Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022814.1 Corchorus olitorius cultivar O-4 contig22847, 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: 95930
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1775 original size:16 final size:16
Alignment explanation
Indices: 1754--1786 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1744 AAAAGGTAAT
1754 AAAAGG-TTCTTCTCAA
1 AAAAGGATT-TTCTCAA
1770 AAAAGGATTTTCTCAA
1 AAAAGGATTTTCTCAA
1786 A
1 A
1787 TCATGTTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (16 bp):
AAAAGGATTTTCTCAA
Found at i:2678 original size:6 final size:6
Alignment explanation
Indices: 2662--2691 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2652 ATATGAATCC
*
2662 TAAAAA GAAAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
2692 GAAACTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (6 bp):
TAAAAA
Found at i:2684 original size:11 final size:12
Alignment explanation
Indices: 2662--2695 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
2652 ATATGAATCC
2662 TAAAAAGAAAAA
1 TAAAAAGAAAAA
*
2674 TAAAAATAAAAA
1 TAAAAAGAAAAA
2686 TAAAAAGAAA
1 TAAAAAGAAA
2696 CTAAAATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (12 bp):
TAAAAAGAAAAA
Found at i:6923 original size:11 final size:11
Alignment explanation
Indices: 6907--6932 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6897 CTAGCCCTAA
6907 AAAACTAGAAG
1 AAAACTAGAAG
6918 AAAACTAGAAG
1 AAAACTAGAAG
6929 AAAA
1 AAAA
6933 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:7554 original size:19 final size:18
Alignment explanation
Indices: 7521--7556 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
7511 TTGAAATAGA
7521 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
7539 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
7557 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:8791 original size:43 final size:43
Alignment explanation
Indices: 8730--8815 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
8720 CATAACATAC
8730 TTTCATAATTGTAATTTCAATAAAGATTAAACACAAGTTCTAA
1 TTTCATAATTGTAATTTCAATAAAGATTAAACACAAGTTCTAA
8773 TTTCATAATTGTAATTTCAATAAAGATTAAACACAAGTTCTAA
1 TTTCATAATTGTAATTTCAATAAAGATTAAACACAAGTTCTAA
8816 AAATAGGCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (43 bp):
TTTCATAATTGTAATTTCAATAAAGATTAAACACAAGTTCTAA
Found at i:9234 original size:21 final size:22
Alignment explanation
Indices: 9194--9236 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
9184 GACCCAAACA
*
9194 AGCAATTCAAAGCATCAATCAT
1 AGCAATTCAAAGCATAAATCAT
*
9216 AGCAA-TCATAGCATAAATCAT
1 AGCAATTCAAAGCATAAATCAT
9237 TATAAAGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.23
Consensus pattern (22 bp):
AGCAATTCAAAGCATAAATCAT
Found at i:9332 original size:16 final size:15
Alignment explanation
Indices: 9311--9357 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
9301 AGGAATAGGC
9311 AATCAATCAAAGCAA
1 AATCAATCAAAGCAA
*
9326 TAATCAATCAGAGCAA
1 -AATCAATCAAAGCAA
9342 AA-CAATGCAAAG-AA
1 AATCAAT-CAAAGCAA
9356 AA
1 AA
9358 AGTAAATGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 8 0.29
15 6 0.21
16 14 0.50
ACGTcount: A:0.60, C:0.17, G:0.11, T:0.13
Consensus pattern (15 bp):
AATCAATCAAAGCAA
Found at i:11848 original size:26 final size:28
Alignment explanation
Indices: 11817--11883 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 28
11807 AAAATTTTGG
11817 AAAACGCAAAAAC-A-CTTTTTTTCTCA
1 AAAACGCAAAAACAATCTTTTTTTCTCA
* *
11843 AAAACGCAAAAACAAATTTTTTTTTTTCA
1 AAAACGCAAAAAC-AATCTTTTTTTCTCA
11872 AAAACGCAAAAA
1 AAAACGCAAAAA
11884 AAAAAAGAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 13 0.36
28 1 0.03
29 22 0.61
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.28
Consensus pattern (28 bp):
AAAACGCAAAAACAATCTTTTTTTCTCA
Found at i:12980 original size:11 final size:11
Alignment explanation
Indices: 12964--12989 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12954 CTAACCCTAA
12964 AAAACTAGAAG
1 AAAACTAGAAG
12975 AAAACTAGAAG
1 AAAACTAGAAG
12986 AAAA
1 AAAA
12990 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:13610 original size:19 final size:18
Alignment explanation
Indices: 13577--13612 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13567 TTGAAATAGA
13577 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
13595 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
13613 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:28011 original size:17 final size:18
Alignment explanation
Indices: 27976--28011 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
27966 CTCCTCTTGC
*
27976 ATGAAAACACTTGTTTTT
1 ATGAAAACAATTGTTTTT
27994 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTGTTTTT
28011 A
1 A
28012 ACTACCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (18 bp):
ATGAAAACAATTGTTTTT
Found at i:31126 original size:32 final size:31
Alignment explanation
Indices: 31054--31134 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
31044 TATTTATTTA
* **
31054 TTTTAGAAAACGCAAAAACACCCACTTTTTT
1 TTTTAAAAAACGCAAAAACAAACACTTTTTT
* *
31085 TTTTCAAAAACGCAAAAACAAATA-TTTTTT
1 TTTTAAAAAACGCAAAAACAAACACTTTTTT
31115 TTTATGAAAAAACGCAAAAA
1 TTT-T-AAAAAACGCAAAAA
31135 AGAAAAATTC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 9 0.21
31 20 0.48
32 13 0.31
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (31 bp):
TTTTAAAAAACGCAAAAACAAACACTTTTTT
Found at i:34952 original size:15 final size:16
Alignment explanation
Indices: 34932--34965 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
34922 ACTAATGCAT
34932 AAAAACTAAGA-AAAC
1 AAAAACTAAGACAAAC
*
34947 AAAAACTAATACAAAC
1 AAAAACTAAGACAAAC
34963 AAA
1 AAA
34966 GATTCCACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.74, C:0.15, G:0.03, T:0.09
Consensus pattern (16 bp):
AAAAACTAAGACAAAC
Found at i:44355 original size:21 final size:21
Alignment explanation
Indices: 44331--44379 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
44321 AACTCTTTGC
* *
44331 ACAATTCATTAATGCACAACA
1 ACAATTCATGAATACACAACA
*
44352 ACAATTCATGAGTACACAACA
1 ACAATTCATGAATACACAACA
*
44373 ATAATTC
1 ACAATTC
44380 CAGCAAGAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.24
Consensus pattern (21 bp):
ACAATTCATGAATACACAACA
Found at i:45467 original size:5 final size:6
Alignment explanation
Indices: 45453--45489 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
45443 TCTTCCTCTC
45453 AAAAA- AAAAAT AAAAAT AAAAAT AAAAAT -AAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
45490 GTAGTAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 10 0.33
6 20 0.67
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:45473 original size:12 final size:12
Alignment explanation
Indices: 45453--45489 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
45443 TCTTCCTCTC
45453 AAAAA-AAAAAT
1 AAAAATAAAAAT
45464 AAAAATAAAAAT
1 AAAAATAAAAAT
45476 AAAAAT-AAAAT
1 AAAAATAAAAAT
45487 AAA
1 AAA
45490 GTAGTAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 13 0.52
12 12 0.48
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:49794 original size:15 final size:15
Alignment explanation
Indices: 49764--49805 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
49754 TTATTTTGTT
49764 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
49780 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
49795 TTGTTTTCTGT
1 TTGTTTTCTGT
49806 CAACCTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:73809 original size:10 final size:11
Alignment explanation
Indices: 73792--73819 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
73782 AAAACTGATG
73792 CAAAAAAAAAA
1 CAAAAAAAAAA
73803 CAAAAAAAAAA
1 CAAAAAAAAAA
73814 CAAAAA
1 CAAAAA
73820 CTAATCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:73829 original size:17 final size:17
Alignment explanation
Indices: 73777--73829 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
73767 CCTTCTAAAC
*
73777 AAACAAAAACTGATGCAA
1 AAACAAAAACTAAT-CAA
* **
73795 AAA-AAAAACAAAAAAA
1 AAACAAAAACTAATCAA
73811 AAACAAAAACTAATCAA
1 AAACAAAAACTAATCAA
73828 AA
1 AA
73830 GCTTAATACT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
16 5 0.19
17 19 0.70
18 3 0.11
ACGTcount: A:0.75, C:0.13, G:0.04, T:0.08
Consensus pattern (17 bp):
AAACAAAAACTAATCAA
Found at i:74971 original size:15 final size:16
Alignment explanation
Indices: 74947--74984 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
74937 ATAAATCAAA
*
74947 AGAAAGAAGAGA-AAG
1 AGAAAAAAGAGACAAG
74962 AGAAAAAAGAGACCAAG
1 AGAAAAAAGAGA-CAAG
74979 AGAAAA
1 AGAAAA
74985 GGGGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
17 9 0.45
ACGTcount: A:0.68, C:0.05, G:0.26, T:0.00
Consensus pattern (16 bp):
AGAAAAAAGAGACAAG
Found at i:76459 original size:65 final size:65
Alignment explanation
Indices: 76347--77074 Score: 886
Period size: 63 Copynumber: 11.1 Consensus size: 65
76337 TTTTGAAACA
* * * * **
76347 AAACTATCGACCAGAGACCTCAAACATGATTTTTTTTTTAATGAAACAGATTTTGAATTGAAATG
1 AAACTCTCTACCAGAGACCTCGAACAAGA-TTTTTTTAAAATGAAACAGATTTTGAATTGAAATG
76412 G
65 G
* *
76413 AAACTCTCTACCAGAGACCTCGAACATGATTTTTTTAAAATGAAACAGATTTTGGATTGAAATGG
1 AAACTCTCTACCAGAGACCTCGAACAAGATTTTTTTAAAATGAAACAGATTTTGAATTGAAATGG
* * * * * *
76478 AAACTTTCTACTAAAGGCCTCGAAC-AGA-ATTTTTAAAATGAAACAGGTTTTGAATTGAAATGG
1 AAACTCTCTACCAGAGACCTCGAACAAGATTTTTTTAAAATGAAACAGATTTTGAATTGAAATGG
* * *
76541 AAACTCTCTACCAGAGACCTCGCACAAGA--TTTTTAAAATGAAATAGATTTTGAATTAAAATGG
1 AAACTCTCTACCAGAGACCTCGAACAAGATTTTTTTAAAATGAAACAGATTTTGAATTGAAATGG
* * *
76604 AAACTCTCTACCAGAGACCTCGCACAAGA--TTTTTAAAATGAAATAGATTTTGAATTAAAATGG
1 AAACTCTCTACCAGAGACCTCGAACAAGATTTTTTTAAAATGAAACAGATTTTGAATTGAAATGG
76667 AAACTCTCTACCAGAGACCTCGAACAAGATTTTTTTAAAAATGAAACAGATTTTGAATTGAAATG
1 AAACTCTCTACCAGAGACCTCGAACAAGATTTTTTT-AAAATGAAACAGATTTTGAATTGAAATG
76732 G
65 G
* * *
76733 AAA--CTCTACCGGAAACCTCGAACATGATTTTTTTTCAAAAAAAAAATTGAAACAGATTTTGAA
1 AAACTCTCTACCAGAGACCTCGAACAAGA-TTTTTTT-------AAAA-TGAAACAGATTTTGAA
*
76796 TTGAAATAG
57 TTGAAATGG
*
76805 AAACTCTCTACCAGAGACCTCGAACAGGA--TTTTTAAAATGAAACAGATTTTGAATTGAAATGG
1 AAACTCTCTACCAGAGACCTCGAACAAGATTTTTTTAAAATGAAACAGATTTTGAATTGAAATGG
* * *
76868 AAACTCTCTATCAGAGACCTCGAACAAGATTTTTTAAAAATGAAACAGATTTTGAATTGAAATAG
1 AAACTCTCTACCAGAGACCTCGAACAAGATTTTTTTAAAATGAAACAGATTTTGAATTGAAATGG
* * *
76933 AAACTCTTTACCAGAAACCTCGAACATGATTTTTTTTTTTGAAAAAATGAAACAGATTTTGAATT
1 AAACTCTCTACCAGAGACCTCGAACAAGA----TTTTTTT---AAAATGAAACAGATTTTGAATT
76998 GAAATGG
59 GAAATGG
* * * **
77005 AAACTCTCTACCAGAGACCTCGAACAGGA--TTTTCAAAATGAAACAGATTTTGAATTAAAACAG
1 AAACTCTCTACCAGAGACCTCGAACAAGATTTTTTTAAAATGAAACAGATTTTGAATTGAAATGG
77068 AAACTCT
1 AAACTCT
77075 AGTAAAAGCT
Statistics
Matches: 589, Mismatches: 50, Indels: 49
0.86 0.07 0.07
Matches are distributed among these distances:
63 258 0.44
64 30 0.05
65 123 0.21
66 60 0.10
69 6 0.01
71 10 0.02
72 81 0.14
74 21 0.04
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (65 bp):
AAACTCTCTACCAGAGACCTCGAACAAGATTTTTTTAAAATGAAACAGATTTTGAATTGAAATGG
Found at i:77027 original size:200 final size:194
Alignment explanation
Indices: 76356--77074 Score: 963
Period size: 200 Copynumber: 3.7 Consensus size: 194
76346 AAAACTATCG
* *
76356 ACCAGAGACCTCAAACATGATTTTTTTTTT--AATGAAACAGATTTTGAATTGAAATGGAAACTC
1 ACCAGAAACCTCGAACATGATTTTTTTTTTAAAATGAAACAGATTTTGAATTGAAATGGAAACTC
* * * *
76419 TCTACCAGAGACCTCGAACATGATTTTTTTAAAATGAAACAGATTTTGGATTGAAATGGAAACTT
66 TCTACCAGAGACCTCGAACAGGA--TTTTTAAAATGAAACAGATTTTGAATTAAAATGGAAACTC
* * * *
76484 TCTACTAAAGGCCTCGAAC-AGAATTTTT-AAAATGAAACAGGTTTTGAATTGAAATGGAAACTC
129 TCTAC-AGAGACCTCGAACAAGATTTTTTAAAAATGAAACAGATTTTGAATTGAAATGGAAACTC
76547 TCT
193 T-T
* * * * *
76550 ACCAGAGACCTCGCACAAGA-----TTTTTAAAATGAAATAGATTTTGAATTAAAATGGAAACTC
1 ACCAGAAACCTCGAACATGATTTTTTTTTTAAAATGAAACAGATTTTGAATTGAAATGGAAACTC
* * *
76610 TCTACCAGAGACCTCGCACAAGATTTTTAAAATGAAATAGATTTTGAATTAAAATGGAAACTCTC
66 TCTACCAGAGACCTCGAACAGGATTTTTAAAATGAAACAGATTTTGAATTAAAATGGAAACTCTC
76675 TACCAGAGACCTCGAACAAGATTTTTTTAAAAATGAAACAGATTTTGAATTGAAATGGAAACTC-
131 TA-CAGAGACCTCGAACAAGA-TTTTTTAAAAATGAAACAGATTTTGAATTGAAATGGAAACTCT
76739 T
194 T
* ** *
76740 ACCGGAAACCTCGAACATGATTTTTTTTCAAAAAAAAAATTGAAACAGATTTTGAATTGAAATAG
1 ACCAGAAACCTCGAACATGATTTTTTTT-----TTAAAA-TGAAACAGATTTTGAATTGAAATGG
*
76805 AAACTCTCTACCAGAGACCTCGAACAGGATTTTTAAAATGAAACAGATTTTGAATTGAAATGGAA
60 AAACTCTCTACCAGAGACCTCGAACAGGATTTTTAAAATGAAACAGATTTTGAATTAAAATGGAA
*
76870 ACTCTCTATCAGAGACCTCGAACAAGATTTTTTAAAAATGAAACAGATTTTGAATTGAAATAGAA
125 ACTCTCTA-CAGAGACCTCGAACAAGATTTTTTAAAAATGAAACAGATTTTGAATTGAAATGGAA
76935 ACTCTTT
189 ACTC-TT
76942 ACCAGAAACCTCGAACATGATTTTTTTTTTTGAAAAAATGAAACAGATTTTGAATTGAAATGGAA
1 ACCAGAAACCTCGAACATGA-TTTTTTTTTT---AAAATGAAACAGATTTTGAATTGAAATGGAA
* **
77007 ACTCTCTACCAGAGACCTCGAACAGGATTTTCAAAATGAAACAGATTTTGAATTAAAACAGAAAC
62 ACTCTCTACCAGAGACCTCGAACAGGATTTTTAAAATGAAACAGATTTTGAATTAAAATGGAAAC
77072 TCT
127 TCT
77075 AGTAAAAGCT
Statistics
Matches: 464, Mismatches: 38, Indels: 40
0.86 0.07 0.07
Matches are distributed among these distances:
189 56 0.12
190 21 0.05
191 57 0.12
192 34 0.07
194 17 0.04
195 3 0.01
200 135 0.29
201 113 0.24
202 20 0.04
203 8 0.02
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (194 bp):
ACCAGAAACCTCGAACATGATTTTTTTTTTAAAATGAAACAGATTTTGAATTGAAATGGAAACTC
TCTACCAGAGACCTCGAACAGGATTTTTAAAATGAAACAGATTTTGAATTAAAATGGAAACTCTC
TACAGAGACCTCGAACAAGATTTTTTAAAAATGAAACAGATTTTGAATTGAAATGGAAACTCTT
Found at i:78504 original size:23 final size:23
Alignment explanation
Indices: 78478--78526 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
78468 CAAAGGGTAA
* *
78478 TTTTTCATGGCAGTCTCTATAAG
1 TTTTTCATGCCAGTCCCTATAAG
78501 TTTTTCATGCCAGTCCCTATAAG
1 TTTTTCATGCCAGTCCCTATAAG
78524 TTT
1 TTT
78527 CTTGTTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.45
Consensus pattern (23 bp):
TTTTTCATGCCAGTCCCTATAAG
Found at i:82315 original size:11 final size:11
Alignment explanation
Indices: 82301--82338 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
82291 ATTCATAACA
82301 AATTTATAATT
1 AATTTATAATT
82312 AATTTATAATT
1 AATTTATAATT
82323 -ATTTGATAATT
1 AATTT-ATAATT
*
82334 TATTT
1 AATTT
82339 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:85987 original size:29 final size:30
Alignment explanation
Indices: 85918--85991 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 30
85908 AAATAGCCTT
*
85918 TTTGCCCCCTGAACTTTGCAAATTTAGGCCAG
1 TTTGCCCCCTGAACTTT-CAAATTTA-GCCAC
*
85950 ATTGCCCCCTGAACTTT-AAATTGT-GCCAC
1 TTTGCCCCCTGAACTTTCAAATT-TAGCCAC
85979 TTTGCCCCCTGAA
1 TTTGCCCCCTGAA
85992 TTTGTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 16 0.42
30 5 0.13
31 1 0.03
32 16 0.42
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (30 bp):
TTTGCCCCCTGAACTTTCAAATTTAGCCAC
Found at i:86092 original size:19 final size:18
Alignment explanation
Indices: 86056--86094 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
86046 TTAAGTCCCA
*
86056 CAAATTTTGATGATGTGG
1 CAAATTTTGATGACGTGG
*
86074 CAAACTTTTGCTGACGTGG
1 CAAA-TTTTGATGACGTGG
86093 CA
1 CA
86095 CTTCCACGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (18 bp):
CAAATTTTGATGACGTGG
Found at i:86311 original size:29 final size:30
Alignment explanation
Indices: 86260--86338 Score: 74
Period size: 32 Copynumber: 2.6 Consensus size: 30
86250 GCCTGATTTC
* *
86260 ACAAA-TTCAAGGGGCAAAGTGG-CACAA-T
1 ACAAAGTTCAGGGGGCAAACTGGCCA-AATT
* *
86288 ATAAAGTTCAGGGGGCAATCTGGCCTAAATTT
1 ACAAAGTTCAGGGGGCAAACTGGCC-AAA-TT
86320 ACAAAGTTCAGGGGGCAAA
1 ACAAAGTTCAGGGGGCAAA
86339 TGGGCTATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
28 4 0.10
29 14 0.35
30 3 0.08
31 1 0.03
32 18 0.45
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.19
Consensus pattern (30 bp):
ACAAAGTTCAGGGGGCAAACTGGCCAAATT
Found at i:89489 original size:17 final size:18
Alignment explanation
Indices: 89459--89499 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
89449 TAGTTATTTT
89459 ATTATTTGACTATAATTA
1 ATTATTTGACTATAATTA
89477 ATTATTT-ACTATAATTA
1 ATTATTTGACTATAATTA
*
89494 TTTATT
1 ATTATT
89500 ATTGTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTATTTGACTATAATTA
Found at i:94932 original size:15 final size:15
Alignment explanation
Indices: 94905--94943 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
94895 TTTTGTTTTG
94905 TTTTCTAGTTTAATTA
1 TTTTCT-GTTTAATTA
*
94921 TTTTCTGTTTAATTG
1 TTTTCTGTTTAATTA
94936 TTTTCTGT
1 TTTTCTGT
94944 CAACCTCTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.15, C:0.08, G:0.10, T:0.67
Consensus pattern (15 bp):
TTTTCTGTTTAATTA
Found at i:95899 original size:26 final size:26
Alignment explanation
Indices: 95870--95928 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
95860 CACCTGCGGA
*
95870 AATAATAAATGAATAC-ATTAATAAAT
1 AATAATAAAT-AATACGACTAATAAAT
*
95896 AATAATAAATATTACGACTAATAAAT
1 AATAATAAATAATACGACTAATAAAT
95922 AATAATA
1 AATAATA
95929 CC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 4 0.13
26 26 0.87
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (26 bp):
AATAATAAATAATACGACTAATAAAT
Done.