Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019752.1 Corchorus olitorius cultivar O-4 contig19785, 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: 42646
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1477 original size:10 final size:10
Alignment explanation
Indices: 1449--1479 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
1439 TAGCAACTAC
1449 AAAAAAATAA
1 AAAAAAATAA
1459 AAAATAAATAA
1 AAAA-AAATAA
1470 AAAAAAATAA
1 AAAAAAATAA
1480 CAAAGTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:3138 original size:13 final size:13
Alignment explanation
Indices: 3120--3145 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3110 CTTGGCATGA
3120 GTGATGATTTTTG
1 GTGATGATTTTTG
3133 GTGATGATTTTTG
1 GTGATGATTTTTG
3146 TTGTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:6072 original size:54 final size:54
Alignment explanation
Indices: 5977--6138 Score: 238
Period size: 54 Copynumber: 3.0 Consensus size: 54
5967 GTAATCATTG
* *
5977 TCGTCCATCCA-TTTGGTGTTTGAATTGAGATTTCAGAAATAATACAATTCAAAC
1 TCGTCCATTCATTTTGATGTTTGAATTG-GATTTCAGAAATAATACAATTCAAAC
*
6031 TTGTCCATTCATTTTGATGTTTGAATTCGGATTTCAG-AATAATACAATTCAAAC
1 TCGTCCATTCATTTTGATGTTTGAATT-GGATTTCAGAAATAATACAATTCAAAC
* *
6085 TCATCCATTCATTTTGATGTTTGAATTGGGATTTCAGAAATAATATAATTCAAA
1 TCGTCCATTCATTTTGATGTTTGAATT-GGATTTCAGAAATAATACAATTCAAA
6139 AAAAATTAAG
Statistics
Matches: 98, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
54 60 0.61
55 37 0.38
56 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (54 bp):
TCGTCCATTCATTTTGATGTTTGAATTGGATTTCAGAAATAATACAATTCAAAC
Found at i:7841 original size:22 final size:22
Alignment explanation
Indices: 7816--8354 Score: 154
Period size: 22 Copynumber: 24.7 Consensus size: 22
7806 TATATATCCT
7816 TATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAATCTTCC
* * *
7838 TATGAAATTTTAATAA-CGATAC
1 TATGAAATTTTGATAATC-TTCC
* * * **
7860 TATGGAATTTCGATAACCTTTT
1 TATGAAATTTTGATAATCTTCC
* ** * *
7882 TATAAAATTTTTTTAACCTTCT
1 TATGAAATTTTGATAATCTTCC
** *
7904 TATGAAATTTTTTTAATCTCCC
1 TATGAAATTTTGATAATCTTCC
* * *
7926 TAAGGAATTTTGA-AGA-CCTCAC
1 TATGAAATTTTGATA-ATCTTC-C
*
7948 TATTAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAATCTT-CC
* * * **
7970 AAAGAAATTTTAATAATCAACAC
1 TATGAAATTTTGATAATCTTC-C
* * * *
7993 TATGAGATGTTGATAA-CCTCTA
1 TATGAAATTTTGATAATCTTC-C
* * * *
8015 TATGATATATTGATAATC-ACGT
1 TATGAAATTTTGATAATCTTC-C
* * * * *
8037 TATGAAAATTTAAAAACCTTCA
1 TATGAAATTTTGATAATCTTCC
*
8059 TATG-AATTGTT-AGTAATC-ACAC
1 TATGAAATT-TTGA-TAATCTTC-C
* *
8081 TCTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAATCTTC-C
* *
8103 TATGAAATTGTGATAA-CCTCGC
1 TATGAAATTTTGATAATCTTC-C
* *
8125 TATAAAATTTTGATAAAGCTTCC
1 TATGAAATTTTGAT-AATCTTCC
* *
8148 TATAAAATTTTGATAAATCTCCC
1 TATGAAATTTTGAT-AATCTTCC
*
8171 TATAAAATTTTGATAATC-TCC
1 TATGAAATTTTGATAATCTTCC
*
8192 TTATGAAATCTTGATAA-----C
1 -TATGAAATTTTGATAATCTTCC
* *
8210 TA-CAAATTTTGATAA-CTTCAT
1 TATGAAATTTTGATAATCTTC-C
* * *
8231 TATGAAATTTTGAT-CTACATAC
1 TATGAAATTTTGATAAT-CTTCC
* * *
8253 TATGAAATTTTGATAACCCTAC
1 TATGAAATTTTGATAATCTTCC
* * **
8275 TATGAAATTTT-AAAAACTAAAC
1 TATGAAATTTTGATAATCT-TCC
* * *
8297 TATAAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAATCTTCC
*
8319 TATGAAATTTTGAT-ATCCTGCC
1 TATGAAATTTTGATAAT-CTTCC
8341 --TGAAATTTTGATAA
1 TATGAAATTTTGATAA
8355 CTCCATAGTA
Statistics
Matches: 385, Mismatches: 100, Indels: 65
0.70 0.18 0.12
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 12 0.03
21 20 0.05
22 268 0.70
23 68 0.18
24 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAATCTTCC
Found at i:8591 original size:88 final size:88
Alignment explanation
Indices: 8433--8599 Score: 221
Period size: 88 Copynumber: 1.9 Consensus size: 88
8423 AAAAATACCA
* * * * *
8433 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTAATAAACTC
1 CTATAAAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTAATAAACAC
*
8498 TCTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* * *
8521 CTATAAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAATA-
1 CTATAAAATTTTGATAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTAATAA-AC
8584 ACACTATAAAATTTTG
64 ACACTATAAAATTTTG
8600 ATATTCTTCT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
88 65 0.96
89 3 0.04
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (88 bp):
CTATAAAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTAATAAACAC
ACTATAAAATTTTGTTGACCCCT
Found at i:8595 original size:22 final size:22
Alignment explanation
Indices: 8431--8602 Score: 85
Period size: 22 Copynumber: 7.8 Consensus size: 22
8421 CCAAAAATAC
* *
8431 CACTATGAAATTTTGGTAATCA
1 CACTATAAAATTTTGATAATCA
* * * *
8453 CATTTTGAAAA-TTTGATAACCT
1 CACTAT-AAAATTTTGATAATCA
** * * * *
8475 CTTTATGAAATTTTAATAAACT
1 CACTATAAAATTTTGATAATCA
* * * * *
8497 CTCTATAAAATTTTGTTGACCC
1 CACTATAAAATTTTGATAATCA
*
8519 CTCTATAAAATTTTGATAATCA
1 CACTATAAAATTTTGATAATCA
* ** * *
8541 CATTATGTAATTTTGATAACCT
1 CACTATAAAATTTTGATAATCA
* * * *
8563 CGCTTTGAAATTTTGATAATAA
1 CACTATAAAATTTTGATAATCA
8585 CACTATAAAATTTTGATA
1 CACTATAAAATTTTGATA
8603 TTCTTCTTAT
Statistics
Matches: 110, Mismatches: 38, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
21 3 0.03
22 104 0.95
23 3 0.03
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (22 bp):
CACTATAAAATTTTGATAATCA
Found at i:8597 original size:44 final size:43
Alignment explanation
Indices: 8436--8625 Score: 127
Period size: 44 Copynumber: 4.3 Consensus size: 43
8426 AATACCACTA
* * * * *
8436 TGAAATTTTGGTAATCACATTTTGAAAA-TTTGATAACCTCTTT
1 TGAAATTTTGATAATAACACTAT-AAAATTTTGATAACCTCCTT
* * * * *
8479 ATGAAATTTTAATAA-ACTCTCTATAAAATTTTGTTGACC-CCTCT
1 -TGAAATTTTGATAATA-ACACTATAAAATTTTGATAACCTCCT-T
* * * **
8523 ATAAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT
1 -TGAAATTTTGATAATAACACTATAAAATTTTGATAACCTC-CTT
** *
8568 TGAAATTTTGATAATAACACTATAAAATTTTGATATTCTTCTT
1 TGAAATTTTGATAATAACACTATAAAATTTTGATAACCTCCTT
8611 AT-AAATTTTGATAAT
1 -TGAAATTTTGATAAT
8626 CTGATCTTTA
Statistics
Matches: 111, Mismatches: 28, Indels: 15
0.72 0.18 0.10
Matches are distributed among these distances:
43 22 0.20
44 85 0.77
45 2 0.02
46 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (43 bp):
TGAAATTTTGATAATAACACTATAAAATTTTGATAACCTCCTT
Found at i:8614 original size:88 final size:87
Alignment explanation
Indices: 8433--8626 Score: 214
Period size: 88 Copynumber: 2.2 Consensus size: 87
8423 AAAAATACCA
* * * *
8433 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTAATAAACTC
1 CTAT-AAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTAATAAACAC
* *
8498 TCTATAAAATTTTGTTGACCCCT
65 ACTATAAAATTTTGATGACCCCT
* * *
8521 CTATAAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAATA-
1 CTAT-AAATTTTGATAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTAATAA-AC
** *
8584 ACACTATAAAATTTTGAT-ATTCTT
63 ACACTATAAAATTTTGATGACCCCT
8608 CTTATAAATTTTGATAATC
1 C-TATAAATTTTGATAATC
8627 TGATCTTTAT
Statistics
Matches: 90, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
87 18 0.20
88 69 0.77
89 3 0.03
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (87 bp):
CTATAAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTAATAAACACA
CTATAAAATTTTGATGACCCCT
Found at i:8676 original size:20 final size:22
Alignment explanation
Indices: 8634--8685 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 22
8624 ATCTGATCTT
8634 TATGAAATTTCGATAACCATTC
1 TATGAAATTTCGATAACCATTC
*
8656 TATGAGATTT-GATAA-CATTC
1 TATGAAATTTCGATAACCATTC
*
8676 TATCAAATTT
1 TATGAAATTT
8686 TAGCACTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 13 0.48
21 5 0.19
22 9 0.33
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTCGATAACCATTC
Found at i:10382 original size:12 final size:13
Alignment explanation
Indices: 10364--10396 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
10354 GTGGGTTTAA
10364 TAGTTTGTTTATT
1 TAGTTTGTTTATT
*
10377 TA-TTTGTTTGTT
1 TAGTTTGTTTATT
10389 TAGTTTGT
1 TAGTTTGT
10397 AATTACTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.12, C:0.00, G:0.18, T:0.70
Consensus pattern (13 bp):
TAGTTTGTTTATT
Found at i:12807 original size:13 final size:13
Alignment explanation
Indices: 12788--12823 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
12778 TTCAAATTTA
12788 ATAAAATTTTATT
1 ATAAAATTTTATT
* *
12801 TTAAAATTTAATT
1 ATAAAATTTTATT
12814 ATAAAATTTT
1 ATAAAATTTT
12824 TCAATTCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATAAAATTTTATT
Found at i:13436 original size:22 final size:22
Alignment explanation
Indices: 13376--13437 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
13366 GAGACGATTT
* *
13376 AAATTTTATTGTGTGATTATCA
1 AAATTTTATAGTGTGGTTATCA
*
13398 AAATTTGATAGTGTGGTTATCA
1 AAATTTTATAGTGTGGTTATCA
* *
13420 AGATTTTATAGTATGGTT
1 AAATTTTATAGTGTGGTT
13438 TTTAAGAGGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (22 bp):
AAATTTTATAGTGTGGTTATCA
Found at i:13594 original size:22 final size:21
Alignment explanation
Indices: 13498--13931 Score: 153
Period size: 22 Copynumber: 19.9 Consensus size: 21
13488 TGATAGTTTG
*
13498 GTTATCAAAATTACATAGGGA
1 GTTATCAAAATTTCATAGGGA
* **
13519 GGTTATCATAATTTCATAGTATA
1 -GTTATCAAAATTTCATAG-GGA
* * *
13542 GTTGTCAAAATTTAATA-GTA
1 GTTATCAAAATTTCATAGGGA
*
13562 TGGTTTTCAAAATTTCATAGGGA
1 --GTTATCAAAATTTCATAGGGA
* * * *
13585 GATTAACAAAATTCCGTAAGGA
1 G-TTATCAAAATTTCATAGGGA
* *
13607 TGTTATGAAAAATTCATAGGGA
1 -GTTATCAAAATTTCATAGGGA
*
13629 GGTTATAAAAATTTCATAGGGTA
1 -GTTATCAAAATTTCATAGGG-A
*
13652 GTTATCAAAATTTCA-AGAGGTG
1 GTTATCAAAATTTCATAG-GG-A
*
13674 GTTATCGAAATTTCAT-GAGGA
1 GTTATCAAAATTTCATAG-GGA
*
13695 GATTATCAAAATTTCAGAAGAGG-
1 G-TTATCAAAATTTCA-TAG-GGA
* * **
13718 GTTATCAAAATTTTACAGAAA
1 GTTATCAAAATTTCATAGGGA
* **
13739 GCTTTATCAAAATTTTATAATGA
1 G--TTATCAAAATTTCATAGGGA
* * *
13762 GGTTATCACAATTTGATAGTGA
1 -GTTATCAAAATTTCATAGGGA
* * * * *
13784 -TCACCAACATTTTATAGGAA
1 GTTATCAAAATTTCATAGGGA
* * *
13804 GGTGATCAAAATTTCGTA-GTA
1 -GTTATCAAAATTTCATAGGGA
* * * * *
13825 TGCTTACCAACATTCCACATGGA
1 -G-TTATCAAAATTTCATAGGGA
* * * *
13848 GGTTATTAAAATATCATAGTGT
1 -GTTATCAAAATTTCATAGGGA
*
13870 GCTTATC-AAATTTCATAAGGA
1 G-TTATCAAAATTTCATAGGGA
* *
13891 GGTTATCAAAATTTCATAAGTA
1 -GTTATCAAAATTTCATAGGGA
* *
13913 GCTTATTAAATTTTCATAG
1 G-TTATCAAAATTTCATAG
13932 TTTCGTTATC
Statistics
Matches: 306, Mismatches: 82, Indels: 48
0.70 0.19 0.11
Matches are distributed among these distances:
20 15 0.05
21 27 0.09
22 234 0.76
23 25 0.08
24 5 0.02
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (21 bp):
GTTATCAAAATTTCATAGGGA
Found at i:13749 original size:23 final size:24
Alignment explanation
Indices: 13697--13755 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 24
13687 CATGAGGAGA
*
13697 TTATCAAAA-TTT-CAGAAGAGGG
1 TTATCAAAATTTTACAGAAGAGCG
*
13719 TTATCAAAATTTTACAGAA-AGCT
1 TTATCAAAATTTTACAGAAGAGCG
13742 TTATCAAAATTTTA
1 TTATCAAAATTTTA
13756 TAATGAGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 9 0.27
23 19 0.58
24 5 0.15
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (24 bp):
TTATCAAAATTTTACAGAAGAGCG
Found at i:13859 original size:44 final size:43
Alignment explanation
Indices: 13803--13917 Score: 124
Period size: 43 Copynumber: 2.7 Consensus size: 43
13793 TTTTATAGGA
* * *
13803 AGGTGATCAAAATTTCGTAGTATGCTTACCAACATTCCACATGG
1 AGGTTATCAAAATTTCATAGTATGCTTACCAA-ATTCCACAAGG
* * * * * *
13847 AGGTTATTAAAATATCATAGTGTGCTTATCAAATTTCATAAGG
1 AGGTTATCAAAATTTCATAGTATGCTTACCAAATTCCACAAGG
13890 AGGTTATCAAAATTTCATAAGTA-GCTTA
1 AGGTTATCAAAATTTCAT-AGTATGCTTA
13918 TTAAATTTTC
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
43 29 0.50
44 29 0.50
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (43 bp):
AGGTTATCAAAATTTCATAGTATGCTTACCAAATTCCACAAGG
Found at i:14986 original size:12 final size:11
Alignment explanation
Indices: 14969--15016 Score: 59
Period size: 9 Copynumber: 4.6 Consensus size: 11
14959 ACTTTTATGT
14969 TATATATATATA
1 TATATATATA-A
14981 TATATATATAA
1 TATATATATAA
14992 TA-ATA-ATAA
1 TATATATATAA
15001 TA-ATA-ATAA
1 TATATATATAA
15010 TATATAT
1 TATATAT
15017 TATTGGCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
9 15 0.44
10 6 0.18
11 3 0.09
12 10 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATATATATAA
Found at i:17919 original size:19 final size:18
Alignment explanation
Indices: 17882--17926 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
17872 TGAAATTTAT
17882 TAATTATTTATTAAATAA
1 TAATTATTTATTAAATAA
17900 TAATTATTT-TTCAGAATAA
1 TAATTATTTATT-A-AATAA
*
17919 TTATTATT
1 TAATTATT
17927 GAATATCCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 2 0.08
18 10 0.42
19 12 0.50
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTATTTATTAAATAA
Found at i:18900 original size:26 final size:28
Alignment explanation
Indices: 18856--18913 Score: 84
Period size: 26 Copynumber: 2.1 Consensus size: 28
18846 TTGCTATAAG
*
18856 AAGAGGGAGAAATTGTCCATCGTCCATC
1 AAGAAGGAGAAATTGTCCATCGTCCATC
*
18884 AAGAAGGA-AAATT-TCCATCTTCCATC
1 AAGAAGGAGAAATTGTCCATCGTCCATC
18910 AAGA
1 AAGA
18914 GGGATGATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 16 0.57
27 5 0.18
28 7 0.25
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (28 bp):
AAGAAGGAGAAATTGTCCATCGTCCATC
Found at i:19715 original size:22 final size:22
Alignment explanation
Indices: 19690--19874 Score: 134
Period size: 22 Copynumber: 8.5 Consensus size: 22
19680 GGGACATTAA
* *
19690 CAAAATCTCATAGGGAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* *
19712 CAAAA-ATCATAAGAAGGTTA-
1 CAAAATTTCATAGGAAGGTTAT
19732 CAAAATTTCATAGGAAGGTTTAAT
1 CAAAATTTCATAGGAAGG-TT-AT
***
19756 -AAAATTTCATATTTAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* *
19777 CAAAGTTTCATATGG-AGTTTAT
1 CAAAATTTCATA-GGAAGGTTAT
* *
19799 CACATTTTCATAGGTAA--TTAT
1 CAAAATTTCATAGG-AAGGTTAT
* *
19820 C-AAATTTCATAGCAAGATTAT
1 CAAAATTTCATAGGAAGGTTAT
* *
19841 CAAAATTTAATAGGGTA-GTTAT
1 CAAAATTTCATA-GGAAGGTTAT
19863 CAAAATTTCATA
1 CAAAATTTCATA
19875 AAAATATTCA
Statistics
Matches: 129, Mismatches: 22, Indels: 24
0.74 0.13 0.14
Matches are distributed among these distances:
19 2 0.02
20 14 0.11
21 36 0.28
22 59 0.46
23 18 0.14
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:19729 original size:21 final size:21
Alignment explanation
Indices: 19689--19751 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
19679 AGGGACATTA
* * *
19689 ACAAAATCTCATAGGGAGGTT
1 ACAAAATATCATAAGAAGGTT
19710 ATCAAAA-ATCATAAGAAGGTT
1 A-CAAAATATCATAAGAAGGTT
* *
19731 ACAAAATTTCATAGGAAGGTT
1 ACAAAATATCATAAGAAGGTT
19752 TAATAAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 5 0.14
21 25 0.71
22 5 0.14
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.25
Consensus pattern (21 bp):
ACAAAATATCATAAGAAGGTT
Found at i:19863 original size:43 final size:42
Alignment explanation
Indices: 19772--19874 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 42
19762 TCATATTTAG
* * * * *
19772 GTTATCAAAGTTTCATATGGAGTTTATCACATTTTCATAGGTA
1 GTTATCAAA-TTTCATATGAAGATTATCAAAATTTAATAGGTA
*
19815 ATTATCAAATTTCATA-GCAAGATTATCAAAATTTAATAGGGTA
1 GTTATCAAATTTCATATG-AAGATTATCAAAATTTAATA-GGTA
19858 GTTATCAAAATTTCATA
1 GTTATC-AAATTTCATA
19875 AAAATATTCA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
41 1 0.02
42 22 0.44
43 17 0.34
44 10 0.20
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.39
Consensus pattern (42 bp):
GTTATCAAATTTCATATGAAGATTATCAAAATTTAATAGGTA
Found at i:22837 original size:21 final size:22
Alignment explanation
Indices: 22813--22881 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
22803 GTTTATCACT
*
22813 ATTTTATA-GGTAATTATCAAA
1 ATTTAATACGGTAATTATCAAA
* *
22834 ATTTCATACGGTGATTATCAAA
1 ATTTAATACGGTAATTATCAAA
* *
22856 ATTTAATAGGGTAGTTATCAAA
1 ATTTAATACGGTAATTATCAAA
22878 ATTT
1 ATTT
22882 CATAAAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
21 7 0.17
22 34 0.83
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (22 bp):
ATTTAATACGGTAATTATCAAA
Found at i:26322 original size:24 final size:24
Alignment explanation
Indices: 26289--26341 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
26279 GCCAATGAAT
*
26289 AACTATACAGATCCATTCTAGGAC
1 AACTACACAGATCCATTCTAGGAC
*
26313 AACTACACAGATCCATTCTTGGAC
1 AACTACACAGATCCATTCTAGGAC
26337 AACTA
1 AACTA
26342 AATATGCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.25
Consensus pattern (24 bp):
AACTACACAGATCCATTCTAGGAC
Found at i:39570 original size:25 final size:27
Alignment explanation
Indices: 39540--39617 Score: 106
Period size: 30 Copynumber: 2.9 Consensus size: 27
39530 TTGCTGTAGG
39540 AAGTGGCGCAGGGCCTGAGAGAA-G-A
1 AAGTGGCGCAGGGCCTGAGAGAAGGTA
*
39565 AAGTGGCGCAGGGCCTGGGGAAAGAAGGTA
1 AAGTGGCGCAGGGCCT---GAGAGAAGGTA
39595 AAGTGGCGCAGGGCCTGAGAGAA
1 AAGTGGCGCAGGGCCTGAGAGAA
39618 AATAAGCACG
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
25 16 0.35
27 6 0.13
28 6 0.13
29 1 0.02
30 17 0.37
ACGTcount: A:0.31, C:0.15, G:0.45, T:0.09
Consensus pattern (27 bp):
AAGTGGCGCAGGGCCTGAGAGAAGGTA
Found at i:42298 original size:16 final size:17
Alignment explanation
Indices: 42266--42299 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42256 TTTTATTTTT
*
42266 TATTTGTTGATATATAA
1 TATTTATTGATATATAA
42283 TATTTATTGA-ATATAA
1 TATTTATTGATATATAA
42299 T
1 T
42300 TTATACGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (17 bp):
TATTTATTGATATATAA
Found at i:42445 original size:14 final size:13
Alignment explanation
Indices: 42409--42447 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
42399 ATTTTATATT
*
42409 TATAATTATATTTA
1 TATAATTA-ATTAA
42423 TATAATTAATTAA
1 TATAATTAATTAA
42436 TATAATTTAATT
1 TATAA-TTAATT
42448 TTTAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATAATTAATTAA
Done.