Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015361.1 Corchorus olitorius cultivar O-4 contig15394, 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: 87666
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:493 original size:53 final size:53
Alignment explanation
Indices: 413--518 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
403 GATATAGTTG
413 TGTCTATGTCCAGGACACCATCCTCATCCAAGGGACTGCCAGTTTTACCAACT
1 TGTCTATGTCCAGGACACCATCCTCATCCAAGGGACTGCCAGTTTTACCAACT
466 TGTCTATGTCCAGGACACCATCCTCATCCAAGGGACTGCCAGTTTTACCAACT
1 TGTCTATGTCCAGGACACCATCCTCATCCAAGGGACTGCCAGTTTTACCAACT
519 CCTGCATGCG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (53 bp):
TGTCTATGTCCAGGACACCATCCTCATCCAAGGGACTGCCAGTTTTACCAACT
Found at i:630 original size:18 final size:18
Alignment explanation
Indices: 607--644 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
597 CAAATGTTGA
*
607 ATAAATTTTCTACTCTGC
1 ATAAATTTTCTACTCCGC
625 ATAAATTTTCTACTCCGC
1 ATAAATTTTCTACTCCGC
643 AT
1 AT
645 TTGTCTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.42
Consensus pattern (18 bp):
ATAAATTTTCTACTCCGC
Found at i:657 original size:22 final size:22
Alignment explanation
Indices: 629--677 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
619 CTCTGCATAA
629 ATTTTCTACTCCGCATTTGTCT
1 ATTTTCTACTCCGCATTTGTCT
651 ATTTTCTACTCCGCATTTGTCT
1 ATTTTCTACTCCGCATTTGTCT
673 ATTTT
1 ATTTT
678 GGCCTTGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.14, C:0.24, G:0.08, T:0.53
Consensus pattern (22 bp):
ATTTTCTACTCCGCATTTGTCT
Found at i:877 original size:72 final size:73
Alignment explanation
Indices: 760--982 Score: 358
Period size: 72 Copynumber: 3.0 Consensus size: 73
750 GTCTGGCAGA
760 CGGGCCACATGTCATCAACATTGACATTGAAGATCCTGTTTGCTTGAAACTCTTGCAAACAAATT
1 CGGGCCACATGTCATCAACATTGACATTGAAGATCCTGTTTGCTTGAAACTCTTGCAAACAAATT
825 CCAAGGT-
66 CCAAGGTC
*
832 CGGGCCACATGTCATCAACATTGACATTGAAGATCTTGTTTGCTTGAAACTCTTGCAAACAAATT
1 CGGGCCACATGTCATCAACATTGACATTGAAGATCCTGTTTGCTTGAAACTCTTGCAAACAAATT
897 CCAAGGTCCGGC
66 CCAAGGT----C
909 AGACGGGCCACATGTCATCAACATTGACATTGAAGATCCTGTTTGCTTGAAACTCTTGCAAACAA
1 ---CGGGCCACATGTCATCAACATTGACATTGAAGATCCTGTTTGCTTGAAACTCTTGCAAACAA
*
974 ATTTCAAGG
63 ATTCCAAGG
983 CCCACGCAGC
Statistics
Matches: 140, Mismatches: 3, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
72 71 0.51
80 69 0.49
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (73 bp):
CGGGCCACATGTCATCAACATTGACATTGAAGATCCTGTTTGCTTGAAACTCTTGCAAACAAATT
CCAAGGTC
Found at i:933 original size:80 final size:80
Alignment explanation
Indices: 832--982 Score: 284
Period size: 80 Copynumber: 1.9 Consensus size: 80
822 ATTCCAAGGT
*
832 CGGGCCACATGTCATCAACATTGACATTGAAGATCTTGTTTGCTTGAAACTCTTGCAAACAAATT
1 CGGGCCACATGTCATCAACATTGACATTGAAGATCCTGTTTGCTTGAAACTCTTGCAAACAAATT
897 CCAAGGTCCGGCAGA
66 CCAAGGTCCGGCAGA
912 CGGGCCACATGTCATCAACATTGACATTGAAGATCCTGTTTGCTTGAAACTCTTGCAAACAAATT
1 CGGGCCACATGTCATCAACATTGACATTGAAGATCCTGTTTGCTTGAAACTCTTGCAAACAAATT
*
977 TCAAGG
66 CCAAGG
983 CCCACGCAGC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 69 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (80 bp):
CGGGCCACATGTCATCAACATTGACATTGAAGATCCTGTTTGCTTGAAACTCTTGCAAACAAATT
CCAAGGTCCGGCAGA
Found at i:6263 original size:18 final size:19
Alignment explanation
Indices: 6237--6276 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
6227 CCCTCTGGCG
*
6237 AAATAAAAAAA-GAAAAAA
1 AAATAAAAAAACCAAAAAA
*
6255 AAATTAAAAAACCAAAAAA
1 AAATAAAAAAACCAAAAAA
6274 AAA
1 AAA
6277 AAGAAACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.85, C:0.05, G:0.03, T:0.07
Consensus pattern (19 bp):
AAATAAAAAAACCAAAAAA
Found at i:6264 original size:19 final size:19
Alignment explanation
Indices: 6240--6276 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6230 TCTGGCGAAA
*
6240 TAAAAAAAGAAAAAAAAAT
1 TAAAAAAACAAAAAAAAAT
*
6259 TAAAAAACCAAAAAAAAA
1 TAAAAAAACAAAAAAAAA
6277 AAGAAACAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.84, C:0.05, G:0.03, T:0.08
Consensus pattern (19 bp):
TAAAAAAACAAAAAAAAAT
Found at i:8384 original size:13 final size:13
Alignment explanation
Indices: 8366--8390 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8356 TAGTACCTTT
8366 AAAAAAAAGGGAA
1 AAAAAAAAGGGAA
8379 AAAAAAAAGGGA
1 AAAAAAAAGGGA
8391 CTAAAGTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGGGAA
Found at i:14093 original size:23 final size:23
Alignment explanation
Indices: 14062--14131 Score: 72
Period size: 26 Copynumber: 2.9 Consensus size: 23
14052 GTAACATCTC
*
14062 AACTTGTAAATTTCTTGGAAAAA
1 AACTAGTAAATTTCTTGGAAAAA
14085 AACTAGTAAATTTC--GGCCAAAAAAAA
1 AACTAGTAAATTTCTTGG-----AAAAA
14111 AACTAGTAAATTTCTTGGAAA
1 AACTAGTAAATTTCTTGGAAA
14132 TGCCAATGCA
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
21 2 0.05
23 16 0.41
26 19 0.49
28 2 0.05
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (23 bp):
AACTAGTAAATTTCTTGGAAAAA
Found at i:14607 original size:2 final size:2
Alignment explanation
Indices: 14600--14629 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
14590 CATATTCTGC
14600 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
14630 TTCTAATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15138 original size:6 final size:6
Alignment explanation
Indices: 15123--15164 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
15113 TTTCTGGCCA
* * *
15123 AATA-T AATACT AATACT ACTACT AATAAT AATAAT AATACT A
1 AATACT AATACT AATACT AATACT AATACT AATACT AATACT A
15165 TATTTAAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (6 bp):
AATACT
Found at i:22192 original size:13 final size:14
Alignment explanation
Indices: 22174--22208 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
22164 TAGAGATCTA
22174 GAATTGTGA-TTGT
1 GAATTGTGATTTGT
22187 GAATTGTGATTTGT
1 GAATTGTGATTTGT
*
22201 GATTTGTG
1 GAATTGTG
22209 TTACATAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (14 bp):
GAATTGTGATTTGT
Found at i:23156 original size:50 final size:50
Alignment explanation
Indices: 23028--23163 Score: 200
Period size: 50 Copynumber: 2.7 Consensus size: 50
23018 GTTCTCGGCC
* * * * *
23028 GTAAGATCCCATGACGGGTCGTAAGACCAACGAGCATTGATCGAACGACC
1 GTAAGACCCCATGACGGGCCGTAAGACCGATGAGCATTGATCGAACGACA
* * *
23078 GTAAGACCCCATGACGGGCCGTAAGACCGATAAGCATTGATCGAATGGCA
1 GTAAGACCCCATGACGGGCCGTAAGACCGATGAGCATTGATCGAACGACA
23128 GTAAGACCCCATGACGGGCCGTAAGACCGATGAGCA
1 GTAAGACCCCATGACGGGCCGTAAGACCGATGAGCA
23164 ATCGGCACGA
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 77 1.00
ACGTcount: A:0.32, C:0.26, G:0.28, T:0.15
Consensus pattern (50 bp):
GTAAGACCCCATGACGGGCCGTAAGACCGATGAGCATTGATCGAACGACA
Found at i:23338 original size:32 final size:32
Alignment explanation
Indices: 23309--23444 Score: 175
Period size: 32 Copynumber: 4.2 Consensus size: 32
23299 TAAAAATAGT
* **
23309 GGCTTTTTGTTCTGTAGACGCTACTAAATAAG
1 GGCTTTTTGTTCTTTAGACGCCGCTAAATAAG
*
23341 GGCGTTTTGTTCTTTAGACGCCGCTAAATAAG
1 GGCTTTTTGTTCTTTAGACGCCGCTAAATAAG
* *
23373 GGCATTTTGTTTTTTAGACGCCGCTAAATAAG
1 GGCTTTTTGTTCTTTAGACGCCGCTAAATAAG
* *
23405 GGCGTTTTT-TTCTATAGACGCTGCTAAATAAG
1 GGC-TTTTTGTTCTTTAGACGCCGCTAAATAAG
*
23437 GGCGTTTT
1 GGCTTTTT
23445 CTTTTCACAC
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
31 4 0.04
32 84 0.91
33 4 0.04
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.38
Consensus pattern (32 bp):
GGCTTTTTGTTCTTTAGACGCCGCTAAATAAG
Found at i:23403 original size:64 final size:64
Alignment explanation
Indices: 23313--23449 Score: 193
Period size: 64 Copynumber: 2.1 Consensus size: 64
23303 AATAGTGGCT
* * *
23313 TTTTGTTCTGTAGACGCTACTAAATAAGGGCGTTTTGTTCTTTAGACGCCGCTAAATAAGGGCA
1 TTTTGTTTTGTAGACGCCACTAAATAAGGGCGTTTTGTTCTATAGACGCCGCTAAATAAGGGCA
* * * * *
23377 TTTTGTTTTTTAGACGCCGCTAAATAAGGGCGTTTTTTTCTATAGACGCTGCTAAATAAGGGCG
1 TTTTGTTTTGTAGACGCCACTAAATAAGGGCGTTTTGTTCTATAGACGCCGCTAAATAAGGGCA
*
23441 TTTTCTTTT
1 TTTTGTTTT
23450 CACACATGCT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (64 bp):
TTTTGTTTTGTAGACGCCACTAAATAAGGGCGTTTTGTTCTATAGACGCCGCTAAATAAGGGCA
Found at i:23820 original size:6 final size:6
Alignment explanation
Indices: 23809--23849 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
23799 AAAGTTACCA
*
23809 CCATCG CCATCG CCATCG CCATCG CCATCG CCATCT CCATC
1 CCATCG CCATCG CCATCG CCATCG CCATCG CCATCG CCATC
23850 ATCACCGGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.17, C:0.51, G:0.12, T:0.20
Consensus pattern (6 bp):
CCATCG
Found at i:25838 original size:160 final size:161
Alignment explanation
Indices: 25566--25939 Score: 466
Period size: 160 Copynumber: 2.3 Consensus size: 161
25556 GGCGAGAGAA
* * * *
25566 TTTTCCCTCCAAAACAA-AGAAAAAAAAATTCTTTCACTCCATATATTACAATTGCGGCGTTTCC
1 TTTTCCCTCCAAAA-AAGAGAAAAAAAAA-TC--TCTCTCCATATATTAAAATAGCGGCGTTTCA
* * * ** * **
25630 TTTCCTTGATGCCACTAATTAGTGGCGTCTGGTGAGAAAATTCCGCTATATATTATAGGCGTAGA
62 TTTCCTAGACGCCACTAATTAGCGGCGTCTGAAGACAAAACGCCGCTATATATTATAGGCGTAGA
25695 GTTGG-AACATTTCTTTGTTTTA-GGGGGAGGGAAT
127 GTTGGAAAC-TTTCTTTGTTTTAGGGGGGAGGGAAT
* * *
25729 TTTTCCCTCCAAAAAAGGGAAAAAAATATCTCTCTCCATATATTAAAATAGCGGCGTTTCATTTT
1 TTTTCCCTCCAAAAAAGAGAAAAAAAAATCTCTCTCCATATATTAAAATAGCGGCGTTTCATTTC
* * * *
25794 CTAGACGTCACTACTTAGCGGCGTCTGAAGTCAAAACGCCGCTATATATTATAGGTGTAGAGTTG
66 CTAGACGCCACTAATTAGCGGCGTCTGAAGACAAAACGCCGCTATATATTATAGGCGTAGAGTTG
25859 GAAACTTTCTTTGTTTTAGGGGGGAGGGAAT
131 GAAACTTTCTTTGTTTTAGGGGGGAGGGAAT
*
25890 TTTTTCCTCCAAAAAAAAGAGAAAAAAAAATCTCTCCCTCCATATATTAA
1 TTTTCCCTCC--AAAAAAGAGAAAAAAAAATCTCT--CTCCATATATTAA
25940 TATGGCGGTG
Statistics
Matches: 182, Mismatches: 22, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
160 97 0.53
161 24 0.13
162 4 0.02
163 44 0.24
165 13 0.07
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (161 bp):
TTTTCCCTCCAAAAAAGAGAAAAAAAAATCTCTCTCCATATATTAAAATAGCGGCGTTTCATTTC
CTAGACGCCACTAATTAGCGGCGTCTGAAGACAAAACGCCGCTATATATTATAGGCGTAGAGTTG
GAAACTTTCTTTGTTTTAGGGGGGAGGGAAT
Found at i:26625 original size:96 final size:96
Alignment explanation
Indices: 26511--26730 Score: 296
Period size: 96 Copynumber: 2.3 Consensus size: 96
26501 GCGCACTATT
*
26511 AAAATGCCGATCGCGCAAATGATGAGTGCACCTCAGAAGGGAATAGAATGCACGAGCGAAGATCG
1 AAAATGCCGATCGCGCAAATGATGAATGCACCTCAGAAGGGAATAGAATGCACGAGCGAAGATCG
*
26576 CGCACCACAAGAATGTCGATCGCACGAATGA
66 CGCACCACAAGAATGTCGATCGCACAAATGA
* * ** * * * *** *
26607 AAAATTCTGATCGCGCAAATGAAAAATGCTCCTCAGAAGGGAGTAGCATGTGTGAGCGAAGATTG
1 AAAATGCCGATCGCGCAAATGATGAATGCACCTCAGAAGGGAATAGAATGCACGAGCGAAGATCG
* *
26672 CGCACCATAAGAATGTCGATCGCGCAAATGA
66 CGCACCACAAGAATGTCGATCGCACAAATGA
*
26703 AAAATGCCGATCGCGCAAATTATGAATG
1 AAAATGCCGATCGCGCAAATGATGAATG
26731 TCGATTGCGC
Statistics
Matches: 104, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
96 104 1.00
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.17
Consensus pattern (96 bp):
AAAATGCCGATCGCGCAAATGATGAATGCACCTCAGAAGGGAATAGAATGCACGAGCGAAGATCG
CGCACCACAAGAATGTCGATCGCACAAATGA
Found at i:26708 original size:22 final size:22
Alignment explanation
Indices: 26683--26752 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
26673 GCACCATAAG
*
26683 AATGTCGATCGCGCAAATGAAA
1 AATGTCGATCGCGCAAATAAAA
* * **
26705 AATGCCGATCGCGCAAATTATG
1 AATGTCGATCGCGCAAATAAAA
* *
26727 AATGTCGATTGCGCAATTAAAA
1 AATGTCGATCGCGCAAATAAAA
26749 AATG
1 AATG
26753 CTCCTCAAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (22 bp):
AATGTCGATCGCGCAAATAAAA
Found at i:30332 original size:53 final size:53
Alignment explanation
Indices: 30252--30517 Score: 265
Period size: 53 Copynumber: 5.1 Consensus size: 53
30242 TATTTATTCA
30252 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
* *
30305 ATTGAACTTATTAAATAAACACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
** * * * * ** * * *** *** * * *
30358 ATTGAA--TAATTCTATTA-TATA-TTA-TTATTATTA-ATTGTGTTGTTTATTCA
1 ATTGAACCT-ATTAAATAAGCACACATACCAAATAATACAAAATG-CAATGA-ACT
30408 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
*
30461 ATTGAACCTATTAATTAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
30514 ATTG
1 ATTG
30518 GATTTAAAGA
Statistics
Matches: 163, Mismatches: 41, Indels: 18
0.73 0.18 0.08
Matches are distributed among these distances:
48 3 0.02
49 7 0.04
50 9 0.06
51 9 0.06
52 9 0.06
53 116 0.71
54 7 0.04
55 3 0.02
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (53 bp):
ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
Found at i:30490 original size:156 final size:156
Alignment explanation
Indices: 30206--30517 Score: 579
Period size: 156 Copynumber: 2.0 Consensus size: 156
30196 ATTATAAAAT
30206 AATAATTCTATTATATAATATTATTATTAATTGTGTTATTTATTCAATTGAACCTATTAAATAAG
1 AATAATTCTATTATATAATATTATTATTAATTGTGTTATTTATTCAATTGAACCTATTAAATAAG
*
30271 CACACATACCAAATAATACAAAATGCAATGAACTATTGAACTTATTAAATAAACACACATACCAA
66 CACACATACCAAATAATACAAAATGCAATGAACTATTGAACCTATTAAATAAACACACATACCAA
30336 ATAATACAAAATGCAATGAACTATTG
131 ATAATACAAAATGCAATGAACTATTG
* *
30362 AATAATTCTATTATATATTATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAG
1 AATAATTCTATTATATAATATTATTATTAATTGTGTTATTTATTCAATTGAACCTATTAAATAAG
* *
30427 CACACATACCAAATAATACAAAATGCAATGAACTATTGAACCTATTAATTAAGCACACATACCAA
66 CACACATACCAAATAATACAAAATGCAATGAACTATTGAACCTATTAAATAAACACACATACCAA
30492 ATAATACAAAATGCAATGAACTATTG
131 ATAATACAAAATGCAATGAACTATTG
30518 GATTTAAAGA
Statistics
Matches: 151, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 151 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.34
Consensus pattern (156 bp):
AATAATTCTATTATATAATATTATTATTAATTGTGTTATTTATTCAATTGAACCTATTAAATAAG
CACACATACCAAATAATACAAAATGCAATGAACTATTGAACCTATTAAATAAACACACATACCAA
ATAATACAAAATGCAATGAACTATTG
Found at i:30689 original size:38 final size:39
Alignment explanation
Indices: 30647--30722 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
30637 TTTTAAAAAA
*
30647 AATAAAATATA-ATT-ACTTTTTTAAGTAAATTTTCTTAG
1 AATAAAATATAGATTGA-TTTTTTAAATAAATTTTCTTAG
* * *
30685 AATAACATCTAGATTGATTTTTTAAATTAATTTTCTTA
1 AATAAAATATAGATTGATTTTTTAAATAAATTTTCTTA
30723 ACAAAACTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 9 0.28
39 22 0.69
40 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (39 bp):
AATAAAATATAGATTGATTTTTTAAATAAATTTTCTTAG
Found at i:30816 original size:30 final size:32
Alignment explanation
Indices: 30780--30840 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
30770 ATAAAATGAG
*
30780 TAGCCCA-TATATAA-GTGGGCCGTGCCGTGC
1 TAGCCCATTATATAATATGGGCCGTGCCGTGC
* *
30810 TAGCCCATTTTATAATATGGGTCGTGCCGTG
1 TAGCCCATTATATAATATGGGCCGTGCCGTG
30841 TCAATCCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 7 0.27
31 6 0.23
32 13 0.50
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.30
Consensus pattern (32 bp):
TAGCCCATTATATAATATGGGCCGTGCCGTGC
Found at i:37971 original size:25 final size:26
Alignment explanation
Indices: 37937--37991 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
37927 CAAACAAGGC
37937 ATAAGAATAAGACCCAGAAAA-AAAA
1 ATAAGAATAAGACCCAGAAAAGAAAA
* * *
37962 ATAATAATAAGACCCGGAAAAGGAAA
1 ATAAGAATAAGACCCAGAAAAGAAAA
37988 ATAA
1 ATAA
37992 AAGACAAGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.64, C:0.11, G:0.15, T:0.11
Consensus pattern (26 bp):
ATAAGAATAAGACCCAGAAAAGAAAA
Found at i:42167 original size:16 final size:18
Alignment explanation
Indices: 42134--42170 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
42124 ACTCTTTTCT
42134 AATTTCTAAAATTTTTAG
1 AATTTCTAAAATTTTTAG
42152 AATTT-TAAAA-TTTTAG
1 AATTTCTAAAATTTTTAG
42168 AAT
1 AAT
42171 ACCTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 5 0.26
18 5 0.26
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (18 bp):
AATTTCTAAAATTTTTAG
Found at i:43219 original size:21 final size:20
Alignment explanation
Indices: 43179--43219 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43169 TTCCGTTAGC
*
43179 AAATTACTTAGACCGCTAAT
1 AAATTACTTACACCGCTAAT
*
43199 AAATTACTTAACACCGTTAAT
1 AAATTACTT-ACACCGCTAAT
43220 TTTACATACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (20 bp):
AAATTACTTACACCGCTAAT
Found at i:45425 original size:2 final size:2
Alignment explanation
Indices: 45418--45472 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
45408 TGACTTCTAT
45418 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
45460 AC AC AC AC AC AC A
1 AC AC AC AC AC AC A
45473 TCTATTATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:48076 original size:16 final size:15
Alignment explanation
Indices: 48055--48103 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
48045 AAATAAGATC
48055 TTATATATCATTACTT
1 TTATATATCATTA-TT
48071 TTATATAT--TT-TT
1 TTATATATCATTATT
*
48083 TTATAAATCATTAGTT
1 TTATATATCATTA-TT
48099 TTATA
1 TTATA
48104 ATAATAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
12 9 0.32
14 4 0.14
16 15 0.54
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (15 bp):
TTATATATCATTATT
Found at i:52636 original size:19 final size:18
Alignment explanation
Indices: 52599--52639 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
52589 TTTTTGAAAT
*
52599 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
52617 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
52636 AATT
1 AATT
52640 AATCTTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:53929 original size:60 final size:60
Alignment explanation
Indices: 53840--54000 Score: 177
Period size: 59 Copynumber: 2.7 Consensus size: 60
53830 CTAATTGCTT
* * * **
53840 AAATAAGGGCCTTA-GATTTG-CTAAGATGCTCAAATAAGGGCATGATCTTTTAATTTGGCC
1 AAATAAGGGCCTAACG-TTTGTCGAAAATGCTCAAATAAGGGC-CCATCTTTTAATTTGGCC
* * *
53900 AAATAAGGGCCTAACGTTTGTC-AAAATGCTCAAACAATGGCCCATCTTTTAGTTTGGCC
1 AAATAAGGGCCTAACGTTTGTCGAAAATGCTCAAATAAGGGCCCATCTTTTAATTTGGCC
* * *
53959 AAATTAGAGCCTAACG-TTATCGAAAATGCTCAAATAAGGGCC
1 AAATAAGGGCCTAACGTTTGTCGAAAATGCTCAAATAAGGGCC
54001 TGGAGTCGAA
Statistics
Matches: 86, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
58 4 0.05
59 47 0.55
60 33 0.38
61 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (60 bp):
AAATAAGGGCCTAACGTTTGTCGAAAATGCTCAAATAAGGGCCCATCTTTTAATTTGGCC
Found at i:54078 original size:31 final size:30
Alignment explanation
Indices: 54040--54143 Score: 120
Period size: 31 Copynumber: 3.4 Consensus size: 30
54030 AACTGATGCC
*
54040 AGGCCCTTATTTGACCATTTTCGATAACGTT
1 AGGCCCTTATTTGACCATTTTCAATAAC-TT
* ** * *
54071 AGGCCCTTATTTGGCCAAATTAAAAAAC-T
1 AGGCCCTTATTTGACCATTTTCAATAACTT
*
54100 AGGCCCTTATTTGAGCATTTTCAATAACTTT
1 AGGCCCTTATTTGACCATTTTCAATAAC-TT
54131 AGGCCCTTATTTG
1 AGGCCCTTATTTG
54144 GCCAAATTAA
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
29 23 0.39
31 36 0.61
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (30 bp):
AGGCCCTTATTTGACCATTTTCAATAACTT
Found at i:54111 original size:29 final size:29
Alignment explanation
Indices: 54070--54171 Score: 109
Period size: 29 Copynumber: 3.4 Consensus size: 29
54060 TCGATAACGT
54070 TAGGCCCTTATTTGGCCAAATTAAAAAAC
1 TAGGCCCTTATTTGGCCAAATTAAAAAAC
** * *
54099 TAGGCCCTTATTTGAG-CATTTTCAATAAC
1 TAGGCCCTTATTTG-GCCAAATTAAAAAAC
54128 TTTAGGCCCTTATTTGGCCAAATTAAAAAA-
1 --TAGGCCCTTATTTGGCCAAATTAAAAAAC
*
54158 TCAGACCCTTATTT
1 T-AGGCCCTTATTT
54172 TAGCATTTTG
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
28 1 0.02
29 34 0.58
30 2 0.03
31 22 0.37
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (29 bp):
TAGGCCCTTATTTGGCCAAATTAAAAAAC
Found at i:54133 original size:60 final size:60
Alignment explanation
Indices: 54039--54180 Score: 223
Period size: 60 Copynumber: 2.4 Consensus size: 60
54029 AAACTGATGC
* *
54039 CAGGCCCTTATTTGACCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAAA-
1 CAGGCCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAAAT
*
54098 CTAGGCCCTTATTTGAGCATTTTCAATAACTTTAGGCCCTTATTTGGCCAAATTAAAAAAT
1 C-AGGCCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAAAT
* *
54159 CAGACCCTTATTTTAGCATTTT
1 CAGGCCCTTATTTGAGCATTTT
54181 GGCAAACGTT
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
59 1 0.01
60 74 0.97
61 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAAAT
Found at i:54198 original size:60 final size:60
Alignment explanation
Indices: 54043--54203 Score: 204
Period size: 60 Copynumber: 2.7 Consensus size: 60
54033 TGATGCCAGG
* *
54043 CCCTTATTTGACCATTTT-CGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAAACTAGG
1 CCCTTATTTGAGCATTTTGC-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAAACTAGA
*
54103 CCCTTATTTGAGCATTTT-CAATAACTTTAGGCCCTTATTTGGCCAAATTAAAAAA-TCAGA
1 CCCTTATTTGAGCATTTTGC-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAAACT-AGA
* **
54163 CCCTTATTTTAGCATTTTGGCA-AACGTTACCCCCTTATTTG
1 CCCTTATTTGAGCATTTT-GCATAACGTTAGGCCCTTATTTG
54204 AGCAAGCAGC
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
59 1 0.01
60 87 0.97
61 1 0.01
62 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTGCATAACGTTAGGCCCTTATTTGGCCAAATTAAAAAACTAGA
Found at i:54949 original size:2 final size:2
Alignment explanation
Indices: 54942--54975 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
54932 GGGCCATCAC
*
54942 CA CA CA CA CA CA CA CA CA CA CA CA AA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
54976 ATAACATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:57363 original size:3 final size:3
Alignment explanation
Indices: 57344--57391 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
57334 GCTTTCTTTC
*
57344 TCT TCCT TCT CCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
57390 TC
1 TC
57392 CACTTCAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:69804 original size:5 final size:5
Alignment explanation
Indices: 69794--69820 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
69784 AACTTAGTTC
69794 GTTTT GTTTT GTTTT GTTTT GTTTT GT
1 GTTTT GTTTT GTTTT GTTTT GTTTT GT
69821 AGATAGTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (5 bp):
GTTTT
Found at i:70521 original size:25 final size:25
Alignment explanation
Indices: 70493--70547 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
70483 AATTTAATAT
* * *
70493 ATTTAAAATTTAAATACTATAATTA
1 ATTTAAAATATAAAAAATATAATTA
70518 ATTTAAAATATAAAAAATATAATTA
1 ATTTAAAATATAAAAAATATAATTA
70543 ATTTA
1 ATTTA
70548 TTTAAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAAAATATAAAAAATATAATTA
Found at i:72263 original size:16 final size:16
Alignment explanation
Indices: 72229--72300 Score: 85
Period size: 16 Copynumber: 4.6 Consensus size: 16
72219 CGGGCTCGGG
*
72229 CGGGTTCGGGTA-CTT
1 CGGGTTCGGGTATTTT
72244 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* *
72260 CGGGCTCGGGT-TATGT
1 CGGGTTCGGGTAT-TTT
*
72276 CGGGTTTGGGTATTTT
1 CGGGTTCGGGTATTTT
72292 CGGGTTCGG
1 CGGGTTCGG
72301 TCTCGGGTAG
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
15 13 0.28
16 33 0.70
17 1 0.02
ACGTcount: A:0.06, C:0.15, G:0.42, T:0.38
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:72299 original size:6 final size:6
Alignment explanation
Indices: 72290--72343 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
72280 TTTGGGTATT
* *
72290 TTCGGG TTC-GG TCTCGGG -TAGGG TTCGGG TTCGGG -TCGGG TTCGAG
1 TTCGGG TTCGGG T-TCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
*
72336 CTCGGG TT
1 TTCGGG TT
72344 TGATTTCAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
5 12 0.32
6 24 0.63
7 2 0.05
ACGTcount: A:0.04, C:0.19, G:0.46, T:0.31
Consensus pattern (6 bp):
TTCGGG
Found at i:72308 original size:12 final size:11
Alignment explanation
Indices: 72291--72343 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
72281 TTGGGTATTT
72291 TCGGGTTCGGTC
1 TCGGGTTCGG-C
** *
72303 TCGGGTAGGGT
1 TCGGGTTCGGC
*
72314 TCGGGTTCGGG
1 TCGGGTTCGGC
72325 TCGGGTTCGAGC
1 TCGGGTTCG-GC
72337 TCGGGTT
1 TCGGGTT
72344 TGATTTCAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
11 17 0.52
12 16 0.48
ACGTcount: A:0.04, C:0.19, G:0.47, T:0.30
Consensus pattern (11 bp):
TCGGGTTCGGC
Found at i:72315 original size:17 final size:17
Alignment explanation
Indices: 72293--72342 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
72283 GGGTATTTTC
72293 GGGTTCGGTCTCGGGTA
1 GGGTTCGGTCTCGGGTA
*
72310 GGGTTCGGGT-TCGGGTC
1 GGGTTC-GGTCTCGGGTA
72327 GGGTTCGAG-CTCGGGT
1 GGGTTCG-GTCTCGGGT
72343 TTGATTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 1 0.03
17 25 0.86
18 3 0.10
ACGTcount: A:0.04, C:0.18, G:0.50, T:0.28
Consensus pattern (17 bp):
GGGTTCGGTCTCGGGTA
Found at i:72805 original size:31 final size:30
Alignment explanation
Indices: 72770--72841 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 30
72760 TAAATTATTG
*
72770 CAAATTAAAACAATCTAAG-CATTAAATTAAA
1 CAAATTAAAA-AATCAAAGTC-TTAAATTAAA
*
72801 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA--AAAATCAAAGTCTTAAATTAAA
72832 CAAATTAAAA
1 CAAATTAAAA
72842 GCTGATAGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
30 5 0.14
31 24 0.69
32 6 0.17
ACGTcount: A:0.60, C:0.10, G:0.04, T:0.26
Consensus pattern (30 bp):
CAAATTAAAAAATCAAAGTCTTAAATTAAA
Found at i:73167 original size:21 final size:22
Alignment explanation
Indices: 73126--73167 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
73116 CTTTTTATAT
*
73126 TGATCAATTAATTAATTAATTG
1 TGATCAATTAATTAATAAATTG
73148 TGATC-ATT-ATTATATAAATT
1 TGATCAATTAATTA-ATAAATT
73168 TTATTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (22 bp):
TGATCAATTAATTAATAAATTG
Found at i:74901 original size:22 final size:22
Alignment explanation
Indices: 74873--74925 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
74863 ACATTAAAAA
*
74873 TGGGTCGTGCTGCATCGGTACG
1 TGGGTCGTGCTGCATCGGCACG
**
74895 TGGGTCGTGCTGTGTCGGCACG
1 TGGGTCGTGCTGCATCGGCACG
74917 TGGGTCGTG
1 TGGGTCGTG
74926 TCGTGCCATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.06, C:0.21, G:0.45, T:0.28
Consensus pattern (22 bp):
TGGGTCGTGCTGCATCGGCACG
Found at i:80005 original size:45 final size:45
Alignment explanation
Indices: 79956--80183 Score: 223
Period size: 45 Copynumber: 5.1 Consensus size: 45
79946 GAAGACATTC
*
79956 AAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
1 AAAGAGACAGCCATGACAGTAAATAGCTCAGCTGAGAAGATGAAG
** * * *
80001 AAAGAGACAGTGATGGCAGTAAATAGCTTAGCTGAGAAGGTGAAG
1 AAAGAGACAGCCATGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* * *
80046 AAAGAGA-TGTCCATGACAGTAAATAGTTCAGCTGAGAAGGTGAA-
1 AAAGAGACAG-CCATGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* * * *
80090 AAGAGAAACAG-C-TG-CAGCAAATGGCTCAGCCGAGAAGATGAAG
1 AA-AGAGACAGCCATGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* * * * * * *
80133 AGAGAAACGGCCTTGACAGTAAATGGCTCAGTTGAGAAGACGAAG
1 AAAGAGACAGCCATGACAGTAAATAGCTCAGCTGAGAAGATGAAG
80178 AAAGAG
1 AAAGAG
80184 TTGGCTGTGG
Statistics
Matches: 149, Mismatches: 27, Indels: 14
0.78 0.14 0.07
Matches are distributed among these distances:
42 30 0.20
43 4 0.03
44 6 0.04
45 108 0.72
46 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.30, T:0.15
Consensus pattern (45 bp):
AAAGAGACAGCCATGACAGTAAATAGCTCAGCTGAGAAGATGAAG
Found at i:80169 original size:87 final size:89
Alignment explanation
Indices: 79956--80182 Score: 244
Period size: 87 Copynumber: 2.6 Consensus size: 89
79946 GAAGACATTC
* * * *
79956 AAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAGAAAGAGACAGTGATGGCAGT
1 AAAGAAACGGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAGAAAGAAACAG-GATGGCAGC
* * *
80021 AAATAGCTTAGCTGAGAAGGTGAAG
65 AAATAGCTCAGCCGAGAAGATGAAG
* * * * * * *
80046 AAAGAGATGTCCATGACAGTAAATAGTTCAGCTGAGAAGGTGAA-AAGAGAAACA-GCT-GCAGC
1 AAAGAAACGGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAGAA-AGAAACAGGATGGCAGC
*
80108 AAATGGCTCAGCCGAGAAGATGAAG
65 AAATAGCTCAGCCGAGAAGATGAAG
* * * *
80133 AGAGAAACGGCCTTGACAGTAAATGGCTCAGTTGAGAAGACGAAGAAAGA
1 AAAGAAACGGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAGAAAGA
80183 GTTGGCTGTG
Statistics
Matches: 112, Mismatches: 23, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
87 62 0.55
88 4 0.04
89 2 0.02
90 44 0.39
ACGTcount: A:0.41, C:0.14, G:0.30, T:0.15
Consensus pattern (89 bp):
AAAGAAACGGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAGAAAGAAACAGGATGGCAGCA
AATAGCTCAGCCGAGAAGATGAAG
Found at i:80205 original size:45 final size:45
Alignment explanation
Indices: 80149--80273 Score: 171
Period size: 45 Copynumber: 2.8 Consensus size: 45
80139 ACGGCCTTGA
* *
80149 CAGTAAATGGCTCAGTTGAGAAGACGAAGAAAGAGTTGGCTGTGG
1 CAGTGAATGGCTCAGTTGAAAAGACGAAGAAAGAGTTGGCTGTGG
* * **
80194 CAGTGAGTGGCTCAGCTGAAAAGGTGAAGAAAGAGTTGGCTGTGG
1 CAGTGAATGGCTCAGTTGAAAAGACGAAGAAAGAGTTGGCTGTGG
*
80239 CAGTGAATGGCTCA-TCTGAAAAGACAAAGAAAGAG
1 CAGTGAATGGCTCAGT-TGAAAAGACGAAGAAAGAG
80274 GCAGCCATGA
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
45 68 1.00
ACGTcount: A:0.35, C:0.12, G:0.34, T:0.18
Consensus pattern (45 bp):
CAGTGAATGGCTCAGTTGAAAAGACGAAGAAAGAGTTGGCTGTGG
Done.