Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000059.1 Hibiscus syriacus cultivar Beakdansim tig00000091_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: 71994
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:10165 original size:11 final size:11
Alignment explanation
Indices: 10149--10177 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
10139 AACACTGTGT
10149 ATTGCATCCAC
1 ATTGCATCCAC
10160 ATTGCATCCAC
1 ATTGCATCCAC
10171 ATTGCAT
1 ATTGCAT
10178 TTACTTTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (11 bp):
ATTGCATCCAC
Found at i:14767 original size:134 final size:134
Alignment explanation
Indices: 14590--15165 Score: 508
Period size: 134 Copynumber: 4.3 Consensus size: 134
14580 TTTCAAGCAT
* * * * *
14590 AGTGGAGTGAATCTACATCCCCATG-TCTGATTTTTCCCT-AAGAAGAAGAGGAACATATCACTC
1 AGTGGAATGAATCAAC-TCCCCCTGATCAGA-TTTTCCCTCAAGAAGAAGAGAAACATATCACTC
* * * *
14653 CCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTATGCCTCAATTCAATCTTCCCTG
64 TCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTG
*
14718 AGTGAT
129 AGTGAC
* * * * * * *
14724 AGTGGAATGGATCAACTCCCCCTGATCAGATTTTCCCTCAAGAAGAAGTGGAATAGATCAATATC
1 AGTGGAATGAATCAACTCCCCCTGATCAGATTTTCCCTCAAGAAGAAGAGAAACATATCACTCTC
* ** * **
14789 TTTCAAGATTTGATATTTCCTGAGTAACAGTGGAACAAGTCTATCTCGATTCAATCTACCCTGTC
66 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAG
14854 TGAC
131 TGAC
** * * *
14858 AGTGGAATAAATGAATCAGTGTCCCCAT-ATCTGATTTTCCCTCAAGAAGAAGCA-AAATATATC
1 AGTGG----AATGAATCA-ACTCCCCCTGATCAGATTTTCCCTCAAGAAGAAG-AGAAACATATC
* * * *
14921 A-T-TTTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAATAAGTCTGCCTCGATTCAATCCTC
60 ACTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTC
*
14984 CCTAAGTGAC
125 CCTGAGTGAC
* * * * * * * *
14994 AGTGGAACGAATC-A-TCATCCCTAAATCTGATCTTCCCTCTAA-AAAAAGTGAAACATATCCCT
1 AGTGGAATGAATCAACTC-CCCCT-GATCAGATTTTCCCTC-AAGAAGAAGAGAAACATATCACT
* * * * * * *
15056 CTATTTCAGGATTTGAGATTCCCTGAGTAATAGTGTAATAAGTCTGCCTCGATTCAATCTTCCTT
63 CTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCT
15121 GAGTGAC
128 GAGTGAC
* *
15128 AATGGAATGAATCAACAT-CCCCAGAT-ATGATTTTCCCT
1 AGTGGAATGAATCAAC-TCCCCCTGATCA-GATTTTCCCT
15166 GAGTGAGAGT
Statistics
Matches: 360, Mismatches: 63, Indels: 38
0.78 0.14 0.08
Matches are distributed among these distances:
129 2 0.01
130 3 0.01
132 34 0.09
133 18 0.05
134 187 0.52
135 4 0.01
136 65 0.18
137 2 0.01
138 39 0.11
139 6 0.02
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (134 bp):
AGTGGAATGAATCAACTCCCCCTGATCAGATTTTCCCTCAAGAAGAAGAGAAACATATCACTCTC
TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAG
TGAC
Found at i:15421 original size:134 final size:134
Alignment explanation
Indices: 15150--16477 Score: 1510
Period size: 134 Copynumber: 9.9 Consensus size: 134
15140 CAACATCCCC
* * * * * ** *
15150 AGATATGATTTTCCCTGAGTGAGAGTGGAACAAGTCT-TCACGATTCAAAATTCCATGAGTGACA
1 AGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACA
* * * ** * * * * *
15214 GTAGAATGAATCAA-TGTCCCCACATCTGATTTTTTCTCAAGTAA-AAGTGGAATAGATCCATAT
66 GTGGAATGAATCAACT-CCCCCAGATCTGATTTTCCCTCAAG-AAGAAGCGGAACAAATCCCTCT
* *
15277 CTATCG
129 CTTTCA
* * * *
15283 AGATTTGATATTCCCTGATTGATAGTGGAATAAGTCTACCTCGATTCAATCTTCCCTGAGTGACA
1 AGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACA
* * * * * * *
15348 ATGGAATGAATCAAAGT-CCCCATATCTAACTTTCCCTCCAGAAGAAGCAGAACAAATCCCTCTC
66 GTGGAATGAATC-AACTCCCCCAGATCTGATTTTCCCTCAAGAAGAAGCGGAACAAATCCCTCTC
15412 TTTCA
130 TTTCA
* * * * ** *
15417 AGATTTGATATTTCCTGGGTGATAGTGGGACAAGTCTGCCTCGATTCAATCTTCTTTGAGTGATA
1 AGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACA
* *
15482 GTGGAATGAATCAACTCCCCCAGATCTGATTTTCCCTCAAGAAGAAGC-GAACAAGTTCCTCTCT
66 GTGGAATGAATCAACTCCCCCAGATCTGATTTTCCCTCAAGAAGAAGCGGAACAAATCCCTCTCT
15546 TTCA
131 TTCA
* * * *
15550 AGATTTGATATTCCCTGAGTGACAGTGGGACAAGTATGCCTCGATTCAATCTTCCCTGGGAGACA
1 AGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACA
* * * * * *
15615 GTAGAATGAATCAACTCCCTCAGATCTGATTTTCCCTTAAGAAAAAGCGGAACATATCCATCTCT
66 GTGGAATGAATCAACTCCCCCAGATCTGATTTTCCCTCAAGAAGAAGCGGAACAAATCCCTCTCT
15680 TTCA
131 TTCA
* * * * * * * *
15684 AGATTTGATATTCCCTGAGTGATAGTGGGATAAGTATGACTCGATTCAATATTCCCTAAGTGAAA
1 AGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACA
* * * * *
15749 GTGGAATGAATCAACTCCCCCAAATCTGATTTTCCCTCAAGAAGAAGTGGAGCATATCTCTCAT-
66 GTGGAATGAATCAACTCCCCCAGATCTGATTTTCCCTCAAGAAGAAGCGGAACAAATCCCTC-TC
15813 TTTCA
130 TTTCA
* *
15818 AGATTTGATATTCCCTGAGTGACAGT-GAGACAAGTCTGACTCGATTCAATCTTCCTTGAGTGAC
1 AGATTTGATATTCCCTGAGTGACAGTGGA-ACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGAC
* * * * * *
15882 AGTGGAATGAATCAACTCCCCCAGATCTAATTTTCCCACAAGAAAAAGCGGAACATATCCATCAC
65 AGTGGAATGAATCAACTCCCCCAGATCTGATTTTCCCTCAAGAAGAAGCGGAACAAATCCCTCTC
15947 TTTCA
130 TTTCA
* * * *
15952 AGATTTGATATTCCCTGAGTGACAGTGGAATAAGCCTGTCTCAATTCAATCTTCCCTGAGTGACA
1 AGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACA
* * * *
16017 GTGGAATGAATCAACTCCCTCAGATCTGATTTTCCCTCAAGAAGAAGTGGAACAGATCCTTCTCT
66 GTGGAATGAATCAACTCCCCCAGATCTGATTTTCCCTCAAGAAGAAGCGGAACAAATCCCTCTCT
16082 TTCA
131 TTCA
* * * *
16086 AGATTTGATATTCCCTGAGTGACAATGGAACAAGTCTGTCTCGATTCAATCTTCTCT-AATGACA
1 AGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACA
* *
16150 GTGGAATGAATCAACTCCCCCATATCTGATTTTCCCTTAAGAAGAAGCGGAACAAAT--CTCTCT
66 GTGGAATGAATCAACTCCCCCAGATCTGATTTTCCCTCAAGAAGAAGCGGAACAAATCCCTCTCT
16213 TTCA
131 TTCA
* * * * * * * * *
16217 AGATTTAATATTCCCTAAGAGACATTGGAACAAGTTTTCCTTGATTTAATCTTCCTTGAGTGACA
1 AGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACA
* * * *
16282 GTGGAATGAAT-ATACTCCCCCAAATCTAATTTTCCCTCAAGAATAAGCGGAACAAATCCCTCTT
66 GTGGAATGAATCA-ACTCCCCCAGATCTGATTTTCCCTCAAGAAGAAGCGGAACAAATCCCTCTC
16346 TTTCA
130 TTTCA
* * * *
16351 AGATTTTATATTCTCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGAAA
1 AGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACA
* ** ** * * * *
16416 GTGGAATGAAT-AAATATTCTTAGATATGATTTTCCCTAAAAAAGAAGCGGAACAGATCCCTC
66 GTGGAATGAATCAACT-CCCCCAGATCTGATTTTCCCTCAAGAAGAAGCGGAACAAATCCCTC
16478 ATCATATTCC
Statistics
Matches: 1020, Mismatches: 160, Indels: 29
0.84 0.13 0.02
Matches are distributed among these distances:
131 56 0.05
132 57 0.06
133 216 0.21
134 685 0.67
135 5 0.00
136 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (134 bp):
AGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACA
GTGGAATGAATCAACTCCCCCAGATCTGATTTTCCCTCAAGAAGAAGCGGAACAAATCCCTCTCT
TTCA
Found at i:16158 original size:401 final size:397
Alignment explanation
Indices: 15150--16474 Score: 1633
Period size: 401 Copynumber: 3.3 Consensus size: 397
15140 CAACATCCCC
* * * * * ** *
15150 AGATATGATTTTCCCTGAGTGAGAGTGGAACAAGTCT-TCACGATTCAAAATTCCATGAGTGACA
1 AGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACA
* * ** * * *
15214 GTAGAATGAATCAATGTCCC-CACATCTGATTTTTTCTCAAGTAA-AAGTGGAATAGATCCATAT
66 GTAGAATGAATCAA-CTCCCTCAGATCTGATTTTCCCTCAAG-AAGAAGCGGAACAGATCCATCT
* * *
15277 CTATCGAGATTTGATATTCCCTGATTGATAGTGGAATAAGTCT-ACCTCGATTCAATCTTCCCTG
129 CTTTCAAGATTTGATATTCCCTGAGTGATAGTGGAATAAGTCTGA-CTCGATTCAATCTTCCCT-
* * * * * * *
15341 AGTGACAATGGAATGAATCAAAGT-CCCCATATCTAACTTTCCCTCCAGAAGAAGCAGAACAAAT
192 AATGACAGTGGAATGAATC-AACTCCCCCATATCTGATTTTCCCTCAAGAAGAAGCGGAACAAAT
* * * *
15405 CCCTCTCTTTCAAGATTTGATATTTCCTGGGTGATAGTGGGACAAGTCTGCCTCGATTCAATCTT
256 CTCTCT-TTTCAAGATTTGATATTCCCTGAGTGACAGT-GGACAAGTCTGCCTCGATTCAATCTT
* * * *
15470 CTTTGAGTGATAGTGGAATGAATCAACTCCCCCAGATCTGATTTTCCCTCAAGAAGAAGC-GAAC
319 CCTTGAGTGACAGTGGAATGAATCAACTCCCCCAGATCTAATTTTCCCTCAAGAAAAAGCGGAAC
15534 AAGTTCCTCTCTTTCA
384 AA--TCCTCTCTTTCA
* * * *
15550 AGATTTGATATTCCCTGAGTGACAGTGGGACAAGTATGCCTCGATTCAATCTTCCCTGGGAGACA
1 AGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACA
* * *
15615 GTAGAATGAATCAACTCCCTCAGATCTGATTTTCCCTTAAGAAAAAGCGGAACATATCCATCTCT
66 GTAGAATGAATCAACTCCCTCAGATCTGATTTTCCCTCAAGAAGAAGCGGAACAGATCCATCTCT
* * *
15680 TTCAAGATTTGATATTCCCTGAGTGATAGTGGGATAAGTATGACTCGATTCAATATTCCCTAAGT
131 TTCAAGATTTGATATTCCCTGAGTGATAGTGGAATAAGTCTGACTCGATTCAATCTTCCCTAA-T
* * * * *
15745 GAAAGTGGAATGAATCAACTCCCCCAAATCTGATTTTCCCTCAAGAAGAAGTGGAGCATATCTCT
195 GACAGTGGAATGAATCAACTCCCCCATATCTGATTTTCCCTCAAGAAGAAGCGGAACAAATCTCT
*
15810 CATTTTCAAGATTTGATATTCCCTGAGTGACAGTGAGACAAGTCTGACTCGATTCAATCTTCCTT
260 C-TTTTCAAGATTTGATATTCCCTGAGTGACAGTG-GACAAGTCTGCCTCGATTCAATCTTCCTT
*
15875 GAGTGACAGTGGAATGAATCAACTCCCCCAGATCTAATTTTCCCACAAGAAAAAGCGGAACATAT
323 GAGTGACAGTGGAATGAATCAACTCCCCCAGATCTAATTTTCCCTCAAGAAAAAGCGGAACA-AT
*
15940 CCATCACTTTCA
387 CC-TCTCTTTCA
* * * *
15952 AGATTTGATATTCCCTGAGTGACAGTGGAATAAGCCTGTCTCAATTCAATCTTCCCTGAGTGACA
1 AGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACA
* * *
16017 GTGGAATGAATCAACTCCCTCAGATCTGATTTTCCCTCAAGAAGAAGTGGAACAGATCCTTCTCT
66 GTAGAATGAATCAACTCCCTCAGATCTGATTTTCCCTCAAGAAGAAGCGGAACAGATCCATCTCT
* * * * *
16082 TTCAAGATTTGATATTCCCTGAGTGACAATGGAACAAGTCTGTCTCGATTCAATCTTCTCTAATG
131 TTCAAGATTTGATATTCCCTGAGTGATAGTGGAATAAGTCTGACTCGATTCAATCTTCCCTAATG
*
16147 ACAGTGGAATGAATCAACTCCCCCATATCTGATTTTCCCTTAAGAAGAAGCGGAACAAATCTCTC
196 ACAGTGGAATGAATCAACTCCCCCATATCTGATTTTCCCTCAAGAAGAAGCGGAACAAATCTCTC
* * * * * * * *
16212 -TTTCAAGATTTAATATTCCCTAAGAGACATTGGAACAAGTTTTCCTTGATTTAATCTTCCTTGA
261 TTTTCAAGATTTGATATTCCCTGAGTGACAGTGG-ACAAGTCTGCCTCGATTCAATCTTCCTTGA
* *
16276 GTGACAGTGGAATGAAT-ATACTCCCCCAAATCTAATTTTCCCTCAAGAATAAGCGGAACAAATC
325 GTGACAGTGGAATGAATCA-ACTCCCCCAGATCTAATTTTCCCTCAAGAAAAAGCGGAAC-AAT-
*
16340 CCTCTTTTTCA
387 CCTCTCTTTCA
* * * *
16351 AGATTTTATATTCTCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGAAA
1 AGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACA
* * ** * * * *
16416 GTGGAATGAAT-AAATATTCTTAGATATGATTTTCCCTAAAAAAGAAGCGGAACAGATCC
66 GTAGAATGAATCAACT-CCCTCAGATCTGATTTTCCCTCAAGAAGAAGCGGAACAGATCC
16475 CTCATCATAT
Statistics
Matches: 801, Mismatches: 108, Indels: 33
0.85 0.11 0.04
Matches are distributed among these distances:
398 5 0.01
399 220 0.27
400 46 0.06
401 343 0.43
402 186 0.23
403 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (397 bp):
AGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACA
GTAGAATGAATCAACTCCCTCAGATCTGATTTTCCCTCAAGAAGAAGCGGAACAGATCCATCTCT
TTCAAGATTTGATATTCCCTGAGTGATAGTGGAATAAGTCTGACTCGATTCAATCTTCCCTAATG
ACAGTGGAATGAATCAACTCCCCCATATCTGATTTTCCCTCAAGAAGAAGCGGAACAAATCTCTC
TTTTCAAGATTTGATATTCCCTGAGTGACAGTGGACAAGTCTGCCTCGATTCAATCTTCCTTGAG
TGACAGTGGAATGAATCAACTCCCCCAGATCTAATTTTCCCTCAAGAAAAAGCGGAACAATCCTC
TCTTTCA
Found at i:19284 original size:3 final size:3
Alignment explanation
Indices: 19273--19327 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
19263 ATAATTAGTT
19273 ATA AT- ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19319 ATA ATA ATA
1 ATA ATA ATA
19328 TAACACTTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.08
3 46 0.92
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:19644 original size:89 final size:89
Alignment explanation
Indices: 19542--19716 Score: 262
Period size: 89 Copynumber: 2.0 Consensus size: 89
19532 ATGAATGCTA
* *
19542 GATTGACTCGAAAAGAATCTGCTTCACTACTCTTTCA-TGAAGATCAGATTCAAGGTGGATTTTC
1 GATTGACTCGAAAAGAATCTGCTTCACTACTC-TTCAGTGAAGATCAAATTCAAGGTGGATTTGC
*
19606 TTCCACTACTCTTCCGTGGAGATTG
65 TTCCACTACTCTTCCATGGAGATTG
* * * * *
19631 GATTGATTTGAAAAGAATCTGTTTCACTATTCTTCAGTGAAGATCAAATTCAAGGTTGATTTGCT
1 GATTGACTCGAAAAGAATCTGCTTCACTACTCTTCAGTGAAGATCAAATTCAAGGTGGATTTGCT
19696 TCCACTACTCTTCCATGGAGA
66 TCCACTACTCTTCCATGGAGA
19717 CCAAATCTTC
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
88 4 0.05
89 73 0.95
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.35
Consensus pattern (89 bp):
GATTGACTCGAAAAGAATCTGCTTCACTACTCTTCAGTGAAGATCAAATTCAAGGTGGATTTGCT
TCCACTACTCTTCCATGGAGATTG
Found at i:19754 original size:50 final size:50
Alignment explanation
Indices: 19695--19814 Score: 213
Period size: 50 Copynumber: 2.4 Consensus size: 50
19685 GTTGATTTGC
*
19695 TTCCACTACTCTTCCATGGAGACCAAATCTTCAATATTGGAAAAAACTTG
1 TTCCACTACTCTTCCGTGGAGACCAAATCTTCAATATTGGAAAAAACTTG
* *
19745 TTCCACTACTCTTCCGTGGAGCCCAAATCTTCAATATTGGAAAGAACTTG
1 TTCCACTACTCTTCCGTGGAGACCAAATCTTCAATATTGGAAAAAACTTG
19795 TTCCACTACTCTTCCGTGGA
1 TTCCACTACTCTTCCGTGGA
19815 TATTAGACTC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (50 bp):
TTCCACTACTCTTCCGTGGAGACCAAATCTTCAATATTGGAAAAAACTTG
Found at i:32552 original size:13 final size:12
Alignment explanation
Indices: 32531--32592 Score: 67
Period size: 13 Copynumber: 5.2 Consensus size: 12
32521 CCTGTAACAA
*
32531 AATTGTAATAATT
1 AATTATAATAA-T
32544 AATTATAAT-AT
1 AATTATAATAAT
*
32555 AATAATAATAAT
1 AATTATAATAAT
32567 -A-TATAATAAT
1 AATTATAATAAT
32577 AATATATAATAAT
1 AAT-TATAATAAT
32590 AAT
1 AAT
32593 ATTATAACAC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
10 8 0.19
11 11 0.26
12 3 0.07
13 20 0.48
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (12 bp):
AATTATAATAAT
Found at i:32559 original size:3 final size:3
Alignment explanation
Indices: 32536--32593 Score: 73
Period size: 3 Copynumber: 18.7 Consensus size: 3
32526 AACAAAATTG
*
32536 TAA TAA TTAA TTA TAA T-A TAA TAA TAA TAA TATA TAA TAA TAA TATA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A
32583 TAA TAA TAA TA
1 TAA TAA TAA TA
32594 TTATAACACT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 2 0.04
3 38 0.78
4 9 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:32572 original size:16 final size:15
Alignment explanation
Indices: 32536--32598 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 15
32526 AACAAAATTG
32536 TAATAATTAATTATAATA
1 TAATAA-TAA-TAT-ATA
32554 TAATAATAATAATATA
1 TAATAATAAT-ATATA
32570 TAATAATAATATATAA
1 TAATAATAATATAT-A
*
32586 TAATAATATTATA
1 TAATAATAATATA
32599 ACACTTATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
15 4 0.10
16 27 0.64
17 5 0.12
18 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAATATATA
Found at i:32593 original size:13 final size:13
Alignment explanation
Indices: 32543--32599 Score: 87
Period size: 13 Copynumber: 4.2 Consensus size: 13
32533 TTGTAATAAT
*
32543 TAATTATAATATAA
1 TAATAATAATAT-A
32557 TAATAATAATATA
1 TAATAATAATATA
32570 TAATAATAATATA
1 TAATAATAATATA
32583 TAATAATAATATTA
1 TAATAATAATA-TA
32597 TAA
1 TAA
32600 CACTTATAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
13 25 0.61
14 16 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATAATAATATA
Found at i:34159 original size:131 final size:130
Alignment explanation
Indices: 33960--34327 Score: 470
Period size: 131 Copynumber: 2.8 Consensus size: 130
33950 CGATATTGAG
** * * * * * * *
33960 AATAGTAATATCT-TTTCATTTCGGTTGAAGTAATAAATGATCGCTTTAAGGTATGAGAGATCAT
1 AATAGTAATATCTCTTT-ATTTCAATTG-AGTAATAAATGATTGTTTTAACGCACGAAAGGTCAT
* * * *
34024 TTATTCTCAATTGGAAATAATTTGATATTGTCGTTTTCTCTCGAATTAATA-CCAATTTTTAAGA
64 TTATTCTCAATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATCCAA-TTTTAAGA
34088 CGA
128 CGA
34091 AATAGTAATATCTCTTTATTTCAATTAGAGTAATAAATGATTGTTTTAACGCACGAAAGGTCATT
1 AATAGTAATATCTCTTTATTTCAATT-GAGTAATAAATGATTGTTTTAACGCACGAAAGGTCATT
* * ** **
34156 TATTCTCGATTGGAAATTATTAGATATTATCGTTTTCACTCGAATCGCTATTGAATTTTAAGACG
65 TATTCTCAATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATCCAATTTTAAGACG
34221 A
130 A
* * *
34222 AATAGTAATATCTCTTTATTTTAATTGGGGTAATAAATGATTGTTTTAATGCACGAAAGGTCATT
1 AATAGTAATATCTCTTTATTTCAATT-GAGTAATAAATGATTGTTTTAACGCACGAAAGGTCATT
*
34287 TATTCTCAATTGGAAATAATTAGATATTATCGTTTTTACTC
65 TATTCTCAATTGGAAATAATTAGATATTATCGTTTTCACTC
34328 TTAAAATTAT
Statistics
Matches: 208, Mismatches: 26, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
131 202 0.97
132 6 0.03
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (130 bp):
AATAGTAATATCTCTTTATTTCAATTGAGTAATAAATGATTGTTTTAACGCACGAAAGGTCATTT
ATTCTCAATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATCCAATTTTAAGACGA
Found at i:40292 original size:34 final size:33
Alignment explanation
Indices: 40216--40293 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
40206 TAAAATCAAG
*
40216 AACAAAAGA-AAAGCTTGATTTTGAGAATGAAA
1 AACAAAATAGAAAGCTTGATTTTGAGAATGAAA
* *
40248 AACCAGATAGAAAGCTTGATTTT-AGGAATGAAA
1 AACAAAATAGAAAGCTTGATTTTGA-GAATGAAA
40281 ATACAAAATAGAA
1 A-ACAAAATAGAA
40294 GAAAAATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
32 7 0.18
33 22 0.58
34 9 0.24
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.22
Consensus pattern (33 bp):
AACAAAATAGAAAGCTTGATTTTGAGAATGAAA
Found at i:48748 original size:18 final size:18
Alignment explanation
Indices: 48725--48759 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
48715 TATGTGATAT
48725 GTGGTCCTACGGGACATA
1 GTGGTCCTACGGGACATA
*
48743 GTGGTCCTTCGGGACAT
1 GTGGTCCTACGGGACAT
48760 TTCTACGCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
GTGGTCCTACGGGACATA
Found at i:49600 original size:21 final size:22
Alignment explanation
Indices: 49574--49618 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
49564 TGTAGCAGTA
49574 CTGTAGCA-GGGTATCGATACC
1 CTGTAGCAGGGGTATCGATACC
49595 CTGTAGCAGGGGTATCGATACC
1 CTGTAGCAGGGGTATCGATACC
49617 CT
1 CT
49619 TGAAGCAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.24
Consensus pattern (22 bp):
CTGTAGCAGGGGTATCGATACC
Found at i:49680 original size:12 final size:12
Alignment explanation
Indices: 49648--49682 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
49638 TTTAACATTC
*
49648 GGTACTATTCAT
1 GGTACTGTTCAT
49660 GGTACTGTTCAT
1 GGTACTGTTCAT
*
49672 GGTATTGTTCA
1 GGTACTGTTCA
49683 GCACTGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (12 bp):
GGTACTGTTCAT
Found at i:55840 original size:17 final size:17
Alignment explanation
Indices: 55818--55851 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55808 TAAAATTACC
55818 TATTTTTATTCTATTTT
1 TATTTTTATTCTATTTT
*
55835 TATTTTTATTTTATTTT
1 TATTTTTATTCTATTTT
55852 AGTTGCCCAA
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:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (17 bp):
TATTTTTATTCTATTTT
Found at i:56729 original size:16 final size:17
Alignment explanation
Indices: 56708--56739 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
56698 AATTCAAATT
56708 TTTTATTAA-TAATTTA
1 TTTTATTAATTAATTTA
56724 TTTTATTAATTAATTT
1 TTTTATTAATTAATTT
56740 TGAAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTAATTAATTTA
Found at i:57995 original size:16 final size:17
Alignment explanation
Indices: 57958--58002 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 17
57948 ATTTATGAGT
57958 GAATTGGAATCTGTGAAG
1 GAATTGGAATCTGT-AAG
57976 GAATTGGAATCTGT-AG
1 GAATTGGAATCTGTAAG
57992 GAATTGGAATC
1 GAATTGGAATC
58003 CAATTCTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 13 0.48
18 14 0.52
ACGTcount: A:0.33, C:0.07, G:0.31, T:0.29
Consensus pattern (17 bp):
GAATTGGAATCTGTAAG
Found at i:58623 original size:38 final size:37
Alignment explanation
Indices: 58566--58654 Score: 126
Period size: 38 Copynumber: 2.4 Consensus size: 37
58556 CCTAAACCCG
58566 AACCCGACCCGACCTGACCCAAATATCACACTTAAAAA
1 AACCCGACCCGACCTGACCCAAATATCACACTT-AAAA
* *
58604 AACCCGACCCGA-TTCGACCCGAATATCACACTTAAAA
1 AACCCGACCCGACCT-GACCCAAATATCACACTTAAAA
*
58641 AACCTGACCCGACC
1 AACCCGACCCGACC
58655 CGAACAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
37 16 0.36
38 29 0.64
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.13
Consensus pattern (37 bp):
AACCCGACCCGACCTGACCCAAATATCACACTTAAAA
Found at i:61355 original size:169 final size:169
Alignment explanation
Indices: 61076--61395 Score: 430
Period size: 169 Copynumber: 1.9 Consensus size: 169
61066 GATCAAAGGC
* *
61076 CCCAAAACAATTCGCTGATAGCCGTCGCCGTTCGCCGGAATCAAGCCCTTGAAGTTTCACTGAAA
1 CCCAAAACAATTCGCTGATAGCCGTCGCCGTTCACCGGAATCAAGCCCTTGAAGTTTCACCGAAA
* * *
61141 ACCCACCCCGACGCCTCAGATTTTGAACAGTTCCGGCCGCCTCGGACCTCCGTTTGCCTCATCGC
66 ACCCACCCCGACGCCTCAGATTTTGAACAGTTCCGGCCACCTCGGACCTCCGTTCGCCTCACCGC
61206 AACCATAGTTAGCTTCCTCGTCCCTTTCATCTAAAAACT
131 AACCATAGTTAGCTTCCTCGTCCCTTTCATCTAAAAACT
* * * *
61245 CCCAAAACAATTCG-TGCATATCCGTCTCCGTTCACCGGAATCGAGCCCTTGAAGTTTCGCCGAA
1 CCCAAAACAATTCGCTG-ATAGCCGTCGCCGTTCACCGGAATCAAGCCCTTGAAGTTTCACCGAA
* * * * * **
61309 AACCTACTCTGACGCCTC-GAATTTTGGAC-GATTCTGGCCACCTCGGACCTTTGTTCGCCTCAC
65 AACCCACCCCGACGCCTCAG-ATTTTGAACAG-TTCCGGCCACCTCGGACCTCCGTTCGCCTCAC
* *
61372 CGCCACCATATTTAGCTTCCTCGT
128 CGCAACCATAGTTAGCTTCCTCGT
61396 TGCCGTCTGC
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
168 4 0.03
169 126 0.97
ACGTcount: A:0.22, C:0.35, G:0.17, T:0.26
Consensus pattern (169 bp):
CCCAAAACAATTCGCTGATAGCCGTCGCCGTTCACCGGAATCAAGCCCTTGAAGTTTCACCGAAA
ACCCACCCCGACGCCTCAGATTTTGAACAGTTCCGGCCACCTCGGACCTCCGTTCGCCTCACCGC
AACCATAGTTAGCTTCCTCGTCCCTTTCATCTAAAAACT
Found at i:61520 original size:22 final size:22
Alignment explanation
Indices: 61477--61517 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
61467 GTTAGGATTT
61477 GGGTTTTTTTGTAAATAAATAA
1 GGGTTTTTTTGTAAATAAATAA
61499 GGGTTTTTTT-T-AATAAATA
1 GGGTTTTTTTGTAAATAAATA
61518 TAATAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (22 bp):
GGGTTTTTTTGTAAATAAATAA
Found at i:61533 original size:12 final size:12
Alignment explanation
Indices: 61518--61549 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
61508 TTAATAAATA
61518 TAATAATATTTT
1 TAATAATATTTT
61530 TAATAATATTTT
1 TAATAATATTTT
*
61542 TAAAAATA
1 TAATAATA
61550 AATTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATAATATTTT
Found at i:61556 original size:14 final size:14
Alignment explanation
Indices: 61519--61560 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
61509 TAATAAATAT
*
61519 AATAATATTTTTAAT
1 AATAA-ATTTTTAAA
61534 AAT--ATTTTTAAA
1 AATAAATTTTTAAA
61546 AATAAATTTTTAAA
1 AATAAATTTTTAAA
61560 A
1 A
61561 TTACCAGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
12 11 0.46
14 10 0.42
15 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATAAATTTTTAAA
Found at i:63247 original size:24 final size:24
Alignment explanation
Indices: 63202--63247 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
63192 ACCCTATATT
* **
63202 TTTATACTGTAATGATTGTAATAA
1 TTTATAATGTAATGATAATAATAA
*
63226 TTTATAATGTTATGATAATAAT
1 TTTATAATGTAATGATAATAAT
63248 TGGTTTTAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (24 bp):
TTTATAATGTAATGATAATAATAA
Found at i:64655 original size:3 final size:3
Alignment explanation
Indices: 64647--64676 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
64637 CCATAAACCC
*
64647 CTT CTT CTT CTT CTT CTT CAT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
64677 TATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Done.