Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011568.1 Corchorus capsularis cultivar CVL-1 contig11589, 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: 64468
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3886 original size:49 final size:49
Alignment explanation
Indices: 3827--3924 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
3817 AAATGATGTG
* *
3827 GCATTGATGGACTATTTGACGCGATATTATTAGGTAGATCACGGATGAT
1 GCATTGATGGACTAGTTGACGCGATATTATTAGGTAGATCACAGATGAT
3876 GCATTGATGGACTAGTTGACGCGATATTATTAGGTAGATCACAGATGAT
1 GCATTGATGGACTAGTTGACGCGATATTATTAGGTAGATCACAGATGAT
3925 TTGATGGACC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.32
Consensus pattern (49 bp):
GCATTGATGGACTAGTTGACGCGATATTATTAGGTAGATCACAGATGAT
Found at i:5223 original size:20 final size:19
Alignment explanation
Indices: 5189--5228 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
5179 TAAAAAGTAC
5189 AATTAATTCAGAAAAACAA
1 AATTAATTCAGAAAAACAA
*
5208 AATTTATTCAGAAAAACAA
1 AATTAATTCAGAAAAACAA
5227 AA
1 AA
5229 CATATCGGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.23
Consensus pattern (19 bp):
AATTAATTCAGAAAAACAA
Found at i:11309 original size:87 final size:85
Alignment explanation
Indices: 11208--11380 Score: 283
Period size: 87 Copynumber: 2.0 Consensus size: 85
11198 GGTCAATCGC
* *
11208 CGATCAAACCGGTTGTTGACCGGGCCAAAACCCTCCCGGAAAACCCCACTCTCCGGGGACCGGAT
1 CGATCAAACCGGTTGTTGACCGGGCCAAAACCCTCCCAGAAAACCCCACTCTCC--GGACAGGAT
11273 AGGCCTCCGGGTCCCAGTTAAA
64 AGGCCTCCGGGTCCCAGTTAAA
*
11295 CGATCAAACTGGTTGTTGACCGGGCCAAAACCCTCCCAGAAAACCCCACTCTCCGGACAGGATAG
1 CGATCAAACCGGTTGTTGACCGGGCCAAAACCCTCCCAGAAAACCCCACTCTCCGGACAGGATAG
* *
11360 GTCTCTGGGTCCCAGTTAAA
66 GCCTCCGGGTCCCAGTTAAA
11380 C
1 C
11381 CGGTCCGACC
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
85 29 0.36
87 52 0.64
ACGTcount: A:0.25, C:0.34, G:0.24, T:0.17
Consensus pattern (85 bp):
CGATCAAACCGGTTGTTGACCGGGCCAAAACCCTCCCAGAAAACCCCACTCTCCGGACAGGATAG
GCCTCCGGGTCCCAGTTAAA
Found at i:14560 original size:19 final size:20
Alignment explanation
Indices: 14538--14579 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
14528 TCTTTTATTT
*
14538 AAATAAAGAT-TACTTTTTA
1 AAATAAAAATATACTTTTTA
*
14557 AAATAAAAATATATTTTTTA
1 AAATAAAAATATACTTTTTA
14577 AAA
1 AAA
14580 AAATTAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
AAATAAAAATATACTTTTTA
Found at i:14621 original size:20 final size:20
Alignment explanation
Indices: 14596--14636 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
14586 AGAAAAAAAT
14596 AGAATATTGACTCAGAATTC
1 AGAATATTGACTCAGAATTC
14616 AGAATATTGACTCAGAATTC
1 AGAATATTGACTCAGAATTC
14636 A
1 A
14637 CGAGTTGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (20 bp):
AGAATATTGACTCAGAATTC
Found at i:16189 original size:30 final size:28
Alignment explanation
Indices: 16154--16213 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
16144 GCTCTATAAT
*
16154 TTTTTTTTCAATATTATAAGCTGAATTTTA
1 TTTTTTATCAATA--ATAAGCTGAATTTTA
*
16184 TTTTTTATGAATAATAAGCTGAATTTTA
1 TTTTTTATCAATAATAAGCTGAATTTTA
16212 TT
1 TT
16214 GGTTTCAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 17 0.61
30 11 0.39
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (28 bp):
TTTTTTATCAATAATAAGCTGAATTTTA
Found at i:25370 original size:20 final size:20
Alignment explanation
Indices: 25325--25364 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
25315 ATACTATTCT
*
25325 CAAAAAAAAATTAATTTAAC
1 CAAAAAAAAATTAATCTAAC
25345 CAAAAAAAAATTAATACTAA
1 CAAAAAAAAATTAAT-CTAA
25365 GAAAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (20 bp):
CAAAAAAAAATTAATCTAAC
Found at i:25370 original size:21 final size:20
Alignment explanation
Indices: 25326--25370 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
25316 TACTATTCTC
* *
25326 AAAAAAAAATTAATTTAACC
1 AAAAAAAAATTAATCTAACA
*
25346 AAAAAAAAATTAATACTAAGA
1 AAAAAAAAATTAAT-CTAACA
25367 AAAA
1 AAAA
25371 TTAAGTTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAAAAAAATTAATCTAACA
Found at i:30014 original size:73 final size:74
Alignment explanation
Indices: 29926--30076 Score: 243
Period size: 74 Copynumber: 2.1 Consensus size: 74
29916 ATTAAGGAAT
* * * *
29926 GTGTAATTAC-GAAAAAGGTAGAAGGAAAAGGAATGGGGGAAACTCATAGAGGGGCTTTTTAGTC
1 GTGTAATTACAAAAAAAGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAAGGGCATTTTAGTC
29990 ATCC-GAAAA
66 A-CCTGAAAA
29999 GTGTAATTACAAAAAAAGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAAGGGCATTTTAGTC
1 GTGTAATTACAAAAAAAGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAAGGGCATTTTAGTC
30064 ACCTGAAAA
66 ACCTGAAAA
30073 GTGT
1 GTGT
30077 GAAAAGATCA
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
73 12 0.17
74 60 0.83
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (74 bp):
GTGTAATTACAAAAAAAGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAAGGGCATTTTAGTC
ACCTGAAAA
Found at i:32233 original size:12 final size:12
Alignment explanation
Indices: 32216--32245 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
32206 CTTTCTTCTG
32216 ATTTCATCACCA
1 ATTTCATCACCA
32228 ATTTCATCACCA
1 ATTTCATCACCA
32240 ATTTCA
1 ATTTCA
32246 ACTTTTTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (12 bp):
ATTTCATCACCA
Found at i:32926 original size:45 final size:45
Alignment explanation
Indices: 32868--32953 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
32858 AAGACATCAA
* * *
32868 TATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACCT-CCATATGAAATATTGATAACCAACAC
* *
32913 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCA
32954 CGTTATGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAACAC
Found at i:32947 original size:22 final size:22
Alignment explanation
Indices: 32825--33288 Score: 142
Period size: 22 Copynumber: 20.9 Consensus size: 22
32815 ATCCACTTCT
*
32825 TATGAAATTTTGTTAACCTCCCA
1 TATGAAATTTTGATAACCT-CCA
* * *
32848 -A-GGAATTTTGA-AGACATCAA
1 TATGAAATTTTGATA-ACCTCCA
*
32868 TATGAAATTTTGATAACTTCCCA
1 TATGAAATTTTGATAACCT-CCA
**
32891 -ATGAAATTTTGATAACCAACA
1 TATGAAATTTTGATAACCTCCA
* *
32912 CTATGAGATGTTGATAACCTCCA
1 -TATGAAATTTTGATAACCTCCA
* * * **
32935 TATGATATATTGATAACCACGT
1 TATGAAATTTTGATAACCTCCA
* *
32957 TATGAAAATTT-AAAAGCCTCCA
1 TATGAAATTTTGATAA-CCTCCA
32979 TATG-AATTGTT-AGTAA--TCACA
1 TATGAAATT-TTGA-TAACCTC-CA
*
33000 CTCTGAAATTTTGATAA--TCACA
1 -TATGAAATTTTGATAACCTC-CA
* *
33022 CTACGAAATTTTGATAAATCTTCC-
1 -TATGAAATTTTGAT-AA-CCTCCA
* *
33046 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCA
* *
33069 TATAAAATTTTGATAACTTCCTTA
1 TATGAAATTTTGATAACCTCC--A
*
33093 TAACTACAAATTTTGATAACCTCTC-
1 T-A-T-GAAATTTTGATAACCTC-CA
** *
33118 TATGATTTTTTGATAGCCT-CA
1 TATGAAATTTTGATAACCTCCA
* * * *
33139 TTATGAATTTTTGTTAATCTCCC
1 -TATGAAATTTTGATAACCTCCA
* * *
33162 TATGAAATTTTGATCTACATAC-
1 TATGAAATTTTGAT-AACCTCCA
*
33184 TATG-AATCTTTGATAACC-CTCT
1 TATGAAAT-TTTGATAACCTC-CA
* * **
33206 TATGAAAATTTGA-AAACTAAA
1 TATGAAATTTTGATAACCTCCA
*
33227 CTATGAAATTTTGATATCCTCC-
1 -TATGAAATTTTGATAACCTCCA
* *
33249 -CTGAAATTTTGATTA-CTCCA
1 TATGAAATTTTGATAACCTCCA
* * *
33269 TAATAAAAGTTTAATAACCT
1 T-ATGAAATTTTGATAACCT
33289 TCCTAATTTG
Statistics
Matches: 327, Mismatches: 74, Indels: 80
0.68 0.15 0.17
Matches are distributed among these distances:
19 4 0.01
20 18 0.06
21 31 0.09
22 180 0.55
23 70 0.21
24 2 0.01
25 3 0.01
26 3 0.01
27 15 0.05
28 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:33053 original size:23 final size:23
Alignment explanation
Indices: 33027--33084 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
33017 TCACACTACG
* *
33027 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
33050 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
33073 AAATTTTGATAA
1 AAATTTTGATAA
33085 CTTCCTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.40
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:33546 original size:22 final size:22
Alignment explanation
Indices: 33342--33591 Score: 142
Period size: 22 Copynumber: 11.5 Consensus size: 22
33332 AGAAATACCA
33342 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCAC-T
* * * *
33365 -TTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * * * *
33386 TTATAAAATTTTGTTGATCCCT
1 CTATGAAATTTTGATAATCACT
* *
33408 CTATCAAATTCTGATAATCACAT
1 CTATGAAATTTTGATAATCAC-T
* * * *
33431 -TATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACT
* *
33452 CTTTGAAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATC-ACT
*
33474 CTATGAAATTTTGATAATC-TT
1 CTATGAAATTTTGATAATCACT
33495 CTTAT-AAATTTTGATAATCTGATCT
1 C-TATGAAATTTTGATAATC--A-CT
*
33520 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCACT
* *
33542 CTATGAGA-TTTGATAATC-TT
1 CTATGAAATTTTGATAATCACT
* * *
33562 CTATCAAATTTTGGTACTC-CT
1 CTATGAAATTTTGATAATCACT
33583 -TATGAAATT
1 CTATGAAATT
33592 AAGACTTTTA
Statistics
Matches: 173, Mismatches: 41, Indels: 29
0.71 0.17 0.12
Matches are distributed among these distances:
20 15 0.09
21 39 0.23
22 98 0.57
23 3 0.02
24 3 0.02
25 15 0.09
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:33794 original size:22 final size:22
Alignment explanation
Indices: 33766--33904 Score: 147
Period size: 22 Copynumber: 6.3 Consensus size: 22
33756 TTGTGATGAT
*
33766 TAACCACCATATGAAATTTTGG
1 TAACCACCATATGAAATTTTGA
*
33788 TAACCACAATATGAAATTTTGA
1 TAACCACCATATGAAATTTTGA
** *
33810 TAACTTCCATATGAAATTTTGG
1 TAACCACCATATGAAATTTTGA
33832 TAACCA-CACTATGAAATTTTGA
1 TAACCACCA-TATGAAATTTTGA
* * *
33854 TAACCTCC-TCATGAAATTATAA
1 TAACCACCAT-ATGAAATTTTGA
* * *
33876 TAATCATCTTATGAAATTTTGA
1 TAACCACCATATGAAATTTTGA
33898 TAACCAC
1 TAACCAC
33905 ATAGAGACAA
Statistics
Matches: 94, Mismatches: 19, Indels: 8
0.78 0.16 0.07
Matches are distributed among these distances:
21 3 0.03
22 89 0.95
23 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (22 bp):
TAACCACCATATGAAATTTTGA
Found at i:33825 original size:44 final size:44
Alignment explanation
Indices: 33766--33902 Score: 170
Period size: 44 Copynumber: 3.1 Consensus size: 44
33756 TTGTGATGAT
*
33766 TAACCACCATATGAAATTTTGGTAACCACAATATGAAATTTTGA
1 TAACCTCCATATGAAATTTTGGTAACCACAATATGAAATTTTGA
* *
33810 TAACTTCCATATGAAATTTTGGTAACCACACTATGAAATTTTGA
1 TAACCTCCATATGAAATTTTGGTAACCACAATATGAAATTTTGA
* ** * *
33854 TAACCTCC-TCATGAAATTATAATAATCATC-TTATGAAATTTTGA
1 TAACCTCCAT-ATGAAATTTTGGTAACCA-CAATATGAAATTTTGA
33898 TAACC
1 TAACC
33903 ACATAGAGAC
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
43 1 0.01
44 80 0.98
45 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (44 bp):
TAACCTCCATATGAAATTTTGGTAACCACAATATGAAATTTTGA
Found at i:33868 original size:66 final size:67
Alignment explanation
Indices: 33766--33905 Score: 162
Period size: 66 Copynumber: 2.1 Consensus size: 67
33756 TTGTGATGAT
* * * *
33766 TAACCAC-CATATGAAATTTTGGTAACCACAATATGAAATTTTGATAA-CTTCCATATGAAATTT
1 TAACCACACATATGAAATTTTGATAACCACAATATGAAATTATAATAATCAT-CATATGAAATTT
*
33829 TGG
65 TGA
* * *
33832 TAACCACAC-TATGAAATTTTGATAACCTC-CTCATGAAATTATAATAATCATCTTATGAAATTT
1 TAACCACACATATGAAATTTTGATAACCACAAT-ATGAAATTATAATAATCATCATATGAAATTT
33895 TGA
65 TGA
33898 TAACCACA
1 TAACCACA
33906 TAGAGACAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
65 1 0.02
66 59 0.94
67 3 0.05
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.34
Consensus pattern (67 bp):
TAACCACACATATGAAATTTTGATAACCACAATATGAAATTATAATAATCATCATATGAAATTTT
GA
Found at i:34464 original size:31 final size:31
Alignment explanation
Indices: 34429--34494 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
34419 TGGCAATTTA
**
34429 GAAATATGATTTTTTAAA-AAGGGTACAATAG
1 GAAATAT-ATTTTAAAAATAAGGGTACAATAG
* *
34460 GAAATATATTTTAAAAATAAGGGTATAATCG
1 GAAATATATTTTAAAAATAAGGGTACAATAG
34491 GAAA
1 GAAA
34495 ACATAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.48, C:0.03, G:0.18, T:0.30
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATAG
Found at i:34721 original size:96 final size:98
Alignment explanation
Indices: 34611--34790 Score: 256
Period size: 98 Copynumber: 1.9 Consensus size: 98
34601 TTATACCCCA
** * ** *
34611 TTTTTCAAATATATTTCAAAATTGTCATT-A-TTAAAATATTTTAATTATGTCATTATTAAAATA
1 TTTTTCAAATATATTTCAAAATTGTCATTAAGAAAAAATATTTTAAGTATACCATTAGTAAAATA
34674 TAATTTTATGTAATTTTTTTCCGATTGTACTAT
66 TAATTTTATGTAATTTTTTTCCGATTGTACTAT
**
34707 TTTTTCAAATATATTTTTAAATTGTCATTAAGAAAAAATATTTTAAGTATACCATTAGTAAAATA
1 TTTTTCAAATATATTTCAAAATTGTCATTAAGAAAAAATATTTTAAGTATACCATTAGTAAAATA
* *
34772 TAATTTTGTGTACTTTTTT
66 TAATTTTATGTAATTTTTT
34791 CAAATATATT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
96 27 0.38
97 1 0.01
98 44 0.61
ACGTcount: A:0.37, C:0.07, G:0.06, T:0.51
Consensus pattern (98 bp):
TTTTTCAAATATATTTCAAAATTGTCATTAAGAAAAAATATTTTAAGTATACCATTAGTAAAATA
TAATTTTATGTAATTTTTTTCCGATTGTACTAT
Found at i:35826 original size:546 final size:541
Alignment explanation
Indices: 34753--35834 Score: 1767
Period size: 546 Copynumber: 2.0 Consensus size: 541
34743 AATATTTTAA
34753 GTATACCATTAGTAAAATATAATTTTGTGTACTTTTTTCAAATATATTTCTAAGTTCATAATCTT
1 GTATACCATTAGTAAAATATAATTTTGTGTACTTTTTTCAAATATATTTCTAAGTTCATAATCTT
*
34818 TACAAAATATAATTTTTTTAATTAGAAACTAATTCTGAAAAAGGTTGAAAAGCGAGATTAGAAGT
66 TACAAAATATAATTTTTTTAATTAGAAACTAATTCGGAAAAAGGTTGAAAAGCGAGATTAGAAGT
* * *
34883 GTGAGAAGCCCTTCATTCTTTTTGGCGTTGAGTTATATATTTTTTATTAGTGTTGTAGCCCGAAA
131 GTGAGAAGCCCTTCATTCTTTTTGGCGTTGAGTTATATATTTTTTAATAGTATTGTAGCCCAAAA
* *
34948 TTGAGGAGAAATTTCTCAAGTCAATTTTTGCAAAGTTTGAGCTGAAATCGTGTATTGACCATCAC
196 TTGAGGAGAAATTTCTCAAGTCAATTTTTGCAAAGTTTGAGCTGAAATCGTGTACTAACCATCAC
* *
35013 GGTTTTTGACTAAAAACACGTTCCGGAGCCCCGGTTCCATTTTGCAAGATTTTGGGAGCTAAGTC
261 GGTTTTTGACTAAAAACACGTTCCAGAGCCCCGGTTCCATTTTGCAAGATTTTGGGAGCCAAGTC
* *
35078 TCATTGAAAATCTATATCCATCTAACCAAATCTTACCCATATTGGATTTAAGGATTTGTTTTTAC
326 TCATTGAAAATCTATATCCATATAACCAAATCTTACCCACATTGGATTTAAGGATTTGTTTTTAC
*
35143 GAGCATATGAATCATGTTTCGATTTAATTAGGAACTAATTCAGAAAAAAATAGGAAAACGAGATT
391 GAGCATATGAATCATGTTTCGATTCAATTAGGAACTAATTCAGAAAAAAATAGGAAAACGAGATT
*
35208 AGAAGCGTGAATAGCCTTTCAATCTTTTTGGTGTTGAATTATATATTTTTATGATTATCGTGGCT
456 AAAAGCGTGAATAGCCTTTCAATCTTTTTGGTGTTGAATTATATATTTTTATGATTATCGTGGCT
35273 AAAAATTGAAGAAAATTATTT
521 AAAAATTGAAGAAAATTATTT
*
35294 GTATACCATTATTAAAATATAATTTTGTGTACTTTTTTTCAAATATATTTCTAAGTGTTCATAAT
1 GTATACCATTAGTAAAATATAATTTTGTGTAC-TTTTTTCAAATATATTTCTAA--GTTCATAAT
* * *
35359 TTTTACAAAATATAATTTTTTTAATTAGAAATTAATTCGGAAAAAGGTTGGAAAAGCGATATTAG
63 CTTTACAAAATATAATTTTTTTAATTAGAAACTAATTCGGAAAAAGGTT-GAAAAGCGAGATTAG
*
35424 AAGTGTGAGAAGCCCTTCATTCTTTTTGGCGTTGAGTTATATATTTTTTAATAGTATTGTAGGCC
127 AAGTGTGAGAAGCCCTTCATTCTTTTTGGCGTTGAGTTATATATTTTTTAATAGTATTGTAGCCC
* *
35489 AAAATTGAGGAGAAATTTCTCAGGTCAATTTTTGCAAAGTTTTAGCTGAAATCGTGTACTAACCA
192 AAAATTGAGGAGAAATTTCTCAAGTCAATTTTTGCAAAGTTTGAGCTGAAATCGTGTACTAACCA
* * * *
35554 TCACGATTTTTTGACTAAAAACACGTTTCAGAGCCTCGGTT-CAGTTTTGCACGATTTTGGGAGC
257 TCACG-GTTTTTGACTAAAAACACGTTCCAGAGCCCCGGTTCCA-TTTTGCAAGATTTTGGGAGC
* *
35618 CAAGTCTCATTGAAAATCTATATCCATATAACCAAATTTTACCCACATTGGATTTAAGTATTTGT
320 CAAGTCTCATTGAAAATCTATATCCATATAACCAAATCTTACCCACATTGGATTTAAGGATTTGT
*
35683 TTTTACGAGCATATATGAATCATGTTTCGATTCAATTAGGAATTAATTC-GAAAAAAATAGGAAA
385 TTTTACGAGC--ATATGAATCATGTTTCGATTCAATTAGGAACTAATTCAGAAAAAAATAGG-AA
* * * *
35747 AACGATATTAAAAGTGTGAATAGCCTTTCAATTTTTTTGGTGTTGAATTATAT-TTTTT-TTATT
447 AACGAGATTAAAAGCGTGAATAGCCTTTCAATCTTTTTGGTGTTGAATTATATATTTTTATGATT
* *
35810 ATCGTGGCTGAAAATTGAGGAAAAT
512 ATCGTGGCTAAAAATTGAAGAAAAT
35835 ACTTTCGGGT
Statistics
Matches: 500, Mismatches: 32, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
541 31 0.06
542 21 0.04
544 55 0.11
545 143 0.29
546 147 0.29
547 17 0.03
548 86 0.17
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.38
Consensus pattern (541 bp):
GTATACCATTAGTAAAATATAATTTTGTGTACTTTTTTCAAATATATTTCTAAGTTCATAATCTT
TACAAAATATAATTTTTTTAATTAGAAACTAATTCGGAAAAAGGTTGAAAAGCGAGATTAGAAGT
GTGAGAAGCCCTTCATTCTTTTTGGCGTTGAGTTATATATTTTTTAATAGTATTGTAGCCCAAAA
TTGAGGAGAAATTTCTCAAGTCAATTTTTGCAAAGTTTGAGCTGAAATCGTGTACTAACCATCAC
GGTTTTTGACTAAAAACACGTTCCAGAGCCCCGGTTCCATTTTGCAAGATTTTGGGAGCCAAGTC
TCATTGAAAATCTATATCCATATAACCAAATCTTACCCACATTGGATTTAAGGATTTGTTTTTAC
GAGCATATGAATCATGTTTCGATTCAATTAGGAACTAATTCAGAAAAAAATAGGAAAACGAGATT
AAAAGCGTGAATAGCCTTTCAATCTTTTTGGTGTTGAATTATATATTTTTATGATTATCGTGGCT
AAAAATTGAAGAAAATTATTT
Found at i:38067 original size:30 final size:31
Alignment explanation
Indices: 38013--38077 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
38003 AACTTTATGT
* *
38013 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCCTATTTTTAAAACATA
38044 TTTCCAATTGTACCCCT-TTTTTAAAACATA
1 TTTCCAATTGTACCCCTATTTTTAAAACATA
38074 TTTC
1 TTTC
38078 TAAATTGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.28, C:0.22, G:0.05, T:0.46
Consensus pattern (31 bp):
TTTCCAATTGTACCCCTATTTTTAAAACATA
Found at i:38084 original size:31 final size:31
Alignment explanation
Indices: 38019--38085 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 31
38009 ATGTTTTCCG
* *
38019 ATTGTACCCTTATTTTTAAAACATATTTCCA
1 ATTGTACCCCTATTTTTAAAACATATTTCAA
38050 ATTGTACCCCT-TTTTTAAAACATATTTCTAA
1 ATTGTACCCCTATTTTTAAAACATATTTC-AA
38081 ATTGT
1 ATTGT
38086 CATTATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.31, C:0.18, G:0.04, T:0.46
Consensus pattern (31 bp):
ATTGTACCCCTATTTTTAAAACATATTTCAA
Found at i:38201 original size:30 final size:31
Alignment explanation
Indices: 38147--38211 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
38137 AACTTTATGT
* *
38147 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCATTATTTTTAAAACATA
38178 TTTCCAATTGTACCATT-TTTTTAAAACATA
1 TTTCCAATTGTACCATTATTTTTAAAACATA
38208 TTTC
1 TTTC
38212 TTTTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCATTATTTTTAAAACATA
Found at i:40863 original size:29 final size:31
Alignment explanation
Indices: 40803--40863 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
40793 AACTTTATGT
* * *
40803 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTATACCCTTATTTTTAAAAAATA
40834 TTTCCAATTATACCC-T-TTTTTAAAAAATA
1 TTTCCAATTATACCCTTATTTTTAAAAAATA
40863 T
1 T
40864 ATTTCTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 13 0.48
30 1 0.04
31 13 0.48
ACGTcount: A:0.33, C:0.18, G:0.03, T:0.46
Consensus pattern (31 bp):
TTTCCAATTATACCCTTATTTTTAAAAAATA
Found at i:40868 original size:31 final size:31
Alignment explanation
Indices: 40803--40863 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
40793 AACTTTATGT
* * *
40803 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTATACCCTTATTTTAAAAACATA
40834 TTTCCAATTATACCCTT-TTTTAAAAA-ATA
1 TTTCCAATTATACCCTTATTTTAAAAACATA
40863 T
1 T
40864 ATTTCTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 4 0.15
30 8 0.30
31 15 0.56
ACGTcount: A:0.33, C:0.18, G:0.03, T:0.46
Consensus pattern (31 bp):
TTTCCAATTATACCCTTATTTTAAAAACATA
Found at i:44384 original size:22 final size:22
Alignment explanation
Indices: 44343--44384 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
44333 GACAAACCCG
**
44343 TAACCCGAATAATCTGAGAAGT
1 TAACCCGAATAATCCAAGAAGT
*
44365 TAACCCGAATGATCCAAGAA
1 TAACCCGAATAATCCAAGAA
44385 CATTATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (22 bp):
TAACCCGAATAATCCAAGAAGT
Found at i:44961 original size:2 final size:2
Alignment explanation
Indices: 44954--45017 Score: 58
Period size: 2 Copynumber: 32.0 Consensus size: 2
44944 CTCGTACTTT
* * * *
44954 TA TA TA TA GTA TA GA TA GA TA TA GA TA TA TA TA TA TA TA GA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
44997 TA GA TA GA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
45018 ATGTAACATG
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
1 1 0.02
2 45 0.94
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (2 bp):
TA
Found at i:49023 original size:2 final size:2
Alignment explanation
Indices: 49016--49060 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
49006 GGTATTGCAG
49016 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
49059 AT
1 AT
49061 TATTTTAGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:51577 original size:21 final size:21
Alignment explanation
Indices: 51519--51590 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 21
51509 CATACTATAG
* *
51519 TATCAAAAAATTATAGAGAGAT
1 TATC-AAAAATCATAGAGAGGT
* *
51541 TAACAAAATCTCATAGAGAGGT
1 TATCAAAA-ATCATAGAGAGGT
51563 TATCAAAAATCATAG-GAAGGT
1 TATCAAAAATCATAGAG-AGGT
51584 TA-CAAAA
1 TATCAAAA
51591 TTTCGTAGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 6 0.14
21 16 0.38
22 20 0.48
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.24
Consensus pattern (21 bp):
TATCAAAAATCATAGAGAGGT
Found at i:51658 original size:21 final size:21
Alignment explanation
Indices: 51605--51707 Score: 91
Period size: 22 Copynumber: 4.8 Consensus size: 21
51595 GTAGGAAGGT
* *
51605 TTATTAAAATTTCATATGGTGT
1 TTATCAAAATTTCATA-GGTGA
* *
51627 TTATCACAATTTCATAGGTAA
1 TTATCAAAATTTCATAGGTGA
*
51648 ATATCAAAATTTCATAGCGTGA
1 TTATCAAAATTTCATAG-GTGA
* *
51670 TTATCAAAATTTAATGGGAT-A
1 TTATCAAAATTTCATAGG-TGA
*
51691 GTTATCAAAAATTCATA
1 -TTATCAAAATTTCATA
51708 AAAAATTCAA
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
21 20 0.31
22 45 0.69
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGTGA
Found at i:53571 original size:40 final size:40
Alignment explanation
Indices: 53516--53596 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
53506 TGTCCTAAAG
53516 TTAGCAATAAAAAGTAGATATTAGTTTGTACATGGACAGA
1 TTAGCAATAAAAAGTAGATATTAGTTTGTACATGGACAGA
53556 TTAGCAATAAAAAGTAGATATTAGTTTGTACATGGACAGA
1 TTAGCAATAAAAAGTAGATATTAGTTTGTACATGGACAGA
53596 T
1 T
53597 GCAATAGCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (40 bp):
TTAGCAATAAAAAGTAGATATTAGTTTGTACATGGACAGA
Found at i:54814 original size:28 final size:28
Alignment explanation
Indices: 54755--54814 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
54745 TATTTTTTAG
* * * *
54755 ATAAATACTTGAGTTTTTTTGAGGGAAG
1 ATAAATACTTGAGTTCTGTTGAGGAAAA
54783 ATAAATACTTGAGTTCTGTTG-GGAAATA
1 ATAAATACTTGAGTTCTGTTGAGGAAA-A
54811 ATAA
1 ATAA
54815 TTAAAAGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (28 bp):
ATAAATACTTGAGTTCTGTTGAGGAAAA
Found at i:55220 original size:22 final size:22
Alignment explanation
Indices: 55195--55239 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
55185 TTTTTAATTG
*
55195 AGTAAAATTA-TAAAAGTAAAAT
1 AGTAAAA-TAGTAAAAATAAAAT
55217 AGTAAAATAGTAAAAATAAAAT
1 AGTAAAATAGTAAAAATAAAAT
55239 A
1 A
55240 ATTATAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (22 bp):
AGTAAAATAGTAAAAATAAAAT
Found at i:55246 original size:93 final size:93
Alignment explanation
Indices: 55118--55302 Score: 255
Period size: 93 Copynumber: 2.0 Consensus size: 93
55108 GCTTTTTAAT
* * * * *
55118 TAAATTAGTAATATGGTAAAAATAAAATAGGTATAA-AGATATTTGATTAAATTAAATAAAAATA
1 TAAAATAGTAAAATAGTAAAAATAAAATAAGTATAAGA-ATATTAGATTAAATTAAATAAAAATA
* *
55182 AAGTTTTTAATTGAGTAAAATTATAAAAG
65 AAGTTATTAATTGACTAAAATTATAAAAG
* * *
55211 TAAAATAGTAAAATAGTAAAAATAAAATAATTATAAGAATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATAGTAAAAATAAAATAAGTATAAGAATATTAGATTAAATTAAATAAAAATAA
*
55276 AGTTATTAGTTGACTAAAATTATAAAA
66 AGTTATTAATTGACTAAAATTATAAAA
55303 ATTTATTCAA
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
93 79 0.99
94 1 0.01
ACGTcount: A:0.56, C:0.01, G:0.10, T:0.34
Consensus pattern (93 bp):
TAAAATAGTAAAATAGTAAAAATAAAATAAGTATAAGAATATTAGATTAAATTAAATAAAAATAA
AGTTATTAATTGACTAAAATTATAAAAG
Found at i:61650 original size:79 final size:79
Alignment explanation
Indices: 61518--61692 Score: 264
Period size: 79 Copynumber: 2.2 Consensus size: 79
61508 GAGAGGGTTT
**
61518 GTGATGAAATCAGATCGGTTTGAATCATTAGTGTTCAAGTTGGGCGTTCCGAATCTTCACGCGCC
1 GTGATGAAATCAGATCAATTTGAATCATTAGTGTTCAAGTTGGGCGTTCCGAATCTTCACGCGCC
61583 AACTTGA-GAAGGGA
66 AACTTGAGGAA-GGA
* * *
61597 GTGATGAAATCAGATCAATTTGAATGATTAGTGTTCAAGTTGGGCGTTGCGAATCTTCACGCTCC
1 GTGATGAAATCAGATCAATTTGAATCATTAGTGTTCAAGTTGGGCGTTCCGAATCTTCACGCGCC
*
61662 AACTTGAGGAAGGC
66 AACTTGAGGAAGGA
*
61676 GTGATGGAATCA-ATCAA
1 GTGATGAAATCAGATCAA
61693 GCAGGTCTAC
Statistics
Matches: 88, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
78 5 0.06
79 80 0.91
80 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.28
Consensus pattern (79 bp):
GTGATGAAATCAGATCAATTTGAATCATTAGTGTTCAAGTTGGGCGTTCCGAATCTTCACGCGCC
AACTTGAGGAAGGA
Found at i:64407 original size:2 final size:2
Alignment explanation
Indices: 64400--64463 Score: 101
Period size: 2 Copynumber: 31.5 Consensus size: 2
64390 TTTTGATCAC
* *
64400 TA TA TA TA TA TA TGA TC CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
64443 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
64464 TAGTC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
2 55 0.96
3 2 0.04
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Done.