Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015493.1 Corchorus olitorius cultivar O-4 contig15526, 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: 30259
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:370 original size:205 final size:203
Alignment explanation
Indices: 19--431 Score: 727
Period size: 205 Copynumber: 2.0 Consensus size: 203
9 GCTTAATAAC
19 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAAATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAAATTACTAACAAAGTTGTAGTGAATAA
* * *
84 GATACAATACATTATTATTATATATATAAAACTATACCCAAAAAAAGTAGTTGAACATTAGTGGT
66 GATACAACACATTACTATTATATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGT
*
149 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAAATTCAAAATTATAAAAGATATTAAAGA
131 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAAATTCAAAAATATAAAAGATATT-AAGA
*
214 TCCGATTTA
195 TCCAATTTA
*
223 TTTATCAATGGTGAATGTTATTAATTTTTTAAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
1 TTTATCAATGGTGAATGTTATTAATTTTTT-AAGTCTAAAATTACTAACAAAGTTGTAGTGAATA
* *
288 AGATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGG
65 AGATACAACACATTACTATTATATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGG
*
353 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAAATATAAAAGATATTAAGA
130 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAAATTCAAAAATATAAAAGATATTAAGA
418 TCCAATTTA
195 TCCAATTTA
427 TTTAT
1 TTTAT
432 TATTAAGGAA
Statistics
Matches: 199, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
204 47 0.24
205 152 0.76
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (203 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAAATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGT
TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAAATTCAAAAATATAAAAGATATTAAGAT
CCAATTTA
Found at i:482 original size:29 final size:29
Alignment explanation
Indices: 440--514 Score: 150
Period size: 29 Copynumber: 2.6 Consensus size: 29
430 ATTATTAAGG
440 AAACAATATTTCTTTTTTTTTGGCCAACA
1 AAACAATATTTCTTTTTTTTTGGCCAACA
469 AAACAATATTTCTTTTTTTTTGGCCAACA
1 AAACAATATTTCTTTTTTTTTGGCCAACA
498 AAACAATATTTCTTTTT
1 AAACAATATTTCTTTTT
515 AGTCAATACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (29 bp):
AAACAATATTTCTTTTTTTTTGGCCAACA
Found at i:624 original size:39 final size:40
Alignment explanation
Indices: 570--650 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
560 ATACCTAAGA
* *
570 ATTTAATTAATGTAAGTATTTTGGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
609 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
649 AT
1 AT
651 AGGAATTACA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
Found at i:1619 original size:22 final size:23
Alignment explanation
Indices: 1573--1771 Score: 134
Period size: 22 Copynumber: 9.1 Consensus size: 23
1563 TAAATATTTT
*
1573 TATGAAATTTTG-TAAACTACCC
1 TATGAAATTTTGATAATCTACCC
* *
1595 TATTAAATTTTGATAATC-ACGC
1 TATGAAATTTTGATAATCTACCC
* *
1617 TATGAAATTCTGATAAT-TA-CT
1 TATGAAATTTTGATAATCTACCC
* * *
1638 TATGAAATTGTGATAAACT-CCA
1 TATGAAATTTTGATAATCTACCC
* *
1660 TATGAAATTTTGATAACCTA-AC
1 TATGAAATTTTGATAATCTACCC
* * *
1682 TATGAAATTTTAATAAACCT-TCC
1 TATGAAATTTTGAT-AATCTACCC
*
1705 TATGAAATTTTG-TAATCT-TCC
1 TATGAAATTTTGATAATCTACCC
* * *
1726 TATG-ATTTTTGATAA-CTTCCT
1 TATGAAATTTTGATAATCTACCC
* *
1747 TATGAGATTTTGTTAATCT-CCC
1 TATGAAATTTTGATAATCTACCC
1769 TAT
1 TAT
1772 AATTTTTTGA
Statistics
Matches: 141, Mismatches: 25, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
20 8 0.06
21 34 0.24
22 76 0.54
23 23 0.16
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.42
Consensus pattern (23 bp):
TATGAAATTTTGATAATCTACCC
Found at i:1699 original size:44 final size:42
Alignment explanation
Indices: 1573--1758 Score: 130
Period size: 43 Copynumber: 4.3 Consensus size: 42
1563 TAAATATTTT
* * * *
1573 TATGAAATTTTG-TAAACTACCCTATTAAATTTTGATAATCACGC
1 TATGAAATTTTGAT-AACTA-ACTATGAAATTTTGATAAACTC-C
* * *
1617 TATGAAATTCTGATAA-TTACTTATGAAATTGTGATAAACTCC
1 TATGAAATTTTGATAACTAAC-TATGAAATTTTGATAAACTCC
*
1659 ATATGAAATTTTGATAACCTAACTATGAAATTTTAATAAACCTTCC
1 -TATGAAATTTTGATAA-CTAACTATGAAATTTTGATAAA-C-TCC
** *
1705 TATGAAATTTTG-TAATCTTCCTATG-ATTTTTGAT-AACTTCC
1 TATGAAATTTTGATAA-CTAACTATGAAATTTTGATAAAC-TCC
*
1746 TTATGAGATTTTG
1 -TATGAAATTTTG
1759 TTAATCTCCC
Statistics
Matches: 117, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
41 5 0.04
42 15 0.13
43 39 0.33
44 38 0.32
45 17 0.15
46 3 0.03
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.41
Consensus pattern (42 bp):
TATGAAATTTTGATAACTAACTATGAAATTTTGATAAACTCC
Found at i:1744 original size:20 final size:20
Alignment explanation
Indices: 1700--1777 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 20
1690 TTTAATAAAC
1700 CTTCCTATGAAATTTTGTAAT
1 CTTCCTATG-AATTTTGTAAT
*
1721 CTTCCTATGATTTTTGATAA-
1 CTTCCTATGAATTTTG-TAAT
1741 CTTCCTTATGAGATTTTGTTAAT
1 CTTCC-TATGA-ATTTTG-TAAT
*
1764 CTCCCTAT-AATTTT
1 CTTCCTATGAATTTT
1778 TTGATGCTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
20 16 0.33
21 18 0.37
22 11 0.22
23 4 0.08
ACGTcount: A:0.24, C:0.17, G:0.09, T:0.50
Consensus pattern (20 bp):
CTTCCTATGAATTTTGTAAT
Found at i:2052 original size:45 final size:45
Alignment explanation
Indices: 1988--2079 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
1978 GGCAATCTAA
*
1988 TCCGGTTTAACTCTTATAGTATGATTATACATTTAAAAATTCAAC
1 TCCGGTTTAACTCTTATAGTATGATTATACATTTAAAAATCCAAC
** *
2033 TCCGGTTTAGTTCTTATAGTATGATTATACGTTTAAAAATCCAAC
1 TCCGGTTTAACTCTTATAGTATGATTATACATTTAAAAATCCAAC
2078 TC
1 TC
2080 GTTTGAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (45 bp):
TCCGGTTTAACTCTTATAGTATGATTATACATTTAAAAATCCAAC
Found at i:3703 original size:32 final size:32
Alignment explanation
Indices: 3667--3732 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
3657 CATAAAGCTA
3667 AAGCAGGATCATCTTGAAACCAAAAGGGTTAC
1 AAGCAGGATCATCTTGAAACCAAAAGGGTTAC
* *
3699 AAGCAGGATCATCTTGAAGCCAAAAGGTTTAC
1 AAGCAGGATCATCTTGAAACCAAAAGGGTTAC
3731 AA
1 AA
3733 ATGGTAGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (32 bp):
AAGCAGGATCATCTTGAAACCAAAAGGGTTAC
Found at i:6542 original size:4 final size:4
Alignment explanation
Indices: 6535--6560 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
6525 AAAAAAAAAA
6535 AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AA
6561 TGGGCTAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:6922 original size:28 final size:28
Alignment explanation
Indices: 6854--6928 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 28
6844 TATGGGCATA
* *
6854 AAATTACCGTTTTACCCTAAGAATGAAT
1 AAATTACAGTTTTACCCTTAGAATGAAT
**
6882 AAATTACCA-TTTTACCCTTAGAA-GGTT
1 AAATTA-CAGTTTTACCCTTAGAATGAAT
*
6909 AAATTTACAGTTTTAACCTT
1 AAA-TTACAGTTTTACCCTT
6929 GTACTTTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 7 0.18
28 31 0.79
29 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.37
Consensus pattern (28 bp):
AAATTACAGTTTTACCCTTAGAATGAAT
Found at i:9850 original size:22 final size:22
Alignment explanation
Indices: 9825--9904 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
9815 TACATAGAAA
*
9825 GGTTATCAATATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* *
9847 GGTTACCAAAATTTCATA-TGGA
1 GGTTATCAAAATTTCATAGT-GT
* * *
9869 GGTTATCGAAACTTCACAGTGT
1 GGTTATCAAAATTTCATAGTGT
*
9891 AGTTATCAAAATTT
1 GGTTATCAAAATTT
9905 TATATAGAAA
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
21 1 0.02
22 43 0.96
23 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGT
Found at i:9874 original size:44 final size:44
Alignment explanation
Indices: 9824--9909 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
9814 ATACATAGAA
* * *
9824 AGGTTATC-AATATTTCATAGTGTGGTTACCAAAATTTCATATGG
1 AGGTTATCGAA-ACTTCACAGTGTAGTTACCAAAATTTCATATGG
* *
9868 AGGTTATCGAAACTTCACAGTGTAGTTATCAAAATTTTATAT
1 AGGTTATCGAAACTTCACAGTGTAGTTACCAAAATTTCATAT
9910 AGAAATTACA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
44 34 0.94
45 2 0.06
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (44 bp):
AGGTTATCGAAACTTCACAGTGTAGTTACCAAAATTTCATATGG
Found at i:10006 original size:110 final size:110
Alignment explanation
Indices: 9808--10018 Score: 262
Period size: 110 Copynumber: 1.9 Consensus size: 110
9798 ACAATTACAC
* * * * * * *
9808 CAAAAAATACATAGAAAGGTTATCAATATTTCATAGTGTGGTTACCAAAATTTCATATGGAGGTT
1 CAAAAAATACATAAAAAGATTATCAAAATTTCATAGAGTGGTTAACAAAATTTCATACGAAGGTT
9873 ATCGAAACTTCACAGTGTAGTTATCAAAATTTTATATAGAAATTA
66 ATCGAAACTTCACAGTGTAGTTATCAAAATTTTATATAGAAATTA
* * * *
9918 CAAAAATTTCATAAAAAGATTATCAAAATTTCTTAGAGAT-GTTAACAACATTTCATACGAAGGT
1 CAAAAAATACATAAAAAGATTATCAAAATTTCATAGAG-TGGTTAACAAAATTTCATACGAAGGT
* * * * *
9982 TATCGATATTTTATAGTGTGGTTATCAAAATTTTATA
65 TATCGAAACTTCACAGTGTAGTTATCAAAATTTTATA
10019 AGGATGTTAA
Statistics
Matches: 84, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
110 83 0.99
111 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (110 bp):
CAAAAAATACATAAAAAGATTATCAAAATTTCATAGAGTGGTTAACAAAATTTCATACGAAGGTT
ATCGAAACTTCACAGTGTAGTTATCAAAATTTTATATAGAAATTA
Found at i:10027 original size:22 final size:24
Alignment explanation
Indices: 10002--10062 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 24
9992 TTATAGTGTG
*
10002 GTTATCAAAATTTTATA-A-GGAT
1 GTTATCAAAATTTCATAGAGGGAT
*
10024 GTTAACAAAATTTCATAGGGAGGGAT
1 GTTATCAAAATTTCATA--GAGGGAT
10050 GTTATCAAAATTT
1 GTTATCAAAATTT
10063 GTGCTTATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 15 0.47
25 1 0.03
26 16 0.50
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (24 bp):
GTTATCAAAATTTCATAGAGGGAT
Found at i:10257 original size:22 final size:22
Alignment explanation
Indices: 10181--10441 Score: 196
Period size: 22 Copynumber: 12.0 Consensus size: 22
10171 CTCATATGGA
*
10181 GGTTATCGAAA-TTTCATGGTGT
1 GGTTATC-AAATTTTCATAGTGT
* *
10203 GATTA-CAAAATTTT-ATGAG-GA
1 GGTTATC-AAATTTTCAT-AGTGT
10224 GGTTATCAAATTTTTCATAGTGT
1 GGTTATCAAA-TTTTCATAGTGT
*
10247 GGTTA-CCAATTTT-ATAGTGT
1 GGTTATCAAATTTTCATAGTGT
* * * *
10267 GATTATCAAAATTTAATAGTGA
1 GGTTATCAAATTTTCATAGTGT
* * * * *
10289 GATTATCACATTTTCACACTGA
1 GGTTATCAAATTTTCATAGTGT
* * *
10311 GGTAATCAAAATTTCATAGTGC
1 GGTTATCAAATTTTCATAGTGT
* *
10333 GCTTATCAAAATTTCATAGTGT
1 GGTTATCAAATTTTCATAGTGT
* *
10355 GGTTATCAAAATTTCACAGTGT
1 GGTTATCAAATTTTCATAGTGT
10377 GGTTATCAAATTTTCATAAG-GT
1 GGTTATCAAATTTTCAT-AGTGT
* * *
10399 GGTTATCCAGA-TTTCATAATGA
1 GGTTAT-CAAATTTTCATAGTGT
*
10421 GGTTATCAAATTTTCAAAGTG
1 GGTTATCAAATTTTCATAGTG
10442 GGATTATTAA
Statistics
Matches: 191, Mismatches: 36, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
20 11 0.06
21 28 0.15
22 139 0.73
23 13 0.07
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.39
Consensus pattern (22 bp):
GGTTATCAAATTTTCATAGTGT
Found at i:10405 original size:66 final size:65
Alignment explanation
Indices: 10181--10441 Score: 239
Period size: 66 Copynumber: 4.0 Consensus size: 65
10171 CTCATATGGA
* *
10181 GGTTATCGAAA-TTTCAT-GGTGTGATTA-CAAAATTTTATGAG-GAGGTTATCAAATTTTTCAT
1 GGTTATC-AAATTTTCATAGGTG-G-TTATCAAAATTTCAT-AGTGAGGTTATCAAA-TTTTCAC
10242 AGTGT
61 AGTGT
* * * * * *
10247 GGTTA-CCAATTTT-ATAGTGTGATTATCAAAATTTAATAGTGAGATTATCACATTTTCACACTG
1 GGTTATCAAATTTTCATAG-GTGGTTATCAAAATTTCATAGTGAGGTTATCAAATTTTCACAGTG
*
10310 A
65 T
* * * *
10311 GGTAATCAAAATTTCATA-GTGCGCTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAGT
1 GGTTATCAAATTTTCATAGGTG-G-TTATCAAAATTTCATAGTGAGGTTATCAAATTTTCACAGT
10375 GT
64 GT
* * * *
10377 GGTTATCAAATTTTCATAAGGTGGTTATCCAGATTTCATAATGAGGTTATCAAATTTTCAAAGTG
1 GGTTATCAAATTTTCAT-AGGTGGTTATCAAAATTTCATAGTGAGGTTATCAAATTTTCACAGTG
10442 GGATTATTAA
Statistics
Matches: 157, Mismatches: 27, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
64 25 0.16
65 31 0.20
66 96 0.61
67 2 0.01
68 3 0.02
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.39
Consensus pattern (65 bp):
GGTTATCAAATTTTCATAGGTGGTTATCAAAATTTCATAGTGAGGTTATCAAATTTTCACAGTGT
Found at i:12071 original size:28 final size:28
Alignment explanation
Indices: 12027--12084 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
12017 TAAAAAAAAT
12027 CATAGCTTTACACAGAAAGAAAGAAACC
1 CATAGCTTTACACAGAAAGAAAGAAACC
*
12055 CATAGCTTTACATAGAAAGAAAGAAACC
1 CATAGCTTTACACAGAAAGAAAGAAACC
12083 CA
1 CA
12085 AAGGGCCAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.50, C:0.21, G:0.14, T:0.16
Consensus pattern (28 bp):
CATAGCTTTACACAGAAAGAAAGAAACC
Found at i:13169 original size:42 final size:42
Alignment explanation
Indices: 13079--13194 Score: 121
Period size: 42 Copynumber: 2.7 Consensus size: 42
13069 ATCATTCAAC
* *
13079 TTTTTTTATTAATTATGGAAAGATATTGTAAATCCAATATTTAA
1 TTTTTTTA-AAATTATGGAAAGATATTTTAAATCC-ATATTTAA
*
13123 -TTTTTTAAAATTATGAAAAGATATTTTAAAT-C-TATCTTAA
1 TTTTTTTAAAATTATGGAAAGATATTTTAAATCCATAT-TTAA
** *
13163 TTTTTTTTTGAATTATGGAAATATATTTTAAA
1 -TTTTTTTAAAATTATGGAAAGATATTTTAAA
13195 AATAATTAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
39 3 0.05
40 4 0.06
41 1 0.02
42 47 0.76
43 7 0.11
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (42 bp):
TTTTTTTAAAATTATGGAAAGATATTTTAAATCCATATTTAA
Found at i:13879 original size:13 final size:13
Alignment explanation
Indices: 13861--13889 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
13851 AAGATTTATT
13861 TTTCTTTAGTTCA
1 TTTCTTTAGTTCA
13874 TTTCTTTAGTTCA
1 TTTCTTTAGTTCA
13887 TTT
1 TTT
13890 GTAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (13 bp):
TTTCTTTAGTTCA
Found at i:14161 original size:21 final size:20
Alignment explanation
Indices: 14135--14182 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
14125 TAATATATAC
* * *
14135 CATTATGACTTTTTTGATAA
1 CATTATAACTTCTTTAATAA
14155 TCATTATAACTTCTTTAATAA
1 -CATTATAACTTCTTTAATAA
14176 CATTATA
1 CATTATA
14183 TTAAAAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.35, C:0.12, G:0.04, T:0.48
Consensus pattern (20 bp):
CATTATAACTTCTTTAATAA
Found at i:15202 original size:30 final size:30
Alignment explanation
Indices: 15163--15247 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
15153 TAGTAGGGCC
* * *
15163 AATACTATAAAATTTTGATTTTA-ATGGGGTT
1 AATA-TATAAAACTTTCATTTTAGA-AGGGTT
15194 AATATATAAAACTTTCATTTTAGAAGGGTT
1 AATATATAAAACTTTCATTTTAGAAGGGTT
*
15224 AATATTGTAAAAC-TTCAATTTTAG
1 AATA-TATAAAACTTTC-ATTTTAG
15248 TGGAGTCAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
30 28 0.60
31 19 0.40
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (30 bp):
AATATATAAAACTTTCATTTTAGAAGGGTT
Found at i:15238 original size:31 final size:30
Alignment explanation
Indices: 15189--15247 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
15179 GATTTTAATG
15189 GGGTTAATATATAAAACTTTC-ATTTTAGAA
1 GGGTTAATATATAAAAC-TTCAATTTTAGAA
*
15219 GGGTTAATATTGTAAAACTTCAATTTTAG
1 GGGTTAATA-TATAAAACTTCAATTTTAG
15248 TGGAGTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (30 bp):
GGGTTAATATATAAAACTTCAATTTTAGAA
Found at i:15879 original size:22 final size:22
Alignment explanation
Indices: 15854--15970 Score: 64
Period size: 22 Copynumber: 5.3 Consensus size: 22
15844 ACAATCAAAC
15854 CAAAATTACATAGGAAGGTTAT
1 CAAAATTACATAGGAAGGTTAT
* * *
15876 CAAAATTTA-GTAGTG-TGGTTAC
1 CAAAA-TTACATAG-GAAGGTTAT
* *
15898 CAAAATTTCATATGG-GGGTTAT
1 CAAAATTACATA-GGAAGGTTAT
*
15920 CAAAACTT-CATAGTATA-GTTAT
1 CAAAA-TTACATAGGA-AGGTTAT
** **
15942 CAAAATTTTATAAAAAGGTTAT
1 CAAAATTACATAGGAAGGTTAT
15964 CAAAATT
1 CAAAATT
15971 TCTTAGACTC
Statistics
Matches: 74, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
21 6 0.08
22 61 0.82
23 7 0.09
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.34
Consensus pattern (22 bp):
CAAAATTACATAGGAAGGTTAT
Found at i:16254 original size:22 final size:22
Alignment explanation
Indices: 16185--16259 Score: 55
Period size: 22 Copynumber: 3.4 Consensus size: 22
16175 TCTTAGGGAG
* * *
16185 GTTAACAAAATTTCGTACGAAG
1 GTTAACAAAATTTCATAAGAAT
* **
16207 GTTATCAAAACTTT-AT-AGTGT
1 GTTAACAAAA-TTTCATAAGAAT
*
16228 AGTTATCAAAATTTCATAAGAAT
1 -GTTAACAAAATTTCATAAGAAT
16251 GTTAACAAA
1 GTTAACAAA
16260 GTATCATTGG
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
21 4 0.10
22 30 0.75
23 6 0.15
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (22 bp):
GTTAACAAAATTTCATAAGAAT
Found at i:16337 original size:22 final size:22
Alignment explanation
Indices: 16294--16390 Score: 92
Period size: 22 Copynumber: 4.5 Consensus size: 22
16284 ATATTCGTGC
*
16294 TTATCAAAATTTCCT--GGAGG
1 TTATCAAAATTTCATAGGGAGG
*
16314 TTAACAAAATTTCATAGGGAGG
1 TTATCAAAATTTCATAGGGAGG
* *
16336 TTATGAAAATTTCAT-GGAGAAG
1 TTATCAAAATTTCATAGG-GAGG
* *
16358 TTATCAAAATTACATAGAGAGG
1 TTATCAAAATTTCATAGGGAGG
* *
16380 ATATCACAATT
1 TTATCAAAATT
16391 CACAATTTCA
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 13 0.21
21 2 0.03
22 46 0.74
23 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGAGG
Found at i:16346 original size:42 final size:43
Alignment explanation
Indices: 16294--16390 Score: 115
Period size: 44 Copynumber: 2.3 Consensus size: 43
16284 ATATTCGTGC
* * *
16294 TTATCAAAATTTCCTGGAG-GTTAACAAAATTTCATAGGGAGG
1 TTATCAAAATTTCATGGAGAGTTAACAAAATTACATAGAGAGG
* *
16336 TTATGAAAATTTCATGGAGAAGTTATCAAAATTACATAGAGAGG
1 TTATCAAAATTTCATGGAG-AGTTAACAAAATTACATAGAGAGG
* *
16380 ATATCACAATT
1 TTATCAAAATT
16391 CACAATTTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
42 17 0.38
44 28 0.62
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (43 bp):
TTATCAAAATTTCATGGAGAGTTAACAAAATTACATAGAGAGG
Found at i:16489 original size:22 final size:22
Alignment explanation
Indices: 16464--16643 Score: 168
Period size: 22 Copynumber: 8.3 Consensus size: 22
16454 GCACGGTTAC
* * *
16464 AATTTTATAGTTTGATTATCAA
1 AATTTCATAGTGTGGTTATCAA
* * *
16486 AATTTCATAGGGAGATTATCAA
1 AATTTCATAGTGTGGTTATCAA
* * *
16508 AATTTCACACTGAGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
16530 AATTTCATAGTGTGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
*
16552 AATTTCACAGTGTGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
* * * *
16574 ACTTTCATAGGGAGGTTATCGA
1 AATTTCATAGTGTGGTTATCAA
* *
16596 AA-TTCTATAATGAGGTTATCAA
1 AATTTC-ATAGTGTGGTTATCAA
*
16618 ATTTTC--AGTGTGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
*
16638 TATTTC
1 AATTTC
16644 TACATTGGAG
Statistics
Matches: 130, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.12
21 3 0.02
22 108 0.83
23 3 0.02
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (22 bp):
AATTTCATAGTGTGGTTATCAA
Found at i:16529 original size:44 final size:44
Alignment explanation
Indices: 16479--16624 Score: 186
Period size: 44 Copynumber: 3.3 Consensus size: 44
16469 TATAGTTTGA
* *
16479 TTATCAAAATTTCATAGGGAGATTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCACAATGAGG
* * * *
16523 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAGTGTGG
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCACAATGAGG
* * *
16567 TTATCAAACTTTCATAGGGAGGTTATCGAAA-TTCTATAATGAGG
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTC-ACAATGAGG
*
16611 TTATCAAATTTTCA
1 TTATCAAAATTTCA
16625 GTGTGGTTAT
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
43 3 0.03
44 85 0.97
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.36
Consensus pattern (44 bp):
TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCACAATGAGG
Found at i:23249 original size:60 final size:59
Alignment explanation
Indices: 23133--23249 Score: 130
Period size: 60 Copynumber: 2.0 Consensus size: 59
23123 AAATTGTCTC
** * * * *
23133 ATTTTGATAGTTTAGGGGTGAAAGTTTCAAATTAAAAGTTCAAGAGAGAAATTGTCCTG
1 ATTTTGATAGTTTAGGACTGAAAGTTCCAAAATAAAAATTCAAGAGAGAAAATGTCCTG
*
23192 ATTTTGATAGTTTAAGGACT-ACAAGTTCCAAAATAAAAATTCAGGAG-GAAAAATGTCC
1 ATTTTGATAGTTT-AGGACTGA-AAGTTCCAAAATAAAAATTCAAGAGAG-AAAATGTCC
23250 CTTTTGTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
59 15 0.31
60 33 0.69
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (59 bp):
ATTTTGATAGTTTAGGACTGAAAGTTCCAAAATAAAAATTCAAGAGAGAAAATGTCCTG
Found at i:30070 original size:128 final size:119
Alignment explanation
Indices: 29799--30114 Score: 343
Period size: 128 Copynumber: 2.6 Consensus size: 119
29789 ATGTAGCTAG
* *
29799 TGCCTCGTTAAAAACCTTAAG-CTGGAAAACCCAATGGGACAAAACC-AGTCATAAGGAAAAAAG
1 TGCCTCATTAAAAACCTTAAGTC-GGAAAACCCAATGGGACAAAACCGA-TCATAAGGGAAAAAG
** * * *
29862 AGTGCAGCATATCAAGTCCATTTGTCTTCTGGACAAATATTACATGTGCTCTTTAT
64 AGTGCAGCATATCAAGTCCATTTGTCTTCAAGACAAACATTAAATGTGCTCATTAT
** * * *
29918 TGCCTCATTAAAAACCTTGTGTCGGAAAACCCAATTGGACAAAACCGAACAGAAGGGAAAAAGAG
1 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG
* *
29983 TGCTAGAGCA-ATTTAAGTCCATGTAAATGTCTTCAAGACAATTACATCTAAATGTGCT-ATTGT
66 TGC---AGCATA-TCAAGTCCAT-T---TGTCTTCAAGACAA--ACAT-TAAATGTGCTCATTAT
**
30046 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCTGTGGGACAAAACCGATCATAAGGGAAAAAGAG
1 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG
30111 TGCA
66 TGCA
30115 ACGCACTTTA
Statistics
Matches: 163, Mismatches: 21, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
119 57 0.35
120 2 0.01
121 1 0.01
122 13 0.08
123 1 0.01
125 1 0.01
126 12 0.07
128 67 0.41
129 9 0.06
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (119 bp):
TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG
TGCAGCATATCAAGTCCATTTGTCTTCAAGACAAACATTAAATGTGCTCATTAT
Done.