Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014774.1 Corchorus olitorius cultivar O-4 contig14807, 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: 118026
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1342 original size:4 final size:4
Alignment explanation
Indices: 1329--1368 Score: 64
Period size: 4 Copynumber: 10.0 Consensus size: 4
1319 AACCCCTTGG
1329 TAAA -AAA TAAA TAAA TAAA TAAA TAAA TAAA TAAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T-AAA TAAA
1369 ATAATTCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 3 0.09
4 27 0.79
5 4 0.12
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:1925 original size:252 final size:251
Alignment explanation
Indices: 1478--1981 Score: 848
Period size: 252 Copynumber: 2.0 Consensus size: 251
1468 GCTGAAAGGA
*
1478 GGTAAAAGTACCCGGAAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTGTACTTTTTTT
1 GGTAAAAGTACCCGGAAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTCTAC-TTTTTT
* ***
1543 TTTCTACAAATTCGTCTCTATACTATCAGAACCTATCACCCGAGATCCCTCACGTTAGTGTGCCG
65 TTTCTACAAATTCGTCCCTATACTATCAGAACCTATCACCCGAGATCCCTCACGTTAACATGCCG
* * *
1608 TGACAGGCCCGTCAAATATGCTGACGTGGCACTAACACCGTTTTTTTTGCTGATGTGGCAGGTGA
130 TGACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGA
1673 CACGTGGAATAAAAATTAAATATTTTTTTAATATATTTTATTTTATTGAAATTTATTTT
195 CACGTGGAATAAAAATTAAATA--TTTTTAATATATTTTATTTTATTGAAATTTATTTT
* *
1732 GGTAAAAGTATCCGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTCTAC-TTTTTT
1 GGTAAAAGTACCCGGAAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTCTACTTTTTTT
* *
1796 TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGATCCCTCATGTTAACATGCCGT
66 TTCTACAAATTCGTCCCTATACTATCAGAACCTATCACCCGAGATCCCTCACGTTAACATGCCGT
* *
1861 GACAGACCCGTCATATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGTAGGTGAC
131 GACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGAC
1926 ACGTGGAATAAAAATTAAATATTTTTAATATATTTTATTTTATTGAAATTTATTTT
196 ACGTGGAATAAAAATTAAATATTTTTAATATATTTTATTTTATTGAAATTTATTTT
1982 TTAAAAAAAT
Statistics
Matches: 236, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
250 35 0.15
252 146 0.62
254 55 0.23
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (251 bp):
GGTAAAAGTACCCGGAAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTCTACTTTTTTT
TTCTACAAATTCGTCCCTATACTATCAGAACCTATCACCCGAGATCCCTCACGTTAACATGCCGT
GACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGAC
ACGTGGAATAAAAATTAAATATTTTTAATATATTTTATTTTATTGAAATTTATTTT
Found at i:3647 original size:31 final size:31
Alignment explanation
Indices: 3580--3720 Score: 147
Period size: 31 Copynumber: 4.5 Consensus size: 31
3570 TCCTTTTGTG
** **
3580 CACATGGCATGCCATATGTCACTTTTTGAAA
1 CACATGGCATGCCACGTGTCACTTTTTGGTA
* * *
3611 TACATGGCATGTCACGTGTCACTTTTGGGTA
1 CACATGGCATGCCACGTGTCACTTTTTGGTA
* ** *
3642 CACATGGCGTGATACGTGTCACTTTTTTGTA
1 CACATGGCATGCCACGTGTCACTTTTTGGTA
* * *
3673 CACATGGCGTGCCACATGTCGCTTTTTGGTA
1 CACATGGCATGCCACGTGTCACTTTTTGGTA
*
3704 CACGTGGCATGCCACGT
1 CACATGGCATGCCACGT
3721 CGGACACCGT
Statistics
Matches: 89, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 89 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (31 bp):
CACATGGCATGCCACGTGTCACTTTTTGGTA
Found at i:5594 original size:30 final size:29
Alignment explanation
Indices: 5521--5598 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
5511 ATTTGTAGCG
* *
5521 TTTGGACGTTTTGTCCCATGAACTTCAAT
1 TTTGGACGTTTTGCCCCCTGAACTTCAAT
* * *
5550 TTTGAACATTTTGCCCCCTGAATTTCAAT
1 TTTGGACGTTTTGCCCCCTGAACTTCAAT
5579 TTTGGGACGTTTTGCCCCCT
1 TTT-GGACGTTTTGCCCCCT
5599 TAGGCTAACG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 27 0.66
30 14 0.34
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.41
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCCCTGAACTTCAAT
Found at i:5675 original size:33 final size:33
Alignment explanation
Indices: 5632--5711 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
5622 GCTGACGTGG
*
5632 CATTGCCACGTCAGACCAACCCGACCCACATGA
1 CATTGTCACGTCAGACCAACCCGACCCACATGA
5665 CATTGTCACGTCAGACCAACCCGACCCACATGA
1 CATTGTCACGTCAGACCAACCCGACCCACATGA
5698 CATTGTCACGTCAG
1 CATTGTCACGTCAG
5712 CATCTTGACG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.29, C:0.39, G:0.16, T:0.16
Consensus pattern (33 bp):
CATTGTCACGTCAGACCAACCCGACCCACATGA
Found at i:5783 original size:29 final size:30
Alignment explanation
Indices: 5736--5795 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
5726 TATTAGTCCG
5736 AGGGGGTAAAACATCCCAAAATTAAAGTTT
1 AGGGGGTAAAACATCCCAAAATTAAAGTTT
** *
5766 AGGGGGTAAAATGT-CCAAAATTGAAGTTT
1 AGGGGGTAAAACATCCCAAAATTAAAGTTT
5795 A
1 A
5796 TGAGCAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (30 bp):
AGGGGGTAAAACATCCCAAAATTAAAGTTT
Found at i:6865 original size:273 final size:274
Alignment explanation
Indices: 6238--6965 Score: 786
Period size: 274 Copynumber: 2.7 Consensus size: 274
6228 TATTTACTGT
*
6238 CATATCTTAGATTTA-AAATATTTATCAAAACTAAGTAAGCTGGAATACTTGGATCTTGGAGGAA
1 CATATCTTAGATTTACAAA-CTTTATCAAAACTAAGTAAGCTGGAATACTTGGATCTTGGAGGAA
* * * * *
6302 ATAAATTCAAGAGCAACGATTTTGTGATGTGTTTGGTATCTCTTCCGTCACTTAAATCTCTCAAT
65 ATAAATTCAAGAACAAAGATATTGTGATGTGTTTGGGATCTCTCCCGTCACTTAAATCTCTCAAT
* * ** *
6367 CTTAAAT-GGAATTATATGGAGGGCTGTTTGTGTGACCAAGGTATGTCTTATATTTAATTTAATT
130 C-TAAATGGGAATTCTATGGAGGGCTCTTTGACTGACCAAGGTATGTATTATATTTAATTTAATT
* * * *
6431 ATTTGGTTAATTAATAACATTATTATTCAAATAAAGTTTGATTTGATCATATAAAAGTTATAATG
194 ATATGATTAATTAATAACATTACTATTCAAATAAAGTTTGATTTGATCATATAAAAGTCATAATG
*
6496 TTGACATGACATGACC
259 TTAACATGACATGACC
6512 CATATCTTAGATTT-CAAACATGTTA-CAAAACTAAGTAAGCTGGAATACTTGGATCTTGGAGGA
1 CATATCTTAGATTTACAAAC-T-TTATCAAAACTAAGTAAGCTGGAATACTTGGATCTTGGAGGA
* * * * * * *
6575 AATAGATTCACGAACAAAGATATTGTGATGTGTTTGGGAGCTCTCCCGTCCCTTAAATTTGTTAA
64 AATAAATTCAAGAACAAAGATATTGTGATGTGTTTGGGATCTCTCCCGTCACTTAAATCTCTCAA
* * * * **
6640 TCTCAATGGGAATTCTATGGGGGGAC-CTTTGACTGACCATGGTATGTATTATATTT-CTTTGCT
129 TCTAAATGGGAATTCTATGGAGGG-CTCTTTGACTGACCAAGGTATGTATTATATTTAATTTAAT
* * *
6703 T-TAT-ATTATATTTATTA-A-TACTATTCAAATGAAAGTTTGATTTTGA-CATAATTATATCA-
193 TATATGATTA-ATTAATAACATTACTATTCAAAT-AAAGTTTGA-TTTGATCAT-A-TA-A-AAG
* *
6762 TCATTAAT-TTAAATATTAC-TG-CC
251 TCA-TAATGTT-AACATGACATGACC
* * **
6785 CATATCTTAGATTTACAAGCTTTATCAAAACTAAGTAAGCTGGAGTACTTAAATCTTGGAGGAAA
1 CATATCTTAGATTTACAAACTTTATCAAAACTAAGTAAGCTGGAATACTTGGATCTTGGAGGAAA
* * *
6850 TAAATTCAAGAACAAAGATATTGTGAGGTGTTTGGGATTTCTCCCGTCGCTTAAATCTCTCAATC
66 TAAATTCAAGAACAAAGATATTGTGATGTGTTTGGGATCTCTCCCGTCACTTAAATCTCTCAATC
* * * * * * *
6915 TTACTGGCAATTCTATGGAGGGCTTTTTGTCCGACGAAGGTATGTA-TATAT
131 TAAATGGGAATTCTATGGAGGGCTCTTTGACTGACCAAGGTATGTATTATAT
6966 CTTCATTAAT
Statistics
Matches: 381, Mismatches: 56, Indels: 36
0.81 0.12 0.08
Matches are distributed among these distances:
270 11 0.03
271 16 0.04
272 23 0.06
273 156 0.41
274 161 0.42
275 14 0.04
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.37
Consensus pattern (274 bp):
CATATCTTAGATTTACAAACTTTATCAAAACTAAGTAAGCTGGAATACTTGGATCTTGGAGGAAA
TAAATTCAAGAACAAAGATATTGTGATGTGTTTGGGATCTCTCCCGTCACTTAAATCTCTCAATC
TAAATGGGAATTCTATGGAGGGCTCTTTGACTGACCAAGGTATGTATTATATTTAATTTAATTAT
ATGATTAATTAATAACATTACTATTCAAATAAAGTTTGATTTGATCATATAAAAGTCATAATGTT
AACATGACATGACC
Found at i:9773 original size:7 final size:7
Alignment explanation
Indices: 9761--9788 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
9751 TAAAATTACT
9761 CCTAAAC
1 CCTAAAC
9768 CCTAAAC
1 CCTAAAC
9775 CCTAAAC
1 CCTAAAC
9782 CCTAAAC
1 CCTAAAC
9789 TTTTTTCCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.14
Consensus pattern (7 bp):
CCTAAAC
Found at i:10219 original size:14 final size:14
Alignment explanation
Indices: 10200--10233 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
10190 TTTTATAATT
10200 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
10214 ATTTTATTTTTACT
1 ATTTTATTTTTACC
10228 ATTTTA
1 ATTTTA
10234 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:10281 original size:15 final size:15
Alignment explanation
Indices: 10261--10291 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
10251 GATTAACATG
10261 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
10276 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
10291 T
1 T
10292 AATGTATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Found at i:11987 original size:20 final size:20
Alignment explanation
Indices: 11964--12003 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
11954 TGTATATATG
11964 GACTATTTGATCCTCAAGTC
1 GACTATTTGATCCTCAAGTC
11984 GACTATTTGATCCTCAAGTC
1 GACTATTTGATCCTCAAGTC
12004 AATTGATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (20 bp):
GACTATTTGATCCTCAAGTC
Found at i:13342 original size:42 final size:42
Alignment explanation
Indices: 13286--13391 Score: 131
Period size: 42 Copynumber: 2.5 Consensus size: 42
13276 CTCTCATGAG
* * *
13286 AGTCTCGAAGAAGAAGATGATGATGAAGATAGTGATGAAATTTTC
1 AGTCTGGAAGAAGAAGA--AT-ATGAAGATACTGATGAAACTTTC
* * *
13331 AGTCTGGAAGAAGAAGAATCTGAGGATTCTGATGAAACTTTC
1 AGTCTGGAAGAAGAAGAATATGAAGATACTGATGAAACTTTC
13373 AGTCTGGAAGAAGAAGAAT
1 AGTCTGGAAGAAGAAGAAT
13392 CTGATGAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
42 37 0.67
43 2 0.04
45 16 0.29
ACGTcount: A:0.40, C:0.08, G:0.27, T:0.25
Consensus pattern (42 bp):
AGTCTGGAAGAAGAAGAATATGAAGATACTGATGAAACTTTC
Found at i:13396 original size:33 final size:33
Alignment explanation
Indices: 13358--13422 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
13348 ATCTGAGGAT
*
13358 TCTGATGAAACTTTCAGTCTGGAAGAAGAAGAA
1 TCTGATGAAACTTTCAGTCTGGAAAAAGAAGAA
*
13391 TCTGATGAAATTTTCAGTCTGGAAAAAGAAGA
1 TCTGATGAAACTTTCAGTCTGGAAAAAGAAGA
13423 TGAAGACACC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (33 bp):
TCTGATGAAACTTTCAGTCTGGAAAAAGAAGAA
Found at i:53805 original size:20 final size:20
Alignment explanation
Indices: 53780--53822 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
53770 AACCTTTTGG
53780 AATAATAAATCAAGTAAAAA
1 AATAATAAATCAAGTAAAAA
53800 AATAATAAATCAAGTAAAAA
1 AATAATAAATCAAGTAAAAA
53820 AAT
1 AAT
53823 GTAGTTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.21
Consensus pattern (20 bp):
AATAATAAATCAAGTAAAAA
Found at i:59208 original size:23 final size:23
Alignment explanation
Indices: 59182--59226 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
59172 TGTTCAATAT
*
59182 TCACCTTTTAAAGACAAATACTC
1 TCACCTTTTAAAAACAAATACTC
59205 TCACCTTTTAAAAACAAATACT
1 TCACCTTTTAAAAACAAATACT
59227 TTTAATAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.24, G:0.02, T:0.31
Consensus pattern (23 bp):
TCACCTTTTAAAAACAAATACTC
Found at i:59296 original size:19 final size:20
Alignment explanation
Indices: 59267--59329 Score: 83
Period size: 21 Copynumber: 3.1 Consensus size: 20
59257 TGACACTGTC
59267 TAGCAACTGTACAGATGAGAT
1 TAGC-ACTGTACAGATGAGAT
*
59288 TA-CACTGTACAGATTAGAT
1 TAGCACTGTACAGATGAGAT
*
59307 TAAGTACTGTACAGATGAGAT
1 T-AGCACTGTACAGATGAGAT
59328 TA
1 TA
59330 TTAGAACAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 16 0.43
20 3 0.08
21 18 0.49
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.29
Consensus pattern (20 bp):
TAGCACTGTACAGATGAGAT
Found at i:62604 original size:39 final size:39
Alignment explanation
Indices: 62561--62639 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
62551 CCCCGTCGCT
62561 CACCTGGTTATGGTGGGTGAGTCTACCAACGGGGGCAGC
1 CACCTGGTTATGGTGGGTGAGTCTACCAACGGGGGCAGC
62600 CACCTGGTTATGGTGGGTGAGTCTACCAACGGGGGCAGC
1 CACCTGGTTATGGTGGGTGAGTCTACCAACGGGGGCAGC
62639 C
1 C
62640 GCGTACGCAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.18, C:0.24, G:0.38, T:0.20
Consensus pattern (39 bp):
CACCTGGTTATGGTGGGTGAGTCTACCAACGGGGGCAGC
Found at i:64427 original size:7 final size:7
Alignment explanation
Indices: 64415--64446 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
64405 TGTGATCGCC
64415 AAAAAGA
1 AAAAAGA
64422 AAAAAGA
1 AAAAAGA
64429 AAAAAGA
1 AAAAAGA
64436 AAAAA-A
1 AAAAAGA
64442 AAAAA
1 AAAAA
64447 CAGAGTCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:65577 original size:19 final size:19
Alignment explanation
Indices: 65544--65625 Score: 61
Period size: 19 Copynumber: 4.5 Consensus size: 19
65534 CCGTTTAGTA
65544 ATAT-TTATA-AT-TAAAT
1 ATATATTATATATATAAAT
65560 ATATATTATATATATAAA-
1 ATATATTATATATATAAAT
*
65578 ATAATATTAGATATATATAAT
1 AT-ATATTATATATATA-AAT
*
65599 -TACA-TATAT-TATAATAT
1 ATATATTATATATATAA-AT
65616 ATATAATTAT
1 ATAT-ATTAT
65626 TAAACGGTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
16 5 0.10
17 11 0.21
18 10 0.19
19 20 0.38
20 6 0.12
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (19 bp):
ATATATTATATATATAAAT
Found at i:65600 original size:14 final size:13
Alignment explanation
Indices: 65542--65624 Score: 55
Period size: 11 Copynumber: 7.2 Consensus size: 13
65532 GACCGTTTAG
*
65542 TAATATTTATAAT
1 TAATATATATAAT
65555 TAA-ATATAT-AT
1 TAATATATATAAT
65566 T-ATATATAT-A-
1 TAATATATATAAT
65576 -AA-ATA-AT-AT
1 TAATATATATAAT
65585 TAGATATATATAAT
1 TA-ATATATATAAT
65599 TACATATAT-T-A-
1 TA-ATATATATAAT
65610 TAATATATATAAT
1 TAATATATATAAT
65623 TA
1 TA
65625 TTAAACGGTT
Statistics
Matches: 57, Mismatches: 2, Indels: 22
0.70 0.02 0.27
Matches are distributed among these distances:
8 3 0.05
9 3 0.05
10 9 0.16
11 14 0.25
12 10 0.18
13 8 0.14
14 10 0.18
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (13 bp):
TAATATATATAAT
Found at i:77062 original size:36 final size:33
Alignment explanation
Indices: 76985--77064 Score: 92
Period size: 33 Copynumber: 2.3 Consensus size: 33
76975 ACCTTTTGTT
*
76985 TCCTTATT-GCTGTCTCCTATCCCCTGTTGACTC
1 TCCTT-TTGGCTGCCTCCTATCCCCTGTTGACTC
77018 T-CTGTTTGGCTGCCTCCTATCCCCTGTTGACGACTC
1 TCCT-TTTGGCTGCCTCCTATCCCCTGTT---GACTC
77054 TCCTTTTGGCT
1 TCCTTTTGGCT
77065 TCTGGAGAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
32 4 0.10
33 21 0.52
36 13 0.32
37 2 0.05
ACGTcount: A:0.07, C:0.35, G:0.16, T:0.41
Consensus pattern (33 bp):
TCCTTTTGGCTGCCTCCTATCCCCTGTTGACTC
Found at i:84231 original size:6 final size:6
Alignment explanation
Indices: 84217--84258 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
84207 AAGAGAGGTA
*
84217 ATATAT ATATCT ATATCT ATATACT ATATCT ATATACT ATAT
1 ATATCT ATATCT ATATCT ATAT-CT ATATCT ATAT-CT ATAT
84259 AAGTCTAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
6 21 0.64
7 12 0.36
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATCT
Found at i:84245 original size:13 final size:13
Alignment explanation
Indices: 84220--84258 Score: 69
Period size: 13 Copynumber: 2.9 Consensus size: 13
84210 AGAGGTAATA
84220 TATATATCTATATC
1 TATATA-CTATATC
84234 TATATACTATATC
1 TATATACTATATC
84247 TATATACTATAT
1 TATATACTATAT
84259 AAGTCTAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (13 bp):
TATATACTATATC
Found at i:84531 original size:39 final size:40
Alignment explanation
Indices: 84475--84555 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
84465 TTTAATTCCT
*
84475 ATGTAATATATATAATAAGTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
84515 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
84554 AT
1 AT
84556 TCTTAGGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:84582 original size:25 final size:24
Alignment explanation
Indices: 84546--84592 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
84536 AATACTTACA
84546 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
84570 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
84593 GTGCAGACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Found at i:85612 original size:36 final size:36
Alignment explanation
Indices: 85572--85641 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
85562 GAGATTTTGG
* *
85572 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
* *
85608 AGAAATATGATAACCAAAATCACAGAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
85642 GGTTATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.59, C:0.09, G:0.11, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:88200 original size:14 final size:14
Alignment explanation
Indices: 88181--88208 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
88171 GATAATCTTA
88181 TTCTTATTTTTTGC
1 TTCTTATTTTTTGC
88195 TTCTTATTTTTTGC
1 TTCTTATTTTTTGC
88209 ATCAGAGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.14, G:0.07, T:0.71
Consensus pattern (14 bp):
TTCTTATTTTTTGC
Found at i:88563 original size:27 final size:27
Alignment explanation
Indices: 88525--88578 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
88515 ATATATATAT
88525 GCAATTGTGAAAGTTTGAAATTCGTAA
1 GCAATTGTGAAAGTTTGAAATTCGTAA
88552 GCAATTGTGAAAGTTTGAAATTCGTAA
1 GCAATTGTGAAAGTTTGAAATTCGTAA
88579 TTGGTGCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.33
Consensus pattern (27 bp):
GCAATTGTGAAAGTTTGAAATTCGTAA
Found at i:92846 original size:15 final size:16
Alignment explanation
Indices: 92828--92857 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
92818 ATAAATAATA
92828 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
92843 ATATTATAATCTAAA
1 ATATTATAATCTAAA
92858 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:93215 original size:21 final size:22
Alignment explanation
Indices: 93168--93227 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
93158 GAATATTTTT
93168 TTATGAAATTTTGATAACTACC
1 TTATGAAATTTTGATAACTACC
* *
93190 CTATGAAATTTTG-TAAC-ATTC
1 TTATGAAATTTTGATAACTA-CC
*
93211 TTATG-ATTTTTGATAAC
1 TTATGAAATTTTGATAAC
93228 CTTATTAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 7 0.22
21 13 0.41
22 12 0.38
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TTATGAAATTTTGATAACTACC
Found at i:95051 original size:3 final size:3
Alignment explanation
Indices: 95033--95097 Score: 116
Period size: 3 Copynumber: 22.3 Consensus size: 3
95023 TATATAGTAA
95033 AAT AA- AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
95079 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
95098 TAGTAAAATA
Statistics
Matches: 60, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.07
3 56 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:95113 original size:13 final size:13
Alignment explanation
Indices: 95091--95125 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
95081 TAATAATAAT
*
95091 AATAATATAGTAA
1 AATAAGATAGTAA
95104 AATAAGATAGTAA
1 AATAAGATAGTAA
*
95117 GATAAGATA
1 AATAAGATA
95126 TAGCTTCCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (13 bp):
AATAAGATAGTAA
Found at i:98175 original size:46 final size:46
Alignment explanation
Indices: 98108--98200 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
98098 TACTCGTAAT
98108 AATATTCCTTCTTGCAGCCTCTGCAGCTACAATTGCTAATCTGTGG
1 AATATTCCTTCTTGCAGCCTCTGCAGCTACAATTGCTAATCTGTGG
98154 AATATTCCTTCTTGCAGCCTCTGCAGCTACAATTGCTAATCTGTGG
1 AATATTCCTTCTTGCAGCCTCTGCAGCTACAATTGCTAATCTGTGG
98200 A
1 A
98201 GGAAATCGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (46 bp):
AATATTCCTTCTTGCAGCCTCTGCAGCTACAATTGCTAATCTGTGG
Found at i:99095 original size:12 final size:12
Alignment explanation
Indices: 99078--99102 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
99068 AACTTCTTAG
99078 GGAAAGGGTCTA
1 GGAAAGGGTCTA
99090 GGAAAGGGTCTA
1 GGAAAGGGTCTA
99102 G
1 G
99103 TTATCGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.44, T:0.16
Consensus pattern (12 bp):
GGAAAGGGTCTA
Found at i:104020 original size:160 final size:160
Alignment explanation
Indices: 103756--104076 Score: 615
Period size: 160 Copynumber: 2.0 Consensus size: 160
103746 ACAAGGCATA
** *
103756 TAATCTTGAGAATACATAGACATATTGTCCTGTTGATAATGCATGGTTTTTATTAGTACAAACTG
1 TAATCTTGAGAATACATAGACATATTGTCCTCCTGATAATGCATGATTTTTATTAGTACAAACTG
103821 TTTATACCTCAATTTACAATTGAGGGTAAATTGGTCTTCACATAAATAATATCAAGATGAGTGGT
66 TTTATACCTCAATTTACAATTGAGGGTAAATTGGTCTTCACATAAATAATATCAAGATGAGTGGT
103886 CAAGATTTGATTAAAAATCCTGATGAAACT
131 CAAGATTTGATTAAAAATCCTGATGAAACT
103916 TAATCTTGAGAATACATAGACATATTGTCCTCCTGATAATGCATGATTTTTATTAGTACAAACTG
1 TAATCTTGAGAATACATAGACATATTGTCCTCCTGATAATGCATGATTTTTATTAGTACAAACTG
103981 TTTATACCTCAATTTACAATTGAGGGTAAATTGGTCTTCACATAAATAATATCAAGATGAGTGGT
66 TTTATACCTCAATTTACAATTGAGGGTAAATTGGTCTTCACATAAATAATATCAAGATGAGTGGT
104046 CAAGATTTGATTAAAAATCCTGATGAAACT
131 CAAGATTTGATTAAAAATCCTGATGAAACT
104076 T
1 T
104077 GGTTTCCGCA
Statistics
Matches: 158, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
160 158 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (160 bp):
TAATCTTGAGAATACATAGACATATTGTCCTCCTGATAATGCATGATTTTTATTAGTACAAACTG
TTTATACCTCAATTTACAATTGAGGGTAAATTGGTCTTCACATAAATAATATCAAGATGAGTGGT
CAAGATTTGATTAAAAATCCTGATGAAACT
Found at i:107516 original size:31 final size:31
Alignment explanation
Indices: 107481--107545 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
107471 GACACGGATC
107481 ACCCTAATCTTATTTGGATTAATTTAGAAAA
1 ACCCTAATCTTATTTGGATTAATTTAGAAAA
107512 ACCCTAATCTTATTTGGATTAATTTAGAAAA
1 ACCCTAATCTTATTTGGATTAATTTAGAAAA
107543 ACC
1 ACC
107546 TTTACCTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.37
Consensus pattern (31 bp):
ACCCTAATCTTATTTGGATTAATTTAGAAAA
Found at i:107855 original size:18 final size:18
Alignment explanation
Indices: 107832--107875 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
107822 TAAGCCAACT
* *
107832 AACTAATATATTAAGTCC
1 AACTAATACATTAAGCCC
**
107850 AACTAACGCATTAAGCCC
1 AACTAATACATTAAGCCC
107868 AACTAATA
1 AACTAATA
107876 ACCAATGTAT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.25
Consensus pattern (18 bp):
AACTAATACATTAAGCCC
Found at i:111989 original size:31 final size:31
Alignment explanation
Indices: 111932--111990 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
111922 TTCGGCTCAT
*
111932 CTGGATTCAGGTCATTCAGGTCTCGGGTCTG
1 CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
* *
111963 CTGGATTTAGGGTCATGCGGGT-TCGGGT
1 CTGGATTCA-GGTCATGCAGGTCTCGGGT
111991 TTTGGCCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.58
32 10 0.42
ACGTcount: A:0.12, C:0.19, G:0.37, T:0.32
Consensus pattern (31 bp):
CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
Found at i:116532 original size:141 final size:142
Alignment explanation
Indices: 116299--116641 Score: 446
Period size: 141 Copynumber: 2.4 Consensus size: 142
116289 TTGGTTTTGG
* * * *
116299 GAGAGGTCTAGAAGTTTAAGAGAAGTCAAATTGTTCAAGCATTGAGGTAGGTTTCCTTCG-AGAC
1 GAGAGGTCTAGAACTTTAAGAGAAGTCAAATTGTTTAAGCATGGAGGAAGGTTTCCTTCGAAGAC
* * * *
116363 TATTACGCCCCAGAACCAACCATTGAAGAG-AGCTAGACAACAAATCGCAAGGGATGGTCCCACT
66 TATTACGCCCAAGAAACAACCATCGAAGAGAAG-TAGACAACAAATCGCAAGAGATGGTCCCACT
116427 GAA-TCGATTCCCA
130 GAATTC-ATTCCCA
* * *
116440 TAGAGGTCTAGAACTTTAAGAGAAATCGAATTGTTTAAGCATGGAGGAAGGTTTCCTTCGAAG-C
1 GAGAGGTCTAGAACTTTAAGAGAAGTCAAATTGTTTAAGCATGGAGGAAGGTTTCCTTCGAAGAC
* * * *
116504 TATTACTG-CTAAGAAACAACTC-TCGAAGAGAAGTTGACAATAAATCGCAAGAGATGGTCCCAT
66 TATTAC-GCCCAAGAAACAAC-CATCGAAGAGAAGTAGACAACAAATCGCAAGAGATGGTCCCAC
*
116567 TGAATTCATTCCCG
129 TGAATTCATTCCCA
* *
116581 GAGAGGTCTAGAACTTTAAGAGAAGTCAAATTGTTTAAACATGGAGGAAGGGTTCCTTCGA
1 GAGAGGTCTAGAACTTTAAGAGAAGTCAAATTGTTTAAGCATGGAGGAAGGTTTCCTTCGA
116642 GATCATTAAA
Statistics
Matches: 176, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
141 168 0.95
142 8 0.05
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (142 bp):
GAGAGGTCTAGAACTTTAAGAGAAGTCAAATTGTTTAAGCATGGAGGAAGGTTTCCTTCGAAGAC
TATTACGCCCAAGAAACAACCATCGAAGAGAAGTAGACAACAAATCGCAAGAGATGGTCCCACTG
AATTCATTCCCA
Done.