Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011605.1 Corchorus capsularis cultivar CVL-1 contig11626, 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: 43169
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1580 original size:24 final size:24
Alignment explanation
Indices: 1548--1595 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1538 GAGGTTGGAG
* *
1548 GTCTTCAAGTGACTTCTCTTCATC
1 GTCTTCAAGTGACTCCTCATCATC
1572 GTCTTCAAGTGACTCCTCATCATC
1 GTCTTCAAGTGACTCCTCATCATC
1596 ATCTCCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.31, G:0.12, T:0.38
Consensus pattern (24 bp):
GTCTTCAAGTGACTCCTCATCATC
Found at i:7595 original size:30 final size:31
Alignment explanation
Indices: 7541--7605 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
7531 AACTTTATGT
* *
7541 TTTCCGATTGTACCCTTATTTTTAAAATATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
7572 TTTCCAATTGTACCCTT-TTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
7602 TTTC
1 TTTC
7606 TAAATTGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:7612 original size:31 final size:31
Alignment explanation
Indices: 7547--7613 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
7537 ATGTTTTCCG
* *
7547 ATTGTACCCTTATTTTTAAAATATATTTCCA
1 ATTGTACCCTTATTTTTAAAACATATTTCAA
7578 ATTGTACCCTT-TTTTTAAAACATATTTCTAA
1 ATTGTACCCTTATTTTTAAAACATATTTC-AA
7609 ATTGT
1 ATTGT
7614 CATTACTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 16 0.48
31 17 0.52
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.49
Consensus pattern (31 bp):
ATTGTACCCTTATTTTTAAAACATATTTCAA
Found at i:7956 original size:23 final size:22
Alignment explanation
Indices: 7928--7985 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
7918 ATGTGATTAT
*
7928 CAAAATTTCATAGATGGGGTCAA
1 CAAAATTTCATAGA-GAGGTCAA
* * *
7951 CAAAATTTTTATAGAGAGGTTAT
1 CAAAA-TTTCATAGAGAGGTCAA
7974 CAAAATTTCATA
1 CAAAATTTCATA
7986 AAGAAGTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 6 0.21
23 15 0.52
24 8 0.28
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAGAGAGGTCAA
Found at i:7997 original size:22 final size:22
Alignment explanation
Indices: 7898--8029 Score: 88
Period size: 22 Copynumber: 5.9 Consensus size: 22
7888 TTCAAAGCGC
* *
7898 GAGGTTATCAAAATTACATAAT
1 GAGGTTATCAAAATTTCATAAA
* * *
7920 GTGATTATCAAAATTTCATAGAT
1 GAGGTTATCAAAATTTCATA-AA
* * * * *
7943 GGGGTCAACAAAATTTTTATAGA
1 GAGGTTATCAAAA-TTTCATAAA
7966 GAGGTTATCAAAATTTCATAAA
1 GAGGTTATCAAAATTTCATAAA
*
7988 GAAGTTATC-AAATTCTCA-AAA
1 GAGGTTATCAAAATT-TCATAAA
* * *
8009 TGTGATTACCAAAATTTCATA
1 -GAGGTTATCAAAATTTCATA
8030 GTGGTACTTC
Statistics
Matches: 84, Mismatches: 20, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
21 8 0.10
22 43 0.51
23 27 0.32
24 6 0.07
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAAA
Found at i:8205 original size:44 final size:43
Alignment explanation
Indices: 8114--8252 Score: 154
Period size: 44 Copynumber: 3.2 Consensus size: 43
8104 TGGAGTAATA
* * ** *
8114 AAAATTTCATATGAAGGCTATCAAAATTTCATAGTTTAG-TTTTC
1 AAAATTTCATAAG-AGGTTATCAAAATTTCATAG-GGAGATTATC
*
8158 AAAATTTCATAAGAGGGTTATCAAAATTTCATAGGGAGATTAAC
1 AAAATTTCATAAGA-GGTTATCAAAATTTCATAGGGAGATTATC
***
8202 AAAATTTCATAATGAGGTTATCAAAAAACCATAGGGAGATTATC
1 AAAATTTCATAA-GAGGTTATCAAAATTTCATAGGGAGATTATC
8246 AAAATTT
1 AAAATTT
8253 GTAGTTATCA
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
43 3 0.04
44 77 0.94
45 2 0.02
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.33
Consensus pattern (43 bp):
AAAATTTCATAAGAGGTTATCAAAATTTCATAGGGAGATTATC
Found at i:8290 original size:22 final size:22
Alignment explanation
Indices: 8114--8299 Score: 111
Period size: 22 Copynumber: 8.7 Consensus size: 22
8104 TGGAGTAATA
* * *
8114 AAAATTTCATATGAAGGCTATC
1 AAAATTTCATAAGGAGGTTATC
* *
8136 AAAATTTCAT-AGTTTA-GTTTTC
1 AAAATTTCATAAG--GAGGTTATC
8158 AAAATTTCATAA-GAGGGTTATC
1 AAAATTTCATAAGGA-GGTTATC
* * *
8180 AAAATTTCATAGGGAGATTAAC
1 AAAATTTCATAAGGAGGTTATC
*
8202 AAAATTTCATAATGAGGTTATC
1 AAAATTTCATAAGGAGGTTATC
*** * *
8224 AAAAAACCATAGGGAGATTATC
1 AAAATTTCATAAGGAGGTTATC
*
8246 AAAA-TT--T--GTA-GTTATC
1 AAAATTTCATAAGGAGGTTATC
* *
8262 AAGATTTCATAAGGAGGTTATT
1 AAAATTTCATAAGGAGGTTATC
* *
8284 AAAATTTTATAGGGAG
1 AAAATTTCATAAGGAG
8300 ATTTATATAG
Statistics
Matches: 123, Mismatches: 29, Indels: 24
0.70 0.16 0.14
Matches are distributed among these distances:
16 8 0.07
17 4 0.03
19 2 0.02
20 1 0.01
21 3 0.02
22 101 0.82
23 4 0.03
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.34
Consensus pattern (22 bp):
AAAATTTCATAAGGAGGTTATC
Found at i:8510 original size:45 final size:45
Alignment explanation
Indices: 8423--8511 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 45
8413 TTTCATAACG
* * * *
8423 TGGTTATCAATATATCATATGGAGGTTATCAACATCTTATAGTGT
1 TGGTTATCAAAATATCATATGAAAGTTATCAAAATCTTATAGTGT
* *
8468 TGGTTATCAAAATTTCATTTGAAAGTTATCAAAAT-TTCATAGTG
1 TGGTTATCAAAATATCATATGAAAGTTATCAAAATCTT-ATAGTG
8512 AGGTCTTCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
44 2 0.05
45 35 0.95
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGAAAGTTATCAAAATCTTATAGTGT
Found at i:8521 original size:22 final size:22
Alignment explanation
Indices: 8392--8561 Score: 92
Period size: 22 Copynumber: 7.7 Consensus size: 22
8382 TTACTGACAA
* * * *
8392 TTCATATGGAGGTTTTTAAATT
1 TTCATAGGGAGGTTATCAAAAT
** * *
8414 TTCATAACGTGGTTATCAATAT
1 TTCATAGGGAGGTTATCAAAAT
* * *
8436 ATCATATGGAGGTTATCAACAT
1 TTCATAGGGAGGTTATCAAAAT
**
8458 CTT-ATAGTGTTGGTTATCAAAAT
1 -TTCATAG-GGAGGTTATCAAAAT
** * *
8481 TTCATTTGAAAGTTATCAAAAT
1 TTCATAGGGAGGTTATCAAAAT
*
8503 TTCATAGTGAGGTCT-TCAAAAT
1 TTCATAGGGAGGT-TATCAAAAT
* * *
8525 TCCTTAGGGAGGTTAACAAAAT
1 TTCATAGGGAGGTTATCAAAAT
* *
8547 TTCATAAGAAGGTTA
1 TTCATAGGGAGGTTA
8562 AAAAAAAAAT
Statistics
Matches: 108, Mismatches: 35, Indels: 10
0.71 0.23 0.07
Matches are distributed among these distances:
21 1 0.01
22 91 0.84
23 16 0.15
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (22 bp):
TTCATAGGGAGGTTATCAAAAT
Found at i:8746 original size:62 final size:61
Alignment explanation
Indices: 8611--8750 Score: 226
Period size: 61 Copynumber: 2.3 Consensus size: 61
8601 TCGTTATTGA
* *
8611 AATTTCATAGGAAGCTTATCAAAATTTCATAAGGACGTCATAAAAATAGTGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATATCATAAGGACGTCATAAAAATAGTGTAATTATCAT
* *
8672 AATTTCATAGGAAGGTTATCAAAATATCATAAGTACGTCATTAAAAATAGTGTAATTATTAT
1 AATTTCATAGGAAGGTTATCAAAATATCATAAGGACGTCA-TAAAAATAGTGTAATTATCAT
*
8734 AATTTAATAGGAAGGTT
1 AATTTCATAGGAAGGTT
8751 TTCATACTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
61 37 0.51
62 36 0.49
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (61 bp):
AATTTCATAGGAAGGTTATCAAAATATCATAAGGACGTCATAAAAATAGTGTAATTATCAT
Found at i:8958 original size:15 final size:16
Alignment explanation
Indices: 8939--8975 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
8929 TATTGTTTGT
8939 TTATATTAAAGTATAA
1 TTATATTAAAGTATAA
8955 -TATATTAAAGTATAA
1 TTATATTAAAGTATAA
8970 TTATAT
1 TTATAT
8976 ATTTTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (16 bp):
TTATATTAAAGTATAA
Found at i:21401 original size:18 final size:18
Alignment explanation
Indices: 21380--21415 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21370 AATTATTATT
21380 ATTAAGCCTAAATAATTG
1 ATTAAGCCTAAATAATTG
21398 ATTAAGCCTAAATAATTG
1 ATTAAGCCTAAATAATTG
21416 GAAAGAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (18 bp):
ATTAAGCCTAAATAATTG
Found at i:21444 original size:2 final size:2
Alignment explanation
Indices: 21437--21463 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21427 CCTTTGTTAG
21437 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
21464 GTTAATAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22572 original size:20 final size:21
Alignment explanation
Indices: 22535--22574 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
22525 AAGGTTTTTC
*
22535 CAAAATTCCAATAAATCAAAT
1 CAAAATTCCAAAAAATCAAAT
22556 CAAAATT-CAAAAAATCAAA
1 CAAAATTCCAAAAAATCAAA
22575 AATTTTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.20
Consensus pattern (21 bp):
CAAAATTCCAAAAAATCAAAT
Found at i:25065 original size:23 final size:23
Alignment explanation
Indices: 25039--25084 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
25029 TTGTATGCAC
25039 TGTTAGAGTGCATTATGAAGGAA
1 TGTTAGAGTGCATTATGAAGGAA
25062 TGTTAGAGTGCATTATGAAGGAA
1 TGTTAGAGTGCATTATGAAGGAA
25085 GGTCTAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.30, T:0.30
Consensus pattern (23 bp):
TGTTAGAGTGCATTATGAAGGAA
Found at i:25985 original size:29 final size:29
Alignment explanation
Indices: 25894--25986 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
25884 AACCAATTCA
***
25894 GGATATAACGTTTGCTGCATGATCAATTTG
1 GGATATAACGTTT-CAAAATGATCAATTTG
* * * * *
25924 GGATGTAACGTTTTAGAACT-A-CCATTTCA
1 GGATATAACGTTTCA-AAATGATCAATTT-G
25953 GGATATAACGTTTCAAAATGATCAATTTG
1 GGATATAACGTTTCAAAATGATCAATTTG
25982 GGATA
1 GGATA
25987 AAATTCACGT
Statistics
Matches: 46, Mismatches: 13, Indels: 9
0.68 0.19 0.13
Matches are distributed among these distances:
28 8 0.17
29 20 0.43
30 18 0.39
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.34
Consensus pattern (29 bp):
GGATATAACGTTTCAAAATGATCAATTTG
Found at i:26118 original size:29 final size:31
Alignment explanation
Indices: 26054--26118 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
26044 TCCGTTAGAC
* *
26054 TATATCCTGATTTGGTCGTTTTCAGTAACGT
1 TATATCCTGAATTGGTCGTTTTCAGAAACGT
*
26085 TATATCCTGAATTGG-CGTTTT-TGAAACGT
1 TATATCCTGAATTGGTCGTTTTCAGAAACGT
26114 TATAT
1 TATAT
26119 TCCAAATTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 11 0.35
30 6 0.19
31 14 0.45
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (31 bp):
TATATCCTGAATTGGTCGTTTTCAGAAACGT
Found at i:28071 original size:22 final size:22
Alignment explanation
Indices: 28012--28056 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
28002 AACATATGTA
28012 TAAACAAAAGAAAAGAAAAAAT
1 TAAACAAAAGAAAAGAAAAAAT
28034 TAAACAAAAGAAAAGAAAAAAT
1 TAAACAAAAGAAAAGAAAAAAT
28056 T
1 T
28057 GATTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.11
Consensus pattern (22 bp):
TAAACAAAAGAAAAGAAAAAAT
Found at i:28335 original size:2 final size:2
Alignment explanation
Indices: 28322--28368 Score: 67
Period size: 2 Copynumber: 23.0 Consensus size: 2
28312 AATCAAACCC
* *
28322 TA TA TCA TA TA TA TA TA TA CA TA TA TA TA GA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28365 TA TA
1 TA TA
28369 ACTAACAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:30395 original size:44 final size:44
Alignment explanation
Indices: 30341--30494 Score: 125
Period size: 55 Copynumber: 3.3 Consensus size: 44
30331 AATTTGTTTG
30341 TTCAAGATCAAGTCGCCAAGACCCTTGAATCAAATTATCATCAA
1 TTCAAGATCAAGTCGCCAAGACCCTTGAATCAAATTATCATCAA
* * * *
30385 TTCGAGATCAAGTCATCAAAGACCCTCGAATCAAATCAAATTCCCAAGTCATCAA
1 TTCAAGATCAAGTC-GCCAAGACCCT----T-GAATCAAATT----A-TCATCAA
* *
30440 TTCAAGATCAAGTCGTCAAGACCCTTGAATTAAA-T-T-ATCAA
1 TTCAAGATCAAGTCGCCAAGACCCTTGAATCAAATTATCATCAA
*
30481 TTCAAGACCAAGTC
1 TTCAAGATCAAGTC
30495 ATTCGACCCT
Statistics
Matches: 88, Mismatches: 11, Indels: 25
0.71 0.09 0.20
Matches are distributed among these distances:
41 18 0.20
42 1 0.01
44 13 0.15
45 9 0.10
48 1 0.01
49 7 0.08
50 10 0.11
54 9 0.10
55 20 0.23
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.25
Consensus pattern (44 bp):
TTCAAGATCAAGTCGCCAAGACCCTTGAATCAAATTATCATCAA
Found at i:30524 original size:99 final size:97
Alignment explanation
Indices: 30341--30519 Score: 240
Period size: 99 Copynumber: 1.9 Consensus size: 97
30331 AATTTGTTTG
* *
30341 TTCAAGATCAAGTCGCCAAGACCCTTGAATCAAATTATCATCAATTCGAGATCAAGTCATCAAAG
1 TTCAAGATCAAGTCGCCAAGACCCTTGAATCAAATTATCATCAATTCAAGACCAAGTCATC--AG
*
30406 ACCCTCGAATCAAATCAAATTCCCAAGTCATCAA
64 ACCCTCAAATCAAATCAAATTCCCAAGTCATCAA
* *
30440 TTCAAGATCAAGTCGTCAAGACCCTTGAATTAAA-T-T-ATCAATTCAAGACCAAGTCATTC-GA
1 TTCAAGATCAAGTCGCCAAGACCCTTGAATCAAATTATCATCAATTCAAGACCAAGTCA-TCAGA
**
30501 CCCTTGAATCAAATCAAAT
65 CCCTCAAATCAAATCAAAT
30520 CAAATCAAGT
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
94 20 0.27
96 18 0.24
97 3 0.04
98 1 0.01
99 32 0.43
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (97 bp):
TTCAAGATCAAGTCGCCAAGACCCTTGAATCAAATTATCATCAATTCAAGACCAAGTCATCAGAC
CCTCAAATCAAATCAAATTCCCAAGTCATCAA
Found at i:32212 original size:60 final size:61
Alignment explanation
Indices: 32119--32248 Score: 226
Period size: 60 Copynumber: 2.1 Consensus size: 61
32109 AATCAACCAA
*
32119 AAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAG-
1 AAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGC
*
32179 AAAAAAAAAGGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGC
1 AAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGC
*
32240 ACAAAAAAA
1 AAAAAAAAA
32249 TGAACTACGT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
60 58 0.88
61 8 0.12
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (61 bp):
AAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGC
Found at i:38553 original size:15 final size:15
Alignment explanation
Indices: 38535--38565 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
38525 TGCATCATTG
38535 ATTGGTGCATGCTAC
1 ATTGGTGCATGCTAC
38550 ATTGGTGCATGCTAC
1 ATTGGTGCATGCTAC
38565 A
1 A
38566 GTTCAAATGC
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:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (15 bp):
ATTGGTGCATGCTAC
Found at i:39674 original size:36 final size:34
Alignment explanation
Indices: 39627--39743 Score: 125
Period size: 36 Copynumber: 3.4 Consensus size: 34
39617 TCTTTTCTAG
* *
39627 ATTAAGCTCTTTATTGACTTCATTTAATTACCTTGA
1 ATTAAGTTCTTTATTGAC-TCACTTAATTACC-TGA
39663 ATTAAGTTCTTTATT--CT-ACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACTCACTTAATTA-CCTGA
*
39695 ATTAAG-CCTTTTATTGACCTCACTTAATTACACTGA
1 ATTAAGTTC-TTTATTGA-CTCACTTAATTAC-CTGA
39731 ATTAAGTTCTTTA
1 ATTAAGTTCTTTA
39744 CTTTACTTAA
Statistics
Matches: 69, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
31 1 0.01
32 23 0.33
33 3 0.04
34 1 0.01
35 3 0.04
36 37 0.54
37 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (34 bp):
ATTAAGTTCTTTATTGACTCACTTAATTACCTGA
Found at i:39696 original size:32 final size:32
Alignment explanation
Indices: 39650--39755 Score: 117
Period size: 32 Copynumber: 3.2 Consensus size: 32
39640 TTGACTTCAT
*
39650 TTAATTACCTTGAATTAAGTTCTTTATTCTAC
1 TTAATTACCCTGAATTAAGTTCTTTATTCTAC
*
39682 TTAATTACCCTGAATTAAG-CCTTTTATTGACCTCAC
1 TTAATTACCCTGAATTAAGTTC-TTTATT---CT-AC
*
39718 TTAATTACACTGAATTAAGTTCTTTACTT-TAC
1 TTAATTACCCTGAATTAAGTTCTTTA-TTCTAC
39750 TTAATT
1 TTAATT
39756 TCCTTTCCTG
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
31 1 0.02
32 32 0.51
33 1 0.02
35 2 0.03
36 24 0.38
37 3 0.05
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.46
Consensus pattern (32 bp):
TTAATTACCCTGAATTAAGTTCTTTATTCTAC
Found at i:39708 original size:68 final size:68
Alignment explanation
Indices: 39627--39755 Score: 192
Period size: 68 Copynumber: 1.9 Consensus size: 68
39617 TCTTTTCTAG
* *
39627 ATTAAGCTCTTTATTGACTTCATTTAATTAC-CTTGAATTAAGTTCTTTA-TTCTACTTAATTAC
1 ATTAAGCTCTTTATTGACCTCACTTAATTACAC-TGAATTAAGTTCTTTACTT-TACTTAATTAC
39690 CCTGA
64 CCTGA
39695 ATTAAGC-CTTTTATTGACCTCACTTAATTACACTGAATTAAGTTCTTTACTTTACTTAATT
1 ATTAAGCTC-TTTATTGACCTCACTTAATTACACTGAATTAAGTTCTTTACTTTACTTAATT
39756 TCCTTTCCTG
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
67 1 0.02
68 52 0.93
69 3 0.05
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.47
Consensus pattern (68 bp):
ATTAAGCTCTTTATTGACCTCACTTAATTACACTGAATTAAGTTCTTTACTTTACTTAATTACCC
TGA
Found at i:39810 original size:35 final size:34
Alignment explanation
Indices: 39759--40480 Score: 838
Period size: 35 Copynumber: 20.5 Consensus size: 34
39749 CTTAATTTCC
*
39759 TTTCC-TGAAATTAAGCCTATGTCTT-TTTACTTAA
1 TTTCCTTGAAATTAAGCC-A-GTCTTCTTTACCTAA
39793 TTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCT-TCTTTACCTAA
* *
39828 TTTCCTAGAAATTAAGCCAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTC--TTCTTTACCTAA
* * *
39864 TTTCCTTGAAACTAAGCCAGTTCTTTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAG-TCTTCTTTACCTAA
* *
39899 TTTCCTAGAAATTAAGCCAGCCTAT-TTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCT-TCTTTACCTAA
39933 TTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCT-TCTTTACCTAA
* *
39968 TTTCCTTGAAATTAAGCCAGTTTTGTCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAG-TCT-TCTTTACCTAA
* * *
40004 TTTCCTTGAAACTAAGCCAGTCCTTTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGT-CTTCTTTACCTAA
*
40039 TTCCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCT-TCTTTACCTAA
*
40074 TTTCCTTGAAATTAAGCCAATCTATCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCT-TCTTTACCTAA
** * * **
40109 AATCCTTGAAATTAAGCTAGTTTTTTCTTTACCTCG
1 TTTCCTTGAAATTAAGCCAG--TCTTCTTTACCTAA
* * *
40145 TTTCCTTGAAACTAAGCCAGTTCTTTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAG-TCTTCTTTACCTAA
*
40180 TTCCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCT-TCTTTACCTAA
* * *
40215 TTTTCTTGAAATTAAGCCAGTGTTTACTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGT-CTT-CTTTACCTAA
40251 TTTCCTTGAAATTAAGCCAGTCTTTACTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTC-TT-CTTTACCTAA
* * *
40287 TTTCCTTGAAACTAAGCCAGTCTTGGTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTT-CTTTACCTAA
*
40322 TTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCT-TCTTTACCTAA
* *
40357 TTTCCTTGAAATTAAGCCAGTCTTGTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTT-CTTTACCTAA
* *
40392 TTTCCTTGAAATTAAGCCAATCTATTCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTC--TTCTTTACCTAA
*
40428 TTTCCTTGAAACTAAGCCAGTCTATCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCT-TCTTTACCTAA
*
40463 TTTCCTTGAAATTTAGCC
1 TTTCCTTGAAATTAAGCC
40481 CTTTTTATTC
Statistics
Matches: 591, Mismatches: 75, Indels: 43
0.83 0.11 0.06
Matches are distributed among these distances:
33 4 0.01
34 47 0.08
35 357 0.60
36 176 0.30
37 7 0.01
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.42
Consensus pattern (34 bp):
TTTCCTTGAAATTAAGCCAGTCTTCTTTACCTAA
Found at i:39894 original size:106 final size:106
Alignment explanation
Indices: 39759--40480 Score: 867
Period size: 106 Copynumber: 6.8 Consensus size: 106
39749 CTTAATTTCC
*
39759 TTTCC-TGAAATTAAGCCTATGTC--TTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATCTT
1 TTTCCTTGAAATTAAGCC-A-GTCTATTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTT
* *
39821 TACCTAATTTCCTAGAAATTAAGCCAGTCTTTTCTTTACCTAG
64 TACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAA
* * * *
39864 TTTCCTTGAAACTAAGCCAGTTCT-TTTTTACTTAATTTCCTAGAAATTAAGCCAGCCTAT-TTT
1 TTTCCTTGAAATTAAGCCAG-TCTATTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTT
*
39927 ACCTAATTTCCTTGAAATTAAGCCAGTC-TATCTTTACCTAA
65 ACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAA
* * * *
39968 TTTCCTTGAAATTAAGCCAGT-TTTGTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCCT-TTT
1 TTTCCTTGAAATTAAGCCAGTCTAT-T-TTTACCTAATTTCCTTGAAATTAAGCCAGT-CTATCT
* * *
40031 TTACTTAATTCCCTTGAAATTAAGCCAGTC-TATCTTTACCTAA
63 TTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAA
* * ** * * *
40074 TTTCCTTGAAATTAAGCCAATCTATCTTTACCTAAAATCCTTGAAATTAAGCTAGTTTTTTCTTT
1 TTTCCTTGAAATTAAGCCAGTCTATTTTTACCTAATTTCCTTGAAATTAAGCCAG-TCTATCTTT
** * *
40139 ACCTCGTTTCCTTGAAACTAAGCCAGT-TCTTT-TTTACTTAA
65 ACCTAATTTCCTTGAAATTAAGCCAGTCT-TTTCTTTACCTAA
* * * * *
40180 TTCCCTTGAAATTAAGCCAGTCTATCTTTACCTAATTTTCTTGAAATTAAGCCAGTGTTTACTTT
1 TTTCCTTGAAATTAAGCCAGTCTATTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTAT-CTTT
* *
40245 ACCTAGTTTCCTTGAAATTAAGCCAGTCTTTACTTTACCTAA
65 ACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAA
* * *
40287 TTTCCTTGAAACTAAGCCAGTCT-TGGTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATCTTT
1 TTTCCTTGAAATTAAGCCAGTCTAT-TTTTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTT
* * *
40351 ACCTAGTTTCCTTGAAATTAAGCCAGTCTTGT-TTTACTTAA
65 ACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAA
* * *
40392 TTTCCTTGAAATTAAGCCAATCTATTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTATCTTT
1 TTTCCTTGAAATTAAGCCAGTCTATT-TTTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTT
*
40457 ACCTAATTTCCTTGAAATTTAGCC
65 ACCTAATTTCCTTGAAATTAAGCC
40481 CTTTTTATTC
Statistics
Matches: 538, Mismatches: 60, Indels: 37
0.85 0.09 0.06
Matches are distributed among these distances:
102 1 0.00
103 2 0.00
104 32 0.06
105 122 0.23
106 317 0.59
107 64 0.12
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.42
Consensus pattern (106 bp):
TTTCCTTGAAATTAAGCCAGTCTATTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTA
CCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAA
Found at i:40131 original size:141 final size:140
Alignment explanation
Indices: 39759--40480 Score: 1069
Period size: 141 Copynumber: 5.1 Consensus size: 140
39749 CTTAATTTCC
*
39759 TTTCC-TGAAATTAAGCCTATGTCT-T-TTTACTTAATTTCCTTGAAATTAAGCCAGTCTATCTT
1 TTTCCTTGAAATTAAGCC-A-GTCTATCTTTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTT
*
39821 TACCTAATTTCCTAGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTT
64 TACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAG-T
39886 CTTTTTTACTTAA
128 CTTTTTTACTTAA
* *
39899 TTTCCTAGAAATTAAGCCAGCCTAT-TTTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTA
1 TTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTA
39963 CCTAATTTCCTTGAAATTAAGCCAGT-TTTGTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCC
66 CCTAATTTCCTTGAAATTAAGCCAGTCTTT-TCTTTACCTAGTTTCCTTGAAACTAAGCCAGT-C
40027 TTTTTTACTTAA
129 TTTTTTACTTAA
* *
40039 TTCCCTTGAAATTAAGCCAGTCTATCTTTACCTAATTTCCTTGAAATTAAGCCAATCTATCTTTA
1 TTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTA
** * * *
40104 CCTAAAATCCTTGAAATTAAGCTAGTTTTTTCTTTACCTCGTTTCCTTGAAACTAAGCCAGTTCT
66 CCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAG-TCT
40169 TTTTTACTTAA
130 TTTTTACTTAA
* * * *
40180 TTCCCTTGAAATTAAGCCAGTCTATCTTTACCTAATTTTCTTGAAATTAAGCCAGTGTTTACTTT
1 TTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAATTTCCTTGAAATTAAGCCAGTCTAT-CTTT
* * *
40245 ACCTAGTTTCCTTGAAATTAAGCCAGTCTTTACTTTACCTAATTTCCTTGAAACTAAGCCAGTCT
65 ACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCT
*
40310 TGGTTTACTTAA
130 T-TTTTACTTAA
* *
40322 TTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAGTTTCCTTGAAATTAAGCCAGTCT-TGTTTT
1 TTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAATTTCCTTGAAATTAAGCCAGTCTAT-CTTT
* * *
40386 ACTTAATTTCCTTGAAATTAAGCCAATCTATTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCT
65 ACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCT
* *
40451 ATCTTTACCTAA
130 -TTTTTACTTAA
*
40463 TTTCCTTGAAATTTAGCC
1 TTTCCTTGAAATTAAGCC
40481 CTTTTTATTC
Statistics
Matches: 532, Mismatches: 40, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
139 7 0.01
140 136 0.26
141 263 0.49
142 126 0.24
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.42
Consensus pattern (140 bp):
TTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTA
CCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTT
TTTTACTTAA
Found at i:41265 original size:32 final size:32
Alignment explanation
Indices: 41229--41324 Score: 97
Period size: 36 Copynumber: 2.9 Consensus size: 32
41219 TAAATTATCT
*
41229 TGAATTAAGTTCTTTATTCTACTTAATTACCC
1 TGAATTAAGTTCTTTATTCTACTTAATTACAC
* *
41261 TGAATTAAG-CCTTTTATTGACCTCACATAATTACAC
1 TGAATTAAGTTC-TTTATT---CT-ACTTAATTACAC
41297 TGAATTAAGTTCTTTACTT-TACTTAATT
1 TGAATTAAGTTCTTTA-TTCTACTTAATT
41325 TCCTCTCCTG
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 1 0.02
32 22 0.42
33 1 0.02
35 2 0.04
36 23 0.44
37 3 0.06
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (32 bp):
TGAATTAAGTTCTTTATTCTACTTAATTACAC
Found at i:41379 original size:35 final size:35
Alignment explanation
Indices: 41333--42438 Score: 1278
Period size: 35 Copynumber: 31.5 Consensus size: 35
41323 TTTCCTCTCC
*
41333 TGAAATTAAGCCTATGTC-TT-TTTACTTAATTTCCT
1 TGAAATTAAGCC-A-GTCTTTCTTTACCTAATTTCCT
*
41368 TGAAATTAAGCCAGTCTATCTTTACCTAATTTCCT
1 TGAAATTAAGCCAGTCTTTCTTTACCTAATTTCCT
*
41403 TGAAATTAAGCCAGTCTTGTCTTTACCTAGTTTCCT
1 TGAAATTAAGCCAGTCTT-TCTTTACCTAATTTCCT
* * * * *
41439 TTAAACTAAGCCAGACCTTT-TTTACTTAATTCCCT
1 TGAAATTAAGCCAG-TCTTTCTTTACCTAATTTCCT
*
41474 TGAAATTAAGCCAGTCTATCTTTACCTAATTTCCT
1 TGAAATTAAGCCAGTCTTTCTTTACCTAATTTCCT
*
41509 TGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCT
1 TGAAATTAAGCCAGTC-TTTCTTTACCTAATTTCCT
* * *
41545 TGAAACTAAGCCAGTTCTTT-TTTACTTAATTTTCT
1 TGAAATTAAGCCAG-TCTTTCTTTACCTAATTTCCT
* *
41580 TGAAATTAAGCCAATCTATCTTTACCTAATTTCCT
1 TGAAATTAAGCCAGTCTTTCTTTACCTAATTTCCT
*
41615 TGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCT
1 TGAAATTAAGCCAGTC-TTTCTTTACCTAATTTCCT
*
41651 TGAAATTAAGCCAGTTCTTT-TTTACTTAATTTCCT
1 TGAAATTAAGCCAG-TCTTTCTTTACCTAATTTCCT
* *
41686 TGAAATTAAGCCAGTCTATCTTTACCTAATTTCTT
1 TGAAATTAAGCCAGTCTTTCTTTACCTAATTTCCT
* * *
41721 TGAAATTAAGCTAGTCTATCTTTATCTAATTTCCT
1 TGAAATTAAGCCAGTCTTTCTTTACCTAATTTCCT
* * *
41756 TGAAATTAAGTCAGTTTTGTCTTTACCTAGTTTCCT
1 TGAAATTAAGCCAGTCTT-TCTTTACCTAATTTCCT
* * *
41792 TGAAACTAAGCCAGTCCTTT-TTTACTTAATTCCCT
1 TGAAATTAAGCCAGT-CTTTCTTTACCTAATTTCCT
*
41827 TGAAATTAAGCCAGTCTATCTTTACCTAATTTCCT
1 TGAAATTAAGCCAGTCTTTCTTTACCTAATTTCCT
* **
41862 TGAAATTAAGCCAGTCTATCTTTACCTAAAATCCT
1 TGAAATTAAGCCAGTCTTTCTTTACCTAATTTCCT
**
41897 TGAAATTAAGCCAGTCTTTTCTTTACCTCGTTT-CT
1 TGAAATTAAGCCAGTC-TTTCTTTACCTAATTTCCT
* * * *
41932 TGAAACTAACCCAGTTCTTT-TTTACTTAATTCCCT
1 TGAAATTAAGCCAG-TCTTTCTTTACCTAATTTCCT
*
41967 TGAAATTAAGCCAGTCTATCTTTACCTAATTTCCT
1 TGAAATTAAGCCAGTCTTTCTTTACCTAATTTCCT
*
42002 TGAAATTAAGCCAGTCTTGT-TTTACTTAATTTCCT
1 TGAAATTAAGCCAGTCTT-TCTTTACCTAATTTCCT
* * *
42037 TGAAATTAAGCTAGTCTATTATTTACCTAGTTTCCT
1 TGAAATTAAGCCAGTCT-TTCTTTACCTAATTTCCT
*
42073 TGAAACTAAGCCAGTCTATT-TTTACCTAATTTCCT
1 TGAAATTAAGCCAGTCT-TTCTTTACCTAATTTCCT
*
42108 TGAAATTAAGCCAGTC--T-TTT--CT--TTACCT
1 TGAAATTAAGCCAGTCTTTCTTTACCTAATTTCCT
* * * *
42136 TGAAACTAAGCCAATTCTTT-TTTACTTAATTCCCT
1 TGAAATTAAGCC-AGTCTTTCTTTACCTAATTTCCT
*
42171 TGAAATTAAGCCAGTCTATCTTTACCTAATTTCCT
1 TGAAATTAAGCCAGTCTTTCTTTACCTAATTTCCT
* *
42206 TAAAATTAAGCCAGTCTTTACTTTACCTAGTTTCCT
1 TGAAATTAAGCCAGTCTTT-CTTTACCTAATTTCCT
*
42242 TGAAACTAAGCCAGTCTTTACTTTTACCTAATTTCCT
1 TGAAATTAAGCCAGTCTTT-C-TTTACCTAATTTCCT
* * * ** * *
42279 TGAAACTAATCCTGTCTTGGTTTACTTAATTTCAT
1 TGAAATTAAGCCAGTCTTTCTTTACCTAATTTCCT
* * *
42314 TGAAATTAAGCCAGTCTATCTTTACCTAGTTTTCT
1 TGAAATTAAGCCAGTCTTTCTTTACCTAATTTCCT
*
42349 TGAAATTAAGCCAGTCTTGT-TTTACTTAATTTCCT
1 TGAAATTAAGCCAGTCTT-TCTTTACCTAATTTCCT
*
42384 TGAAATTAAGCCAGTCTATTCTTTACCTAGTTTCCT
1 TGAAATTAAGCCAGTCT-TTCTTTACCTAATTTCCT
* * *
42420 TGAAACTAAGACAATCTTT
1 TGAAATTAAGCCAGTCTTT
42439 TATCAGTCTA
Statistics
Matches: 915, Mismatches: 122, Indels: 68
0.83 0.11 0.06
Matches are distributed among these distances:
28 16 0.02
29 3 0.00
30 2 0.00
31 4 0.00
32 4 0.00
33 4 0.00
34 33 0.04
35 576 0.63
36 234 0.26
37 39 0.04
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.43
Consensus pattern (35 bp):
TGAAATTAAGCCAGTCTTTCTTTACCTAATTTCCT
Found at i:41462 original size:106 final size:105
Alignment explanation
Indices: 41333--42429 Score: 1280
Period size: 106 Copynumber: 10.4 Consensus size: 105
41323 TTTCCTCTCC
*
41333 TGAAATTAAGCCTATGTC--TTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTA
1 TGAAATTAAGCC-A-GTCTATTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTA
*
41396 ATTTCCTTGAAATTAAGCCAGTCTTGTCTTTACCTAGTTTCCT
64 ATTTCCTTGAAATTAAGCCAGTCTT-TCTTTACCTAATTTCCT
* * * * *
41439 TTAAACTAAGCCAGACCT-TTTTTACTTAATTCCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
1 TGAAATTAAGCCAG-TCTATTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
*
41503 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCT
65 TTTCCTTGAAATTAAGCCAGTC-TTTCTTTACCTAATTTCCT
* * * *
41545 TGAAACTAAGCCAGTTCT-TTTTTACTTAATTTTCTTGAAATTAAGCCAATCTATCTTTACCTAA
1 TGAAATTAAGCCAG-TCTATTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
*
41609 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCT
65 TTTCCTTGAAATTAAGCCAGTC-TTTCTTTACCTAATTTCCT
*
41651 TGAAATTAAGCCAGTTCT-TTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
1 TGAAATTAAGCCAG-TCTATTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
* * * *
41715 TTTCTTTGAAATTAAGCTAGTCTATCTTTATCTAATTTCCT
65 TTTCCTTGAAATTAAGCCAGTCTTTCTTTACCTAATTTCCT
* * * * * *
41756 TGAAATTAAGTCAGT-TTTGTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCCT-TTTTTACTT
1 TGAAATTAAGCCAGTCTAT-T-TTTACCTAATTTCCTTGAAATTAAGCCAGT-CTATCTTTACCT
* *
41819 AATTCCCTTGAAATTAAGCCAGTCTATCTTTACCTAATTTCCT
63 AATTTCCTTGAAATTAAGCCAGTCTTTCTTTACCTAATTTCCT
* ** * **
41862 TGAAATTAAGCCAGTCTATCTTTACCTAAAATCCTTGAAATTAAGCCAGTCTTTTCTTTACCTCG
1 TGAAATTAAGCCAGTCTATTTTTACCTAATTTCCTTGAAATTAAGCCAGTC-TATCTTTACCTAA
* * * *
41927 TTT-CTTGAAACTAACCCAGTTCTTT-TTTACTTAATTCCCT
65 TTTCCTTGAAATTAAGCCAG-TCTTTCTTTACCTAATTTCCT
* * *
41967 TGAAATTAAGCCAGTCTATCTTTACCTAATTTCCTTGAAATTAAGCCAGTCT-TGTTTTACTTAA
1 TGAAATTAAGCCAGTCTATTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTAT-CTTTACCTAA
* * *
42031 TTTCCTTGAAATTAAGCTAGTCTATTATTTACCTAGTTTCCT
65 TTTCCTTGAAATTAAGCCAGTCT-TTCTTTACCTAATTTCCT
*
42073 TGAAACTAAGCCAGTCTATTTTTACCTAATTTCCTTGAAATTAAGCCAGTC--T-TTT--CT--T
1 TGAAATTAAGCCAGTCTATTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAAT
* * * * *
42131 TACCTTGAAACTAAGCCAATTCTTT-TTTACTTAATTCCCT
66 TTCCTTGAAATTAAGCC-AGTCTTTCTTTACCTAATTTCCT
* * * *
42171 TGAAATTAAGCCAGTCTATCTTTACCTAATTTCCTTAAAATTAAGCCAGTCTTTACTTTACCTAG
1 TGAAATTAAGCCAGTCTATTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTAT-CTTTACCTAA
*
42236 TTTCCTTGAAACTAAGCCAGTCTTTACTTTTACCTAATTTCCT
65 TTTCCTTGAAATTAAGCCAGTCTTT-C-TTTACCTAATTTCCT
* * * * * * *
42279 TGAAACTAATCCTGTCT-TGGTTTACTTAATTTCATTGAAATTAAGCCAGTCTATCTTTACCTAG
1 TGAAATTAAGCCAGTCTAT-TTTTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
* *
42343 TTTTCTTGAAATTAAGCCAGTCTTGT-TTTACTTAATTTCCT
65 TTTCCTTGAAATTAAGCCAGTCTT-TCTTTACCTAATTTCCT
* *
42384 TGAAATTAAGCCAGTCTATTCTTTACCTAGTTTCCTTGAAACTAAG
1 TGAAATTAAGCCAGTCTATT-TTTACCTAATTTCCTTGAAATTAAG
42430 ACAATCTTTT
Statistics
Matches: 867, Mismatches: 93, Indels: 62
0.85 0.09 0.06
Matches are distributed among these distances:
98 60 0.07
99 17 0.02
100 5 0.01
101 1 0.00
102 3 0.00
103 5 0.01
104 19 0.02
105 185 0.21
106 475 0.55
107 39 0.04
108 58 0.07
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.43
Consensus pattern (105 bp):
TGAAATTAAGCCAGTCTATTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAAT
TTCCTTGAAATTAAGCCAGTCTTTCTTTACCTAATTTCCT
Found at i:41484 original size:141 final size:137
Alignment explanation
Indices: 41313--42429 Score: 1291
Period size: 141 Copynumber: 7.9 Consensus size: 137
41303 AAGTTCTTTA
* *
41313 CTTTACTTAATTTCCTCTCCTGAAATTAAGCCTATGTCT-T-TTTACTTAATTTCCTTGAAATTA
1 CTTTACTTAATTT-C-CT--TGAAATTAAGCC-A-GTCTATCTTTACCTAGTTTCCTTGAAATTA
* * *
41376 AGCCAGTCTATCTTTACCTAATTTCCTTGAAATTAAGCCAGTCTTGTCTTTACCTAGTTTCCTTT
60 AGCCAGTCT-TTTTTACCTAATTTCCTTGAAATTAAGCCAGTC-T-TCTTTACCTAATTTCCTTG
*
41441 AAACTAAGCCAGACCTT
122 AAACTAAGCCAG-TCTT
* * *
41458 TTTTACTTAATTCCCTTGAAATTAAGCCAGTCTATCTTTACCTAATTTCCTTGAAATTAAGCCAG
1 CTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAGTTTCCTTGAAATTAAGCCAG
* * * * * *
41523 TCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTTCTTTTTTACTTAATTTTCTTGAAATTA
66 TC-TTT-TTTACCTAATTTCCTTGAAATTAAGCCAG-TCTTCTTTACCTAATTTCCTTGAAACTA
*
41588 AGCCAATCTAT
128 AGCCAGTCT-T
* *
41599 CTTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAATTAAGCCA
1 CTTTACTTAATTTCCTTGAAATTAAGCCAGTC-TATCTTTACCTAGTTTCCTTGAAATTAAGCCA
* * *
41664 GTTCTTTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAATTTCTTTGAAATTA
65 G-TCTTTTTTACCTAATTTCCTTGAAATTAAGCCAGTCT-TCTTTACCTAATTTCCTTGAAACTA
*
41729 AGCTAGTCTAT
128 AGCCAGTCT-T
* * * *
41740 CTTTA-TCTAATTTCCTTGAAATTAAGTCAGTTTTGTCTTTACCTAGTTTCCTTGAAACTAAGCC
1 CTTTACT-TAATTTCCTTGAAATTAAGCCAG-TCTATCTTTACCTAGTTTCCTTGAAATTAAGCC
* * *
41804 AGTCCTTTTTTACTTAATTCCCTTGAAATTAAGCCAGTCTATCTTTACCTAATTTCCTTGAAATT
64 AGT-CTTTTTTACCTAATTTCCTTGAAATTAAGCCAGTCT-TCTTTACCTAATTTCCTTGAAACT
41869 AAGCCAGTCTAT
127 AAGCCAGTCT-T
* ** * * * *
41881 CTTTACCTAAAATCCTTGAAATTAAGCCAGTCTTTTCTTTACCTCGTTT-CTTGAAACTAACCCA
1 CTTTACTTAATTTCCTTGAAATTAAGCCAGTC-TATCTTTACCTAGTTTCCTTGAAATTAAGCCA
* * *
41945 GTTCTTTTTTACTTAATTCCCTTGAAATTAAGCCAGTCTATCTTTACCTAATTTCCTTGAAATTA
65 G-TCTTTTTTACCTAATTTCCTTGAAATTAAGCCAGTCT-TCTTTACCTAATTTCCTTGAAACTA
42010 AGCCAGTCTT
128 AGCCAGTCTT
* * * *
42020 GTTTTACTTAATTTCCTTGAAATTAAGCTAGTCTATTATTTACCTAGTTTCCTTGAAACTAAGCC
1 -CTTTACTTAATTTCCTTGAAATTAAGCCAGTCTA-TCTTTACCTAGTTTCCTTGAAATTAAGCC
*
42085 AGTCTATTTTTACCTAATTTCCTTGAAATTAAGCCAGTC-T-TTT--CT--TTACCTTGAAACTA
64 AGTCT-TTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTTCTTTACCTAATTTCCTTGAAACTA
*
42144 AGCCAATTCTT
128 AGCC-AGTCTT
* * * *
42155 TTTTACTTAATTCCCTTGAAATTAAGCCAGTCTATCTTTACCTAATTTCCTTAAAATTAAGCCAG
1 CTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAGTTTCCTTGAAATTAAGCCAG
* *
42220 TCTTTACTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTACTTTTACCTAATTTCCTTGAAAC
66 TCTTT--TTTACCTAATTTCCTTGAAATTAAGCCAGTC-TT-C-TTTACCTAATTTCCTTGAAAC
* *
42285 TAATCCTGTCTT
126 TAAGCCAGTCTT
* * *
42297 GGTTTACTTAATTTCATTGAAATTAAGCCAGTCTATCTTTACCTAGTTTTCTTGAAATTAAGCCA
1 -CTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAGTTTCCTTGAAATTAAGCCA
* *
42362 GTCTTGTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATTCTTTACCTAGTTTCCTTGAAACT
65 GTCTT-TTTTACCTAATTTCCTTGAAATTAAGCCAGTC--TTCTTTACCTAATTTCCTTGAAACT
42427 AAG
127 AAG
42430 ACAATCTTTT
Statistics
Matches: 856, Mismatches: 82, Indels: 72
0.85 0.08 0.07
Matches are distributed among these distances:
132 2 0.00
133 30 0.04
134 77 0.09
135 5 0.01
136 3 0.00
138 3 0.00
139 10 0.01
140 137 0.16
141 392 0.46
142 97 0.11
143 87 0.10
144 2 0.00
145 11 0.01
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.43
Consensus pattern (137 bp):
CTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAGTTTCCTTGAAATTAAGCCAG
TCTTTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTTCTTTACCTAATTTCCTTGAAACTAAGC
CAGTCTT
Found at i:42172 original size:63 final size:62
Alignment explanation
Indices: 42070--42197 Score: 195
Period size: 63 Copynumber: 2.0 Consensus size: 62
42060 TACCTAGTTT
* *
42070 CCTTGAAACTAAGCCAGTCTATTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTA
1 CCTTGAAACTAAGCCAGTCTATTTTTACCTAATTCCCTTGAAATTAAGCCAGTC-TATCTTTA
* *
42133 CCTTGAAACTAAGCCAATTCT-TTTTTACTTAATTCCCTTGAAATTAAGCCAGTCTATCTTTA
1 CCTTGAAACTAAGCC-AGTCTATTTTTACCTAATTCCCTTGAAATTAAGCCAGTCTATCTTTA
42195 CCT
1 CCT
42198 AATTTCCTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
62 10 0.17
63 46 0.77
64 4 0.07
ACGTcount: A:0.27, C:0.23, G:0.09, T:0.41
Consensus pattern (62 bp):
CCTTGAAACTAAGCCAGTCTATTTTTACCTAATTCCCTTGAAATTAAGCCAGTCTATCTTTA
Found at i:42457 original size:11 final size:11
Alignment explanation
Indices: 42441--42511 Score: 65
Period size: 11 Copynumber: 6.5 Consensus size: 11
42431 CAATCTTTTA
42441 TCAGTCTAATT
1 TCAGTCTAATT
**
42452 TCAGTCTTCTT
1 TCAGTCTAATT
* *
42463 TCAATCTGATT
1 TCAGTCTAATT
42474 TCAG-CTTAATT
1 TCAGTC-TAATT
*
42485 ATCAGTCT-TTT
1 -TCAGTCTAATT
42496 TCAGTCTAATT
1 TCAGTCTAATT
42507 TCAGT
1 TCAGT
42512 TTTGTTTCAG
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
10 8 0.17
11 33 0.70
12 5 0.11
13 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.48
Consensus pattern (11 bp):
TCAGTCTAATT
Found at i:42519 original size:22 final size:23
Alignment explanation
Indices: 42438--42522 Score: 63
Period size: 22 Copynumber: 3.8 Consensus size: 23
42428 AGACAATCTT
* *
42438 TTATCAGTCTAATTTCAGTCTT-C
1 TTATCAGTCT-TTTTCAGTCTTAA
* *
42461 TT-TCAATCTGATTTCAG-CTTAA
1 TTATCAGTCT-TTTTCAGTCTTAA
42483 TTATCAGTCTTTTTCAGTC-TAA
1 TTATCAGTCTTTTTCAGTCTTAA
*
42505 TT-TCAGTTTTGTTTCAGT
1 TTATCAGTCTT-TTTCAGT
42523 TTTCTTTTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
21 10 0.19
22 33 0.63
23 9 0.17
ACGTcount: A:0.21, C:0.18, G:0.11, T:0.51
Consensus pattern (23 bp):
TTATCAGTCTTTTTCAGTCTTAA
Found at i:42548 original size:12 final size:12
Alignment explanation
Indices: 42516--42548 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
42506 TTCAGTTTTG
*
42516 TTTCAGTTTTCT
1 TTTCAGTCTTCT
42528 TTT-AGTCTTCT
1 TTTCAGTCTTCT
42539 TTTCAGTCTT
1 TTTCAGTCTT
42549 TTTCTTTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.09, C:0.18, G:0.09, T:0.64
Consensus pattern (12 bp):
TTTCAGTCTTCT
Done.