Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010839.1 Corchorus capsularis cultivar CVL-1 contig10860, 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: 137938
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7544 original size:87 final size:87
Alignment explanation
Indices: 7409--7585 Score: 300
Period size: 87 Copynumber: 2.0 Consensus size: 87
7399 TTCAATGCAC
** *
7409 TTCTTTGTCCTCTCGGATTCCTCATTTTCCTCCTTGCACTCTTCCCCATCTAATTCTCGGCAGTT
1 TTCTTTGTCCTCTCAAATTCCTCATTTTCCTCCCTGCACTCTTCCCCATCTAATTCTCGGCAGTT
*
7474 TTCTGACTCAGCTTCAGATCTT
66 TTCTGAATCAGCTTCAGATCTT
* *
7496 TTCTTTTTCCTCTCAAATTCCTCATTTTCCTCCCTGCACTCTTCCCCATCTAATTCTTGGCAGTT
1 TTCTTTGTCCTCTCAAATTCCTCATTTTCCTCCCTGCACTCTTCCCCATCTAATTCTCGGCAGTT
7561 TTCTGAATCAGCTTCAGATCTT
66 TTCTGAATCAGCTTCAGATCTT
7583 TTC
1 TTC
7586 CTCTGAGGAA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.14, C:0.33, G:0.10, T:0.44
Consensus pattern (87 bp):
TTCTTTGTCCTCTCAAATTCCTCATTTTCCTCCCTGCACTCTTCCCCATCTAATTCTCGGCAGTT
TTCTGAATCAGCTTCAGATCTT
Found at i:14166 original size:2 final size:2
Alignment explanation
Indices: 14159--14194 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
14149 GTTTTGAATA
*
14159 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14195 GATTATGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:15806 original size:22 final size:22
Alignment explanation
Indices: 15780--15826 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
15770 ATTTATTCAT
15780 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
15802 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
15824 TAT
1 TAT
15827 ATAGTATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:15822 original size:11 final size:11
Alignment explanation
Indices: 15780--15822 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
15770 ATTTATTCAT
*
15780 TATTAATTAAC
1 TATTAATTAGC
*
15791 TATTAATTAGA
1 TATTAATTAGC
15802 TATTAATTAGC
1 TATTAATTAGC
15813 TATTAATTAG
1 TATTAATTAG
15823 ATATATAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:16762 original size:20 final size:19
Alignment explanation
Indices: 16721--16766 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
16711 CATGTCATCA
*
16721 TTGACTTTGACTTTGATAG
1 TTGACTTTGACTTTGACAG
*
16740 TTGACTATTGACTTTGACCG
1 TTGACT-TTGACTTTGACAG
16760 TTGACTT
1 TTGACTT
16767 CCATGAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.46
Consensus pattern (19 bp):
TTGACTTTGACTTTGACAG
Found at i:19151 original size:13 final size:13
Alignment explanation
Indices: 19114--19171 Score: 61
Period size: 12 Copynumber: 4.7 Consensus size: 13
19104 TTATGCACCC
*
19114 AAAACATTTAT-C
1 AAAACATTTATAT
19126 AAAACATTT-TAT
1 AAAACATTTATAT
19138 AAAACATTTATAT
1 AAAACATTTATAT
*
19151 AAAA-ATAGTA-AT
1 AAAACAT-TTATAT
19163 AAAACATTT
1 AAAACATTT
19172 CCTCAACGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 1 0.03
12 27 0.69
13 11 0.28
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (13 bp):
AAAACATTTATAT
Found at i:20422 original size:60 final size:60
Alignment explanation
Indices: 20329--20494 Score: 260
Period size: 60 Copynumber: 2.8 Consensus size: 60
20319 GCTAATTGTT
* * *
20329 CAAATAAGGGCCTAAGGTTTGACAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTGAATTTGGC
** *
20389 CAAATAAATGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTCCGATCTTTGAATTTGGC
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTGAATTTGGC
* *
20449 CGAATAAGGGCCTAATGTTTGCCAAAATGCCCAAATAAGGGTCTGA
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTCTGA
20495 CTCACGCGTC
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 95 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTGAATTTGGC
Found at i:20487 original size:31 final size:30
Alignment explanation
Indices: 20329--20489 Score: 103
Period size: 31 Copynumber: 5.3 Consensus size: 30
20319 GCTAATTGTT
* *
20329 CAAATAAGGGCCTAAGGTTTGACAAAATGCT
1 CAAATAAGGGCCTAATGTTTG-CAAAATGCC
* * * * ** *
20360 CAAATAAGGGTCTGATCTTT-TAATTTGGC
1 CAAATAAGGGCCTAATGTTTGCAAAATGCC
** *
20389 CAAATAAATGCCTAATGTTTGCCAAAATGCT
1 CAAATAAGGGCCTAATGTTTG-CAAAATGCC
* * ** *
20420 CAAATAAGGGTCC-GATCTTTG-AATTTGGC
1 CAAATAAGGG-CCTAATGTTTGCAAAATGCC
*
20449 CGAATAAGGGCCTAATGTTTGCCAAAATGCC
1 CAAATAAGGGCCTAATGTTTG-CAAAATGCC
20480 CAAATAAGGG
1 CAAATAAGGG
20490 TCTGACTCAC
Statistics
Matches: 90, Mismatches: 34, Indels: 12
0.66 0.25 0.09
Matches are distributed among these distances:
28 2 0.02
29 38 0.42
31 48 0.53
32 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (30 bp):
CAAATAAGGGCCTAATGTTTGCAAAATGCC
Found at i:20559 original size:31 final size:31
Alignment explanation
Indices: 20524--20591 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
20514 GATACCAAGA
*
20524 CCTTATCCGAGCATTTTCGATAACGTTAGGC
1 CCTTATCCGAGCATTTTCGATAACGTTAGAC
** *
20555 CCTTATTTGAGTATTTTCGATAACGTTAGAC
1 CCTTATCCGAGCATTTTCGATAACGTTAGAC
20586 CCTTAT
1 CCTTAT
20592 TTGGCCAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (31 bp):
CCTTATCCGAGCATTTTCGATAACGTTAGAC
Found at i:20619 original size:60 final size:60
Alignment explanation
Indices: 20552--20714 Score: 238
Period size: 60 Copynumber: 2.7 Consensus size: 60
20542 GATAACGTTA
* *
20552 GGCCCTTATTTGAGTATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAACATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAACATCG
* * *
20612 GGCCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTAGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAACATCG
* * *
20672 GACCCTTATTTAAGCATTTTGGCA-AACGTTAGGCCCTTATTTG
1 GGCCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
20715 AGCAATTAGC
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
60 91 0.99
61 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAACATCG
Found at i:20623 original size:29 final size:29
Alignment explanation
Indices: 20585--20682 Score: 90
Period size: 29 Copynumber: 3.3 Consensus size: 29
20575 TAACGTTAGA
20585 CCCTTATTTGGCCAAATTAAAACATCGGG
1 CCCTTATTTGGCCAAATTAAAACATCGGG
** * **
20614 CCCTTATTTGAG-CATTTTCAATAACGTTAGG
1 CCCTTATTTG-GCCAAATT-AA-AACATCGGG
* * *
20645 CCCTTATTTAGCCAAATTAAAAGATCGGA
1 CCCTTATTTGGCCAAATTAAAACATCGGG
20674 CCCTTATTT
1 CCCTTATTT
20683 AAGCATTTTG
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
29 27 0.52
30 6 0.12
31 19 0.37
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTAAAACATCGGG
Found at i:20650 original size:31 final size:30
Alignment explanation
Indices: 20532--20718 Score: 134
Period size: 31 Copynumber: 6.2 Consensus size: 30
20522 GACCTTATCC
*
20532 GAGCATTTTCGATAACGTTAGGCCCTTATTT
1 GAGCATTTTC-AAAACGTTAGGCCCTTATTT
* * *
20563 GAGTATTTTCGATAACGTTAGACCCTTATTT
1 GAGCATTTTC-AAAACGTTAGGCCCTTATTT
** * **
20594 G-GCCAAATT-AAAACATCGGGCCCTTATTT
1 GAG-CATTTTCAAAACGTTAGGCCCTTATTT
20623 GAGCATTTTCAATAACGTTAGGCCCTTATTT
1 GAGCATTTTCAA-AACGTTAGGCCCTTATTT
** * *
20654 -AGCCAAATT-AAAA-GATCGGACCCTTATTT
1 GAG-CATTTTCAAAACGTTAGG-CCCTTATTT
*
20683 AAGCATTTTGGC-AAACGTTAGGCCCTTATTT
1 GAGCATTTT--CAAAACGTTAGGCCCTTATTT
20714 GAGCA
1 GAGCA
20719 ATTAGCCTTT
Statistics
Matches: 121, Mismatches: 24, Indels: 22
0.72 0.14 0.13
Matches are distributed among these distances:
28 4 0.03
29 35 0.29
30 10 0.08
31 68 0.56
32 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (30 bp):
GAGCATTTTCAAAACGTTAGGCCCTTATTT
Found at i:22635 original size:31 final size:29
Alignment explanation
Indices: 22600--22677 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
22590 TTTAATACCT
22600 AAATTAGCCCCTTAACTATTCATTTTGGGAC
1 AAATTAGCCCCTTAACT-TT-ATTTTGGGAC
* * * *
22631 AAATTGGCTCTTTAACTTTTTTTTGGGAC
1 AAATTAGCCCCTTAACTTTATTTTGGGAC
22660 AAATT-GACCCC-TAACTTT
1 AAATTAG-CCCCTTAACTTT
22678 TAAAAACGAG
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 8 0.20
29 16 0.40
30 2 0.05
31 14 0.35
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.40
Consensus pattern (29 bp):
AAATTAGCCCCTTAACTTTATTTTGGGAC
Found at i:22675 original size:28 final size:29
Alignment explanation
Indices: 22622--22678 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
22612 TAACTATTCA
* **
22622 TTTTGGGACAAATTGGCTCTTTAACTTTT
1 TTTTGGGACAAATTGACTCCCTAACTTTT
22651 TTTTGGGACAAATTGAC-CCCTAACTTTT
1 TTTTGGGACAAATTGACTCCCTAACTTTT
22679 AAAAACGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.44
Consensus pattern (29 bp):
TTTTGGGACAAATTGACTCCCTAACTTTT
Found at i:27443 original size:7 final size:7
Alignment explanation
Indices: 27430--27459 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
27420 TAATTCTCTC
27430 ACTCGCA
1 ACTCGCA
*
27437 CCTCGCA
1 ACTCGCA
27444 ACTCGCA
1 ACTCGCA
27451 ACTCGCA
1 ACTCGCA
27458 AC
1 AC
27460 AGCCTAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.27, C:0.47, G:0.13, T:0.13
Consensus pattern (7 bp):
ACTCGCA
Found at i:27588 original size:40 final size:40
Alignment explanation
Indices: 27533--27612 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
27523 TCAGTCTTGG
27533 GCATGCGTTTTCAAAATCTAGTCTTTCTTCTTAATTTGAT
1 GCATGCGTTTTCAAAATCTAGTCTTTCTTCTTAATTTGAT
27573 GCATGCGTTTTCAAAATCTAGTCTTTCTTCTTAATTTGAT
1 GCATGCGTTTTCAAAATCTAGTCTTTCTTCTTAATTTGAT
27613 ACATATATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.47
Consensus pattern (40 bp):
GCATGCGTTTTCAAAATCTAGTCTTTCTTCTTAATTTGAT
Found at i:39723 original size:14 final size:14
Alignment explanation
Indices: 39702--39735 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
39692 TAAGAGCAGA
39702 CCTTTTTTTTTT-T
1 CCTTTTTTTTTTCT
39715 CCTTTTTTTTTTCT
1 CCTTTTTTTTTTCT
39729 CCTTTTT
1 CCTTTTT
39736 ACGTTAGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
CCTTTTTTTTTTCT
Found at i:39734 original size:12 final size:13
Alignment explanation
Indices: 39702--39735 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
39692 TAAGAGCAGA
*
39702 CCTTTTTTTTTTT
1 CCTTTTTTTTTCT
39715 CCTTTTTTTTTTCT
1 CC-TTTTTTTTTCT
39729 CCTTTTT
1 CCTTTTT
39736 ACGTTAGAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
CCTTTTTTTTTCT
Found at i:50342 original size:7 final size:7
Alignment explanation
Indices: 50331--50385 Score: 83
Period size: 7 Copynumber: 7.9 Consensus size: 7
50321 CTGAGGACCC
50331 ACCCCAA
1 ACCCCAA
*
50338 TCCCCAA
1 ACCCCAA
*
50345 TCCCCAA
1 ACCCCAA
*
50352 TCCCCAA
1 ACCCCAA
50359 ACCCCAA
1 ACCCCAA
50366 ACCCCAA
1 ACCCCAA
50373 ACCCCAA
1 ACCCCAA
50380 ACCCCA
1 ACCCCA
50386 TACCGTGTCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.36, C:0.58, G:0.00, T:0.05
Consensus pattern (7 bp):
ACCCCAA
Found at i:59893 original size:23 final size:22
Alignment explanation
Indices: 59835--59899 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 22
59825 GATGATTATT
*
59835 CCTCTATTCCTTTTTAATTGTC
1 CCTCTATTTCTTTTTAATTGTC
59857 CATCTCCCTTATTTCTTTTTAATTGTC
1 C--CT--C-TATTTCTTTTTAATTGTC
59884 CCTCATATTTCTTTTT
1 CCTC-TATTTCTTTTT
59900 CAGAAATACG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
22 1 0.03
23 12 0.33
24 2 0.06
25 2 0.06
26 1 0.03
27 18 0.50
ACGTcount: A:0.14, C:0.26, G:0.03, T:0.57
Consensus pattern (22 bp):
CCTCTATTTCTTTTTAATTGTC
Found at i:72379 original size:19 final size:20
Alignment explanation
Indices: 72342--72382 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
72332 TAGCTCTAGC
*
72342 ACTAAGAGATGTAAAAATTG
1 ACTAAGACATGTAAAAATTG
72362 ACTAAGACATGT-AAAATTG
1 ACTAAGACATGTAAAAATTG
72381 AC
1 AC
72383 ACAGTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.24
Consensus pattern (20 bp):
ACTAAGACATGTAAAAATTG
Found at i:73008 original size:73 final size:72
Alignment explanation
Indices: 72890--73036 Score: 267
Period size: 73 Copynumber: 2.0 Consensus size: 72
72880 TCTGCATCAC
72890 AAATTTGAGGATTACAAACAGGTTCTATGCTACTTTTAGTAAATCAAACAACTATTCAAGCTCTA
1 AAATTTGAGGATTACAAACAGGTTCTATGCTACTTTTAGTAAATCAAACAACTATTCAAGCTCTA
72955 CAAAATG
66 CAAAATG
* *
72962 AAATTTGAGGATTACAAACAGGTTTCTATGCTACTTTTAGTAAATCAAAGAACTATTCGAGCTCT
1 AAATTTGAGGATTACAAACAGG-TTCTATGCTACTTTTAGTAAATCAAACAACTATTCAAGCTCT
73027 ACAAAATG
65 ACAAAATG
73035 AA
1 AA
73037 TAAGACAAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
72 22 0.31
73 50 0.69
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.31
Consensus pattern (72 bp):
AAATTTGAGGATTACAAACAGGTTCTATGCTACTTTTAGTAAATCAAACAACTATTCAAGCTCTA
CAAAATG
Found at i:77197 original size:12 final size:11
Alignment explanation
Indices: 77170--77195 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
77160 ATTTGCTGTC
77170 TTTTCTTTTTT
1 TTTTCTTTTTT
77181 TTTTCTTTTTT
1 TTTTCTTTTTT
77192 TTTT
1 TTTT
77196 TCGCTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:100464 original size:4 final size:4
Alignment explanation
Indices: 100455--100485 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
100445 TATTTTTTTC
100455 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
100486 ATACTTCCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TCTT
Found at i:103435 original size:6 final size:6
Alignment explanation
Indices: 103426--103452 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
103416 ATCTGCAGCA
103426 GCAGGG GCAGGG GCAGGG GCAGGG GCA
1 GCAGGG GCAGGG GCAGGG GCAGGG GCA
103453 TCGGCTGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.63, T:0.00
Consensus pattern (6 bp):
GCAGGG
Found at i:110122 original size:33 final size:32
Alignment explanation
Indices: 110080--110160 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 32
110070 TACACTGAGT
110080 CTCCCCACTAGGACGCTTCAGCCAC-GGCAGAGC
1 CTCCCCACTAGGACGCTTCA-CCACGGGCA-AGC
*
110113 CTCCCCACTAGGGCGGCTTCACCACGGGCAAGC
1 CTCCCCACTAGGAC-GCTTCACCACGGGCAAGC
* *
110146 CGCCCCACTGGGACG
1 CTCCCCACTAGGACG
110161 GCACGAGTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 1 0.02
33 31 0.74
34 10 0.24
ACGTcount: A:0.19, C:0.43, G:0.27, T:0.11
Consensus pattern (32 bp):
CTCCCCACTAGGACGCTTCACCACGGGCAAGC
Found at i:115604 original size:2 final size:2
Alignment explanation
Indices: 115599--115704 Score: 83
Period size: 2 Copynumber: 53.5 Consensus size: 2
115589 AAGAAACGTT
* * * *
115599 TC TC TC TT TC TC TT TC TC TC TC TC TC TC TC CC TC TC TG TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * *
115641 TC TC TGC TC TG TG TC TC TT TC TC TC TC -C TC GC T- TC TC TT TC
1 TC TC T-C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
115682 TT TC TC TC TC TAC T- TC TC TC TC T
1 TC TC TC TC TC T-C TC TC TC TC TC T
115705 TTATATTTCA
Statistics
Matches: 81, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
1 3 0.04
2 74 0.91
3 4 0.05
ACGTcount: A:0.01, C:0.42, G:0.05, T:0.53
Consensus pattern (2 bp):
TC
Found at i:132619 original size:45 final size:47
Alignment explanation
Indices: 132570--132659 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 47
132560 TTCAACAATA
*
132570 AAAAATTG-AATAC-ATTTT-TAGAA-AAATCAATTGAACAAAAAAATT
1 AAAAA-TGAAATACAATTTTATA-AATAAATCAATAGAACAAAAAAATT
*
132615 AAAAATGAAATACAATTTTATAAATAAATCAATAGAATAAAAAAA
1 AAAAATGAAATACAATTTTATAAATAAATCAATAGAACAAAAAAA
132660 AGCTTCACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
44 2 0.05
45 10 0.26
46 7 0.18
47 20 0.51
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.27
Consensus pattern (47 bp):
AAAAATGAAATACAATTTTATAAATAAATCAATAGAACAAAAAAATT
Found at i:132816 original size:19 final size:18
Alignment explanation
Indices: 132782--132835 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 18
132772 TTTTAATAAG
*
132782 TATTCTTTTTAGTAATT-
1 TATTTTTTTTAGTAATTC
132799 TATTTTTTTTGAGATAATTC
1 TATTTTTTTT-AG-TAATTC
* *
132819 AATTTTTTTTATTAATT
1 TATTTTTTTTAGTAATT
132836 ATGGAAAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 9 0.29
18 7 0.23
19 6 0.19
20 9 0.29
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.65
Consensus pattern (18 bp):
TATTTTTTTTAGTAATTC
Found at i:132976 original size:21 final size:20
Alignment explanation
Indices: 132937--132979 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
132927 TTTTTCGATT
*
132937 ATAATATAATATATTTAATC
1 ATAATATAATATATATAATC
*
132957 ATAATATTATAATATATAATC
1 ATAATATAAT-ATATATAATC
132978 AT
1 AT
132980 GAAACTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAATATAATATATATAATC
Found at i:134250 original size:323 final size:320
Alignment explanation
Indices: 133539--134380 Score: 906
Period size: 323 Copynumber: 2.6 Consensus size: 320
133529 TTTAGCCGAT
* * * * * * * *
133539 ATCATGTACTAAGCATCACGGTTTTTGGATAGAAACCCGT-TTAGGAGCCCCGACTCAA-TTTTG
1 ATCATGTACTAACCACCACGGTTTTGGGCTAAAAACACGTATCAGG-GTCCCGACT-AAGTTTTG
* * * * * *
133602 CATGATTTTTGGCGCAAAGACTCCATGAAATATCTATATTCATCGAATCAAATGT-CAGTCACAT
64 CATGATTTTTGACGAAAAGATTCCTTGAAATATCTATATTCATCGAACCAAAT-TCCAGCCACAT
* * * * * *
133666 TGGATATATGGTTTTGTTTTTACAAGCATCTGAATCTTAATTATTTTGATTTAATAAGAAATTAA
128 TGGATATAAGGATTTGTTTTTACGAGCATCTGAATC----TTGTTTCGATTTAATTAGAAATTAA
* * * *
133731 TTCGGAAAAAAAGGGAAAACGGTATTAGAAGCGTGAAAGGCCCGAAAATAATTTTGACATTGAAT
189 TTCGGAAAAAAAGGAAAAACGATATTAGAAACGTGAAAAGCCCGAAAATAATTTTGACATTGAAT
* *
133796 TATATATTTTTTCGGAGTATTGTGGTAAAAAATTGAGAAAAAACTCTTCAGGTCAATTTTGAGTC
254 TATATATTTTTTC-GAGTATTGTGGAAAAAAATAGAGAAAAAACTCTTCAGGTCAATTTTGAGTC
133861 AAA
318 AAA
* * * *
133864 ATCGTGTACTAACCATCACGGTTTTGGGCTAAAAACGCGTATCAGGGTCCCGACTCAGTTTTGCA
1 ATCATGTACTAACCACCACGGTTTTGGGCTAAAAACACGTATCAGGGTCCCGACTAAGTTTTGCA
*
133929 TGATTTTTGACTGAAAAGATTCCTTAAAATATCTATATTCATCGAACCAAATTCCAGCCACATTG
66 TGATTTTTGAC-GAAAAGATTCCTTGAAATATCTATATTCATCGAACCAAATTCCAGCCACATTG
133994 GATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGA
130 GATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGA
* * ** * ** * *
134059 AAAAATGGAAAAATGATATTAGAAACGTGAAAAGCCCGTCATTCGTTTTGGCGTTGAATTATATA
195 AAAAAAGGAAAAACGATATTAGAAACGTGAAAAGCCCGAAAATAATTTTGACATTGAATTATATA
* * * * * *
134124 TGTTATTT-GAGTGTTGTGGCAAAAAAATAGAGAAAAAACTCTTCATGTTAGTTTTTAGTCGAA
260 T-TT-TTTCGAGTATTGTGG-AAAAAAATAGAGAAAAAACTCTTCAGGTCAATTTTGAGTCAAA
* * * *** *
134187 ATCATGTACTAACCACCACTGTTTTGTGCTAAAAACACGTTTCAGGGTTGTGCCTAAGTTTTGCA
1 ATCATGTACTAACCACCACGGTTTTGGGCTAAAAACACGTATCAGGGTCCCGACTAAGTTTTGCA
* * * *
134252 TGATTTTTGGAAGAAATGCTT-CTTGAAATATCTATATTCGTCTAATCAAACCAAA-TCTCAGCC
66 TGATTTTT-GACGAAAAGATTCCTTGAAATATCTATA-T--TC--ATCGAACCAAATTC-CAGCC
* * * * *
134315 ACAATGAATTTAAAGATGTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA-TAA
124 ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
134379 TT
189 TT
134381 TTTTTTTTAA
Statistics
Matches: 439, Mismatches: 64, Indels: 27
0.83 0.12 0.05
Matches are distributed among these distances:
322 105 0.24
323 108 0.25
324 6 0.01
325 62 0.14
326 87 0.20
327 71 0.16
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (320 bp):
ATCATGTACTAACCACCACGGTTTTGGGCTAAAAACACGTATCAGGGTCCCGACTAAGTTTTGCA
TGATTTTTGACGAAAAGATTCCTTGAAATATCTATATTCATCGAACCAAATTCCAGCCACATTGG
ATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAA
AAAAAGGAAAAACGATATTAGAAACGTGAAAAGCCCGAAAATAATTTTGACATTGAATTATATAT
TTTTTCGAGTATTGTGGAAAAAAATAGAGAAAAAACTCTTCAGGTCAATTTTGAGTCAAA
Found at i:134288 original size:322 final size:319
Alignment explanation
Indices: 133539--134380 Score: 881
Period size: 322 Copynumber: 2.6 Consensus size: 319
133529 TTTAGCCGAT
* * * * * * * *
133539 ATCATGTACTAAGCATCACGGTTTTTGGATAGAAACCCGT-TTAGGAGCCCCGACTCAA-TTTTG
1 ATCATGTACTAACCACCACGGTTTTGGGCTAAAAACACGTATCAGG-GTCCCGACT-AAGTTTTG
* * * * *
133602 CATGATTTTTGG-CGCAAAGACTCCATGAAATATCTATATTCATCGAATCAAATGT-CAGTCACA
64 CATGATTTTTGGAAG-AAAG-CTTCTTGAAATATCTATATTCATCGAACCAAAT-TCCAGCCACA
* * * * * *
133665 TTGGATATATGGTTTTGTTTTTACAAGCATCTGAATCTTAATTATTTTGATTTAATAAGAAATTA
126 TTGGATATAAGGATTTGTTTTTACGAGCATCTGAATC----TTGTTTCGATTTAATTAGAAATTA
* * * *
133730 ATTCGGAAAAAAAGGGAAAACGGTATTAGAAGCGTGAAAGGCCCGAAAATAATTTTGACATTGAA
187 ATTCGGAAAAAAAGGAAAAACGATATTAGAAACGTGAAAAGCCCGAAAATAATTTTGACATTGAA
* *
133795 TTATATATTTTTTCGGAGTATTGTGGTAAAAAATTGAGAAAAAACTCTTCAGGTCAATTTTGAGT
252 TTATATATTTTTTC-GAGTATTGTGGAAAAAAATAGAGAAAAAACTCTTCAGGTCAATTTTGAGT
133860 CAAA
316 CAAA
* * * *
133864 ATCGTGTACTAACCATCACGGTTTTGGGCTAAAAACGCGTATCAGGGTCCCGACTCAGTTTTGCA
1 ATCATGTACTAACCACCACGGTTTTGGGCTAAAAACACGTATCAGGGTCCCGACTAAGTTTTGCA
* * *
133929 TGATTTTT-GACTGAAAAGATTCCTTAAAATATCTATATTCATCGAACCAAATTCCAGCCACATT
66 TGATTTTTGGA-AG-AAAGCTT-CTTGAAATATCTATATTCATCGAACCAAATTCCAGCCACATT
133993 GGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG
128 GGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG
* * ** * ** * *
134058 AAAAAATGGAAAAATGATATTAGAAACGTGAAAAGCCCGTCATTCGTTTTGGCGTTGAATTATAT
193 AAAAAAAGGAAAAACGATATTAGAAACGTGAAAAGCCCGAAAATAATTTTGACATTGAATTATAT
* * * * * *
134123 ATGTTATTT-GAGTGTTGTGGCAAAAAAATAGAGAAAAAACTCTTCATGTTAGTTTTTAGTCGAA
258 AT-TT-TTTCGAGTATTGTGG-AAAAAAATAGAGAAAAAACTCTTCAGGTCAATTTTGAGTCAAA
* * * *** *
134187 ATCATGTACTAACCACCACTGTTTTGTGCTAAAAACACGTTTCAGGGTTGTGCCTAAGTTTTGCA
1 ATCATGTACTAACCACCACGGTTTTGGGCTAAAAACACGTATCAGGGTCCCGACTAAGTTTTGCA
*
134252 TGATTTTTGGAAGAAATGCTTCTTGAAATATCTATATTCGTCTAATCAAACCAAA-TCTCAGCCA
66 TGATTTTTGGAAGAAA-GCTTCTTGAAATATCTATA-T--TC--ATCGAACCAAATTC-CAGCCA
* * * * *
134316 CAATGAATTTAAAGATGTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA-TAAT
124 CATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAAT
134380 T
189 T
134381 TTTTTTTTAA
Statistics
Matches: 436, Mismatches: 64, Indels: 33
0.82 0.12 0.06
Matches are distributed among these distances:
322 108 0.25
323 105 0.24
324 7 0.02
325 61 0.14
326 84 0.19
327 71 0.16
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (319 bp):
ATCATGTACTAACCACCACGGTTTTGGGCTAAAAACACGTATCAGGGTCCCGACTAAGTTTTGCA
TGATTTTTGGAAGAAAGCTTCTTGAAATATCTATATTCATCGAACCAAATTCCAGCCACATTGGA
TATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAA
AAAAGGAAAAACGATATTAGAAACGTGAAAAGCCCGAAAATAATTTTGACATTGAATTATATATT
TTTTCGAGTATTGTGGAAAAAAATAGAGAAAAAACTCTTCAGGTCAATTTTGAGTCAAA
Found at i:136069 original size:322 final size:321
Alignment explanation
Indices: 134672--136718 Score: 2763
Period size: 321 Copynumber: 6.4 Consensus size: 321
134662 ATTCCACTCG
* *
134672 CAAATCCTTATATCCAATGTGGCTGATATTTGATTCGATGAATATAGATATTTCAAGGAGTTTTT
1 CAAATCCTTATATCCAATGTGGCTGACATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTT
* * ** *
134737 GCGCAAAAAATCATGCAAAATTAAGCCAAGGCTCCGGAACGCATTTTTAGCCAAAAACCGTGATG
66 GCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
* * * *
134802 GTTATTACACGATTTCGGCTAAAAATTGTCCCGAAAAATATTTTCT-AAATTTTTGAACACAATA
131 GTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAACATTTTCTCAAATTTTT-AACACAATA
* * * * *
134866 GTTAG-AAAAATTTATAATTCAACGCCAAAAATATTGGCAGGTTTTACACGGTTCAAATATGGTT
195 ATCAGAAAAAATTTATAATTCAACGCCAAAAAGATTGGCAGGTTTTTCAC-CTTCAAATATGGTT
* *
134930 TTTCCATTTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGA-TTGAGATACTCGTAAAAA
259 TTTCCA-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGACTT-AGATGCTCGTAAAAA
** * * * * *
134994 CAAATCCTTATATCCAATGCAGCTCACA-TTGATTTGATAAATATAGATATTTTAAGGAGTTTTT
1 CAAATCCTTATATCCAATGTGGCTGACATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTT
* *
135058 GCG-CAAAAATCATGCAAAATTGAGTCGGGGCTTCGGAACGCGTTTTTAGCCAAAAACCGTGATG
66 GCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
* * *
135122 GTTAGTACACGATTTCGACTAAAAACTGACCCGAAAAACATTTTCACAATTTTTTAACACAATAA
131 GTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAACATTTTCTCAAATTTTTAACACAATAA
*
135187 TCAGAAAAAATTTATAATTCAACGCCAAAAAGATTGACAGGTTTTTCATCCTTCAAATATGGTTT
196 TCAGAAAAAATTTATAATTCAACGCCAAAAAGATTGGCAGGTTTTTCA-CCTTCAAATATGGTTT
* *
135252 TTCCATCTTTTTTCTGAATTAATTTTTAATTAAATCGAAACAAGACTTAGATGCTCGTAAAAA
260 TTCCAT-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGACTTAGATGCTCGTAAAAA
* *
135315 CAAATCCTTATATCCAATGTGGCTGACATTTGATTCGATGAATATAGATATTTCGAGGAATCTTT
1 CAAATCCTTATATCCAATGTGGCTGACATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTT
* * *
135380 GCTCCAAAAATCATGCAAAATTGAGCCGGGGCTACGGAACGCGTTTTTAGCCAAAAACTGTGATG
66 GCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
135445 GTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAACATTTTCTCAAATTTTTAACACAATAA
131 GTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAACATTTTCTCAAATTTTTAACACAATAA
135510 TCAGAAAAAAATTTATAATTCAACGCCAAAAAGATTGGCAGGTTTTTCATACCATTCAAATATGG
196 TCAG-AAAAAATTTATAATTCAACGCCAAAAAGATTGGCAGGTTTTTC--ACC-TTCAAATATGG
*
135575 TTTTTCCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGACTTAGATGCACGTAAAA
257 TTTTTCCA-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGACTTAGATGCTCGTAAAA
135640 A
321 A
* * * *
135641 CAAATCCTTATATCCAATGTGGCTGACATTAGATTCGACGAATATAGATATTTCGAGGAATCTTT
1 CAAATCCTTATATCCAATGTGGCTGACATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTT
* *
135706 GCTCCAAAAATCATGCAAAATTGAGCCGGGGCTCTGGAACGCGTTTTTAGCCAAAAACCGTGATG
66 GCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
*
135771 GTTAGTACACGATTTCGGCTAAAAGCTGACCCGAAAAACATTTTCTCAAATTTTTAACACAATAA
131 GTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAACATTTTCTCAAATTTTTAACACAATAA
*
135836 TCAGAAAAAATTTATAATTCAACGCCAAAAATATTGGCAGGTTTTTCACCATTCAAATATGGTTT
196 TCAGAAAAAATTTATAATTCAACGCCAAAAAGATTGGCAGGTTTTTCACC-TTCAAATATGGTTT
* *
135901 TTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGACTTAGATGCACGTAAATA
260 TTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGACTTAGATGCTCGTAAAAA
* * * *
135963 CAAATCCTAATATCCAATGTGGCTGACATTTGATTCCATGAATATAGATATTTCAAAGAGTATTT
1 CAAATCCTTATATCCAATGTGGCTGACATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTT
* *
136028 GCGCCAAAAATCATGCAAAATTAAGCCGGGGCTCCGGAACGCGTTTTT-------ATCC---A--
66 GCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
* * ** *
136081 ---AGTACACGATTTCGGCTAAAAACTGACCCGAAAAGCATTTTCTCAATTTTTTGCCACAATAG
131 GTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAACATTTTCTCAAATTTTTAACACAATAA
*
136143 TCAGAAAAAATTTATAATTCAACGGCAAAAAGATTGGCAGGTTTTTCACGCTTCAAATATGGTTT
196 TCAGAAAAAATTTATAATTCAACGCCAAAAAGATTGGCAGGTTTTTCAC-CTTCAAATATGGTTT
* ** * *
136208 TTCCATTTTTTTCCTAATTAATTTCTAATTAAATCGAATGAAGACTGAGATGCGCGTAAAAA
260 TTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGACTTAGATGCTCGTAAAAA
* * **
136270 CAAATCCTTATATCCAATGTGGTTGACATTTGATTCGACGAATATAGATATTTTGAGGAGTCTTT
1 CAAATCCTTATATCCAATGTGGCTGACATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTT
* * * * * * * *
136335 GCTCCAAAAATCATTCAAAATTGA-CCCGGGATCCGAAACACATTTTTAGCCAAAAACTGTGATG
66 GCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
* ** * * * ** * *
136399 GTTACTACACGATTTCGATTAAAAACTGTCCTGAAAAACATTTTCTCAATTTTTTCCCACAACAC
131 GTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAACATTTTCTCAAATTTTTAACACAATAA
* * * * * * *** **
136464 TCAGAAAAAATATATAATTCAACGCTAAAAATATTAGCGGGTTGTTCACGCTTCCTGTATCATTT
196 TCAGAAAAAATTTATAATTCAACGCCAAAAAGATTGGCAGGTTTTTCAC-CTTCAAATATGGTTT
* * * *
136529 TTCCA-TTTTTTCTGGATTAATTTCTAATTAAATCGAAACAAGA-TTGAGATGCTCTTAAATA
260 TTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGACTT-AGATGCTCGTAAAAA
* * * * * *
136590 CAAATCTTTATATCCAATGTGGCTGACATTTGATTCCATGAATGTAGATATTTCAAAGAGTATAT
1 CAAATCCTTATATCCAATGTGGCTGACATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTT
* ** * * *
136655 GCGCCAAAAACCATGCAAAATAAAGTCAGGGCTTCGGAACGCGTTTTTAGCCAAAAACCGTGAT
66 GCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGAT
136719 TTTTAACATA
Statistics
Matches: 1541, Mismatches: 154, Indels: 61
0.88 0.09 0.03
Matches are distributed among these distances:
306 18 0.01
307 251 0.16
308 1 0.00
312 1 0.00
313 2 0.00
315 3 0.00
316 1 0.00
319 1 0.00
320 226 0.15
321 320 0.21
322 217 0.14
323 147 0.10
324 42 0.03
325 44 0.03
326 266 0.17
327 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (321 bp):
CAAATCCTTATATCCAATGTGGCTGACATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTT
GCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
GTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAACATTTTCTCAAATTTTTAACACAATAA
TCAGAAAAAATTTATAATTCAACGCCAAAAAGATTGGCAGGTTTTTCACCTTCAAATATGGTTTT
TCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGACTTAGATGCTCGTAAAAA
Found at i:137622 original size:323 final size:322
Alignment explanation
Indices: 136735--137938 Score: 1517
Period size: 324 Copynumber: 3.7 Consensus size: 322
136725 CATATTAAAT
* *
136735 AGAAAAAATTTATAATTCAACGCCAAAAAGATTGGCAGGTTTTTCACGCTTCAAATATGGGTTTT
1 AGAAAAAATTTATAATTCAACGCCAAAAAGATTGACAGGTTTTTCACGCTTCAAATATGGTTTTT
*
136800 CCATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATACTCGTAAAAGCAAAT
66 CCATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGTAAAA-CAAAT
* * * ** *
136865 CTTTATCTCCAATG-CAGCTCACATTTGATTTGATGAATATAGATATTTCAAGGAGTCTTTGCGC
130 CCTTATATCCAATGTCA-CTGACATTTGATTCAATGAATATAGATATTTCAAAGAGTCTTTGCGC
* **
136929 CAAAAATTATGCAAAAATTGAGCCGGGGCTCCAGAACACGTTTTTAGCCAAAATTCGTGATGGTT
194 CAAAAATCATGC-AAAATTGAGCCGGGGCTCCAGAACACGTTTTTAGCCAAAAACCGTGATGGTT
*
136994 AGTACACGATTTCGGCTAAAAACTGACCCGAAAA-CTATTTTCTCAATTTTTTTGCCACAATAGT
258 AGTACACGATTTCGGCTAAAAACTGACCCGAAAAGC-ATTTTCTCAATTTTTTTACCACAATAGT
137058 C
322 C
* * *
137059 AGAAAAGATTTATAATTCAACGCCAAAAAGATTGACAGGTTTTTCACGCTTCGAATATAGTTTTT
1 AGAAAAAATTTATAATTCAACGCCAAAAAGATTGACAGGTTTTTCACGCTTCAAATATGGTTTTT
** ** * * * * *
137124 CCATTCGAATACGCTTCAAATAGTTAATTTATAATTAAATCGAAATAAGACTGATATGCTTGTAA
66 CCATT----T--TTTTCTGA-A-TTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGT-A
** * * * * * * *
137189 AAACAAATCCTTATATCCAATGTGGCTGAAATTTAATTCGACGAATAAAGATATTTC-AAGGGTT
122 AAACAAATCCTTATATCCAATGTCACTGACATTTGATTCAATGAATATAGATATTTCAAAGAGTC
* *
137253 TTGTGCACCAAAAATCGTGCAAAATTGAGCCGGGGCTCCAGAACACG-TTTTAGCCAAAAACCGT
187 TT-TGCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCAGAACACGTTTTTAGCCAAAAACCGT
* * * * *
137317 AATGGTTAGTACACGATTTCGGCTAAAAATTGTCCCGAAAAGCAATTTCTCAATTTTTTTAACAC
251 GATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGCATTTTCTCAATTTTTTTACCAC
137382 AATAGTC
316 AATAGTC
*
137389 AGAAAAAAATTTATAATTCAACGCCAAAAAGATTGGCAGGTTTTTCACGCTTCAAATATGGTTTT
1 AG-AAAAAATTTATAATTCAACGCCAAAAAGATTGACAGGTTTTTCACGCTTCAAATATGGTTTT
* * *
137454 TCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATAGAGATGCTCATAAATACAAA
65 TCCATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGTAAA-ACAAA
* *
137519 TCCTAATATCCAATGTCACTGACATTTGATTCAATGAATATAGATATTTCAAAGAGTATTTGCGC
129 TCCTTATATCCAATGTCACTGACATTTGATTCAATGAATATAGATATTTCAAAGAGTCTTTGCGC
* *
137584 CAAAAATCATGCAAAATTAAGCCGGGGCTCCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTA
194 CAAAAATCATGCAAAATTGAGCCGGGGCTCCAGAACACGTTTTTAGCCAAAAACCGTGATGGTTA
* * * * * *
137649 CTACACGATTTCGACTAAAAACTGACCAGAAAAGCATTTTCTCAA--TTTTTCCCACAACACTC
259 GTACACGATTTCGGCTAAAAACTGACCCGAAAAGCATTTTCTCAATTTTTTTACCACAATAGTC
* * * * * * *
137711 AGAAAAAATATATAATTCATCGCTAAAAATATTGAC-GGCTTTTTCACACTTCCAATATCGTTTT
1 AGAAAAAATTTATAATTCAACGCCAAAAAGATTGACAGG-TTTTTCACGCTTCAAATATGGTTTT
137775 TCCA-TTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGTAAAA-AAAT
65 TCCATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGTAAAACAAAT
** * * * * * *
137838 CCTTATATCCAATCACACTGAGATTTTGCTTCAATGAAAATAGATATTTTAAGGAGCCTTTGCGC
130 CCTTATATCCAATGTCACTGACA-TTTGATTCAATGAATATAGATATTTCAAAGAGTCTTTGCGC
** * *
137903 CAAAAATCCGGCAAAATTGAGCCGGTGCTCCGGAAC
194 CAAAAATCATGCAAAATTGAGCCGGGGCTCCAGAAC
Statistics
Matches: 758, Mismatches: 104, Indels: 41
0.84 0.12 0.05
Matches are distributed among these distances:
318 23 0.03
319 68 0.09
320 53 0.07
321 55 0.07
322 18 0.02
323 120 0.16
324 136 0.18
325 4 0.01
327 1 0.00
328 1 0.00
330 85 0.11
331 99 0.13
332 91 0.12
333 4 0.01
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (322 bp):
AGAAAAAATTTATAATTCAACGCCAAAAAGATTGACAGGTTTTTCACGCTTCAAATATGGTTTTT
CCATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGTAAAACAAATC
CTTATATCCAATGTCACTGACATTTGATTCAATGAATATAGATATTTCAAAGAGTCTTTGCGCCA
AAAATCATGCAAAATTGAGCCGGGGCTCCAGAACACGTTTTTAGCCAAAAACCGTGATGGTTAGT
ACACGATTTCGGCTAAAAACTGACCCGAAAAGCATTTTCTCAATTTTTTTACCACAATAGTC
Done.