Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000461.1 Hibiscus syriacus cultivar Beakdansim tig00000856_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: 78931
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:471 original size:31 final size:30
Alignment explanation
Indices: 436--498 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
426 AGTCATCATC
436 ATTATAAACTAATACAATTAACTCCATATTA
1 ATTATAAACTAATACAATTAACTCCAT-TTA
* ** *
467 ATTATAAATTTGTACAATTGACTCCATTTA
1 ATTATAAACTAATACAATTAACTCCATTTA
497 AT
1 AT
499 ATTTAATCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (30 bp):
ATTATAAACTAATACAATTAACTCCATTTA
Found at i:642 original size:2 final size:2
Alignment explanation
Indices: 637--666 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
627 ATATATGCTA
637 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
667 GGTGGAACGA
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:1548 original size:136 final size:136
Alignment explanation
Indices: 1304--1575 Score: 499
Period size: 136 Copynumber: 2.0 Consensus size: 136
1294 AGAAGGATTT
* *
1304 TTGTTGAGGCGTGTATAAACAGTTTCCTTAAGACAGATTCGTCATCTCTTAGGTGCTTTGAGTAA
1 TTGTTGAGGCATGTATAAACAGTTTCCTTAAGACAGATTCGTCATCTCCTAGGTGCTTTGAGTAA
* * *
1369 CGTTGGATGTCGGTCTCCCAGATACAACAACAAACGATCACAACAGTATGCACAATCGTAGCGAT
66 CATTGGACGTCGGTCTCCCAGATACAACAACAAACGATCACAACAGTAAGCACAATCGTAGCGAT
1434 CAGTCG
131 CAGTCG
1440 TTGTTGAGGCATGTATAAACAGTTTCCTTAAGACAGATTCGTCATCTCCTAGGTGCTTTGAGTAA
1 TTGTTGAGGCATGTATAAACAGTTTCCTTAAGACAGATTCGTCATCTCCTAGGTGCTTTGAGTAA
1505 CATTGGACGTCGGTCTCCCAGATACAACAACAAACGATCACAACAGTAAGCACAATCGTAGCGAT
66 CATTGGACGTCGGTCTCCCAGATACAACAACAAACGATCACAACAGTAAGCACAATCGTAGCGAT
1570 CAGTCG
131 CAGTCG
1576 AACATAATTT
Statistics
Matches: 131, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
136 131 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (136 bp):
TTGTTGAGGCATGTATAAACAGTTTCCTTAAGACAGATTCGTCATCTCCTAGGTGCTTTGAGTAA
CATTGGACGTCGGTCTCCCAGATACAACAACAAACGATCACAACAGTAAGCACAATCGTAGCGAT
CAGTCG
Found at i:1760 original size:21 final size:21
Alignment explanation
Indices: 1736--1830 Score: 93
Period size: 21 Copynumber: 4.5 Consensus size: 21
1726 AGGTTAAGAC
*
1736 CTTTTGATGAAAGGACTTAAT
1 CTTTTGATGAAAGGATTTAAT
* * *
1757 CTTTTGATTAAAAGATTT-CT
1 CTTTTGATGAAAGGATTTAAT
* *
1777 CCTTTTGATGAAAGGGTTTAAC
1 -CTTTTGATGAAAGGATTTAAT
*
1799 CTTTTCATGAAAGGATTTAAT
1 CTTTTGATGAAAGGATTTAAT
* *
1820 ATTTTCATGAA
1 CTTTTGATGAA
1831 GAGAATTGTT
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
20 1 0.02
21 58 0.98
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (21 bp):
CTTTTGATGAAAGGATTTAAT
Found at i:1816 original size:42 final size:42
Alignment explanation
Indices: 1735--1816 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
1725 AAGGTTAAGA
* * *
1735 CCTTTTGATGAAAGGACTTAATCTTTTGATTAAAAGATTTCT
1 CCTTTTGATGAAAGGACTTAACCTTTTCATGAAAAGATTTCT
** *
1777 CCTTTTGATGAAAGGGTTTAACCTTTTCATGAAAGGATTT
1 CCTTTTGATGAAAGGACTTAACCTTTTCATGAAAAGATTT
1817 AATATTTTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.41
Consensus pattern (42 bp):
CCTTTTGATGAAAGGACTTAACCTTTTCATGAAAAGATTTCT
Found at i:3659 original size:21 final size:21
Alignment explanation
Indices: 3635--3688 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
3625 AAAGACTTCT
* *
3635 CCTTTTGATGAAAGGGTTTAA
1 CCTTTTCATGAAAGGATTTAA
3656 CCTTTTCATGAAAGGATTTAA
1 CCTTTTCATGAAAGGATTTAA
*
3677 TCTTTTCATGAA
1 CCTTTTCATGAA
3689 GAGAATTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (21 bp):
CCTTTTCATGAAAGGATTTAA
Found at i:5968 original size:6 final size:6
Alignment explanation
Indices: 5954--5983 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5944 ATGTATCTTT
*
5954 CATAAA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA
5984 TGTATGTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (6 bp):
CATATA
Found at i:8481 original size:130 final size:130
Alignment explanation
Indices: 8248--8503 Score: 485
Period size: 130 Copynumber: 2.0 Consensus size: 130
8238 ATTTATTTAA
*
8248 TTTTATATATTTGGGGTACCGAATTCTGATATTGTGTTCGTAATACTTTTAAGAAAAATGAAGAG
1 TTTTATATATTTAGGGTACCGAATTCTGATATTGTGTTCGTAATACTTTTAAGAAAAATGAAGAG
*
8313 ACGGAACAACATTTTGACAAGCATACCTCTTTTAAATAATCAAAATCTTTGTTCACAAAAGGAAT
66 ACGGAACAACATTTTGACAAGCATACCTCTTTCAAATAATCAAAATCTTTGTTCACAAAAGGAAT
8378 TTTTATATATTTAGGGTACCGAATTCTGATATTGTGTTCGTAATACTTTTAAGAAAAATGAAGAG
1 TTTTATATATTTAGGGTACCGAATTCTGATATTGTGTTCGTAATACTTTTAAGAAAAATGAAGAG
*
8443 ACGGAGCAACATTTTGACAAGCATACCTCTTTCAAATAATCAAAATCTTTGTTCACAAAAG
66 ACGGAACAACATTTTGACAAGCATACCTCTTTCAAATAATCAAAATCTTTGTTCACAAAAG
8504 AAAAAAGAGA
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 123 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (130 bp):
TTTTATATATTTAGGGTACCGAATTCTGATATTGTGTTCGTAATACTTTTAAGAAAAATGAAGAG
ACGGAACAACATTTTGACAAGCATACCTCTTTCAAATAATCAAAATCTTTGTTCACAAAAGGAAT
Found at i:15495 original size:18 final size:18
Alignment explanation
Indices: 15474--15508 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15464 CTCTCCAAAG
* *
15474 CAAGCTAACGGGGAGAAA
1 CAAGATAACGGGAAGAAA
15492 CAAGATAACGGGAAGAA
1 CAAGATAACGGGAAGAA
15509 TGCAACAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.14, G:0.31, T:0.06
Consensus pattern (18 bp):
CAAGATAACGGGAAGAAA
Found at i:15839 original size:28 final size:29
Alignment explanation
Indices: 15788--15848 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
15778 AATCCTACGC
* * *
15788 TTAATATTTTAATATATATTTTTATCTTG
1 TTAATAATTTAATATATATGTTTACCTTG
*
15817 TTAATAATTT-ATATATATGTTTACCTTT
1 TTAATAATTTAATATATATGTTTACCTTG
15845 TTAA
1 TTAA
15849 AAAATATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (29 bp):
TTAATAATTTAATATATATGTTTACCTTG
Found at i:16313 original size:29 final size:30
Alignment explanation
Indices: 16252--16322 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
16242 TTAGTATACT
16252 AAAAATGAAACATTAAGTATGATTTTGGAA
1 AAAAATGAAACATTAAGTATGATTTTGGAA
*
16282 AAAAATGAAACATTAATTATGATTTTGGAA
1 AAAAATGAAACATTAAGTATGATTTTGGAA
*
16312 AAAAATAAAAC
1 AAAAATGAAAC
16323 TTTTTTACTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.55, C:0.04, G:0.13, T:0.28
Consensus pattern (30 bp):
AAAAATGAAACATTAAGTATGATTTTGGAA
Found at i:21098 original size:48 final size:49
Alignment explanation
Indices: 21031--21126 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 49
21021 ATATACCAAT
* *
21031 TTTTTTACTAAACCTACCAAAAGATTAGTGTAATGATTATGTTTTTTCA
1 TTTTTTACTAAAACTACCAAAAGATTAATGTAATGATTATGTTTTTTCA
*
21080 TTTTTTATTAAAAC-ACCAAAAGATTAATGTAATGATTATGTTTTTTC
1 TTTTTTACTAAAACTACCAAAAGATTAATGTAATGATTATGTTTTTTC
21127 TTTATATGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 32 0.73
49 12 0.27
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.46
Consensus pattern (49 bp):
TTTTTTACTAAAACTACCAAAAGATTAATGTAATGATTATGTTTTTTCA
Found at i:23763 original size:73 final size:73
Alignment explanation
Indices: 23644--23789 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
23634 TCATAATTAA
23644 ATTACACTTTGATTATTTGAAAATAAAAAAGTCAAAATATAAAGGAAACAGAAAAAGATGTGTAA
1 ATTACACTTTGATTATTTGAAAATAAAAAAGTCAAAATATAAAGGAAACAGAAAAAGATGTGTAA
23709 TGTTTTAC
66 TGTTTTAC
*
23717 ATTACACTTTGATTATTTGAAAATAAAAAAGTCAAAATATAAAGGAAATAGAAAAAGATGTGTAA
1 ATTACACTTTGATTATTTGAAAATAAAAAAGTCAAAATATAAAGGAAACAGAAAAAGATGTGTAA
23782 TGTTTTAC
66 TGTTTTAC
23790 CTGCATCGTA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (73 bp):
ATTACACTTTGATTATTTGAAAATAAAAAAGTCAAAATATAAAGGAAACAGAAAAAGATGTGTAA
TGTTTTAC
Found at i:24505 original size:5 final size:5
Alignment explanation
Indices: 24487--24553 Score: 50
Period size: 5 Copynumber: 13.8 Consensus size: 5
24477 TTCCTGCAAC
* * * * *
24487 AAAAT -AAA- AAAAT AGAAT AAAAT ACATT TATAT AAAAT AAAAT AAAAGT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T
*
24536 -ATAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAA
24554 AATCAGACCC
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
4 7 0.15
5 38 0.83
6 1 0.02
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:24527 original size:20 final size:20
Alignment explanation
Indices: 24515--24553 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
24505 AAAATACATT
24515 TATATAAAATAAAATAAAAG
1 TATATAAAATAAAATAAAAG
24535 TATATAAAATAAAATAAAA
1 TATATAAAATAAAATAAAA
24554 AATCAGACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
TATATAAAATAAAATAAAAG
Found at i:25411 original size:12 final size:12
Alignment explanation
Indices: 25394--25421 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
25384 TTTTCAATAT
25394 ATTAAATAGTGA
1 ATTAAATAGTGA
25406 ATTAAATAGTGA
1 ATTAAATAGTGA
25418 ATTA
1 ATTA
25422 TATATGTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (12 bp):
ATTAAATAGTGA
Found at i:26011 original size:72 final size:71
Alignment explanation
Indices: 25909--26052 Score: 193
Period size: 72 Copynumber: 2.0 Consensus size: 71
25899 AAAAAAAAAT
*
25909 ATTATTGTACATAGAGAGAGTACTTAAATCCAAATCCAACAAGTTTCAACTTCATCCAATTTAAA
1 ATTATTGTACATAGAGAGAGTAATTAAATCCAAATCCAACAAGTTTCAACTTCATCCAATTT-AA
*
25974 CAATATC
65 CAAGATC
* * * *
25981 ATTATTGTACATAGAGATG-GTAAATT-AATCCCAATCCATCAGGTTTCAACTTCATTCAATTTA
1 ATTATTGTACATAGAGA-GAGT-AATTAAATCCAAATCCAACAAGTTTCAACTTCATCCAATTTA
26044 ACAAGATC
64 ACAAGATC
26052 A
1 A
26053 ATTTTTTATT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
71 9 0.14
72 51 0.80
73 4 0.06
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.32
Consensus pattern (71 bp):
ATTATTGTACATAGAGAGAGTAATTAAATCCAAATCCAACAAGTTTCAACTTCATCCAATTTAAC
AAGATC
Found at i:32193 original size:2 final size:2
Alignment explanation
Indices: 32186--32212 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
32176 TCTCAGCAAC
32186 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
32213 ATTGTTGGAA
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:34175 original size:20 final size:20
Alignment explanation
Indices: 34138--34178 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
34128 ACGCGACATT
*
34138 TAAAATATATTTTTTAAAAA
1 TAAAATATATTTTCTAAAAA
34158 TAAAATA-ATATTTCTAAAAA
1 TAAAATATAT-TTTCTAAAAA
34178 T
1 T
34179 TTATCTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAATATATTTTCTAAAAA
Found at i:36233 original size:52 final size:52
Alignment explanation
Indices: 36125--36238 Score: 126
Period size: 52 Copynumber: 2.2 Consensus size: 52
36115 TAATTAATTT
* * *
36125 TCAATGTGAACTGATTAATAAATTAAAATAAAATCATAAATTAATCATATTC
1 TCAATGTGAACTGATTAATAAATCAAAATAAAATAAAAAATTAATCATATTC
* * * *
36177 -CAATGTTAATTGATTAATAATATCCAAATAAAATAAAAAATTAA-CCT-TGTC
1 TCAATGTGAACTGATTAATAA-ATCAAAATAAAATAAAAAATTAATCATAT-TC
36228 TCAATGTGAAC
1 TCAATGTGAAC
36239 ATGAATCATA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
50 1 0.02
51 22 0.44
52 27 0.54
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.33
Consensus pattern (52 bp):
TCAATGTGAACTGATTAATAAATCAAAATAAAATAAAAAATTAATCATATTC
Found at i:37019 original size:24 final size:24
Alignment explanation
Indices: 36988--37070 Score: 121
Period size: 24 Copynumber: 3.4 Consensus size: 24
36978 TTTAAGATTA
*
36988 AGGGTTTTTAGGTTAAAATAGTTT
1 AGGGTTTTTAGGTTAAAGTAGTTT
37012 AGGGTTTTTAGGTTAAAGTAGTTT
1 AGGGTTTTTAGGTTAAAGTAGTTT
* *
37036 TGGGTTTTTTTAGGTTAAAGTGGTTT
1 AGGG--TTTTTAGGTTAAAGTAGTTT
37062 AGGGTTTTT
1 AGGGTTTTT
37071 TTAAAAATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
24 31 0.58
26 22 0.42
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (24 bp):
AGGGTTTTTAGGTTAAAGTAGTTT
Found at i:37052 original size:26 final size:26
Alignment explanation
Indices: 36992--37073 Score: 123
Period size: 26 Copynumber: 3.2 Consensus size: 26
36982 AGATTAAGGG
*
36992 TTTTTAGGTTAAAATAGTTTAGGG--
1 TTTTTAGGTTAAAGTAGTTTAGGGTT
*
37016 TTTTTAGGTTAAAGTAGTTTTGGGTT
1 TTTTTAGGTTAAAGTAGTTTAGGGTT
*
37042 TTTTTAGGTTAAAGTGGTTTAGGGTT
1 TTTTTAGGTTAAAGTAGTTTAGGGTT
37068 TTTTTA
1 TTTTTA
37074 AAAATAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 22 0.42
26 30 0.58
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (26 bp):
TTTTTAGGTTAAAGTAGTTTAGGGTT
Found at i:37081 original size:27 final size:26
Alignment explanation
Indices: 37025--37081 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
37015 GTTTTTAGGT
* ***
37025 TAAAGTAGTTTTGGGTTTTTTTAGGT
1 TAAAGTAGTTTAGGGTTTTTTTAAAA
*
37051 TAAAGTGGTTTAGGGTTTTTTTAAAAA
1 TAAAGTAGTTTAGGGTTTTTTT-AAAA
37078 TAAA
1 TAAA
37082 ATGTTAATCA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (26 bp):
TAAAGTAGTTTAGGGTTTTTTTAAAA
Found at i:37398 original size:53 final size:51
Alignment explanation
Indices: 37328--37441 Score: 167
Period size: 53 Copynumber: 2.2 Consensus size: 51
37318 TAGAAAATAC
37328 ACATTGAAAATATTAGAAAATACA-ATTACATTAAAATATTAGAAACAAGCACAT
1 ACATTG-AAATATTAGAAAATA-ATATTACATTAAAATATTAGAAA-AA-CACAT
*
37382 ACATTGAAATATTAGAAAATAATATTACATTGAAATATTAGAAAAACACAT
1 ACATTGAAATATTAGAAAATAATATTACATTAAAATATTAGAAAAACACAT
*
37433 ACATAGAAA
1 ACATTGAAA
37442 ATAAAATTAC
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
51 13 0.23
52 3 0.05
53 35 0.61
54 6 0.11
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (51 bp):
ACATTGAAATATTAGAAAATAATATTACATTAAAATATTAGAAAAACACAT
Found at i:37443 original size:26 final size:28
Alignment explanation
Indices: 37328--37444 Score: 135
Period size: 26 Copynumber: 4.4 Consensus size: 28
37318 TAGAAAATAC
37328 ACATTGAAAATATTAGAAAATACA-ATT
1 ACATTGAAAATATTAGAAAATACACATT
37355 ACATT-AAAATATTAGAAACA-AGCACA-T
1 ACATTGAAAATATTAGAAA-ATA-CACATT
*
37382 ACATTG-AAATATTAGAAAATA-ATATT
1 ACATTGAAAATATTAGAAAATACACATT
37408 ACATTG-AAATATTAGAAAA-ACACA-T
1 ACATTGAAAATATTAGAAAATACACATT
*
37433 ACATAGAAAATA
1 ACATTGAAAATA
37445 AAATTACATA
Statistics
Matches: 79, Mismatches: 3, Indels: 17
0.80 0.03 0.17
Matches are distributed among these distances:
25 9 0.11
26 42 0.53
27 27 0.34
28 1 0.01
ACGTcount: A:0.56, C:0.09, G:0.08, T:0.26
Consensus pattern (28 bp):
ACATTGAAAATATTAGAAAATACACATT
Found at i:46427 original size:21 final size:22
Alignment explanation
Indices: 46403--46479 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 22
46393 TTGTGCACAG
*
46403 TGTATCGATACATCCTTG-CTA
1 TGTATCGATACATCCTTGAATA
*
46424 TGTATTGATACA--CTATGAATA
1 TGTATCGATACATCCT-TGAATA
* *
46445 TGTACCGATACATTCCTTGAATG
1 TGTATCGATACA-TCCTTGAATA
46468 TGTATCGATACA
1 TGTATCGATACA
46480 CTCAAGAGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.04
20 2 0.04
21 23 0.51
23 16 0.36
24 2 0.04
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (22 bp):
TGTATCGATACATCCTTGAATA
Found at i:46993 original size:12 final size:13
Alignment explanation
Indices: 46970--47003 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
46960 CATATTATGA
46970 TTTCAAACAATA-T
1 TTTCAAA-AATAGT
46983 TTTCAAAAATAGT
1 TTTCAAAAATAGT
46996 TTTCAAAA
1 TTTCAAAA
47004 TTGCCCATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (13 bp):
TTTCAAAAATAGT
Found at i:48771 original size:12 final size:13
Alignment explanation
Indices: 48745--48778 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
48735 ATTTTTAGTA
*
48745 ATTTTCAAAATTG
1 ATTTTCAAAAATG
48758 ATTTT-AAAAATG
1 ATTTTCAAAAATG
48770 ATTTTCAAA
1 ATTTTCAAA
48779 GAAAAATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:49292 original size:21 final size:21
Alignment explanation
Indices: 49266--49305 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
49256 ATTTTACACT
*
49266 GAGTGTATCGATACACCTAGA
1 GAGTGTACCGATACACCTAGA
49287 GAGTGTACCGATACACCTA
1 GAGTGTACCGATACACCTA
49306 CGCTCTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.23
Consensus pattern (21 bp):
GAGTGTACCGATACACCTAGA
Found at i:55864 original size:6 final size:6
Alignment explanation
Indices: 55848--55885 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
55838 AAATAATAAA
*
55848 TTTATT ATTATT TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TT
55886 GTTTGTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:60846 original size:170 final size:170
Alignment explanation
Indices: 60310--60924 Score: 681
Period size: 170 Copynumber: 3.6 Consensus size: 170
60300 GCAACAATTT
* * * *
60310 TTCACTTAATAATAGCCATAAATGATGTCCCCCATTGGGGAACTATTCTCATCAACTCCTATCT-
1 TTCAGTTAATAATAGCCATAAATGATGTCCCCCATTGGGAAACTATTCACATCAACCCCTAT-TA
* * *
60374 TGTTTGATAGGATGTGACACTATGGCATGGA-AGAGATTCTCTGGAAAAGGTGAAAGCGCTTCTT
65 TGTTTGATGGGATGAGACACTATGGCAT-GACAGAGATTCTCTGAAAAAGGTGAAAGCGCTTCTT
* * *
60438 GTGGGACGCG-TCTTCCCTTTTCGTCAAAGATTCTCTGT-ATTA
129 GTGGGACGCGCT-TTCCCTTTTCGTTAGAGATTCTCT-TCATTC
* * * *
60480 TTTAGTTAATGATAGCCATAAATGATGTCCCCCGTTGGAGAAA-TATTCACGTCAACCCCTATTA
1 TTCAGTTAATAATAGCCATAAATGATGTCCCCCATTGG-GAAACTATTCACATCAACCCCTATTA
* * * * * ** * * *
60544 TATTTGAAGGGATTAGATACTATGACATGGTAGAGATTCTCTGGAAAAA-GAGAAAACGCTTATT
65 TGTTTGATGGGATGAGACACTATGGCATGACAGAGATTCTCT-GAAAAAGGTGAAAGCGCTTCTT
* * ** *
60608 -TGGAACGCGCCTTCTATTTTC-TTCAGAGATTCTCTGCATTC
129 GTGGGACGCGCTTTCCCTTTTCGTT-AGAGATTCTCTTCATTC
* * *
60649 TTCAGTTAATAATAGCCATAAATGATGTCTCTCATTGGGAAACTATTCACGTCAACCCCTATTAT
1 TTCAGTTAATAATAGCCATAAATGATGTCCCCCATTGGGAAACTATTCACATCAACCCCTATTAT
* * * *
60714 GTTTGATGGGATGAGACATTATGGCATGACAGAGATTATCTAAAAAAGGTGAAAGCACTTCTTGT
66 GTTTGATGGGATGAGACACTATGGCATGACAGAGATTCTCTGAAAAAGGTGAAAGCGCTTCTTGT
* *
60779 GGGATGTGCTTTCCCTTTTCGTTAGAGATTCTCTTCATTC
131 GGGACGCGCTTTCCCTTTTCGTTAGAGATTCTCTTCATTC
* * **
60819 TTCAGTTAATAATAGCCATAAATGATGTCCCCTATAAGGG-AACTATTCACATCAACCTTTATTA
1 TTCAGTTAATAATAGCCATAAATGATGTCCCCCAT-TGGGAAACTATTCACATCAACCCCTATTA
* * * *
60883 TGTTTGCTGGGATGAGACATTATAGCATTACAGAGATTCTCT
65 TGTTTGATGGGATGAGACACTATGGCATGACAGAGATTCTCT
60925 TATCACATCA
Statistics
Matches: 368, Mismatches: 65, Indels: 24
0.81 0.14 0.05
Matches are distributed among these distances:
168 10 0.03
169 129 0.35
170 216 0.59
171 13 0.04
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (170 bp):
TTCAGTTAATAATAGCCATAAATGATGTCCCCCATTGGGAAACTATTCACATCAACCCCTATTAT
GTTTGATGGGATGAGACACTATGGCATGACAGAGATTCTCTGAAAAAGGTGAAAGCGCTTCTTGT
GGGACGCGCTTTCCCTTTTCGTTAGAGATTCTCTTCATTC
Found at i:61091 original size:33 final size:34
Alignment explanation
Indices: 61016--61118 Score: 138
Period size: 33 Copynumber: 3.1 Consensus size: 34
61006 TATATATAAG
*
61016 ATTTTGTTTGTGGTCCTAACTTTTAAAACTTCTC
1 ATTTTGTTTGTGGTCCTAACTTTCAAAACTTCTC
* *
61050 ATTGTGTTTGTGGTCTTAACTTTCAAAA-TTCTC
1 ATTTTGTTTGTGGTCCTAACTTTCAAAACTTCTC
** *
61083 ATTTTGTTTGTGGTCCTCGCCTTC-AAACTTCTC
1 ATTTTGTTTGTGGTCCTAACTTTCAAAACTTCTC
61116 ATT
1 ATT
61119 AAGTTTCTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
32 3 0.05
33 32 0.53
34 25 0.42
ACGTcount: A:0.18, C:0.19, G:0.14, T:0.49
Consensus pattern (34 bp):
ATTTTGTTTGTGGTCCTAACTTTCAAAACTTCTC
Found at i:61798 original size:6 final size:6
Alignment explanation
Indices: 61775--61839 Score: 71
Period size: 6 Copynumber: 10.8 Consensus size: 6
61765 TTGTAATGTC
* * *
61775 AATTTG AATGTA AATTTG AATTTG AATTT- AGATTTG AATTTG GATTTG
1 AATTTG AATTTG AATTTG AATTTG AATTTG A-ATTTG AATTTG AATTTG
61823 TAA-TTG AATTTG AATTT
1 -AATTTG AATTTG AATTT
61840 TTATTTTTAG
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
5 3 0.06
6 44 0.90
7 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (6 bp):
AATTTG
Found at i:62583 original size:41 final size:42
Alignment explanation
Indices: 62498--62583 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 42
62488 AATATGTTTC
* *
62498 TAATGGTAAGGTAATGTACTCTAAGGTTCATGATAATGCTTT
1 TAATGGTAAGGTAATGTACTCTAAGGTTCATGATAATACATT
*
62540 TAAT-GTAAGGTAATGTACTCTAATG-TCATG-TAATTAACATT
1 TAATGGTAAGGTAATGTACTCTAAGGTTCATGATAA-T-ACATT
62581 TAA
1 TAA
62584 CAAACACAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
39 3 0.08
40 6 0.15
41 26 0.67
42 4 0.10
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.38
Consensus pattern (42 bp):
TAATGGTAAGGTAATGTACTCTAAGGTTCATGATAATACATT
Found at i:62660 original size:37 final size:37
Alignment explanation
Indices: 62619--62690 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
62609 AATGAAAATG
* *
62619 TTAAACATTTAACAACCATAAAGACAA-ATTAAAAAAA
1 TTAAACATTTAACAAACATAAACA-AATATTAAAAAAA
62656 TTAAACATTTAACAAACATAAACAAATATTAAAAA
1 TTAAACATTTAACAAACATAAACAAATATTAAAAA
62691 CATAACATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 2 0.06
37 30 0.94
ACGTcount: A:0.62, C:0.12, G:0.01, T:0.24
Consensus pattern (37 bp):
TTAAACATTTAACAAACATAAACAAATATTAAAAAAA
Found at i:62677 original size:17 final size:17
Alignment explanation
Indices: 62620--62679 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
62610 ATGAAAATGT
*
62620 TAAACATTTAACAACCA
1 TAAACATTTAACAAACA
* *
62637 TAAAGACAAATTAA-AAAAA
1 T-AA-AC-ATTTAACAAACA
62656 TTAAACATTTAACAAACA
1 -TAAACATTTAACAAACA
62674 TAAACA
1 TAAACA
62680 AATATTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
17 12 0.36
18 8 0.24
19 7 0.21
20 6 0.18
ACGTcount: A:0.62, C:0.15, G:0.02, T:0.22
Consensus pattern (17 bp):
TAAACATTTAACAAACA
Found at i:65009 original size:19 final size:19
Alignment explanation
Indices: 64960--65010 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
64950 CACAAATAAT
* *
64960 TAATAAAATTAAATATATTT
1 TAATAAAA-TAAAAATATTA
* *
64980 TAATTATATAAAAATATTA
1 TAATAAAATAAAAATATTA
64999 TAATAAAATAAA
1 TAATAAAATAAA
65011 TATAACCATT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATAAAATAAAAATATTA
Found at i:65053 original size:20 final size:20
Alignment explanation
Indices: 64970--65147 Score: 74
Period size: 20 Copynumber: 9.2 Consensus size: 20
64960 TAATAAAATT
**
64970 AAATATATTTTAATTATATAA
1 AAATATATAATAATTA-ATAA
64991 AAATAT-T-ATAA-TAA-AA
1 AAATATATAATAATTAATAA
* **
65007 TAA-ATATAACCATTAATAA
1 AAATATATAATAATTAATAA
*
65026 TTAA-ATATAATAATTAATAA
1 -AAATATATAATAATTAATAA
*
65046 AAATATATTAT-ATTATATAA
1 AAATATATAATAATTA-ATAA
*
65066 TAATATAATAATAATTAA-AA
1 AAATAT-ATAATAATTAATAA
** *
65086 ATTAAT-TA-AA-AAAAAAAAA
1 A--AATATATAATAATTAATAA
* * * *
65105 AAAAAAATAA-AAATATTAA
1 AAATATATAATAATTAATAA
65124 AAATAATATAATAATTAATAA
1 AAAT-ATATAATAATTAATAA
65145 AAA
1 AAA
65148 ATTATTACCT
Statistics
Matches: 119, Mismatches: 22, Indels: 32
0.69 0.13 0.18
Matches are distributed among these distances:
15 2 0.02
16 5 0.04
17 5 0.04
18 10 0.08
19 27 0.23
20 41 0.34
21 22 0.18
22 7 0.06
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATATATAATAATTAATAA
Found at i:65071 original size:38 final size:37
Alignment explanation
Indices: 64954--65087 Score: 111
Period size: 38 Copynumber: 3.6 Consensus size: 37
64944 AATTATCACA
* *
64954 AATAAT-TAATAA-AAT-TAAATATATTTTAATTATAT
1 AATAATATAATAATAATAAAAATATATTAT-ATTATAT
* * *
64989 AAAAATATTATAATAA-AATAAATATA--ACCATTA-AT
1 AATAATATAATAATAATAA-AAATATATTA-TATTATAT
65024 AATTAAATATAATAATTAATAAAAATATATTATATTATAT
1 AA-T-AATATAATAA-TAATAAAAATATATTATATTATAT
65064 AATAATATAATAATAATTAAAAAT
1 AATAATATAATAATAA-TAAAAAT
65088 TAATTAAAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
35 9 0.12
36 9 0.12
37 14 0.18
38 34 0.44
39 7 0.09
40 5 0.06
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (37 bp):
AATAATATAATAATAATAAAAATATATTATATTATAT
Found at i:65091 original size:11 final size:10
Alignment explanation
Indices: 65064--65154 Score: 58
Period size: 10 Copynumber: 8.8 Consensus size: 10
65054 TATATTATAT
*
65064 AATAATATAAT
1 AATAAT-TAAA
65075 AATAATTAAA
1 AATAATTAAA
65085 AATTAATTAAA
1 AA-TAATTAAA
* **
65096 AAAAAAAAAA
1 AATAATTAAA
* *
65106 AAAAAATAAA
1 AATAATTAAA
65116 AAT-ATTAAA
1 AATAATTAAA
65125 AATAATATAATA
1 AATAAT-TAA-A
* *
65137 ATTAATAAAA
1 AATAATTAAA
*
65147 AATTATTA
1 AATAATTA
65155 CCTAATAATA
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
9 8 0.12
10 29 0.45
11 21 0.33
12 6 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AATAATTAAA
Found at i:69188 original size:21 final size:21
Alignment explanation
Indices: 69140--69200 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
69130 TTCAAAAATT
* * **
69140 ATTTCACGAAAAGATTAAATC
1 ATTTCATGAAAAGGTTAAGGC
69161 ATTTCATGAAAAGGTTAAGGC
1 ATTTCATGAAAAGGTTAAGGC
* *
69182 ATTTCATCAAAAGGATAAG
1 ATTTCATGAAAAGGTTAAG
69201 TCTTTTAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.28
Consensus pattern (21 bp):
ATTTCATGAAAAGGTTAAGGC
Found at i:69215 original size:21 final size:22
Alignment explanation
Indices: 69191--69236 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
69181 CATTTCATCA
* *
69191 AAAGGA-TAAGTCTTTTAATTG
1 AAAGGACTAAGTCCTTTAATCG
69212 AAA-GACTAAGTCCTTTAATCG
1 AAAGGACTAAGTCCTTTAATCG
69233 AAAG
1 AAAG
69237 TGTTGAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.30
Consensus pattern (22 bp):
AAAGGACTAAGTCCTTTAATCG
Found at i:77691 original size:131 final size:130
Alignment explanation
Indices: 77453--77813 Score: 451
Period size: 131 Copynumber: 2.8 Consensus size: 130
77443 TCGATATTGA
* * *
77453 AAATAGTAATATCTCATTATTT-GGTTGGAGTAATAAATGACTACTTTAAGGCATGAGAGGTCAT
1 AAATAGTAATATCTCTTTATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
* * * * * * * *
77517 TTATTCTCGATTGGAAAGAATAAGATATTACCATTTTCTCTCGAGTTAATATTGATTTTTAAGAC
66 TTATTCTCGATTGGAAATAATTAGATATTATC-TTTTCACTCGAATCAATATTAAATTTTAAGAC
77582 G
130 G
* * * *
77583 GAATAGTGATATCTCTTTATTTCGATTGGAGTAATAAAT-AGTTGCTATAAGGCATGAGAGGTCA
1 AAATAGTAATATCTCTTTATTTCGATTGGAGTAATAAATGA-CTGCTTTAAGGCATGAGAGGTCA
* *
77647 TTTATTCTCGTTTGGAAATCATTAGATATTATCGTTTTCACTCGAATCAATATTAAATTTTAAGA
65 TTTATTCTCGATTGGAAATAATTAGATATTATC-TTTTCACTCGAATCAATATTAAATTTTAAGA
77712 CG
129 CG
* * * * * *
77714 AAATAGTAATATCTCTTCATTTC-AATGGGGTAA-GAATGACTGTTTTAAGGCATGAAAGGTCAT
1 AAATAGTAATATCTCTTTATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
*
77777 TTATTATCGATTGGAAATAATTAGATATTATCTTTTC
66 TTATTCTCGATTGGAAATAATTAGATATTATCTTTTC
77814 TCTTAAATTA
Statistics
Matches: 197, Mismatches: 31, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
128 5 0.03
129 52 0.26
130 29 0.15
131 111 0.56
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (130 bp):
AAATAGTAATATCTCTTTATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
TTATTCTCGATTGGAAATAATTAGATATTATCTTTTCACTCGAATCAATATTAAATTTTAAGACG
Done.