Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021296.1 Corchorus olitorius cultivar O-4 contig21329, 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: 61030
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2144 original size:29 final size:29
Alignment explanation
Indices: 2111--2175 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
2101 TCTTTCTGGT
* *
2111 TTTGTTTAAGTGCAGATTGTGCACTTGTG
1 TTTGTTTAAGTGCAGATTGTACACTTGGG
* **
2140 TTTGTTCAAGTGTGGATTGTACACTTGGG
1 TTTGTTTAAGTGCAGATTGTACACTTGGG
*
2169 ATTGTTT
1 TTTGTTT
2176 TGAGTGTGGG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.09, G:0.28, T:0.46
Consensus pattern (29 bp):
TTTGTTTAAGTGCAGATTGTACACTTGGG
Found at i:3421 original size:21 final size:22
Alignment explanation
Indices: 3395--3436 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3385 GCTCCCATCA
3395 GAAAAGAA-AAAAAGAAAAAGT
1 GAAAAGAATAAAAAGAAAAAGT
*
3416 GAAAAGAATAAAAAGGAAAAG
1 GAAAAGAATAAAAAGAAAAAG
3437 AAAGAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (22 bp):
GAAAAGAATAAAAAGAAAAAGT
Found at i:3428 original size:16 final size:15
Alignment explanation
Indices: 3396--3438 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
3386 CTCCCATCAG
* *
3396 AAAA-GAAAAAAAGA
1 AAAAGGAAAAGAATA
3410 AAAAGTGAAAAGAATA
1 AAAAG-GAAAAGAATA
3426 AAAAGGAAAAGAA
1 AAAAGGAAAAGAA
3439 AGAGAAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.16
15 8 0.32
16 13 0.52
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.05
Consensus pattern (15 bp):
AAAAGGAAAAGAATA
Found at i:3444 original size:21 final size:19
Alignment explanation
Indices: 3394--3445 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 19
3384 AGCTCCCATC
3394 AGAAAAGAAAAAAAGAAAA
1 AGAAAAGAAAAAAAGAAAA
*
3413 AGTGAAAAGAATAAAAAGGAAA
1 A--GAAAAGAA-AAAAAGAAAA
3435 AGAAAGAGAAA
1 AGAAA-AGAAA
3446 TTGAATTGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
20 5 0.18
21 12 0.43
22 10 0.36
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (19 bp):
AGAAAAGAAAAAAAGAAAA
Found at i:5082 original size:35 final size:35
Alignment explanation
Indices: 5043--5306 Score: 101
Period size: 35 Copynumber: 8.1 Consensus size: 35
5033 CGGTCTTTCC
*
5043 TCAGTTAGTTTCAATTGATCCAGGGCGATCATTCT
1 TCAGTTAGCTTCAATTGATCCAGGGCGATCATTCT
**
5078 TCAGTTTA-CTTCAATCAATCC-GGAGCG---A----
1 TCAG-TTAGCTTCAATTGATCCAGG-GCGATCATTCT
* * * *
5106 TC--TT-GCTTCAAGTTGACCCAAGGCGGTCCTTCT
1 TCAGTTAGCTTCAA-TTGATCCAGGGCGATCATTCT
* *
5139 TCAGTTAGTTTCAATTGATCTAGGGCGATCATTCT
1 TCAGTTAGCTTCAATTGATCCAGGGCGATCATTCT
* * *
5174 TCAATTTA-CTTCAATTGATCTAGAGCG---A----
1 TC-AGTTAGCTTCAATTGATCCAGGGCGATCATTCT
* * * * *
5202 TC--TT-GCTTCAAGTGGACCCAGGGCGGT-TTTTT
1 TCAGTTAGCTTCAA-TTGATCCAGGGCGATCATTCT
* *
5234 TCAGTTAGTTTCAATTGATCCAGGGCGATCACTCT
1 TCAGTTAGCTTCAATTGATCCAGGGCGATCATTCT
* * *
5269 TCAGTTTA-CTTCAATTGATCTAGAGCGATCTTTCT
1 TCAG-TTAGCTTCAATTGATCCAGGGCGATCATTCT
5304 TCA
1 TCA
5307 AGTTGACCCA
Statistics
Matches: 166, Mismatches: 34, Indels: 58
0.64 0.13 0.22
Matches are distributed among these distances:
25 16 0.10
26 16 0.10
27 1 0.01
28 4 0.02
32 4 0.02
33 2 0.01
34 16 0.10
35 91 0.55
36 16 0.10
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (35 bp):
TCAGTTAGCTTCAATTGATCCAGGGCGATCATTCT
Found at i:5277 original size:95 final size:96
Alignment explanation
Indices: 4990--5332 Score: 499
Period size: 96 Copynumber: 3.6 Consensus size: 96
4980 CATGGTTCAT
* * * * *
4990 CTTCAATCGATCCGGAGCGATATTGCTTCAAGTTGACCCACGACGGTCTTTCCTCAGTTAGTTTC
1 CTTCAATCGATCCAGAGCGATCTTGCTTCAAGTTGACCCAGGGCGGTCTTTCTTCAGTTAGTTTC
5055 AATTGATCCAGGGCGATCATTCTTCAGTTTA
66 AATTGATCCAGGGCGATCATTCTTCAGTTTA
* * * *
5086 CTTCAATCAATCCGGAGCGATCTTGCTTCAAGTTGACCCAAGGCGGTCCTTCTTCAGTTAGTTTC
1 CTTCAATCGATCCAGAGCGATCTTGCTTCAAGTTGACCCAGGGCGGTCTTTCTTCAGTTAGTTTC
* *
5151 AATTGATCTAGGGCGATCATTCTTCAATTTA
66 AATTGATCCAGGGCGATCATTCTTCAGTTTA
* * * *
5182 CTTCAATTGATCTAGAGCGATCTTGCTTCAAGTGGACCCAGGGCGGT-TTTTTTCAGTTAGTTTC
1 CTTCAATCGATCCAGAGCGATCTTGCTTCAAGTTGACCCAGGGCGGTCTTTCTTCAGTTAGTTTC
*
5246 AATTGATCCAGGGCGATCACTCTTCAGTTTA
66 AATTGATCCAGGGCGATCATTCTTCAGTTTA
* * * *
5277 CTTCAATTGATCTAGAGCGATCTTTCTTCAAGTTGACCCAGGGTGGTCTTTCTTCA
1 CTTCAATCGATCCAGAGCGATCTTGCTTCAAGTTGACCCAGGGCGGTCTTTCTTCA
5333 ATTTATTTCA
Statistics
Matches: 223, Mismatches: 23, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
95 87 0.39
96 136 0.61
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (96 bp):
CTTCAATCGATCCAGAGCGATCTTGCTTCAAGTTGACCCAGGGCGGTCTTTCTTCAGTTAGTTTC
AATTGATCCAGGGCGATCATTCTTCAGTTTA
Found at i:5392 original size:22 final size:22
Alignment explanation
Indices: 5364--5416 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
5354 GGTGGCCTTT
**
5364 CTTCAATTTCAATACTCCAATG
1 CTTCAATTTCAATACTCCAAAA
* *
5386 CTTCAATTTCAATTCTTCAAAA
1 CTTCAATTTCAATACTCCAAAA
5408 CTTCAATTT
1 CTTCAATTT
5417 TTCAAGTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.02, T:0.42
Consensus pattern (22 bp):
CTTCAATTTCAATACTCCAAAA
Found at i:5428 original size:24 final size:24
Alignment explanation
Indices: 5385--5463 Score: 108
Period size: 24 Copynumber: 3.4 Consensus size: 24
5375 ATACTCCAAT
* *
5385 GCTTCAA--TTTCAATTCTTCAAA
1 GCTTCAATTTTTCAAGTATTCAAA
*
5407 ACTTCAATTTTTCAAGTATTCAAA
1 GCTTCAATTTTTCAAGTATTCAAA
*
5431 GCCTCAATTTTTCAAGTATTCAAA
1 GCTTCAATTTTTCAAGTATTCAAA
5455 GCTTCAATT
1 GCTTCAATT
5464 CTCCAATGCT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
22 6 0.12
24 43 0.88
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (24 bp):
GCTTCAATTTTTCAAGTATTCAAA
Found at i:5738 original size:54 final size:54
Alignment explanation
Indices: 5491--5728 Score: 326
Period size: 54 Copynumber: 4.5 Consensus size: 54
5481 ACTTTAATGT
* * *
5491 TCCAGTGCGGTCAATCAA-AAACTTT-CAAGTGGCTTAAGTTTATCTTCAAACTGA
1 TCCAGTGCGGTCAATCAAGAAAGTTTAC-AGTGGTTTAAGTTTATCTTC-AAGTGA
* * *
5545 TCCGGTGCGATCAATC--G--AGTTTACAGTGGTTTAAGTTTATCTTCAAGCGA
1 TCCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTTTAAGTTTATCTTCAAGTGA
5595 TCCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTTTAAGTTTATCTTCAAGTGA
1 TCCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTTTAAGTTTATCTTCAAGTGA
**
5649 TCCAGTGCGGTCGGTCAAGAAAGTTTACAGTGGTTTAAGTTTATCTTCAAGTGA
1 TCCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTTTAAGTTTATCTTCAAGTGA
* *
5703 TCTAGTACGGTCAATCAAGAAAGTTT
1 TCCAGTGCGGTCAATCAAGAAAGTTT
5729 CTGATGGTTT
Statistics
Matches: 163, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
50 18 0.11
51 23 0.14
52 2 0.01
54 120 0.74
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.33
Consensus pattern (54 bp):
TCCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTTTAAGTTTATCTTCAAGTGA
Found at i:5824 original size:96 final size:97
Alignment explanation
Indices: 5640--5817 Score: 277
Period size: 96 Copynumber: 1.8 Consensus size: 97
5630 TAAGTTTATC
* *
5640 TTCAAGTGATCCAGTGCGGTCGGTCAAGAAAGTTTACAGTGGTTTAAGTTTATCTTCAAGTGATC
1 TTCAAGTGATCCAGTGCGATCGGTCAAGAAAGTTTACAGTGGTTTAAATTTATCTTCAAGTGATC
*
5705 TAGTACGGTCAATCAAGAAAGTTTCTGATGGT
66 CAGTACGGTCAATCAAGAAAGTTTCTGATGGT
* * *
5737 TTCAAGTGATCCAGTGCGATTGTTC-AGAAAGTTTCCAGTGGTTTAAATTTATCTTCAAGTGATC
1 TTCAAGTGATCCAGTGCGATCGGTCAAGAAAGTTTACAGTGGTTTAAATTTATCTTCAAGTGATC
* *
5801 CAGTGCGGTCAGTCAAG
66 CAGTACGGTCAATCAAG
5818 GGAGTTTTCA
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
96 51 0.70
97 22 0.30
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (97 bp):
TTCAAGTGATCCAGTGCGATCGGTCAAGAAAGTTTACAGTGGTTTAAATTTATCTTCAAGTGATC
CAGTACGGTCAATCAAGAAAGTTTCTGATGGT
Found at i:5996 original size:90 final size:88
Alignment explanation
Indices: 5894--6312 Score: 482
Period size: 90 Copynumber: 4.9 Consensus size: 88
5884 TTCAAAGATG
* * *
5894 GATTCGGTGAATCAGGTTAATGCAGTGCATTAGTTCTTCAAGATTGGATTCGATGAGCTCGGTGC
1 GATTCGGTGAATCAAGTTAATGCGGTGCATTAGTTCTTCAAGATTGGATTCGGTGAGCTCGGTGC
*
5959 AGCACATTTTCAAACAGTTCAGGGT
66 AGCACA-TTTCAAACA-TTCAGGAT
*
5984 GATTCGGTGAATCAAGTTAATACGGTGCATT-GTTTCTTCAAGATTGGATTCGGTGAGCTCGGTG
1 GATTCGGTGAATCAAGTTAATGCGGTGCATTAG-TTCTTCAAGATTGGATTCGGTGAGCTCGGTG
6048 CAG--CA--T-----ATTCAGGAT
65 CAGCACATTTCAAACATTCAGGAT
* *
6063 GATTCGGTGAATCAAGTTAATGCGGTGCATT-GTTTCTTTAAGATTGGATTTGGTGAGCTCGGTG
1 GATTCGGTGAATCAAGTTAATGCGGTGCATTAG-TTCTTCAAGATTGGATTCGGTGAGCTCGGTG
6127 CAG--CA--T-----ATTCAGGAT
65 CAGCACATTTCAAACATTCAGGAT
* * * * * *
6142 GATTCGGTGAATCAAGTTGATGCGGTGCACTATTTTTTCAAGATTGGATTCGGTGAGCTCGATGT
1 GATTCGGTGAATCAAGTTAATGCGGTGCATTAGTTCTTCAAGATTGGATTCGGTGAGCTCGGTGC
*
6207 AGCATATTTTCAAACAGTTCAGGAT
66 AGCACA-TTTCAAACA-TTCAGGAT
* **
6232 GATTCGGTGAATCAAGTTGATGCGGTGCATTAGTTCTTCAAGATTGGATTCGGTGAGCTCGACGC
1 GATTCGGTGAATCAAGTTAATGCGGTGCATTAGTTCTTCAAGATTGGATTCGGTGAGCTCGGTGC
6297 AGCACATCTTCAAACA
66 AGCACAT-TTCAAACA
6313 AGTGTTCCTT
Statistics
Matches: 292, Mismatches: 23, Indels: 28
0.85 0.07 0.08
Matches are distributed among these distances:
79 141 0.48
80 1 0.00
81 1 0.00
84 1 0.00
85 1 0.00
88 2 0.01
89 3 0.01
90 142 0.49
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (88 bp):
GATTCGGTGAATCAAGTTAATGCGGTGCATTAGTTCTTCAAGATTGGATTCGGTGAGCTCGGTGC
AGCACATTTCAAACATTCAGGAT
Found at i:6107 original size:79 final size:79
Alignment explanation
Indices: 5976--6292 Score: 420
Period size: 79 Copynumber: 3.9 Consensus size: 79
5966 TTTCAAACAG
* *
5976 TTCAGGGTGATTCGGTGAATCAAGTTAATACGGTGCATTGTTTCTTCAAGATTGGATTCGGTGAG
1 TTCAGGATGATTCGGTGAATCAAGTTAATGCGGTGCATTGTTTCTTCAAGATTGGATTCGGTGAG
6041 CTCGGTGCAGCATA
66 CTCGGTGCAGCATA
* *
6055 TTCAGGATGATTCGGTGAATCAAGTTAATGCGGTGCATTGTTTCTTTAAGATTGGATTTGGTGAG
1 TTCAGGATGATTCGGTGAATCAAGTTAATGCGGTGCATTGTTTCTTCAAGATTGGATTCGGTGAG
6120 CTCGGTGCAGCATA
66 CTCGGTGCAGCATA
* * * *
6134 TTCAGGATGATTCGGTGAATCAAGTTGATGCGGTGCACTATTTTTTCAAGATTGGATTCGGTGAG
1 TTCAGGATGATTCGGTGAATCAAGTTAATGCGGTGCATTGTTTCTTCAAGATTGGATTCGGTGAG
* *
6199 CTCGATGTAGCATATTTTCAAACA
66 CTCG--GT-GC--A---GC--ATA
*
6223 GTTCAGGATGATTCGGTGAATCAAGTTGATGCGGTGCATTAG-TTCTTCAAGATTGGATTCGGTG
1 -TTCAGGATGATTCGGTGAATCAAGTTAATGCGGTGCATT-GTTTCTTCAAGATTGGATTCGGTG
6287 AGCTCG
64 AGCTCG
6293 ACGCAGCACA
Statistics
Matches: 211, Mismatches: 15, Indels: 13
0.88 0.06 0.05
Matches are distributed among these distances:
79 138 0.65
81 2 0.01
82 2 0.01
84 1 0.00
87 1 0.00
89 2 0.01
90 65 0.31
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.34
Consensus pattern (79 bp):
TTCAGGATGATTCGGTGAATCAAGTTAATGCGGTGCATTGTTTCTTCAAGATTGGATTCGGTGAG
CTCGGTGCAGCATA
Found at i:6715 original size:46 final size:46
Alignment explanation
Indices: 6411--6788 Score: 413
Period size: 46 Copynumber: 8.2 Consensus size: 46
6401 AAGTTCAAGG
* ** * * *
6411 TTGATTCGGTGAATCAAGTTAATTCAATACAATATTTATTCAAAGT
1 TTGATTCGGTGAATCAAGTTAATGCGGTGCAGTATTTCTTCAAAGT
*
6457 TTGATTCGGTGAATCAAGTTAATGCGGTGCAATATTTCTTCAAAGT
1 TTGATTCGGTGAATCAAGTTAATGCGGTGCAGTATTTCTTCAAAGT
* * * *
6503 TTGATCCGGTGAATCAAGTTAATTCAGTACAGTATTTCTTCAAAGT
1 TTGATTCGGTGAATCAAGTTAATGCGGTGCAGTATTTCTTCAAAGT
* * * *
6549 TTGATTCGGTGGATCAAGTTAATGCAGTGCA-TCATTTCTTTAAAGA
1 TTGATTCGGTGAATCAAGTTAATGCGGTGCAGT-ATTTCTTCAAAGT
* * *
6595 TTGATTCGGTTAATCAAGTTAATGCGGTGCAGTATTTCTTTAGAGT
1 TTGATTCGGTGAATCAAGTTAATGCGGTGCAGTATTTCTTCAAAGT
* * * *
6641 TTGATTCGGTGGATCAAGTTAATGCGGTGCACTATTTCTTCAAGGA
1 TTGATTCGGTGAATCAAGTTAATGCGGTGCAGTATTTCTTCAAAGT
* * ** *
6687 TTGATTCGGTGAATCAAGTTATTTCGGTGTGGTATTTCTTC--ATT
1 TTGATTCGGTGAATCAAGTTAATGCGGTGCAGTATTTCTTCAAAGT
* * * * *
6731 TGTGATTCGGTGAATCAAATTAACT-TGGTGCGGTGTTTCTTCAAAGA
1 T-TGATTCGGTGAATCAAGTTAA-TGCGGTGCAGTATTTCTTCAAAGT
6778 TTGATTCGGTG
1 TTGATTCGGTG
6789 TGGTCTTTCT
Statistics
Matches: 282, Mismatches: 44, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
44 1 0.00
45 34 0.12
46 244 0.87
47 3 0.01
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (46 bp):
TTGATTCGGTGAATCAAGTTAATGCGGTGCAGTATTTCTTCAAAGT
Found at i:6770 original size:45 final size:45
Alignment explanation
Indices: 6688--6773 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
6678 CTTCAAGGAT
* * *
6688 TGATTCGGTGAATCAAGTTATTTCGGTGTGGTATTTCTTCATTTG
1 TGATTCGGTGAATCAAATTACTTCGGTGCGGTATTTCTTCATTTG
*
6733 TGATTCGGTGAATCAAATTAACTT-GGTGCGGTGTTTCTTCA
1 TGATTCGGTGAATCAAATT-ACTTCGGTGCGGTATTTCTTCA
6774 AAGATTGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
45 33 0.92
46 3 0.08
ACGTcount: A:0.20, C:0.13, G:0.24, T:0.43
Consensus pattern (45 bp):
TGATTCGGTGAATCAAATTACTTCGGTGCGGTATTTCTTCATTTG
Found at i:14601 original size:21 final size:21
Alignment explanation
Indices: 14576--14619 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
14566 TTACTAGTAT
*
14576 TATACTTATATTTTATGCATG
1 TATACTTACATTTTATGCATG
14597 TATACTTACATTTTATGCATG
1 TATACTTACATTTTATGCATG
14618 TA
1 TA
14620 GTTATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (21 bp):
TATACTTACATTTTATGCATG
Found at i:16711 original size:436 final size:433
Alignment explanation
Indices: 15856--16720 Score: 1159
Period size: 436 Copynumber: 2.0 Consensus size: 433
15846 AAAAATATTA
* * * * *
15856 GTTTATGGAGACGAAACATAAAAATTGCCTTTTGAACCCTTAATGAAACTAATGAATCAAATTCA
1 GTTTATGGAGACCAAACATAAAAATTGCCTCTCGAACCATTAACGAAACTAATGAATCAAATTCA
* * *
15921 ACTTTCAGGCCCTTAATGAAAATCGTAGATCACAAATAACCTTTTATCCGACACTTGAACAACTT
66 ACTTTCAGGCCCTTAACGAAAATCGTAGATCACAAATAACATTTTATCCGACACTTGAACAACCT
* ** * *
15986 CAATCGGACAAGTGGACCAAAAATTATACAACATTAAATAGATCGGCAATTGAAACCACAAGATT
131 CAATCGGACAAGTGGACCAAAAATTATACAACATTAAATAGACCAACAATCGAAACCACAAAATT
* * * *
16051 TCAGAAGCATTTTTAGAATTAAAACATTAAAATTGACTTCTAAGTTCTTCATGGAAGTTGTAGAT
196 TCAGAAACATTTTTAGAATCAAAACATTAAAATTGACTTCTAAGTCCTTCATGAAAGTTGTAGAT
* * * * * *
16116 CATGAAATCACCTTTTCATAGACACTTGAATCAGCTTGATCGGACAAATAGAACAGAAAATACAA
261 CATGAAATCACCTTTTAATAGACACTGGAATCACCTTGATCGGACAAACAAAACAAAAAATACAA
* * *
16181 AAGTAAAAGCCGAAGCGTTAAATCATCCAACCCACAATTGTAAAGGATTAAATAGCATAAAGCAT
326 AAATAAAAGCCGAAACGTTAAATCATCCAACCCACAATTGTAAAGGACTAAATAGCATAAAGCAT
16246 AAAAGTATGAGGATCATTTGATAAATAATCACACAAAAAAAAAT
391 AAAAGTATGAGGATCATTTGATAAATAATC-CACAAAAAAAAAT
* * *
16290 GTTTATGGAGACCAAACATAAAAATT-CTCTCTCGAA-CATTCCACGAAACTCATTAATCAAATT
1 GTTTATGGAGACCAAACATAAAAATTGC-CTCTCGAACCATT-AACGAAACTAATGAATCAAATT
* *
16353 CAGCTTTCAGGCCCTTGACGAAAATCGTAGATCACACAATAACATTTTAAT-CGACACTTGAACA
64 CAACTTTCAGGCCCTTAACGAAAATCGTAGATCACA-AATAACATTTT-ATCCGACACTTGAACA
* * * *
16417 ACCTCAATCGGACAAGTGGACCGAAAATTATACAATATTAGATAGACCAACAATCGAGACCACAA
127 ACCTCAATCGGACAAGTGGACCAAAAATTATACAACATTAAATAGACCAACAATCGAAACCACAA
* * *
16482 AATTTCAGAAACATTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGTCCTTCATGAAAGTTG
192 AATTTCAGAAACA-TTTTTAGAATCAAAACATTAAAATTGACTTCTAAGTCCTTCATGAAAGTTG
* * * *
16547 TAGATCATGAAATTACCTTTTAATAGACACTGGAATCACCTTGATTGGAGAAGCAAAACAAAAAA
256 TAGATCATGAAATCACCTTTTAATAGACACTGGAATCACCTTGATCGGACAAACAAAACAAAAAA
* * * *
16612 TA-AAAGAATTAAAGCCGAAACGTTCAATCATCCAACCCATAATTTGT-GAGGAACTAAATAGCA
321 TACAAA-AATAAAAGCCGAAACGTTAAATCATCCAACCCACAA-TTGTAAAGG-ACTAAATAGCA
* *
16675 TAAAGTATAAAAGTAT-AGGGATCATTTGAT-AATAATCCAGAAAAAA
383 TAAAGCATAAAAGTATGA-GGATCATTTGATAAATAATCCACAAAAAA
16721 TGATTTGTTT
Statistics
Matches: 374, Mismatches: 48, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
433 4 0.01
434 82 0.22
435 101 0.27
436 146 0.39
437 41 0.11
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.26
Consensus pattern (433 bp):
GTTTATGGAGACCAAACATAAAAATTGCCTCTCGAACCATTAACGAAACTAATGAATCAAATTCA
ACTTTCAGGCCCTTAACGAAAATCGTAGATCACAAATAACATTTTATCCGACACTTGAACAACCT
CAATCGGACAAGTGGACCAAAAATTATACAACATTAAATAGACCAACAATCGAAACCACAAAATT
TCAGAAACATTTTTAGAATCAAAACATTAAAATTGACTTCTAAGTCCTTCATGAAAGTTGTAGAT
CATGAAATCACCTTTTAATAGACACTGGAATCACCTTGATCGGACAAACAAAACAAAAAATACAA
AAATAAAAGCCGAAACGTTAAATCATCCAACCCACAATTGTAAAGGACTAAATAGCATAAAGCAT
AAAAGTATGAGGATCATTTGATAAATAATCCACAAAAAAAAAT
Found at i:21866 original size:88 final size:89
Alignment explanation
Indices: 21763--21947 Score: 266
Period size: 89 Copynumber: 2.1 Consensus size: 89
21753 ATGATAATAT
* *
21763 ACCAATAATCACTAATAATTAACATTAATCAAATCACCTT-ATCAAATATTTACTCCAATTAA-T
1 ACCAA-AATCACTAATAATTAACATTAATCAAATCACCTTGATAAAATATTTACACCAA-TAATT
*
21826 TCTTATTAATAAAACAATTAATAAGA
64 TCTTATTAACAAAACAATTAATAAGA
* * *
21852 ACCAAAATCACTAATAATTAACATTAATCAAATGACTTTGATAAAATATTTACACCAATAATTTT
1 ACCAAAATCACTAATAATTAACATTAATCAAATCACCTTGATAAAATATTTACACCAATAATTTC
*
21917 TTATTAACAAAACAATTAGTAAGA
66 TTATTAACAAAACAATTAATAAGA
*
21941 ACAAAAA
1 ACCAAAA
21948 AATAATAATG
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
88 35 0.41
89 51 0.59
ACGTcount: A:0.50, C:0.15, G:0.03, T:0.32
Consensus pattern (89 bp):
ACCAAAATCACTAATAATTAACATTAATCAAATCACCTTGATAAAATATTTACACCAATAATTTC
TTATTAACAAAACAATTAATAAGA
Found at i:22737 original size:438 final size:440
Alignment explanation
Indices: 22091--22931 Score: 1167
Period size: 438 Copynumber: 1.9 Consensus size: 440
22081 AACTCTTCAT
* * * * * * *
22091 GAAACTCGTTGATTAAATTCAGCTTTCAGGCCCTTTATGAAAGTCGTAGATCATACAATAACATT
1 GAAACTCATTAATCAAATTCAGCTTTCAAGCCCTTGACGAAAGTCGTAGATCACACAATAACATT
* * * * * *
22156 TTAAATGACACTTGAACAACTTCAATGTGTCAAGTGGATCGAGAATTATACAATATTAGATAGAT
66 TTAAACGACACTTGAACAACCTCAATGTGACAAGTGGACCGAAAATTATACAATATTAGATAGAC
* * * **
22221 CGTTAATCGAGACCACCAAATTTTAGAAACATTTTTGAGAATTGAAACATTAAAGTTGACTTTTG
131 CGTCAATCAAGACCACAAAATTTTAGAAACATTTTTGAGAATCAAAACATTAAAGTTGACTTTTG
* * *
22286 AGTTCTTCATGAAAATTGTAGATCATGAAATTATCTTTTCA-TAGACACTTGAATCACCTTGATC
196 AGTCCTTCATGAAAATTGTAGATCATGAAATTACCTTTT-AGTAGACACTTAAATCACCTTGATC
* * * *
22350 AGACAAATAGAAC-AAAAAATACAAA-AATAAAAGTTGAAGCGTTAAATCGTCCAACCC-AA-TT
260 AGACAAACAAAACAAAAAAATA-AAAGAATAAAAGTCGAAACGTTAAATCGTCCAACCCAAATTT
* *
22411 GTAAAGGATTAAATAGTATAAAGCATAAAAAGTATGA-GGATCATTTGATAAATAATCCAGCAAA
324 GTAAAGGACTAAATAGCATAAAGCATAAAAA-TAT-ATGGATCATTTGATAAATAATCCAGCAAA
22475 AAGAAT-ATTTGTTTATGGAGACCAAAAATAAAAATTCTCTCTCGAACATTCCAC
387 AA-AATGATTTGTTTATGGAGACCAAAAATAAAAATTCTCTCTCGAACATTCCAC
* * * *
22529 GAAACTCATTAATCAAATTTAGCTTTCAAGTCCTTGACGAAAGTTGTAGATCACACAATAACCTT
1 GAAACTCATTAATCAAATTCAGCTTTCAAGCCCTTGACGAAAGTCGTAGATCACACAATAACATT
*
22594 TTAACCGACACTTGAACAACCTCAATCG-GACAAGTGGACCGAAAATTATACAATATTAGATAGA
66 TTAAACGACACTTGAACAACCTCAAT-GTGACAAGTGGACCGAAAATTATACAATATTAGATAGA
* * **
22658 CCGTCAATCAAGACCACAAAATTTTAGAAGCATTTTTTAGAATCAAAACATTAAAGTTGGTTTTT
130 CCGTCAATCAAGACCACAAAATTTTAGAAACATTTTTGAGAATCAAAACATTAAAGTTGACTTTT
*
22723 GAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAGTAGACACTTAAATCACCTTGATC
195 GAGTCCTTCATGAAAATTGTAGATCATGAAATTACCTTTTAGTAGACACTTAAATCACCTTGATC
* *
22788 GGACAAACAAAACAAAAAAATAAAAGAATTAAAGTCGAAACGTTAAATCGTCCAACCCAGAATTT
260 AGACAAACAAAACAAAAAAATAAAAGAATAAAAGTCGAAACGTTAAATCGTCCAACCCA-AATTT
* * * **
22853 GTGAGGGACTAAATGGCATAAATTATAAAAATATATGGATCATTTGATAAATAATCCAGCAAAAA
324 GTAAAGGACTAAATAGCATAAAGCATAAAAATATATGGATCATTTGATAAATAATCCAGCAAAAA
22918 AATGATTTGTTTAT
389 AATGATTTGTTTAT
22932 TAAGAGCGGG
Statistics
Matches: 350, Mismatches: 44, Indels: 15
0.86 0.11 0.04
Matches are distributed among these distances:
437 1 0.00
438 237 0.68
439 38 0.11
440 4 0.01
441 44 0.13
442 26 0.07
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.29
Consensus pattern (440 bp):
GAAACTCATTAATCAAATTCAGCTTTCAAGCCCTTGACGAAAGTCGTAGATCACACAATAACATT
TTAAACGACACTTGAACAACCTCAATGTGACAAGTGGACCGAAAATTATACAATATTAGATAGAC
CGTCAATCAAGACCACAAAATTTTAGAAACATTTTTGAGAATCAAAACATTAAAGTTGACTTTTG
AGTCCTTCATGAAAATTGTAGATCATGAAATTACCTTTTAGTAGACACTTAAATCACCTTGATCA
GACAAACAAAACAAAAAAATAAAAGAATAAAAGTCGAAACGTTAAATCGTCCAACCCAAATTTGT
AAAGGACTAAATAGCATAAAGCATAAAAATATATGGATCATTTGATAAATAATCCAGCAAAAAAA
TGATTTGTTTATGGAGACCAAAAATAAAAATTCTCTCTCGAACATTCCAC
Found at i:24855 original size:165 final size:165
Alignment explanation
Indices: 24649--24981 Score: 558
Period size: 165 Copynumber: 2.0 Consensus size: 165
24639 TGTTATATTA
* *
24649 TATTAAATTGTTAAAAAGTCAAAAATACCCTTAGAAGTTTGTGGGGATAACGAAAAAACCAATAT
1 TATTAAATTGTTAAAAAGTCAAAAATACCCTTAGAAGTTTGTGAGAATAACGAAAAAACCAATAT
* * *
24714 TGGAATGACGGAAAAACCAAGCTAAATAGTAATCAAATTAATAAGGTTAAATCTTTTGATTGGTC
66 TGGAATGACGAAAAAACCAAGCTAAATAGTAATCAAATTAATAAGATTAAATCTTTTGACTGGTC
* *
24779 TTTTAGTACTTTCACTTCTCATAATTATTGTTTTT
131 TTTTAATACTTTCACTTCCCATAATTATTGTTTTT
* *
24814 TATTAAATTGTTAGAAAGTCAAAAATACCCTTAGGAGTTTGTGAGAATAACGAAAAAACCAATAT
1 TATTAAATTGTTAAAAAGTCAAAAATACCCTTAGAAGTTTGTGAGAATAACGAAAAAACCAATAT
* *
24879 TGGAATGACGAAAAAACCAAGCTAAATAGTAATTAAATTAATAAGATTAAATCTTTTGACTGGTT
66 TGGAATGACGAAAAAACCAAGCTAAATAGTAATCAAATTAATAAGATTAAATCTTTTGACTGGTC
*
24944 TTTTAATATTTTCACTTCCCATAATTATTGTTTTT
131 TTTTAATACTTTCACTTCCCATAATTATTGTTTTT
24979 TAT
1 TAT
24982 AATAATATAT
Statistics
Matches: 156, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
165 156 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.36
Consensus pattern (165 bp):
TATTAAATTGTTAAAAAGTCAAAAATACCCTTAGAAGTTTGTGAGAATAACGAAAAAACCAATAT
TGGAATGACGAAAAAACCAAGCTAAATAGTAATCAAATTAATAAGATTAAATCTTTTGACTGGTC
TTTTAATACTTTCACTTCCCATAATTATTGTTTTT
Found at i:24991 original size:2 final size:2
Alignment explanation
Indices: 24986--25023 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
24976 TTTTATAATA
24986 AT AT AT AT AT AT A- AT AT AT AT A- 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 AT AT AT AT
25024 TGTTATAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:25001 original size:13 final size:12
Alignment explanation
Indices: 24979--25020 Score: 66
Period size: 13 Copynumber: 3.3 Consensus size: 12
24969 TATTGTTTTT
24979 TATAATAATATA
1 TATAATAATATA
24991 TATATATAATATA
1 TATA-ATAATATA
25004 TATAATATATATA
1 TATAATA-ATATA
25017 TATA
1 TATA
25021 TATTGTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.25
13 21 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TATAATAATATA
Found at i:25008 original size:22 final size:21
Alignment explanation
Indices: 24979--25020 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
24969 TATTGTTTTT
24979 TATAATAATATATATATATAA
1 TATAATAATATATATATATAA
25000 TATATATAATATATATATATA
1 TATA-ATAATATATATATATA
25021 TATTGTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATAATAATATATATATATAA
Found at i:26003 original size:1 final size:1
Alignment explanation
Indices: 25997--26027 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
25987 GTGCTTCGCG
25997 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
26028 GCATTATCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:29721 original size:1 final size:1
Alignment explanation
Indices: 29715--29764 Score: 73
Period size: 1 Copynumber: 50.0 Consensus size: 1
29705 AATTCGTTGC
* * *
29715 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTCTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29765 CTTTCCTACT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:35035 original size:13 final size:13
Alignment explanation
Indices: 35017--35041 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35007 CCATTTGTAA
35017 ATATAGCATAACT
1 ATATAGCATAACT
35030 ATATAGCATAAC
1 ATATAGCATAAC
35042 AGATTATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (13 bp):
ATATAGCATAACT
Found at i:37064 original size:21 final size:21
Alignment explanation
Indices: 37040--37079 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
37030 ATTGCACACC
37040 TGGGTGATT-AGACAAACCACA
1 TGGGT-ATTCAGACAAACCACA
*
37061 TGGGTCTTCAGACAAACCA
1 TGGGTATTCAGACAAACCA
37080 TGTGGGCGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.20
Consensus pattern (21 bp):
TGGGTATTCAGACAAACCACA
Found at i:37576 original size:40 final size:39
Alignment explanation
Indices: 37532--37865 Score: 298
Period size: 40 Copynumber: 8.4 Consensus size: 39
37522 CCTTATAACC
* * *
37532 AGGAAAGACATAACAGGAATATGAACAACACCTTCCGATG
1 AGGAAGGACA-AACTGGAATATAAACAACACCTTCCGATG
* *
37572 AGGAAGGGCAAACTGGTAA-ACTTAACAACACCTTCCGATG
1 AGGAAGGACAAACTGG-AATA-TAAACAACACCTTCCGATG
* * * * *
37612 GGGAAGGGCTAACCGGAATGTAAACAACACCTTCCGATG
1 AGGAAGGACAAACTGGAATATAAACAACACCTTCCGATG
* * *
37651 AGGAAGGGCAAATTGAGAATTTAAACAACACCTTCCGATG
1 AGGAAGGACAAACTG-GAATATAAACAACACCTTCCGATG
* * * **
37691 AGGAA-GAGCTAACTGGTAGACTTCACAACACCTTCCGATG
1 AGGAAGGA-CAAACTGGAATA-TAAACAACACCTTCCGATG
* ** * * *
37731 GGGAA-GAGCAAACCAGAATGTAAACAACATCTTCTGATG
1 AGGAAGGA-CAAACTGGAATATAAACAACACCTTCCGATG
* *
37770 AGGAAGGGCAAACTGGGAATGTAAACAACACCTTCCGATG
1 AGGAAGGACAAACT-GGAATATAAACAACACCTTCCGATG
*
37810 AGGAAGGACAAATTGGGAAT-TCAAACAACACCTTCCGATG
1 AGGAAGGACAAACT-GGAATAT-AAACAACACCTTCCGATG
*
37850 AGGAAGGGCAAACTGG
1 AGGAAGGACAAACTGG
37866 TAGATAATCG
Statistics
Matches: 242, Mismatches: 43, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
39 67 0.28
40 175 0.72
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (39 bp):
AGGAAGGACAAACTGGAATATAAACAACACCTTCCGATG
Found at i:37640 original size:79 final size:78
Alignment explanation
Indices: 37555--37858 Score: 346
Period size: 79 Copynumber: 3.8 Consensus size: 78
37545 CAGGAATATG
*
37555 AACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTT-AACAACACCTTCCGATGGGGAAGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGG-AAA-TTAAACAACACCTTCCGATGAGGAAGG
37619 GCTAACCGGAATGTA
64 GCTAACCGGAATGTA
* * *
37634 AACAACACCTTCCGATGAGGAAGGGCAAATTGAGAATTTAAACAACACCTTCCGATGAGGAAGAG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTG-GAAATTAAACAACACCTTCCGATGAGGAAGGG
*
37699 CTAACTGGTAGACT-T-
65 CTAACCGG-A-A-TGTA
* * * ** * *
37714 CACAACACCTTCCGATGGGGAAGAGCAAACCAG-AATGTAAACAACATCTTCTGATGAGGAAGGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGAAAT-TAAACAACACCTTCCGATGAGGAAGGG
* *
37778 CAAACTGGGAATGTA
65 CTAAC-CGGAATGTA
* * *
37793 AACAACACCTTCCGATGAGGAAGGACAAATTGGGAATTCAAACAACACCTTCCGATGAGGAAGGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATT-AAACAACACCTTCCGATGAGGAAGGG
37858 C
65 C
37859 AAACTGGTAG
Statistics
Matches: 188, Mismatches: 26, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
77 1 0.01
78 6 0.03
79 120 0.64
80 58 0.31
81 2 0.01
82 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.17
Consensus pattern (78 bp):
AACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATTAAACAACACCTTCCGATGAGGAAGGGC
TAACCGGAATGTA
Found at i:37725 original size:119 final size:118
Alignment explanation
Indices: 37555--37862 Score: 431
Period size: 119 Copynumber: 2.6 Consensus size: 118
37545 CAGGAATATG
* *
37555 AACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTTAACAACACCTTCCGATGGGGAAGGG
1 AACAACACCTTCCGATGAGGAA-GGCAAACTGGTAGACTTCACAACACCTTCCGATGGGGAAGGG
* * * *
37620 CTAACCGGAATGTAAACAACACCTTCCGATGAGGAAGGGCAAATTGAGAATTTA
65 CAAACCAGAATGTAAACAACACCTTCCGATGAGGAAGGGCAAACTGAGAATGTA
* *
37674 AACAACACCTTCCGATGAGGAAGAGCTAACTGGTAGACTTCACAACACCTTCCGATGGGGAAGAG
1 AACAACACCTTCCGATGAGGAAG-GCAAACTGGTAGACTTCACAACACCTTCCGATGGGGAAGGG
* * *
37739 CAAACCAGAATGTAAACAACATCTTCTGATGAGGAAGGGCAAACTGGGAATGTA
65 CAAACCAGAATGTAAACAACACCTTCCGATGAGGAAGGGCAAACTGAGAATGTA
* * *
37793 AACAACACCTTCCGATGAGGAAGGACAAATTGG--GAATTCAAACAACACCTTCCGATGAGGAAG
1 AACAACACCTTCCGATGAGGAAGG-CAAACTGGTAGACTTC--ACAACACCTTCCGATGGGGAAG
37856 GGCAAAC
63 GGCAAAC
37863 TGGTAGATAA
Statistics
Matches: 169, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
117 5 0.03
118 2 0.01
119 162 0.96
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (118 bp):
AACAACACCTTCCGATGAGGAAGGCAAACTGGTAGACTTCACAACACCTTCCGATGGGGAAGGGC
AAACCAGAATGTAAACAACACCTTCCGATGAGGAAGGGCAAACTGAGAATGTA
Found at i:39824 original size:40 final size:38
Alignment explanation
Indices: 39736--40152 Score: 377
Period size: 40 Copynumber: 10.7 Consensus size: 38
39726 TCAGTAGACT
* **
39736 TAACAACACCTTCCGATGAGGAAGAGCAAACCAGAATG
1 TAACAACACCTTCCGATGAGGAAGGGCAAACTGGAATG
39774 TAAACAACACCTTCCGATGAGGAAGGGCAAACTCGGAATG
1 T-AACAACACCTTCCGATGAGGAAGGGCAAACT-GGAATG
* * *
39814 TAAACAACACCTTCCGATGAGAAATGGCAAACTGGGAATT
1 T-AACAACACCTTCCGATGAGGAAGGGCAAACT-GGAATG
* *
39854 TAAACAACACCTTCCGATGATGAAAGGCAAACTGGTAAACT-
1 T-AACAACACCTTCCGATGAGGAAGGGCAAACTGG--AA-TG
39895 TAACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACT-
1 TAACAACACCTTCCGATGAGGAAGGGCAAACTGG--AA-TG
*
39935 TAACAACACCTTCCGATAAGGAAGGGCAAAC-----TG
1 TAACAACACCTTCCGATGAGGAAGGGCAAACTGGAATG
* *
39968 --ACAACAGCTTCCGATGAGGAAGGGCAAACCGGGAAAT-
1 TAACAACACCTTCCGATGAGGAAGGGCAAA-CTGG-AATG
* * **
40005 TCGACAACACCTTCCGATGAGGAAGGGCAAATTGGGAAAC
1 T-AACAACACCTTCCGATGAGGAAGGGCAAACT-GGAATG
* *
40045 TCAACAACACCTTTCGATTAGGAAGGGCAAACTGGTAATG
1 T-AACAACACCTTCCGATGAGGAAGGGCAAACTGG-AATG
* ** *
40085 CTAACAACACCTTTCGATGAGGAAGCACAAACTGAAAAATG
1 -TAACAACACCTTCCGATGAGGAAGGGCAAACTG--GAATG
*
40126 CTGACAACACCTTCCGATGAGGAAGGG
1 -TAACAACACCTTCCGATGAGGAAGGG
40153 TAATTTAGGA
Statistics
Matches: 324, Mismatches: 33, Indels: 41
0.81 0.08 0.10
Matches are distributed among these distances:
31 26 0.08
32 2 0.01
38 2 0.01
39 35 0.11
40 227 0.70
41 31 0.10
42 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (38 bp):
TAACAACACCTTCCGATGAGGAAGGGCAAACTGGAATG
Found at i:39972 original size:31 final size:31
Alignment explanation
Indices: 39937--39996 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
39927 GGTAAACTTA
39937 ACAACACCTTCCGATAAGGAAGGGCAAACTG
1 ACAACACCTTCCGATAAGGAAGGGCAAACTG
* *
39968 ACAACAGCTTCCGATGAGGAAGGGCAAAC
1 ACAACACCTTCCGATAAGGAAGGGCAAAC
39997 CGGGAAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.38, C:0.25, G:0.25, T:0.12
Consensus pattern (31 bp):
ACAACACCTTCCGATAAGGAAGGGCAAACTG
Found at i:39982 original size:71 final size:71
Alignment explanation
Indices: 39817--40035 Score: 224
Period size: 71 Copynumber: 3.0 Consensus size: 71
39807 CGGAATGTAA
* * * * *
39817 ACAACACCTTCCGATGAGAAATGGCAAACTGGGAATTTAAACAACACCTTCCGATGATGAAAGGC
1 ACAACACCTTCCGATGAGGAAGGGCAAACCGGGAAATTCAACAACACCTTCC---GAT--AAGG-
* * *
39882 AAACTGGTAAACTTA
60 -AA-GGGCAAAC-TG
* *
39897 ACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTT-AACAACACCTTCCGATAAGGAAGGG
1 ACAACACCTTCCGATGAGGAAGGGCAAACCGGGAAA-TTCAACAACACCTTCCGATAAGGAAGGG
39961 CAAACTG
65 CAAACTG
* * *
39968 ACAACAGCTTCCGATGAGGAAGGGCAAACCGGGAAATTCGACAACACCTTCCGATGAGGAAGGGC
1 ACAACACCTTCCGATGAGGAAGGGCAAACCGGGAAATTCAACAACACCTTCCGATAAGGAAGGGC
40033 AAA
66 AAA
40036 TTGGGAAACT
Statistics
Matches: 125, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
70 2 0.02
71 61 0.49
72 6 0.05
73 2 0.02
75 4 0.03
77 3 0.02
80 45 0.36
81 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (71 bp):
ACAACACCTTCCGATGAGGAAGGGCAAACCGGGAAATTCAACAACACCTTCCGATAAGGAAGGGC
AAACTG
Found at i:40015 original size:151 final size:151
Alignment explanation
Indices: 39817--40119 Score: 419
Period size: 151 Copynumber: 2.0 Consensus size: 151
39807 CGGAATGTAA
* * * *
39817 ACAACACCTTCCGATGAGAAATGGCAAACTGGGAATTTAAACAACACCTTCCGATGATGAAAGGC
1 ACAACACCTTCCGATGAGAAAGGGCAAACCGGGAAATTAAACAACACCTTCCGATGAGGAAAGGC
* *
39882 AAACTGGTAAACTTAACAACACCTTCCGATGAGGAAGGGCAAACTGGTAA-ACTTAACAACACCT
66 AAACTGGGAAACTCAACAACACCTTCCGATGAGGAAGGGCAAACTGGTAATAC-TAACAACACCT
**
39946 TCCGATAAGGAAGGGCAAACTG
130 TCCGATAAGGAAGCACAAACTG
* * ** *
39968 ACAACAGCTTCCGATGAGGAAGGGCAAACCGGGAAATTCGACAACACCTTCCGATGAGGAAGGGC
1 ACAACACCTTCCGATGAGAAAGGGCAAACCGGGAAATTAAACAACACCTTCCGATGAGGAAAGGC
* * * *
40033 AAATTGGGAAACTCAACAACACCTTTCGATTAGGAAGGGCAAACTGGTAATGCTAACAACACCTT
66 AAACTGGGAAACTCAACAACACCTTCCGATGAGGAAGGGCAAACTGGTAATACTAACAACACCTT
* *
40098 TCGATGAGGAAGCACAAACTG
131 CCGATAAGGAAGCACAAACTG
40119 A
1 A
40120 AAAATGCTGA
Statistics
Matches: 132, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
151 131 0.99
152 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (151 bp):
ACAACACCTTCCGATGAGAAAGGGCAAACCGGGAAATTAAACAACACCTTCCGATGAGGAAAGGC
AAACTGGGAAACTCAACAACACCTTCCGATGAGGAAGGGCAAACTGGTAATACTAACAACACCTT
CCGATAAGGAAGCACAAACTG
Found at i:40051 original size:111 final size:111
Alignment explanation
Indices: 39857--40078 Score: 329
Period size: 111 Copynumber: 2.0 Consensus size: 111
39847 GGGAATTTAA
* * *
39857 ACAACACCTTCCGATGATGAAAGGCAAACTGGTAAACTTAACAACACCTTCCGATGAGGAAGGGC
1 ACAACACCTTCCGATGAGGAAAGGCAAACCGGGAAACTTAACAACACCTTCCGATGAGGAAGGGC
* *
39922 AAACTGGTAAACTTAACAACACCTTCCGATAAGGAAGGGCAAACTG
66 AAACTGGGAAACTCAACAACACCTTCCGATAAGGAAGGGCAAACTG
* * *
39968 ACAACAGCTTCCGATGAGGAAGGGCAAACCGGGAAA-TTCGACAACACCTTCCGATGAGGAAGGG
1 ACAACACCTTCCGATGAGGAAAGGCAAACCGGGAAACTT-AACAACACCTTCCGATGAGGAAGGG
* * *
40032 CAAATTGGGAAACTCAACAACACCTTTCGATTAGGAAGGGCAAACTG
65 CAAACTGGGAAACTCAACAACACCTTCCGATAAGGAAGGGCAAACTG
40079 GTAATGCTAA
Statistics
Matches: 99, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
110 2 0.02
111 97 0.98
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.16
Consensus pattern (111 bp):
ACAACACCTTCCGATGAGGAAAGGCAAACCGGGAAACTTAACAACACCTTCCGATGAGGAAGGGC
AAACTGGGAAACTCAACAACACCTTCCGATAAGGAAGGGCAAACTG
Done.