Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014650.1 Corchorus capsularis cultivar CVL-1 contig14671, 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: 93320
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Found at i:3152 original size:20 final size:18
Alignment explanation
Indices: 3132--3168 Score: 51
Period size: 16 Copynumber: 2.1 Consensus size: 18
3122 TACCCAGCCA
3132 AAAATATTGATACAAAACC
1 AAAA-ATTGATACAAAACC
3151 --AAATTGATACAAAACC
1 AAAAATTGATACAAAACC
3167 AA
1 AA
3169 TCAGGTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 5
0.76 0.00 0.24
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.59, C:0.16, G:0.05, T:0.19
Consensus pattern (18 bp):
AAAAATTGATACAAAACC
Found at i:3158 original size:16 final size:16
Alignment explanation
Indices: 3137--3168 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3127 AGCCAAAAAT
3137 ATTGATACAAAACCAA
1 ATTGATACAAAACCAA
3153 ATTGATACAAAACCAA
1 ATTGATACAAAACCAA
3169 TCAGGTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.19, G:0.06, T:0.19
Consensus pattern (16 bp):
ATTGATACAAAACCAA
Found at i:4514 original size:22 final size:22
Alignment explanation
Indices: 4431--4521 Score: 85
Period size: 22 Copynumber: 4.1 Consensus size: 22
4421 AATTTTGAAG
* *
4431 ACCTCAATATGAAATTTTGATA
1 ACCTCCATATGAAATATTGATA
* *
4453 ACTTCCCA-ATGAAATTTTGATA
1 ACCT-CCATATGAAATATTGATA
** *
4475 ACCAACATTATGAGATATTGATA
1 ACCTCCA-TATGAAATATTGATA
*
4498 ACCTCCATATGATATATTGATA
1 ACCTCCATATGAAATATTGATA
4520 AC
1 AC
4522 TACGTTATGA
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
21 2 0.04
22 35 0.62
23 19 0.34
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (22 bp):
ACCTCCATATGAAATATTGATA
Found at i:4581 original size:22 final size:22
Alignment explanation
Indices: 4549--4630 Score: 80
Period size: 22 Copynumber: 3.7 Consensus size: 22
4539 AAAACCTCCG
*
4549 TATGAATTGTT-AGTAATCACAC
1 TATGAAATGTTGA-TAATCACAC
*
4571 TCTGAAATGTTGATAATCACAC
1 TATGAAATGTTGATAATCACAC
* *
4593 TATGAAAT-TGTGATAATCTCGC
1 TATGAAATGT-TGATAATCACAC
4615 TATGAAAT-TTCGATAA
1 TATGAAATGTT-GATAA
4631 ATCTTCCTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
21 2 0.04
22 49 0.94
23 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
TATGAAATGTTGATAATCACAC
Found at i:4640 original size:23 final size:22
Alignment explanation
Indices: 4592--4698 Score: 78
Period size: 23 Copynumber: 4.7 Consensus size: 22
4582 GATAATCACA
4592 CTATGAAATTGTGAT-AATC-TC
1 CTATGAAATT-TGATAAATCTTC
4613 GCTATGAAATTTCGATAAATCTTC
1 -CTATGAAATTT-GATAAATCTTC
* *
4637 CTATAAAATTTTGATAAA-CCTC
1 CTATGAAA-TTTGATAAATCTTC
* *
4659 CTTATAAAATTTTGATAACT-TTC
1 C-TATGAAA-TTTGATAAATCTTC
*
4682 TTATGAAATCTTGATAA
1 CTATGAAAT-TTGATAA
4699 CTACAAATTT
Statistics
Matches: 72, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.03
22 30 0.42
23 35 0.49
24 5 0.07
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.40
Consensus pattern (22 bp):
CTATGAAATTTGATAAATCTTC
Found at i:4690 original size:22 final size:22
Alignment explanation
Indices: 4592--4700 Score: 87
Period size: 22 Copynumber: 4.9 Consensus size: 22
4582 GATAATCACA
* *
4592 CTATGAAATTGTGATAA-TCTC
1 CTATGAAATTTTGATAACTTTC
* *
4613 GCTATGAAATTTCGATAAATCTTC
1 -CTATGAAATTTTGATAACT-TTC
* *
4637 CTATAAAATTTTGATAAAC-CTC
1 CTATGAAATTTTGAT-AACTTTC
*
4659 CTTATAAAATTTTGATAACTTTC
1 C-TATGAAATTTTGATAACTTTC
* *
4682 TTATGAAATCTTGATAACT
1 CTATGAAATTTTGATAACT
4701 ACAAATTTTA
Statistics
Matches: 71, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
22 37 0.52
23 30 0.42
24 4 0.06
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (22 bp):
CTATGAAATTTTGATAACTTTC
Found at i:4736 original size:22 final size:22
Alignment explanation
Indices: 4706--4880 Score: 77
Period size: 22 Copynumber: 8.0 Consensus size: 22
4696 TAACTACAAA
* *
4706 TTTTAATAACCTCCCTATGATT
1 TTTTGATAACCTCCCTATGAAT
** *
4728 TTTTGATAACCTCATTATGAGT
1 TTTTGATAACCTCCCTATGAAT
* * *
4750 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCTCCCTATGAAT
* * ** *
4772 TTTTGATCTACAT-ATTATGAAA
1 TTTTGAT-AACCTCCCTATGAAT
* * *
4794 TTTTGATAACC-CTCTTGTGAAA
1 TTTTGATAACCTC-CCTATGAAT
* ** *
4816 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCT-CCCTATGAAT
* * * *
4838 TTTTGATAACCACACTATAAAA
1 TTTTGATAACCTCCCTATGAAT
*
4860 TTTTGATAACCTCCCCATGAA
1 TTTTGATAACCTCCCTATGAA
4881 ATATTTAATG
Statistics
Matches: 114, Mismatches: 33, Indels: 12
0.72 0.21 0.08
Matches are distributed among these distances:
21 5 0.04
22 104 0.91
23 5 0.04
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (22 bp):
TTTTGATAACCTCCCTATGAAT
Found at i:5054 original size:22 final size:22
Alignment explanation
Indices: 5026--5155 Score: 129
Period size: 22 Copynumber: 5.9 Consensus size: 22
5016 CTAAGTGATT
*
5026 CTATGAAATTTTGGTAACCATA
1 CTATGAAATTTTGATAACCATA
* *
5048 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCATA
* * **
5070 CTATGGAATTTTGGTAACCACG
1 CTATGAAATTTTGATAACCATA
* *
5092 CTATGGAATTTTGATAACC-TC
1 CTATGAAATTTTGATAACCATA
* *
5113 CTCATGAAATTATAATAACCAT-
1 CT-ATGAAATTTTGATAACCATA
5135 CTTATGAAATTTTGATAACCA
1 C-TATGAAATTTTGATAACCA
5156 CATAGAGACA
Statistics
Matches: 94, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
21 2 0.02
22 90 0.96
23 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCATA
Found at i:5089 original size:44 final size:43
Alignment explanation
Indices: 5026--5157 Score: 149
Period size: 44 Copynumber: 3.0 Consensus size: 43
5016 CTAAGTGATT
*
5026 CTATGAAATTTTGGTAACCATACTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCAT-CTATGAAATTTTGATAACCACA
* * * *
5070 CTATGGAATTTTGGTAACCACGCTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGGTAACCA-TCTATGAAATTTTGATAACCACA
* **
5113 CTCATGAAATTATAATAACCATCTTATGAAATTTTGATAACCACA
1 CT-ATGAAATTTTGGTAACCATC-TATGAAATTTTGATAACCACA
5158 TAGAGACAAG
Statistics
Matches: 72, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
43 3 0.04
44 69 0.96
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (43 bp):
CTATGAAATTTTGGTAACCATCTATGAAATTTTGATAACCACA
Found at i:5132 original size:66 final size:66
Alignment explanation
Indices: 5026--5156 Score: 149
Period size: 66 Copynumber: 2.0 Consensus size: 66
5016 CTAAGTGATT
* * ** * *
5026 CTATGAAATTTTGGTAACCATACTATGAAATTTTGGTAACCA-CACTATGGAATTTTGGTAACCA
1 CTATGAAATTTTGATAACCATACTATGAAATTATAATAACCATC-CTATGAAATTTTGATAACCA
5090 CG
65 CG
* * *
5092 CTATGGAATTTTGATAACC-TCCTCATGAAATTATAATAACCATCTTATGAAATTTTGATAACCA
1 CTATGAAATTTTGATAACCATACT-ATGAAATTATAATAACCATCCTATGAAATTTTGATAACCA
5156 C
65 C
5157 ATAGAGACAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
65 3 0.06
66 50 0.93
67 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (66 bp):
CTATGAAATTTTGATAACCATACTATGAAATTATAATAACCATCCTATGAAATTTTGATAACCAC
G
Found at i:5345 original size:19 final size:20
Alignment explanation
Indices: 5321--5358 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5311 TACTGACATT
5321 TAAAAT-TTGAAATT-AAAAG
1 TAAAATATT-AAATTCAAAAG
5340 TAAAATATTAAATTCAAAA
1 TAAAATATTAAATTCAAAA
5359 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (20 bp):
TAAAATATTAAATTCAAAAG
Found at i:5701 original size:31 final size:31
Alignment explanation
Indices: 5665--5729 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
5655 GACAATTTCA
*
5665 AAATATGA-TTTAAAGA-AAAGGGTACAATTGG
1 AAATAT-ATTTTAAA-ATAAAGGGTACAATCGG
*
5696 AAATATATTTTAAAATTAAGGGTACAATCGG
1 AAATATATTTTAAAATAAAGGGTACAATCGG
5727 AAA
1 AAA
5730 ACATAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.28
Consensus pattern (31 bp):
AAATATATTTTAAAATAAAGGGTACAATCGG
Found at i:6047 original size:63 final size:63
Alignment explanation
Indices: 5948--6075 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
5938 GACCTAAGTG
5948 ACGATAATTCGAAACTCGCTCTCTAACTTTATAAGTCAAAGGAAACATACTCCAAAAATAGAA
1 ACGATAATTCGAAACTCGCTCTCTAACTTTATAAGTCAAAGGAAACATACTCCAAAAATAGAA
*
6011 ACGATAATTCGAAACTCGCTCTCTAACTTTATAAGTCAAAGGAAACATGCTCCAAAAATAGAA
1 ACGATAATTCGAAACTCGCTCTCTAACTTTATAAGTCAAAGGAAACATACTCCAAAAATAGAA
6074 AC
1 AC
6076 AGAGCAATCA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.23
Consensus pattern (63 bp):
ACGATAATTCGAAACTCGCTCTCTAACTTTATAAGTCAAAGGAAACATACTCCAAAAATAGAA
Found at i:6520 original size:78 final size:78
Alignment explanation
Indices: 6385--6621 Score: 289
Period size: 78 Copynumber: 3.2 Consensus size: 78
6375 GTTTTTTAAT
* * * *
6385 TAAAATACTAAAATGGTAAAATAT-A-AGTAATATGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGATAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
6448 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
*
6461 TAAAATAGTAAAATGATAAAATATAATAGTTATAAGGATATTAGATTTAGTTATATAAAAATAGA
1 TAAAATAGTAAAATGATAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
*
6526 GTTTTTAATTGAG
66 GTTTTTAGTTGAG
** * *
6539 TAAAATAGT-AAA--AT---A-A-AATAGTTATAAAAATATTATATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGATAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
*
6596 GTTTTTAGTTAAG
66 GTTTTTAGTTGAG
6609 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
6622 ACCTAAATAA
Statistics
Matches: 144, Mismatches: 13, Indels: 13
0.85 0.08 0.08
Matches are distributed among these distances:
70 53 0.37
71 6 0.04
72 1 0.01
75 2 0.01
76 22 0.15
77 4 0.03
78 56 0.39
ACGTcount: A:0.51, C:0.01, G:0.12, T:0.36
Consensus pattern (78 bp):
TAAAATAGTAAAATGATAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:6551 original size:70 final size:70
Alignment explanation
Indices: 6467--6621 Score: 206
Period size: 70 Copynumber: 2.2 Consensus size: 70
6457 TGAGTAAAAT
* ** * *
6467 AGTAAAAT-GATAAAATATAATAGTTATAAGGATATTAGATTTAGTTATATAAAAATAGAGTTTT
1 AGTAAAATAG-TAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAGTTTT
*
6531 TAATTG
65 TAATTA
*
6537 AGTAAAATAGTAAAATAAAATAGTTATAAAAATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAGTTTTT
*
6602 AGTTA
66 AATTA
6607 AGTAAAACTA-TAAAA
1 AGTAAAA-TAGTAAAA
6622 ACCTAAATAA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
70 72 0.96
71 3 0.04
ACGTcount: A:0.52, C:0.01, G:0.11, T:0.36
Consensus pattern (70 bp):
AGTAAAATAGTAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAGTTTTT
AATTA
Found at i:8345 original size:60 final size:60
Alignment explanation
Indices: 8295--8864 Score: 191
Period size: 60 Copynumber: 9.7 Consensus size: 60
8285 AGGTTGCACT
* *
8295 TCTCGAAAGAAAATACAAACCCGGTTATGTAGTGGACGAAGTTGATGAGAAAATCACACG
1 TCTCGAAAGAAAATACAAACCCGGTTATGTAGTGAACGAAGTTGATGAGAAGATCACACG
* * * * * * *** *
8355 CCTGGAAA-ACAAATATAAGCCGGGTTATGCT-GTAAACGAA---GATGAGAAGATTGTACT
1 TCTCGAAAGA-AAATACAAACCCGGTTATG-TAGTGAACGAAGTTGATGAGAAGATCACACG
* * * * * * **
8412 TCTAGAGAA-CAAATACAAACCCGGTTATGCAGTAAATGAAGTTGACGAGAAGATTGCACG
1 TCTCGA-AAGAAAATACAAACCCGGTTATGTAGTGAACGAAGTTGATGAGAAGATCACACG
* * * * * *
8472 CCTCGAAAGTAAATATAAGCCAGGTTATGCT-GTGAACGAA---GATGAGAAGATCACGC-
1 TCTCGAAAGAAAATACAAACCCGGTTATG-TAGTGAACGAAGTTGATGAGAAGATCACACG
** * * * * * * *
8528 TACTCGAGCGCAAATACAAACCTGGTTATGCAGTGGATGAAGCTGAAGAGAAGATCACACG
1 T-CTCGAAAGAAAATACAAACCCGGTTATGTAGTGAACGAAGTTGATGAGAAGATCACACG
* * ** * * *
8589 TCTTGAAAGAAAATACAAACCTGGTTATGCGGT-AGATGAAGCTGACGAGAAGATTGCACAC-
1 TCTCGAAAGAAAATACAAACCCGGTTATGTAGTGA-ACGAAGTTGATGAGAAGA-T-CACACG
* * * * * * * ***
8650 -CTTGAGAGCAAATATAAGCCAGGTTATGCT-GTGAATGAA---GATGAGAAGATCGTGC-
1 TCTCGAAAGAAAATACAAACCCGGTTATG-TAGTGAACGAAGTTGATGAGAAGATCACACG
* * *** * * *
8705 TCCTCGAAAGAAAATACAACCCCGGTTATGCAGTGGGTGAAGCTAACGAGAAGATCACACG
1 T-CTCGAAAGAAAATACAAACCCGGTTATGTAGTGAACGAAGTTGATGAGAAGATCACACG
* * * * * * * * *
8766 CCTGGAAAGCAAATATAAGCCGGGTTATGCT-GTGAAAGAA---GATGAAAAGATTGCAAAC-
1 TCTCGAAAGAAAATACAAACCCGGTTATG-TAGTGAACGAAGTTGATGAGAAGA-T-CACACG
* * * *
8824 -CTTGAAAGCAAATATAAACCCGGTTATGTAGTGAAAGAAGT
1 TCTCGAAAGAAAATACAAACCCGGTTATGTAGTGAACGAAGT
8865 CAAGGGAGAC
Statistics
Matches: 381, Mismatches: 96, Indels: 67
0.70 0.18 0.12
Matches are distributed among these distances:
55 2 0.01
56 2 0.01
57 160 0.42
58 3 0.01
59 7 0.02
60 198 0.52
61 4 0.01
62 5 0.01
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.20
Consensus pattern (60 bp):
TCTCGAAAGAAAATACAAACCCGGTTATGTAGTGAACGAAGTTGATGAGAAGATCACACG
Found at i:8438 original size:57 final size:56
Alignment explanation
Indices: 8351--8522 Score: 164
Period size: 57 Copynumber: 3.0 Consensus size: 56
8341 GAGAAAATCA
* *
8351 CACGCCTGGAAAACAAATATAAGCCGGGTTATGCTGTAAACGAAGATGAGAAGATTG
1 CACGCCTAG-AAACAAATATAAGCCAGGTTATGCTGTAAACGAAGATGAGAAGATTG
* ** * * * * * *
8408 TACTTCTAGAGAACAAATACAAACCCGGTTATGCAGTAAATGAAGTTGACGAGAAGATTG
1 CACGCCTAGA-AACAAATATAAGCCAGGTTATGCTGTAAACGAA---GATGAGAAGATTG
* * *
8468 CACGCCTCGAAAGTAAATATAAGCCAGGTTATGCTGTGAACGAAGATGAGAAGAT
1 CACGCCTAGAAA-CAAATATAAGCCAGGTTATGCTGTAAACGAAGATGAGAAGAT
8523 CACGCTACTC
Statistics
Matches: 88, Mismatches: 22, Indels: 10
0.73 0.18 0.08
Matches are distributed among these distances:
56 1 0.01
57 43 0.49
59 2 0.02
60 42 0.48
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (56 bp):
CACGCCTAGAAACAAATATAAGCCAGGTTATGCTGTAAACGAAGATGAGAAGATTG
Found at i:8487 original size:117 final size:117
Alignment explanation
Indices: 8305--8618 Score: 360
Period size: 117 Copynumber: 2.7 Consensus size: 117
8295 TCTCGAAAGA
* * * * *
8305 AAATACAAACCCGGTTATGTAGTGGACGAAGTTGATGAGAAAATCACACGCCTGGAAA-ACAAAT
1 AAATACAAACCCGGTTATGCAGTGGATGAAGTTGAAGAGAAGATCACACGCCTCGAAAGA-AAAT
* *** *
8369 ATAAGCCGGGTTATGCTGTAAACGAAGATGAGAAGATTGTACTTCTAGAGAAC
65 ATAAGCCAGGTTATGCTGTAAACGAAGATGAGAAGATCACACTACTAGAGAAC
** * ** *
8422 AAATACAAACCCGGTTATGCAGTAAATGAAGTTGACGAGAAGATTGCACGCCTCGAAAGTAAATA
1 AAATACAAACCCGGTTATGCAGTGGATGAAGTTGAAGAGAAGATCACACGCCTCGAAAGAAAATA
* * * **
8487 TAAGCCAGGTTATGCTGTGAACGAAGATGAGAAGATCACGCTACTCGAGCGC
66 TAAGCCAGGTTATGCTGTAAACGAAGATGAGAAGATCACACTACTAGAGAAC
* * * *
8539 AAATACAAACCTGGTTATGCAGTGGATGAAGCTGAAGAGAAGATCACACGTCTTGAAAGAAAATA
1 AAATACAAACCCGGTTATGCAGTGGATGAAGTTGAAGAGAAGATCACACGCCTCGAAAGAAAATA
* * *
8604 CAAACCTGGTTATGC
66 TAAGCCAGGTTATGC
8619 GGTAGATGAA
Statistics
Matches: 163, Mismatches: 33, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
117 163 1.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.21
Consensus pattern (117 bp):
AAATACAAACCCGGTTATGCAGTGGATGAAGTTGAAGAGAAGATCACACGCCTCGAAAGAAAATA
TAAGCCAGGTTATGCTGTAAACGAAGATGAGAAGATCACACTACTAGAGAAC
Found at i:8605 original size:177 final size:177
Alignment explanation
Indices: 8422--8851 Score: 546
Period size: 177 Copynumber: 2.4 Consensus size: 177
8412 TCTAGAGAAC
* * * *
8422 AAATACAAACCCGGTTATGCAGTAAATGAAGTTGACGAGAAGATTGCACGCCTCGAAAGTAAATA
1 AAATACAAACCCGGTTATGCAGTAAATGAAGATGACGAGAAGATTGCACACCTTGAAAGCAAATA
** * *
8487 TAAGCCAGGTTATGCTGTGAACGAAGATGAGAAGATCACGCTACTCGAGCGCAAATACAAACCTG
66 TAAGCCAGGTTATGCTGTGAACGAAGATGAGAAGATCACGCTACTCGAAAGAAAATACAAACCCG
* *
8552 GTTATGCAGTGGATGAAGCTGAA-GAGAAGATCACACGTCTTGAAAGA
131 GTTATGCAGTGGATGAAGCT-AACGAGAAGATCACACGCCTGGAAAGA
* * * * *
8599 AAATACAAACCTGGTTATGCGGTAGATGAAGCTGACGAGAAGATTGCACACCTTGAGAGCAAATA
1 AAATACAAACCCGGTTATGCAGTAAATGAAGATGACGAGAAGATTGCACACCTTGAAAGCAAATA
* ** * *
8664 TAAGCCAGGTTATGCTGTGAATGAAGATGAGAAGATCGTGCTCCTCGAAAGAAAATACAACCCCG
66 TAAGCCAGGTTATGCTGTGAACGAAGATGAGAAGATCACGCTACTCGAAAGAAAATACAAACCCG
* *
8729 GTTATGCAGTGGGTGAAGCTAACGAGAAGATCACACGCCTGGAAAGC
131 GTTATGCAGTGGATGAAGCTAACGAGAAGATCACACGCCTGGAAAGA
* * * * *
8776 AAATATAAGCCGGGTTATGCTGTGAAA-GAAGATGA--A-AAGATTGCAAACCTTGAAAGCAAAT
1 AAATACAAACCCGGTTATGCAGT-AAATGAAGATGACGAGAAGATTGCACACCTTGAAAGCAAAT
* *
8837 ATAAACCCGGTTATG
65 ATAAGCCAGGTTATG
8852 TAGTGAAAGA
Statistics
Matches: 220, Mismatches: 31, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
174 36 0.16
175 1 0.00
176 2 0.01
177 179 0.81
178 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (177 bp):
AAATACAAACCCGGTTATGCAGTAAATGAAGATGACGAGAAGATTGCACACCTTGAAAGCAAATA
TAAGCCAGGTTATGCTGTGAACGAAGATGAGAAGATCACGCTACTCGAAAGAAAATACAAACCCG
GTTATGCAGTGGATGAAGCTAACGAGAAGATCACACGCCTGGAAAGA
Found at i:8696 original size:117 final size:116
Alignment explanation
Indices: 8575--8851 Score: 322
Period size: 117 Copynumber: 2.4 Consensus size: 116
8565 TGAAGCTGAA
* * * *
8575 GAGAAGATCACACGTCTTGAAAGAAAATACAAACCTGGTTATGCGGTAGATGAAGCTGACGAGAA
1 GAGAAGATCAAAC-TCTTGAAAGAAAATACAAACCCGGTTATGCAGTAGATGAAGCTAACGAGAA
** * * *
8640 GATTGCACACCTTGAGAGCAAATATAAGCCAGGTTATGCTGTGAATGAAGAT
65 GATCACACACCTGGAAAGCAAATATAAGCCAGGTTATGCTGTGAAAGAAGAT
*** * * * *
8692 GAGAAGATCGTGCTCCTCGAAAGAAAATACAACCCCGGTTATGCAGTGGGTGAAGCTAACGAGAA
1 GAGAAGATCAAACT-CTTGAAAGAAAATACAAACCCGGTTATGCAGTAGATGAAGCTAACGAGAA
* *
8757 GATCACACGCCTGGAAAGCAAATATAAGCCGGGTTATGCTGTGAAAGAAGAT
65 GATCACACACCTGGAAAGCAAATATAAGCCAGGTTATGCTGTGAAAGAAGAT
* * *
8809 GAAAAGATTGCAAAC-CTTGAAAGCAAATATAAACCCGGTTATG
1 GAGAAGA-T-CAAACTCTTGAAAGAAAATACAAACCCGGTTATG
8852 TAGTGAAAGA
Statistics
Matches: 132, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
116 1 0.01
117 128 0.97
118 1 0.01
119 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (116 bp):
GAGAAGATCAAACTCTTGAAAGAAAATACAAACCCGGTTATGCAGTAGATGAAGCTAACGAGAAG
ATCACACACCTGGAAAGCAAATATAAGCCAGGTTATGCTGTGAAAGAAGAT
Found at i:8834 original size:57 final size:57
Alignment explanation
Indices: 8359--8863 Score: 252
Period size: 60 Copynumber: 8.6 Consensus size: 57
8349 CACACGCCTG
* * * ** *
8359 GAAAACAAATATAAGCCGGGTTATGCTGT-AAACGAAGATGAGAAGATTGTACTTCTA
1 GAAAGCAAATATAAGCCCGGTTATGCTGTGAAA-GAAGATGAGAAGATTGCACACCTT
* * * * * *
8416 GAGAA-CAAATACAAACCCGGTTATGCAGT-AAATGAAGTTGACGAGAAGATTGCACGCCTC
1 GA-AAGCAAATATAAGCCCGGTTATGCTGTGAAA-GAA---GATGAGAAGATTGCACACCTT
* * * * *
8476 GAAAGTAAATATAAGCCAGGTTATGCTGTGAACGAAGATGAGAAGA-T-CACGCTACTC
1 GAAAGCAAATATAAGCCCGGTTATGCTGTGAAAGAAGATGAGAAGATTGCACAC--CTT
** * * * * ** *
8533 GAGCGCAAATACAAACCTGGTTATGCAGTGGATGAAGCTGAAGAGAAGA-T-CACACGTCTT
1 GAAAGCAAATATAAGCCCGGTTATGCTGT-GA--AAGAAGATGAGAAGATTGCACAC--CTT
* * * * * ** *
8593 GAAAGAAAATACAAACCTGGTTATGCGGTAGATGAAGCTGACGAGAAGATTGCACACCTT
1 GAAAGCAAATATAAGCCCGGTTATGCTGT-GA--AAGAAGATGAGAAGATTGCACACCTT
* * * * ** * *
8653 GAGAGCAAATATAAGCCAGGTTATGCTGTGAATGAAGATGAGAAGATCGTGCTCCTC
1 GAAAGCAAATATAAGCCCGGTTATGCTGTGAAAGAAGATGAGAAGATTGCACACCTT
* * * * *** * ** * *
8710 GAAAGAAAATACAACCCCGGTTATGCAGTGGGTGAAGCTAACGAGAAGATCACACGCCTG
1 GAAAGCAAATATAAGCCCGGTTATGCTGTGAAAGAAG---ATGAGAAGATTGCACACCTT
* * *
8770 GAAAGCAAATATAAGCCGGGTTATGCTGTGAAAGAAGATGAAAAGATTGCAAACCTT
1 GAAAGCAAATATAAGCCCGGTTATGCTGTGAAAGAAGATGAGAAGATTGCACACCTT
*
8827 GAAAGCAAATATAAACCCGGTTATG-TAGTGAAAGAAG
1 GAAAGCAAATATAAGCCCGGTTATGCT-GTGAAAGAAG
8864 TCAAGGGAGA
Statistics
Matches: 347, Mismatches: 84, Indels: 34
0.75 0.18 0.07
Matches are distributed among these distances:
55 5 0.01
56 2 0.01
57 154 0.44
58 4 0.01
59 4 0.01
60 170 0.49
61 3 0.01
62 5 0.01
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.20
Consensus pattern (57 bp):
GAAAGCAAATATAAGCCCGGTTATGCTGTGAAAGAAGATGAGAAGATTGCACACCTT
Found at i:8837 original size:294 final size:293
Alignment explanation
Indices: 8299--8856 Score: 679
Period size: 294 Copynumber: 1.9 Consensus size: 293
8289 TGCACTTCTC
* * * * *
8299 GAAAGAAAATACAAACCCGGTTATGTAGTGGACGAAGTTGATGAGAAAATCACACGCCTGGAAAA
1 GAAAGAAAATACAAACCCGGTTATGCAGTAGACGAAGCTGACGAGAAAATCACACACCTGGAAAA
* * * *
8364 CAAATATAAGCCGGGTTATGCTGTAAACGAAGATGAGAAGATTGTACTTCTAGAGAACAAATACA
66 CAAATATAAGCCAGGTTATGCTGTAAACGAAGATGAGAAGATCGTACTCCTAGAGAAAAAATACA
* * ** *
8429 AACCCGGTTATGCAGTAAATGAAGTTGACGAGAAGATTGCACGCCTCGAAAGTAAATATAAGCCA
131 AACCCGGTTATGCAGTAAATGAAGCTAACGAGAAGATCACACGCCTCGAAAGCAAATATAAGCCA
* * ** ** *
8494 GGTTATGCTGTGAACGAAGATGAGAAGATCACGCTACTCGAGCGCAAATACAAACCTGGTTATGC
196 GGTTATGCTGTGAAAGAAGATGAAAAGATCAAAC-ACTCGAAAGCAAATACAAACCCGGTTATGC
8559 AGTGGATGAAGCTGAAGAGAAGATCACACGTCTT
260 AGTGGATGAAGCTGAAGAGAAGATCACACGTCTT
* * * * ** * * *
8593 GAAAGAAAATACAAACCTGGTTATGCGGTAGATGAAGCTGACGAGAAGATTGCACACCTTGAGAG
1 GAAAGAAAATACAAACCCGGTTATGCAGTAGACGAAGCTGACGAGAAAATCACACACCTGGAAAA
* * * *
8658 CAAATATAAGCCAGGTTATGCTGTGAATGAAGATGAGAAGATCGTGCTCCTCGA-AAGAAAATAC
66 CAAATATAAGCCAGGTTATGCTGTAAACGAAGATGAGAAGATCGTACTCCTAGAGAA-AAAATAC
* *** *
8722 AACCCCGGTTATGCAGTGGGTGAAGCTAACGAGAAGATCACACGCCTGGAAAGCAAATATAAGCC
130 AAACCCGGTTATGCAGTAAATGAAGCTAACGAGAAGATCACACGCCTCGAAAGCAAATATAAGCC
* * *
8787 GGGTTATGCTGTGAAAGAAGATGAAAAGATTGCAAAC-CTTGAAAGCAAATATAAACCCGGTTAT
195 AGGTTATGCTGTGAAAGAAGATGAAAAGA-T-CAAACACTCGAAAGCAAATACAAACCCGGTTAT
*
8851 GTAGTG
258 GCAGTG
8857 AAAGAAGTCA
Statistics
Matches: 218, Mismatches: 43, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
293 2 0.01
294 212 0.97
295 1 0.00
296 3 0.01
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.20
Consensus pattern (293 bp):
GAAAGAAAATACAAACCCGGTTATGCAGTAGACGAAGCTGACGAGAAAATCACACACCTGGAAAA
CAAATATAAGCCAGGTTATGCTGTAAACGAAGATGAGAAGATCGTACTCCTAGAGAAAAAATACA
AACCCGGTTATGCAGTAAATGAAGCTAACGAGAAGATCACACGCCTCGAAAGCAAATATAAGCCA
GGTTATGCTGTGAAAGAAGATGAAAAGATCAAACACTCGAAAGCAAATACAAACCCGGTTATGCA
GTGGATGAAGCTGAAGAGAAGATCACACGTCTT
Found at i:11349 original size:2 final size:2
Alignment explanation
Indices: 11344--11375 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
11334 CTCAAGTGTG
11344 TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
11376 GTGTGTGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13544 original size:14 final size:14
Alignment explanation
Indices: 13527--13554 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13517 CCAAGGTCCA
13527 CTAGCCAAATAAGG
1 CTAGCCAAATAAGG
13541 CTAGCCAAATAAGG
1 CTAGCCAAATAAGG
13555 TCTAAGCCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
CTAGCCAAATAAGG
Found at i:13727 original size:16 final size:16
Alignment explanation
Indices: 13706--13742 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
13696 ACACCCATAA
*
13706 CACTGAAAGTAGATCT
1 CACTGAAAGTAAATCT
13722 CACTG-AAGTAAATCT
1 CACTGAAAGTAAATCT
13737 CACTGA
1 CACTGA
13743 CTAGACTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (16 bp):
CACTGAAAGTAAATCT
Found at i:24520 original size:3 final size:3
Alignment explanation
Indices: 24512--24556 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
24502 ACGAAAAGTG
* * * *
24512 CTT CTT CTT CTT CTT TTT CTT CTT CAT CAT CTT CTT CCT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
24557 TTCCTCCCTC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.04, C:0.33, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:24556 original size:12 final size:12
Alignment explanation
Indices: 24514--24590 Score: 61
Period size: 12 Copynumber: 6.7 Consensus size: 12
24504 GAAAAGTGCT
*
24514 TCTTCTTCTTCT
1 TCTTCTTCTTCC
* *
24526 TTTTCTTCTTCA
1 TCTTCTTCTTCC
*
24538 TCATCTTCTTCC
1 TCTTCTTCTTCC
24550 TCTTCTT-TTCC
1 TCTTCTTCTTCC
*
24561 TC--CCTCTTCC
1 TCTTCTTCTTCC
* *
24571 TCTCCTTCTCCC
1 TCTTCTTCTTCC
*
24583 TTTTCTTC
1 TCTTCTTC
24591 GCATCATCAT
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
9 2 0.04
10 6 0.12
11 6 0.12
12 37 0.73
ACGTcount: A:0.03, C:0.40, G:0.00, T:0.57
Consensus pattern (12 bp):
TCTTCTTCTTCC
Found at i:35096 original size:2 final size:2
Alignment explanation
Indices: 35091--35118 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35081 ACACACATAC
35091 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
35119 GAGGAGTTAG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:44671 original size:20 final size:20
Alignment explanation
Indices: 44639--44677 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
44629 TAAAACAATA
*
44639 TATTATAATTATATATTAAT
1 TATTATAATTATACATTAAT
44659 TATTA-AATCTATACATTAA
1 TATTATAAT-TATACATTAA
44678 AATTAACTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTATAATTATACATTAAT
Found at i:52805 original size:54 final size:54
Alignment explanation
Indices: 52723--52825 Score: 179
Period size: 54 Copynumber: 1.9 Consensus size: 54
52713 CCCAATTCAC
* **
52723 TTGTGAGTCCTCATCTCTCCCCTGTGTGGCCCAACCCGTCAAGTCTTAAGCTAA
1 TTGTGAGTCCCCATCTCTCCCCAATGTGGCCCAACCCGTCAAGTCTTAAGCTAA
52777 TTGTGAGTCCCCATCTCTCCCCAATGTGGCCCAACCCGTCAAGTCTTAA
1 TTGTGAGTCCCCATCTCTCCCCAATGTGGCCCAACCCGTCAAGTCTTAA
52826 ACCAACCGAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.19, C:0.35, G:0.17, T:0.28
Consensus pattern (54 bp):
TTGTGAGTCCCCATCTCTCCCCAATGTGGCCCAACCCGTCAAGTCTTAAGCTAA
Found at i:55607 original size:2 final size:2
Alignment explanation
Indices: 55600--55625 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55590 CATCTTTGTC
55600 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
55626 GTTGAAACAA
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:55845 original size:2 final size:2
Alignment explanation
Indices: 55838--55869 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
55828 TATGATTTGA
55838 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55870 TACGAATCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56183 original size:31 final size:30
Alignment explanation
Indices: 56155--56212 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
56145 TGTTTTCCGG
56155 TTATACCCTTATTTTT-AAAATATATTTCCAA
1 TTATA-CCTT-TTTTTAAAAATATATTTCCAA
*
56186 TTGTACCTTTTTTTAAAAATATATTTC
1 TTATACCTTTTTTTAAAAATATATTTC
56213 TAAATTGCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 5 0.20
30 16 0.64
31 4 0.16
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.52
Consensus pattern (30 bp):
TTATACCTTTTTTTAAAAATATATTTCCAA
Found at i:57620 original size:7 final size:7
Alignment explanation
Indices: 57608--57670 Score: 70
Period size: 7 Copynumber: 10.1 Consensus size: 7
57598 GACCTGGCAA
57608 TTCGTGT
1 TTCGTGT
57615 TTCGTG-
1 TTCGTGT
57621 -TCGTGT
1 TTCGTGT
57627 TTCGTG-
1 TTCGTGT
57633 -TCGTGT
1 TTCGTGT
57639 TTCGTG-
1 TTCGTGT
57645 -TCGTGT
1 TTCGTGT
57651 TTCGTG-
1 TTCGTGT
57657 -TCGTGT
1 TTCGTGT
57663 TTCGTGT
1 TTCGTGT
57670 T
1 T
57671 GTATAAACGT
Statistics
Matches: 48, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
5 20 0.42
7 28 0.58
ACGTcount: A:0.00, C:0.16, G:0.32, T:0.52
Consensus pattern (7 bp):
TTCGTGT
Found at i:57626 original size:12 final size:12
Alignment explanation
Indices: 57609--57669 Score: 122
Period size: 12 Copynumber: 5.1 Consensus size: 12
57599 ACCTGGCAAT
57609 TCGTGTTTCGTG
1 TCGTGTTTCGTG
57621 TCGTGTTTCGTG
1 TCGTGTTTCGTG
57633 TCGTGTTTCGTG
1 TCGTGTTTCGTG
57645 TCGTGTTTCGTG
1 TCGTGTTTCGTG
57657 TCGTGTTTCGTG
1 TCGTGTTTCGTG
57669 T
1 T
57670 TGTATAAACG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 49 1.00
ACGTcount: A:0.00, C:0.16, G:0.33, T:0.51
Consensus pattern (12 bp):
TCGTGTTTCGTG
Found at i:58315 original size:2 final size:2
Alignment explanation
Indices: 58308--58332 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58298 ATTCAAATCC
58308 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
58333 CTTATTAGGC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59008 original size:22 final size:21
Alignment explanation
Indices: 58983--59088 Score: 70
Period size: 22 Copynumber: 4.8 Consensus size: 21
58973 AGATTATACG
*
58983 AATTTCATAGTGTGGTTAACAA
1 AATTTCATAG-GAGGTTAACAA
59005 AATTTCATTAGGAGGTT-ACTAA
1 AATTTCA-TAGGAGGTTAAC-AA
* * *
59027 TATTTCATTGGGAGGTTATCAA
1 AATTTCA-TAGGAGGTTAACAA
* * *
59049 AATTTTATAGCGTGGTTACCAA
1 AATTTCATAG-GAGGTTAACAA
* *
59071 AACTTCATATGAAGGTTA
1 AATTTCATA-GGAGGTTA
59089 TAAAAGTCTC
Statistics
Matches: 66, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
21 4 0.06
22 57 0.86
23 5 0.08
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (21 bp):
AATTTCATAGGAGGTTAACAA
Found at i:59274 original size:66 final size:66
Alignment explanation
Indices: 59199--59370 Score: 195
Period size: 66 Copynumber: 2.6 Consensus size: 66
59189 TTATATGAAA
* * ** * *
59199 GATTATCAAAATTTCTTAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAAT
1 GATTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAAT
59263 GT
65 GT
* * * * * *
59265 GATTATCAAAATTTCATAGAGGGGTGAACAAAATTTTATAAAGAGGTTATCAAATTTTCAAAATG
1 GATTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATG
59330 T
66 T
*
59331 GATTA-CAAAAATTTCATAGAGAGGTTATCATAATTTCATA
1 GATTATC-AAAATTTCATAGAGAGGTTATCAAAATTTCATA
59371 TGAATATTTT
Statistics
Matches: 88, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
65 1 0.01
66 85 0.97
67 2 0.02
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATG
T
Found at i:59318 original size:22 final size:22
Alignment explanation
Indices: 59154--59370 Score: 120
Period size: 22 Copynumber: 9.7 Consensus size: 22
59144 CTTAGAGTGA
* *
59154 TTATCGAAATTTCAAAAAGATCGG
1 TTATCAAAATTTCATAAAGA--GG
*
59178 ATTATCAAAATTT-ATATGAA-AGA
1 -TTATCAAAATTTCATA--AAGAGG
* ** **
59201 TTATCAAAATTTCTTAGTGTTG
1 TTATCAAAATTTCATAAAGAGG
*
59223 TTATCAAAATTTCA-AAGCGAGG
1 TTATCAAAATTTCATAA-AGAGG
* * * *
59245 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAAGAGG
* *
59267 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAAAGAGG
* * *
59289 TGAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
* * *
59311 TTATCAAATTTTCA-AAATGTGA
1 TTATCAAAATTTCATAAA-GAGG
*
59333 TTA-CAAAAATTTCATAGAGAGG
1 TTATC-AAAATTTCATAAAGAGG
*
59355 TTATCATAATTTCATA
1 TTATCAAAATTTCATA
59371 TGAATATTTT
Statistics
Matches: 143, Mismatches: 39, Indels: 23
0.70 0.19 0.11
Matches are distributed among these distances:
21 5 0.03
22 114 0.80
23 8 0.06
24 2 0.01
25 12 0.08
26 2 0.01
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:60694 original size:3 final size:3
Alignment explanation
Indices: 60686--60720 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
60676 TTTATAAGTA
60686 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
60721 GTACTTGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:63197 original size:7 final size:7
Alignment explanation
Indices: 63185--63220 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
63175 AATTTTATTT
63185 TAATATA
1 TAATATA
63192 TAATATA
1 TAATATA
*
63199 TATTAT-
1 TAATATA
63205 TAATATA
1 TAATATA
63212 TAATATA
1 TAATATA
63219 TA
1 TA
63221 TATGTGTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TAATATA
Found at i:63209 original size:20 final size:19
Alignment explanation
Indices: 63180--63221 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 19
63170 GTAAGAATTT
63180 TATTTTAATATATAATATA
1 TATTTTAATATATAATATA
63199 TATTATTAATATATAATATA
1 TATT-TTAATATATAATATA
63219 TAT
1 TAT
63222 ATGTGTGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TATTTTAATATATAATATA
Found at i:78571 original size:12 final size:12
Alignment explanation
Indices: 78554--78608 Score: 83
Period size: 12 Copynumber: 4.5 Consensus size: 12
78544 TTAATACAGG
78554 TATCGACGGATA
1 TATCGACGGATA
78566 TATCGAACGGATA
1 TATCG-ACGGATA
* *
78579 TATTGACGGGTA
1 TATCGACGGATA
78591 TATCGACGGATA
1 TATCGACGGATA
78603 TATCGA
1 TATCGA
78609 GGTATCGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
12 27 0.71
13 11 0.29
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:78592 original size:25 final size:24
Alignment explanation
Indices: 78558--78605 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
78548 TACAGGTATC
78558 GACGGATATATCGAACGGATATATT
1 GACGGATATATCG-ACGGATATATT
*
78583 GACGGGTATATCGACGGATATAT
1 GACGGATATATCGACGGATATAT
78606 CGAGGTATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.27
Consensus pattern (24 bp):
GACGGATATATCGACGGATATATT
Found at i:80053 original size:18 final size:18
Alignment explanation
Indices: 80032--80066 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
80022 TAATATGGAT
*
80032 ATTTATAGATATATCGAG
1 ATTTATAGAGATATCGAG
*
80050 ATTTATCGAGATATCGA
1 ATTTATAGAGATATCGA
80067 TAAATATCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (18 bp):
ATTTATAGAGATATCGAG
Found at i:91054 original size:32 final size:29
Alignment explanation
Indices: 91016--91082 Score: 98
Period size: 32 Copynumber: 2.2 Consensus size: 29
91006 TAATGTTTTG
91016 TAATTAGCAGAATAAAAAATGGAAAATATTAA
1 TAATTAGCAGAATAAAAAATGG--AATATT-A
*
91048 TAATTAGCAGAATAAAACATGGAATATTA
1 TAATTAGCAGAATAAAAAATGGAATATTA
91077 TAATTA
1 TAATTA
91083 TATTAGTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 7 0.21
30 6 0.18
32 21 0.62
ACGTcount: A:0.55, C:0.04, G:0.12, T:0.28
Consensus pattern (29 bp):
TAATTAGCAGAATAAAAAATGGAATATTA
Found at i:92226 original size:27 final size:24
Alignment explanation
Indices: 92159--92228 Score: 68
Period size: 27 Copynumber: 2.7 Consensus size: 24
92149 GTAGATAAAT
*
92159 TACTATAACAAAAAATTATTAGTA
1 TACTATAACAAAAAATAATTAGTA
*
92183 TACTAATTACCAAAAAAATAAATTAGTA
1 TACT-A-TAAC-AAAAAAT-AATTAGTA
92211 TACTATAATCACAAAAAT
1 TACTATAA-CA-AAAAAT
92229 TTTACATTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
24 4 0.11
25 1 0.03
26 6 0.16
27 15 0.41
28 11 0.30
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.30
Consensus pattern (24 bp):
TACTATAACAAAAAATAATTAGTA
Found at i:92226 original size:28 final size:28
Alignment explanation
Indices: 92166--92227 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
92156 AATTACTATA
* *
92166 ACAAAAAATTATTAGTATACTAATTACC
1 ACAAAAAATAATTAGTATACTAATAACC
*
92194 A-AAAAAATAAATTAGTATACT-ATAATC
1 ACAAAAAAT-AATTAGTATACTAATAACC
92221 ACAAAAA
1 ACAAAAA
92228 TTTTACATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 12 0.41
28 17 0.59
ACGTcount: A:0.58, C:0.11, G:0.03, T:0.27
Consensus pattern (28 bp):
ACAAAAAATAATTAGTATACTAATAACC
Found at i:92637 original size:3 final size:3
Alignment explanation
Indices: 92629--92656 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
92619 TTAAGGTAAA
92629 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
92657 GGTTCAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Done.