Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001568.1 Hibiscus syriacus cultivar Beakdansim tig00003103_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: 302910
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
File 2 of 2
Found at i:235065 original size:8 final size:8
Alignment explanation
Indices: 235052--235122 Score: 52
Period size: 8 Copynumber: 8.0 Consensus size: 8
235042 AAAAACATTA
235052 TATTATAT
1 TATTATAT
235060 TATTATAT
1 TATTATAT
235068 TATTATTGTGAT
1 TATTA---T-AT
*
235080 TATCATAT
1 TATTATAT
235088 TATTATTAT
1 TATTA-TAT
*
235097 TATTATTT
1 TATTATAT
*
235105 TAATATAT
1 TATTATAT
235113 ATATATATAT
1 -TAT-TATAT
235123 ATATATTTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
8 27 0.54
9 11 0.22
10 5 0.10
11 1 0.02
12 6 0.12
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (8 bp):
TATTATAT
Found at i:235101 original size:20 final size:20
Alignment explanation
Indices: 235048--235102 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
235038 TTACAAAAAC
*
235048 ATTA-TATTA-TATTATTAT
1 ATTATTATTATTATTATCAT
* *
235066 ATTATTATTGTGATTATCAT
1 ATTATTATTATTATTATCAT
235086 ATTATTATTATTATTAT
1 ATTATTATTATTATTAT
235103 TTTAATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 4 0.13
19 4 0.13
20 22 0.73
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
ATTATTATTATTATTATCAT
Found at i:240510 original size:31 final size:31
Alignment explanation
Indices: 240472--240657 Score: 329
Period size: 31 Copynumber: 6.0 Consensus size: 31
240462 GGGTCGAGGG
240472 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
240503 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
240534 TTACCTATGTTCTTTGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
240565 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
240596 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
240627 TTACCTAGGTTCTTCGGAATC-TATGGACTGT
1 TTACCTATGTTCTTCGGGA-CATATGGACTGT
240658 CCTTCGGGAC
Statistics
Matches: 150, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
31 149 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:244938 original size:31 final size:31
Alignment explanation
Indices: 244900--245084 Score: 327
Period size: 31 Copynumber: 6.0 Consensus size: 31
244890 GGGTTGAGGG
244900 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
244931 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
244962 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
244993 TTACCTATGTTCTTCGGGACATATAGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
245024 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
245055 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
245085 GTCCTTCGGG
Statistics
Matches: 149, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
31 148 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:246745 original size:22 final size:22
Alignment explanation
Indices: 246715--246766 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
246705 TAAGGCGGTT
*
246715 ATTATGGCTGGTCAAAAAAATG
1 ATTACGGCTGGTCAAAAAAATG
246737 ATTACGGCTGGTCAAAAAAATG
1 ATTACGGCTGGTCAAAAAAATG
246759 ATTACGGC
1 ATTACGGC
246767 AAAAGATCCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.25
Consensus pattern (22 bp):
ATTACGGCTGGTCAAAAAAATG
Found at i:256803 original size:2 final size:2
Alignment explanation
Indices: 256796--256823 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
256786 TGTGATGATG
256796 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
256824 TCAAATATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:270438 original size:21 final size:21
Alignment explanation
Indices: 270412--270454 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
270402 TTTCTGGGCC
* *
270412 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
270433 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
270454 A
1 A
270455 ACGAACAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:272320 original size:23 final size:23
Alignment explanation
Indices: 272276--272320 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
272266 ATCATTATAT
*
272276 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
272299 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
272321 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:279243 original size:7 final size:7
Alignment explanation
Indices: 279231--279255 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
279221 GTCAAAGAAA
279231 GTCAACG
1 GTCAACG
279238 GTCAACG
1 GTCAACG
279245 GTCAACG
1 GTCAACG
279252 GTCA
1 GTCA
279256 GATCGGGTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:279272 original size:22 final size:22
Alignment explanation
Indices: 279244--279308 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
279234 AACGGTCAAC
* *
279244 GGTCAACGGTCAGATCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
279266 GGTCAACGGTTGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
279288 TGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
279309 AGACCGGTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.12, C:0.22, G:0.45, T:0.22
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:279323 original size:9 final size:9
Alignment explanation
Indices: 279305--279373 Score: 75
Period size: 9 Copynumber: 7.3 Consensus size: 9
279295 GGTCGGGTCG
*
279305 GGTCAGACC
1 GGTCAAACC
279314 GGTCAAACC
1 GGTCAAACC
*
279323 GGTCAAACT
1 GGTCAAACC
*
279332 GGTTCGAACC
1 GG-TCAAACC
*
279342 GGTTGAAACC
1 GG-TCAAACC
279352 GGTCAAACC
1 GGTCAAACC
279361 GGTCAGAACC
1 GGTCA-AACC
279371 GGT
1 GGT
279374 TGTAAACCGA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
9 29 0.57
10 22 0.43
ACGTcount: A:0.28, C:0.28, G:0.29, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:279351 original size:10 final size:10
Alignment explanation
Indices: 279311--279394 Score: 70
Period size: 9 Copynumber: 8.7 Consensus size: 10
279301 GTCGGGTCAG
279311 ACCGG-TCAA
1 ACCGGTTCAA
279320 ACCGG-TCAA
1 ACCGGTTCAA
* *
279329 ACTGGTTCGA
1 ACCGGTTCAA
*
279339 ACCGGTTGAA
1 ACCGGTTCAA
279349 ACCGG-TCAA
1 ACCGGTTCAA
279358 ACCGG-TCAGA
1 ACCGGTTCA-A
*
279368 ACCGGTTGTAA
1 ACCGGTT-CAA
*
279379 ACCGATT-AA
1 ACCGGTTCAA
279388 ACCGGTT
1 ACCGGTT
279395 TCCAGCAGCC
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
9 32 0.52
10 21 0.34
11 8 0.13
12 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:279354 original size:29 final size:30
Alignment explanation
Indices: 279318--279393 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
279308 CAGACCGGTC
*
279318 AAACCGGTCAAACTGGTTC-GAACCGGTTG-
1 AAACCGGTCAAACCGG-TCAGAACCGGTTGT
279347 AAACCGGTCAAACCGGTCAGAACCGGTTGT
1 AAACCGGTCAAACCGGTCAGAACCGGTTGT
* *
279377 AAACCGATTAAACCGGT
1 AAACCGGTCAAACCGGT
279394 TTCCAGCAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 2 0.05
29 25 0.60
30 15 0.36
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (30 bp):
AAACCGGTCAAACCGGTCAGAACCGGTTGT
Found at i:279360 original size:19 final size:19
Alignment explanation
Indices: 279305--279394 Score: 76
Period size: 19 Copynumber: 4.7 Consensus size: 19
279295 GGTCGGGTCG
*
279305 GGTCAGACCGG-TCAAACC
1 GGTCAAACCGGTTCAAACC
* *
279323 GGTCAAACTGGTTCGAACC
1 GGTCAAACCGGTTCAAACC
*
279342 GGTTGAAACCGG-TCAAACC
1 GG-TCAAACCGGTTCAAACC
*
279361 GGTCAGAACCGGTTGTAAACC
1 GGTCA-AACCGGTT-CAAACC
* *
279382 GATTAAACCGGTT
1 GGTCAAACCGGTT
279395 TCCAGCAGCC
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
18 11 0.19
19 22 0.39
20 16 0.28
21 8 0.14
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:286609 original size:12 final size:12
Alignment explanation
Indices: 286609--286641 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
286599 TCAACGGTCG
286609 GGTCGGGTCAAC
1 GGTCGGGTCAAC
286621 GGTCGGGTCAAC
1 GGTCGGGTCAAC
286633 GGTCGGGTC
1 GGTCGGGTC
286642 GGGTCAGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.12, C:0.24, G:0.45, T:0.18
Consensus pattern (12 bp):
GGTCGGGTCAAC
Found at i:286612 original size:17 final size:17
Alignment explanation
Indices: 286592--286647 Score: 77
Period size: 17 Copynumber: 3.6 Consensus size: 17
286582 GGTCGGATCA
286592 GGTCGGGTCAACGGTCG
1 GGTCGGGTCAACGGTCG
286609 GGTCGGGTCAA----C-
1 GGTCGGGTCAACGGTCG
286621 GGTCGGGTCAACGGTCG
1 GGTCGGGTCAACGGTCG
286638 GGTCGGGTCA
1 GGTCGGGTCA
286648 GACCGGTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 11 0.32
13 1 0.03
16 1 0.03
17 21 0.62
ACGTcount: A:0.12, C:0.23, G:0.46, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCAACGGTCG
Found at i:286624 original size:29 final size:29
Alignment explanation
Indices: 286592--286647 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
286582 GGTCGGATCA
286592 GGTCGGGTCAACGGTCGGGTCGGGTCAAC
1 GGTCGGGTCAACGGTCGGGTCGGGTCAAC
286621 GGTCGGGTCAACGGTCGGGTCGGGTCA
1 GGTCGGGTCAACGGTCGGGTCGGGTCA
286648 GACCGGTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.12, C:0.23, G:0.46, T:0.18
Consensus pattern (29 bp):
GGTCGGGTCAACGGTCGGGTCGGGTCAAC
Found at i:286667 original size:19 final size:19
Alignment explanation
Indices: 286645--286722 Score: 88
Period size: 19 Copynumber: 4.1 Consensus size: 19
286635 TCGGGTCGGG
286645 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
286664 TCAGACCGGTCAAACTGGT
1 TCAGACCGGTCAAACCGGT
*
286683 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
286702 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
286722 T
1 T
286723 GAAAACCGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.06
19 38 0.78
20 8 0.16
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:286673 original size:10 final size:9
Alignment explanation
Indices: 286643--286721 Score: 77
Period size: 10 Copynumber: 8.3 Consensus size: 9
286633 GGTCGGGTCG
*
286643 GGTCAGACC
1 GGTCAAACC
286652 GGTCAAACC
1 GGTCAAACC
*
286661 GGTTCAGACC
1 GG-TCAAACC
*
286671 GGTCAAACT
1 GGTCAAACC
*
286680 GGTTCGAACC
1 GG-TCAAACC
*
286690 GGTTGAAACC
1 GG-TCAAACC
286700 GGTCAAACC
1 GGTCAAACC
286709 GGTCAGAACC
1 GGTCA-AACC
286719 GGT
1 GGT
286722 TGAAAACCGT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
9 28 0.48
10 30 0.52
ACGTcount: A:0.27, C:0.28, G:0.29, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:286726 original size:29 final size:27
Alignment explanation
Indices: 286644--286721 Score: 68
Period size: 29 Copynumber: 2.7 Consensus size: 27
286634 GTCGGGTCGG
*
286644 GTCAGACCGGTCAAACCGGTTCAG-ACCG
1 GTCAAACCGGTCAAACCGG-T-AGAACCG
* * *
286672 GTCAAACTGGTTCGAACCGGTTGAAACCG
1 GTCAAACCGG-TCAAACCGGTAG-AACCG
286701 GTCAAACCGGTCAGAACCGGT
1 GTCAAACCGGTCA-AACCGGT
286722 TGAAAACCGT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
27 1 0.03
28 11 0.28
29 28 0.70
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.17
Consensus pattern (27 bp):
GTCAAACCGGTCAAACCGGTAGAACCG
Found at i:290173 original size:19 final size:19
Alignment explanation
Indices: 290145--290182 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
290135 AACCAAGTGG
*
290145 TTGGATTCGTTTATTTAGA
1 TTGGACTCGTTTATTTAGA
290164 TTGGACTCGTTTATTTAGA
1 TTGGACTCGTTTATTTAGA
290183 CATTCATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.08, G:0.21, T:0.50
Consensus pattern (19 bp):
TTGGACTCGTTTATTTAGA
Found at i:290644 original size:36 final size:38
Alignment explanation
Indices: 290590--290672 Score: 111
Period size: 36 Copynumber: 2.3 Consensus size: 38
290580 TGACAACCAA
290590 CTTTGAAAAA-ATGGTTTTCAAAGTTT-GTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
* *
290626 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
290663 -GTTGAAAAAT
1 CTTTGAAAAAT
290673 CATAATGGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
36 32 0.76
37 10 0.24
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:293621 original size:23 final size:23
Alignment explanation
Indices: 293595--293639 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
293585 CACCACAGCT
*
293595 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
293618 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
293640 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:293887 original size:148 final size:149
Alignment explanation
Indices: 293618--293920 Score: 590
Period size: 148 Copynumber: 2.0 Consensus size: 149
293608 CGAAGTGCCC
293618 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
293683 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
293748 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
293767 CGTAGAATTGCACCGTAGTGCCATAT-ATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
293831 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
293896 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
293915 CGTAGA
1 CGTAGA
293921 CCCTCTACCC
Statistics
Matches: 153, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
148 127 0.83
149 26 0.17
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
CATATGTCCTAAAGAACCG
Found at i:294515 original size:66 final size:65
Alignment explanation
Indices: 294395--294542 Score: 212
Period size: 66 Copynumber: 2.3 Consensus size: 65
294385 TTTTTCTCAT
*
294395 GGGGGAATCGGTTCCCCCCCTGGGGTATCGATTCCCCACTAGCATTCTGGAATTCATATTCGTTG
1 GGGGGTATCGGTT-CCCCCCTGGGGTATCGATTCCCCACTAGCATTCTGGAATTCATATTCGTTG
294460 A
65 A
* *
294461 GGGGGTATCGATTCCCCCCTGGGGGTATCGATTCCCCTA-TA-TATTCTGGAAATTCATATTCGT
1 GGGGGTATCGGTTCCCCCCT-GGGGTATCGATTCCCC-ACTAGCATTCTGG-AATTCATATTCGT
294524 TGA
63 TGA
294527 -GGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
294543 TTGAATGGAT
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
65 29 0.39
66 45 0.60
67 1 0.01
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (65 bp):
GGGGGTATCGGTTCCCCCCTGGGGTATCGATTCCCCACTAGCATTCTGGAATTCATATTCGTTGA
Found at i:294559 original size:66 final size:65
Alignment explanation
Indices: 294395--294565 Score: 179
Period size: 66 Copynumber: 2.6 Consensus size: 65
294385 TTTTTCTCAT
* * * *
294395 GGGGGAATCGGTTCCCCCCCTGGGG-TATCGATTCCCC-ACTAGCATTCTGGAATTCATATTCGT
1 GGGGGTATCGATT-CCCCCCTGGGGATACCGATTCCCCTA-TA-TATTCTGGAATTCATATTCGT
294458 TGA
63 TGA
* *
294461 GGGGGTATCGATTCCCCCCTGGGGGTATCGATTCCCCTATATATTCTGGAAATTCATATTCGTTG
1 GGGGGTATCGATTCCCCCCTGGGGATACCGATTCCCCTATATATTCTGG-AATTCATATTCGTTG
294526 A
65 A
* * *
294527 -GGGGTATCGGTT-CCCCTTGAATGGATACCGATTCCCCTA
1 GGGGGTATCGATTCCCCCCTG--GGGATACCGATTCCCCTA
294566 ACCCAGAAAT
Statistics
Matches: 92, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
64 6 0.07
65 29 0.32
66 56 0.61
67 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (65 bp):
GGGGGTATCGATTCCCCCCTGGGGATACCGATTCCCCTATATATTCTGGAATTCATATTCGTTGA
Found at i:295043 original size:17 final size:19
Alignment explanation
Indices: 295021--295055 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
295011 CGTTTGGGAG
295021 AAGGAAG-A-GAAGAAAAT
1 AAGGAAGAAGGAAGAAAAT
295038 AAGGAAGAAGGAAGAAAA
1 AAGGAAGAAGGAAGAAAA
295056 AAAGAGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (19 bp):
AAGGAAGAAGGAAGAAAAT
Found at i:300833 original size:139 final size:143
Alignment explanation
Indices: 300575--300863 Score: 432
Period size: 139 Copynumber: 2.0 Consensus size: 143
300565 CGAAGTGCCC
300575 CGTAGAATTGCACCGTAGTGGCCATATGATATCCATAAGGACCACATAGAATTCCTTAAGAATCA
1 CGTAGAATTGCACCGTAGTGGCCATATGATATCCATAAGGACCACATAGAATTCCTTAAGAATCA
*
300640 TATACATATATATAGATCAAGTATGTCTTTCAAGACTTCACACATGTTCCAAAGGATATACA-A-
66 TATACATATATAGAGATCAAGTATGTCTTTCAAGACTTCACACATGTTCCAAAGGATATACATAG
300703 TCCTAAAG-ACCG
131 TCCTAAAGAACCG
*
300715 CGTAGAA-TGCACCGTAGT-GCCATATATGATGTCCATAAGGACCACATAGAATTCCTT-A-AAT
1 CGTAGAATTGCACCGTAGTGGCC--ATATGATATCCATAAGGACCACATAGAATTCCTTAAGAAT
* * *
300776 CATATACATA-CTAGGGATCAAGTATGTGTCTTTTAAGACTTCACACATGTTCCAAAGGATATAC
64 CATATACATATATAGAGATCAAGTA--TGTCTTTCAAGACTTCACACATGTTCCAAAGGATATAC
300840 ATATGTCCTAAAGAACCG
127 ATA-GTCCTAAAGAACCG
300858 CGTAGA
1 CGTAGA
300864 CCCTCTACCC
Statistics
Matches: 136, Mismatches: 5, Indels: 13
0.88 0.03 0.08
Matches are distributed among these distances:
137 11 0.08
138 16 0.12
139 50 0.37
140 41 0.30
142 8 0.06
143 10 0.07
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (143 bp):
CGTAGAATTGCACCGTAGTGGCCATATGATATCCATAAGGACCACATAGAATTCCTTAAGAATCA
TATACATATATAGAGATCAAGTATGTCTTTCAAGACTTCACACATGTTCCAAAGGATATACATAG
TCCTAAAGAACCG
Found at i:301451 original size:66 final size:66
Alignment explanation
Indices: 301339--301486 Score: 244
Period size: 67 Copynumber: 2.2 Consensus size: 66
301329 TTTTTCTCAT
*
301339 GGGGGAATCGGTTCCCCCCCGGGGTATCGATTCCCCACTAGCATTCTGG-AATTCATATTCGTTG
1 GGGGGTATCGGTTCCCCCCCGGGGTATCGATTCCCCACTAGCATTCTGGAAATTCATATTCGTTG
301403 A
66 A
* * *
301404 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATTCGTT
1 GGGGGTATCGGTTCCCCCC-CGGGGTATCGATTCCCCACTAGCATTCTGGAAATTCATATTCGTT
301469 GA
65 GA
301471 GGGGGTATCGGTTCCC
1 GGGGGTATCGGTTCCC
301487 TGAATGGGTA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
65 18 0.23
66 27 0.35
67 32 0.42
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCCGGGGTATCGATTCCCCACTAGCATTCTGGAAATTCATATTCGTTG
A
Found at i:301507 original size:66 final size:64
Alignment explanation
Indices: 301339--301486 Score: 215
Period size: 66 Copynumber: 2.2 Consensus size: 64
301329 TTTTTCTCAT
* ** *
301339 GGGGGAATCGGTTCCCCCCCGGGGTATCGATTCCCCACTAGCATTCTGGAATTCATATTCGTTGA
1 GGGGGTATCGGTT-CCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAATTCATATTCGTTGA
*
301404 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATTCGTT
1 GGGGGTATCGGTT--CCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGG-AATTCATATTCGTT
301469 GA
63 GA
301471 GGGGGTATCGGTTCCC
1 GGGGGTATCGGTTCCC
301487 TGAATGGGTA
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
65 15 0.20
66 32 0.42
67 29 0.38
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (64 bp):
GGGGGTATCGGTTCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAATTCATATTCGTTGA
Found at i:301993 original size:24 final size:24
Alignment explanation
Indices: 301963--302008 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
301953 CACGTTTGGG
301963 AGAAGGAAG-AGAAGAAAATAAGGA
1 AGAAGGAAGAAGAAG-AAATAAGGA
301987 AGAAGGAAGAAGAAGAAATAAG
1 AGAAGGAAGAAGAAGAAATAAG
302009 AGAATTCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (24 bp):
AGAAGGAAGAAGAAGAAATAAGGA
Done.