Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008194.1 Hibiscus syriacus cultivar Beakdansim tig00110813_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: 2426039
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 13
Found at i:2376473 original size:44 final size:43
Alignment explanation
Indices: 2376418--2376732 Score: 156
Period size: 44 Copynumber: 7.3 Consensus size: 43
2376408 TTTGCTCAAA
* * *
2376418 TCCATCGCAGAAGAAGTTGGATCAGCGTCAACTTTTAGCTCGAT
1 TCCATCACAGAAG-AGGTGGATCAGCATCAACTTTTAGCTCGAT
* * * * * * * * *
2376462 TCTATCACAGAATGAGGTAGATCAACACCGACATCTCGTTCGAT
1 TCCATCACAGAA-GAGGTGGATCAGCATCAACTTTTAGCTCGAT
** * * *
2376506 TCCATCACAGAATGAGGTGGATC-GACATTTA-GTTT-GCTCAAA
1 TCCATCACAGAA-GAGGTGGATCAG-CATCAACTTTTAGCTCGAT
** * *
2376548 TCCATTGCAGAAGGAGTTGGATCAGCGTCAACTTTTAGCTCGAT
1 TCCATCACAGAA-GAGGTGGATCAGCATCAACTTTTAGCTCGAT
* * * * * * * * *
2376592 TCTATCACAGAGGAGGTAGATTAGCACCAACATCTCGTTCGAT
1 TCCATCACAGAAGAGGTGGATCAGCATCAACTTTTAGCTCGAT
* ** * *
2376635 TCCATCACAAAATGAGGTGGATC-GACATTTA-TTTT-GCTCAAA
1 TCCATCACAGAA-GAGGTGGATCAG-CATCAACTTTTAGCTCGAT
* * * *
2376677 TCCATCGCAGAAGGAGTTGGATCATCGTCAACTTTTAGCTCGAT
1 TCCATCACAGAA-GAGGTGGATCAGCATCAACTTTTAGCTCGAT
*
2376721 TCTATCACAGAA
1 TCCATCACAGAA
2376733 TAAGGTAGAA
Statistics
Matches: 190, Mismatches: 71, Indels: 20
0.68 0.25 0.07
Matches are distributed among these distances:
42 52 0.27
43 44 0.23
44 93 0.49
45 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.28
Consensus pattern (43 bp):
TCCATCACAGAAGAGGTGGATCAGCATCAACTTTTAGCTCGAT
Found at i:2376676 original size:129 final size:131
Alignment explanation
Indices: 2376341--2376845 Score: 692
Period size: 129 Copynumber: 3.8 Consensus size: 131
2376331 CAATACCTTC
* * * *
2376341 AGGAGGTAGATCATCACTAACATCTCGTTCGATTCCATCACAGAAGGAGGTGTATTGACATTTTT
1 AGGAGGTAGATCAACACCAACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGACA-TTTT
*
2376406 ATTTTGCTCAAATCCATCGCAGAAGAAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACA
65 ATTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACA
2376471 GA
130 GA
* * *
2376473 ATGAGGTAGATCAACACCGACATCTCGTTCGATTCCATCACAGAATGAGGTGGATCGACA-TTTA
1 AGGAGGTAGATCAACACCAACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTA
* *
2376537 GTTTGCTCAAATCCATTGCAGAAGGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAG
66 TTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAG
2376602 -
131 A
* * * *
2376602 AGGAGGTAGATTAGCACCAACATCTCGTTCGATTCCATCACAAAATGAGGTGGATCGACA-TTTA
1 AGGAGGTAGATCAACACCAACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTA
*
2376666 TTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCATCGTCAACTTTTAGCTCGATTCTATCACAG
66 TTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAG
2376731 AATAA
131 ----A
* *
2376736 GGTAGAATGAGGTAGATCAACACCAATATCTCATTCGATTCCATCACAGAAGGAGGTGGATCGAC
1 ---AG---GAGGTAGATCAACACCAACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGAC
* * *
2376801 ATTTCTATTTTCGCTCAAATCCATTGCATACGGAGTTGGATCAGC
60 ATTT-TATTTT-GCTCAAATCCATCGCAGAAGGAGTTGGATCAGC
2376846 ATCGTCAACA
Statistics
Matches: 331, Mismatches: 28, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
129 121 0.37
130 66 0.20
132 53 0.16
137 2 0.01
140 52 0.16
141 2 0.01
142 6 0.02
143 29 0.09
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (131 bp):
AGGAGGTAGATCAACACCAACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTA
TTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAG
A
Found at i:2377995 original size:22 final size:21
Alignment explanation
Indices: 2377970--2378015 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
2377960 TGTTGTTTTA
2377970 TTTTAATTTAG-TCACTGTTAAT
1 TTTTAATTTAGCT-ACTGTT-AT
*
2377992 TTTTGATTTAGCTACTGTTAT
1 TTTTAATTTAGCTACTGTTAT
2378013 TTT
1 TTT
2378016 AATATTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 16 0.73
23 1 0.05
ACGTcount: A:0.22, C:0.09, G:0.11, T:0.59
Consensus pattern (21 bp):
TTTTAATTTAGCTACTGTTAT
Found at i:2389561 original size:18 final size:17
Alignment explanation
Indices: 2389529--2389574 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2389519 ATTATATTAG
2389529 TAAAATATAAAATAAAA
1 TAAAATATAAAATAAAA
* *
2389546 TAAAATACTTAAATAAAT
1 TAAAATA-TAAAATAAAA
2389564 TAAATATATAA
1 TAAA-ATATAA
2389575 TATTAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 7 0.29
18 14 0.58
19 3 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAATATAAAATAAAA
Found at i:2389562 original size:23 final size:23
Alignment explanation
Indices: 2389535--2389581 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2389525 TTAGTAAAAT
2389535 ATAAAATAAA-ATAAAATACTTAA
1 ATAAAATAAATATAAAATA-TTAA
* *
2389558 ATAAATTAAATATATAATATTAA
1 ATAAAATAAATATAAAATATTAA
2389581 A
1 A
2389582 AATATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
ATAAAATAAATATAAAATATTAA
Found at i:2392647 original size:25 final size:23
Alignment explanation
Indices: 2392619--2392668 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
2392609 TAAGTTGCAC
*
2392619 TTATGGTTATTAAATTATGTTAAAA
1 TTATGGTT-TTAAATTAT-TAAAAA
* *
2392644 TTATTGTTTTTAATTATTAAAAA
1 TTATGGTTTTAAATTATTAAAAA
2392667 TT
1 TT
2392669 TAAATTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 7 0.32
24 8 0.36
25 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (23 bp):
TTATGGTTTTAAATTATTAAAAA
Found at i:2392880 original size:24 final size:24
Alignment explanation
Indices: 2392848--2392895 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2392838 AATTCTACAA
2392848 AAAAATTCAGAAATTATAAAATTT
1 AAAAATTCAGAAATTATAAAATTT
*
2392872 AAAATTTCAGAAATTATAAAATTT
1 AAAAATTCAGAAATTATAAAATTT
2392896 TAATAAAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (24 bp):
AAAAATTCAGAAATTATAAAATTT
Found at i:2394486 original size:36 final size:36
Alignment explanation
Indices: 2394446--2394531 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
2394436 TTAAAAAAAT
*
2394446 AATAAAAAATTAATAAAAGACAGATTTAATGAGACA
1 AATAAAAAATAAATAAAAGACAGATTTAATGAGACA
* ** **
2394482 AATAAAATATAAATTTACTACAGATTTAATGAGACA
1 AATAAAAAATAAATAAAAGACAGATTTAATGAGACA
*
2394518 AATAAAATATAAAT
1 AATAAAAAATAAAT
2394532 TTACTTATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.59, C:0.06, G:0.08, T:0.27
Consensus pattern (36 bp):
AATAAAAAATAAATAAAAGACAGATTTAATGAGACA
Found at i:2394546 original size:36 final size:36
Alignment explanation
Indices: 2394465--2394536 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
2394455 TTAATAAAAG
2394465 ACAGATTTAATGAGACAAATAAAATATAAATTTACT
1 ACAGATTTAATGAGACAAATAAAATATAAATTTACT
2394501 ACAGATTTAATGAGACAAATAAAATATAAATTTACT
1 ACAGATTTAATGAGACAAATAAAATATAAATTTACT
2394537 TATTTTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (36 bp):
ACAGATTTAATGAGACAAATAAAATATAAATTTACT
Found at i:2395474 original size:23 final size:24
Alignment explanation
Indices: 2395438--2395483 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
2395428 ATTTCGAGTT
*
2395438 TGAGTTTAACTTG-ATTTAGCTTG
1 TGAGTTTAACTTGAATTGAGCTTG
* *
2395461 TGAGTTTGAGTTGAATTGAGCTT
1 TGAGTTTAACTTGAATTGAGCTT
2395484 ACTTTTAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.22, C:0.07, G:0.26, T:0.46
Consensus pattern (24 bp):
TGAGTTTAACTTGAATTGAGCTTG
Found at i:2397076 original size:246 final size:246
Alignment explanation
Indices: 2396642--2397133 Score: 966
Period size: 246 Copynumber: 2.0 Consensus size: 246
2396632 GCTGATCCTG
*
2396642 CTAATTTTCTATCCCCGTTTATCCTCGTTTGTTGGAAACTTTCATTAACAAATATGGCTGGCTAG
1 CTAATTTTCTATCCCCGTTTATCCTCATTTGTTGGAAACTTTCATTAACAAATATGGCTGGCTAG
*
2396707 GTTATATTTTAAATATATTTATAACAGGTTTAATGTAAAAATAATTATTTAAATTATATTTAAAG
66 GTTATATTTTAAATATATTTATAACAGGTTTAATGTAAAAATAAGTATTTAAATTATATTTAAAG
2396772 TTAATTTTTAATTTATAAAAAAATTGTTAAAAATAAGTGTTTAATAATTTTAATGTTTTATTTTT
131 TTAATTTTTAATTTATAAAAAAATTGTTAAAAATAAGTGTTTAATAATTTTAATGTTTTATTTTT
2396837 AAGTGTTTGAACTCTATGTTATTAAATTTGATTTTTAAATTATATATATAT
196 AAGTGTTTGAACTCTATGTTATTAAATTTGATTTTTAAATTATATATATAT
2396888 CTAATTTTCTATCCCCGTTTATCCTCATTTGTTGGAAACTTTCATTAACAAATATGGCTGGCTAG
1 CTAATTTTCTATCCCCGTTTATCCTCATTTGTTGGAAACTTTCATTAACAAATATGGCTGGCTAG
2396953 GTTATATTTTAAATATATTTATAACAGGTTTAATGTAAAAATAAGTATTTAAATTATATTTAAAG
66 GTTATATTTTAAATATATTTATAACAGGTTTAATGTAAAAATAAGTATTTAAATTATATTTAAAG
2397018 TTAATTTTTAATTTATAAAAAAATTGTTAAAAATAAGTGTTTAATAATTTTAATGTTTTATTTTT
131 TTAATTTTTAATTTATAAAAAAATTGTTAAAAATAAGTGTTTAATAATTTTAATGTTTTATTTTT
2397083 AAGTGTTTGAACTCTATGTTATTAAATTTGATTTTTAAATTATATATATAT
196 AAGTGTTTGAACTCTATGTTATTAAATTTGATTTTTAAATTATATATATAT
2397134 ATATATATAT
Statistics
Matches: 244, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
246 244 1.00
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.47
Consensus pattern (246 bp):
CTAATTTTCTATCCCCGTTTATCCTCATTTGTTGGAAACTTTCATTAACAAATATGGCTGGCTAG
GTTATATTTTAAATATATTTATAACAGGTTTAATGTAAAAATAAGTATTTAAATTATATTTAAAG
TTAATTTTTAATTTATAAAAAAATTGTTAAAAATAAGTGTTTAATAATTTTAATGTTTTATTTTT
AAGTGTTTGAACTCTATGTTATTAAATTTGATTTTTAAATTATATATATAT
Found at i:2397714 original size:31 final size:31
Alignment explanation
Indices: 2397667--2397755 Score: 142
Period size: 31 Copynumber: 2.8 Consensus size: 31
2397657 AATTTATATT
* *
2397667 TTTTTTGAGGGATTAACAAGAGTGATTACCTA
1 TTTTTT-AGGGGTTAACGAGAGTGATTACCTA
*
2397699 TTTTTTAGGGGTTAACGAGAGTGATGACCTA
1 TTTTTTAGGGGTTAACGAGAGTGATTACCTA
2397730 TTTTTTAGGGGTTAACGAGAGTGATT
1 TTTTTTAGGGGTTAACGAGAGTGATT
2397756 TCTCTTTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 47 0.89
32 6 0.11
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (31 bp):
TTTTTTAGGGGTTAACGAGAGTGATTACCTA
Found at i:2405778 original size:14 final size:15
Alignment explanation
Indices: 2405761--2405789 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2405751 AATTTTATTA
2405761 TAATTATAC-AATAT
1 TAATTATACGAATAT
2405775 TAATTATACGAATAT
1 TAATTATACGAATAT
2405790 GACATTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (15 bp):
TAATTATACGAATAT
Found at i:2407862 original size:21 final size:21
Alignment explanation
Indices: 2407838--2407880 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2407828 TTTTTCACTT
*
2407838 TTTTAAGAAATTTTTTTAAAA
1 TTTTAAGAAATTTTTTAAAAA
*
2407859 TTTTAAGTAATTTTTTAAAAA
1 TTTTAAGAAATTTTTTAAAAA
2407880 T
1 T
2407881 ATATAAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTTAAGAAATTTTTTAAAAA
Found at i:2408209 original size:26 final size:30
Alignment explanation
Indices: 2408178--2408235 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 30
2408168 GGACATAAAA
2408178 ATGGTATTAAC-AATT-C-C-TAAAATAAT
1 ATGGTATTAACAAATTACTCTTAAAATAAT
2408204 ATGGTATTAACAAATTACTCTTAAAATAAT
1 ATGGTATTAACAAATTACTCTTAAAATAAT
2408234 AT
1 AT
2408236 TATTATCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 11 0.39
27 4 0.14
28 1 0.04
29 1 0.04
30 11 0.39
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (30 bp):
ATGGTATTAACAAATTACTCTTAAAATAAT
Found at i:2409012 original size:2 final size:2
Alignment explanation
Indices: 2409005--2409071 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
2408995 GTTTACTAGT
2409005 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2409047 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 T
2409072 GTGTGTGTGT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2411439 original size:17 final size:17
Alignment explanation
Indices: 2411413--2411453 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
2411403 AACGAAGCAT
*
2411413 GGAGTGGACAGAAACCA
1 GGAGTTGACAGAAACCA
2411430 GGAGTTGACAGAAACCA
1 GGAGTTGACAGAAACCA
2411447 GGAGTTG
1 GGAGTTG
2411454 GACACCTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.37, C:0.15, G:0.37, T:0.12
Consensus pattern (17 bp):
GGAGTTGACAGAAACCA
Found at i:2418687 original size:23 final size:23
Alignment explanation
Indices: 2418640--2418689 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
2418630 AATAACATAT
**
2418640 TAGGTAGCGCTTATATAATGCAA
1 TAGGTAGCGCTTATATAATAAAA
2418663 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
2418686 TAGG
1 TAGG
2418690 CATTTAACCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:2418764 original size:87 final size:87
Alignment explanation
Indices: 2418603--2418765 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
2418593 TATGTTATAT
*
2418603 CATTTAACCGAAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGCAATAGGT
1 CATTTAACCGAAAATATTATCAAGCACAATAACATATTAGGTAACGCTTATATAATGCAATAGGT
**
2418668 AGCGCTTATATAATAAAATAGG
66 AGCAATTATATAATAAAATAGG
* *
2418690 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGCACAATAACATATTAGGTAACGCTTATATAATGCAATAGGT
2418755 AGCAATTATAT
66 AGCAATTATAT
2418766 TGACCTATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAGCACAATAACATATTAGGTAACGCTTATATAATGCAATAGGT
AGCAATTATATAATAAAATAGG
Found at i:2419528 original size:181 final size:182
Alignment explanation
Indices: 2419148--2419824 Score: 1024
Period size: 181 Copynumber: 3.7 Consensus size: 182
2419138 TATTAATATA
* * * *
2419148 TTTTCTCATATTTTTAGCTGTTATATTGTTATCGATCGATACATTTTCATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTATCGACACTT
* *
2419213 TTTA-ACTCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
* * *
2419277 CACTTTCAACATATCCGGTATCCTTTTACCGGTTTTGTCATTTTGAGACCGG
131 CACTTACAACATATCCGGTATCGTTTTACCGGTTTTGTCATTTTGAGATCGG
* *
2419329 TTTTGTTATATTTTTACCTGTTATATTGTTATAGATCGATACATTTT-TTAAAAGTATCGACACT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTCAT-AAAGTATCGACACT
* *
2419393 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTTAGAAAGTGTCGATAATTATATTAAATTATCG
65 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
*
2419458 ACACTTACAACATATCCGGTAGT-GTTTTACCGATTTTGTCATTTTGAGATCGG
130 ACACTTACAACATATCCGGTA-TCGTTTTACCGGTTTTGTCATTTTGAGATCGG
*
2419511 TTTTGTCATA-TTTTACCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTATCGACACTT
*
2419575 TTTAGGCGCTATAACTTATTCTCTTTTAAA-TCAGAAAGTGTCGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
* * *
2419639 CACTTGCAACAAATCCGGTATCGTTTTACCGGTTTTGTCATTTTGAGATTGG
131 CACTTACAACATATCCGGTATCGTTTTACCGGTTTTGTCATTTTGAGATCGG
* * * * **
2419691 TTTTGTCATATTTTTACTTGTAATATTATTATGGATCGATACATTTTTTTAAAGTATCGACACTT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTATCGACACTT
* * * *
2419756 TTTAGGCGCTATAACTTTTTCTCTTTTTATTTCTA-AAAGTGTCGATACTTATATTAAAGTATCG
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTC-AGAAAGTGTCGATACTTATATTAAATTATCG
2419820 ACACT
130 ACACT
2419825 ATTAATTTAC
Statistics
Matches: 453, Mismatches: 35, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
179 1 0.00
180 89 0.20
181 214 0.47
182 147 0.32
183 2 0.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.44
Consensus pattern (182 bp):
TTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTATCGACACTT
TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
CACTTACAACATATCCGGTATCGTTTTACCGGTTTTGTCATTTTGAGATCGG
Found at i:2423820 original size:198 final size:197
Alignment explanation
Indices: 2423443--2423964 Score: 792
Period size: 198 Copynumber: 2.7 Consensus size: 197
2423433 GTAAAAAGTA
* * * * *
2423443 TCGATACATTATGTAGACCTATTTGCTCATAAAACCGGCATATTTAGACCGGTTACATTGTTAAT
1 TCGATACTTTTTGTACACCTATTTTCTCAT-AAACCGGTATATTTAGACCGGTTACATTGTTAAT
* * *
2423508 TTATCTATTA--C---ATTA---TTTCGATGTTTTTAGTATCGACACTTATTATAAATGTATCGA
65 TTACCTATTACTCATAATTATGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCGA
* *
2423565 CACGGTTTAGTGTAATTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTT
130 CACGGATTAGTGCAATTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTT
2423630 GTG
195 GTG
*
2423633 TCGATACTTTTTGTACACCTATTTTCTCATAAACCGATATATTTAGACCGGTTACATTGTTAATT
1 TCGATACTTTTTGTACACCTATTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTAATT
2423698 TACCTATTACTTCATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCG
66 TACCTATTAC-TCATAATTAT-GGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCG
*
2423763 ACAC-GATTAGTGCATTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATT
129 ACACGGATTAGTGCAATTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATT
2423827 TGTG
194 TGTG
* * * *
2423831 TCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTAAATTGTTAATT
1 TCGATACTTTTTGTACACCTATTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTAATT
2423896 TACCTATTACATCATAATTATAGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCG
66 TACCTATTAC-TCATAATTAT-GGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCG
2423961 ACAC
129 ACAC
2423965 TTTTTTCGTG
Statistics
Matches: 303, Mismatches: 19, Indels: 12
0.91 0.06 0.04
Matches are distributed among these distances:
189 41 0.14
190 26 0.09
192 1 0.00
195 4 0.01
198 188 0.62
199 43 0.14
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (197 bp):
TCGATACTTTTTGTACACCTATTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTAATT
TACCTATTACTCATAATTATGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCGAC
ACGGATTAGTGCAATTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTG
TG
Found at i:2424229 original size:24 final size:24
Alignment explanation
Indices: 2424202--2424248 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2424192 ATTTACATTT
2424202 AAATTCAAACTCAAACTCAAATTG
1 AAATTCAAACTCAAACTCAAATTG
* * *
2424226 AAATTTAAATTCAAACTCTAATT
1 AAATTCAAACTCAAACTCAAATT
2424249 ATAAATGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATTCAAACTCAAACTCAAATTG
Found at i:2425486 original size:3 final size:3
Alignment explanation
Indices: 2425478--2425521 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
2425468 ACTTGTTTGG
* * * *
2425478 ATC ATC ATC GTC ATC ATC ATC ATC ATC TTC ATC GTC ATC TTC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
2425522 TGATCACTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (3 bp):
ATC
Found at i:2425495 original size:12 final size:12
Alignment explanation
Indices: 2425478--2425521 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
2425468 ACTTGTTTGG
2425478 ATCATCATCGTC
1 ATCATCATCGTC
*
2425490 ATCATCATCATC
1 ATCATCATCGTC
*
2425502 ATCTTCATCGTC
1 ATCATCATCGTC
*
2425514 ATCTTCAT
1 ATCATCAT
2425522 TGATCACTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (12 bp):
ATCATCATCGTC
Done.