Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016761.1 Corchorus olitorius cultivar O-4 contig16794, 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: 42390
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:67 original size:2 final size:2
Alignment explanation
Indices: 60--92 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
50 ATATTCTCGA
60 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
93 GCTGACTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:414 original size:24 final size:25
Alignment explanation
Indices: 367--415 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
357 TGAATGAAAC
*
367 AAGATTAGTTATATATTACTTTCAAA
1 AAGATTAGTTATATATTA-GTTCAAA
393 AAGATTAGTTATATATT-GTTCAA
1 AAGATTAGTTATATATTAGTTCAA
416 CTTTGTACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
26 17 0.77
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (25 bp):
AAGATTAGTTATATATTAGTTCAAA
Found at i:751 original size:45 final size:45
Alignment explanation
Indices: 693--779 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
683 TACCTAAATT
* *
693 CTACTGCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTA
1 CTACTGCATCTCTAGATAATTCATCAAAATAAAACTAATATTCTA
* *
738 CTACTTCATCTCTAGATAATTCATCAAAATAAAATTAATATT
1 CTACTGCATCTCTAGATAATTCATCAAAATAAAACTAATATT
780 AATTGTTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.36
Consensus pattern (45 bp):
CTACTGCATCTCTAGATAATTCATCAAAATAAAACTAATATTCTA
Found at i:1738 original size:19 final size:19
Alignment explanation
Indices: 1714--1753 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1704 AGTCACTAAA
*
1714 AATAATATATAGTATATAT
1 AATAATATATACTATATAT
*
1733 AATAATCTATACTATATAT
1 AATAATATATACTATATAT
1752 AA
1 AA
1754 AAGTACGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (19 bp):
AATAATATATACTATATAT
Found at i:2630 original size:351 final size:351
Alignment explanation
Indices: 1976--2661 Score: 982
Period size: 351 Copynumber: 2.0 Consensus size: 351
1966 AATCGGTTAG
* * * *
1976 GAGAAGATCAATTCTATCCAGAAATTTCAAGGGCAAAATCGTTCACCGGAACTGCATAAATAAGT
1 GAGAAGATCAATTCTATCCAGAAATTTCAAGGGCAAAATCATCCACCGAAACTGCAGAAATAAGT
*
2041 CTCGAGGTAAACATAAAATTTGTAGATCTTGAAATCCTCTTTCCAACGGTACCTCATTTGCATTT
66 CTCGAGGTAAACATAAAAGTTGTAGATCTTGAAATCCTCTTTCCAACGGTACCTCATTTGCATTT
* * * * * *
2106 TTCTGAGCTCCATATCAAAAGTCATGAATTTTCTTCTTAAAATGTTATTGTGAAGTCCTCTTTTG
131 TGCTGAGCTCCAGATCAAAAGTCATGAACTTTCTTCTCAAAATGCTATTGTGAAGTCCTCCTTTG
* *
2171 AATAGGATTTAACAATGTTGCATCAGGGCTGAATCATTACTGCATCATAATTACTGATTGAAGTT
196 AATAGGATTTAACAATGTTGCATCAGGGCTAAATCATTACTGCATCATAATTACTGATTGAACTT
* * * * *
2236 GGACTCCTTCTTTGGGCTTCCATATTAACGAATTGGATCTAAGAATATCAGATTTAGCCTTCAAG
261 GGACTCCTTCTTTGGGCTTCAACAATAACAAATTGGATCTAAGAATATCAGATTTAGACTTCAAG
2301 ACATATGGCTCTCCAAGCCGGTTTAA
326 ACATATGGCTCTCCAAGCCGGTTTAA
* * * *
2327 GAGAAGATCAATTCTGTCCAGAAATTTTAAGGGCAAAATCATCCACCGAAACTGCAGAATTAGGT
1 GAGAAGATCAATTCTATCCAGAAATTTCAAGGGCAAAATCATCCACCGAAACTGCAGAAATAAGT
* * * **
2392 CTCGAGGTAAACGTAAAAGTTGTAGATTTTGGAATCCTCTTTCCAACGGTATTTCATTTGCATTT
66 CTCGAGGTAAACATAAAAGTTGTAGATCTTGAAATCCTCTTTCCAACGGTACCTCATTTGCATTT
** * *
2457 TGCTGAGCTCTGGATCAAACA-TTATGAACTTTCTTC-CAAAACTGCTCTTGTGAAGTCCTCCTT
131 TGCTGAGCTCCAGATCAAA-AGTCATGAACTTTCTTCTCAAAA-TGCTATTGTGAAGTCCTCCTT
* *
2520 TGAATAGGATTTAACAATGTTGCATCAGGGCTAAATCATTACTGCGTCATAATTACTGATTGGAC
194 TGAATAGGATTTAACAATGTTGCATCAGGGCTAAATCATTACTGCATCATAATTACTGATTGAAC
* * * *
2585 TTGGACTTCTTCTTTGGG-TGTCAACAATAACAAATTGGGTCTAAGAATATCAGATTTCGATTTC
259 TTGGACTCCTTCTTTGGGCT-TCAACAATAACAAATTGGATCTAAGAATATCAGATTTAGACTTC
*
2649 AAGACATCTGGCT
323 AAGACATATGGCT
2662 TGCCAATTTG
Statistics
Matches: 294, Mismatches: 38, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
350 5 0.02
351 288 0.98
352 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (351 bp):
GAGAAGATCAATTCTATCCAGAAATTTCAAGGGCAAAATCATCCACCGAAACTGCAGAAATAAGT
CTCGAGGTAAACATAAAAGTTGTAGATCTTGAAATCCTCTTTCCAACGGTACCTCATTTGCATTT
TGCTGAGCTCCAGATCAAAAGTCATGAACTTTCTTCTCAAAATGCTATTGTGAAGTCCTCCTTTG
AATAGGATTTAACAATGTTGCATCAGGGCTAAATCATTACTGCATCATAATTACTGATTGAACTT
GGACTCCTTCTTTGGGCTTCAACAATAACAAATTGGATCTAAGAATATCAGATTTAGACTTCAAG
ACATATGGCTCTCCAAGCCGGTTTAA
Found at i:3515 original size:27 final size:27
Alignment explanation
Indices: 3477--3550 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
3467 GTTTCCTTTA
3477 TGGATCCCGATGGTCATGAGACAAAAC
1 TGGATCCCGATGGTCATGAGACAAAAC
* ** *
3504 TGGATCCCGATGGTCGTGAGATGAAAT
1 TGGATCCCGATGGTCATGAGACAAAAC
*
3531 TAGATCCCGATGGTCATGAG
1 TGGATCCCGATGGTCATGAG
3551 CAATTTGGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (27 bp):
TGGATCCCGATGGTCATGAGACAAAAC
Found at i:3711 original size:15 final size:15
Alignment explanation
Indices: 3691--3720 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3681 AAAGAAATAG
3691 CACACCATAAAGACA
1 CACACCATAAAGACA
*
3706 CACACCATAAGGACA
1 CACACCATAAAGACA
3721 TCTTATATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.33, G:0.10, T:0.07
Consensus pattern (15 bp):
CACACCATAAAGACA
Found at i:4681 original size:26 final size:26
Alignment explanation
Indices: 4652--4702 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
4642 ATTAACAAAA
4652 TATTTTATTTAGAAAAATTCAATTTT
1 TATTTTATTTAGAAAAATTCAATTTT
4678 TATTTTATTTAGAAAAATTCAATTT
1 TATTTTATTTAGAAAAATTCAATTT
4703 CTACAGTACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (26 bp):
TATTTTATTTAGAAAAATTCAATTTT
Found at i:8877 original size:29 final size:31
Alignment explanation
Indices: 8812--8889 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 31
8802 GATAAAGTAC
* *
8812 CATTTTTCTCCTTGAACTTGTAACGTTTGGA
1 CATTTTACTCCCTGAACTTGTAACGTTTGGA
* * *
8843 CGTTTTGCTCCCTGAACTT-TAA-TTTTGGA
1 CATTTTACTCCCTGAACTTGTAACGTTTGGA
* *
8872 TATTTTACCCCCTGAACT
1 CATTTTACTCCCTGAACT
8890 CTCAATTTGA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 20 0.51
30 3 0.08
31 16 0.41
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (31 bp):
CATTTTACTCCCTGAACTTGTAACGTTTGGA
Found at i:12381 original size:61 final size:61
Alignment explanation
Indices: 12284--12407 Score: 203
Period size: 61 Copynumber: 2.0 Consensus size: 61
12274 TCTGTTCCAA
* *
12284 ATTAATCGACTCTTTTTGAAATTAATATGATTCTTGGGAGTTGAGACGGAAGGAGTATATT
1 ATTAATCGACTCTTTTTGAAATGAATATGATCCTTGGGAGTTGAGACGGAAGGAGTATATT
* * *
12345 ATTAATCGACTCTTTTTGAAATGAATATGATCCTTGGGAGTTGGGACGGAGGGAGTATGTT
1 ATTAATCGACTCTTTTTGAAATGAATATGATCCTTGGGAGTTGAGACGGAAGGAGTATATT
12406 AT
1 AT
12408 ATTATTGTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.36
Consensus pattern (61 bp):
ATTAATCGACTCTTTTTGAAATGAATATGATCCTTGGGAGTTGAGACGGAAGGAGTATATT
Found at i:13517 original size:41 final size:42
Alignment explanation
Indices: 13415--13700 Score: 291
Period size: 41 Copynumber: 6.8 Consensus size: 42
13405 CCCATTAACT
* * *
13415 AAAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCT-TTC
1 AAAAGTCCCCAAACACATTTATAACACAGAGGC-A--CTCTATAC
* * *
13459 TAAAGTCCTCAAACACATTTATAACACAGAGGCA-TCAATAC
1 AAAAGTCCCCAAACACATTTATAACACAGAGGCACTCTATAC
* *
13500 AAAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTC
1 AAAAGTCCCCAAACACATTTATAACACAGAGGCA-CTCTATAC
* *
13543 CAAAGTCCTCAAACACATTTATAACACAGAGGCA-TCTATATC
1 AAAAGTCCCCAAACACATTTATAACACAGAGGCACTCTATA-C
* * *
13585 -AAAGTACCCAAACACAATTATAACACAG-GGCAACTCTCT-C
1 AAAAGTCCCCAAACACATTTATAACACAGAGGC-ACTCTATAC
* *
13625 TAAAAGTCCTCAAACACATTTATAACACAGAGACA-TCTATATC
1 -AAAAGTCCCCAAACACATTTATAACACAGAGGCACTCTATA-C
* *
13668 -AAAGTCCCCAAACACAATTATAACACAGGGGCA
1 AAAAGTCCCCAAACACATTTATAACACAGAGGCA
13701 ATTCTCTCTA
Statistics
Matches: 203, Mismatches: 28, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
40 6 0.03
41 97 0.48
42 31 0.15
43 40 0.20
44 29 0.14
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.21
Consensus pattern (42 bp):
AAAAGTCCCCAAACACATTTATAACACAGAGGCACTCTATAC
Found at i:13662 original size:83 final size:84
Alignment explanation
Indices: 13416--13710 Score: 445
Period size: 83 Copynumber: 3.5 Consensus size: 84
13406 CCATTAACTA
*
13416 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTTTCT-AAAGTCCTCAAACACATTTA
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAA--CTCTCTCTAAAAGTCCTCAAACACATTTA
*
13480 TAACACAGAGGCATCAATA-C
64 TAACACAGAGGCATCTATATC
* * * *
13500 AAAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTAT-TCCAAAGTCCTCAAACACATTTA
1 -AAAGTCCCCAAACACAATTATAACACAGGGGCAACTCTCTCT-AAAAGTCCTCAAACACATTTA
13564 TAACACAGAGGCATCTATATC
64 TAACACAGAGGCATCTATATC
*
13585 AAAGTACCCAAACACAATTATAACACA-GGGCAACTCTCTCTAAAAGTCCTCAAACACATTTATA
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAACTCTCTCTAAAAGTCCTCAAACACATTTATA
*
13649 ACACAGAGACATCTATATC
66 ACACAGAGGCATCTATATC
*
13668 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTCTA
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAACTCTCTCTA
13711 TGGCAAAGAC
Statistics
Matches: 193, Mismatches: 12, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
82 1 0.01
83 81 0.42
84 78 0.40
85 33 0.17
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.22
Consensus pattern (84 bp):
AAAGTCCCCAAACACAATTATAACACAGGGGCAACTCTCTCTAAAAGTCCTCAAACACATTTATA
ACACAGAGGCATCTATATC
Found at i:19516 original size:25 final size:25
Alignment explanation
Indices: 19488--19555 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
19478 TGGGCCATCT
19488 ATGGGCTTGGAGCGGGCTGGAGAAA
1 ATGGGCTTGGAGCGGGCTGGAGAAA
*
19513 ATGGGCTTGGAGCGGGTTGGAGAAA
1 ATGGGCTTGGAGCGGGCTGGAGAAA
**
19538 ATGGGCTTACAGCGGGCT
1 ATGGGCTTGGAGCGGGCT
19556 CGGGTGGGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.22, C:0.13, G:0.46, T:0.19
Consensus pattern (25 bp):
ATGGGCTTGGAGCGGGCTGGAGAAA
Found at i:26919 original size:2 final size:2
Alignment explanation
Indices: 26912--26936 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26902 ATGGTCTTAA
26912 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
26937 CTAAATAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31821 original size:56 final size:55
Alignment explanation
Indices: 31730--31842 Score: 181
Period size: 56 Copynumber: 2.0 Consensus size: 55
31720 TATATGTTTC
* * *
31730 CTTTCACACAATAAATGTTAAAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTAACACAATAAATATTAAAATAAATCATAT-CCCCTATCTCTACTTAATTATT
*
31786 CTTTAACACAATAAATATTATAATAAATCATATCCCCTATCTCTACTTAATTATT
1 CTTTAACACAATAAATATTAAAATAAATCATATCCCCTATCTCTACTTAATTATT
31841 CT
1 CT
31843 ACAAAATAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
55 24 0.45
56 29 0.55
ACGTcount: A:0.37, C:0.23, G:0.01, T:0.39
Consensus pattern (55 bp):
CTTTAACACAATAAATATTAAAATAAATCATATCCCCTATCTCTACTTAATTATT
Found at i:31858 original size:55 final size:56
Alignment explanation
Indices: 31739--31859 Score: 156
Period size: 55 Copynumber: 2.2 Consensus size: 56
31729 CCTTTCACAC
* * * ** * *
31739 AATAAATGTTAAAATAAATCCTATCCCCCTATCTCTACTTAATTATTCTTTAACAC
1 AATAAATATTATAATAAATCATATCCCCCTATCTCTACTTAATTATTCTACAAAAA
31795 AATAAATATTATAATAAATCATAT-CCCCTATCTCTACTTAATTATTCTACAAAATA
1 AATAAATATTATAATAAATCATATCCCCCTATCTCTACTTAATTATTCTACAAAA-A
31851 AAT-AATATT
1 AATAAATATT
31860 TTCTTTTAAG
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
55 33 0.58
56 24 0.42
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.38
Consensus pattern (56 bp):
AATAAATATTATAATAAATCATATCCCCCTATCTCTACTTAATTATTCTACAAAAA
Found at i:31967 original size:42 final size:40
Alignment explanation
Indices: 31908--31986 Score: 140
Period size: 42 Copynumber: 1.9 Consensus size: 40
31898 TAAGGATCAG
31908 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTAC--AGAATTTTCTAT
31950 GATTTGAGTTGAGTATTTCTTAATTTACAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAGAATTTTC
31987 AAGACTTAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 9 0.24
42 28 0.76
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.48
Consensus pattern (40 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAGAATTTTCTAT
Found at i:39802 original size:3 final size:3
Alignment explanation
Indices: 39794--39839 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
39784 TTTTTTAATT
39794 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
39840 CATGTGGGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:40947 original size:130 final size:123
Alignment explanation
Indices: 40803--41048 Score: 366
Period size: 130 Copynumber: 1.9 Consensus size: 123
40793 ATTTAAGAAA
40803 TATATTTAAAAAATTCGAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGATAAATAAAAT
1 TATATTTAAAAAATTCGAATATATATAAGTTTTTTAATTAAAATAGTAAAATGG-T--A-AAAAT
* * *
40868 AGGTATAAGGATATTAGATTTAATTAAATTAAAATTGAGTTTTTAGTTGAGTAAAACTGTAAAAG
62 ---TATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAG
* *
40933 TATATTTAAAAAATTCTAATATATATAATTTTTTTAATTAAAATAGTAAAATGGTAAAAATTATA
1 TATATTTAAAAAATTCGAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTATA
* *
40998 AAGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTTGTGTAAAACT
66 AAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACT
41049 AAAAAAGTTT
Statistics
Matches: 109, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
123 50 0.46
126 5 0.05
127 1 0.01
129 1 0.01
130 52 0.48
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.40
Consensus pattern (123 bp):
TATATTTAAAAAATTCGAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTATA
AAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAG
Found at i:41055 original size:123 final size:127
Alignment explanation
Indices: 40803--41056 Score: 372
Period size: 123 Copynumber: 2.0 Consensus size: 127
40793 ATTTAAGAAA
40803 TATATTTAAAAAATTCGAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGATAAATAAAAT
1 TATATTTAAAAAATTCGAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGAT-AATAAAAT
* * * **
40868 AGGTATAAGGATATTAGATTTAATTAAATTAAAATTGAGTTTTTAGTTGAGTAAAACTGTAAAAG
65 --GTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAAAAAAG
* *
40933 TATATTTAAAAAATTCTAATATATATAATTTTTTTAATTAAAATAGTAAAATGG-T-A-AAAAT-
1 TATATTTAAAAAATTCGAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGATAATAAAATG
* *
40994 TATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTTGTGTAAAACTAAAAAAG
66 TATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAAAAAAG
41056 T
1 T
41057 TTAAACAATG
Statistics
Matches: 115, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
123 56 0.49
126 5 0.04
127 1 0.01
129 1 0.01
130 52 0.45
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.39
Consensus pattern (127 bp):
TATATTTAAAAAATTCGAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGATAATAAAATG
TATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAAAAAAG
Found at i:42022 original size:2 final size:2
Alignment explanation
Indices: 42015--42052 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
42005 CAAGCAATTC
42015 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
42053 AGTCTAAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:42324 original size:39 final size:40
Alignment explanation
Indices: 42268--42348 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
42258 TTTAATTCCT
*
42268 ATGTAATATATATAATAACTAAAATATTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
42308 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
42347 AT
1 AT
42349 CTAGGTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:42380 original size:25 final size:22
Alignment explanation
Indices: 42339--42383 Score: 63
Period size: 25 Copynumber: 1.9 Consensus size: 22
42329 AATACTTACA
42339 TTAATTAAATCTAGGTATTTTT
1 TTAATTAAATCTAGGTATTTTT
42361 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAA-TC-TAGGTATTT
42384 GTGCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 2 0.10
25 9 0.45
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.53
Consensus pattern (22 bp):
TTAATTAAATCTAGGTATTTTT
Done.