Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017627.1 Corchorus olitorius cultivar O-4 contig17660, 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: 82917
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4365 original size:60 final size:59
Alignment explanation
Indices: 4252--4386 Score: 144
Period size: 60 Copynumber: 2.3 Consensus size: 59
4242 AACATTTCTT
* * * ** * * *
4252 GGGGAGAAATTATCCCAATTTTGATAGTTTAAGGGTGAAAGTTTCAAATTAAAAGTTAAA
1 GGGG-GAAATTGTCCCAATTCTGATAGTTAAAGACTGAAAGTTCCAAAATAAAAATTAAA
* * *
4312 GGGGGAAATTGTCCCGATTCTGATAGATTAAAGACTGAAAGTTCCAAAATAAAAATTCAG
1 GGGGGAAATTGTCCCAATTCTGATAG-TTAAAGACTGAAAGTTCCAAAATAAAAATTAAA
*
4372 GGGGGAAAATGTCCC
1 GGGGGAAATTGTCCC
4387 TTTTGTAAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
59 19 0.31
60 43 0.69
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.27
Consensus pattern (59 bp):
GGGGGAAATTGTCCCAATTCTGATAGTTAAAGACTGAAAGTTCCAAAATAAAAATTAAA
Found at i:6601 original size:22 final size:22
Alignment explanation
Indices: 6548--7121 Score: 255
Period size: 22 Copynumber: 26.3 Consensus size: 22
6538 ATTATACTAT
* *
6548 TTTTGATGACC-TCCTTGTGAAA
1 TTTTGATAACCTTCC-TATGAAA
*
6570 TTTTGTTAACCTTCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* ** * *
6592 TTTTAATAACGATACTATGGAA
1 TTTTGATAACCTTCCTATGAAA
* * ** *
6614 TTTCGAGAACCTTTTTATAAAAA
1 TTTTGATAACCTTCCTAT-GAAA
* *
6637 TTTT-TTAACCTTCTTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* * * *
6658 TTTTGTTAACCTCCCTAAGGAA
1 TTTTGATAACCTTCCTATGAAA
6680 TTTTGA-AGACC-TCACTATGAAA
1 TTTTGATA-ACCTTC-CTATGAAA
*
6702 TTTTGATAA-CTTCCCAATGAAA
1 TTTTGATAACCTT-CCTATGAAA
** **
6724 TTTTGATAACCAACACTATGGGA
1 TTTTGATAACCTTC-CTATGAAA
* *
6747 TGTTGATAACC-TCCATATGATA
1 TTTTGATAACCTTCC-TATGAAA
** * *
6769 CATTGATAACC-ACGTTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
* * * *
6791 ATTTAAAAACCTTCATATG-AA
1 TTTTGATAACCTTCCTATGAAA
* * *
6812 TTGTT-AGTAATC-ACACTCTGAAA
1 TT-TTGA-TAACCTTC-CTATGAAA
*
6835 TTTTGATAA--TGACACTATGAAA
1 TTTTGATAACCT-TC-CTATGAAA
*
6857 TTGTGATCAA-C-TCGCTATGAAA
1 TTTTGAT-AACCTTC-CTATGAAA
*
6879 TTTTGATAAACCTTCCTATAAAA
1 TTTTGAT-AACCTTCCTATGAAA
*
6902 TTTTGATAAACC-TCCTTATAAAA
1 TTTTGAT-AACCTTCC-TATGAAA
6925 TTTTGATAACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
* *
6947 TCTTGATAA-----CTA-CAAA
1 TTTTGATAACCTTCCTATGAAA
* **
6963 TTTTGATAACCTCCCTATGAGT
1 TTTTGATAACCTTCCTATGAAA
*
6985 TTTTGATAACC-TCATTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
* * *
7007 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* *
7029 TTTTGATAACCCTCTTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* **
7051 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCT-TCCTATGAAA
*
7073 TTTTGATAACCTTCATATGAAA
1 TTTTGATAACCTTCCTATGAAA
* *
7095 TTTTGATATCCTGCC--TGAAA
1 TTTTGATAACCTTCCTATGAAA
7115 TTTTGAT
1 TTTTGAT
7122 TACTCAATAA
Statistics
Matches: 420, Mismatches: 97, Indels: 72
0.71 0.16 0.12
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
18 1 0.00
20 12 0.03
21 23 0.05
22 296 0.70
23 73 0.17
24 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
TTTTGATAACCTTCCTATGAAA
Found at i:7026 original size:82 final size:84
Alignment explanation
Indices: 6876--7038 Score: 222
Period size: 82 Copynumber: 2.0 Consensus size: 84
6866 ACTCGCTATG
* * *
6876 AAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCCTTATAAAATTTTGATAACCTCCTT
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAAACCTCATTATAAAATTTTGATAACCTCCCT
6941 ATGAAATCTTGATAACTAC
66 ATGAAATCTTGATAACTAC
* ** * * *
6960 AAATTTTGAT-AACCTCCCTATGAGTTTTTGAT-AACCTCATTATGAAATTTTGTTAATCTCCCT
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAAACCTCATTATAAAATTTTGATAACCTCCCT
*
7023 ATGAAATTTTGATAAC
66 ATGAAATCTTGATAAC
7039 CCTCTTATGA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
82 41 0.59
83 18 0.26
84 10 0.14
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (84 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAAACCTCATTATAAAATTTTGATAACCTCCCT
ATGAAATCTTGATAACTAC
Found at i:7253 original size:44 final size:44
Alignment explanation
Indices: 7203--7372 Score: 141
Period size: 44 Copynumber: 3.9 Consensus size: 44
7193 GAAATACCAC
* *
7203 TATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTT
* * * * * *
7247 TATGAAATTTTGATAACCTC-TCTAT-AAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCACAT-TATGAAAA-TTTGATAACCTCTT
* * * *
7291 TATGAAATTTTGATAATCACATTATGTAATTTTCATAACCTCGCT
1 TATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTC-TT
* * *
7336 T-TGAAATTTTGATGATAACACTAT-AAAATTTTGATAA
1 TATGAAATTTTGATAATCACATTATGAAAA-TTTGATAA
7373 TCTTCTTATA
Statistics
Matches: 96, Mismatches: 24, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
43 7 0.07
44 85 0.89
45 4 0.04
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTT
Found at i:7316 original size:22 final size:22
Alignment explanation
Indices: 7203--7374 Score: 100
Period size: 22 Copynumber: 7.8 Consensus size: 22
7193 GAAATACCAC
*
7203 TATGAAATTTTGGTAATCACAT
1 TATGAAATTTTGATAATCACAT
* * * * *
7225 TTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCACAT
* *
7247 TATGAAATTTTGATAACCTC-T
1 TATGAAATTTTGATAATCACAT
* * * * *
7268 CTATAAAATTTTGTTGA-CCCCT
1 -TATGAAATTTTGATAATCACAT
7290 CTATGAAATTTTGATAATCACAT
1 -TATGAAATTTTGATAATCACAT
* * *
7313 TATGTAATTTTCATAACCTCGC-T
1 TATGAAATTTTGATAA--TCACAT
* * *
7336 T-TGAAATTTTGATGATAACAC
1 TATGAAATTTTGATAATCACAT
*
7357 TATAAAATTTTGATAATC
1 TATGAAATTTTGATAATC
7375 TTCTTATAAA
Statistics
Matches: 114, Mismatches: 29, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.02
21 4 0.04
22 100 0.88
23 5 0.04
24 3 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAT
Found at i:7316 original size:66 final size:66
Alignment explanation
Indices: 7227--7374 Score: 161
Period size: 66 Copynumber: 2.2 Consensus size: 66
7217 AATCACATTT
* * * * * * * ** *
7227 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTCTATAAAATTTTGTTGACCCCTCT
1 TGAAATTTTGATAATCACATTATGAAATTTTCATAACCTCGCTATAAAATTTTGATGACAACACT
7292 A
66 A
* * * *
7293 TGAAATTTTGATAATCACATTATGTAATTTTCATAACCTCGCTTTGAAATTTTGATGATAACACT
1 TGAAATTTTGATAATCACATTATGAAATTTTCATAACCTCGCTATAAAATTTTGATGACAACACT
7358 A
66 A
*
7359 TAAAATTTTGATAATC
1 TGAAATTTTGATAATC
7375 TTCTTATAAA
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.41
Consensus pattern (66 bp):
TGAAATTTTGATAATCACATTATGAAATTTTCATAACCTCGCTATAAAATTTTGATGACAACACT
A
Found at i:7360 original size:88 final size:88
Alignment explanation
Indices: 7202--7368 Score: 219
Period size: 88 Copynumber: 1.9 Consensus size: 88
7192 AGAAATACCA
* * * * **
7202 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTTGATAATCACATTATGAAAATTTCATAACCTCCTTATGAAATTTTGATAACAAC
*
7267 TCTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* * * *
7290 CTATGAAATTTTGATAATCACATTATGTAATTTTCATAACCTCGCTT-TGAAATTTTGATGATAA
1 CTATGAAATTTTGATAATCACATTATGAAAATTTCATAACCTC-CTTATGAAATTTTGATAACAA
7354 CACTATAAAATTTTG
65 CACTATAAAATTTTG
7369 ATAATCTTCT
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
88 65 0.97
89 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (88 bp):
CTATGAAATTTTGATAATCACATTATGAAAATTTCATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:7388 original size:12 final size:12
Alignment explanation
Indices: 7371--7397 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
7361 AAATTTTGAT
7371 AATCTTCTTATA
1 AATCTTCTTATA
7383 AATCTTCTTATA
1 AATCTTCTTATA
7395 AAT
1 AAT
7398 TTTGATAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (12 bp):
AATCTTCTTATA
Found at i:9018 original size:44 final size:44
Alignment explanation
Indices: 8956--9048 Score: 179
Period size: 44 Copynumber: 2.1 Consensus size: 44
8946 ATTAACAATC
8956 TAACA-GAAGTACAAAACCCAACAAAACAATGAAAGTAGATATT
1 TAACATGAAGTACAAAACCCAACAAAACAATGAAAGTAGATATT
8999 TAACATGAAGTACAAAACCCAACAAAACAATGAAAGTAGATATT
1 TAACATGAAGTACAAAACCCAACAAAACAATGAAAGTAGATATT
9043 TAACAT
1 TAACAT
9049 AAAGGGGCAC
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 5 0.10
44 44 0.90
ACGTcount: A:0.55, C:0.16, G:0.11, T:0.18
Consensus pattern (44 bp):
TAACATGAAGTACAAAACCCAACAAAACAATGAAAGTAGATATT
Found at i:9071 original size:23 final size:23
Alignment explanation
Indices: 9045--9093 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
9035 TAGATATTTA
9045 ACATAAAGGGGCACAAAATCT-AC
1 ACATAAAGGGGCACAAAA-CTGAC
* *
9068 ACATAAAGTGTCACAAAACTGAC
1 ACATAAAGGGGCACAAAACTGAC
9091 ACA
1 ACA
9094 CAATATACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.49, C:0.22, G:0.14, T:0.14
Consensus pattern (23 bp):
ACATAAAGGGGCACAAAACTGAC
Found at i:15671 original size:109 final size:109
Alignment explanation
Indices: 15480--15697 Score: 382
Period size: 109 Copynumber: 2.0 Consensus size: 109
15470 TAGTCATTTT
*
15480 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTAGTATGTGTGCTT
1 GGTGCTTGTATTTTTCTTCAAATCCAATAGTTCATTGCACTTTGTATTGTTTAGTATGTGTGCTT
15545 ATTTAATAGCTTCAATTGAATAAACAACACAATTAATAATAATA
66 ATTTAATAGCTTCAATTGAATAAACAACACAATTAATAATAATA
* * *
15589 GGTGCTTGTATTTTTCTTCAAATCCAATAGTTCATTGCATTTTGTATTGTTTGGTATGTGTGTTT
1 GGTGCTTGTATTTTTCTTCAAATCCAATAGTTCATTGCACTTTGTATTGTTTAGTATGTGTGCTT
* *
15654 ATTTAATAGGTTCAATTGAATAAACCACACAATTAATAATAATA
66 ATTTAATAGCTTCAATTGAATAAACAACACAATTAATAATAATA
15698 ATATATATAA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
109 103 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (109 bp):
GGTGCTTGTATTTTTCTTCAAATCCAATAGTTCATTGCACTTTGTATTGTTTAGTATGTGTGCTT
ATTTAATAGCTTCAATTGAATAAACAACACAATTAATAATAATA
Found at i:17895 original size:96 final size:95
Alignment explanation
Indices: 17702--17893 Score: 296
Period size: 97 Copynumber: 2.0 Consensus size: 95
17692 GAAAAGACAG
*
17702 ATAGAGTACTTATCTCGATACTCATCAAAAGTTGACGGGGTCTTTAGTAAATTTGGCATATTACA
1 ATAGAGTACTTATCTCGATACTCATCAAAAGTTGACGGGGTCTTTAGTAAATTTAGCATATTACA
* *
17767 ACTCTTAAATACATAGGAGTAAAGACAAAAA
66 ACTCTTAAACACATA-GAGAAAAGACAAAAA
** * *
17798 ATAGAGTTGTTATCTCGATACTCATCAAAAGTTGATTGGGGTCTTTAGTAAATTTAGCTTATTAC
1 ATAGAGTACTTATCTCGATACTCATCAAAAGTTGA-CGGGGTCTTTAGTAAATTTAGCATATTAC
17863 AACTCTTAAACACAT-GAGAAAAGACAAAAA
65 AACTCTTAAACACATAGAGAAAAGACAAAAA
17893 A
1 A
17894 ATGGAGAAGG
Statistics
Matches: 88, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
95 15 0.17
96 33 0.38
97 40 0.45
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (95 bp):
ATAGAGTACTTATCTCGATACTCATCAAAAGTTGACGGGGTCTTTAGTAAATTTAGCATATTACA
ACTCTTAAACACATAGAGAAAAGACAAAAA
Found at i:18826 original size:103 final size:102
Alignment explanation
Indices: 18713--18909 Score: 340
Period size: 103 Copynumber: 1.9 Consensus size: 102
18703 AACTGTTAAT
* * *
18713 GTTTATACAATGTCATTTAAGAAATATATTTAAAAAATTCTAATATATCTAAGTTTTTTAATTAA
1 GTTTATACAATGTCATATAAGAAATAAATTTAAAAAATTCTAATACATCTAAG-TTTTTAATTAA
*
18778 AATAGTAAAATGGTAAAAATAAAATAGTTACCGTAGAA
65 AATAGTAAAATGATAAAAATAAAATAGTTACCGTAGAA
18816 GTTTATACAATGTCATATAAGAAATAAATTTAAAAAATTCTAATACATCTAAGTTTTTAATTAAA
1 GTTTATACAATGTCATATAAGAAATAAATTTAAAAAATTCTAATACATCTAAGTTTTTAATTAAA
*
18881 ATAGTAAAATGATAGAAATAAAATAGTTA
66 ATAGTAAAATGATAAAAATAAAATAGTTA
18910 TAAAGATATT
Statistics
Matches: 89, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
102 39 0.44
103 50 0.56
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (102 bp):
GTTTATACAATGTCATATAAGAAATAAATTTAAAAAATTCTAATACATCTAAGTTTTTAATTAAA
ATAGTAAAATGATAAAAATAAAATAGTTACCGTAGAA
Found at i:19170 original size:13 final size:13
Alignment explanation
Indices: 19152--19178 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19142 AAATCGGACC
19152 AGAAATTAACCCA
1 AGAAATTAACCCA
19165 AGAAATTAACCCA
1 AGAAATTAACCCA
19178 A
1 A
19179 TCGACTTACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.22, G:0.07, T:0.15
Consensus pattern (13 bp):
AGAAATTAACCCA
Found at i:25814 original size:19 final size:22
Alignment explanation
Indices: 25772--25814 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 22
25762 TCATCACTTT
*
25772 AAACATCAAATCACCATAATAA
1 AAACATCAAATCACCATAAAAA
25794 AAACAT-AAA-CA-CATAAAAA
1 AAACATCAAATCACCATAAAAA
25813 AA
1 AA
25815 TAATTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 3 0.15
22 6 0.30
ACGTcount: A:0.67, C:0.19, G:0.00, T:0.14
Consensus pattern (22 bp):
AAACATCAAATCACCATAAAAA
Found at i:34481 original size:31 final size:31
Alignment explanation
Indices: 34438--34523 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 31
34428 TGACATTAGA
34438 GACTGATTTGAGCCGATTTTGCAACG-CAAGG
1 GACTGATTTGAGCCGATTTTGCAACGTCAA-G
* * *
34469 GACTAATTTGAGCCGATTTTGAAACGTTAAG
1 GACTGATTTGAGCCGATTTTGCAACGTCAAG
* *
34500 CACTGATTTGAGCCAATTTTGCAA
1 GACTGATTTGAGCCGATTTTGCAA
34524 TGTTATAAGC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 45 0.96
32 2 0.04
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (31 bp):
GACTGATTTGAGCCGATTTTGCAACGTCAAG
Found at i:35963 original size:2 final size:2
Alignment explanation
Indices: 35956--36000 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
35946 AGGACTGCTC
35956 TA TA TA TA TA -A TA TA TA TA TA TA TA -A TA TA 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
35996 TA TA T
1 TA TA T
36001 TTGGGTTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:35976 original size:15 final size:15
Alignment explanation
Indices: 35956--36000 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
35946 AGGACTGCTC
35956 TATATATATAATATA
1 TATATATATAATATA
35971 TATATATATAATATA
1 TATATATATAATATA
35986 TATATATAT-ATATA
1 TATATATATAATATA
36000 T
1 T
36001 TTGGGTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 6 0.20
15 24 0.80
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATATATAATATA
Found at i:37577 original size:2 final size:2
Alignment explanation
Indices: 37570--37617 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
37560 ATGAGAGGAG
* *
37570 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA AA AA 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
37611 TA TA TA T
1 TA TA TA T
37618 TAAAAATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:37607 original size:21 final size:21
Alignment explanation
Indices: 37581--37624 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
37571 ATATATATAT
37581 ATATATATATATATATTAAAA
1 ATATATATATATATATTAAAA
37602 ATATATATATATATATTAAAA
1 ATATATATATATATATTAAAA
37623 AT
1 AT
37625 TTATTATTTG
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATATATATATATATTAAAA
Found at i:38582 original size:32 final size:33
Alignment explanation
Indices: 38522--38588 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
38512 TGAGAAAAGG
* *
38522 AAAAGGAAAAGAAAAAGAGAAAGAAAAATAGGA
1 AAAAAGAAAAGAAAAAGAGAAAGAAAAATAAGA
*
38555 AAAAAGAAAAG-AAAAGA-AAAGGGAAAATAAGA
1 AAAAAGAAAAGAAAAAGAGAAA-GAAAAATAAGA
38587 AA
1 AA
38589 TGAAATTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 3 0.10
32 17 0.57
33 10 0.33
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (33 bp):
AAAAAGAAAAGAAAAAGAGAAAGAAAAATAAGA
Found at i:38586 original size:25 final size:23
Alignment explanation
Indices: 38514--38593 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 23
38504 TTGAAATTTG
38514 AGAAAAGGAAAAGGAAAAGAA-AAA
1 AGAAAA-GAAAAGGAAAA-AAGAAA
*
38538 GAGAAAGAAAAATAGGAAAAAAGAAA
1 -AGAAA-AGAAA-AGGAAAAAAGAAA
38564 AGAAAAGAAAAGGGAAAATAAGAAA
1 AGAAAAGAAAA-GGAAAA-AAGAAA
*
38589 TGAAA
1 AGAAA
38594 TTTGGGGCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
23 1 0.02
24 10 0.21
25 25 0.53
26 11 0.23
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.04
Consensus pattern (23 bp):
AGAAAAGAAAAGGAAAAAAGAAA
Found at i:44341 original size:15 final size:16
Alignment explanation
Indices: 44321--44356 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
44311 ATTTTAAAGT
44321 ACTTTTATAAGAAAA-
1 ACTTTTATAAGAAAAC
44336 ACTTTTATAAGAAAAC
1 ACTTTTATAAGAAAAC
44352 ACTTT
1 ACTTT
44357 CTTATGAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (16 bp):
ACTTTTATAAGAAAAC
Found at i:44999 original size:182 final size:182
Alignment explanation
Indices: 44693--45237 Score: 1074
Period size: 182 Copynumber: 3.0 Consensus size: 182
44683 ATTTTAAAAA
44693 TACATTTTTATCATTTAATATAAAAATTTCAT-AAAAAAAGGAAGTTATTTAATGTGGTGGTTAA
1 TACATTTTTATCATTTAATATAAAAATTTCATAAAAAAAAGGAAGTTATTTAATGTGGTGGTTAA
44757 CTTAAAAAGAAGAGGATTTTCGAAAAAGACACCATCTCACATGGATTTTGAAATAAGGTTTTTCC
66 CTTAAAAAGAAGAGGATTTTCGAAAAAGACACCATCTCACATGGATTTTGAAATAAGGTTTTTCC
44822 CCCTCTAAAAATCCCTCTCCAATATCCTAAACATATTTAAAAACCCAACTAT
131 CCCTCTAAAAATCCCTCTCCAATATCCTAAACATATTTAAAAACCCAACTAT
44874 TACATTTTTATCATTTAATATAAAAATTTCATAAAAAAAAGGAAGTTATTTAATGTGGTGGTTAA
1 TACATTTTTATCATTTAATATAAAAATTTCATAAAAAAAAGGAAGTTATTTAATGTGGTGGTTAA
44939 CTTAAAAAGAAGAGGATTTTCGAAAAAGACACCATCTCACATGGATTTTGAAATAAGGTTTTTCC
66 CTTAAAAAGAAGAGGATTTTCGAAAAAGACACCATCTCACATGGATTTTGAAATAAGGTTTTTCC
45004 CCCTCTAAAAATCCCTCTCCAATATCCTAAACATATTTAAAAACCCAACTAT
131 CCCTCTAAAAATCCCTCTCCAATATCCTAAACATATTTAAAAACCCAACTAT
45056 TACATTTTTATCATTTAATATAAAAATTTCATAAAAAAAAGGAAGTTATTTAATGTGGTGGTTAA
1 TACATTTTTATCATTTAATATAAAAATTTCATAAAAAAAAGGAAGTTATTTAATGTGGTGGTTAA
45121 CTTAAAAAGAAGAGGATTTTCGAAAAAGACACCATCTCACATGGATTTTGAAATAAGGTTTTTCC
66 CTTAAAAAGAAGAGGATTTTCGAAAAAGACACCATCTCACATGGATTTTGAAATAAGGTTTTTCC
*
45186 CCCTCTAAAAATCCCTCTCCAATATCCTAAACATATTTAAAAATCCAACTAT
131 CCCTCTAAAAATCCCTCTCCAATATCCTAAACATATTTAAAAACCCAACTAT
45238 AATTTTGCCA
Statistics
Matches: 362, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
181 32 0.09
182 330 0.91
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (182 bp):
TACATTTTTATCATTTAATATAAAAATTTCATAAAAAAAAGGAAGTTATTTAATGTGGTGGTTAA
CTTAAAAAGAAGAGGATTTTCGAAAAAGACACCATCTCACATGGATTTTGAAATAAGGTTTTTCC
CCCTCTAAAAATCCCTCTCCAATATCCTAAACATATTTAAAAACCCAACTAT
Found at i:50105 original size:40 final size:37
Alignment explanation
Indices: 50003--50120 Score: 146
Period size: 37 Copynumber: 3.1 Consensus size: 37
49993 AACCTTTGTC
** *
50003 TTAATATTAGACTTTGAAAAGTCTTGGGCCAAGAGCA
1 TTAATATTACCCTTTGAAAAGTCTTGGGCCAAGAACA
* *
50040 TTAATATTCCCCTTTGAAATGTCTTGGGCCAAGAACA
1 TTAATATTACCCTTTGAAAAGTCTTGGGCCAAGAACA
* *
50077 TTAATATCAATAGCCTTTGAAAAGTCTTGGGCCAAGAACT
1 TTAATAT---TACCCTTTGAAAAGTCTTGGGCCAAGAACA
50117 TTAA
1 TTAA
50121 ATTTGTGTCC
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
37 39 0.57
40 30 0.43
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (37 bp):
TTAATATTACCCTTTGAAAAGTCTTGGGCCAAGAACA
Found at i:52970 original size:25 final size:25
Alignment explanation
Indices: 52942--53008 Score: 125
Period size: 25 Copynumber: 2.7 Consensus size: 25
52932 ATCTTGAGCA
52942 CTCTCGCTCGGTCTCTATTTGAGAC
1 CTCTCGCTCGGTCTCTATTTGAGAC
52967 CTCTCGCTCGGTCTCTATTTGAGAC
1 CTCTCGCTCGGTCTCTATTTGAGAC
*
52992 CTCTCGCTCGATCTCTA
1 CTCTCGCTCGGTCTCTA
53009 CAAACCAATC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.12, C:0.34, G:0.18, T:0.36
Consensus pattern (25 bp):
CTCTCGCTCGGTCTCTATTTGAGAC
Found at i:59784 original size:32 final size:32
Alignment explanation
Indices: 59743--59860 Score: 209
Period size: 32 Copynumber: 3.7 Consensus size: 32
59733 GGCTTTAAAC
*
59743 AGATATCACTCATCTCAAAAACAATCTCTCAG
1 AGATATCACTCATCTCAAAAACCATCTCTCAG
*
59775 AGATATCACTCATCTCAAAAACCATCTCTCAC
1 AGATATCACTCATCTCAAAAACCATCTCTCAG
59807 AGATATCACTCATCTCAAAAACCATCTCTCAG
1 AGATATCACTCATCTCAAAAACCATCTCTCAG
*
59839 AGATATCACTCATTTCAAAAAC
1 AGATATCACTCATCTCAAAAAC
59861 TAGCTCTTGA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 82 1.00
ACGTcount: A:0.40, C:0.30, G:0.05, T:0.25
Consensus pattern (32 bp):
AGATATCACTCATCTCAAAAACCATCTCTCAG
Found at i:60442 original size:76 final size:76
Alignment explanation
Indices: 60311--60472 Score: 270
Period size: 76 Copynumber: 2.1 Consensus size: 76
60301 ACAAATTGAC
* * *
60311 TAGCACGCCCCTATGCTGTCATAAAGAATTCTCCACGAAAACTCTAGCAAGAGATTTTTGGCGCA
1 TAGCACGCCCCTATGCTGTCATAAAGAATTCTCCACGAAAACTCTAGAAAAAGATTTTTGACGCA
60376 ACATCTCTTTT
66 ACATCTCTTTT
* * *
60387 TGGCACGCCCCTATGCTGTCATAATGAATTCTCCGCGAAAACTCTAGAAAAAGATTTTTGACGCA
1 TAGCACGCCCCTATGCTGTCATAAAGAATTCTCCACGAAAACTCTAGAAAAAGATTTTTGACGCA
60452 ACATCTCTTTT
66 ACATCTCTTTT
60463 TAGCACGCCC
1 TAGCACGCCC
60473 AGTGGGACAC
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 79 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.28
Consensus pattern (76 bp):
TAGCACGCCCCTATGCTGTCATAAAGAATTCTCCACGAAAACTCTAGAAAAAGATTTTTGACGCA
ACATCTCTTTT
Found at i:63326 original size:19 final size:18
Alignment explanation
Indices: 63302--63337 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
63292 TGAAGACTTA
63302 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
63321 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
63338 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:71835 original size:34 final size:34
Alignment explanation
Indices: 71797--71864 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
71787 GCAATATAAA
71797 GAGACTATGTAAGACAACTAAAAGGGAAAATATT
1 GAGACTATGTAAGACAACTAAAAGGGAAAATATT
* *
71831 GAGACTATGTTAGACAATTAAAAGGGAAAATATT
1 GAGACTATGTAAGACAACTAAAAGGGAAAATATT
71865 TTTGGGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.24
Consensus pattern (34 bp):
GAGACTATGTAAGACAACTAAAAGGGAAAATATT
Found at i:72547 original size:30 final size:30
Alignment explanation
Indices: 72505--72859 Score: 489
Period size: 30 Copynumber: 11.8 Consensus size: 30
72495 TTAACTTATG
* *
72505 AAGCAACGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * *
72535 AAGCGATGATCCTCAATCAGGATCAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
72565 AAGCAATGACCCTCAACCAGGATTAAAATT
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
72595 AAGCAATGATCCTCAACCAGGATT-TAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
72624 AAGCAATGATCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
72654 AGGCAATGATCCTCAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
72684 AAGCAATGATCCTCAAACAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
** *
72714 AAGCAATGATCCTCAAATAGGATTAACTCATA
1 AAGCAATGATCCTCAACCAGGATTAA--AATA
72746 AAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
72776 AAGCAATGATTCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
72806 CAA-CAACGATCCTCAACCAGGATTAAAATG
1 -AAGCAATGATCCTCAACCAGGATTAAAATA
*
72836 AAGTAATGATCCTCAACCAGGATT
1 AAGCAATGATCCTCAACCAGGATT
72860 GTAAATGAAA
Statistics
Matches: 288, Mismatches: 32, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
29 28 0.10
30 232 0.81
31 2 0.01
32 26 0.09
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.21
Consensus pattern (30 bp):
AAGCAATGATCCTCAACCAGGATTAAAATA
Found at i:72799 original size:122 final size:121
Alignment explanation
Indices: 72442--72859 Score: 509
Period size: 122 Copynumber: 3.4 Consensus size: 121
72432 AACTAAAGTG
* * * * * * *
72442 ATGACCCTAAACCAGGATTAAAATGAAACAATCATCCTCAATCAGGACTAAAATTAACTTATGAA
1 ATGATCCTCAACCAGGATTAAAATGAAGCAATGATCCTCAAACAGG------ATTAACTAATAAA
* * * * *
72507 GCAACGATCCTAAACCAGGATTAAAATAAAGCGATGATCCTCAATCAGGATCAAAATAAAGCA
60 GCAATGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAAT-AAGCA
* * *
72570 ATGACCCTCAACCAGGATTAAAATTAAGCAATGATCCTCAACCAGGATT---TAATAAAGCAATG
1 ATGATCCTCAACCAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTAACTAATAAAGCAATG
* *
72632 ATCCTCAAACAGGATTAAAATAAGGCAATGATCCTCAACCAGGATTAAAATGAAGCA
66 ATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAAT-AAGCA
* * *
72689 ATGATCCTCAAACAGGATTAAAATGAAGCAATGATCCTCAAATAGGATTAACTCATAAAGCAATG
1 ATGATCCTCAACCAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTAACTAATAAAGCAATG
* *
72754 ATCCTCAACCAGGATTAAAATAAAGCAATGATTCTCAACCAGGATTAAAATACAACA
66 ATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATA-AGCA
* * *
72811 ACGATCCTCAACCAGGATTAAAATGAAGTAATGATCCTCAACCAGGATT
1 ATGATCCTCAACCAGGATTAAAATGAAGCAATGATCCTCAAACAGGATT
72860 GTAAATGAAA
Statistics
Matches: 256, Mismatches: 30, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
119 104 0.41
121 1 0.00
122 110 0.43
128 41 0.16
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.21
Consensus pattern (121 bp):
ATGATCCTCAACCAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTAACTAATAAAGCAATG
ATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAGCA
Found at i:73250 original size:168 final size:169
Alignment explanation
Indices: 72997--73397 Score: 590
Period size: 168 Copynumber: 2.4 Consensus size: 169
72987 AACAAGGATG
* * **
72997 TTAAACATGAATTTTTGATGAAAAACTTGATGAAATCAAATGGTACCCGGAGGTTTTATTAATTG
1 TTAAACATGAACTTTTGATGAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTG
73062 CCCGGACGACTTATTAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCAGGAGGACTTACCAAT
66 CCCGGACGACTTATTAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCAGGAGGACTTACCAAT
* * *
73127 GCGAACTTTGAA-ATGAGACCTTAAACAAGGATTTTAAAC
131 GCAAACTCTGAATA-GAGACCTTAAACAAGGATTATAAAC
* *
73166 TTAAACATGAA-TTTTGATGAAAAACTTAATGAAATGAAATGGTACCCGGAGGTTTTACCGATTG
1 TTAAACATGAACTTTTGATGAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTG
* * *
73230 CCCGGAGGACTTATTAGAATTACTACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAAT
66 CCCGGACGACTTATTAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCAGGAGGACTTACCAAT
* * *
73295 GTAAACTCTGAATAGAGACCTTGACCAAGGATTATAAAC
131 GCAAACTCTGAATAGAGACCTTAAACAAGGATTATAAAC
* * * * * *
73334 TTAACCATTAACTTTTAATGACAAACTTGATGAAATGAAATGATACCCGGAGGTTTTATCAATT
1 TTAAACATGAACTTTTGATGAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATT
73398 CAAACTCTGA
Statistics
Matches: 208, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
168 150 0.72
169 58 0.28
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (169 bp):
TTAAACATGAACTTTTGATGAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTG
CCCGGACGACTTATTAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCAGGAGGACTTACCAAT
GCAAACTCTGAATAGAGACCTTAAACAAGGATTATAAAC
Found at i:73505 original size:103 final size:102
Alignment explanation
Indices: 73277--73534 Score: 329
Period size: 103 Copynumber: 2.5 Consensus size: 102
73267 TGAATTTGTG
** * * * * *
73277 CCCGGAGGACTTACCAATGTAAACTCTGAATAGAGACCTTGACCAAGGATTATAAACTTAACCAT
1 CCCGGAGGTTTTATCAATGCAAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACAT
* * * *
73342 TAACTTTTAATGACAAACTTGATGAAATGAAATGATA
66 GAACTTTTAATAAAAAACTTGATAAAATGAAATGATA
*
73379 CCCGGAGGTTTTATCAATTCAAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACAT
1 CCCGGAGGTTTTATCAATGCAAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACAT
* * *
73444 GGA-TTTTCGATAAAAAAACTTGATAAAATGAAATGGTA
66 GAACTTTT-AAT-AAAAAACTTGATAAAATGAAATGATA
* * *
73482 CCCGGAGGTTTTATTAATGCAAACTCTGAACAGAGACCTTGAGCAAGGATTTT
1 CCCGGAGGTTTTATCAATGCAAACTCTGAATAGAGACCTTGAACAAGGATTTT
73535 TAACAAGGAA
Statistics
Matches: 135, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
101 4 0.03
102 60 0.44
103 71 0.53
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.28
Consensus pattern (102 bp):
CCCGGAGGTTTTATCAATGCAAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACAT
GAACTTTTAATAAAAAACTTGATAAAATGAAATGATA
Found at i:73717 original size:69 final size:69
Alignment explanation
Indices: 73634--73801 Score: 311
Period size: 69 Copynumber: 2.4 Consensus size: 69
73624 CTTAACTCAC
*
73634 ATGGAAATGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGAC
1 ATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGAC
73699 -TCGT
66 AT-GT
73703 ATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGAC
1 ATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGAC
73768 ATGT
66 ATGT
73772 ATGGAAACGAGTTTGGCTTGTGGAAAAGCC
1 ATGGAAACGAGTTTGGCTTGTGGAAAAGCC
73802 AGAGTATTCG
Statistics
Matches: 97, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
69 96 0.99
70 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (69 bp):
ATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGAC
ATGT
Found at i:75064 original size:21 final size:20
Alignment explanation
Indices: 75040--75078 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
75030 CACCCTAGAG
*
75040 CTCTATTCTTTCCTTTTTCTT
1 CTCT-TTCTTTCATTTTTCTT
*
75061 CTCTTTTTTTCATTTTTC
1 CTCTTTCTTTCATTTTTC
75079 ATTTTTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (20 bp):
CTCTTTCTTTCATTTTTCTT
Found at i:75110 original size:9 final size:8
Alignment explanation
Indices: 75065--75109 Score: 67
Period size: 7 Copynumber: 5.8 Consensus size: 8
75055 TTTCTTCTCT
75065 TTTTTTCA
1 TTTTTTCA
75073 -TTTTTCA
1 TTTTTTCA
75080 -TTTTTCA
1 TTTTTTCA
75087 TTTTTTCA
1 TTTTTTCA
75095 TTTTTTTCA
1 -TTTTTTCA
75104 TTTTTT
1 TTTTTT
75110 TTGCACTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 14 0.40
8 13 0.37
9 8 0.23
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCA
Found at i:81525 original size:21 final size:22
Alignment explanation
Indices: 81492--81532 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
81482 GCATAATTTC
*
81492 TAAAATCAAGGATTAAATTGAA
1 TAAAATCAAGGATCAAATTGAA
*
81514 TAAAAT-AGGGATCAAATTG
1 TAAAATCAAGGATCAAATTG
81533 CATTTAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (22 bp):
TAAAATCAAGGATCAAATTGAA
Found at i:81655 original size:41 final size:41
Alignment explanation
Indices: 81597--81702 Score: 119
Period size: 41 Copynumber: 2.6 Consensus size: 41
81587 TAAAATCCTA
*
81597 AATCAGGG-GCGACATTGAATCAATTAACAAG-TATTTA-CCTC
1 AATCAGGGAGC-AAATTGAATCAATTAA-AAGATA-TTAGCCTC
* * * *
81638 AATCATGGAGTAAATTGAACCAATTAAATGATATTAGCCTC
1 AATCAGGGAGCAAATTGAATCAATTAAAAGATATTAGCCTC
81679 AATCAGGGAGCAAATTGAATCAAT
1 AATCAGGGAGCAAATTGAATCAAT
81703 CAGCATATAA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
40 5 0.09
41 48 0.89
42 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (41 bp):
AATCAGGGAGCAAATTGAATCAATTAAAAGATATTAGCCTC
Done.