Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009709.1 Corchorus capsularis cultivar CVL-1 contig09730, 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: 64864
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:17007 original size:27 final size:27
Alignment explanation
Indices: 16971--17026 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
16961 AGTGCTGCCT
* *
16971 TTGTTTCTTTTTAATTGTCCATTTTCC
1 TTGTTCCTTTTTAATTGTCCATTTCCC
16998 TTGTTCCTTTTTAATTGTCCATTTCCC
1 TTGTTCCTTTTTAATTGTCCATTTCCC
17025 TT
1 TT
17027 ATTTTTCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.11, C:0.21, G:0.07, T:0.61
Consensus pattern (27 bp):
TTGTTCCTTTTTAATTGTCCATTTCCC
Found at i:17852 original size:15 final size:16
Alignment explanation
Indices: 17825--17854 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17815 CACAGAGAAC
17825 AATTAATTTCTATTAT
1 AATTAATTTCTATTAT
17841 AATTAA-TTCTATTA
1 AATTAATTTCTATTA
17855 AGAAGGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTAATTTCTATTAT
Found at i:20454 original size:107 final size:104
Alignment explanation
Indices: 20336--20626 Score: 410
Period size: 107 Copynumber: 2.8 Consensus size: 104
20326 AGGTTTTTTA
* *
20336 TTATAGAGTTTTAGAAATAAAATATAAAATTAATTTCACTAAGTTTAGCCCCAAATTAAAAGTTT
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAA-TTT
* *
20401 ATTTTTATTTTAAGGGTAACTTTCAAAATTAATAATTTATTG
65 ATTTTTATTTTAAGGGTAAATTCCAAAATTAATAA--TATTG
*
20443 TTATAGGGTTTTAGAAATAGAATATAAAACTAACTTT-ACTAAGTTTAGCCCCAAATTAAAATTT
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAA-TTTCACTAAGTTTAGCCCCAAATTAAAATTT
*
20507 ATTTTTATTTTATAGGGTAAATTCCACAATTAATAATATTG
65 ATTTTTATTTTA-AGGGTAAATTCCAAAATTAATAATATTG
* * *
20548 TTATA-GGTTTTAAAAATAAAATATATAACTAA-TTCACTAAGTTTAG-CCCAAATTTAAATTTA
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTT-
*
20610 AATTTTATTTTAAGGGT
65 ATTTTTATTTTAAGGGT
20627 TAGAAAATAT
Statistics
Matches: 169, Mismatches: 11, Indels: 13
0.88 0.06 0.07
Matches are distributed among these distances:
102 21 0.12
103 22 0.13
104 24 0.14
105 10 0.06
106 15 0.09
107 74 0.44
108 3 0.02
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (104 bp):
TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTA
TTTTTATTTTAAGGGTAAATTCCAAAATTAATAATATTG
Found at i:23078 original size:14 final size:14
Alignment explanation
Indices: 23054--23092 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
23044 CGCCAATAAA
*
23054 ATATAAAATATTTT
1 ATATATAATATTTT
* *
23068 TTATATTATATTTT
1 ATATATAATATTTT
23082 ATATATAATAT
1 ATATATAATAT
23093 ATCTAAAGAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATATAATATTTT
Found at i:23141 original size:19 final size:19
Alignment explanation
Indices: 23119--23183 Score: 50
Period size: 18 Copynumber: 3.7 Consensus size: 19
23109 TTTTAGTTTT
23119 AATTTATAATTTATATATA
1 AATTTATAATTTATATATA
* *
23138 AATTTTTAGTTT-TA-AT-
1 AATTTATAATTTATATATA
* * *
23154 ATTTTATAA-TAATTTATA
1 AATTTATAATTTATATATA
23172 AATTTAT-ATTTA
1 AATTTATAATTTA
23184 ACATTTAGAT
Statistics
Matches: 33, Mismatches: 9, Indels: 9
0.65 0.18 0.18
Matches are distributed among these distances:
15 1 0.03
16 7 0.21
17 5 0.15
18 10 0.30
19 10 0.30
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
AATTTATAATTTATATATA
Found at i:23167 original size:26 final size:28
Alignment explanation
Indices: 23103--23168 Score: 75
Period size: 32 Copynumber: 2.3 Consensus size: 28
23093 ATCTAAAGAT
23103 TAATAA-TTTTAGTTTTAATTTATAATTTA
1 TAATAATTTTTAGTTTTAA-TTAT-ATTTA
23132 TATATAAATTTTTAGTTTTAA-TAT-TTTA
1 TA-AT-AATTTTTAGTTTTAATTATATTTA
23160 TAATAATTT
1 TAATAATTT
23169 ATAAATTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
26 5 0.15
27 2 0.06
28 6 0.18
29 2 0.06
30 5 0.15
31 2 0.06
32 12 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (28 bp):
TAATAATTTTTAGTTTTAATTATATTTA
Found at i:25047 original size:439 final size:437
Alignment explanation
Indices: 24139--25354 Score: 1518
Period size: 439 Copynumber: 2.8 Consensus size: 437
24129 GTAGATTATG
* * * *
24139 TCACACATTAACCTTTTAATCGACACTTGAACAACCTCAATCGGACAAGAGGACCGAAAATTATG
1 TCACACAATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAGTGGACCGAAAATTATA
* * * * * **
24204 CAATATATTAAATAGACCGACAATCAAAACCACAAAATTTCAGAAGGATTTTTTATAATTGAAAC
66 C-A-ATATTAAATAGACCGGCAATCGAGACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAAC
* * * *
24269 ATTAAAATTGACTTCTGAATTCTTCATGAAAGTTGTAGATCACGAAATTATCTTTTAATAGACAC
129 ATTAAAATTGACTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTATCTTTTAATAGACAC
* * * * * *
24334 TTGAATCACCTTAATC-G---GAAAAATAGAACA-AAAA-AATCAAA---G---TGTTAAATCGT
194 TTGAATCACCTTCATCGGAAAGAAAAACAAAAAATAAAAGAATTAAAGCCGAAACGTTAAATCGT
* * * *
24387 CCAACCCATAATTT-T-AAAGGATTAAATAGCATAAAGAATAAAAGTAT-GAGAATCATTTGATA
259 CCAACCCAAAATTTGTGAGA-GACTAAATAGCATAAAGAATAAAAGTATAGAG-GTCATTTGATA
* * * *
24449 GATAATCCAGCAAAAAAAATATTTATTTATGGAGACCAAACATTAAAATTCTCTCTCGAACATTC
322 -ATAATCCAGC-AAAAAAATATTTGTTTATGGAGACCAAACATAAAAATTCCCTCTCGAACACTC
* *
24514 CACGAAACTCATTAATCAAATTCAGCTTTCAAACCCTTAACGAAAGTCGTAGA
385 CACGAAACTCATCAATCAAATTCAGCTTTCAAACCCTTAACGAAAGTCATAGA
* * * *
24567 TCATACAATAACCTTTTAATCC-ACACTTGAACAATCTCAATCGGACAACTGGACCAAAAATTAT
1 TCACACAATAACCTTTTAA-CCGACACTTGAACAACCTCAATCGGACAAGTGGACCGAAAATTAT
* *
24631 ACAATATTAAATAGACCGGCAATGGAGACCACAAAATTTCAAAAGCATTTTTTAGAATCAAAACA
65 ACAATATTAAATAGACCGGCAATCGAGACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAACA
* * * *
24696 TTAAAATTGGCTTTTGGGTCCTTCATGAAAGTTATAGATCATGAAATTACCTTTTAATAGACACT
130 TTAAAATTGACTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTATCTTTTAATAGACACT
* *
24761 TGAATCACTTTCATCGGACAAGAAAAACAAAAAATAAAAGAATTAAAGCCGAAACGTTCAATCGT
195 TGAATCACCTTCATCGGA-AAGAAAAACAAAAAATAAAAGAATTAAAGCCGAAACGTTAAATCGT
* ** *
24826 CCAACCCAGAATTTGTGAGAGACTAAATAGCATAAATTATAAAAGTATAGAGGTCATTTGGTAAT
259 CCAACCCAAAATTTGTGAGAGACTAAATAGCATAAAGAATAAAAGTATAGAGGTCATTTGATAAT
* * *
24891 AATCCAGCAAAAAAATTATTTGTTTATGGAGACCAAACATAAAAATTCCCTCTTGAACCCTCCGC
324 AATCCAGCAAAAAAA-TATTTGTTTATGGAGACCAAACATAAAAATTCCCTCTCGAACACTCCAC
* ** * *
24956 GAAACTCATCAATCAAATTCAGCTTTTAGGCCCTTAGCGAAATTCATAGA
388 GAAACTCATCAATCAAATTCAGCTTTCAAACCCTTAACGAAAGTCATAGA
* * *
25006 TTACACAATAACCTTTTAACCGACACTTGAACAACCTCAATCAGACAAGTGGACCGAAATTTATT
1 TCACACAATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAGTGGACCGAAAATTA-T
* * * *
25071 A-GATATCAAATAGACCGGCAATCGTGACCACAAAATTTCAGAAGCATTTTTTTGAATCAAAACA
65 ACAATATTAAATAGACCGGCAATCGAGACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAACA
* *
25135 TTAAAATTGACTTTTGAGTCCTTTATGGAAGTTGTAGATCATGAAATTATCTTTTAATAGACACT
130 TTAAAATTGACTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTATCTTTTAATAGACACT
* *
25200 TGAATCACCTTCATCGGATAA-ACAAAACAAAAAATAAAAGAATTAAAGCCGAAACGTTGAATCC
195 TGAATCACCTTCATCGGA-AAGA-AAAACAAAAAATAAAAGAATTAAAGCCGAAACGTTAAATCG
* * * * *
25264 TCCAACCCAAAAATTGTGAGGGACTAAATAGCATAAAGCATAAAAGTATAG-GGACAATTTGACA
258 TCCAACCCAAAATTTGTGAGAGACTAAATAGCATAAAGAATAAAAGTATAGAGGTC-ATTTGATA
* *
25328 AAAAACCAGC-AAAAAATATTTGTTTAT
322 ATAATCCAGCAAAAAAATATTTGTTTAT
25355 TATAAGCGGG
Statistics
Matches: 679, Mismatches: 87, Indels: 35
0.85 0.11 0.04
Matches are distributed among these distances:
426 123 0.18
427 2 0.00
428 56 0.08
429 1 0.00
431 10 0.01
432 4 0.01
433 6 0.01
436 1 0.00
437 11 0.02
438 19 0.03
439 404 0.59
440 37 0.05
441 5 0.01
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (437 bp):
TCACACAATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAGTGGACCGAAAATTATA
CAATATTAAATAGACCGGCAATCGAGACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAACAT
TAAAATTGACTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTATCTTTTAATAGACACTT
GAATCACCTTCATCGGAAAGAAAAACAAAAAATAAAAGAATTAAAGCCGAAACGTTAAATCGTCC
AACCCAAAATTTGTGAGAGACTAAATAGCATAAAGAATAAAAGTATAGAGGTCATTTGATAATAA
TCCAGCAAAAAAATATTTGTTTATGGAGACCAAACATAAAAATTCCCTCTCGAACACTCCACGAA
ACTCATCAATCAAATTCAGCTTTCAAACCCTTAACGAAAGTCATAGA
Found at i:33823 original size:12 final size:12
Alignment explanation
Indices: 33806--33830 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33796 GCCAGGTAAG
33806 GTTAACTATACA
1 GTTAACTATACA
33818 GTTAACTATACA
1 GTTAACTATACA
33830 G
1 G
33831 AAGTTGTAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (12 bp):
GTTAACTATACA
Found at i:35706 original size:31 final size:31
Alignment explanation
Indices: 35668--35731 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
35658 AATTTATCCT
*
35668 CCAATAGAAATAGTTAGAGGCTAAAATTCAC
1 CCAATAGAAATAGTTAGAGCCTAAAATTCAC
35699 CCAATAGAAATAGTTAGAGCCTAAAATTCAC
1 CCAATAGAAATAGTTAGAGCCTAAAATTCAC
35730 CC
1 CC
35732 GAAGAAGTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.22
Consensus pattern (31 bp):
CCAATAGAAATAGTTAGAGCCTAAAATTCAC
Found at i:36174 original size:48 final size:48
Alignment explanation
Indices: 36074--36180 Score: 146
Period size: 48 Copynumber: 2.2 Consensus size: 48
36064 TCAGATTATT
**
36074 CGGGTTTCGGGTCATTCGGGTCTCGGGTCACACGGGTTTCGGGTCATT
1 CGGGTTTCGGGTCATTCGGGTCTCGGGTCACACGGGTTTCGGGTCAGG
* * *
36122 CGGGTTTCGGGTCATTCGGGTCTTGGGTCTA-TCGGGTTTCGGGTTAGG
1 CGGGTTTCGGGTCATTCGGGTCTCGGGTC-ACACGGGTTTCGGGTCAGG
36170 CGGG-TTCGGGT
1 CGGGTTTCGGGT
36181 TTTGGCCTCG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
47 7 0.13
48 45 0.85
49 1 0.02
ACGTcount: A:0.07, C:0.20, G:0.41, T:0.33
Consensus pattern (48 bp):
CGGGTTTCGGGTCATTCGGGTCTCGGGTCACACGGGTTTCGGGTCAGG
Found at i:36175 original size:16 final size:16
Alignment explanation
Indices: 36033--36165 Score: 146
Period size: 16 Copynumber: 8.4 Consensus size: 16
36023 GACAGTTTTC
*
36033 TCGGATCATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
36049 TCGGGTCATT-TGGAT
1 TCGGGTCATTCGGGTT
* * *
36064 TCAGATTATTCGGGTT
1 TCGGGTCATTCGGGTT
*
36080 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
**
36096 TCGGGTCACACGGGTT
1 TCGGGTCATTCGGGTT
36112 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
36128 TCGGGTCATTCGGGTCT
1 TCGGGTCATTCGGGT-T
36145 T-GGGTC-TATCGGGTT
1 TCGGGTCAT-TCGGGTT
36160 TCGGGT
1 TCGGGT
36166 TAGGCGGGTT
Statistics
Matches: 96, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
15 13 0.14
16 81 0.84
17 2 0.02
ACGTcount: A:0.10, C:0.19, G:0.35, T:0.36
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:38501 original size:32 final size:32
Alignment explanation
Indices: 38465--38546 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 32
38455 GGTTATTCGG
* *
38465 GTCATACGGGTCTCGGGTCA-CTCGAGTTATGA
1 GTCATTCGGGTCTCGGGTCATCT-GAGTTACGA
* * * * *
38497 GTCATTCGGATTTCGAGTCATCTGGGTTACGG
1 GTCATTCGGGTCTCGGGTCATCTGAGTTACGA
38529 GTCATTCGGGTCTCGGGT
1 GTCATTCGGGTCTCGGGT
38547 TGGACGGGTT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
32 37 0.95
33 2 0.05
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.32
Consensus pattern (32 bp):
GTCATTCGGGTCTCGGGTCATCTGAGTTACGA
Found at i:38539 original size:16 final size:16
Alignment explanation
Indices: 38452--38539 Score: 54
Period size: 16 Copynumber: 5.4 Consensus size: 16
38442 GGTTAACTTC
38452 TCGGGTTATTCGGGTCAT
1 TCGGGTTA--CGGGTCAT
* *
38470 ACGGGTCT-CGGGTCAC
1 TCGGGT-TACGGGTCAT
* * *
38486 TCGAGTTATGAGTCAT
1 TCGGGTTACGGGTCAT
* * *
38502 TCGGATTTCGAGTCA-
1 TCGGGTTACGGGTCAT
38517 TCTGGGTTACGGGTCAT
1 TC-GGGTTACGGGTCAT
38534 TCGGGT
1 TCGGGT
38540 CTCGGGTTGG
Statistics
Matches: 52, Mismatches: 14, Indels: 10
0.68 0.18 0.13
Matches are distributed among these distances:
15 3 0.06
16 41 0.79
17 2 0.04
18 5 0.10
19 1 0.02
ACGTcount: A:0.15, C:0.19, G:0.33, T:0.33
Consensus pattern (16 bp):
TCGGGTTACGGGTCAT
Found at i:40589 original size:2 final size:2
Alignment explanation
Indices: 40576--40616 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
40566 GACAAAAATA
40576 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40617 TTTCTTATCC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.06
2 32 0.89
3 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:41342 original size:2 final size:2
Alignment explanation
Indices: 41335--41360 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41325 TCATTAATAC
41335 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
41361 TAGTTTTAAC
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:41450 original size:22 final size:21
Alignment explanation
Indices: 41420--41498 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 21
41410 AATATTTGTA
41420 TAAACTTTTGATAACTACCCTAT
1 TAAA-TTTTGATAA-TACCCTAT
*
41443 TAAATTTTGATAATCACCATAT
1 TAAATTTTGATAAT-ACCCTAT
**
41465 GGAATTTTGATAATTA-CCTAT
1 TAAATTTTGATAA-TACCCTAT
* *
41486 AAAATTGTGATAA
1 TAAATTTTGATAA
41499 ACTCCATAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
21 15 0.32
22 27 0.57
23 5 0.11
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (21 bp):
TAAATTTTGATAATACCCTAT
Found at i:41506 original size:43 final size:44
Alignment explanation
Indices: 41425--41521 Score: 115
Period size: 43 Copynumber: 2.2 Consensus size: 44
41415 TTGTATAAAC
* * * * *
41425 TTTTGATAACTACCCTATTAAATTTTGATAATCACCATATGGAA
1 TTTTGATAACTACCCTATAAAATTGTGATAAACACCATAAGAAA
* *
41469 TTTTGATAATTA-CCTATAAAATTGTGATAAACTCCATAAGAAA
1 TTTTGATAACTACCCTATAAAATTGTGATAAACACCATAAGAAA
*
41512 CTTTGATAAC
1 TTTTGATAAC
41522 CTAACTATGA
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
43 33 0.75
44 11 0.25
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.37
Consensus pattern (44 bp):
TTTTGATAACTACCCTATAAAATTGTGATAAACACCATAAGAAA
Found at i:42436 original size:2 final size:2
Alignment explanation
Indices: 42431--42455 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42421 ATATATATAT
42431 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
42456 ACTACTCCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:45426 original size:22 final size:21
Alignment explanation
Indices: 45401--45603 Score: 131
Period size: 22 Copynumber: 9.3 Consensus size: 21
45391 TCGTGATGGA
*
45401 TAACCTCCTTATAAAATTCTGG
1 TAACCTCC-TATGAAATTCTGG
* * *
45423 TAACCTTCATTTAAAATT-TCGG
1 TAACC-TCCTATGAAATTCT-GG
* * *
45445 TAACCTCCCCATTAAATTTTGG
1 TAACCT-CCTATGAAATTCTGG
* *
45467 TAAACC-CCTATGAGATTTTGG
1 T-AACCTCCTATGAAATTCTGG
* * **
45488 TAACTTTCCTATGAGATTCTAA
1 TAAC-CTCCTATGAAATTCTGG
*
45510 TAACCTCGCTATGAAATTCTAG
1 TAACCTC-CTATGAAATTCTGG
* * *
45532 TAACCTTGCTATGAAATTTTTG
1 TAACC-TCCTATGAAATTCTGG
*
45554 TAACCTCGCTATGAAATTTTGG
1 TAACCTC-CTATGAAATTCTGG
*
45576 TAACCTCCCTATGAAATTCTAG
1 TAACCT-CCTATGAAATTCTGG
45598 TAACCT
1 TAACCT
45604 TCGTAAGAAA
Statistics
Matches: 147, Mismatches: 23, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
20 3 0.02
21 18 0.12
22 117 0.80
23 9 0.06
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (21 bp):
TAACCTCCTATGAAATTCTGG
Found at i:45523 original size:44 final size:44
Alignment explanation
Indices: 45474--45619 Score: 177
Period size: 44 Copynumber: 3.3 Consensus size: 44
45464 TGGTAAACCC
* * * *
45474 CTATGAGATTTTGGTAACTTTCCTATGAGATTCTAATAACCTCG
1 CTATGAAATTTTGGTAACCTTCCTATGAAATTCTAGTAACCTCG
* * * * *
45518 CTATGAAATTCTAGTAACCTTGCTATGAAATTTTTGTAACCTCG
1 CTATGAAATTTTGGTAACCTTCCTATGAAATTCTAGTAACCTCG
*
45562 CTATGAAATTTTGGTAACCTCCCTATGAAATTCTAGTAACCTTCG
1 CTATGAAATTTTGGTAACCTTCCTATGAAATTCTAGTAACC-TCG
*
45607 -TAAGAAATTTTGG
1 CTATGAAATTTTGG
45620 CAACAGTGTG
Statistics
Matches: 85, Mismatches: 16, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
44 82 0.96
45 3 0.04
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (44 bp):
CTATGAAATTTTGGTAACCTTCCTATGAAATTCTAGTAACCTCG
Found at i:45557 original size:66 final size:65
Alignment explanation
Indices: 45474--45619 Score: 177
Period size: 66 Copynumber: 2.2 Consensus size: 65
45464 TGGTAAACCC
* * * *
45474 CTATGAGATTTTGGTAACTTTC-CTATGAGATTCTAATAACCTCGCTATGAAATTCTAGTAACCT
1 CTATGAAATTTTGGTAAC-CTCGCTATGAAATTCTAATAACCTCCCTATGAAATTCTAGTAACCT
45538 T
65 T
* * **
45539 GCTATGAAATTTTTGTAACCTCGCTATGAAATTTTGGTAACCTCCCTATGAAATTCTAGTAACCT
1 -CTATGAAATTTTGGTAACCTCGCTATGAAATTCTAATAACCTCCCTATGAAATTCTAGTAACCT
45604 T
65 T
*
45605 CGTAAGAAATTTTGG
1 C-TATGAAATTTTGG
45620 CAACAGTGTG
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
65 3 0.04
66 65 0.96
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (65 bp):
CTATGAAATTTTGGTAACCTCGCTATGAAATTCTAATAACCTCCCTATGAAATTCTAGTAACCTT
Found at i:45613 original size:22 final size:23
Alignment explanation
Indices: 45487--45615 Score: 135
Period size: 22 Copynumber: 5.9 Consensus size: 23
45477 TGAGATTTTG
* *
45487 GTAACTTTC-CTATGAGATTCTA
1 GTAACCTTCGCTATGAAATTCTA
*
45509 ATAACC-TCGCTATGAAATTCTA
1 GTAACCTTCGCTATGAAATTCTA
* *
45531 GTAACCTT-GCTATGAAATTTTT
1 GTAACCTTCGCTATGAAATTCTA
* *
45553 GTAACC-TCGCTATGAAATTTTG
1 GTAACCTTCGCTATGAAATTCTA
*
45575 GTAACC-TCCCTATGAAATTCTA
1 GTAACCTTCGCTATGAAATTCTA
*
45597 GTAACCTTCG-TAAGAAATT
1 GTAACCTTCGCTATGAAATT
45616 TTGGCAACAG
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.03
22 85 0.93
23 3 0.03
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.36
Consensus pattern (23 bp):
GTAACCTTCGCTATGAAATTCTA
Found at i:50830 original size:416 final size:416
Alignment explanation
Indices: 50086--50837 Score: 1152
Period size: 416 Copynumber: 1.8 Consensus size: 416
50076 GTATTTCTGG
* *
50086 AGAAAAAAAAACAATTGGGTGCACAGATGGTGTAGGGTGTGGTGAAGTGTGAACAAGTCCAAAAA
1 AGAAAAAAAAACAACTGGGTGCACAGATGGTGCAGGGTGTGGTGAAGTGTGAACAAGTCCAAAAA
*
50151 GAACGGGCCACTTAACTGGTTATCCAAGAAATATCGAGTTAGCCGCACGAGGGAGAGCTGTCACA
66 GAACGGGCCACTTAACTGGTTATCCAAGAAATATCGAGTTAGCCACACGAGGGAGAGCTGTCACA
* *
50216 TGTGAACGGGGAAGTTTGTTAGAGTTCACATGTGAGTGTCGCATCCCATATCACAAAAGGATGGG
131 TGTGAACGGGGAAGTTTGTTAGAGTTCAAATGTGAGTGTCGCATCCCACATCACAAAAGGATGGG
* * *
50281 CTATAAAAATGGCATATATACCTGAAAAATCCAAGAACACATAGGCTTAAACTTTTGGGTTTAGA
196 ATATAAAAATGGCATATATACCTGAAAAATCCAAGAACACATAGACTTAAACTTTTGGGTTCAGA
** * * *
50346 TTGGTCTTTGACAGGTATATATGAGCCACATTGGTGGGCCTTGTAACACTAAGGCCGAGTTACTC
261 TTGGTCTCCGACAGGTATATATGAGCCACACTGGTGGGCCTCGTAACACTAAGACCGAGTTACTC
50411 TCTCTCCTACAAATGGTATCAGAGCTAGGTTCGATTGGAGTTCGGTGTTGCAGCTGTGCTAAAAA
326 TCTCTCCTACAAATGGTATCAGAGCTAGGTTCGATTGGAGTTCGGTGTTGCAGCTGTGCTAAAAA
50476 AACAATGATGTGGTATTTCAAGAGAA
391 AACAATGATGTGGTATTTCAAGAGAA
*
50502 AGAAAAAAAAACAACTGGGTGCACAGATGGTGCAGGGTGTGGTTAAGTGTGAACAAGTCCAAAAA
1 AGAAAAAAAAACAACTGGGTGCACAGATGGTGCAGGGTGTGGTGAAGTGTGAACAAGTCCAAAAA
* * *
50567 GAACGGGTCACTTAATTGGTTATCCAAGAAATATCGAGTTAGCCACACGGGGGAGAGCTGTCACA
66 GAACGGGCCACTTAACTGGTTATCCAAGAAATATCGAGTTAGCCACACGAGGGAGAGCTGTCACA
* *
50632 TGTGAACGAGGG-AGTTTGTTGGAGTTCAAATGTGATTGTCGCATCCCACATCAC-AAAGGAATG
131 TGTGAACG-GGGAAGTTTGTTAGAGTTCAAATGTGAGTGTCGCATCCCACATCACAAAAGG-ATG
* * * ** * * *
50695 GGATGTAGAAGTGGGGTATATACCTGAAAGATCCAAGAATACATAGACTTAAGCTTTTGGGTTCA
194 GGATATAAAAATGGCATATATACCTGAAAAATCCAAGAACACATAGACTTAAACTTTTGGGTTCA
* * * *
50760 GATTGGTGTCCGATAGGTATATATGGGCCACACTGGTGGGCCTCGTAACGAC-GAGACCG-GATT
259 GATTGGTCTCCGACAGGTATATATGAGCCACACTGGTGGGCCTCGTAAC-ACTAAGACCGAG-TT
*
50823 GCTCTCTCTCCTACA
322 ACTCTCTCTCCTACA
50838 TATGCTAACT
Statistics
Matches: 300, Mismatches: 32, Indels: 8
0.88 0.09 0.02
Matches are distributed among these distances:
415 6 0.02
416 289 0.96
417 5 0.02
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.25
Consensus pattern (416 bp):
AGAAAAAAAAACAACTGGGTGCACAGATGGTGCAGGGTGTGGTGAAGTGTGAACAAGTCCAAAAA
GAACGGGCCACTTAACTGGTTATCCAAGAAATATCGAGTTAGCCACACGAGGGAGAGCTGTCACA
TGTGAACGGGGAAGTTTGTTAGAGTTCAAATGTGAGTGTCGCATCCCACATCACAAAAGGATGGG
ATATAAAAATGGCATATATACCTGAAAAATCCAAGAACACATAGACTTAAACTTTTGGGTTCAGA
TTGGTCTCCGACAGGTATATATGAGCCACACTGGTGGGCCTCGTAACACTAAGACCGAGTTACTC
TCTCTCCTACAAATGGTATCAGAGCTAGGTTCGATTGGAGTTCGGTGTTGCAGCTGTGCTAAAAA
AACAATGATGTGGTATTTCAAGAGAA
Found at i:56445 original size:22 final size:22
Alignment explanation
Indices: 56415--56624 Score: 111
Period size: 22 Copynumber: 9.5 Consensus size: 22
56405 GTGATCTCAT
*
56415 CCTCATTATGAAGTTTTGGTAA
1 CCTCCTTATGAAGTTTTGGTAA
* * * **
56437 TCTCCTTATCAAATTCCGGTAA
1 CCTCCTTATGAAGTTTTGGTAA
*
56459 CCTCCCTATGAAGTTTTGGTAA
1 CCTCCTTATGAAGTTTTGGTAA
* * **
56481 CCTCCTTATCAAATTCCGGTAA
1 CCTCCTTATGAAGTTTTGGTAA
* * * *
56503 CCTCCCTATGAAATTCTGGTAT
1 CCTCCTTATGAAGTTTTGGTAA
* * *
56525 CC-CCACTATGAAATTGTGGTAA
1 CCTCC-TTATGAAGTTTTGGTAA
* * *
56547 CTTCAC-TATGAAATTATGGTAA
1 CCTC-CTTATGAAGTTTTGGTAA
* * * *
56569 CTTCCCTATGAAATTTGGGTAA
1 CCTCCTTATGAAGTTTTGGTAA
** *
56591 CCTCCCAATGAAATTATT-GTAA
1 CCTCCTTATGAAGTT-TTGGTAA
*
56613 CCTCCCTATGAA
1 CCTCCTTATGAA
56625 CCAACTAATT
Statistics
Matches: 152, Mismatches: 31, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
21 3 0.02
22 146 0.96
23 2 0.01
24 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (22 bp):
CCTCCTTATGAAGTTTTGGTAA
Found at i:56486 original size:44 final size:44
Alignment explanation
Indices: 56421--56621 Score: 208
Period size: 44 Copynumber: 4.6 Consensus size: 44
56411 TCATCCTCAT
* * *
56421 TATGAAGTTTTGGTAATCTCCTTATCAAATTCCGGTAACCTCCC
1 TATGAAATTTTGGTAACCTCCCTATCAAATTCCGGTAACCTCCC
* *
56465 TATGAAGTTTTGGTAACCTCCTTATCAAATTCCGGTAACCTCCC
1 TATGAAATTTTGGTAACCTCCCTATCAAATTCCGGTAACCTCCC
* * * ** * *
56509 TATGAAATTCTGGTATCC-CCACTATGAAATTGTGGTAACTTCAC
1 TATGAAATTTTGGTAACCTCC-CTATCAAATTCCGGTAACCTCCC
* * * **
56553 TATGAAATTATGGTAACTTCCCTATGAAATTTGGGTAACCTCCC
1 TATGAAATTTTGGTAACCTCCCTATCAAATTCCGGTAACCTCCC
*
56597 AATGAAATTATT-GTAACCTCCCTAT
1 TATGAAATT-TTGGTAACCTCCCTAT
56622 GAACCAACTA
Statistics
Matches: 134, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
43 2 0.01
44 129 0.96
45 3 0.02
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (44 bp):
TATGAAATTTTGGTAACCTCCCTATCAAATTCCGGTAACCTCCC
Found at i:56622 original size:66 final size:65
Alignment explanation
Indices: 56432--56624 Score: 192
Period size: 66 Copynumber: 2.9 Consensus size: 65
56422 ATGAAGTTTT
* * * * * * * *
56432 GGTAATCTCCTTATCAAATTCCGGTAACCTCCCTATGAAGTTTTGGTAACCTCCTTATCAAATTC
1 GGTAACCTCCCTATGAAATTCTGGTAACCTCCCTATGAAATTTT-GTAACCTCCCTATGAAATTA
56497 C
65 C
* * * *
56498 GGTAACCTCCCTATGAAATTCTGGTATCC-CCACTATGAAATTGTGGTAACTTCACTATGAAATT
1 GGTAACCTCCCTATGAAATTCTGGTAACCTCC-CTATGAAATT-TTGTAACCTCCCTATGAAATT
*
56562 AT
64 AC
* *
56564 GGTAACTTCCCTATGAAATT-TGGGTAACCTCCCAATGAAATTATTGTAACCTCCCTATGAA
1 GGTAACCTCCCTATGAAATTCT-GGTAACCTCCCTATGAAATT-TTGTAACCTCCCTATGAA
56625 CCAACTAATT
Statistics
Matches: 103, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
65 3 0.03
66 97 0.94
67 3 0.03
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (65 bp):
GGTAACCTCCCTATGAAATTCTGGTAACCTCCCTATGAAATTTTGTAACCTCCCTATGAAATTAC
Found at i:63927 original size:26 final size:28
Alignment explanation
Indices: 63874--63927 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
63864 TTACTCAACT
**
63874 AAAAACTCTATTTTTATTTTTCTGTAAA
1 AAAAACTCTATTTTTATTTTAATGTAAA
63902 AAAAACTCTATTTTTA-TTTAAT-TAAA
1 AAAAACTCTATTTTTATTTTAATGTAAA
63928 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 4 0.17
28 16 0.67
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (28 bp):
AAAAACTCTATTTTTATTTTAATGTAAA
Done.