Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003872.1 Hibiscus syriacus cultivar Beakdansim tig00008342_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: 61749
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1550 original size:23 final size:23
Alignment explanation
Indices: 1534--1593 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
1524 ACCTATTTTA
1534 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTATTACG
1557 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTATTACG
1580 TTATATAAGCGCTA
1 TTATATAAGCGCTA
1594 TCTAATATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (23 bp):
TTATATAAGCGCTACCTATTACG
Found at i:1742 original size:23 final size:23
Alignment explanation
Indices: 1713--1761 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1703 ACCTATTTTA
* *
1713 TATATAAGCGTTACCTATTACGT
1 TATATAAGCGCTACCTAATACGT
*
1736 TATATAAGCGCTACCTAATATGT
1 TATATAAGCGCTACCTAATACGT
1759 TAT
1 TAT
1762 TATGCTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (23 bp):
TATATAAGCGCTACCTAATACGT
Found at i:1750 original size:178 final size:177
Alignment explanation
Indices: 1393--1761 Score: 575
Period size: 178 Copynumber: 2.1 Consensus size: 177
1383 ATAATGCACA
*
1393 ACCTATTACGTTACAAAAGCGCTACATAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAA
1 ACCTATTACGTTATAAAAGCGCTACATAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAA
* *
1458 CTGTTTGTTATCATTGGTAACATTTTAGGTGTTACCTAATATATTGTAATAAAAATTAAGTAATT
66 CGGTTTGTTATCATTGGTAACATTTTAGGTGTTACCTAATATACTGTAATAAAAATTAAGTAATT
1523 AACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCT
131 AACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCT
* *
1570 ACCTATTACGTTATATAAGCGCTATC-TAATATG-TGTTATGC-TGATAATGTTTCCAGTAATTA
1 ACCTATTACGTTATAAAAGCGCTA-CATAATATGTTATTATGCTTGATAATGTTTCCAGTAATTA
* *
1632 ACCGGTTATGTTATCCTTGGTAACATTTTAGGTGTTTACCTAATATGCTGTAATAATAAATTAAG
65 A-CGGTT-TGTTATCATTGGTAACATTTTAGGTG-TTACCTAATATACTGTAATAA-AAATTAAG
*
1697 TAATTAACCTATTTTA-TATATAAGCGTTACCTATTACGTTATATAAGCGCT
126 TAATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCT
* *
1748 ACCTAATATGTTAT
1 ACCTATTACGTTAT
1762 TATGCTTGAT
Statistics
Matches: 177, Mismatches: 10, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
175 22 0.12
176 11 0.06
177 54 0.31
178 66 0.37
179 24 0.14
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (177 bp):
ACCTATTACGTTATAAAAGCGCTACATAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAA
CGGTTTGTTATCATTGGTAACATTTTAGGTGTTACCTAATATACTGTAATAAAAATTAAGTAATT
AACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCT
Found at i:7404 original size:3 final size:3
Alignment explanation
Indices: 7396--7484 Score: 133
Period size: 3 Copynumber: 29.7 Consensus size: 3
7386 ACATGTAAAT
* *
7396 AAC AAC AAC AAC AAC AAC AAA AAC AAC AAC AAT AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* * *
7444 AAC AAC AGC AAC AAC AAT AAT AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
7485 TAATAATAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.67, C:0.28, G:0.01, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:8136 original size:65 final size:65
Alignment explanation
Indices: 7989--8198 Score: 260
Period size: 65 Copynumber: 3.2 Consensus size: 65
7979 TAGGGATTTG
* * * **
7989 TTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGA-CTAAAAAATTT
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACA-ATCT-AAATGTTT
*
8053 GTG
63 GTA
* * * **
8056 TTACAAGGGAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAATGTTCATA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTAAATGTTTGTA
* * *
8121 TTTCAAGGGAAACTGTCTCAAGAGAGATAAAACTTATTTCAAGAGAAACAATCTAAATGTTTGTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTAAATGTTTGTA
8186 TTTCAAGGGAAAC
1 TTTCAAGGGAAAC
8199 AACTTCTGGA
Statistics
Matches: 123, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
65 76 0.62
66 19 0.15
67 28 0.23
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (65 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTAAATGTTTGTA
Found at i:15694 original size:2 final size:2
Alignment explanation
Indices: 15689--15716 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15679 GCGCGCGCGC
15689 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
15717 TATGATTAGA
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:19270 original size:39 final size:37
Alignment explanation
Indices: 19226--19311 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 37
19216 ACCCTTTCAT
* *
19226 TAAATCTTTTTATATTTTCAATTTTGTAAA-AAAATTATA
1 TAAATCTTTTGA-A-TTTAAATTTTGTAAAGAAAA-TATA
* *
19265 TAAATCTTATGAATTTAAATTTTTTAAAGAAAATATA
1 TAAATCTTTTGAATTTAAATTTTGTAAAGAAAATATA
*
19302 TAAATATTTT
1 TAAATCTTTT
19312 CCAACTTGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
37 25 0.62
38 5 0.12
39 10 0.25
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (37 bp):
TAAATCTTTTGAATTTAAATTTTGTAAAGAAAATATA
Found at i:22048 original size:24 final size:24
Alignment explanation
Indices: 22015--22063 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
22005 CTCATTTTTC
*
22015 TTACATAATATAATTCACATGTAT
1 TTACACAATATAATTCACATGTAT
22039 TTACACAATATAATTCACATGTAT
1 TTACACAATATAATTCACATGTAT
22063 T
1 T
22064 CTACTTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (24 bp):
TTACACAATATAATTCACATGTAT
Found at i:23069 original size:77 final size:77
Alignment explanation
Indices: 22942--23099 Score: 316
Period size: 77 Copynumber: 2.1 Consensus size: 77
22932 AGTGGATTTG
22942 TCATCTTAAGTATTATTATGTCTATGGTTATATCATTAAATTATATACTATTTTGTGTGTTTAAT
1 TCATCTTAAGTATTATTATGTCTATGGTTATATCATTAAATTATATACTATTTTGTGTGTTTAAT
23007 GTTTTTAGGACA
66 GTTTTTAGGACA
23019 TCATCTTAAGTATTATTATGTCTATGGTTATATCATTAAATTATATACTATTTTGTGTGTTTAAT
1 TCATCTTAAGTATTATTATGTCTATGGTTATATCATTAAATTATATACTATTTTGTGTGTTTAAT
23084 GTTTTTAGGACA
66 GTTTTTAGGACA
23096 TCAT
1 TCAT
23100 GTTGTATAGA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 81 1.00
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.51
Consensus pattern (77 bp):
TCATCTTAAGTATTATTATGTCTATGGTTATATCATTAAATTATATACTATTTTGTGTGTTTAAT
GTTTTTAGGACA
Found at i:24987 original size:15 final size:16
Alignment explanation
Indices: 24955--24999 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
24945 TAAAGAACCT
24955 AATAAAAATATAACAAAC
1 AATAAAAATA-AA-AAAC
*
24973 AA-ATAAATAAAAAAC
1 AATAAAAATAAAAAAC
24988 AATAAAAATAAA
1 AATAAAAATAAA
25000 TAAGAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 6 0.25
16 10 0.42
17 6 0.25
18 2 0.08
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.16
Consensus pattern (16 bp):
AATAAAAATAAAAAAC
Found at i:24998 original size:20 final size:21
Alignment explanation
Indices: 24973--25030 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 21
24963 TATAACAAAC
24973 AAATAAATAAAAAACAATA-A
1 AAATAAATAAAAAACAATATA
24993 AAATAAATAAGAAAA-AATATA
1 AAATAAATAA-AAAACAATATA
*
25014 AAGA-AAATAGAAAACAA
1 AA-ATAAATAAAAAACAA
25031 GTGAAGACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 18 0.55
21 14 0.42
22 1 0.03
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (21 bp):
AAATAAATAAAAAACAATATA
Found at i:25290 original size:2 final size:2
Alignment explanation
Indices: 25285--25315 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
25275 AAAAAAAAAT
25285 TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
25316 GATACTAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:25442 original size:15 final size:14
Alignment explanation
Indices: 25422--25455 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
25412 ATGCTTAAAG
25422 AAAATAAAATATATA
1 AAAATAAAATATA-A
*
25437 AAAATATAATATAA
1 AAAATAAAATATAA
25451 AAAAT
1 AAAAT
25456 TAGTAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATAAAATATAA
Found at i:28599 original size:6 final size:6
Alignment explanation
Indices: 28588--28648 Score: 54
Period size: 6 Copynumber: 9.8 Consensus size: 6
28578 ACCCACCTTA
*
28588 TTTTTC TTTTTC -TTTTC TTTTGCTC TTTTTC TCTTTT- TTGTTTT TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTT--TC TTTTTC T-TTTTC TT-TTTC TTTTTC
*
28638 TTTTCC TTTTT
1 TTTTTC TTTTT
28649 TTTCCGACTT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
5 6 0.13
6 28 0.61
7 6 0.13
8 6 0.13
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:28616 original size:19 final size:20
Alignment explanation
Indices: 28592--28647 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
28582 ACCTTATTTT
28592 TCTTTTTCTTTTCTTTTG-C
1 TCTTTTTCTTTTCTTTTGTC
* *
28611 TCTTTTTCTCTT-TTTTGTT
1 TCTTTTTCTTTTCTTTTGTC
*
28630 TTTTTTTCTTTTCCTTTT
1 TCTTTTTCTTTT-CTTTT
28648 TTTTCCGACT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 5 0.17
19 21 0.70
21 4 0.13
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.79
Consensus pattern (20 bp):
TCTTTTTCTTTTCTTTTGTC
Found at i:28633 original size:25 final size:24
Alignment explanation
Indices: 28588--28651 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
28578 ACCCACCTTA
28588 TTTTTCTTTTTCTTTTCTTTTGCTC
1 TTTTTCTTTTT-TTTTCTTTTGCTC
**
28613 TTTTTCTCTTTTTTGTT-TTTTTTTC
1 TTTTTCT-TTTTTT-TTCTTTTGCTC
*
28638 TTTTCCTTTTTTTT
1 TTTTTCTTTTTTTT
28652 CCGACTTTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 1 0.03
24 6 0.18
25 21 0.62
26 6 0.18
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (24 bp):
TTTTTCTTTTTTTTTCTTTTGCTC
Found at i:29214 original size:2 final size:2
Alignment explanation
Indices: 29207--29239 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
29197 TTTTAAGAAA
*
29207 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29240 AATAAGATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:29258 original size:23 final size:23
Alignment explanation
Indices: 29223--29266 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
29213 ATATATATAT
*
29223 ATATATATATATTTATAAATAAG
1 ATATATATATATTTAGAAATAAG
* *
29246 ATATTTATTTATTTAGAAATA
1 ATATATATATATTTAGAAATA
29267 TCAGAAAAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
ATATATATATATTTAGAAATAAG
Found at i:31022 original size:3 final size:3
Alignment explanation
Indices: 31014--31055 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
31004 ATTTTTTATT
*
31014 TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31056 AACGAAATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:31325 original size:26 final size:25
Alignment explanation
Indices: 31297--31346 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
31287 CGAAGGCTTT
* *
31297 TTTTTAAAACATCATGCACTGAAGG
1 TTTTGAAAACATCAAGCACTGAAGG
*
31322 TTTTGAAAACATTAAGCACTGAAGG
1 TTTTGAAAACATCAAGCACTGAAGG
31347 GCTTACAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (25 bp):
TTTTGAAAACATCAAGCACTGAAGG
Found at i:31432 original size:45 final size:45
Alignment explanation
Indices: 31315--31451 Score: 238
Period size: 45 Copynumber: 3.0 Consensus size: 45
31305 ACATCATGCA
*
31315 CTGAAGGTTTTGAAAACATTAAGCACTGAAGGGCTTACAGATGAC
1 CTGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGAC
**
31360 CCAAAGGTTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGAC
1 CTGAAGG-TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGAC
31406 CTGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGAC
1 CTGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGAC
31451 C
1 C
31452 CTGAGGCTTT
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
45 44 0.51
46 42 0.49
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (45 bp):
CTGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGAC
Found at i:31455 original size:46 final size:46
Alignment explanation
Indices: 31315--31455 Score: 241
Period size: 46 Copynumber: 3.1 Consensus size: 46
31305 ACATCATGCA
*
31315 CTGAAGGTTTTGAAAACATTAAGCACTGAAGGGCTTACAGATGACC
1 CTGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACC
*
31361 C-AAAGGTTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA-C
1 CTGAAGG-TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACC
31406 CTGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACC
1 CTGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACC
31452 CTGA
1 CTGA
31456 GGCTTTAATA
Statistics
Matches: 89, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
45 43 0.48
46 46 0.52
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (46 bp):
CTGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACC
Found at i:31552 original size:46 final size:46
Alignment explanation
Indices: 31485--32072 Score: 982
Period size: 46 Copynumber: 12.8 Consensus size: 46
31475 TCTTGAACTC
* *
31485 TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGGCCCGAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
31531 TTTTTGATAACATCATGCACTGAAGGGCTTACAGATGACCCGGAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
31577 -TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* * * *
31622 TTTTTGATAACATCATGCATTGAAGGACTTACAGATGACCTGAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* * *
31668 TTTTTGATAACATCATGCACTAAAGGGCTTACAGATGACCCGGAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
31714 -TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
31759 TTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
31805 TTTTTGAAAATATCATGCACTGAAGAGCTTACAGATGACCCGAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
31851 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
31897 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
31943 TTTTTGAAAATATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
31989 TTTTTGAAAACATCATGAACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
32035 TTTTTTGAAAACATCATGCACTGAAGTGCTTACAGATG
1 -TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
32073 TTGGAAATAG
Statistics
Matches: 506, Mismatches: 33, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
45 84 0.17
46 387 0.76
47 35 0.07
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (46 bp):
TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
Found at i:31731 original size:137 final size:138
Alignment explanation
Indices: 31485--32072 Score: 993
Period size: 137 Copynumber: 4.3 Consensus size: 138
31475 TCTTGAACTC
* *
31485 TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGGCCCGAAGGTTTTTGATAACATCATGCA
1 TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCA
*
31550 CTGAAGGGCTTACAGATGACCCGGAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
66 CTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
31614 CCCAAAGG
131 CCCGAAGG
* * * *
31622 TTTTTGATAACATCATGCATTGAAGGACTTACAGATGACCTGAAGGTTTTTGATAACATCATGCA
1 TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCA
* *
31687 CTAAAGGGCTTACAGATGACCCGGAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
66 CTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
31751 CCCGAAGG
131 CCCGAAGG
* *
31759 TTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAATATCATGCA
1 TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCA
*
31824 CTGAAGAGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
66 CTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
31889 CCCGAAGG
131 CCCGAAGG
* *
31897 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAATATCATGCA
1 TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCA
*
31962 CTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGAACTGAAGGGCTTACAGATGA
66 CTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
32027 CCCGAAGG
131 CCCGAAGG
32035 TTTTTTGAAAACATCATGCACTGAAGTG-CTTACAGATG
1 -TTTTTGAAAACATCATGCACTGAAG-GACTTACAGATG
32073 TTGGAAATAG
Statistics
Matches: 431, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
137 216 0.50
138 179 0.42
139 35 0.08
140 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (138 bp):
TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCA
CTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
CCCGAAGG
Found at i:32799 original size:22 final size:22
Alignment explanation
Indices: 32748--32805 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
32738 GATAAAGCTT
* *
32748 TCATCTTCGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
32770 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
32792 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
32806 TGTAGATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:33275 original size:54 final size:54
Alignment explanation
Indices: 33172--33281 Score: 132
Period size: 54 Copynumber: 2.0 Consensus size: 54
33162 TGACTGGTTC
* * * *
33172 GTAAAACATTTGTCAATACATTCATCATCTCATGTGGTTTATGATCAGATGCTA
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGATCAGATACTA
* * * *
33226 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCA-CAGATACTA
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATG-ATCAGATACTA
33280 GT
1 GT
33282 TGACAACACA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
54 46 0.98
55 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.35
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGATCAGATACTA
Found at i:34286 original size:74 final size:75
Alignment explanation
Indices: 34155--34321 Score: 194
Period size: 74 Copynumber: 2.2 Consensus size: 75
34145 GGGTCTTCAG
* * *
34155 CATGCCCCAACATTGGCTAATACAGACGTTCAAAATGTACCAACATTCCTGATTCTGATT-AAAA
1 CATGCCCCAACATTTGCTAATACAAACGTTCAAAATGTACCAACATTCCTGAGTCTGATTGAAAA
34219 GGGCTTTAAA
66 GGGCTTTAAA
* * * * * *
34229 CATGTCCCAACATTTGCTGATACAAATGTTCAAAATG-AGTCAATATTCTTGAGTCTGATTGAAA
1 CATGCCCCAACATTTGCTAATACAAACGTTCAAAATGTA-CCAACATTCCTGAGTCTGATTGAAA
* * *
34293 TGGGCTTTCAG
65 AGGGCTTTAAA
*
34304 CATACCCCAACATTTGCT
1 CATGCCCCAACATTTGCT
34322 TCTTGTTGAT
Statistics
Matches: 77, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
73 1 0.01
74 49 0.64
75 27 0.35
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (75 bp):
CATGCCCCAACATTTGCTAATACAAACGTTCAAAATGTACCAACATTCCTGAGTCTGATTGAAAA
GGGCTTTAAA
Found at i:37216 original size:15 final size:15
Alignment explanation
Indices: 37198--37248 Score: 75
Period size: 15 Copynumber: 3.3 Consensus size: 15
37188 ATTTTTTCAT
37198 TTTTTCCCTTTTTCC
1 TTTTTCCCTTTTTCC
*
37213 TTTTTTCCTTTTTTCC
1 -TTTTTCCCTTTTTCC
*
37229 TTTTTTCCTTTTTCC
1 TTTTTCCCTTTTTCC
37244 TTTTT
1 TTTTT
37249 TTTCCCTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
15 18 0.56
16 14 0.44
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTCCCTTTTTCC
Found at i:37268 original size:8 final size:8
Alignment explanation
Indices: 37189--37267 Score: 99
Period size: 8 Copynumber: 9.8 Consensus size: 8
37179 CTTGGTTTAA
*
37189 TTTTTTCA
1 TTTTTTCC
37197 TTTTTTCC
1 TTTTTTCC
*
37205 CTTTTTCC
1 TTTTTTCC
37213 TTTTTTCC
1 TTTTTTCC
37221 TTTTTTCC
1 TTTTTTCC
37229 TTTTTTCC
1 TTTTTTCC
37237 -TTTTTCC
1 TTTTTTCC
37244 TTTTTTTTCCC
1 --TTTTTT-CC
37255 TTTTTT-C
1 TTTTTTCC
37262 TTTTTT
1 TTTTTT
37268 TTTTCAAGTA
Statistics
Matches: 64, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
7 14 0.22
8 37 0.58
9 6 0.09
10 5 0.08
11 2 0.03
ACGTcount: A:0.01, C:0.23, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTTCC
Found at i:42889 original size:2 final size:2
Alignment explanation
Indices: 42884--42917 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
42874 ATATATTAAG
*
42884 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42918 AATAAGATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42927 original size:24 final size:23
Alignment explanation
Indices: 42900--42944 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
42890 GTATATATAT
*
42900 ATATATATATATATTATAAATAAG
1 ATATATATATAT-TTAGAAATAAG
* *
42924 ATATTTATTTATTTAGAAATA
1 ATATATATATATTTAGAAATA
42945 TCAGAAAAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
ATATATATATATTTAGAAATAAG
Found at i:44695 original size:3 final size:3
Alignment explanation
Indices: 44687--44725 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
44677 ATTTTTTATT
44687 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
44726 AATGAAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:51694 original size:19 final size:18
Alignment explanation
Indices: 51670--51709 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
51660 GTTAATACGA
51670 ATAT-AAAAACATGGAAAAT
1 ATATAAAAAACAT--AAAAT
51689 ATATAAAAAACATAAAAT
1 ATATAAAAAACATAAAAT
51707 ATA
1 ATA
51710 AAATGCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 4 0.20
20 8 0.40
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (18 bp):
ATATAAAAAACATAAAAT
Found at i:52743 original size:4 final size:4
Alignment explanation
Indices: 52734--52780 Score: 71
Period size: 4 Copynumber: 12.0 Consensus size: 4
52724 TTTTTTATCC
52734 ATTT ATTT ATTT ATTT ATTT ATTT A-TT ATTT A-TT ATTTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT ATTT
52781 TATTATTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
3 6 0.15
4 31 0.77
5 3 0.08
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:52769 original size:3 final size:3
Alignment explanation
Indices: 52756--52806 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
52746 ATTTATTTAT
**
52756 TTA TTA TTTA TTA TT- TTA TTTA TT- TTA TTA TTA TTA AAA TTA TTA
1 TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
52801 TTA TTA
1 TTA TTA
52807 CAAACAGCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.10
3 30 0.75
4 6 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:52786 original size:12 final size:11
Alignment explanation
Indices: 52736--52787 Score: 68
Period size: 12 Copynumber: 4.5 Consensus size: 11
52726 TTTTATCCAT
52736 TTATTTATTTA
1 TTATTTATTTA
52747 TTTATTTATTTA
1 -TTATTTATTTA
*
52759 TTATTTATTATT
1 TTATTTATT-TA
52771 TTATTTATTTTA
1 TTATTTA-TTTA
52783 TTATT
1 TTATT
52788 ATTAAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
11 9 0.25
12 25 0.69
13 2 0.06
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:52787 original size:27 final size:27
Alignment explanation
Indices: 52734--52790 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
52724 TTTTTTATCC
52734 ATTTATTTATTTATTTATTTATTTATT
1 ATTTATTTATTTATTTATTTATTTATT
52761 ATTTA-TTATTTTATTTATTT-TATTATT
1 ATTTATTTA-TTTATTTATTTAT-TTATT
52788 ATT
1 ATT
52791 AAAATTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (27 bp):
ATTTATTTATTTATTTATTTATTTATT
Found at i:52789 original size:15 final size:14
Alignment explanation
Indices: 52734--52805 Score: 71
Period size: 15 Copynumber: 5.2 Consensus size: 14
52724 TTTTTTATCC
52734 ATTTATTTA-T-TT
1 ATTTATTTATTATT
52746 ATTTATTTATTTATT
1 ATTTATTTA-TTATT
52761 ATTTA-TTATT-TT
1 ATTTATTTATTATT
52773 ATTTATTTTATTATT
1 ATTTA-TTTATTATT
* *
52788 ATTAAAATTATTATT
1 ATT-TATTTATTATT
52803 ATT
1 ATT
52806 ACAAACAGCC
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
12 16 0.31
13 2 0.04
14 9 0.18
15 23 0.45
16 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTATTTATTATT
Found at i:52789 original size:23 final size:23
Alignment explanation
Indices: 52736--52791 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 23
52726 TTTTATCCAT
52736 TTATTTATT-TATTTATTTATTTA
1 TTATTTATTAT-TTTATTTATTTA
52759 TTATTTATTATTTTATTTATTTTA
1 TTATTTATTATTTTATTTA-TTTA
52783 TTA-TTATTA
1 TTATTTATTA
52792 AAATTATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 23 0.74
24 8 0.26
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (23 bp):
TTATTTATTATTTTATTTATTTA
Found at i:52801 original size:27 final size:27
Alignment explanation
Indices: 52743--52802 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
52733 CATTTATTTA
**
52743 TTTATTTATTTATTTATTATTTATTAT
1 TTTATTTATTTATTTATTATTTAAAAT
52770 TTTATTTATTT-TATTATTA-TTAAAAT
1 TTTATTTATTTAT-TTATTATTTAAAAT
52796 TATTATT
1 T-TTATT
52803 ATTACAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTATTTATTTATTTATTATTTAAAAT
Found at i:54248 original size:2 final size:2
Alignment explanation
Indices: 54241--54266 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54231 TTATTTGTCA
54241 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
54267 TTATCTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55110 original size:3 final size:3
Alignment explanation
Indices: 55104--55129 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
55094 TTTTAAATAC
55104 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
55130 TTTTATGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.