Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012743.1 Corchorus olitorius cultivar O-4 contig12776, 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: 104300
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3878 original size:35 final size:34
Alignment explanation
Indices: 3839--3921 Score: 139
Period size: 35 Copynumber: 2.4 Consensus size: 34
3829 AAATAAGGAA
*
3839 ATGGGTTCTGAAAATAAAGAGAAAGGATGTTACCT
1 ATGGGTTCT-AAAATAAAGAGAAAGGATATTACCT
3874 ATGGGTTCTAAAAATAAAGAGAAAGGATATTACCT
1 ATGGGTTCT-AAAATAAAGAGAAAGGATATTACCT
3909 ATGGGTTCTAAAA
1 ATGGGTTCTAAAA
3922 GAAATAAATG
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 4 0.09
35 42 0.91
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (34 bp):
ATGGGTTCTAAAATAAAGAGAAAGGATATTACCT
Found at i:9437 original size:16 final size:16
Alignment explanation
Indices: 9416--9471 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
9406 ATTAAGAAGA
9416 AGATAAATAGTGTAGG
1 AGATAAATAGTGTAGG
* * *
9432 AGATAAAT-TTGGAAGA
1 AGATAAATAGT-GTAGG
*
9448 AGATGAATAGTGTAGG
1 AGATAAATAGTGTAGG
9464 AGATAAAT
1 AGATAAAT
9472 TTATGAGATG
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
15 1 0.03
16 28 0.93
17 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.29, T:0.25
Consensus pattern (16 bp):
AGATAAATAGTGTAGG
Found at i:9448 original size:32 final size:32
Alignment explanation
Indices: 9411--9473 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
9401 TGGAGATTAA
9411 GAAGAAGATAAATAGTGTAGGAGATAAATTTG
1 GAAGAAGATAAATAGTGTAGGAGATAAATTTG
*
9443 GAAGAAGATGAATAGTGTAGGAGATAAATTT
1 GAAGAAGATAAATAGTGTAGGAGATAAATTT
9474 ATGAGATGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.46, C:0.00, G:0.29, T:0.25
Consensus pattern (32 bp):
GAAGAAGATAAATAGTGTAGGAGATAAATTTG
Found at i:11945 original size:19 final size:19
Alignment explanation
Indices: 11921--11966 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
11911 ATCCTAATAC
11921 AAATTAGTAATATAATATT
1 AAATTAGTAATATAATATT
11940 AAATTAGTAATATAATATT
1 AAATTAGTAATATAATATT
11959 AATATTAG
1 AA-ATTAG
11967 CAGATTGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (19 bp):
AAATTAGTAATATAATATT
Found at i:13580 original size:25 final size:25
Alignment explanation
Indices: 13546--13679 Score: 241
Period size: 25 Copynumber: 5.4 Consensus size: 25
13536 TGATAAAGAA
13546 GAAATTATGTGGAGACAACGGTCTC
1 GAAATTATGTGGAGACAACGGTCTC
13571 GAAATTATGTGGAGACAACGGTCTC
1 GAAATTATGTGGAGACAACGGTCTC
*
13596 GAAATTATGTGGAGACAACAGTCTC
1 GAAATTATGTGGAGACAACGGTCTC
*
13621 GAAATTATGTGGAGACAACAGTCTC
1 GAAATTATGTGGAGACAACGGTCTC
13646 GAAATTATGTGGAGACAACGGTCTC
1 GAAATTATGTGGAGACAACGGTCTC
*
13671 AAAATTATG
1 GAAATTATG
13680 CTTTATAGGA
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 106 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (25 bp):
GAAATTATGTGGAGACAACGGTCTC
Found at i:22470 original size:2 final size:2
Alignment explanation
Indices: 22463--22489 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22453 TTTTAATAAC
22463 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
22490 TATGATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23462 original size:98 final size:98
Alignment explanation
Indices: 23347--23547 Score: 393
Period size: 98 Copynumber: 2.1 Consensus size: 98
23337 ATGAATTTAG
23347 TTCCTTCATACCGAACAACAAAAAAGACATGTAACTTTCTTTTCATTCCCTTCCTATTTCATTCC
1 TTCCTTCATACCGAACAACAAAAAAGACATGTAACTTTCTTTTCATTCCCTTCCTATTTCATTCC
23412 CTTCGCTAGTTCTTTTCTATGCAATTTCTTTCC
66 CTTCGCTAGTTCTTTTCTATGCAATTTCTTTCC
*
23445 TTCCTTCATACCGAACAACAAAAAAGACATGTAACTTTCTTTTCTTTCCCTTCCTATTTCATTCC
1 TTCCTTCATACCGAACAACAAAAAAGACATGTAACTTTCTTTTCATTCCCTTCCTATTTCATTCC
23510 CTTCGCTAGTTCTTTTCTATGCAATTTCTTTCC
66 CTTCGCTAGTTCTTTTCTATGCAATTTCTTTCC
23543 TTCCT
1 TTCCT
23548 GCCGAACATA
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 102 1.00
ACGTcount: A:0.22, C:0.29, G:0.06, T:0.43
Consensus pattern (98 bp):
TTCCTTCATACCGAACAACAAAAAAGACATGTAACTTTCTTTTCATTCCCTTCCTATTTCATTCC
CTTCGCTAGTTCTTTTCTATGCAATTTCTTTCC
Found at i:30412 original size:40 final size:40
Alignment explanation
Indices: 30368--30849 Score: 347
Period size: 40 Copynumber: 12.2 Consensus size: 40
30358 AAGCCACTGG
*
30368 TCCTGAATAGGATTTTTGAAATTGA-CTGATAAAGCAAGGA
1 TCCTGAATAGGA-TTTTGAAATTAATCTGATAAAGCAAGGA
* * * *
30408 TCCTGAATATGATTTTGAAGTTAATTTGATAAAGCAATGA
1 TCCTGAATAGGATTTTGAAATTAATCTGATAAAGCAAGGA
** *
30448 TCCTGAGCAGGATTTTGAAATTAATTTGATAAA--AAGATGA
1 TCCTGAATAGGATTTTGAAATTAATCTGATAAAGCAAG--GA
* *** * * *
30488 TCATGTGCAGGATTCTGAAATTAATTTGATAAAGCAATGA
1 TCCTGAATAGGATTTTGAAATTAATCTGATAAAGCAAGGA
* * * * *
30528 TCCTGAGTCGGA--TTGAAATTAATTTGATAAAACAATGA
1 TCCTGAATAGGATTTTGAAATTAATCTGATAAAGCAAGGA
* * * *
30566 TCCTGAGTAGGATTTTGAAGTTAATTTGATAAAGCAATGA
1 TCCTGAATAGGATTTTGAAATTAATCTGATAAAGCAAGGA
** *
30606 TCCTGAGCAGGATTTTGAAATTAATTTGATAAA--AAGATGA
1 TCCTGAATAGGATTTTGAAATTAATCTGATAAAGCAAG--GA
*** * * *
30646 TCCTGTGCAGGATTCTGAAATTAATTTGATAAAGCAATGA
1 TCCTGAATAGGATTTTGAAATTAATCTGATAAAGCAAGGA
** * * *
30686 TCCTGAGCAGGA--TTGAAATTAATTTGATAAAACAATGA
1 TCCTGAATAGGATTTTGAAATTAATCTGATAAAGCAAGGA
* * * * *
30724 TCCTGAGTAGGATTTTGAAGTTAATTTAATAAAGCAATGA
1 TCCTGAATAGGATTTTGAAATTAATCTGATAAAGCAAGGA
** *
30764 TCCTGAGCAGGATTTTGAAATTAATTTGATAAA--AAGATGA
1 TCCTGAATAGGATTTTGAAATTAATCTGATAAAGCAAG--GA
**** * * *
30804 TCCTCTGCAGGATTCTGAAATTAATTTGATAAAGCAATGA
1 TCCTGAATAGGATTTTGAAATTAATCTGATAAAGCAAGGA
30844 TCCTGA
1 TCCTGA
30850 GTAGCATTGA
Statistics
Matches: 379, Mismatches: 46, Indels: 34
0.83 0.10 0.07
Matches are distributed among these distances:
38 76 0.20
39 10 0.03
40 287 0.76
42 6 0.02
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.33
Consensus pattern (40 bp):
TCCTGAATAGGATTTTGAAATTAATCTGATAAAGCAAGGA
Found at i:30579 original size:118 final size:118
Alignment explanation
Indices: 30376--30850 Score: 586
Period size: 118 Copynumber: 4.0 Consensus size: 118
30366 GGTCCTGAAT
* * * ** * *
30376 AGGATTTTTGAAATTGA-CTGATAAAGCAAGGATCCTGAATATGATTTTGAAGTTAATTTGATAA
1 AGGA-TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGA-TTTGAAATTAATTTGATAA
* * *
30440 AGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAAAGATGATCATGTGC
64 AACAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAAA-ATGATCCTGAGC
*
30496 AGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGTC-GGA-TTGAAATTAATTTGATAAA
1 AGGATTTTGAAATTAATTTGATAAAGCAATGATCCTGAG-CAGGATTTGAAATTAATTTGATAAA
* * *
30559 ACAATGATCCTGAGTAGGATTTTGAAGTTAATTTGATAAAGCAATGATCCTGAGC
65 ACAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAA-AAATGATCCTGAGC
* *
30614 AGGATTTTGAAATTAATTTGATAAA-AAGATGATCCTGTGCAGGATTCTGAAATTAATTTGATAA
1 AGGATTTTGAAATTAATTTGATAAAGCA-ATGATCCTGAGCAGGATT-TGAAATTAATTTGATAA
* *
30678 AGCAATGATCCTGAGCAGGA--TTGAAATTAATTTGATAAAACAATGATCCTGAGT
64 AACAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAA-AATGATCCTGAGC
* *
30732 AGGATTTTGAAGTTAATTTAATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAA
1 AGGATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGA-TTTGAAATTAATTTGATAAA
** * *
30797 A-AGATGATCCTCTGCAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAG
65 ACA-ATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAA-AAATGATCCTGAG
30851 TAGCATTGAA
Statistics
Matches: 310, Mismatches: 31, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
117 3 0.01
118 202 0.65
119 15 0.05
120 90 0.29
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (118 bp):
AGGATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTGAAATTAATTTGATAAAA
CAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAAAATGATCCTGAGC
Found at i:30682 original size:158 final size:158
Alignment explanation
Indices: 30394--30863 Score: 843
Period size: 158 Copynumber: 3.0 Consensus size: 158
30384 TGAAATTGAC
* * * *
30394 TGATAAAGCAAGGATCCTGAATATGATTTTGAAGTTAATTTGATAAAGCAATGATCCTGAGCAGG
1 TGATAAAACAATGATCCTGAGTAGGATTTTGAAGTTAATTTGATAAAGCAATGATCCTGAGCAGG
*
30459 ATTTTGAAATTAATTTGATAAAAAGATGATCATGTGCAGGATTCTGAAATTAATTTGATAAAGCA
66 ATTTTGAAATTAATTTGATAAAAAGATGATCCTGTGCAGGATTCTGAAATTAATTTGATAAAGCA
30524 ATGATCCTGAGTCGGATTGAAATTAATT
131 ATGATCCTGAGTCGGATTGAAATTAATT
30552 TGATAAAACAATGATCCTGAGTAGGATTTTGAAGTTAATTTGATAAAGCAATGATCCTGAGCAGG
1 TGATAAAACAATGATCCTGAGTAGGATTTTGAAGTTAATTTGATAAAGCAATGATCCTGAGCAGG
30617 ATTTTGAAATTAATTTGATAAAAAGATGATCCTGTGCAGGATTCTGAAATTAATTTGATAAAGCA
66 ATTTTGAAATTAATTTGATAAAAAGATGATCCTGTGCAGGATTCTGAAATTAATTTGATAAAGCA
30682 ATGATCCTGAG-CAGGATTGAAATTAATT
131 ATGATCCTGAGTC-GGATTGAAATTAATT
*
30710 TGATAAAACAATGATCCTGAGTAGGATTTTGAAGTTAATTTAATAAAGCAATGATCCTGAGCAGG
1 TGATAAAACAATGATCCTGAGTAGGATTTTGAAGTTAATTTGATAAAGCAATGATCCTGAGCAGG
*
30775 ATTTTGAAATTAATTTGATAAAAAGATGATCCTCTGCAGGATTCTGAAATTAATTTGATAAAGCA
66 ATTTTGAAATTAATTTGATAAAAAGATGATCCTGTGCAGGATTCTGAAATTAATTTGATAAAGCA
* *
30840 ATGATCCTGAGTAGCATTGAAATT
131 ATGATCCTGAGTCGGATTGAAATT
30864 GACTGGTAAA
Statistics
Matches: 301, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
157 1 0.00
158 300 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.33
Consensus pattern (158 bp):
TGATAAAACAATGATCCTGAGTAGGATTTTGAAGTTAATTTGATAAAGCAATGATCCTGAGCAGG
ATTTTGAAATTAATTTGATAAAAAGATGATCCTGTGCAGGATTCTGAAATTAATTTGATAAAGCA
ATGATCCTGAGTCGGATTGAAATTAATT
Found at i:31490 original size:145 final size:144
Alignment explanation
Indices: 31137--31989 Score: 1287
Period size: 145 Copynumber: 6.0 Consensus size: 144
31127 CGAAGGTTTC
* * * * *
31137 TGAAATGGTGCCCGGAGGATTTATCAGAATTAATAACC-AGAGATTTCTGAAATTGTGCCTGGAG
1 TGAAATGATACCCGGAGGATTTATCAGAATTAATACCCGA-AGGTTTCTGAAATTGTGCCCGGAG
*
31201 GTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAAC-TAAGCACAGCTTTGAT
65 GTCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACAC-GCTTTGAT
31265 TAAAAACTTGATGAAA
129 TAAAAACTTGATGAAA
31281 TGAAATGATACCC---GGATTTATCAGAATTAATACCCGAAGGTTTCTGAAATTGTGCCCGGAGG
1 TGAAATGATACCCGGAGGATTTATCAGAATTAATACCCGAAGGTTTCTGAAATTGTGCCCGGAGG
* *
31343 TCTTTCAAATGCAAACTCAACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACACGTCTTTGATT
66 TCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACACG-CTTTGATT
* *
31408 AAAAATTTAATGAAA
130 AAAAACTTGATGAAA
* * * * *
31423 TGAAACGATACCCGGAGGACTTATCAGAATTAATACCCGGAGGCTTCTGAAATGGTGCCCGGAGG
1 TGAAATGATACCCGGAGGATTTATCAGAATTAATACCCGAAGGTTTCTGAAATTGTGCCCGGAGG
* *
31488 TCTTACAAATGCAAACTCGACCATGAGCAAGGTTTTGATTTTGAAACTTAAACACAGGTTTGATT
66 TCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACAC-GCTTTGATT
31553 AAAAACTTGATGAAA
130 AAAAACTTGATGAAA
* *
31568 TGAAATGATGCCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGG
1 TGAAATGATACCCGGAGGATTTATCAGAATTAATACCCGAAGGTTTCTGAAATTGTGCCCGGAGG
31633 TCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACACTGCTTTGATT
66 TCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACAC-GCTTTGATT
31698 AAAAACTTGATGAAA
130 AAAAACTTGATGAAA
* * * * *
31713 TGAAATGTTACCCGAAGGATTTATTAGAATTAATACCCGAAGGTTTCTAAAATTGTGCCCGAAGG
1 TGAAATGATACCCGGAGGATTTATCAGAATTAATACCCGAAGGTTTCTGAAATTGTGCCCGGAGG
*
31778 TCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACACAACTTTGATT
66 TCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACAC-GCTTTGATT
*
31843 AAAAACTTGATGGAA
130 AAAAACTTGATGAAA
*
31858 TGAAATGATACCC---GGATTTATCAGAATTAATACACGAAGGTTTCTGAAATTGTGCCCGGAGG
1 TGAAATGATACCCGGAGGATTTATCAGAATTAATACCCGAAGGTTTCTGAAATTGTGCCCGGAGG
* * * *
31920 TCTTACAAATGCAAACTCAACCTTGAGCAAGG-TTT--TTTTGAAATTTAAACGCAACTTTGATT
66 TCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACAC-GCTTTGATT
31982 AAAAACTT
130 AAAAACTT
31990 ACCAAAATGG
Statistics
Matches: 655, Mismatches: 47, Indels: 19
0.91 0.07 0.03
Matches are distributed among these distances:
139 33 0.05
141 93 0.14
142 116 0.18
144 11 0.02
145 401 0.61
146 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (144 bp):
TGAAATGATACCCGGAGGATTTATCAGAATTAATACCCGAAGGTTTCTGAAATTGTGCCCGGAGG
TCTTACAAATGCAAACTCGACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACACGCTTTGATTA
AAAACTTGATGAAA
Found at i:32920 original size:4 final size:4
Alignment explanation
Indices: 32911--32972 Score: 96
Period size: 4 Copynumber: 16.5 Consensus size: 4
32901 GCTTTATTCC
32911 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC- TTC-
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
32957 TTCT TT-T TT-T TTCT TT
1 TTCT TTCT TTCT TTCT TT
32973 TTTTTTTTGC
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
3 12 0.21
4 44 0.79
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:32977 original size:12 final size:12
Alignment explanation
Indices: 32914--32980 Score: 62
Period size: 12 Copynumber: 5.2 Consensus size: 12
32904 TTATTCCTTC
* *
32914 TTTCTTTCTTTC
1 TTTCTTTTTTTT
* *
32926 TTTCTTTCTTTC
1 TTTCTTTTTTTT
32938 TTTCTTTCTTTCTT
1 TTTCTTT-TTT-TT
32952 TCTTCTTCTTTTTT
1 T-TTCTT-TTTTTT
32966 TTTCTTTTTTTT
1 TTTCTTTTTTTT
32978 TTT
1 TTT
32981 GCACTTGAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
12 28 0.57
13 7 0.14
14 5 0.10
15 8 0.16
16 1 0.02
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:33321 original size:19 final size:19
Alignment explanation
Indices: 33278--33321 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
33268 ACTTTTTTCA
33278 ATTTTCAATTTTCACATTT
1 ATTTTCAATTTTCACATTT
* *
33297 ACTTTCAATTTTCACTTTT
1 ATTTTCAATTTTCACATTT
*
33316 TTTTTC
1 ATTTTC
33322 GTTTTCTTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTCAATTTTCACATTT
Found at i:33326 original size:9 final size:8
Alignment explanation
Indices: 33314--33373 Score: 59
Period size: 8 Copynumber: 7.5 Consensus size: 8
33304 ATTTTCACTT
33314 TTTTTTTC
1 TTTTTTTC
*
33322 GTTTTCTTC
1 -TTTTTTTC
*
33331 TTTTTTTG
1 TTTTTTTC
*
33339 TTTTTTTG
1 TTTTTTTC
*
33347 TTTTTGTC
1 TTTTTTTC
*
33355 TTTTTTGC
1 TTTTTTTC
33363 TTTTTTT-
1 TTTTTTTC
33370 TTTT
1 TTTT
33374 AGCATATGTA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
7 4 0.09
8 32 0.74
9 7 0.16
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:33349 original size:24 final size:24
Alignment explanation
Indices: 33314--33373 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
33304 ATTTTCACTT
33314 TTTTTTTCGTTTTCT-TCTTTTTTTG-
1 TTTTTTT-GTTTT-TGTC-TTTTTTGC
33339 TTTTTTTGTTTTTGTCTTTTTTGC
1 TTTTTTTGTTTTTGTCTTTTTTGC
33363 TTTTTTT-TTTT
1 TTTTTTTGTTTT
33374 AGCATATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
23 12 0.36
24 14 0.42
25 7 0.21
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.83
Consensus pattern (24 bp):
TTTTTTTGTTTTTGTCTTTTTTGC
Found at i:37990 original size:43 final size:42
Alignment explanation
Indices: 37925--38013 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 42
37915 TGAAAACTTG
37925 GCAAACATGTTGCCTTGGGGCAGGTTGGTTCACCTATTGTGA
1 GCAAACATGTTGCCTTGGGGCAGGTTGGTTCACCTATTGTGA
37967 GCAAGACATGTTGCCTTGGGGCAGGTTGGTTCACCTATTGTGA
1 GCAA-ACATGTTGCCTTGGGGCAGGTTGGTTCACCTATTGTGA
38010 GCAA
1 GCAA
38014 TGCAATTACT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 4 0.09
43 42 0.91
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.29
Consensus pattern (42 bp):
GCAAACATGTTGCCTTGGGGCAGGTTGGTTCACCTATTGTGA
Found at i:53095 original size:15 final size:16
Alignment explanation
Indices: 53075--53104 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
53065 GTTTTCTAGT
53075 TTAATTGTT-TTCTTC
1 TTAATTGTTATTCTTC
53090 TTAATTGTTATTCTT
1 TTAATTGTTATTCTT
53105 AACCCTCTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.67
Consensus pattern (16 bp):
TTAATTGTTATTCTTC
Found at i:57541 original size:17 final size:18
Alignment explanation
Indices: 57519--57555 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
57509 CATTGAAAAA
57519 AAGGG-TTAAATGCTATC
1 AAGGGTTTAAATGCTATC
57536 AAGGGTTTAAATGCTATC
1 AAGGGTTTAAATGCTATC
57554 AA
1 AA
57556 TTTATCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.30
Consensus pattern (18 bp):
AAGGGTTTAAATGCTATC
Found at i:59636 original size:17 final size:18
Alignment explanation
Indices: 59614--59652 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
59604 AAGAGATGTC
59614 ATCTCAACCCAATTTGT-
1 ATCTCAACCCAATTTGTG
59631 ATCTCAACCCAATTTGTG
1 ATCTCAACCCAATTTGTG
59649 ATCT
1 ATCT
59653 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (18 bp):
ATCTCAACCCAATTTGTG
Found at i:64178 original size:48 final size:47
Alignment explanation
Indices: 64025--64289 Score: 182
Period size: 48 Copynumber: 5.5 Consensus size: 47
64015 CGCGTTCGGC
* * * *
64025 GAGCGTTCTCCGTTTCGCGACCTCGAGCATTCTTAATTTGCGCTCGAG
1 GAGCATTCTCCATTTCGCGA-CTCGGGCATTCTTCATTTGCGCTCGAG
* * * * **
64073 GAGCATTCTCCATTCCGCG-CTCAGCGCGTTCTACGCTT-CGCATTCG-G
1 GAGCATTCTCCATTTCGCGACTC-GGGCATTCTTCATTTGCGC--TCGAG
* *
64120 CAAGCGTTCTCCATTTCGCGAACTCGGGCATTCTTCATTTGCGCTCGAG
1 -GAGCATTCTCCATTTCGCG-ACTCGGGCATTCTTCATTTGCGCTCGAG
** * * * *
64169 GAGCATTCTCCATTTCGCG-CTCAGCGAGTGTTCTACGCTTCGCGTTCG-G
1 GAGCATTCTCCATTTCGCGACTC-G-G-GCATTCTTC-ATTTGCGCTCGAG
* * * *
64218 CAAGCGTTCTCCATTTCGCGACCTCGGGCATTCTTTATTTGCACTCGAG
1 -GAGCATTCTCCATTTCGCGA-CTCGGGCATTCTTCATTTGCGCTCGAG
64267 GAGCATTCTCCATTTCGCG-CTCG
1 GAGCATTCTCCATTTCGCGACTCG
64290 ACAAGCGTTC
Statistics
Matches: 164, Mismatches: 37, Indels: 34
0.70 0.16 0.14
Matches are distributed among these distances:
46 13 0.08
47 11 0.07
48 80 0.49
49 24 0.15
50 32 0.20
51 1 0.01
52 3 0.02
ACGTcount: A:0.14, C:0.32, G:0.23, T:0.31
Consensus pattern (47 bp):
GAGCATTCTCCATTTCGCGACTCGGGCATTCTTCATTTGCGCTCGAG
Found at i:64202 original size:25 final size:25
Alignment explanation
Indices: 64078--64237 Score: 73
Period size: 25 Copynumber: 6.6 Consensus size: 25
64068 TCGAGGAGCA
*
64078 TTCTCCATTCCGCGCTCAGC--GCG
1 TTCTCCATTTCGCGCTCAGCAAGCG
* ** ** *
64101 TTCTACGCTTCGCATTCGGCAAGCG
1 TTCTCCATTTCGCGCTCAGCAAGCG
* *
64126 TTCTCCATTTCGCGAACTC-G--GGCA
1 TTCTCCATTTCGCG--CTCAGCAAGCG
* * *
64150 TTCTTCATTT-GCGCTCGAG-GAGCA
1 TTCTCCATTTCGCGCTC-AGCAAGCG
* *
64174 TTCTCCATTTCGCGCTCAGCGAGTG
1 TTCTCCATTTCGCGCTCAGCAAGCG
* ** * *
64199 TTCTACGCTTCGCGTTCGGCAAGCG
1 TTCTCCATTTCGCGCTCAGCAAGCG
64224 TTCTCCATTTCGCG
1 TTCTCCATTTCGCG
64238 ACCTCGGGCA
Statistics
Matches: 99, Mismatches: 29, Indels: 16
0.69 0.20 0.11
Matches are distributed among these distances:
21 3 0.03
23 17 0.17
24 25 0.25
25 51 0.52
26 1 0.01
27 2 0.02
ACGTcount: A:0.13, C:0.33, G:0.23, T:0.31
Consensus pattern (25 bp):
TTCTCCATTTCGCGCTCAGCAAGCG
Found at i:64319 original size:25 final size:25
Alignment explanation
Indices: 64280--64348 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 25
64270 CATTCTCCAT
* * *
64280 TTCGCGCTCGACAAGCGTTCCACGC
1 TTCGCGTTCGGCAAGAGTTCCACGC
* *
64305 TTTGCGTTCGGCAAGAGTTCTACGC
1 TTCGCGTTCGGCAAGAGTTCCACGC
64330 TTCGCGTTCGGCAAGAGTT
1 TTCGCGTTCGGCAAGAGTT
64349 ATACGTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.16, C:0.29, G:0.28, T:0.28
Consensus pattern (25 bp):
TTCGCGTTCGGCAAGAGTTCCACGC
Found at i:64335 original size:98 final size:97
Alignment explanation
Indices: 64004--64325 Score: 477
Period size: 98 Copynumber: 3.3 Consensus size: 97
63994 CTTGGCGAAA
* * * *
64004 GTTCAACGCTTCGCGTTCGGCGAGCGTTCTCCGTTTCGCGACCTCGAGCATTCTTAATTTGCGCT
1 GTTCTACGCTTCGCGTTCGGCAAGCGTTCTCCATTTCGCGACCTCGGGCATTCTTAATTTGCGCT
*
64069 CGAGGAGCATTCTCCATTCCGCGCTCAGC-GC
66 CGAGGAGCATTCTCCATTTCGCGCTCAGCAGC
* * *
64100 GTTCTACGCTTCGCATTCGGCAAGCGTTCTCCATTTCGCGAACTCGGGCATTCTTCATTTGCGCT
1 GTTCTACGCTTCGCGTTCGGCAAGCGTTCTCCATTTCGCGACCTCGGGCATTCTTAATTTGCGCT
*
64165 CGAGGAGCATTCTCCATTTCGCGCTCAGCGAGT
66 CGAGGAGCATTCTCCATTTCGCGCTCAGC-AGC
* *
64198 GTTCTACGCTTCGCGTTCGGCAAGCGTTCTCCATTTCGCGACCTCGGGCATTCTTTATTTGCACT
1 GTTCTACGCTTCGCGTTCGGCAAGCGTTCTCCATTTCGCGACCTCGGGCATTCTTAATTTGCGCT
64263 CGAGGAGCATTCTCCATTTCGCGCTC-GACAAGC
66 CGAGGAGCATTCTCCATTTCGCGCTCAG-C-AGC
* * *
64296 GTTCCACGCTTTGCGTTCGGCAAGAGTTCT
1 GTTCTACGCTTCGCGTTCGGCAAGCGTTCT
64326 ACGCTTCGCG
Statistics
Matches: 205, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
96 86 0.42
97 1 0.00
98 118 0.58
ACGTcount: A:0.15, C:0.31, G:0.24, T:0.30
Consensus pattern (97 bp):
GTTCTACGCTTCGCGTTCGGCAAGCGTTCTCCATTTCGCGACCTCGGGCATTCTTAATTTGCGCT
CGAGGAGCATTCTCCATTTCGCGCTCAGCAGC
Found at i:64407 original size:21 final size:21
Alignment explanation
Indices: 64367--64521 Score: 197
Period size: 21 Copynumber: 7.4 Consensus size: 21
64357 TTCGTTCGAC
64367 GAGCATTCTCCTCT-CTTGGG
1 GAGCATTCTCCTCTCCTTGGG
64387 GAGCATTCTCCTCTCCTTGGG
1 GAGCATTCTCCTCTCCTTGGG
64408 GAGCATTCTCCTCTCCTTGGG
1 GAGCATTCTCCTCTCCTTGGG
* * * * *
64429 GAGCACTCTTCTATCCGTGGA
1 GAGCATTCTCCTCTCCTTGGG
*
64450 GATCATTCTCCTCTCCTTGGG
1 GAGCATTCTCCTCTCCTTGGG
* * *
64471 GAGCATTCTTCAT-TCTTTGGA
1 GAGCATTC-TCCTCTCCTTGGG
*
64492 GAGCATTCTCCTCTACTTGGG
1 GAGCATTCTCCTCTCCTTGGG
64513 GAGCATTCT
1 GAGCATTCT
64522 TCATTTTTTG
Statistics
Matches: 113, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
20 17 0.15
21 93 0.82
22 3 0.03
ACGTcount: A:0.14, C:0.29, G:0.23, T:0.35
Consensus pattern (21 bp):
GAGCATTCTCCTCTCCTTGGG
Found at i:64457 original size:42 final size:42
Alignment explanation
Indices: 64367--64548 Score: 226
Period size: 42 Copynumber: 4.4 Consensus size: 42
64357 TTCGTTCGAC
* * *
64367 GAGCATTCTCCTCT-CTTGGGGAGCATTCTCCTCTCCTTGGG
1 GAGCATTCTCCTCTCCTTGGGGAGCATTCTTCTATCCTTGGA
* *
64408 GAGCATTCTCCTCTCCTTGGGGAGCACTCTTCTATCCGTGGA
1 GAGCATTCTCCTCTCCTTGGGGAGCATTCTTCTATCCTTGGA
* *
64450 GATCATTCTCCTCTCCTTGGGGAGCATTCTTC-ATTCTTTGGA
1 GAGCATTCTCCTCTCCTTGGGGAGCATTCTTCTA-TCCTTGGA
* **
64492 GAGCATTCTCCTCTACTTGGGGAGCATTCTTC-ATTTTTTGGA
1 GAGCATTCTCCTCTCCTTGGGGAGCATTCTTCTA-TCCTTGGA
*
64534 GAGCATTTTCCTCTC
1 GAGCATTCTCCTCTC
64549 TTCGCCTTTC
Statistics
Matches: 125, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
41 15 0.12
42 110 0.88
ACGTcount: A:0.14, C:0.28, G:0.21, T:0.37
Consensus pattern (42 bp):
GAGCATTCTCCTCTCCTTGGGGAGCATTCTTCTATCCTTGGA
Found at i:64532 original size:21 final size:21
Alignment explanation
Indices: 64466--64540 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
64456 TCTCCTCTCC
* *
64466 TTGGGGAGCATTCTTCATTCT
1 TTGGAGAGCATTCTTCATTAT
* *
64487 TTGGAGAGCATTC-TCCTCTAC
1 TTGGAGAGCATTCTTCAT-TAT
* *
64508 TTGGGGAGCATTCTTCATTTT
1 TTGGAGAGCATTCTTCATTAT
64529 TTGGAGAGCATT
1 TTGGAGAGCATT
64541 TTCCTCTCTT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 3 0.07
21 37 0.86
22 3 0.07
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (21 bp):
TTGGAGAGCATTCTTCATTAT
Found at i:65066 original size:123 final size:122
Alignment explanation
Indices: 64788--65551 Score: 813
Period size: 123 Copynumber: 6.3 Consensus size: 122
64778 GCGCGCCTAA
* * * *
64788 TTGGAGTTGGGCCCTTTGAGGGCTTTATCATCATTTTCCCATGC-CTGGTCAGGGATGATTCTGT
1 TTGGCGTTGGGCCCCTTGAGGGC--T-TCATCA-TTTCCCATACTC-GGTCAGGGATGGTTCT-T
* * * * * * * *
64852 GTCGGTCGCCTGCCAGTCGAGGGCCATACTTGGTCGAGGTTGG-CTATGTC-GAGCGCTCGCCTA
60 G-CGATCGCCTGCCAGTCGGGGGCCATACTAGGTCGAGCTCGGCCT-TGCCTGATCGCTCGCCTG
** * * * * * * *
64915 TCAGCGTT-GGACTCTTTAGGGGTTTCATCATTTCCCATACTCGGCCAAGGATGGTTCATGTCGA
1 TTGGCGTTGGGCCCCTTGA-GGGCTTCATCATTTCCCATACTCGGTCAGGGATGGTTCTTG-CGA
* * * * *
64979 TCGCCAGCCAGTCGAGGGCCATAATAGGTCGAGCTCGGCCTTGTCTGATCGCTCGCCCG
64 TCGCCTGCCAGTCGGGGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCTCGCCTG
* *
65038 TTGGCGTTGGGCCCCTTGAAGGCTTCATCATTTCCCATACTCGGTCAGGGATGGTCCTTGCTGAT
1 TTGGCGTTGGGCCCCTTGAGGGCTTCATCATTTCCCATACTCGGTCAGGGATGGTTCTTGC-GAT
* * * * * * *
65103 TGCCTGCCGGTCGAGGGCCATACTAGGTCGAGCTCGG-TTGTGCCTGACCGCTCGGCTA
65 CGCCTGCCAGTCGGGGGCCATACTAGGTCGAGCTCGGCCT-TGCCTGATCGCTCGCCTG
* * * * * *
65161 TTGGTGTTGGGCTCCTTGAGGGCTTCATCATTTCCCGTACTCGGTTAGGAATGGTCCTTGCTGAT
1 TTGGCGTTGGGCCCCTTGAGGGCTTCATCATTTCCCATACTCGGTCAGGGATGGTTCTTGC-GAT
65226 CGCCTGCCAGTCGGGGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCTCG-CTAG
65 CGCCTGCCAGTCGGGGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCTCGCCT-G
* *
65284 TTGGCGTTGGGCCCCTTGAGGGCTTCATTATTTCCCATGCTCGGTCAGGGATGGTT-TT----T-
1 TTGGCGTTGGGCCCCTTGAGGGCTTCATCATTTCCCATACTCGGTCAGGGATGGTTCTTGCGATC
65343 G-C--CCA-TCGGGGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCTCGCCTG
66 GCCTGCCAGTCGGGGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCTCGCCTG
* * ** * *
65396 TTAGCGTAGGGCCTTTTGAGGGCTTCATCATTTACCATACTCGGTCAGGGATGGTTGTTGCCGAT
1 TTGGCGTTGGGCCCCTTGAGGGCTTCATCATTTCCCATACTCGGTCAGGGATGGTTCTTG-CGAT
* *
65461 CGCCTGCCAGTCGGGGGCCATAATAGGTCGAGGTCGGCCTTGCCTGATCGCTCGCCTG
65 CGCCTGCCAGTCGGGGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCTCGCCTG
*
65519 TTGGCGTTGGGCCCGTTGAGGGCTTCATCATTT
1 TTGGCGTTGGGCCCCTTGAGGGCTTCATCATTT
65552 TTTCCATTCT
Statistics
Matches: 540, Mismatches: 76, Indels: 46
0.82 0.11 0.07
Matches are distributed among these distances:
112 94 0.17
113 7 0.01
115 1 0.00
116 1 0.00
117 1 0.00
118 1 0.00
119 1 0.00
120 1 0.00
122 51 0.09
123 352 0.65
124 15 0.03
125 1 0.00
126 6 0.01
127 8 0.01
ACGTcount: A:0.13, C:0.27, G:0.31, T:0.29
Consensus pattern (122 bp):
TTGGCGTTGGGCCCCTTGAGGGCTTCATCATTTCCCATACTCGGTCAGGGATGGTTCTTGCGATC
GCCTGCCAGTCGGGGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCTCGCCTG
Found at i:65500 original size:235 final size:240
Alignment explanation
Indices: 64868--65551 Score: 821
Period size: 235 Copynumber: 2.8 Consensus size: 240
64858 CGCCTGCCAG
* * * * * * * * *
64868 TCGAGGGCCATACTTGGTCGAGGTTGGCTATGTC-GAGCGCTCGCCTATCAGCGTTGGACT-CTT
1 TCGAGGGCCATACTAGGTCGAGCTCGGCTGTGCCTGACCGCTCGCCTATTAGCGTAGGGCTCCTT
* * * * * * * *
64931 TAGGGGTTTCATCATTTCCCATACTCGGCCAAGGATGGTTCATGTCGATCGCCAGCCAGTCGAGG
66 GA-GGGCTTCATCATTTCCCATACTCGGTCAGGGATGGTTCTTGCCGATCGCCTGCCAGTCGGGG
* * *
64996 GCCATAATAGGTCGAGCTCGGCCTTGTCTGATCGCTCGCCCGTTGGCGTTGGGCCCCTTGAAGGC
130 GCCATAATAGGTCGAGCTCGGCCTTGCCTGATCGCTCG-CTGTTGGCGTTGGGCCCCTTGAGGGC
*
65061 TTCATCATTTCCCATACTCGGTCAGGGATGGTCCTTGCTGATTGCCTGCCGG
194 TTCATCATTTCCCATACTCGGTCAGGGATGG--CTT-CT-ATTGCC-GCCGA
* * * * *
65113 TCGAGGGCCATACTAGGTCGAGCTCGGTTGTGCCTGACCGCTCGGCTATTGGTGTTGGGCTCCTT
1 TCGAGGGCCATACTAGGTCGAGCTCGGCTGTGCCTGACCGCTCGCCTATTAGCGTAGGGCTCCTT
* * * * *
65178 GAGGGCTTCATCATTTCCCGTACTCGGTTAGGAATGGTCCTTGCTGATCGCCTGCCAGTCGGGGG
66 GAGGGCTTCATCATTTCCCATACTCGGTCAGGGATGGTTCTTGCCGATCGCCTGCCAGTCGGGGG
*
65243 CCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCTCGCTAGTTGGCGTTGGGCCCCTTGAGGGCT
131 CCATAATAGGTCGAGCTCGGCCTTGCCTGATCGCTCGCT-GTTGGCGTTGGGCCCCTTGAGGGCT
* *
65308 TCATTATTTCCCATGCTCGGTCAGGGATGG-TT-T-TTG-C-CC-A
195 TCATCATTTCCCATACTCGGTCAGGGATGGCTTCTATTGCCGCCGA
* * * *
65348 TCGGGGGCCATACTAGGTCGAGCTCGGCCT-TGCCTGATCGCTCGCCTGTTAGCGTAGGGC-CTT
1 TCGAGGGCCATACTAGGTCGAGCTCGG-CTGTGCCTGACCGCTCGCCTATTAGCGTAGGGCTC-C
* *
65411 TTGAGGGCTTCATCATTTACCATACTCGGTCAGGGATGGTTGTTGCCGATCGCCTGCCAGTCGGG
64 TTGAGGGCTTCATCATTTCCCATACTCGGTCAGGGATGGTTCTTGCCGATCGCCTGCCAGTCGGG
* *
65476 GGCCATAATAGGTCGAGGTCGGCCTTGCCTGATCGCTCGCCTGTTGGCGTTGGGCCCGTTGAGGG
129 GGCCATAATAGGTCGAGCTCGGCCTTGCCTGATCGCTCG-CTGTTGGCGTTGGGCCCCTTGAGGG
65541 CTTCATCATTT
193 CTTCATCATTT
65552 TTTCCATTCT
Statistics
Matches: 381, Mismatches: 52, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
234 1 0.00
235 177 0.46
236 5 0.01
238 1 0.00
239 3 0.01
241 1 0.00
243 2 0.01
245 29 0.08
246 158 0.41
247 4 0.01
ACGTcount: A:0.13, C:0.27, G:0.31, T:0.28
Consensus pattern (240 bp):
TCGAGGGCCATACTAGGTCGAGCTCGGCTGTGCCTGACCGCTCGCCTATTAGCGTAGGGCTCCTT
GAGGGCTTCATCATTTCCCATACTCGGTCAGGGATGGTTCTTGCCGATCGCCTGCCAGTCGGGGG
CCATAATAGGTCGAGCTCGGCCTTGCCTGATCGCTCGCTGTTGGCGTTGGGCCCCTTGAGGGCTT
CATCATTTCCCATACTCGGTCAGGGATGGCTTCTATTGCCGCCGA
Found at i:66424 original size:21 final size:21
Alignment explanation
Indices: 66394--66439 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
66384 CATGACACTG
* * *
66394 ACCACCTGGGTGATCAGGCAA
1 ACCACATGGGTCATCAGACAA
*
66415 ACCACATGGGTCTTCAGACAA
1 ACCACATGGGTCATCAGACAA
66436 ACCA
1 ACCA
66440 TGTGGGTGCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.30, G:0.22, T:0.15
Consensus pattern (21 bp):
ACCACATGGGTCATCAGACAA
Found at i:69257 original size:2 final size:2
Alignment explanation
Indices: 69247--69277 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
69237 TCCGTGTGTG
*
69247 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
69278 GTTCACTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:70162 original size:14 final size:14
Alignment explanation
Indices: 70143--70171 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
70133 TCATTACTAA
70143 ATTTAGTTTTTTGG
1 ATTTAGTTTTTTGG
70157 ATTTAGTTTTTTGG
1 ATTTAGTTTTTTGG
70171 A
1 A
70172 CCTTCACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.21, T:0.62
Consensus pattern (14 bp):
ATTTAGTTTTTTGG
Found at i:76406 original size:36 final size:36
Alignment explanation
Indices: 76359--76428 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
76349 TTCAATAACC
* *
76359 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
76395 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
76429 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:76734 original size:31 final size:31
Alignment explanation
Indices: 76699--76764 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
76689 ATGAATGATC
76699 AATGTGATCTAAAATAACATAGCAAAAAGGT
1 AATGTGATCTAAAATAACATAGCAAAAAGGT
76730 AATGTGATCTAAAATAACATAGCAAAAAGGT
1 AATGTGATCTAAAATAACATAGCAAAAAGGT
76761 AATG
1 AATG
76765 ATCTTATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.23
Consensus pattern (31 bp):
AATGTGATCTAAAATAACATAGCAAAAAGGT
Found at i:77502 original size:25 final size:24
Alignment explanation
Indices: 77468--77514 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
77458 ACGTTTGCAC
* *
77468 AAATAGCTAAGAATTTGAATTAAAA
1 AAATACCTAAAAATTT-AATTAAAA
77493 AAATACCTAAAAATTTAATTAA
1 AAATACCTAAAAATTTAATTAA
77515 TGTAAGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAAAATTTAATTAAAA
Found at i:78249 original size:2 final size:2
Alignment explanation
Indices: 78244--78269 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
78234 TGTTTATAGA
78244 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
78270 GCATGCTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:79340 original size:30 final size:29
Alignment explanation
Indices: 79274--79341 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
79264 ACACAAAACG
***
79274 GCCAAATAAGCCCCTGAACTCTAAGTGCA
1 GCCAAATAAGCCCCTGAACTCTAAGAAAA
79303 GCCAAATAAGCCCCTGAACTCTTAA-AAAA
1 GCCAAATAAGCCCCTGAACTC-TAAGAAAA
79332 GCCCAAATAA
1 G-CCAAATAA
79342 ACCCTTTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 23 0.68
30 11 0.32
ACGTcount: A:0.41, C:0.29, G:0.13, T:0.16
Consensus pattern (29 bp):
GCCAAATAAGCCCCTGAACTCTAAGAAAA
Found at i:80007 original size:14 final size:15
Alignment explanation
Indices: 79979--80007 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
79969 TGCTGTCAAC
79979 GTTTTCCTCTTTTTT
1 GTTTTCCTCTTTTTT
79994 GTTTTCCT-TTTTTT
1 GTTTTCCTCTTTTTT
80008 AAAATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (15 bp):
GTTTTCCTCTTTTTT
Found at i:83691 original size:21 final size:21
Alignment explanation
Indices: 83652--83691 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
83642 AGGATATGTC
*
83652 AAAGATGCCATTTGATCCATT
1 AAAGATGCCATTAGATCCATT
*
83673 AAAGATGCCATTAGGTCCA
1 AAAGATGCCATTAGATCCA
83692 AAGACAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAGATGCCATTAGATCCATT
Found at i:85637 original size:21 final size:21
Alignment explanation
Indices: 85598--85637 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
85588 GGGTGATGCC
*
85598 AAAGATGCCATTTGATCCATT
1 AAAGATGCCATTAGATCCATT
*
85619 AAAGATGCCATTAGGTCCA
1 AAAGATGCCATTAGATCCA
85638 AAGACAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAGATGCCATTAGATCCATT
Found at i:87199 original size:21 final size:21
Alignment explanation
Indices: 87160--87199 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
87150 GGATGATGCC
*
87160 AAAGATGCCATTTGATCCATT
1 AAAGATGCCATTAGATCCATT
*
87181 AAAGATGCCATTAGGTCCA
1 AAAGATGCCATTAGATCCA
87200 AAGACAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAGATGCCATTAGATCCATT
Found at i:91222 original size:22 final size:21
Alignment explanation
Indices: 91192--91232 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
91182 TTTATGAATG
91192 AAAAAAAAAACAAAAAAAAAT
1 AAAAAAAAAACAAAAAAAAAT
*
91213 AAAAAGAAAAACTAAAAAAA
1 AAAAA-AAAAACAAAAAAAA
91233 GGAAGCATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.88, C:0.05, G:0.02, T:0.05
Consensus pattern (21 bp):
AAAAAAAAAACAAAAAAAAAT
Found at i:92204 original size:31 final size:31
Alignment explanation
Indices: 92169--92305 Score: 166
Period size: 31 Copynumber: 4.4 Consensus size: 31
92159 GTGTCCAACA
* *
92169 TGGCATGCCACGTGTACCAAAAAGCGACATG
1 TGGCATGCCACGTGTACCAAAAAGTGACACG
* **
92200 TGGCACGCCACGTGTATTAAAAAGTGACACG
1 TGGCATGCCACGTGTACCAAAAAGTGACACG
** * *
92231 TATCACGCCATGTGTACCAAAAAGTGACACG
1 TGGCATGCCACGTGTACCAAAAAGTGACACG
* **
92262 TGGCATGCCATGTGTTTCAAAAAGTGACACG
1 TGGCATGCCACGTGTACCAAAAAGTGACACG
92293 TGGCATGCCACGT
1 TGGCATGCCACGT
92306 ACACAAAAGG
Statistics
Matches: 90, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 90 1.00
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (31 bp):
TGGCATGCCACGTGTACCAAAAAGTGACACG
Found at i:94227 original size:67 final size:67
Alignment explanation
Indices: 94119--94253 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
94109 CCCAAAGGCC
94119 TTACAGGTTTGTCATTTCCAAAAGACACCTCACAAATTTGGATTGGATCTCTATATATAAACCAC
1 TTACAGGTTTGTCATTTCCAAAAGACACCTCACAAATTTGGATTGGATCTCTATATATAAACCAC
94184 AA
66 AA
94186 TTACAGGTTTGTCATTTCCAAAAGACACCTCACAAATTTGGATTGGATCTCTATATATAAACCAC
1 TTACAGGTTTGTCATTTCCAAAAGACACCTCACAAATTTGGATTGGATCTCTATATATAAACCAC
94251 AA
66 AA
94253 T
1 T
94254 AACCACAACA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.32
Consensus pattern (67 bp):
TTACAGGTTTGTCATTTCCAAAAGACACCTCACAAATTTGGATTGGATCTCTATATATAAACCAC
AA
Found at i:95005 original size:17 final size:17
Alignment explanation
Indices: 94981--95043 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 17
94971 TATTTATTAC
94981 TATATATATTACTATAAT
1 TATATATATTA-TATAAT
94999 T-TATATATTATAATAAT
1 TATATATATTAT-ATAAT
*
95016 TATATTTATTATTATATAT
1 TATATATATTA-TATA-AT
*
95035 AATATATAT
1 TATATATAT
95044 AAATAAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 1 0.03
17 15 0.39
18 12 0.32
19 10 0.26
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATATATTATATAAT
Found at i:95044 original size:25 final size:24
Alignment explanation
Indices: 94971--95044 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 24
94961 TAGGAAATCT
*
94971 TATTTATTACTATATATATTACTATA
1 TATTTATTA-TATATATAATA-TATA
94997 -ATTTA-TATAT-TATAATA-ATTA
1 TATTTATTATATATATAATATA-TA
95018 TATTTATTATTATATATAATATATA
1 TATTTATTA-TATATATAATATATA
95043 TA
1 TA
95045 AATAAATTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
20 1 0.02
21 2 0.05
22 11 0.27
23 5 0.12
24 5 0.12
25 16 0.39
26 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTTATTATATATATAATATATA
Found at i:95439 original size:19 final size:19
Alignment explanation
Indices: 95417--95481 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
95407 ATTCAAAACA
95417 AAATAAAAACTACCATCTT
1 AAATAAAAACTACCATCTT
*
95436 AAATAAAAACTACCATCCT
1 AAATAAAAACTACCATCTT
95455 -AA-AAAAACTATCC-T-TT
1 AAATAAAAACTA-CCATCTT
*
95471 AAAAAAAAACT
1 AAATAAAAACT
95482 GCCACAAACT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
16 1 0.02
17 11 0.27
18 11 0.27
19 18 0.44
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (19 bp):
AAATAAAAACTACCATCTT
Found at i:102903 original size:1 final size:1
Alignment explanation
Indices: 102897--102933 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
102887 GGTTCTAGGG
102897 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
102934 GGGATTAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.