Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001709.1 Hibiscus syriacus cultivar Beakdansim tig00003435_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: 1326839
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1245296 original size:17 final size:17
Alignment explanation
Indices: 1245274--1245307 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1245264 CGGTGAGCCT
1245274 CTGTCGTTCAGCCGCCG
1 CTGTCGTTCAGCCGCCG
*
1245291 CTGTCGTTCGGCCGCCG
1 CTGTCGTTCAGCCGCCG
1245308 TTGATCGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.41, G:0.32, T:0.24
Consensus pattern (17 bp):
CTGTCGTTCAGCCGCCG
Found at i:1246722 original size:40 final size:39
Alignment explanation
Indices: 1246618--1246734 Score: 162
Period size: 39 Copynumber: 3.0 Consensus size: 39
1246608 TTGTTATCTA
*
1246618 GGGGTAACACGGCTCCTGCGCGATGAGGAGATCTGGTCG
1 GGGGTGACACGGCTCCTGCGCGATGAGGAGATCTGGTCG
*
1246657 GGGGTGACACGGCTCCTGCACGATGAGGAGATCTGGTCG
1 GGGGTGACACGGCTCCTGCGCGATGAGGAGATCTGGTCG
* * * * *
1246696 GGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGTC
1 GGGG-TGACACGGCTCCTGCGCGATGAGGAGATCTGGTC
1246735 ATCTTTAGGA
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
39 41 0.59
40 28 0.41
ACGTcount: A:0.20, C:0.21, G:0.39, T:0.20
Consensus pattern (39 bp):
GGGGTGACACGGCTCCTGCGCGATGAGGAGATCTGGTCG
Found at i:1246789 original size:173 final size:174
Alignment explanation
Indices: 1246505--1246847 Score: 465
Period size: 173 Copynumber: 2.0 Consensus size: 174
1246495 GTTCCTACGA
* *
1246505 GATGAGGAAATCTGGTCAGGGGATGACACGACTCATACATGATGAAGAGTTTTGGTCATCTTTTG
1 GATGAGGAAATCTGGTCAGGGGATGACACGACTCATACATGATGAAGAGTTCTGGTCATCTTTAG
* ** * * *
1246570 GAATGGTGATAACTCAGTTCCTATGCGATGTGGACGACTTGTTATCTAGGGGTAACACGGCTCCT
66 GAAGGGCAATAACTCAGTTCCTACGCGATGAGGACGACTGGTTATCTAGGGGTAACACGGCTCCT
* * *
1246635 GCGCGATGAGGAGATCTGGTC-GGGGGTGACACGGCTCCTGCAC
131 ACGCGATGAGGAGATCTGATCAGGGGATGACACGGCTCCTGCAC
* * * *
1246678 GATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGTCATCTTTAG
1 GATGAGGAAATCTGGTCAGGGGATGACACGACTCATACATGATGAAGAGTTCTGGTCATCTTTAG
* * *
1246743 GAAGGGCAATGACTC-GATTCCTACGCGATGAGGACGGCTGGTTATCTAGGGGTGACACGGCTCC
66 GAAGGGCAATAACTCAG-TTCCTACGCGATGAGGACGACTGGTTATCTAGGGGTAACACGGCTCC
* * * *
1246807 TACGTGATGAGGAGGTTTGATCAGGGGATGACACGGTTCCT
130 TACGCGATGAGGAGATCTGATCAGGGGATGACACGGCTCCT
1246848 ACGTTGTGAG
Statistics
Matches: 146, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
172 1 0.01
173 129 0.88
174 16 0.11
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.25
Consensus pattern (174 bp):
GATGAGGAAATCTGGTCAGGGGATGACACGACTCATACATGATGAAGAGTTCTGGTCATCTTTAG
GAAGGGCAATAACTCAGTTCCTACGCGATGAGGACGACTGGTTATCTAGGGGTAACACGGCTCCT
ACGCGATGAGGAGATCTGATCAGGGGATGACACGGCTCCTGCAC
Found at i:1246925 original size:28 final size:28
Alignment explanation
Indices: 1246885--1246981 Score: 90
Period size: 28 Copynumber: 3.4 Consensus size: 28
1246875 AGTGATTATG
** *
1246885 GTTTCAAGGGAAACCGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
1246913 GTTTCAAAAGAAACAGACTCAATA-ATTT
1 GTTTCAAAAGAAACAGACTCAA-AGATTT
* *
1246941 GTCTCAAGAA-AAACAAACTCAAAGATGATGT
1 GTTTCAA-AAGAAACAGACTCAAAGAT--T-T
1246972 GTTTCAAAAG
1 GTTTCAAAAG
1246982 CAACTGTCTC
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.02
28 42 0.75
29 3 0.05
30 3 0.05
31 7 0.12
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.25
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGACTCAAAGATTT
Found at i:1247065 original size:63 final size:66
Alignment explanation
Indices: 1246957--1247106 Score: 164
Period size: 63 Copynumber: 2.3 Consensus size: 66
1246947 AGAAAAACAA
* *
1246957 ACTCAAAGATGATGTGTTTCAAAAGCAACTGTCTCAAAAGAGACAAAATTCGT-TTCAAGGGAAA
1 ACTCAAAGATGA-GTGTTTCAAAAGAAAATGTCTCAAAAGAGACAAAATTCGTGTTCAAGGGAAA
1247021 GG
65 GG
* ** * *
1247023 ACTCAAAGATGA-TGTTT-AAAGGAAAATGTCTCAAGCGAGACAAAATTTGTGTTTAAGGGAAAC
1 ACTCAAAGATGAGTGTTTCAAAAGAAAATGTCTCAAAAGAGACAAAATTCGTGTTCAAGGGAAA-
*
1247086 GT
65 GG
*
1247088 TCTCAAAGAT-AGGTGTTTC
1 ACTCAAAGATGA-GTGTTTC
1247107 GAGAAAAACA
Statistics
Matches: 70, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
63 27 0.39
64 16 0.23
65 10 0.14
66 17 0.24
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (66 bp):
ACTCAAAGATGAGTGTTTCAAAAGAAAATGTCTCAAAAGAGACAAAATTCGTGTTCAAGGGAAAG
G
Found at i:1247144 original size:32 final size:33
Alignment explanation
Indices: 1247101--1247170 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 33
1247091 CAAAGATAGG
*
1247101 TGTTTCGAGAAAAACAAACTCAAAGATGTT-TT
1 TGTTTCAAGAAAAACAAACTCAAAGATGTTGTT
* *
1247133 TGTTTCAAGAAAAACATACTCAAAGATTTTGTT
1 TGTTTCAAGAAAAACAAACTCAAAGATGTTGTT
1247166 TGTTT
1 TGTTT
1247171 TGTTTCATGG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 27 0.79
33 7 0.21
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Consensus pattern (33 bp):
TGTTTCAAGAAAAACAAACTCAAAGATGTTGTT
Found at i:1247736 original size:65 final size:64
Alignment explanation
Indices: 1247635--1247757 Score: 174
Period size: 65 Copynumber: 1.9 Consensus size: 64
1247625 GTGGGTATTT
* *
1247635 TCAAAAGAAATTATCTCGAGAGACAAAATCTTGTTTCAAATGAAACAAACTCAAAGATTTTTTC
1 TCAAAAGAAATTATCTCAAGAGACAAAATCTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTC
* * * * *
1247699 TCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TCAAAAGAAATTATC-TCAAGAGACAAAATCTTGTTTCAAAAGAAACAAACTCAAAGAT
1247758 AGATTACATC
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
64 14 0.27
65 37 0.73
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (64 bp):
TCAAAAGAAATTATCTCAAGAGACAAAATCTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTC
Found at i:1249659 original size:19 final size:18
Alignment explanation
Indices: 1249635--1249682 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 18
1249625 TTGTCATCTT
1249635 TTTGTTCTTTGCTCTTTTC
1 TTTGTT-TTTGCTCTTTTC
*
1249654 TTTGTTTTTGCTTTTTTTC
1 TTTGTTTTTGC-TCTTTTC
1249673 TTTGCTTTTT
1 TTTG-TTTTT
1249683 TTCTCTTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 5 0.19
19 16 0.62
20 5 0.19
ACGTcount: A:0.00, C:0.15, G:0.10, T:0.75
Consensus pattern (18 bp):
TTTGTTTTTGCTCTTTTC
Found at i:1249696 original size:13 final size:13
Alignment explanation
Indices: 1249660--1249686 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1249650 TTTCTTTGTT
1249660 TTTGCTTTTTTTC
1 TTTGCTTTTTTTC
1249673 TTTGCTTTTTTTC
1 TTTGCTTTTTTTC
1249686 T
1 T
1249687 CTTTGTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (13 bp):
TTTGCTTTTTTTC
Found at i:1251002 original size:13 final size:14
Alignment explanation
Indices: 1250984--1251014 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1250974 TTAAAAATTG
1250984 AAATGCAAATATA-
1 AAATGCAAATATAC
1250997 AAATGCAAATATAC
1 AAATGCAAATATAC
1251011 AAAT
1 AAAT
1251015 CCAGATGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.61, C:0.10, G:0.06, T:0.23
Consensus pattern (14 bp):
AAATGCAAATATAC
Found at i:1253332 original size:60 final size:60
Alignment explanation
Indices: 1253225--1253348 Score: 160
Period size: 60 Copynumber: 2.1 Consensus size: 60
1253215 GATGGTCATG
* * * * *
1253225 GTTTAGGGATGAAATTAGAATGTTTAAAAGTTTAAGAATTAATTTAAAATAAAAATAATA
1 GTTTAGGGATGAAACTAAAATATTTAAAAGTTTAAGAATCAACTTAAAATAAAAATAATA
* * *
1253285 GTTTAGGGATGAAACTAAAATATTTAAAAGTTTAAGGAA-CAACTTAAAATGAAAGTTATA
1 GTTTAGGGATGAAACTAAAATATTTAAAAGTTTAA-GAATCAACTTAAAATAAAAATAATA
1253345 GTTT
1 GTTT
1253349 GAGTTCATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 52 0.95
61 3 0.05
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (60 bp):
GTTTAGGGATGAAACTAAAATATTTAAAAGTTTAAGAATCAACTTAAAATAAAAATAATA
Found at i:1254994 original size:36 final size:36
Alignment explanation
Indices: 1254923--1254995 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
1254913 GTTGGAAAAT
* *
1254923 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
1254959 ATTTATATAATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTGAAAATCATAAA
1254995 A
1 A
1254996 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 18 0.55
37 15 0.45
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
Found at i:1256133 original size:59 final size:61
Alignment explanation
Indices: 1256070--1256184 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 61
1256060 TCTATGACTA
* ** *
1256070 TCATTCTAGATTAGTCTTC-AAAC-TTTTGAATATT-TCAATTTTATCCCAAACTATGGCAT
1 TCATTCTAAATTAGTCCCCTAAACTTTTTGAACATTCT-AATTTTATCCCAAACTATGGCAT
* *
1256129 TCATTCTAAATTGGTCCCCTAAACTTTTTGAACATTCTAATTTTATCTCAAACTAT
1 TCATTCTAAATTAGTCCCCTAAACTTTTTGAACATTCTAATTTTATCCCAAACTAT
1256185 ATGTATATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 15 0.32
60 4 0.09
61 27 0.57
62 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (61 bp):
TCATTCTAAATTAGTCCCCTAAACTTTTTGAACATTCTAATTTTATCCCAAACTATGGCAT
Found at i:1257457 original size:74 final size:73
Alignment explanation
Indices: 1257363--1257503 Score: 219
Period size: 74 Copynumber: 1.9 Consensus size: 73
1257353 ATCTTTTAAC
* *
1257363 TTTTAATTTATAATTATCAATATTTATCCAAATAAATTATTAGATGGGTAACTTGTATCTAAATA
1 TTTTAATTTATAAATATCAATATTTATCCAAATAAATTATTAGAT-GGTAACTCGTATCTAAATA
1257428 AATCTAAAA
65 AATCTAAAA
* * * *
1257437 TTTTAGTTTATAAATGTCAATATTTATCCAAATAAATTTTTATATGGTAACTCGTATCTAAATAA
1 TTTTAATTTATAAATATCAATATTTATCCAAATAAATTATTAGATGGTAACTCGTATCTAAATAA
1257502 AT
66 AT
1257504 TTATTAACCT
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 21 0.34
74 40 0.66
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (73 bp):
TTTTAATTTATAAATATCAATATTTATCCAAATAAATTATTAGATGGTAACTCGTATCTAAATAA
ATCTAAAA
Found at i:1258390 original size:43 final size:43
Alignment explanation
Indices: 1258343--1258425 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
1258333 AGGGTATGTT
* *
1258343 TTTCTTTCTGTGTTT-TTATTTTTTTGATCTTTCATTGAGATCC
1 TTTCTTTCTGTGTTTGTTAGTTTTTTGATCTTCCA-TGAGATCC
* * *
1258386 TTTCTTTGTTTGTTTGTTGGTTTTTTGATCTTCCATGAGA
1 TTTCTTTCTGTGTTTGTTAGTTTTTTGATCTTCCATGAGA
1258426 ATTTTCAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 18 0.53
44 16 0.47
ACGTcount: A:0.11, C:0.12, G:0.16, T:0.61
Consensus pattern (43 bp):
TTTCTTTCTGTGTTTGTTAGTTTTTTGATCTTCCATGAGATCC
Found at i:1292351 original size:3 final size:3
Alignment explanation
Indices: 1292343--1292367 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1292333 TATAAACAAG
1292343 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1292368 TTGTTAGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1300764 original size:16 final size:16
Alignment explanation
Indices: 1300740--1300774 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1300730 AAAATTCATC
*
1300740 TTATATGAATAATTTT
1 TTATATGAATAATTCT
*
1300756 TTATCTGAATAATTCT
1 TTATATGAATAATTCT
1300772 TTA
1 TTA
1300775 AACAAGATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (16 bp):
TTATATGAATAATTCT
Found at i:1306241 original size:26 final size:26
Alignment explanation
Indices: 1306187--1306240 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
1306177 AGGGATAATG
* *
1306187 AAACAATTTCAAATATTAAAAGAATA
1 AAACAATTTCAAAAATCAAAAGAATA
1306213 AAACAATTT-AAAAATCAAAATG-ATA
1 AAACAATTTCAAAAATCAAAA-GAATA
1306238 AAA
1 AAA
1306241 AATAGAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.65, C:0.07, G:0.04, T:0.24
Consensus pattern (26 bp):
AAACAATTTCAAAAATCAAAAGAATA
Found at i:1311435 original size:56 final size:56
Alignment explanation
Indices: 1311308--1311759 Score: 314
Period size: 51 Copynumber: 8.6 Consensus size: 56
1311298 TGACGAGCCT
* *
1311308 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTC-ATAAAACGTGTCT
1 GCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * * *
1311363 GCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * *
1311419 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAAAATCTTCAAT-AAACAGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAATAAAACGGGTCC
* * * ** **
1311474 GCTCCCTATTCTTTCAGGGAGTATAGGACT----CAATCTTCAA-CGAACTAGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* ** **
1311525 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* ** * ** **
1311576 GCTCTCTATTTATTCAGAGAGTATAGGACT----CAATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * ** **
1311627 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* ** **
1311678 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
*
1311729 GCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTC
1311760 AATCTTCAAC
Statistics
Matches: 363, Mismatches: 28, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
51 241 0.66
55 71 0.20
56 51 0.14
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (56 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
Found at i:1311530 original size:51 final size:51
Alignment explanation
Indices: 1311415--1311769 Score: 557
Period size: 51 Copynumber: 6.9 Consensus size: 51
1311405 AATAAAACGG
* * ** **
1311415 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAG
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACGAACTT
* * *
1311470 GTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCAATCTTCAACGAACTA
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1311521 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
* **
1311572 GTCCGCTCTCTATTTATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
1311623 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1311674 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1311725 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
1311770 AAACGAATTT
Statistics
Matches: 283, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
51 252 0.89
55 31 0.11
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (51 bp):
GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:1311600 original size:102 final size:102
Alignment explanation
Indices: 1311308--1311773 Score: 567
Period size: 102 Copynumber: 4.4 Consensus size: 102
1311298 TGACGAGCCT
* * * *
1311308 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATA-AAACGTGTCTGCTCTCTA
1 GCTCCCTATTCCTTCAGAG-AGTATAGGACT----CAATCTTCA-ACAAACTTGTCCGCTCCCTA
* * ** **
1311371 TTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCC
60 TTCATTCAGAGAGTATAGGAC-T---CAATCTTCAA-CGAACTTGTCC
* * * **
1311419 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAGGTCCGCTCCCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACAAACTTGTCCGCTCCCTATT
* * *
1311484 CTTTCAGGGAGTATAGGACTCAATCTTCAACGAACTAGTCC
62 CATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
* * *
1311525 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCTCTATTTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTATTCATT
1311590 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
66 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
* * *
1311627 GCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCCTT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTATTCATT
1311692 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
66 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
1311729 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAAC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAAC
1311774 GAATTTGCTT
Statistics
Matches: 317, Mismatches: 32, Indels: 21
0.86 0.09 0.06
Matches are distributed among these distances:
102 203 0.64
106 36 0.11
107 10 0.03
110 2 0.01
111 65 0.21
112 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (102 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTATTCATT
CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
Found at i:1313148 original size:25 final size:25
Alignment explanation
Indices: 1313093--1313201 Score: 78
Period size: 25 Copynumber: 4.2 Consensus size: 25
1313083 CCTTTATTTA
* **
1313093 TCTTTTTCATTTTTCTCTT-TCCTT
1 TCTTTTCCATTTTTCTCTTCTTTTT
*
1313117 CCTTTTTCCATTTTTCTCTTCTTTTT
1 TC-TTTTCCATTTTTCTCTTCTTTTT
** *
1313143 TCTTTTCGTTTTTTC-CATCATTTTT
1 TCTTTTCCATTTTTCTCTTC-TTTTT
* *
1313168 TCGTTTTTCTCATTTTTTTCTTCTTTTC
1 TC--TTTTC-CATTTTTCTCTTCTTTTT
1313196 TCTTTT
1 TCTTTT
1313202 ATTTCTTCTT
Statistics
Matches: 65, Mismatches: 13, Indels: 12
0.72 0.14 0.13
Matches are distributed among these distances:
24 4 0.06
25 34 0.52
26 8 0.12
27 5 0.08
28 11 0.17
29 3 0.05
ACGTcount: A:0.05, C:0.23, G:0.02, T:0.71
Consensus pattern (25 bp):
TCTTTTCCATTTTTCTCTTCTTTTT
Found at i:1313158 original size:44 final size:46
Alignment explanation
Indices: 1313110--1313195 Score: 113
Period size: 44 Copynumber: 1.9 Consensus size: 46
1313100 CATTTTTCTC
* *
1313110 TTTCCTTCCTTTTTCCATTTTTCTC-TTCTTTT-TTCTTTTCGTTT
1 TTTCCATCATTTTTCCATTTTTCTCATTCTTTTCTTCTTTTCGTTT
* * *
1313154 TTTCCATCATTTTTTCGTTTTTCTCATTTTTTTCTTCTTTTC
1 TTTCCATCATTTTTCCATTTTTCTCATTCTTTTCTTCTTTTC
1313196 TCTTTTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 21 0.60
45 6 0.17
46 8 0.23
ACGTcount: A:0.05, C:0.23, G:0.02, T:0.70
Consensus pattern (46 bp):
TTTCCATCATTTTTCCATTTTTCTCATTCTTTTCTTCTTTTCGTTT
Found at i:1313186 original size:20 final size:20
Alignment explanation
Indices: 1313139--1313186 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1313129 TTTCTCTTCT
1313139 TTTTTCTTTTCGTTTTTTCCA
1 TTTTT-TTTTCGTTTTTTCCA
**
1313160 TCATTTTTTCG-TTTTTCTCA
1 TTTTTTTTTCGTTTTTTC-CA
1313180 TTTTTTT
1 TTTTTTT
1313187 CTTCTTTTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 6 0.27
20 13 0.59
21 3 0.14
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.73
Consensus pattern (20 bp):
TTTTTTTTTCGTTTTTTCCA
Found at i:1313194 original size:19 final size:18
Alignment explanation
Indices: 1313163--1313211 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
1313153 TTTTCCATCA
*
1313163 TTTTTTCGT-TTTTCTCAT
1 TTTTTTCTTCTTTTCTC-T
1313181 TTTTTTCTTCTTTTCTCT
1 TTTTTTCTTCTTTTCTCT
1313199 TTTATTTCTTCTT
1 TTT-TTTCTTCTT
1313212 CAAGCAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTTTCTTCTTTTCTCT
Found at i:1322916 original size:44 final size:46
Alignment explanation
Indices: 1322852--1322949 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 46
1322842 TTGTTATTCA
1322852 CAAAAATAAATCCTAACCGCATGATATCTAATTCGCATG-TTTATT
1 CAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGATTTATT
*
1322897 CAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATT
1 CAAAAATAAATCCTAACCGCATGATATCTAATTCGCATG-ATTTATT
1322943 CGAAAAA
1 C-AAAAA
1322950 ACGAAAATAA
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
44 27 0.55
45 10 0.20
46 7 0.14
47 5 0.10
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (46 bp):
CAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGATTTATT
Done.