Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014177.1 Corchorus olitorius cultivar O-4 contig14210, 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: 45488
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:3468 original size:3 final size:3
Alignment explanation
Indices: 3460--3494 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
3450 AAATTCTTTA
*
3460 TTC TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3495 GCATTAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:16684 original size:6 final size:6
Alignment explanation
Indices: 16673--16703 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
16663 ATATATATGA
16673 TGAAAT TGAAAT TGAAAT TGAAAT TGAAAT T
1 TGAAAT TGAAAT TGAAAT TGAAAT TGAAAT T
16704 TGTTTACTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.35
Consensus pattern (6 bp):
TGAAAT
Found at i:17160 original size:25 final size:25
Alignment explanation
Indices: 17132--17182 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
17122 GCCAGAATTT
17132 TATTT-TTAATTAATTAATTTACTTA
1 TATTTATTAATT-ATTAATTTACTTA
* *
17157 TATTTATTTATTATTAATTTATTTA
1 TATTTATTAATTATTAATTTACTTA
17182 T
1 T
17183 CATAAAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
TATTTATTAATTATTAATTTACTTA
Found at i:17324 original size:22 final size:22
Alignment explanation
Indices: 17296--17341 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
17286 ATCAAAGAGG
17296 AATTAATCTATACTATATATAA
1 AATTAATCTATACTATATATAA
*
17318 AATTAATCTATATTATATATAA
1 AATTAATCTATACTATATATAA
17340 AA
1 AA
17342 GTACGAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTAATCTATACTATATATAA
Found at i:18324 original size:3 final size:3
Alignment explanation
Indices: 18316--18358 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
18306 ATTTCTACTA
18316 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
18359 TATGATTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:19672 original size:21 final size:21
Alignment explanation
Indices: 19646--19692 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
19636 TCTTAGACAG
19646 AGGTTAGCAAA-AATCATAGGA
1 AGGTTA-CAAATAATCATAGGA
**
19667 AGGTTACAAATTTTCATAGGA
1 AGGTTACAAATAATCATAGGA
19688 AGGTT
1 AGGTT
19693 TATTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (21 bp):
AGGTTACAAATAATCATAGGA
Found at i:19708 original size:23 final size:21
Alignment explanation
Indices: 19646--19753 Score: 67
Period size: 22 Copynumber: 5.0 Consensus size: 21
19636 TCTTAGACAG
*
19646 AGGTTAGCAAAA-ATCATAGGA
1 AGGTTA-CAAAATTTCATAGGA
*
19667 AGGTTACAAATTTTCATAGGA
1 AGGTTACAAAATTTCATAGGA
* **
19688 AGGTTTATTAAAATTTCATAGTT
1 AGG-TTA-CAAAATTTCATAGGA
* *
19711 AGATTATCAAAGTTTCATATGG-
1 AGGTTA-CAAAATTTCATA-GGA
* *
19733 AGTTTATCACAATTTCATAGG
1 AGGTTA-CAAAATTTCATAGG
19754 TAAATCATCA
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
20 4 0.06
21 19 0.27
22 33 0.47
23 14 0.20
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (21 bp):
AGGTTACAAAATTTCATAGGA
Found at i:19726 original size:22 final size:22
Alignment explanation
Indices: 19692--19813 Score: 106
Period size: 22 Copynumber: 5.5 Consensus size: 22
19682 ATAGGAAGGT
*
19692 TTATTAAAATTTCATAGTTAGA
1 TTATCAAAATTTCATAGTTAGA
* * *
19714 TTATCAAAGTTTCATA-TGGAGT
1 TTATCAAAATTTCATAGT-TAGA
* * *
19736 TTATCACAATTTCATAGGTAAA
1 TTATCAAAATTTCATAGTTAGA
*
19758 TCATCAAAATTTCATAGTGT-GA
1 TTATCAAAATTTCATAGT-TAGA
* *
19780 TTATCAAAATTTAATAGGGTAG-
1 TTATCAAAATTTCATA-GTTAGA
19802 TTATCAAAATTT
1 TTATCAAAATTT
19814 TATAAAAATA
Statistics
Matches: 78, Mismatches: 17, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
21 1 0.01
22 74 0.95
23 3 0.04
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTTAGA
Found at i:19738 original size:44 final size:45
Alignment explanation
Indices: 19673--19774 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 45
19663 AGGAAGGTTA
* * * * *
19673 CAAATTTTCATAGGAAGGTTTATTAAAATTTCATAGTTAGATTAT
1 CAAAATTTCATAGGAAGGTTTATCAAAATTTCATAGGTAAATCAT
* *
19718 CAAAGTTTCATATGG-A-GTTTATCACAATTTCATAGGTAAATCAT
1 CAAAATTTCATA-GGAAGGTTTATCAAAATTTCATAGGTAAATCAT
19762 CAAAATTTCATAG
1 CAAAATTTCATAG
19775 TGTGATTATC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
43 1 0.02
44 34 0.69
45 12 0.24
46 2 0.04
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (45 bp):
CAAAATTTCATAGGAAGGTTTATCAAAATTTCATAGGTAAATCAT
Found at i:19808 original size:44 final size:42
Alignment explanation
Indices: 19692--19813 Score: 120
Period size: 44 Copynumber: 2.8 Consensus size: 42
19682 ATAGGAAGGT
* * *
19692 TTATTAAAATTTCATAGTTAGATTATCAAAGTTTCATATGGAG
1 TTATCAAAATTTCATAGGTAG-TTATCAAAATTTCATATGGAG
* * *
19735 TTTATCACAATTTCATAGGTAAATCATCAAAATTTCATAGTGTGA-
1 -TTATCAAAATTTCATAGGT-AGTTATCAAAATTTCATA-TG-GAG
*
19780 TTATCAAAATTTAATAGGGTAGTTATCAAAATTT
1 TTATCAAAATTTCATA-GGTAGTTATCAAAATTT
19814 TATAAAAATA
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
44 56 0.88
45 6 0.09
46 2 0.03
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (42 bp):
TTATCAAAATTTCATAGGTAGTTATCAAAATTTCATATGGAG
Found at i:25503 original size:21 final size:21
Alignment explanation
Indices: 25477--25518 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
25467 GCACCTTAGG
*
25477 CAACTCCGATGAGCTTGAAAC
1 CAACTCAGATGAGCTTGAAAC
25498 CAACTCAGATGAGCTTGAAAC
1 CAACTCAGATGAGCTTGAAAC
25519 TTCTTTGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (21 bp):
CAACTCAGATGAGCTTGAAAC
Found at i:27401 original size:33 final size:33
Alignment explanation
Indices: 27331--27468 Score: 129
Period size: 33 Copynumber: 4.2 Consensus size: 33
27321 ATGATCAACC
** *
27331 AAAACAGATTT-GTTTTCATCACAATTAGCATCC-
1 AAAACAGATTTAG-TTTCATCACAAACAACA-CCT
27364 AAAACAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAG-ATTTAGTTTCATCACAAACAACACCT
* *
27397 AAAACAGATTTAGTGTCATCACAAACAACACTT
1 AAAACAGATTTAGTTTCATCACAAACAACACCT
** * * * *
27430 AAATTAGGTTTAGTATCATCACTAACAACATCT
1 AAAACAGATTTAGTTTCATCACAAACAACACCT
27463 AAAACA
1 AAAACA
27469 CTCTTTGCAA
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
32 6 0.07
33 77 0.88
34 5 0.06
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (33 bp):
AAAACAGATTTAGTTTCATCACAAACAACACCT
Found at i:29906 original size:21 final size:21
Alignment explanation
Indices: 29876--29917 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
29866 GCGCCTTAGG
29876 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
*
29897 CAACTTCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
29918 TTCTTTGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:37455 original size:60 final size:60
Alignment explanation
Indices: 37368--37530 Score: 256
Period size: 60 Copynumber: 2.7 Consensus size: 60
37358 GCTAATTGCT
* *
37368 CAAATAAGGGTCTAACGTTTATC-AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAAC-ATTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
* * *
37428 CAAATAAGGACCTAACATTATCGAAAATGCTTAAATAAGGGCCCGGTCTTTTAATTTGGC
1 CAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
37488 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGGCC
37531 TAGCGTCGAA
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
59 5 0.05
60 89 0.95
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:37526 original size:31 final size:31
Alignment explanation
Indices: 37364--37532 Score: 97
Period size: 31 Copynumber: 5.6 Consensus size: 31
37354 ATAGGCTAAT
*
37364 TGCTCAAATAAGGGTCTAACGTTTATC-AAAA
1 TGCTCAAATAAGGGCCTAACG-TTATCGAAAA
* * * **
37395 TGCTCAAATAAGGGCCCGATC-TT-T-TAATT
1 TGCTCAAATAAGGG-CCTAACGTTATCGAAAA
* *
37424 TGGC-CAAATAAGGACCTAACATTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTATCGAAAA
* ** **
37455 TGCTTAAATAAGGGCC---CGGTCT-TTTAATT
1 TGCTCAAATAAGGGCCTAAC-GT-TATCGAAAA
37484 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTATCGAAAA
37515 TGCTCAAATAAGGGCCTA
1 TGCTCAAATAAGGGCCTA
37533 GCGTCGAAAA
Statistics
Matches: 100, Mismatches: 23, Indels: 30
0.65 0.15 0.20
Matches are distributed among these distances:
28 5 0.05
29 31 0.31
30 13 0.13
31 47 0.47
32 4 0.04
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTATCGAAAA
Found at i:37548 original size:28 final size:29
Alignment explanation
Indices: 37488--37549 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
37478 TTAATTTGGC
37488 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACG-T-TCGAAAATGCT
* *
37519 CAAATAAGGGCCTAGCG-TCGAAAATTCT
1 CAAATAAGGGCCTAACGTTCGAAAATGCT
37547 CAA
1 CAA
37550 GCGTCATCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 13 0.45
31 16 0.55
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (29 bp):
CAAATAAGGGCCTAACGTTCGAAAATGCT
Found at i:37611 original size:31 final size:29
Alignment explanation
Indices: 37573--37737 Score: 122
Period size: 31 Copynumber: 5.5 Consensus size: 29
37563 TGACGCCAGA
*
37573 CCCTTATTTGAGCATTTTCGATAATGTTAGG
1 CCCTTATTTGAGCATTTT-GA-AAAGTTAGG
** * *
37604 CCCTTATTT-AGCCAAATT-AAAAGATCAGA
1 CCCTTATTTGAG-CATTTTGAAAAG-TTAGG
*
37633 CCCTTATTTGAGCATTTTGACAAACGTTAAG
1 CCCTTATTTGAGCATTTTGA-AAA-GTTAGG
* * *
37664 CCCTTATTTGA-CAAATTT-AAAAGATCAGA
1 CCCTTATTTGAGC-ATTTTGAAAAG-TTAGG
*
37693 CCCTTATTTGTGCATTTTGACAAATGTTAGG
1 CCCTTATTTGAGCATTTTGA-AAA-GTTAGG
37724 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
37738 ATTAGCCTAC
Statistics
Matches: 103, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
28 4 0.04
29 36 0.35
30 9 0.09
31 52 0.50
32 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (29 bp):
CCCTTATTTGAGCATTTTGAAAAGTTAGG
Found at i:37641 original size:29 final size:28
Alignment explanation
Indices: 37604--37701 Score: 83
Period size: 29 Copynumber: 3.3 Consensus size: 28
37594 TAATGTTAGG
37604 CCCTTATTTAGCCAAATTAAAAGATCAGA
1 CCCTTATTTAG-CAAATTAAAAGATCAGA
** * *
37633 CCCTTATTTGAGCATTTTGACAAACGTTAAG-
1 CCCTTATTT-AGCAAATT-A-AAA-GATCAGA
37664 CCCTTATTT-GACAAATTTAAAAGATCAGA
1 CCCTTATTTAG-CAAA-TTAAAAGATCAGA
37693 CCCTTATTT
1 CCCTTATTT
37702 GTGCATTTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
28 4 0.07
29 26 0.48
30 6 0.11
31 14 0.26
32 4 0.07
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (28 bp):
CCCTTATTTAGCAAATTAAAAGATCAGA
Found at i:37648 original size:60 final size:60
Alignment explanation
Indices: 37569--37734 Score: 255
Period size: 60 Copynumber: 2.8 Consensus size: 60
37559 AAATTGACGC
* *
37569 CAGACCCTTATTTGAGCATTTTCGA-TAATGTTAGGCCCTTATTTAGCCAAA-TTAAAAGAT
1 CAGACCCTTATTTGAGCATTTT-GACAAATGTTAGGCCCTTATTT-GACAAATTTAAAAGAT
* *
37629 CAGACCCTTATTTGAGCATTTTGACAAACGTTAAGCCCTTATTTGACAAATTTAAAAGAT
1 CAGACCCTTATTTGAGCATTTTGACAAATGTTAGGCCCTTATTTGACAAATTTAAAAGAT
*
37689 CAGACCCTTATTTGTGCATTTTGACAAATGTTAGGCCCTTATTTGA
1 CAGACCCTTATTTGAGCATTTTGACAAATGTTAGGCCCTTATTTGA
37735 GCAATTAGCC
Statistics
Matches: 97, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
59 7 0.07
60 90 0.93
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (60 bp):
CAGACCCTTATTTGAGCATTTTGACAAATGTTAGGCCCTTATTTGACAAATTTAAAAGAT
Found at i:37870 original size:21 final size:21
Alignment explanation
Indices: 37844--37886 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
37834 TTTCTCATTT
37844 TTCGGGTGACTAAAAAGTCCC
1 TTCGGGTGACTAAAAAGTCCC
37865 TTCGGGTGACTAAAAAGTCCC
1 TTCGGGTGACTAAAAAGTCCC
37886 T
1 T
37887 CGATGAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (21 bp):
TTCGGGTGACTAAAAAGTCCC
Found at i:38125 original size:131 final size:131
Alignment explanation
Indices: 37928--38193 Score: 487
Period size: 131 Copynumber: 2.0 Consensus size: 131
37918 TCCCTTTTTG
37928 TAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGTGTGGATAT
1 TAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGTGTGGATAT
* *
37993 TAGGATTTACCGGTTCAAATTCTCTTCCGGAATTCCAAAATATTGGTGCTATAAATGTATCTACA
66 TAGGATTTACCAGTTCAAATCCTCTTCCGGAATTCCAAAATATTGGTGCTATAAATGTATCTACA
38058 A
131 A
38059 TAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGTGTGGATAT
1 TAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGTGTGGATAT
* * *
38124 TAGGATTTACCAGTTCAACTCCTCTTCCGGAATTCCAAAGTATTGGTGCTATAAATGTATCTGCA
66 TAGGATTTACCAGTTCAAATCCTCTTCCGGAATTCCAAAATATTGGTGCTATAAATGTATCTACA
38189 A
131 A
38190 TAAT
1 TAAT
38194 GGTTGATTCA
Statistics
Matches: 130, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
131 130 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (131 bp):
TAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGTGTGGATAT
TAGGATTTACCAGTTCAAATCCTCTTCCGGAATTCCAAAATATTGGTGCTATAAATGTATCTACA
A
Found at i:39314 original size:16 final size:16
Alignment explanation
Indices: 39282--39311 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39272 AATTAAAAAA
39282 TATATAAAAAATTAAT
1 TATATAAAAAATTAAT
39298 TATA-AAAAAATTAA
1 TATATAAAAAATTAA
39312 ATTCAAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TATATAAAAAATTAAT
Found at i:41684 original size:2 final size:2
Alignment explanation
Indices: 41677--41741 Score: 60
Period size: 2 Copynumber: 33.0 Consensus size: 2
41667 GTAAACACAT
* * * *
41677 TA TA TA TA TA TA TA TA TA TA TA TA TG TG TG TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
41719 TA TG TA TG TA TG TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
41742 GGTCCTTATT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (2 bp):
TA
Found at i:41712 original size:20 final size:21
Alignment explanation
Indices: 41689--41741 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
41679 TATATATATA
*
41689 TATATATATATATG-TGTGTG
1 TATATATATATATGATGTATG
41709 TATATATATATATGTATGTATG
1 TATATATATATATG-ATGTATG
41731 TATA-ATATATA
1 TATATATATATA
41742 GGTCCTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 14 0.47
21 7 0.23
22 9 0.30
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (21 bp):
TATATATATATATGATGTATG
Found at i:41715 original size:22 final size:22
Alignment explanation
Indices: 41677--41741 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
41667 GTAAACACAT
* *
41677 TATATATATATATATATATATA
1 TATATGTATGTATATATATATA
* *
41699 TATGTGTGTGTATATATATATA
1 TATATGTATGTATATATATATA
*
41721 TGTATGTATGTATA-ATATATA
1 TATATGTATGTATATATATATA
41742 GGTCCTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
21 7 0.19
22 29 0.81
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (22 bp):
TATATGTATGTATATATATATA
Found at i:41717 original size:24 final size:24
Alignment explanation
Indices: 41683--41741 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
41673 ACATTATATA
*
41683 TATATATATATATATATATGTGTG
1 TATATATATATATATATATGTATG
* *
41707 TGTATATATATATATGTATGTATG
1 TATATATATATATATATATGTATG
41731 TATA-ATATATA
1 TATATATATATA
41742 GGTCCTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 7 0.23
24 24 0.77
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (24 bp):
TATATATATATATATATATGTATG
Found at i:42874 original size:11 final size:11
Alignment explanation
Indices: 42860--42890 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
42850 GATTAAAGTC
42860 AAGGAAAAGGA
1 AAGGAAAAGGA
42871 AAGGAAAAGGA
1 AAGGAAAAGGA
42882 AAGGAAAAG
1 AAGGAAAAG
42891 CTAGCTACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (11 bp):
AAGGAAAAGGA
Found at i:43140 original size:2 final size:2
Alignment explanation
Indices: 43133--43160 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43123 AAGAAATGAG
43133 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
43161 GTGTGTGATG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43729 original size:22 final size:22
Alignment explanation
Indices: 43703--43744 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
43693 GGCAAATTCA
* *
43703 TAACCTAAATGACCCGAGAAGT
1 TAACCCAAATGACCCAAGAAGT
*
43725 TAACCCGAATGACCCAAGAA
1 TAACCCAAATGACCCAAGAA
43745 TATTATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.26, G:0.17, T:0.14
Consensus pattern (22 bp):
TAACCCAAATGACCCAAGAAGT
Found at i:44260 original size:41 final size:43
Alignment explanation
Indices: 44211--44303 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 43
44201 AGTGCATTAT
*
44211 CTAA-ATTCTA-CTACATCTCTAGGGAATTCATCAAAA-AAAG
1 CTAATATTCTACCTACATCTCTAGAGAATTCATCAAAATAAAG
* *
44251 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTACATCTCTAGAGAATTCATCAAAATAAAG
*
44296 TTAATATT
1 CTAATATT
44304 AATTGTTGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
40 4 0.09
41 6 0.14
44 23 0.52
45 11 0.25
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.33
Consensus pattern (43 bp):
CTAATATTCTACCTACATCTCTAGAGAATTCATCAAAATAAAG
Done.