Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007897.1 Corchorus capsularis cultivar CVL-1 contig07918, 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: 83689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:246 original size:90 final size:89
Alignment explanation
Indices: 37--285 Score: 303
Period size: 90 Copynumber: 2.8 Consensus size: 89
27 CGGTGTAGCA
* * * *
37 TCTTTAAAG-TTGG-ATTTGGTGAGCTCGGTGCAGCACCATTTTCAAATAGTTCGGGATGGTTCG
1 TCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAGCA-CATTTTCAAACAGTTCGGGATGATTCG
*
100 GTGAATCAAGTTAATGCGGTGCATT
65 GTGAATCAAGTAAATGCGGTGCATT
* * *
125 TCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAGCAAATTCTCAAACAATTCGGGATGATTCGG
1 TCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCGGGATGATTCGG
190 TGAATCAAG-AAGATGCGGTGCATTATT
66 TGAATCAAGTAA-ATGCGGTGC---ATT
* *
217 TCTTC-AAGATTGG-GTTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTC-AGATTGATTCG
1 TCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCGGGA-TGATTCG
*
279 GTAAATC
65 GTGAATC
286 GATTAGTTTT
Statistics
Matches: 140, Mismatches: 14, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
88 9 0.06
89 47 0.34
90 68 0.49
91 8 0.06
92 8 0.06
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (89 bp):
TCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCGGGATGATTCGG
TGAATCAAGTAAATGCGGTGCATT
Found at i:3671 original size:6 final size:6
Alignment explanation
Indices: 3654--3689 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
3644 CTCATATGTT
*
3654 TCTTTC -CTTTC TCTTTC TCTTTC TCTTTT TCTTTC T
1 TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC T
3690 TTAAATCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
TCTTTC
Found at i:9371 original size:26 final size:26
Alignment explanation
Indices: 9331--9386 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
9321 GTAATCAACT
* *
9331 TAATTCAGTGCAATTAAGTGAATTGG
1 TAATTCAGTGAAATTAAGTAAATTGG
*
9357 TAATTCGGTGAAATTAAGTAAATTGG
1 TAATTCAGTGAAATTAAGTAAATTGG
9383 TAAT
1 TAAT
9387 CAATTTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (26 bp):
TAATTCAGTGAAATTAAGTAAATTGG
Found at i:9403 original size:35 final size:35
Alignment explanation
Indices: 9357--9850 Score: 492
Period size: 35 Copynumber: 13.7 Consensus size: 35
9347 AGTGAATTGG
*
9357 TAATTCGGTGAAATTAAGTAAATTGGTAATCAATT
1 TAATTCGGTGAAATTAAGTAAATTGGTAATCAACT
*
9392 TAATTCGGTGAAATTAAGTAAATTGGTAATCTACT
1 TAATTCGGTGAAATTAAGTAAATTGGTAATCAACT
9427 TAATTCGGTGAAATTTAAGTAAATTGGTAATCAACT
1 TAATTCGGTGAAA-TTAAGTAAATTGGTAATCAACT
9463 TAATTCGGTGAAATTAAGTAAATTGGTAATCAACT
1 TAATTCGGTGAAATTAAGTAAATTGGTAATCAACT
*
9498 TAATTCGGTGTAATTAAGTAAATTGGTAATCAACT
1 TAATTCGGTGAAATTAAGTAAATTGGTAATCAACT
*
9533 TAATTCGGTGAAATTAAGTAAATTGGTAATCAGCT
1 TAATTCGGTGAAATTAAGTAAATTGGTAATCAACT
*
9568 TAATTCGGT-ATAATTAAGTAAATTGGAAATCAACT
1 TAATTCGGTGA-AATTAAGTAAATTGGTAATCAACT
* **
9603 TAATT-GGTAATTAAATTAAGTAAATTGGTAATCAGTT
1 TAATTCGG---TGAAATTAAGTAAATTGGTAATCAACT
* **
9640 TAATTCGATGTAATTAAGTAAATAAGTAAATTGGTAGTTAATTTAACT
1 TAATTCG--GTGA--AA-T---TAAGTAAATTGGTA---ATC--AACT
* *
9688 TAATTCGGTGTAATTAAGTAAATTGGTAATTAACT
1 TAATTCGGTGAAATTAAGTAAATTGGTAATCAACT
* * * * * *
9723 AAATTCGG-CACAAGTAAGCAAATCGGTAGGT-AACT
1 TAATTCGGTGA-AATTAAGTAAATTGGTA-ATCAACT
* * * *
9758 TAATTCGGTGTAATTAAGCAAATTGATAATTAACT
1 TAATTCGGTGAAATTAAGTAAATTGGTAATCAACT
* * * ** * *
9793 TAGTTCGGTGTAATTAAGTGAATCAGTAATTAGCT
1 TAATTCGGTGAAATTAAGTAAATTGGTAATCAACT
* *
9828 TAATTCGGTGTAATCAAGTAAAT
1 TAATTCGGTGAAATTAAGTAAAT
9851 AATCAAATGG
Statistics
Matches: 392, Mismatches: 43, Indels: 48
0.81 0.09 0.10
Matches are distributed among these distances:
34 4 0.01
35 273 0.70
36 35 0.09
37 31 0.08
38 2 0.01
39 2 0.01
40 16 0.04
43 15 0.04
44 2 0.01
46 3 0.01
48 9 0.02
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (35 bp):
TAATTCGGTGAAATTAAGTAAATTGGTAATCAACT
Found at i:9618 original size:21 final size:21
Alignment explanation
Indices: 9594--9634 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9584 AGTAAATTGG
*
9594 AAATCAACTTAATTGGTAATT
1 AAATCAACTAAATTGGTAATT
* *
9615 AAATTAAGTAAATTGGTAAT
1 AAATCAACTAAATTGGTAAT
9635 CAGTTTAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (21 bp):
AAATCAACTAAATTGGTAATT
Found at i:9718 original size:16 final size:16
Alignment explanation
Indices: 9697--9727 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9687 TTAATTCGGT
*
9697 GTAATTAAGTAAATTG
1 GTAATTAACTAAATTG
9713 GTAATTAACTAAATT
1 GTAATTAACTAAATT
9728 CGGCACAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.39
Consensus pattern (16 bp):
GTAATTAACTAAATTG
Found at i:14710 original size:34 final size:35
Alignment explanation
Indices: 14645--14714 Score: 92
Period size: 34 Copynumber: 2.0 Consensus size: 35
14635 CACAAGATAA
14645 GCCTAAACAAATTAAGTATAACATGAACAAATCAAT
1 GCCTAAACAAATTAAG-ATAACATGAACAAATCAAT
14681 GCCTAAACAAAATT-A-ATAACAT-AATCAAATCAAT
1 GCCTAAAC-AAATTAAGATAACATGAA-CAAATCAAT
14715 ATATAAAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
33 2 0.06
34 16 0.50
36 9 0.28
37 5 0.16
ACGTcount: A:0.54, C:0.17, G:0.06, T:0.23
Consensus pattern (35 bp):
GCCTAAACAAATTAAGATAACATGAACAAATCAAT
Found at i:15610 original size:32 final size:31
Alignment explanation
Indices: 15574--15659 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 31
15564 CCGCGATAAA
*
15574 CGCACACTATAATAATATTTGTGTGCTTCTCC
1 CGCACACTATAAT-ATATTTGTGTGCATCTCC
15606 CGCACACTATAATGATATTTGTGTGCATCTCC
1 CGCACACTATAAT-ATATTTGTGTGCATCTCC
*
15638 CGCACAAC-ATAATATCTTTGTG
1 CGCAC-ACTATAATATATTTGTG
15660 CACTCACACA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
31 8 0.16
32 40 0.80
33 2 0.04
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (31 bp):
CGCACACTATAATATATTTGTGTGCATCTCC
Found at i:15706 original size:28 final size:28
Alignment explanation
Indices: 15627--15730 Score: 86
Period size: 28 Copynumber: 3.6 Consensus size: 28
15617 ATGATATTTG
* **
15627 TGTGCATCTCCCGCACAACATAATATCTT
1 TGTGCA-CTCCCGCATAACATAATATCCA
* *
15656 TGTGCACTCACACACAT-A-GTAATATCCA
1 TGTGCACTC-C-CGCATAACATAATATCCA
*
15684 TGTGCACTCCCGCATAACATAATGATACCCG
1 TGTGCACTCCCGCATAACATAAT-AT--CCA
15715 TGTGCACTCCCGCATA
1 TGTGCACTCCCGCATA
15731 TAATAGTATT
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
26 4 0.07
27 2 0.03
28 23 0.38
29 10 0.17
30 3 0.05
31 18 0.30
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (28 bp):
TGTGCACTCCCGCATAACATAATATCCA
Found at i:16611 original size:21 final size:21
Alignment explanation
Indices: 16569--16613 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
16559 TTTATAATTT
* *
16569 TTATTAATACTATATTACTAA
1 TTATTAATACTATAATAATAA
16590 TTATTAATA-TATAAATAATAA
1 TTATTAATACTAT-AATAATAA
16611 TTA
1 TTA
16614 AATAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (21 bp):
TTATTAATACTATAATAATAA
Found at i:16990 original size:29 final size:31
Alignment explanation
Indices: 16930--16990 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
16920 AACTTTAGGT
* * *
16930 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCATATTTTTAAAAAATA
16961 TTTCCAATTGTA-CCAT-TTTTTAAAAAATA
1 TTTCCAATTGTACCCATATTTTTAAAAAATA
16990 T
1 T
16991 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 3 0.11
31 11 0.41
ACGTcount: A:0.33, C:0.16, G:0.05, T:0.46
Consensus pattern (31 bp):
TTTCCAATTGTACCCATATTTTTAAAAAATA
Found at i:16995 original size:31 final size:31
Alignment explanation
Indices: 16930--16990 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
16920 AACTTTAGGT
* * *
16930 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCATTATTTTAAAAACATA
16961 TTTCCAATTGTACCATT-TTTTAAAAA-ATA
1 TTTCCAATTGTACCATTATTTTAAAAACATA
16990 T
1 T
16991 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:0.16, G:0.05, T:0.46
Consensus pattern (31 bp):
TTTCCAATTGTACCATTATTTTAAAAACATA
Found at i:18340 original size:19 final size:20
Alignment explanation
Indices: 18313--18350 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
18303 TACTATTATT
18313 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
18333 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
18351 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:18542 original size:22 final size:22
Alignment explanation
Indices: 18514--18675 Score: 112
Period size: 22 Copynumber: 7.3 Consensus size: 22
18504 TGTCTCTATG
18514 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
18536 TGGTTATTATAATTTCATGAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
18558 AGGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
18580 TGGTTACCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
18602 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
18624 TCAGGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
** * *
18648 TGGTTATTGAAATTTCATAGGT
1 TGGTTATCAAAATTTCATAAGA
18670 TGGTTA
1 TGGTTA
18676 ATTATTACAA
Statistics
Matches: 117, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
21 2 0.02
22 96 0.82
23 1 0.01
24 18 0.15
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:18687 original size:26 final size:24
Alignment explanation
Indices: 18611--18693 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 24
18601 GTGGTTACCA
*
18611 AAATTTCATAGGATCAGGTTATTA--
1 AAATTTCATAGG-T-TGGTTATTATT
* *
18635 AAATTTCTTAGGTTGGTTA-T-TG
1 AAATTTCATAGGTTGGTTATTATT
18657 AAATTTCATAGGTTGGTTAATTATT
1 AAATTTCATAGGTTGGTT-ATTATT
*
18682 ACAATTTTATAG
1 A-AATTTCATAG
18694 AAAGGTTATC
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
21 1 0.02
22 22 0.46
23 2 0.04
24 12 0.25
25 2 0.04
26 9 0.19
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.45
Consensus pattern (24 bp):
AAATTTCATAGGTTGGTTATTATT
Found at i:18748 original size:21 final size:22
Alignment explanation
Indices: 18707--18748 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
18697 GGTTATCAAA
18707 GAGATTATCAAAATGTCATAGC
1 GAGATTATCAAAATGTCATAGC
18729 GAGATTAT-AAGAAT-TCATAG
1 GAGATTATCAA-AATGTCATAG
18749 TGTGGTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (22 bp):
GAGATTATCAAAATGTCATAGC
Found at i:18777 original size:22 final size:21
Alignment explanation
Indices: 18752--18849 Score: 74
Period size: 22 Copynumber: 4.5 Consensus size: 21
18742 TTCATAGTGT
18752 GGTTAACAAAATTTCATTAGGA
1 GGTTAACAAAATTTCATT-GGA
* *
18774 GGTT-ACTAATATTTCATGGGGA
1 GGTTAAC-AAAATTTCAT-TGGA
* * *
18796 GGTTATCAAAATTTTATTGTGT
1 GGTTAACAAAATTTCATTG-GA
* *
18818 GGTTATCAAAATTTCATATGAA
1 GGTTAACAAAATTTCAT-TGGA
18840 GGTTAA-AAAA
1 GGTTAACAAAA
18850 GTCTCAATTT
Statistics
Matches: 60, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
21 7 0.12
22 50 0.83
23 3 0.05
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (21 bp):
GGTTAACAAAATTTCATTGGA
Found at i:18926 original size:22 final size:23
Alignment explanation
Indices: 18889--19095 Score: 134
Period size: 22 Copynumber: 9.3 Consensus size: 23
18879 TGATAGAATG
18889 TTATC-AAATCTT-ATAGAGTA-A
1 TTATCAAAAT-TTCATAGAGTAGA
*
18910 TTATCGAAATTTCATAGAGATCAGA
1 TTATCAAAATTTCATAGAG-T-AGA
*
18935 TTATCAAAATTT-ATAG-GAAGA
1 TTATCAAAATTTCATAGAGTAGA
* *
18956 TTATCAAAATTTCATAGTGTTG-
1 TTATCAAAATTTCATAGAGTAGA
* * *
18978 TTATCAAAATTTCAAAGCG-AGG
1 TTATCAAAATTTCATAGAGTAGA
*
19000 TTATCAAAATTACATA-ATGT-GA
1 TTATCAAAATTTCATAGA-GTAGA
* * *
19022 TTATCAGAATTTCATAGAG-GGG
1 TTATCAAAATTTCATAGAGTAGA
* * *
19044 TCATCAAAATTTTATAAAG-AGGA
1 TTATCAAAATTTCATAGAGTA-GA
* *
19067 -TATCAAAATTTCATAAAG-AGG
1 TTATCAAAATTTCATAGAGTAGA
19088 TTATCAAA
1 TTATCAAA
19096 TCTTCAAAAT
Statistics
Matches: 149, Mismatches: 23, Indels: 27
0.75 0.12 0.14
Matches are distributed among these distances:
21 24 0.16
22 102 0.68
23 6 0.04
24 5 0.03
25 12 0.08
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (23 bp):
TTATCAAAATTTCATAGAGTAGA
Found at i:19026 original size:44 final size:45
Alignment explanation
Indices: 18910--19123 Score: 160
Period size: 44 Copynumber: 4.8 Consensus size: 45
18900 TATAGAGTAA
* * *
18910 TTATCGAAATTTCATAGA-GATCAGATTATCAAAATTT-ATAG-GAAGA
1 TTATCAAAATTTCATA-ATGAT--GATTATCAAAATTTCAAAGAG-AGG
* * *
18956 TTATCAAAATTTCATAGTGTTG-TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAATGATGATTATCAAAATTTCAAAGAGAGG
* * * *
19000 TTATCAAAATTACATAATG-TGATTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAATGATGATTATCAAAATTTCAAAGAGAGG
* * * *
19044 TCATCAAAATTTTATAAAGAGGA-TATCAAAATTTCATAA-AGAGG
1 TTATCAAAATTTCATAATGATGATTATCAAAATTTCA-AAGAGAGG
*
19088 TTATC-AAATCTTCAAAATG-TGATTA-CAAAAATTTCA
1 TTATCAAAAT-TTCATAATGATGATTATC-AAAATTTCA
19124 TAATGGTATT
Statistics
Matches: 135, Mismatches: 24, Indels: 20
0.75 0.13 0.11
Matches are distributed among these distances:
43 21 0.16
44 93 0.69
45 4 0.03
46 17 0.13
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (45 bp):
TTATCAAAATTTCATAATGATGATTATCAAAATTTCAAAGAGAGG
Found at i:19033 original size:66 final size:66
Alignment explanation
Indices: 18954--19082 Score: 161
Period size: 66 Copynumber: 2.0 Consensus size: 66
18944 TTTATAGGAA
* ** * * *
18954 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAAT
1 GATTATCAAAATTTCATAGAGGGGTCATCAAAATTTCATAA-AGAGGATATCAAAATTACATAAT
19018 GT
65 GT
* * *
19020 GATTATCAGAATTTCATAGAGGGGTCATCAAAATTTTATAAAGAGGATATCAAAATTTCATAA
1 GATTATCAAAATTTCATAGAGGGGTCATCAAAATTTCATAAAGAGGATATCAAAATTACATAA
19083 AGAGGTTATC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
66 51 0.96
67 2 0.04
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGGGGTCATCAAAATTTCATAAAGAGGATATCAAAATTACATAATG
T
Found at i:19092 original size:66 final size:64
Alignment explanation
Indices: 18936--19101 Score: 149
Period size: 66 Copynumber: 2.5 Consensus size: 64
18926 GAGATCAGAT
* ** * *
18936 TATCAAAATTT-ATAGGAAGA-TTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAG
1 TATCAAAATTTCATA--AAGAGTTATC-AAATTTCATAGAGGGGTCATCAAAATTTCAAAGAGAG
*
18999 GT
63 GA
* * * *
19001 TATCAAAATTACATAATGTGATTATCAGAATTTCATAGAGGGGTCATCAAAATTTTATAA-AGAG
1 TATCAAAATTTCATAAAGAG-TTATCA-AATTTCATAGAGGGGTCATCAAAATTTCA-AAGAGAG
19065 GA
63 GA
19067 TATCAAAATTTCATAAAGAGGTTATCAAATCTTCA
1 TATCAAAATTTCATAAAGA-GTTATCAAAT-TTCA
19102 AAATGTGATT
Statistics
Matches: 81, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
64 2 0.02
65 14 0.17
66 62 0.77
67 3 0.04
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (64 bp):
TATCAAAATTTCATAAAGAGTTATCAAATTTCATAGAGGGGTCATCAAAATTTCAAAGAGAGGA
Found at i:19232 original size:20 final size:20
Alignment explanation
Indices: 19207--19258 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
19197 TTATGGAGTA
19207 ATCAAAATTTCAGAGAGGAT
1 ATCAAAATTTCAGAGAGGAT
*
19227 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTTCAGAGAGGAT
19247 ATCAAAATTTCA
1 ATCAAAATTTCA
19259 TATGAAGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (20 bp):
ATCAAAATTTCAGAGAGGAT
Found at i:19278 original size:22 final size:22
Alignment explanation
Indices: 19207--19540 Score: 160
Period size: 22 Copynumber: 15.5 Consensus size: 22
19197 TTATGGAGTA
* *
19207 ATCAAAATTTCAGA-G-AGGAT
1 ATCAAAATTTCATATGAAGGTT
* * *
19227 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATATGAAGGTT
19247 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
* **
19269 ATTAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* *
19291 TTCAAAATTTCATA-AAAGGGTT
1 ATCAAAATTTCATATGAA-GGTT
* ** *
19313 ATCAAAATTTCATA-GTATATAG
1 ATCAAAATTTCATATGAAGGT-T
* *
19335 ATCAAAATTTCATATGGAGATT
1 ATCAAAATTTCATATGAAGGTT
*
19357 AACAAAATTTCATAATG-AGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
** * *
19379 ATCAAAAAATCATAAGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
*
19401 ATCAAAA--T--T-TGTA-GTT
1 ATCAAAATTTCATATGAAGGTT
* * *
19417 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
19439 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATATGAAGG-TT
* * *
19462 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATATGAAG-GTT
*
19485 ATCAAAATTTCATA-GCGAGGTT
1 ATCAAAATTTCATATG-AAGGTT
* * * *
19507 ATCACAATTTTATAATG-TGATT
1 ATCAAAATTTCAT-ATGAAGGTT
19529 ATCAAAATTTCA
1 ATCAAAATTTCA
19541 GAGTGTGATT
Statistics
Matches: 246, Mismatches: 46, Indels: 42
0.74 0.14 0.13
Matches are distributed among these distances:
16 9 0.04
17 2 0.01
18 3 0.01
19 1 0.00
20 30 0.12
21 5 0.02
22 148 0.60
23 47 0.19
24 1 0.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:19465 original size:23 final size:23
Alignment explanation
Indices: 19437--19520 Score: 116
Period size: 23 Copynumber: 3.7 Consensus size: 23
19427 CATAAGAAAG
19437 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
19460 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* *
19483 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
*
19505 TTATCACAATTTTATA
1 TTATCAAAATTTTATA
19521 ATGTGATTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 14 0.26
23 39 0.74
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:19717 original size:21 final size:22
Alignment explanation
Indices: 19679--19726 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
19669 TTCCTTAGGG
** *
19679 AGGTTAACAAAATTTTATAAGA
1 AGGTTAACAAAAAATTATAAAA
19701 AGGTTAA-AAAAAATTATAAAA
1 AGGTTAACAAAAAATTATAAAA
19722 AGGTT
1 AGGTT
19727 CTTGAAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.29
Consensus pattern (22 bp):
AGGTTAACAAAAAATTATAAAA
Found at i:20222 original size:33 final size:33
Alignment explanation
Indices: 20178--20298 Score: 134
Period size: 33 Copynumber: 3.7 Consensus size: 33
20168 GGCGCGGTGC
* * *
20178 CCAACCGTGGTGTGCCGTCCTCGTAGGATGACA
1 CCAACCATGGTGTGCCGTCCTCGTAGGACGGCA
* *
20211 CCAACCATGGTGTGCCGTCTTCCTAGGACGGCA
1 CCAACCATGGTGTGCCGTCCTCGTAGGACGGCA
* ** * * *
20244 TCAACTGTGGTGTGCCGTCCTAGGAGGACGGTA
1 CCAACCATGGTGTGCCGTCCTCGTAGGACGGCA
*
20277 CCAACCATGGTGTACCGTCCTC
1 CCAACCATGGTGTGCCGTCCTC
20299 CGGGGACGGC
Statistics
Matches: 70, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 70 1.00
ACGTcount: A:0.18, C:0.31, G:0.29, T:0.22
Consensus pattern (33 bp):
CCAACCATGGTGTGCCGTCCTCGTAGGACGGCA
Found at i:20295 original size:66 final size:66
Alignment explanation
Indices: 20179--20309 Score: 172
Period size: 66 Copynumber: 2.0 Consensus size: 66
20169 GCGCGGTGCC
* * * * * *
20179 CAACCGTGGTGTGCCGTCCTCGTAGGATGACACCAACCATGGTGTGCCGTCTTCCTAGGACGGCA
1 CAACCGTGGTGTGCCGTCCTAGGAGGACGACACCAACCATGGTGTACCGTCCTCCGAGGACGGCA
20244 T
66 T
* ** *
20245 CAACTGTGGTGTGCCGTCCTAGGAGGACGGTACCAACCATGGTGTACCGTCCTCCGGGGACGGCA
1 CAACCGTGGTGTGCCGTCCTAGGAGGACGACACCAACCATGGTGTACCGTCCTCCGAGGACGGCA
20310 GCGTGTCTAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.18, C:0.30, G:0.31, T:0.21
Consensus pattern (66 bp):
CAACCGTGGTGTGCCGTCCTAGGAGGACGACACCAACCATGGTGTACCGTCCTCCGAGGACGGCA
T
Found at i:20441 original size:24 final size:24
Alignment explanation
Indices: 20406--20452 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20396 CTAGGCACGA
* *
20406 CACACCACGGTTGGTGCCGTCCTT
1 CACACCACGGTTGATACCGTCCTT
*
20430 CACACCATGGTTGATACCGTCCT
1 CACACCACGGTTGATACCGTCCT
20453 AGGAGGACGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.36, G:0.21, T:0.26
Consensus pattern (24 bp):
CACACCACGGTTGATACCGTCCTT
Found at i:20475 original size:33 final size:33
Alignment explanation
Indices: 20430--20541 Score: 143
Period size: 33 Copynumber: 3.4 Consensus size: 33
20420 TGCCGTCCTT
* *
20430 CACACCATGGTTGATACCGTCCTAGGAGGACGG
1 CACACCACGGTTGATGCCGTCCTAGGAGGACGG
*
20463 GACACCACGGTTGATGCCGTCCTAGGAGGACGG
1 CACACCACGGTTGATGCCGTCCTAGGAGGACGG
* * * ***
20496 CACACCATGGTTGGTGCCTTCCTCCTAGGACGG
1 CACACCACGGTTGATGCCGTCCTAGGAGGACGG
20529 CACACCACGGTTG
1 CACACCACGGTTG
20542 GTGTCGTGGA
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.21, C:0.30, G:0.30, T:0.19
Consensus pattern (33 bp):
CACACCACGGTTGATGCCGTCCTAGGAGGACGG
Found at i:26462 original size:7 final size:7
Alignment explanation
Indices: 26450--26521 Score: 89
Period size: 7 Copynumber: 10.6 Consensus size: 7
26440 AGTTGTTTTG
26450 TTTTGTT
1 TTTTGTT
26457 TTTTG-T
1 TTTTGTT
26463 TTTTG--
1 TTTTGTT
26468 TTTT-TT
1 TTTTGTT
26474 TTTTGTT
1 TTTTGTT
26481 TTTTGTT
1 TTTTGTT
26488 TTTTGTT
1 TTTTGTT
*
26495 TTTTGTAA
1 TTTTGT-T
26503 TTTTGTT
1 TTTTGTT
26510 TTTGTGTT
1 TTT-TGTT
26518 TTTT
1 TTTT
26522 TGGAAGCCCT
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
5 4 0.07
6 10 0.17
7 31 0.53
8 13 0.22
ACGTcount: A:0.03, C:0.00, G:0.14, T:0.83
Consensus pattern (7 bp):
TTTTGTT
Found at i:26466 original size:18 final size:18
Alignment explanation
Indices: 26445--26511 Score: 82
Period size: 18 Copynumber: 3.5 Consensus size: 18
26435 AAAAAAGTTG
26445 TTTTGTTTTGTTTTTTGT
1 TTTTGTTTTGTTTTTTGT
26463 TTTTGTTTT-TTTTTTGTT
1 TTTTGTTTTGTTTTTTG-T
26481 TTTTGTTTTTTGTTTTTTGT
1 TTTTG--TTTTGTTTTTTGT
26501 AATTTTGTTTT
1 --TTTTGTTTT
26512 TGTGTTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.16
18 15 0.35
20 9 0.21
21 7 0.16
22 5 0.12
ACGTcount: A:0.03, C:0.00, G:0.13, T:0.84
Consensus pattern (18 bp):
TTTTGTTTTGTTTTTTGT
Found at i:26468 original size:23 final size:22
Alignment explanation
Indices: 26442--26523 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 22
26432 AATAAAAAAG
26442 TTGTTTTGTTTTGTTTTTTGTTT
1 TTGTTTT-TTTTGTTTTTTGTTT
26465 TTGTTTTTTTTTTGTTTTTTGTTT
1 TTG--TTTTTTTTGTTTTTTGTTT
* *
26489 TT-TGTTTTTTGTAATTTTGTTT
1 TTGTTTTTTTTGT-TTTTTGTTT
26511 TTGTGTTTTTTTG
1 TTGT-TTTTTTTG
26524 GAAGCCCTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
21 9 0.18
22 10 0.20
23 4 0.08
24 24 0.47
25 4 0.08
ACGTcount: A:0.02, C:0.00, G:0.16, T:0.82
Consensus pattern (22 bp):
TTGTTTTTTTTGTTTTTTGTTT
Found at i:29037 original size:2 final size:2
Alignment explanation
Indices: 29030--29084 Score: 69
Period size: 2 Copynumber: 27.5 Consensus size: 2
29020 TTTGCCCTGT
*
29030 TA TA TA TA TA TGA -A TA TA TA TG TA TA TA TA TGA -A TA TA TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
29072 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
29085 TCTACCTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
1 2 0.04
2 43 0.91
3 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:29057 original size:20 final size:20
Alignment explanation
Indices: 29030--29080 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
29020 TTTGCCCTGT
29030 TATATATATATGAATATATA
1 TATATATATATGAATATATA
*
29050 TGTATATATATGAATATATA
1 TATATATATATGAATATATA
29070 TATATATATAT
1 TATATATATAT
29081 ATATTCTACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (20 bp):
TATATATATATGAATATATA
Found at i:39064 original size:9 final size:9
Alignment explanation
Indices: 39050--39083 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
39040 ATCAGAAACG
39050 AAAAAATGAA
1 AAAAAATG-A
39060 AAAAAATGA
1 AAAAAATGA
*
39069 AAAGAATGA
1 AAAAAATGA
39078 AAAAAA
1 AAAAAA
39084 AGAAGAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (9 bp):
AAAAAATGA
Found at i:39065 original size:10 final size:10
Alignment explanation
Indices: 39050--39084 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
39040 ATCAGAAACG
39050 AAAAAATGAA
1 AAAAAATGAA
39060 AAAAAATG-A
1 AAAAAATGAA
*
39069 AAAGAATGAA
1 AAAAAATGAA
39079 AAAAAA
1 AAAAAA
39085 GAAGAAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (10 bp):
AAAAAATGAA
Found at i:39078 original size:19 final size:18
Alignment explanation
Indices: 39049--39098 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
39039 CATCAGAAAC
39049 GAAAAAATGAAAAAAAAT
1 GAAAAAATGAAAAAAAAT
39067 GAAAAGAATGAAAAAAAA-
1 GAAAA-AATGAAAAAAAAT
*
39085 GAAGAAA-GAAAAAA
1 GAAAAAATGAAAAAA
39099 GAGAGAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 7 0.23
17 2 0.07
18 9 0.30
19 12 0.40
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (18 bp):
GAAAAAATGAAAAAAAAT
Found at i:39098 original size:14 final size:13
Alignment explanation
Indices: 39079--39118 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
39069 AAAGAATGAA
39079 AAAAAAGAAGAAAG
1 AAAAAAG-AGAAAG
*
39093 AAAAAAGAGAGAG
1 AAAAAAGAGAAAG
39106 AAAAAAAGAGAAA
1 -AAAAAAGAGAAA
39119 TTGAATTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAAAAGAGAAAG
Found at i:39602 original size:23 final size:22
Alignment explanation
Indices: 39558--39607 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
39548 GTGAATGAAA
* *
39558 AGAAAAGCAAAAAGGAGGAATG
1 AGAAAAGAAAAAAGGAGAAATG
*
39580 AGAAAAGAAAAAAGATAGAAATG
1 AGAAAAGAAAAAAG-GAGAAATG
*
39603 CGAAA
1 AGAAA
39608 TTCAACAAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.64, C:0.04, G:0.26, T:0.06
Consensus pattern (22 bp):
AGAAAAGAAAAAAGGAGAAATG
Found at i:42790 original size:30 final size:30
Alignment explanation
Indices: 42754--42813 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
42744 GGCATCTTAA
*
42754 TGGCATCTCCATGAGGCTTTGCGATTCCAT
1 TGGCATCTCCATGAGACTTTGCGATTCCAT
* *
42784 TGGCATCTTCATGATACTTTGCGATTCCAT
1 TGGCATCTCCATGAGACTTTGCGATTCCAT
42814 CCTCTCCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (30 bp):
TGGCATCTCCATGAGACTTTGCGATTCCAT
Found at i:50725 original size:15 final size:15
Alignment explanation
Indices: 50705--50734 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
50695 GAACCTATAA
*
50705 GAAAAATGAAAAATT
1 GAAAAATAAAAAATT
50720 GAAAAATAAAAAATT
1 GAAAAATAAAAAATT
50735 CTAACTATAA
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:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (15 bp):
GAAAAATAAAAAATT
Found at i:67507 original size:26 final size:25
Alignment explanation
Indices: 67427--67508 Score: 67
Period size: 27 Copynumber: 3.1 Consensus size: 25
67417 TGGGTCACAT
* *
67427 AGGGGCATTTTGGGTCATTTTTATAC
1 AGGGGCATTTT-GGTCATTTTAATTC
* *
67453 TAAGGGCATTCTT-GTCATTTGCACATTC
1 -AGGGGCATT-TTGGTCATTT-TA-ATTC
67481 AGGGGCATTTTGGTCATTTTAAGTTC
1 AGGGGCATTTTGGTCATTTTAA-TTC
67507 AG
1 AG
67509 TTAGTTTAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
25 1 0.02
26 15 0.34
27 23 0.52
28 5 0.11
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.40
Consensus pattern (25 bp):
AGGGGCATTTTGGTCATTTTAATTC
Found at i:67788 original size:21 final size:21
Alignment explanation
Indices: 67764--67807 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
67754 ATTTTGCTAA
67764 GTAGTTTTCATTATAAGCATT
1 GTAGTTTTCATTATAAGCATT
67785 GTAGTTTTCATTATAAGCATT
1 GTAGTTTTCATTATAAGCATT
67806 GT
1 GT
67808 CACTGAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.48
Consensus pattern (21 bp):
GTAGTTTTCATTATAAGCATT
Found at i:68953 original size:15 final size:15
Alignment explanation
Indices: 68933--68962 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
68923 AAAATGACCA
*
68933 TCAAGCTAAATGGGC
1 TCAAGCCAAATGGGC
68948 TCAAGCCAAATGGGC
1 TCAAGCCAAATGGGC
68963 AGCAGTTACA
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:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (15 bp):
TCAAGCCAAATGGGC
Found at i:70610 original size:19 final size:18
Alignment explanation
Indices: 70577--70614 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
70567 TTGAAATAAT
*
70577 TCTTCAATAATCTTCAAA
1 TCTTCAAAAATCTTCAAA
70595 TCTTCAAAATATCTTCAAA
1 TCTTCAAAA-ATCTTCAAA
70614 T
1 T
70615 ACGAACTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAA
Found at i:73491 original size:22 final size:21
Alignment explanation
Indices: 73443--73491 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
73433 TAAAATGGAA
* *
73443 ATTTTCAAAGCAAAATAAAAG
1 ATTTTAAAAACAAAATAAAAG
*
73464 ACTTTAAAAACAAAAGTAAAAG
1 ATTTTAAAAACAAAA-TAAAAG
*
73486 GTTTTA
1 ATTTTA
73492 TCACAGCATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (21 bp):
ATTTTAAAAACAAAATAAAAG
Found at i:75031 original size:42 final size:42
Alignment explanation
Indices: 74972--75057 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
74962 GGTGCTACAA
74972 GTTCATCATCTAAGACTCACATTAAGTGTAGTGAAGAGGAAG
1 GTTCATCATCTAAGACTCACATTAAGTGTAGTGAAGAGGAAG
*
75014 GTTCATCATCTAAGACTCACATTAAGTGTAGTGAAGCGGAAG
1 GTTCATCATCTAAGACTCACATTAAGTGTAGTGAAGAGGAAG
75056 GT
1 GT
75058 GATTTTAATC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (42 bp):
GTTCATCATCTAAGACTCACATTAAGTGTAGTGAAGAGGAAG
Done.