Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001462.1 Hibiscus syriacus cultivar Beakdansim tig00002826_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: 75062
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:181 original size:60 final size:59
Alignment explanation
Indices: 87--242 Score: 140
Period size: 60 Copynumber: 2.6 Consensus size: 59
77 CGGGTGATCA
* * *
87 ATTT-GTAACTTTTAATA-ATCGGATGACTCAACAAAACATCG-TCTTATAGTTGGAA-AAT
1 ATTTGGTAACTTTTTATAGA-CGAATAACTCAACAAAACATCGCT-TTATAGTT-GAAGAAT
* * * * * * *
145 AATTTGGTAATTTTTTGTAGTCGAATAATTCAACAAAGCATTGCTTTATAGTTGAAGGACT
1 -ATTTGGTAACTTTTTATAGACGAATAACTCAACAAAACATCGCTTTATAGTTGAA-GAAT
*
206 ATTTTGTAACTTTTTATAGACGAATAACTCAACAAAA
1 ATTTGGTAACTTTTTATAGACGAATAACTCAACAAAA
243 TATCACCCTA
Statistics
Matches: 76, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
59 7 0.09
60 66 0.87
61 3 0.04
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (59 bp):
ATTTGGTAACTTTTTATAGACGAATAACTCAACAAAACATCGCTTTATAGTTGAAGAAT
Found at i:2176 original size:2 final size:2
Alignment explanation
Indices: 2169--2245 Score: 133
Period size: 2 Copynumber: 40.0 Consensus size: 2
2159 ATAGCTTATC
2169 AT AT AT AT AT AT AT AT -T AT A- 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
2209 AT AT A- 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 AT AT AT
2246 TGAAATGTGG
Statistics
Matches: 72, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 3 0.04
2 69 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3471 original size:2 final size:2
Alignment explanation
Indices: 3464--3506 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3454 TTAATAAAAT
3464 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
3506 T
1 T
3507 TGTGTGGCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3628 original size:2 final size:2
Alignment explanation
Indices: 3621--3658 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3611 CCCCACCCCC
3621 AT AT AT 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 AT AT AT
3659 GATCAAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21359 original size:18 final size:17
Alignment explanation
Indices: 21338--21376 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
21328 ATTTTATAAA
*
21338 ATTAATCAAATAATATAT
1 ATTAATAAAATAATAT-T
*
21356 ATTATTAAAATAATATT
1 ATTAATAAAATAATATT
21373 ATTA
1 ATTA
21377 TTAATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTAATAAAATAATATT
Found at i:21388 original size:21 final size:18
Alignment explanation
Indices: 21345--21380 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
21335 AAAATTAATC
21345 AAATAATATATATTATTA
1 AAATAATATATATTATTA
21363 AAATAATAT-TATTATTA
1 AAATAATATATATTATTA
21380 A
1 A
21381 TTTAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATAATATATATTATTA
Found at i:22765 original size:3 final size:3
Alignment explanation
Indices: 22757--22820 Score: 65
Period size: 3 Copynumber: 20.3 Consensus size: 3
22747 TAATATATTT
* *
22757 TAA TAA TAA TATA TATA TATA TAA TAA TAT TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
22805 TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
22821 TTAAGTAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 41 0.79
4 11 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (3 bp):
TAA
Found at i:22772 original size:18 final size:17
Alignment explanation
Indices: 22747--22820 Score: 84
Period size: 18 Copynumber: 4.4 Consensus size: 17
22737 TTTGGGCTTG
22747 TAAT-ATATTTTAATAA
1 TAATAATATTTTAATAA
*
22763 TAAT-ATA-TAT-ATATA
1 TAATAATATTTTAATA-A
22778 TAATAATATTTATAATAA
1 TAATAATATTT-TAATAA
22796 TAATAATAATTTTAATAA
1 TAATAAT-ATTTTAATAA
22814 TAATAAT
1 TAATAAT
22821 TTAAGTAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 3 0.06
15 7 0.14
16 10 0.20
17 1 0.02
18 22 0.44
19 7 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAATAATATTTTAATAA
Found at i:23075 original size:76 final size:76
Alignment explanation
Indices: 22973--23612 Score: 1145
Period size: 76 Copynumber: 8.4 Consensus size: 76
22963 GAGGTCTTAA
* * * *
22973 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCTCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
23038 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
23049 AAACATCATGCACTGAAGGGCTTACAGAAGACCCGAAGGTTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
23114 AGGCTTTTTTGG
66 AGGC-TTTTTGG
*
23126 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
23191 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
23202 AAACATCATGCACTGAAGGGCTTACAGAAGACCCGAAGGTTTTAAAAACATCAAAAAGCTCTCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
23267 AGGCTTTTTTGG
66 AGGC-TTTTTGG
23279 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
23344 AGGCTTTTTGG
66 AGGCTTTTTGG
*
23355 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
23420 AGGCTTTTTGG
66 AGGCTTTTTGG
23431 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
23496 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
23507 AAACATCATGCACTGAAGGGCTTACAGATGAACCGAAGGTTTTGAGAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
23572 AGGCTTTTTGG
66 AGGCTTTTTGG
23583 AAACATCATGCACTGAAGGGCTTACAGATG
1 AAACATCATGCACTGAAGGGCTTACAGATG
23613 TGGGAAATAG
Statistics
Matches: 542, Mismatches: 20, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
76 396 0.73
77 146 0.27
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:23374 original size:229 final size:228
Alignment explanation
Indices: 22973--23612 Score: 1154
Period size: 229 Copynumber: 2.8 Consensus size: 228
22963 GAGGTCTTAA
* * *
22973 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCTCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCTCGA
* *
23038 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAAGACCCGAAGGTTTTAAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAA
23103 AAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTT
131 AAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTT
*
23168 TGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGG
195 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
* *
23202 AAACATCATGCACTGAAGGGCTTACAGAAGACCCGAAGGTTTTAAAAACATCAAAAAGCTCTCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCTCGA
23267 AGGCTTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
66 AGGC-TTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
23332 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTT
130 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTT
*
23397 TGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGG
195 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
*
23431 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCTCGA
* *
23496 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGAACCGAAGGTTTTGAGAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAA
23561 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATG
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATG
23613 TGGGAAATAG
Statistics
Matches: 396, Mismatches: 14, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
228 111 0.28
229 211 0.53
230 74 0.19
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (228 bp):
AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCTCGA
AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTT
GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
Found at i:23639 original size:152 final size:153
Alignment explanation
Indices: 22973--23612 Score: 1149
Period size: 153 Copynumber: 4.2 Consensus size: 153
22963 GAGGTCTTAA
* * * *
22973 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCTCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
23038 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAAGACCCGAAGGTTTTAAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAAGACCCGAAGGTTTTAAAAACATCAA
23103 AAAGCTCCCGAAGGCTTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTTGG
*
23126 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
23191 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAAGACCCGAAGGTTTTAAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAAGACCCGAAGGTTTTAAAAACATCAA
*
23256 AAAGCTCTCGAAGGCTTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTTGG
23279 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
* *
23344 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAAGACCCGAAGGTTTTAAAAACATCAA
*
23409 AAAGCTCCTGAAGGC-TTTTTGG
131 AAAGCTCCCGAAGGCTTTTTTGG
23431 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
* * * *
23496 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGAACCGAAGGTTTTGAGAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAAGACCCGAAGGTTTTAAAAACATCAA
23561 AAAGCTCCCGAAGGC-TTTTTGG
131 AAAGCTCCCGAAGGCTTTTTTGG
23583 AAACATCATGCACTGAAGGGCTTACAGATG
1 AAACATCATGCACTGAAGGGCTTACAGATG
23613 TGGGAAATAG
Statistics
Matches: 473, Mismatches: 14, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
152 186 0.39
153 287 0.61
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (153 bp):
AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAAGACCCGAAGGTTTTAAAAACATCAA
AAAGCTCCCGAAGGCTTTTTTGG
Found at i:24314 original size:22 final size:23
Alignment explanation
Indices: 24289--24343 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
24279 AATAAAGCTT
* *
24289 TCATTTTTGAAAAGA-GAATCTA
1 TCATCTTTGAAAAAAGGAATCTA
*
24311 TCATCTTT-AAAAAAGGAGTCTA
1 TCATCTTTGAAAAAAGGAATCTA
24333 TCATCTTTGAA
1 TCATCTTTGAA
24344 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.18
22 21 0.75
23 2 0.07
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (23 bp):
TCATCTTTGAAAAAAGGAATCTA
Found at i:31729 original size:278 final size:278
Alignment explanation
Indices: 31232--31789 Score: 1071
Period size: 278 Copynumber: 2.0 Consensus size: 278
31222 ACAGTAATAA
*
31232 AAAAATGTAATGCAAATGCGAAAATGCATAAATTCCAAAAATAAAAATGCAAACTTTGCAATTCA
1 AAAAATGTAATGCAAATGCGAAAATGCATAAATTCCAAAAATAAAAATGCAAACTGTGCAATTCA
31297 AAGGCAAATATAAAAGTATGAATGCAAAATGGAAATGCAAAGATGTAAAAAGTAAAAATAAGAAT
66 AAGGCAAATATAAAAGTATGAATGCAAAATGGAAATGCAAAGATGTAAAAAGTAAAAATAAGAAT
31362 GTAAATACATGTATGAAAAGGTGTTACTCAAGAGTGATCATCTTAGAACAGATTTCATTGAACAC
131 GTAAATACATGTATGAAAAGGTGTTACTCAAGAGTGATCATCTTAGAACAGATTTCATTGAACAC
31427 AAAAGCTTCAGTACATCAAACAAAACTTTTACATGTAGGGGACAACTTTTAGTCCTAACTTCAAA
196 AAAAGCTTCAGTACATCAAACAAAACTTTTACATGTAGGGGACAACTTTTAGTCCTAACTTCAAA
31492 AAAACTTTACATATAGGG
261 AAAACTTTACATATAGGG
*
31510 AAAAATGTAATGCAAATGCGAAAATGCATAAATTCTAAAAATAAAAATGCAAACTGTGCAATTCA
1 AAAAATGTAATGCAAATGCGAAAATGCATAAATTCCAAAAATAAAAATGCAAACTGTGCAATTCA
31575 AAGGCAAATATAAAAGTATGAATGCAAAATGGAAATGCAAAGATGTAAAAAGTAAAAATAAGAAT
66 AAGGCAAATATAAAAGTATGAATGCAAAATGGAAATGCAAAGATGTAAAAAGTAAAAATAAGAAT
*
31640 GTAAATGCATGTATGAAAAGGTGTTACTCAAGAGTGATCATCTTAGAACAGATTTCATTGAACAC
131 GTAAATACATGTATGAAAAGGTGTTACTCAAGAGTGATCATCTTAGAACAGATTTCATTGAACAC
*
31705 AAAAGCTTCAGTACATCAAACAAAACTTTTACATGTAGGGGACAACTTTTAGTCCTAACTTCAAC
196 AAAAGCTTCAGTACATCAAACAAAACTTTTACATGTAGGGGACAACTTTTAGTCCTAACTTCAAA
*
31770 AAAACTTTACATATATGG
261 AAAACTTTACATATAGGG
31788 AA
1 AA
31790 TAACTTTCCC
Statistics
Matches: 275, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
278 275 1.00
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.25
Consensus pattern (278 bp):
AAAAATGTAATGCAAATGCGAAAATGCATAAATTCCAAAAATAAAAATGCAAACTGTGCAATTCA
AAGGCAAATATAAAAGTATGAATGCAAAATGGAAATGCAAAGATGTAAAAAGTAAAAATAAGAAT
GTAAATACATGTATGAAAAGGTGTTACTCAAGAGTGATCATCTTAGAACAGATTTCATTGAACAC
AAAAGCTTCAGTACATCAAACAAAACTTTTACATGTAGGGGACAACTTTTAGTCCTAACTTCAAA
AAAACTTTACATATAGGG
Found at i:34763 original size:22 final size:22
Alignment explanation
Indices: 34738--34808 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
34728 TTTTTATAAA
*
34738 ATTAATCAAATAATATATTAAT
1 ATTAATAAAATAATATATTAAT
*
34760 ATTATTAAAATAATATATTAAT
1 ATTAATAAAATAATATATTAAT
*
34782 ATTATTAAAATAATA-A-TAATT
1 ATTAATAAAATAATATATTAA-T
34803 ATTAAT
1 ATTAAT
34809 TTAAATATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
20 3 0.07
21 7 0.16
22 35 0.78
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTAATAAAATAATATATTAAT
Found at i:34815 original size:22 final size:22
Alignment explanation
Indices: 34745--34796 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
34735 AAAATTAATC
34745 AAATAATATATTAATATTATTA
1 AAATAATATATTAATATTATTA
34767 AAATAATATATTAATATTATTA
1 AAATAATATATTAATATTATTA
34789 AAATAATA
1 AAATAATA
34797 ATAATTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATAATATATTAATATTATTA
Found at i:36195 original size:3 final size:3
Alignment explanation
Indices: 36189--36262 Score: 82
Period size: 3 Copynumber: 25.3 Consensus size: 3
36179 ATAATATATT
* *
36189 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TAT TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
**
36232 TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
36263 TTAAGTAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
2 6 0.10
3 50 0.85
4 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:36209 original size:9 final size:9
Alignment explanation
Indices: 36179--36242 Score: 58
Period size: 9 Copynumber: 6.7 Consensus size: 9
36169 TGGGCTTGTA
36179 ATAATATAT
1 ATAATATAT
*
36188 TTAATAATAAT
1 ATAAT-AT-AT
36199 ATAATATAT
1 ATAATATAT
36208 ATAATATAAT
1 ATAATAT-AT
*
36218 AATAATATTT
1 -ATAATATAT
36228 ATAATA-AT
1 ATAATATAT
36236 AATAATA
1 -ATAATA
36243 ATAATTTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
8 1 0.02
9 25 0.54
10 7 0.15
11 13 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
ATAATATAT
Found at i:36258 original size:12 final size:12
Alignment explanation
Indices: 36177--36259 Score: 73
Period size: 12 Copynumber: 6.8 Consensus size: 12
36167 TTTGGGCTTG
36177 TAATAATATATT-
1 TAATAATA-ATTA
36189 TAATAATAA-TA
1 TAATAATAATTA
*
36200 TAATATATATAATA
1 TAATA-ATA-ATTA
36214 TAATAATAA-TA
1 TAATAATAATTA
* *
36225 TTTATAATAATAA
1 -TAATAATAATTA
*
36238 TAATAATAATTT
1 TAATAATAATTA
36250 TAATAATAAT
1 TAATAATAAT
36260 AATTTAAGTA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
10 1 0.02
11 8 0.13
12 39 0.65
13 5 0.08
14 7 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAATAATAATTA
Found at i:36264 original size:15 final size:15
Alignment explanation
Indices: 36177--36263 Score: 79
Period size: 15 Copynumber: 5.7 Consensus size: 15
36167 TTTGGGCTTG
36177 TAATAATATATT-TAA
1 TAATAATA-ATTATAA
*
36192 TAATAATATAATATATA
1 TAATAATA-ATTATA-A
*
36209 TAAT-ATAATAATAA
1 TAATAATAATTATAA
* * *
36223 TATTTATAATAATAA
1 TAATAATAATTATAA
*
36238 TAATAATAATTTTAA
1 TAATAATAATTATAA
36253 TAATAATAATT
1 TAATAATAATT
36264 TAAGTAAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
14 4 0.07
15 47 0.77
16 5 0.08
17 5 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATAATAATTATAA
Found at i:43432 original size:32 final size:32
Alignment explanation
Indices: 43391--43454 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
43381 ACTTCATCAC
43391 AATCAATAGGGGAATAGCTCCTGAACAGAGAT
1 AATCAATAGGGGAATAGCTCCTGAACAGAGAT
43423 AATCAATAGGGGAATAGCTCCTGAACAGAGAT
1 AATCAATAGGGGAATAGCTCCTGAACAGAGAT
43455 GAACTGTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.19
Consensus pattern (32 bp):
AATCAATAGGGGAATAGCTCCTGAACAGAGAT
Found at i:43543 original size:24 final size:23
Alignment explanation
Indices: 43495--43548 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
43485 GATTAAATTG
**
43495 TGAA-AAATAAGTTATTTAATTT
1 TGAATAAATAAGTTATTTAAAAT
43517 TGAAATAAATAAAGTT-TTTAAAAT
1 TG-AATAAAT-AAGTTATTTAAAAT
43541 TGAATAAA
1 TGAATAAA
43549 CCATGAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 2 0.07
23 8 0.30
24 12 0.44
25 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (23 bp):
TGAATAAATAAGTTATTTAAAAT
Found at i:46075 original size:41 final size:41
Alignment explanation
Indices: 46030--46110 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
46020 CCAACGATGT
*
46030 TGAACATTGATACAAGAATGTACCAAAGTTGAACTGATAAC
1 TGAACATTGATACAAGAATGTACCAAAGCTGAACTGATAAC
* *
46071 TGAACATTGATACACGAATGTACCAAAGCTGAATTGATAA
1 TGAACATTGATACAAGAATGTACCAAAGCTGAACTGATAA
46111 GCACTCACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (41 bp):
TGAACATTGATACAAGAATGTACCAAAGCTGAACTGATAAC
Found at i:46263 original size:18 final size:18
Alignment explanation
Indices: 46240--46305 Score: 87
Period size: 18 Copynumber: 3.7 Consensus size: 18
46230 TCTTATAATT
* *
46240 ATCTGATTACTGTAAATC
1 ATCTGATAACTGAAAATC
46258 ATCTGATAACTGAAAATC
1 ATCTGATAACTGAAAATC
* * *
46276 ATATGATCACTGAAAATT
1 ATCTGATAACTGAAAATC
46294 ATCTGATAACTG
1 ATCTGATAACTG
46306 TAAACATTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (18 bp):
ATCTGATAACTGAAAATC
Found at i:48855 original size:29 final size:30
Alignment explanation
Indices: 48787--48857 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
48777 TTTAATTTTG
* *
48787 AAATTTATATTTTTAGTCCTTAAACTTTTAC
1 AAATTTACA-TTTTAGTCCTTAAACTTTTAA
*
48818 AACTTTACATTTTAGT-CTCTAAAC-TTTAA
1 AAATTTACATTTTAGTCCT-TAAACTTTTAA
48847 AAATTTACATT
1 AAATTTACATT
48858 CCAGTCACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 16 0.46
30 12 0.34
31 7 0.20
ACGTcount: A:0.35, C:0.14, G:0.03, T:0.48
Consensus pattern (30 bp):
AAATTTACATTTTAGTCCTTAAACTTTTAA
Found at i:48863 original size:29 final size:30
Alignment explanation
Indices: 48807--48863 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
48797 TTTTAGTCCT
* * **
48807 TAAACTTTTACAACTTTACATTTTAGTCTC
1 TAAACTTTTAAAAATTTACATTCCAGTCTC
48837 TAAAC-TTTAAAAATTTACATTCCAGTC
1 TAAACTTTTAAAAATTTACATTCCAGTC
48864 ACTATTTCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 18 0.78
30 5 0.22
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (30 bp):
TAAACTTTTAAAAATTTACATTCCAGTCTC
Found at i:52076 original size:41 final size:41
Alignment explanation
Indices: 52019--52099 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
52009 CCAACGATAT
52019 TGAACATTGATACACGAATGTACCAAAGCTGAACTGATAAC
1 TGAACATTGATACACGAATGTACCAAAGCTGAACTGATAAC
* * *
52060 TGAACATTGATACACGAATGTACTAAATCTGAATTGATAA
1 TGAACATTGATACACGAATGTACCAAAGCTGAACTGATAA
52100 GCACTCACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (41 bp):
TGAACATTGATACACGAATGTACCAAAGCTGAACTGATAAC
Found at i:52258 original size:18 final size:18
Alignment explanation
Indices: 52195--52297 Score: 72
Period size: 18 Copynumber: 5.9 Consensus size: 18
52185 ATTATTTTAT
52195 ATCTGATAACTGTGAAAT-
1 ATCTGATAACTGT-AAATC
* *
52213 ATCTGGT--CT-TATAATT
1 ATCTGATAACTGTA-AATC
* *
52229 ATTTGATTACTGTAAATC
1 ATCTGATAACTGTAAATC
52247 ATCTGATAACTG-AAATC
1 ATCTGATAACTGTAAATC
** * **
52264 ATAGGATCACTAAAAATC
1 ATCTGATAACTGTAAATC
52282 ATCTGATAACTGTAAA
1 ATCTGATAACTGTAAA
52298 CATTTAGAAT
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
14 1 0.02
15 4 0.06
16 7 0.11
17 13 0.20
18 37 0.58
19 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.35
Consensus pattern (18 bp):
ATCTGATAACTGTAAATC
Found at i:63563 original size:27 final size:28
Alignment explanation
Indices: 63523--63576 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
63513 AATTGACCTA
* *
63523 AAAATAAATCAAATTAATGTTAAATAAT
1 AAAATAAATCAAATAAATATTAAATAAT
63551 AAAATAAAT-AAATAAATATTAAATAA
1 AAAATAAATCAAATAAATATTAAATAA
63577 ATAGAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAATAAATCAAATAAATATTAAATAAT
Found at i:64260 original size:23 final size:24
Alignment explanation
Indices: 64216--64260 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
64206 GCAAAAATGC
*
64216 TTTGCTCGGTTTTGTTTTGGTTAT
1 TTTGCTCGGTTGTGTTTTGGTTAT
64240 TTTGCTCGGTTGT-TTTTGGTT
1 TTTGCTCGGTTGTGTTTTGGTT
64261 TTGGCCGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.02, C:0.09, G:0.27, T:0.62
Consensus pattern (24 bp):
TTTGCTCGGTTGTGTTTTGGTTAT
Found at i:64813 original size:25 final size:26
Alignment explanation
Indices: 64771--64841 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 26
64761 TGATAAGCCT
64771 AATATAT-ATATATATATATTAAAAA
1 AATATATAATATATATATATTAAAAA
***
64796 AATATATAATATAT-TATATTTTCAA
1 AATATATAATATATATATATTAAAAA
*
64821 AATCATATAATATGTATATAT
1 AAT-ATATAATATATATATAT
64842 ATTTTAAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 18 0.46
26 16 0.41
27 5 0.13
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (26 bp):
AATATATAATATATATATATTAAAAA
Found at i:64861 original size:28 final size:26
Alignment explanation
Indices: 64772--64863 Score: 89
Period size: 28 Copynumber: 3.4 Consensus size: 26
64762 GATAAGCCTA
* *
64772 ATATATATATATATATA-TTAAAAAA
1 ATATATATATATATATATTTTAAAAT
64797 ATATATA-ATATATTATATTTTCAAAAT
1 ATATATATATATA-TATATTTT-AAAAT
*
64824 CATATAATATGTATATATATTTTAAAACT
1 -ATAT-ATATATATATATATTTTAAAA-T
64853 ATACTATATAT
1 ATA-TATATAT
64864 TTTCAAAAAC
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
24 5 0.09
25 11 0.20
26 2 0.04
27 4 0.07
28 16 0.29
29 13 0.24
30 4 0.07
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (26 bp):
ATATATATATATATATATTTTAAAAT
Found at i:64945 original size:44 final size:43
Alignment explanation
Indices: 64835--64990 Score: 167
Period size: 44 Copynumber: 3.5 Consensus size: 43
64825 ATATAATATG
*
64835 TATATAT-ATTTT-AAAACTATACTATATATTTTCAAAAACTATA
1 TATATATGTTTTTAAAAACTATACTATATATTTTCAAAAAC--TA
**
64878 TATTATATGTTTTTTGAAACTATA-TAATATATTTTCAAAAACTA
1 TA-TATATGTTTTTAAAAACTATACT-ATATATTTTCAAAAACTA
* *
64922 TACCATATGTTTTTAAAAACTATACTATATATTTTCAAAAACCA
1 TA-TATATGTTTTTAAAAACTATACTATATATTTTCAAAAACTA
64966 TATATTAT-TTTTTGACAAAACTATA
1 TATA-TATGTTTTT-A-AAAACTATA
64991 TATTATAAAT
Statistics
Matches: 97, Mismatches: 8, Indels: 14
0.82 0.07 0.12
Matches are distributed among these distances:
43 8 0.08
44 50 0.52
45 15 0.15
46 24 0.25
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (43 bp):
TATATATGTTTTTAAAAACTATACTATATATTTTCAAAAACTA
Found at i:64978 original size:22 final size:22
Alignment explanation
Indices: 64847--64996 Score: 119
Period size: 22 Copynumber: 6.7 Consensus size: 22
64837 TATATATTTT
*
64847 AAAACTATACTA-TATATTTTCA
1 AAAACTATA-TATTATTTTTTCA
**
64869 AAAACTATATATTATATGTTTTTT
1 AAAACTATATATTAT-T-TTTTCA
* * *
64893 GAAACTATATAATATATTTTCA
1 AAAACTATATATTATTTTTTCA
*
64915 AAAACTATACCA-TATGTTTTT-A
1 AAAACTATA-TATTAT-TTTTTCA
*
64937 AAAACTATACTA-TATATTTTCA
1 AAAACTATA-TATTATTTTTTCA
* *
64959 AAAACCATATATTATTTTTTGA
1 AAAACTATATATTATTTTTTCA
64981 CAAAACTATATATTAT
1 -AAAACTATATATTAT
64997 AAATTATCAT
Statistics
Matches: 103, Mismatches: 17, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
21 8 0.08
22 59 0.57
23 19 0.18
24 17 0.17
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (22 bp):
AAAACTATATATTATTTTTTCA
Found at i:65805 original size:50 final size:51
Alignment explanation
Indices: 65720--65815 Score: 133
Period size: 50 Copynumber: 1.9 Consensus size: 51
65710 CGAGTCCAGA
** *
65720 TTGAATGTTCTTCTGAGCTGGATATCATTCGTTGTGAAGTTGAAATCCAAC
1 TTGAATGTTCTTCTGAGCTCAATATCATTCATTGTGAAGTTGAAATCCAAC
*
65771 TTGAATGTTCTTC-GAGTTCAATAT-ACTTCATTGTGAAGTTGAAAT
1 TTGAATGTTCTTCTGAGCTCAATATCA-TTCATTGTGAAGTTGAAAT
65816 TGACTCTAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
49 1 0.03
50 26 0.65
51 13 0.32
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.40
Consensus pattern (51 bp):
TTGAATGTTCTTCTGAGCTCAATATCATTCATTGTGAAGTTGAAATCCAAC
Found at i:73734 original size:26 final size:26
Alignment explanation
Indices: 73705--73757 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
73695 GGTCTGATGT
*
73705 GGCAGTTTCTAGAAGGTCCAGTCAGC
1 GGCAGTTTCTAGAAGATCCAGTCAGC
* *
73731 GGCAGTTTCTAGATGATCTAGTCAGC
1 GGCAGTTTCTAGAAGATCCAGTCAGC
73757 G
1 G
73758 CCTTCTGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (26 bp):
GGCAGTTTCTAGAAGATCCAGTCAGC
Done.