCAAGGTCGAAAAGAA
Found at i:1593624 original size:44 final size:43
Alignment explanation
Indices: 1593555--1593637 Score: 139
Period size: 44 Copynumber: 1.9 Consensus size: 43
1593545 ATAAATACAG
* *
1593555 TGTTTCAAGGTGGAAAGAATGTTTCAAGGTCTCAAAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGGGAA
1593598 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAG
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAG
1593638 ATAGAATGTC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
43 11 0.30
44 26 0.70
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.27
Consensus pattern (43 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGGGAA
Found at i:1593635 original size:20 final size:20
Alignment explanation
Indices: 1593555--1593636 Score: 76
Period size: 20 Copynumber: 4.0 Consensus size: 20
1593545 ATAAATACAG
**
1593555 TGTTTCAAGGT-GGAAAGAA
1 TGTTTCAAGGTCTCAAAGAA
1593574 TGTTTCAAGGTCTCAAAGAGGGAA
1 TGTTTCAAGGTCTC-AA-A--GAA
**
1593598 TGTTTCAAGGTCGAAAAGAA
1 TGTTTCAAGGTCTCAAAGAA
*
1593618 TATTTCAAGGTCTCAAAGA
1 TGTTTCAAGGTCTCAAAGA
1593637 GATAGAATGT
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
19 11 0.22
20 19 0.37
21 2 0.04
22 2 0.04
23 2 0.04
24 15 0.29
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.27
Consensus pattern (20 bp):
TGTTTCAAGGTCTCAAAGAA
Found at i:1599838 original size:34 final size:34
Alignment explanation
Indices: 1599792--1599863 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
1599782 AAAAGAAAAC
*
1599792 ACATAAAATTTGAAATAACCCCAAAATATTGAAG
1 ACATAAAATTTGAAATAACCCCAAAACATTGAAG
*
1599826 ACATAAATTTTGAAATAACCCCAAAACATTGAAG
1 ACATAAAATTTGAAATAACCCCAAAACATTGAAG
1599860 ACAT
1 ACAT
1599864 TCGTTTCAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.24
Consensus pattern (34 bp):
ACATAAAATTTGAAATAACCCCAAAACATTGAAG
Found at i:1600780 original size:21 final size:21
Alignment explanation
Indices: 1600756--1600800 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
1600746 TTTATTCATG
1600756 TTAATTTAC-ATTTAAAAATTA
1 TTAA-TTACTATTTAAAAATTA
1600777 TTAATTACTATTTAAAAATTA
1 TTAATTACTATTTAAAAATTA
1600798 TTA
1 TTA
1600801 CACATATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAATTACTATTTAAAAATTA
Found at i:1600808 original size:20 final size:21
Alignment explanation
Indices: 1600765--1600812 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1600755 GTTAATTTAC
*
1600765 ATTTAAAAATTATTAATTACT
1 ATTTAAAAATTATTAATCACT
1600786 ATTTAAAAATTATT-A-CACAT
1 ATTTAAAAATTATTAATCAC-T
1600806 ATTTAAA
1 ATTTAAA
1600813 TAATAATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 9 0.36
21 14 0.56
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTTAAAAATTATTAATCACT
Found at i:1601990 original size:134 final size:129
Alignment explanation
Indices: 1601826--1602087 Score: 461
Period size: 134 Copynumber: 2.0 Consensus size: 129
1601816 GATTCAGCTC
1601826 GTGTTCTGTCCAAGTAAAGCAAAGATTCCGTTCGTGGTGGCAGAATTGGAGGAAAGCAAAGCATG
1 GTGTTCTGTCCAAGTAAAGCAAAGATTCCGTTCGTGGTGGCAGAATTGGAGGAAAGCAAAGCATG
1601891 TCTGCTTTCTTGTTCTCAGATGCTACATAACGGCCGGGTTTTCACTCTGTCTCCTCTTTGAACGA
66 --TGCTTTC-TGTTCTCAGATGCTACATAACGGCCGGGTTTTCACTCTG--TCCTCTTTGAACGA
1601956 TTTT
126 TTTT
* *
1601960 GTGTTCTGTTCGAGTAAAGCAAAGATTCCGTTCGTGGTGGCAGAATTGGAGGAAAGCAAAGCATG
1 GTGTTCTGTCCAAGTAAAGCAAAGATTCCGTTCGTGGTGGCAGAATTGGAGGAAAGCAAAGCATG
1602025 TGCTTTCTGTTCTCAGATGCTACATAACGGCCGGGTTTTCACTCTGTCCTCTTTGAACGATTT
66 TGCTTTCTGTTCTCAGATGCTACATAACGGCCGGGTTTTCACTCTGTCCTCTTTGAACGATTT
1602088 ATTTGGCTTG
Statistics
Matches: 126, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
129 17 0.13
131 39 0.31
132 7 0.06
134 63 0.50
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (129 bp):
GTGTTCTGTCCAAGTAAAGCAAAGATTCCGTTCGTGGTGGCAGAATTGGAGGAAAGCAAAGCATG
TGCTTTCTGTTCTCAGATGCTACATAACGGCCGGGTTTTCACTCTGTCCTCTTTGAACGATTTT
Found at i:1604084 original size:62 final size:63
Alignment explanation
Indices: 1603962--1604086 Score: 227
Period size: 62 Copynumber: 2.0 Consensus size: 63
1603952 AAATCCATTA
1603962 TTTCCAACAAATGGTTAGCAACTCCTCTTGTTACTACTCCGACTTCTCCTCACCTATTATGTT
1 TTTCCAACAAATGGTTAGCAACTCCTCTTGTTACTACTCCGACTTCTCCTCACCTATTATGTT
1604025 TTTCCAACAAATGGTTAGCAACTCC-C-TGTTACTATCTCCGACTTCTCCTCACCTATTATGTT
1 TTTCCAACAAATGGTTAGCAACTCCTCTTGTTACTA-CTCCGACTTCTCCTCACCTATTATGTT
1604087 CGTGTAGTTG
Statistics
Matches: 61, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
61 8 0.13
62 28 0.46
63 25 0.41
ACGTcount: A:0.22, C:0.30, G:0.10, T:0.38
Consensus pattern (63 bp):
TTTCCAACAAATGGTTAGCAACTCCTCTTGTTACTACTCCGACTTCTCCTCACCTATTATGTT
Found at i:1607719 original size:18 final size:18
Alignment explanation
Indices: 1607696--1607731 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1607686 GACTATTCTG
1607696 GTTGATCATTGTCCACTC
1 GTTGATCATTGTCCACTC
1607714 GTTGATCATTGTCCACTC
1 GTTGATCATTGTCCACTC
1607732 TCACGAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.39
Consensus pattern (18 bp):
GTTGATCATTGTCCACTC
Found at i:1608403 original size:2 final size:2
Alignment explanation
Indices: 1608396--1608422 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1608386 CAACACTCCG
1608396 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1608423 CAGAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1613583 original size:30 final size:28
Alignment explanation
Indices: 1613549--1613605 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 28
1613539 TCTGTAAATT
1613549 ATATTTAGATGATTTTTTTTATTGATTAAG
1 ATATTTAGATGA-TTTTTTTATT-ATTAAG
*
1613579 ATATTTAGATTATTTTTTTATTATTAA
1 ATATTTAGATGATTTTTTTATTATTAA
1613606 AATTTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 5 0.19
29 10 0.38
30 11 0.42
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (28 bp):
ATATTTAGATGATTTTTTTATTATTAAG
Found at i:1614175 original size:2 final size:2
Alignment explanation
Indices: 1614168--1614199 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1614158 CAAGAGAAGA
1614168 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
1614200 TCAAATCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1629926 original size:2 final size:2
Alignment explanation
Indices: 1629919--1629952 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1629909 TAGATGAGGA
* *
1629919 AT AT AT AT AT AT AT AT AT AT AT GT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1629953 TTATGTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1629957 original size:16 final size:16
Alignment explanation
Indices: 1629919--1629959 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1629909 TAGATGAGGA
*
1629919 ATATATATATATATAT
1 ATATATGTATATATAT
*
1629935 ATATATGTATATTTAT
1 ATATATGTATATATAT
*
1629951 ATTTATGTA
1 ATATATGTA
1629960 ATTCATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (16 bp):
ATATATGTATATATAT
Found at i:1630718 original size:22 final size:22
Alignment explanation
Indices: 1630678--1630721 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1630668 CTTTATTTTC
* *
1630678 TTTACCAAATTAAGCTTTAGAT
1 TTTACCAAATCAAGATTTAGAT
*
1630700 TTTACCAAATCAATATTTAGAT
1 TTTACCAAATCAAGATTTAGAT
1630722 ATAAATCTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.41
Consensus pattern (22 bp):
TTTACCAAATCAAGATTTAGAT
Done.