Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014779.1 Corchorus olitorius cultivar O-4 contig14812, 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: 203591
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:360 original size:198 final size:197
Alignment explanation
Indices: 12--409 Score: 753
Period size: 198 Copynumber: 2.0 Consensus size: 197
2 TTAATTTATA
12 TATGGGTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTG
1 TATGGGTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTG
*
77 ACACATGTCATTTTTTTGATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATG
66 ACACATGTCATTTTTTTGATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGACACATG
*
142 TCACCCTTTAGGTACCGCTTGTGTAGTCTGTTAAACTCCACTGACGGTGTATTATATATTTAGCC
131 TCACCCTTTAGGTACCGCTTGTGTAGTCTGCTAAACTCCACTGACGGTGTATTATATATTTAGCC
207 TT
196 TT
209 TATGGGTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTG
1 TATGGGTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTG
274 ACACATGTCCATTTTTTTGATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGACACAT
66 ACACATGT-CATTTTTTTGATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGACACAT
339 GTCACCCTTTAGG-ACCCGCTTGTGTAGTCTGCTAAACTCCACTGACGGTGTATTATATATTTAG
130 GTCACCCTTTAGGTA-CCGCTTGTGTAGTCTGCTAAACTCCACTGACGGTGTATTATATATTTAG
403 CCTT
194 CCTT
407 TAT
1 TAT
410 ATATATAGTT
Statistics
Matches: 197, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
197 74 0.38
198 123 0.62
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.37
Consensus pattern (197 bp):
TATGGGTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTG
ACACATGTCATTTTTTTGATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGACACATG
TCACCCTTTAGGTACCGCTTGTGTAGTCTGCTAAACTCCACTGACGGTGTATTATATATTTAGCC
TT
Found at i:1387 original size:31 final size:31
Alignment explanation
Indices: 1351--1409 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1341 TAAGTTTATA
*
1351 CTCTTCTTCATATGGACAAGAAATGCCTACT
1 CTCTTCTTCATATGGACAAGAAAGGCCTACT
*
1382 CTCTTCTTCATATGGACATGAAAGGCCT
1 CTCTTCTTCATATGGACAAGAAAGGCCT
1410 GAAGGGAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.32
Consensus pattern (31 bp):
CTCTTCTTCATATGGACAAGAAAGGCCTACT
Found at i:6081 original size:29 final size:28
Alignment explanation
Indices: 6037--6091 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
6027 CTTAAAAAAA
6037 TTAACACCATCTCTCCTCTAATCTAAGC
1 TTAACACCATCTCTCCTCTAATCTAAGC
*
6065 TTAACAACCGTCTCTCCTCTAATCTAA
1 TTAAC-ACCATCTCTCCTCTAATCTAA
6092 ATTCTAAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.29, C:0.35, G:0.04, T:0.33
Consensus pattern (28 bp):
TTAACACCATCTCTCCTCTAATCTAAGC
Found at i:7452 original size:41 final size:41
Alignment explanation
Indices: 7395--7475 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
7385 GGATTTAAAT
* *
7395 CTTGTGTACTACAAAACAATTTACTACTTAGAGTTAGATGA
1 CTTGTGTACTACAAAACAAGTCACTACTTAGAGTTAGATGA
*
7436 CTTGTGTACTACAAAACAAGTCACTACTTGGAGTTAGATG
1 CTTGTGTACTACAAAACAAGTCACTACTTAGAGTTAGATG
7476 CTTATAATAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (41 bp):
CTTGTGTACTACAAAACAAGTCACTACTTAGAGTTAGATGA
Found at i:12228 original size:2 final size:2
Alignment explanation
Indices: 12221--12246 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12211 GTTGGAACTA
12221 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
12247 TTGGAATTCC
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:13460 original size:19 final size:20
Alignment explanation
Indices: 13432--13469 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
13422 AATTCAAAAC
*
13432 TAAATAAAAACTACTCATTT
1 TAAATAAAAACAACTCATTT
13452 TAAAT-AAAACAACTCATT
1 TAAATAAAAACAACTCATT
13470 AGATGATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAATAAAAACAACTCATTT
Found at i:14865 original size:48 final size:48
Alignment explanation
Indices: 14794--14886 Score: 177
Period size: 48 Copynumber: 1.9 Consensus size: 48
14784 TTTCATACTT
14794 TAAAGGAATTGGGATGAATGGAGAGTTGGTTTGGTCGAGAATTTCTCG
1 TAAAGGAATTGGGATGAATGGAGAGTTGGTTTGGTCGAGAATTTCTCG
*
14842 TAAAGGAATTGGGATGAATGGAGAGTTGGTTTGGTCGAGACTTTC
1 TAAAGGAATTGGGATGAATGGAGAGTTGGTTTGGTCGAGAATTTC
14887 GAGAAATTCT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.27, C:0.06, G:0.35, T:0.31
Consensus pattern (48 bp):
TAAAGGAATTGGGATGAATGGAGAGTTGGTTTGGTCGAGAATTTCTCG
Found at i:26719 original size:332 final size:336
Alignment explanation
Indices: 26159--27024 Score: 883
Period size: 332 Copynumber: 2.6 Consensus size: 336
26149 TATATATATA
* * * * * * *
26159 TAATTCAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTG
1 TAATTAAACGCAAAAAAGATTGAAGCACTTTTCATGCTTTTAATATCGTTTTCCATATTTTTCCG
* *
26224 AATTAA----T--TTAAATTGAAACAAGATTCAGATGCTCGTAAAAGCAAAATTCTTAAATCCAA
66 AATTAATTTCTAATTAAAATGAAACAAGATTCAGATGCTCGTAAAA-C-AAATCCTTAAATCCAA
* * * *
26283 TGTAGCTGAGATTTGATTAGATGAATATGGATATCTCAAAGAGTCTTGGCACCAAAAATCATGCA
129 TGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAAGAGTCTTAGCACCAAAAATCATGCA
* * * * * *
26348 AAATTTAGCCGGGGCCTCGGAACGCGATTTTAACC-AAAAAACCGTGGTG-GTT-A-TTAC-AT-
194 AAACTAAACCGGAGCCTCGGAACGCGATTTTAACCAAAAAAAAC-T-GTGAGTTCACTAACGATA
* * * *
26407 GATTTCGGCTAA-A-TTTTGCAAAAATTGACCCGAAAGT-TATTTCCTC-AATTTTTAGCCACAA
257 GATTTCGACTAATATTTTTGCAAAAATCGACCAGAAA-TATATTTCCTCAAATTTTT-GCCAAAA
26468 TACTCATAAAA-ATCA-T
320 TACTCATAAAATA-CACT
* *** *
26484 ATAATTCAACGCAAAAAAGATTGAAGGGTTTTTCATGCTTTTAATATCGTTTTCCCTATTATTTT
1 -TAATTAAACGCAAAAAAGATTGAAGCACTTTTCATGCTTTTAATATCGTTTTCCATA-T-TTTT
* * ***
26549 CCGAATTAATTTCTAATTAAAATGAAACATGATTCAGATGCTTGTTTCACAAATCCTTAAATCCA
63 CCGAATTAATTTCTAATTAAAATGAAACAAGATTCAGATGCTCGTAAAACAAATCCTTAAATCCA
* * * * * *
26614 ATGTGGCTGAGATTTGGTTAAATGAATATCGATATTTCAAGGAGTTTTAGCGCCAAAAATCATGC
128 ATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAAGAGTCTTAGCACCAAAAATCATGC
* * * * *
26679 AACACTAAATCGGAG-CTCTGGAACGCGTTTTTAGCCAAAAAAAACTGTGATTTCGACTAACGTA
193 AAAACTAAACCGGAGCCTC-GGAACGCGATTTTAACCAAAAAAAACTGTGAGTTC-ACTAACG-A
* * *
26743 TACGATTTCGACTAATATTTTTGCAAAAATCGACCAGAAATATTTTTCCTCAAATTTTTTCTAAA
255 TA-GATTTCGACTAATATTTTTGCAAAAATCGACCAGAAATATATTTCCTCAAATTTTTGCCAAA
26808 ATACTCATAAAATACACT
319 ATACTCATAAAATACACT
* * * * * *
26826 TAATTAAACTCTAAAAAGATTGGAGCACTTTTCATTCTTTTAATATCGTTTTTCATATTTTTCTG
1 TAATTAAACGCAAAAAAGATTGAAGCACTTTTCATGCTTTTAATATCGTTTTCCATATTTTTCCG
* *
26891 AATTAATTTCTAATT-AAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATGCAA
66 AATTAATTTCTAATTAAAAT-GAAACAAGATTCAGATGCTCGT-AAAACAAATCCTTAAATCCAA
* * * * * *
26955 TGTGGCTGAAATATGATTTGATGAATATAGATATTTCAACGAGTC-TCGACACCAAATATCATGC
129 TGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAAGAGTCTTAG-CACCAAAAATCATGC
27019 AAAACT
193 AAAACT
27025 GAGTTGGGAT
Statistics
Matches: 441, Mismatches: 72, Indels: 40
0.80 0.13 0.07
Matches are distributed among these distances:
326 50 0.11
327 1 0.00
328 12 0.03
331 6 0.01
332 98 0.22
333 8 0.02
334 28 0.06
335 3 0.01
337 2 0.00
338 4 0.01
339 53 0.12
340 75 0.17
341 92 0.21
342 9 0.02
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (336 bp):
TAATTAAACGCAAAAAAGATTGAAGCACTTTTCATGCTTTTAATATCGTTTTCCATATTTTTCCG
AATTAATTTCTAATTAAAATGAAACAAGATTCAGATGCTCGTAAAACAAATCCTTAAATCCAATG
TGGCTGAGATTTGATTAGATGAATATAGATATTTCAAAGAGTCTTAGCACCAAAAATCATGCAAA
ACTAAACCGGAGCCTCGGAACGCGATTTTAACCAAAAAAAACTGTGAGTTCACTAACGATAGATT
TCGACTAATATTTTTGCAAAAATCGACCAGAAATATATTTCCTCAAATTTTTGCCAAAATACTCA
TAAAATACACT
Found at i:41355 original size:39 final size:39
Alignment explanation
Indices: 41301--41380 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
41291 TTATAGATTC
41301 AATTCAAACATGAAGAGCAACCATATAATTACTGATCAT
1 AATTCAAACATGAAGAGCAACCATATAATTACTGATCAT
41340 AATTCAAACATGAAGAGCAACCATATAATTACTGATCAT
1 AATTCAAACATGAAGAGCAACCATATAATTACTGATCAT
41379 AA
1 AA
41381 AATCACTTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.25
Consensus pattern (39 bp):
AATTCAAACATGAAGAGCAACCATATAATTACTGATCAT
Found at i:42487 original size:7 final size:8
Alignment explanation
Indices: 42471--42503 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
42461 TTTTTTCCCC
42471 TTTTCTTT
1 TTTTCTTT
42479 TTTTCTTT
1 TTTTCTTT
42487 TTTTC-TT
1 TTTTCTTT
42494 TTTTCTTT
1 TTTTCTTT
42502 TT
1 TT
42504 GCCTTTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTCTTT
Found at i:42489 original size:15 final size:16
Alignment explanation
Indices: 42471--42503 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
42461 TTTTTTCCCC
42471 TTTTCTTTTTTTCTTT
1 TTTTCTTTTTTTCTTT
42487 TTTTC-TTTTTTCTTT
1 TTTTCTTTTTTTCTTT
42502 TT
1 TT
42504 GCCTTTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTCTTTTTTTCTTT
Found at i:42509 original size:15 final size:15
Alignment explanation
Indices: 42477--42510 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
42467 CCCCTTTTCT
**
42477 TTTTTTCTTTTTTTC
1 TTTTTTCTTTTTGCC
42492 TTTTTTCTTTTTGCC
1 TTTTTTCTTTTTGCC
42507 TTTT
1 TTTT
42511 CAATTCTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTTTTCTTTTTGCC
Found at i:44370 original size:23 final size:23
Alignment explanation
Indices: 44344--44412 Score: 58
Period size: 23 Copynumber: 3.1 Consensus size: 23
44334 GCATATACAC
44344 ACAGCAGACAAATGGAACTTAAA
1 ACAGCAGACAAATGGAACTTAAA
* * *
44367 ACAGTAG----ATGGCA-TATACAC
1 ACAGCAGACAAATGGAACT-TA-AA
44387 ACAGCAGACAAATGGAACTTAAA
1 ACAGCAGACAAATGGAACTTAAA
44410 ACA
1 ACA
44413 ATTACTTTGC
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
18 1 0.03
19 7 0.21
20 7 0.21
23 10 0.30
24 7 0.21
25 1 0.03
ACGTcount: A:0.49, C:0.19, G:0.17, T:0.14
Consensus pattern (23 bp):
ACAGCAGACAAATGGAACTTAAA
Found at i:44387 original size:43 final size:43
Alignment explanation
Indices: 44326--44412 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
44316 TAGCTCATGA
44326 AGTAGATGGCATATACACACAGCAGACAAATGGAACTTAAAAC
1 AGTAGATGGCATATACACACAGCAGACAAATGGAACTTAAAAC
44369 AGTAGATGGCATATACACACAGCAGACAAATGGAACTTAAAAC
1 AGTAGATGGCATATACACACAGCAGACAAATGGAACTTAAAAC
44412 A
1 A
44413 ATTACTTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.16
Consensus pattern (43 bp):
AGTAGATGGCATATACACACAGCAGACAAATGGAACTTAAAAC
Found at i:52940 original size:22 final size:22
Alignment explanation
Indices: 52912--52955 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
52902 TTATCCGACT
52912 CGCATCATGCACTTAGTTTCGG
1 CGCATCATGCACTTAGTTTCGG
*
52934 CGCATCATGTACTTAGTTTCGG
1 CGCATCATGCACTTAGTTTCGG
52956 TGAATGAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (22 bp):
CGCATCATGCACTTAGTTTCGG
Found at i:53659 original size:29 final size:28
Alignment explanation
Indices: 53627--53718 Score: 67
Period size: 29 Copynumber: 3.1 Consensus size: 28
53617 AATAAGGATT
53627 TAATCTTTTAATTTGGCCAAATAAGGGCC
1 TAATCTTTTAATTT-GCCAAATAAGGGCC
* ** * *
53656 TAATATTATTGAAAATACTCAAATAAGGACC
1 TAATCTT-TT-AATTTGC-CAAATAAGGGCC
* * *
53687 CAGTCATTTAATTTAGCCAAATAAGGGCC
1 TAATCTTTTAATTT-GCCAAATAAGGGCC
53716 TAA
1 TAA
53719 CGTTATCGAA
Statistics
Matches: 44, Mismatches: 15, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
29 21 0.48
30 6 0.14
31 17 0.39
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.30
Consensus pattern (28 bp):
TAATCTTTTAATTTGCCAAATAAGGGCC
Found at i:53671 original size:60 final size:60
Alignment explanation
Indices: 53585--53743 Score: 194
Period size: 60 Copynumber: 2.6 Consensus size: 60
53575 CAAATTGCTT
* * *** * *
53585 AAATAAGGGTCTAATGTT-TGTCAAAATGCTCAAATAAGGATTTAATCTTTTAATTTGGCC
1 AAATAAGGGCCTAATGTTAT-TGAAAATGCTCAAATAAGGACCCAATCATTTAATTTAGCC
* * *
53645 AAATAAGGGCCTAATATTATTGAAAATACTCAAATAAGGACCCAGTCATTTAATTTAGCC
1 AAATAAGGGCCTAATGTTATTGAAAATGCTCAAATAAGGACCCAATCATTTAATTTAGCC
* *
53705 AAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGG
1 AAATAAGGGCCTAATGTTATTGAAAATGCTCAAATAAGG
53744 GTCTGGTGTC
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 83 0.99
61 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (60 bp):
AAATAAGGGCCTAATGTTATTGAAAATGCTCAAATAAGGACCCAATCATTTAATTTAGCC
Found at i:53928 original size:29 final size:29
Alignment explanation
Indices: 53836--53928 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
53826 TTTGGCCAAA
* *
53836 TTAAAAGATCGAGTCATTATTTGAGCATT
1 TTAAAAGATCGAGCCCTTATTTGAGCATT
* * * * **
53865 TTCGATAACGTTAG-GCCCTTATTTGGGCAAA
1 TT--A-AAAGATCGAGCCCTTATTTGAGCATT
53896 TTAAAAGATCGAGCCCTTATTTGAGCATT
1 TTAAAAGATCGAGCCCTTATTTGAGCATT
53925 TTAA
1 TTAA
53929 CAAACGTTAG
Statistics
Matches: 46, Mismatches: 14, Indels: 8
0.68 0.21 0.12
Matches are distributed among these distances:
28 5 0.11
29 21 0.46
31 15 0.33
32 5 0.11
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.35
Consensus pattern (29 bp):
TTAAAAGATCGAGCCCTTATTTGAGCATT
Found at i:53935 original size:60 final size:60
Alignment explanation
Indices: 53788--53949 Score: 231
Period size: 60 Copynumber: 2.7 Consensus size: 60
53778 CTTATGTCAG
*
53788 GCCCTTATTTGAGCATTTTCGATAACGTTA-GACCTGTATTTGGCCAAATTAAAAGATCGA
1 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCT-TATTTGGCCAAATTAAAAGATCGA
* * *
53848 GTCATTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGGCAAATTAAAAGATCGA
1 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGA
*
53908 GCCCTTATTTGAGCATTTTAAC-A-AACGTTAGGCTCTTATTTG
1 GCCCTTATTTGAGCATTTT--CGATAACGTTAGGCCCTTATTTG
53950 AATAATTAGC
Statistics
Matches: 92, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
60 86 0.93
61 5 0.05
62 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGA
Found at i:59637 original size:25 final size:25
Alignment explanation
Indices: 59603--59652 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
59593 GGTATTGTAG
59603 AAATTGAATTTTTCTAAATAAAATA
1 AAATTGAATTTTTCTAAATAAAATA
59628 AAATTGAATTTTTCTAAATAAAATA
1 AAATTGAATTTTTCTAAATAAAATA
59653 TTTTAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (25 bp):
AAATTGAATTTTTCTAAATAAAATA
Found at i:59875 original size:10 final size:10
Alignment explanation
Indices: 59851--59887 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
59841 TTCGTACTTT
*
59851 TATATATAG-
1 TATAGATAGA
59860 TATAGATAGA
1 TATAGATAGA
59870 TATAGATAGA
1 TATAGATAGA
59880 TATAGATA
1 TATAGATA
59888 TATTTCTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (10 bp):
TATAGATAGA
Found at i:61922 original size:29 final size:30
Alignment explanation
Indices: 61864--61924 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
61854 GTTCTAATTA
* *
61864 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATTATATT
*
61894 ATGTATAAATAT-AATTATTTAATTATATT
1 ATGTATAAATATAAATTATTCAATTATATT
61923 AT
1 AT
61925 ACTTATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATTATATT
Found at i:70262 original size:48 final size:48
Alignment explanation
Indices: 70191--70289 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
70181 TTCCTTTCTT
70191 TCACTAAAACAATTTGACAAATCATATTACTCACAAGTTATCACTACG
1 TCACTAAAACAATTTGACAAATCATATTACTCACAAGTTATCACTACG
70239 TCACTAAAACAATTTGACAAATCATATTACTCACAAGTTATCACTACG
1 TCACTAAAACAATTTGACAAATCATATTACTCACAAGTTATCACTACG
70287 TCA
1 TCA
70290 TATATGGCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.41, C:0.23, G:0.06, T:0.29
Consensus pattern (48 bp):
TCACTAAAACAATTTGACAAATCATATTACTCACAAGTTATCACTACG
Found at i:83495 original size:98 final size:98
Alignment explanation
Indices: 83307--83483 Score: 309
Period size: 98 Copynumber: 1.8 Consensus size: 98
83297 CTTTAGGATT
83307 ATTTATTTATTAGCTGCAACTTGCAAGTCTGCATCTGCAATAGTCATTGTTAAATATTAATAGTA
1 ATTTATTTATTAGCTGCAACTTGCAAGTCTGCATCTGCAATAGTCATTGTTAAATATTAATAGTA
** *
83372 CTAAAATATGTACTACACTGGAGTTTAGATTGA
66 CTAAAATATACACTACACGGGAGTTTAGATTGA
* *
83405 ATTTATTTATTAGCTGCAACTTGCAAGTCTGCATTTGCAATAGTCATTGTTTAATATTAATAGTA
1 ATTTATTTATTAGCTGCAACTTGCAAGTCTGCATCTGCAATAGTCATTGTTAAATATTAATAGTA
83470 CTAAAATATACACT
66 CTAAAATATACACT
83484 TAGGGTTAGT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 75 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (98 bp):
ATTTATTTATTAGCTGCAACTTGCAAGTCTGCATCTGCAATAGTCATTGTTAAATATTAATAGTA
CTAAAATATACACTACACGGGAGTTTAGATTGA
Found at i:84724 original size:21 final size:23
Alignment explanation
Indices: 84681--84724 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
84671 AAATAAGTAC
*
84681 AAAAAGAAACCATATCTTTGTAT
1 AAAAAGAAACCATATCATTGTAT
84704 AAAAA-AAACCATAT-ATTGTAT
1 AAAAAGAAACCATATCATTGTAT
84725 TTTCTGATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 9 0.45
23 5 0.25
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (23 bp):
AAAAAGAAACCATATCATTGTAT
Found at i:88984 original size:31 final size:30
Alignment explanation
Indices: 88943--89059 Score: 123
Period size: 31 Copynumber: 3.8 Consensus size: 30
88933 AAAATTGTTC
*
88943 CTGGTGCTCTGTTTCTCTTGTTAATTTTTAT
1 CTGGTACTCTGTTTCTCTTGTTAATTTTT-T
**
88974 CTGGTACTCTGTTTCTTACTCT-TT--TTTTCC
1 CTGGTACTCTGTTTC-T-CT-TGTTAATTTTTT
*
89004 CTGGAACTCTGTTTCTCTTGTTAACTTTTTT
1 CTGGTACTCTGTTTCTCTTGTTAA-TTTTTT
*
89035 CTGGTACTCTGTTTTTCTTGTTAAT
1 CTGGTACTCTGTTTCTCTTGTTAAT
89060 AATAATGCTA
Statistics
Matches: 71, Mismatches: 8, Indels: 15
0.76 0.09 0.16
Matches are distributed among these distances:
27 1 0.01
28 4 0.06
29 1 0.01
30 15 0.21
31 44 0.62
32 1 0.01
33 4 0.06
34 1 0.01
ACGTcount: A:0.10, C:0.20, G:0.14, T:0.56
Consensus pattern (30 bp):
CTGGTACTCTGTTTCTCTTGTTAATTTTTT
Found at i:100777 original size:18 final size:18
Alignment explanation
Indices: 100754--100791 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
100744 AAATTAATTC
100754 TTGGTCTACAAAGTCATT
1 TTGGTCTACAAAGTCATT
100772 TTGGTCTACAAAGTCATT
1 TTGGTCTACAAAGTCATT
100790 TT
1 TT
100792 TAGAGGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (18 bp):
TTGGTCTACAAAGTCATT
Found at i:102152 original size:47 final size:47
Alignment explanation
Indices: 102099--102196 Score: 169
Period size: 47 Copynumber: 2.1 Consensus size: 47
102089 CAAACTCTCA
*
102099 ATCTAATCAACCCAACATTGGTGATTCTCTCACAACAACATAAAGCT
1 ATCTAATCAACCCAACATGGGTGATTCTCTCACAACAACATAAAGCT
* *
102146 ATCTAATCAACCCAACATGGGTGATTGTCTCACAACAACATAAAGTT
1 ATCTAATCAACCCAACATGGGTGATTCTCTCACAACAACATAAAGCT
102193 ATCT
1 ATCT
102197 TAGCTTTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.27
Consensus pattern (47 bp):
ATCTAATCAACCCAACATGGGTGATTCTCTCACAACAACATAAAGCT
Found at i:122076 original size:5 final size:5
Alignment explanation
Indices: 122041--122086 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
122031 TGGACCTGGA
* **
122041 AAAAA AAAAC -AAAC AAAA- AAAAC TGAAC AAAAC AAAAC AAAAC AAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAA
122087 CTAGAGTTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
4 8 0.24
5 26 0.76
ACGTcount: A:0.80, C:0.15, G:0.02, T:0.02
Consensus pattern (5 bp):
AAAAC
Found at i:132231 original size:6 final size:7
Alignment explanation
Indices: 132205--132230 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
132195 TCAACTTCAA
132205 AAAAAAT
1 AAAAAAT
132212 AAAAAAT
1 AAAAAAT
132219 AAAAAAT
1 AAAAAAT
132226 AAAAA
1 AAAAA
132231 TTCACAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:153833 original size:25 final size:26
Alignment explanation
Indices: 153796--153847 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
153786 TTATGATTTC
*
153796 TTTAATTCATTTTGATTATCAATCATG
1 TTTAATT-ATTTTGATAATCAATCATG
**
153823 TTTAATT-TTTTTCTAATCAATCATG
1 TTTAATTATTTTGATAATCAATCATG
153848 AATTATTGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 15 0.68
27 7 0.32
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.54
Consensus pattern (26 bp):
TTTAATTATTTTGATAATCAATCATG
Found at i:154661 original size:25 final size:25
Alignment explanation
Indices: 154631--154699 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
154621 TGCAGGAAGG
*
154631 GGCGCAGGGCCTGATAGAAGAAAGT
1 GGCGCAGGGCCTGAGAGAAGAAAGT
*
154656 GGCGCAGGGCCTGAGAGAGGAAAGT
1 GGCGCAGGGCCTGAGAGAAGAAAGT
154681 GGCGCAGGGCCTGAGAGAA
1 GGCGCAGGGCCTGAGAGAA
154700 AATAAGCACG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.29, C:0.17, G:0.45, T:0.09
Consensus pattern (25 bp):
GGCGCAGGGCCTGAGAGAAGAAAGT
Found at i:157540 original size:22 final size:23
Alignment explanation
Indices: 157501--157543 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
157491 AATCCTAATC
157501 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
157524 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
157544 ACTCCTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:160458 original size:30 final size:30
Alignment explanation
Indices: 160422--160517 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
160412 CACAAACAAA
160422 TCCTTCATCAAA-AACA-AAATCAGAATCTTC
1 TCCTTCA-CAAACAA-AGAAATCAGAATCTTC
*
160452 TCCTTCACAAACAAAGAGATCAGAATCTTC
1 TCCTTCACAAACAAAGAAATCAGAATCTTC
* **
160482 TCCTTCACAATCAAAGAGCTCAGAATCTTC
1 TCCTTCACAAACAAAGAAATCAGAATCTTC
*
160512 TTCTTC
1 TCCTTC
160518 CTCCTCGTCA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
29 5 0.08
30 55 0.92
ACGTcount: A:0.36, C:0.28, G:0.07, T:0.28
Consensus pattern (30 bp):
TCCTTCACAAACAAAGAAATCAGAATCTTC
Found at i:172660 original size:28 final size:28
Alignment explanation
Indices: 172609--172682 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 28
172599 GCTAAATACT
*
172609 CAAAAAAATCCCTTATGTTTTTTTTTTGGGAA
1 CAAAATAATCCCTTATG---TTTTTTT-GGAA
*
172641 -AAAATAATCTCTTATGTTTTTTTGGAA
1 CAAAATAATCCCTTATGTTTTTTTGGAA
*
172668 CAAATTAATCCCTTA
1 CAAAATAATCCCTTA
172683 CATCTCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
27 4 0.11
28 19 0.51
31 14 0.38
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (28 bp):
CAAAATAATCCCTTATGTTTTTTTGGAA
Found at i:176129 original size:653 final size:629
Alignment explanation
Indices: 174529--177235 Score: 1948
Period size: 652 Copynumber: 4.2 Consensus size: 629
174519 GTCATTACAG
* * ** * * * * * * * * *
174529 TTTTTGGCTAAAAACGAGTTCCGGGGACCTGGCTCAATTTTGTATGATTTTTGGCTCCGAGACTA
1 TTTTTTGCTAAAAACGCGTTCCGAAGCCCCGACTCAGTTTTGCATGATTTTTTGCGCCAAGACTC
* *
174594 CTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTATTTTTACG
66 CTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACG
* * * *** * *
174659 AGCATCTGAATTTTGTTTCGATTTAATTAGAAAATAATTTTAAAAAATA-GGAAAACAATATTAA
131 AGCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAACGATATTAA
** * * ** * * ** **
174723 AAATGTCAAAATCCCTAAAATCTTTTTGGCGTTGAATTATATATTTTTTATGTTTATTTTATTTA
196 AAGCGTAAAAAGCCCTTCAATCTTTTTGTCATTGAATTATATATTTTTTATGAGTATTTTA-CAA
* * * * * *
174788 AAAATTAAGGAAATATCTTTCGGGTCAATTTTTACAAAATTTTAGTCGAAATTGTGTAATAACCA
260 AAAATTGAGAAAATATCTTTCCGGTCAATTTTTGCAAAATTTTAG-C------GT-CAA-AATCA
* ** * * * * * * *
174853 TCACAGTTTTTGGCTAAAAAAACGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTATGGCGTCA
316 T-A-GGTTTTT-GCTAAAAACGCG-TTC-GAGCCCCGGTTCAGTTTTGAATGATTTTTTGCGCCG
* * * *
174918 AAACTCCTT-AAGATAT-TCATATTCATCTAATCAAATCTCAACCACATTGGATTTAAGAATTTG
376 AGACTCCTTGAA-ATATCT-ATATTCATCTAACCAAATC-CTAGC-C-----A-TT--G---TT-
* * * * * * * *
174981 TCTCTACGAGTATCTCAATCTTGTTTCGATTTAATTGGAAATAAATTC---ATAAAAATATGAAA
425 T-T-TACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATAGGAAA
* * * * * ** *
175043 AACGATATTAAAAGAGTGAAAGGTCCTCCAATCTTTTTGAAATTAAATTATATA--TATTATGAG
488 AACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGACGTTAAATTATATATTTTTTATGAG
* * ** * * * *
175106 TCTTTTTTCCAAAAATTGA-GAAAAAA-AT-GGGTCATTTTTTGCAAAATTTTAGCCAAAATCGT
553 TATTGTGGCTAAAAATTGAGGAAAAAATTTCGGGTCAATTTTTGCAAAA-TTTAGCCGAAATC-T
*
175168 GT-ACGTATCACG--G
616 GTAAC--ATCACGTTT
* * * * * ** * *
175181 GTTTTGGCTAAAAGCGAGTTTCGGGGCCCCTG-CTCAGTTTTGCATGATTTTTTG-GCCTGATAC
1 TTTTTTGCTAAAAACGCGTTCCGAAGCCCC-GACTCAGTTTTGCATGATTTTTTGCGCC-AAGAC
* * *
175244 TCATTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGGATTTGTTTTTA
64 TCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTA
* * * * * * *
175309 CGGGAATATGAATCTTGTTTCGATTTAATTAGAAATTATTTTAGAAAAAAATACGACAAACGATA
129 CGAGCATATGAATCTTGTTTCGATTTAATTAGAAATTA-ATTCG-GAAAAATATGAAAAACGATA
* * *
175374 TAAAAAGCG-AGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTAT
192 TTAAAAGCGTA-AAAAGCCCTTCAATCTTTTTGTCATTGAATTATATATTTTTTATGAGTATT-T
** * * * *
175438 GGCTAAAAATTGAGGAAATACCTTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAATCGTATAAT
255 TACAAAAAATTGAGAAAATATCTTTCCGGTCAATTTTTGCAAAATTTTAGC-G---TC----AA-
* * * *
175503 AATCATCACGGTTTTTAACTAAAAACGCGTT-GAGACCCGGTTCAATTTTGAATGATTTTTTGCA
311 AATCAT-A-GGTTTTT-GCTAAAAACGCGTTCGAGCCCCGGTTCAGTTTTGAATGATTTTTTGCG
175567 CCGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCTAGCCATTGTTTTTACAAGCATCT
373 CCGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCTAGCCATTGTTTTTACAAGCATCT
* * *
175632 GAATCATGTTTCGTTTTAATTAGAAATTAATTCGGAAAAAAAAATTAGGATAAACGGTATTAGAA
438 GAATCATGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAAAA-TAGGAAAAACGATATTAGAA
* * * *
175697 GCGTGAAAAACCCTTCAATATTTTTGTCGTTTAATTATATATTTTTTATGAGTATTGTGGCTAAA
501 GCGTGAAAAGCCCTTCAATCTTTTTGACGTTAAATTATATATTTTTTATGAGTATTGTGGCTAAA
175762 AATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATATTAGCCGAAATCATGTAACATCACGG
566 AATTGAGGAAAAA-ATTTCGGGTCAATTTTTGCAAAAT-TTAGCCGAAATC-TGTAACATCAC-G
175827 TTTTTTT
627 ----TTT
** * * *
175834 TTTTGTTGCTAAAAACGCGTTCCGAAGCCCCGGGTCAGTTTTGCATGATTTTTAGTGTCAAGACT
1 TTTT-TTGCTAAAAACGCGTTCCGAAGCCCCGACTCAGTTTTGCATGATTTTTTGCGCCAAGACT
** * * * *
175899 CCTTGAAATATCTATATTCATCTAATCAAATCTCAATCACATAGGATTT-ATGAATTGTTTTTAC
65 CCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTAC
* * *
175963 GAGCATCTAAATCTTATTTCGATTTAATTAGAAATTAATTCGGAAAAAGTATGAAAAACGATATT
130 GAGCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAA-TATGAAAAACGATATT
* * *
176028 AAAAGCGTAAAAACCCCTTCAATATTTTTGTCATTGAATTATATATTTTTTTGTGAGTATTTTAC
194 AAAAGCGTAAAAAGCCCTTCAATCTTTTTGTCATTGAATTATATA-TTTTTTATGAGTATTTTA-
*
176093 CAAAAAATTGAGAAAATATCTTTCCGGTCAATTTTTGCAAAATTTTA--GTCAAAATC-GA-GTT
257 CAAAAAATTGAGAAAATATCTTTCCGGTCAATTTTTGCAAAATTTTAGCGTCAAAATCATAGGTT
* * * * * ** *
176154 TTTGGCTAAAAACGCGTTCTAGGGCCCCGAG-TCAGTTTTGTATTATATTTGGCGCTAAGACTTC
322 TTT-GCTAAAAACGCGTTC--GAGCCCCG-GTTCAGTTTTGAATGATTTTTTGCGCCGAGACTCC
* * * * * * ***
176218 TAGAGATATCCATATTCATCTAATCAAATCTCGACCACATTGCATTTAAGGATTTGTTTTTTTTA
383 TTGAAATATCTATATTCATCTAACCAAA--T----C-C-TAGC-------CA-TTGTTTTTACAA
* * * *
176283 GCAT-TCGAATCTTGTTTCGATTTAATTAGAAATTAATTC--ATAAAAAATATGAAAAACAATAT
432 GCATCT-GAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATAGGAAAAACGATAT
* * * * * * * * **
176345 GAAAAGCGTGAAAAGTCCTCCAATCTTTTTGACGTTAAATTATATATATTTCATGATTATTTTAT
496 TAGAAGCGTGAAAAGCCCTTCAATCTTTTTGACGTTAAATTATATATTTTTTATGAGTATTGTGG
* * * * *
176410 CCAAAAATTGAGG--AAAATTTCTGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTAACTAACC
561 CTAAAAATTGAGGAAAAAATTTCGGGTCAATTTTTGCAAAA-TTTAGCCGAAATC-T--GTAA-C
*
176473 ATCACG--A
621 ATCACGTTT
* * * * * *
176480 TTTTTTGCTAAAAATGCGTTTCGAGGCCCCGACTCAGTTTTCCATGATTTTTTGCGTCGAGACTC
1 TTTTTTGCTAAAAACGCGTTCCGAAGCCCCGACTCAGTTTTGCATGATTTTTTGCGCCAAGACTC
176545 CTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACG
66 CTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACG
* * *
176610 AGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAGAAACGATATTAA
131 AGCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAACGATATTAA
*** ** * * * * *
176675 AAGCGTGTTAAGTGCTCCAATCTTTTTGT-ATTTAAAT-TATATGTTTTATGAGTATTTTAGACA
196 AAGCGTAAAAAGCCCTTCAATCTTTTTGTCATTGAATTATATATTTTTTATGAGTATTTTACA-A
* * ** * * * *
176738 AAAATTAAGGAAAA-ATATTTATGATCAAGTTTTGCAAAATATTAGC--CAAAATCAT-GATTTT
260 AAAATTGA-GAAAATATCTTTCCGGTCAATTTTTGCAAAATTTTAGCGTCAAAATCATAGGTTTT
* * * * * * * *
176799 TGGTTAAAACGTGTTCCGAGGCCCCGGTTCAGTGTTGCATGATTTTTTACGCCGAAACTCCTTAA
324 TGCTAAAAACGCGTT-CGA-GCCCCGGTTCAGTTTTGAATGATTTTTTGCGCCGAGACTCCTTGA
176864 AATATCTATATTCATCTAACCAAAT-CTCAGCCATATTGGATTTAAGAATTTGTAAAACAAGCAT
387 AATATCTATATTCATCTAACCAAATCCT-AGCC--ATT-G---T-----TTT-T---ACAAGCAT
* * *
176928 CTGAATCATGTTTCGATTTAATTAGAAATTAATTCGG-AAAATAATAGGAAAAACGACAATAGAA
436 CTGAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATAGGAAAAACGATATTAGAA
* * * * * *
176992 GCATGAAAAGCCCTTCAATCTTTGTGGCGTTGAATTATTTAATTTTTATGAGTATTGTGGCTAAA
501 GCGTGAAAAGCCCTTCAATCTTTTTGACGTTAAATTATATATTTTTTATGAGTATTGTGGCTAAA
* * *
177057 AATTGAGGAAATAACTTTCGAGTCAATTTTTGCAAAATTCTAGCCGAAATTGTGTGATAATCATC
566 AATTGAGGAAA-AAATTTCGGGTCAATTTTTGCAAAATT-TAGCCGAAA---TCTG-TAA-CATC
177122 ACAG-TT
624 AC-GTTT
* * * * *
177128 TTTTTTGCTAAAAACGCATTCCGGAGCCCCGACTAAGTTTTGTATGATTTTTGGCGCCAAGACTC
1 TTTTTTGCTAAAAACGCGTTCCGAAGCCCCGACTCAGTTTTGCATGATTTTTTGCGCCAAGACTC
* * * * *
177193 TTTGAGATATCCATATTCATCTAATCAAATCCCAGCTACATTG
66 CTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTG
177236 TGTCATGGTC
Statistics
Matches: 1643, Mismatches: 305, Indels: 218
0.76 0.14 0.10
Matches are distributed among these distances:
628 2 0.00
629 2 0.00
632 1 0.00
633 1 0.00
634 3 0.00
636 37 0.02
637 4 0.00
638 21 0.01
639 2 0.00
640 8 0.00
641 141 0.09
642 202 0.12
643 40 0.02
644 17 0.01
645 165 0.10
646 77 0.05
647 37 0.02
648 96 0.06
649 5 0.00
650 35 0.02
651 14 0.01
652 257 0.16
653 193 0.12
654 104 0.06
655 132 0.08
656 3 0.00
657 44 0.03
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (629 bp):
TTTTTTGCTAAAAACGCGTTCCGAAGCCCCGACTCAGTTTTGCATGATTTTTTGCGCCAAGACTC
CTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACG
AGCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAACGATATTAA
AAGCGTAAAAAGCCCTTCAATCTTTTTGTCATTGAATTATATATTTTTTATGAGTATTTTACAAA
AAATTGAGAAAATATCTTTCCGGTCAATTTTTGCAAAATTTTAGCGTCAAAATCATAGGTTTTTG
CTAAAAACGCGTTCGAGCCCCGGTTCAGTTTTGAATGATTTTTTGCGCCGAGACTCCTTGAAATA
TCTATATTCATCTAACCAAATCCTAGCCATTGTTTTTACAAGCATCTGAATCATGTTTCGATTTA
ATTAGAAATTAATTCGGAAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATC
TTTTTGACGTTAAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAAATTTCGG
GTCAATTTTTGCAAAATTTAGCCGAAATCTGTAACATCACGTTT
Found at i:179104 original size:17 final size:17
Alignment explanation
Indices: 179078--179110 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
179068 CCCTTTGTAC
179078 AGGATCTATTTTAAAAG
1 AGGATCTATTTTAAAAG
*
179095 AGGATTTATTTTAAAA
1 AGGATCTATTTTAAAA
179111 TGGGGCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.39
Consensus pattern (17 bp):
AGGATCTATTTTAAAAG
Found at i:179153 original size:85 final size:83
Alignment explanation
Indices: 179010--179172 Score: 272
Period size: 85 Copynumber: 1.9 Consensus size: 83
179000 CCCTTTGTAC
179010 AGGATTTATTTTAAAAGGGGGCTAAACCTTAGGCTAATATCTCAAAATTGGAGACTTACCCTTTG
1 AGGATTTATTTTAAAAGGGGGCTAAACCTTAGGCTAATATCTCAAAATTGGAGACTTACCC--TG
179075 TACAGGATCTATTTTAAAAG
64 TACAGGATCTATTTTAAAAG
* * *
179095 AGGATTTATTTTAAAATGGGGCTAAACCTTAGGCTAATATCTCAAATTTGGAGACTTACCCTGTG
1 AGGATTTATTTTAAAAGGGGGCTAAACCTTAGGCTAATATCTCAAAATTGGAGACTTACCCTGTA
*
179160 CATGATCTATTTT
66 CAGGATCTATTTT
179173 TAAACGGGCA
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
83 15 0.20
85 59 0.80
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (83 bp):
AGGATTTATTTTAAAAGGGGGCTAAACCTTAGGCTAATATCTCAAAATTGGAGACTTACCCTGTA
CAGGATCTATTTTAAAAG
Found at i:179442 original size:113 final size:113
Alignment explanation
Indices: 179244--179469 Score: 452
Period size: 113 Copynumber: 2.0 Consensus size: 113
179234 ATTCTAATGG
179244 TTAGCCCCATGGATGACGTGGTGGGTCCGTCCCACCTAATAATTTCTCATCCATCAAATATCTAA
1 TTAGCCCCATGGATGACGTGGTGGGTCCGTCCCACCTAATAATTTCTCATCCATCAAATATCTAA
179309 ATGAGAATCCAACCCATCTTAAATAACCTACTTAACAAACTATCAATC
66 ATGAGAATCCAACCCATCTTAAATAACCTACTTAACAAACTATCAATC
179357 TTAGCCCCATGGATGACGTGGTGGGTCCGTCCCACCTAATAATTTCTCATCCATCAAATATCTAA
1 TTAGCCCCATGGATGACGTGGTGGGTCCGTCCCACCTAATAATTTCTCATCCATCAAATATCTAA
179422 ATGAGAATCCAACCCATCTTAAATAACCTACTTAACAAACTATCAATC
66 ATGAGAATCCAACCCATCTTAAATAACCTACTTAACAAACTATCAATC
179470 AAACAAACAA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 113 1.00
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (113 bp):
TTAGCCCCATGGATGACGTGGTGGGTCCGTCCCACCTAATAATTTCTCATCCATCAAATATCTAA
ATGAGAATCCAACCCATCTTAAATAACCTACTTAACAAACTATCAATC
Found at i:181918 original size:20 final size:21
Alignment explanation
Indices: 181893--181932 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
181883 CTTCTGAGAC
181893 AAAATAATT-CTTACGTTTCA
1 AAAATAATTCCTTACGTTTCA
181913 AAAATAATTCCTTACGTTTC
1 AAAATAATTCCTTACGTTTC
181933 CTTAAGTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (21 bp):
AAAATAATTCCTTACGTTTCA
Found at i:183598 original size:21 final size:21
Alignment explanation
Indices: 183555--183602 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
183545 GCTGTTTATT
*
183555 ATCTCATCTGTACAGTACCTA
1 ATCTCATCTGTACAATACCTA
* **
183576 ATCTGATCTGTACAATATTTA
1 ATCTCATCTGTACAATACCTA
183597 ATCTCA
1 ATCTCA
183603 CAATCTCAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (21 bp):
ATCTCATCTGTACAATACCTA
Found at i:192493 original size:2 final size:2
Alignment explanation
Indices: 192486--192519 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
192476 CTAGTTGGCA
192486 AT AT AT AT 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 AT AT AT AT
192520 GATGGTAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:193648 original size:30 final size:30
Alignment explanation
Indices: 193614--193675 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
193604 ATTTTTATCT
* *
193614 TGACTTTTCTCTTATACCCTCTAATTTTAA
1 TGACTTTTCTCTTATACCCTCAAATTTCAA
193644 TGACTTTTCTCTTATACCCTCAAATTTCAA
1 TGACTTTTCTCTTATACCCTCAAATTTCAA
193674 TG
1 TG
193676 GCTTATTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.47
Consensus pattern (30 bp):
TGACTTTTCTCTTATACCCTCAAATTTCAA
Found at i:195697 original size:5 final size:5
Alignment explanation
Indices: 195634--195696 Score: 119
Period size: 5 Copynumber: 12.8 Consensus size: 5
195624 GTATTAAGAT
195634 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
195684 TTTTA TTTT- TTTT
1 TTTTA TTTTA TTTT
195697 TGCTTTGATG
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.07
5 54 0.93
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:202463 original size:18 final size:18
Alignment explanation
Indices: 202440--202493 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
202430 AAAATTTTAT
202440 TTTTTCCCCTACTCTTTC
1 TTTTTCCCCTACTCTTTC
202458 TTTTTCCCCTACTCTTTC
1 TTTTTCCCCTACTCTTTC
**
202476 CCTTTCCCCTACTCTTTC
1 TTTTTCCCCTACTCTTTC
202494 AACTCTGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.06, C:0.43, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTTTCCCCTACTCTTTC
Done.