Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005114.1 Hibiscus syriacus cultivar Beakdansim tig00011501_pilon, 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: 90943
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:938 original size:18 final size:17
Alignment explanation
Indices: 915--953 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
905 ATAATTCATA
915 TAAAATACAAAAAATATT
1 TAAAATACAAAAAAT-TT
*
933 TAAAATACAAATAATTT
1 TAAAATACAAAAAATTT
950 TAAA
1 TAAA
954 TTTCTAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAATACAAAAAATTT
Found at i:5105 original size:2 final size:2
Alignment explanation
Indices: 5098--5173 Score: 129
Period size: 2 Copynumber: 39.0 Consensus size: 2
5088 AAGTTTGACA
5098 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5138 AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5174 GTATGTATGT
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
1 2 0.03
2 68 0.97
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6544 original size:68 final size:68
Alignment explanation
Indices: 6472--6602 Score: 235
Period size: 68 Copynumber: 1.9 Consensus size: 68
6462 AATTTTTTTT
* **
6472 GGATTTGTCAAAATGACCAACAAAATTGCAATTCGATCGCTAATTCGCAACGCGATCTCCATTTT
1 GGATTTGTCAAAATGACCAACAAAATCGCAATGAGATCGCTAATTCGCAACGCGATCTCCATTTT
6537 TCC
66 TCC
6540 GGATTTGTCAAAATGACCAACAAAATCGCAATGAGATCGCTAATTCGCAACGCGATCTCCATT
1 GGATTTGTCAAAATGACCAACAAAATCGCAATGAGATCGCTAATTCGCAACGCGATCTCCATT
6603 ATCGCAAATC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 60 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (68 bp):
GGATTTGTCAAAATGACCAACAAAATCGCAATGAGATCGCTAATTCGCAACGCGATCTCCATTTT
TCC
Found at i:6695 original size:21 final size:21
Alignment explanation
Indices: 6644--6696 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
6634 ATTATGACTA
6644 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* **
6665 TTGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
6686 TCGCAATGCGA
1 TCGCAATGCGA
6697 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:6729 original size:21 final size:21
Alignment explanation
Indices: 6686--6758 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
6676 TTTTCCCAAT
* *
6686 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTAGAAAA
6706 TCGCAATGCGAATTTAGAAAA
1 TCGCAATGCGAATTTAGAAAA
*
6727 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTAGAAAA
*
6748 TCGCAACGCGA
1 TCGCAATGCGA
6759 TACTAACTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
20 12 0.25
21 36 0.75
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTTAGAAAA
Found at i:6772 original size:20 final size:20
Alignment explanation
Indices: 6747--6841 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 20
6737 AATTTGGAAA
6747 ATCGCAACGCGATACTAACT
1 ATCGCAACGCGATACTAACT
* **
6767 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATACTA-ACT
*
6788 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTAACT
* *
6808 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTAACT
* *
6828 TTCGCAACGAGATA
1 ATCGCAACGCGATA
6842 ATACATAATC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
20 49 0.75
21 16 0.25
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGATACTAACT
Found at i:6820 original size:41 final size:41
Alignment explanation
Indices: 6744--6821 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
6734 GCGAATTTGG
6744 AAAATCGCAACGCGATACTAACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTAACTATCGCAACGCGATAATAC
* *
6785 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA
1 AAAATCGCAACGCGATACTAACTATCGCAACGCGATA
6822 CTGACTTTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTAACTATCGCAACGCGATAATAC
Found at i:7055 original size:22 final size:22
Alignment explanation
Indices: 7028--7090 Score: 117
Period size: 22 Copynumber: 2.9 Consensus size: 22
7018 CACTCTCTCA
*
7028 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGGCGAAATCCGTC
7050 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGGCGAAATCCGTC
7072 CCCATCTCCGGCGAAATCC
1 CCCATCTCCGGCGAAATCC
7091 ATCTATCTCC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.46, G:0.16, T:0.17
Consensus pattern (22 bp):
CCCATCTCCGGCGAAATCCGTC
Found at i:7402 original size:20 final size:20
Alignment explanation
Indices: 7353--7411 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
7343 TTTATTCTCT
* **
7353 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
7373 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
7393 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
7412 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:7602 original size:25 final size:24
Alignment explanation
Indices: 7548--7602 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
7538 TGTTTATTAT
* *
7548 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
7572 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
7598 TGTTT
1 TGTTT
7603 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:8752 original size:18 final size:18
Alignment explanation
Indices: 8731--8778 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
8721 TCCACTTCGG
8731 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
8749 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
8767 GAGCCATCACCT
1 GAGCCATCACCT
8779 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:9369 original size:19 final size:20
Alignment explanation
Indices: 9326--9370 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
9316 CGCAACACGA
*
9326 AAATGACTATCGTAATGCGG
1 AAATGACTATCGCAATGCGG
*
9346 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCGG
9365 AAATGA
1 AAATGA
9371 AAATCGCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:9376 original size:19 final size:19
Alignment explanation
Indices: 9354--9450 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
9344 GGAAATGGCT
9354 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
9373 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
9387 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
9406 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
9420 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
9439 ATCGCAATGCGA
1 ATCGCAATGCGA
9451 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:9389 original size:14 final size:14
Alignment explanation
Indices: 9370--9428 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
9360 ATGCGAAATG
9370 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
9384 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
9403 AAAATCGCAACGAC
1 AAAATCGCAACGAC
9417 AAAATCGCAACG
1 AAAATCGCAACG
9429 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:9396 original size:33 final size:33
Alignment explanation
Indices: 9354--9445 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
9344 GGAAATGGCT
9354 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
9387 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
9420 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
9446 TGCGATTTGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:9494 original size:33 final size:33
Alignment explanation
Indices: 9457--9533 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 33
9447 GCGATTTGTG
*
9457 TTTCGCGTTGCAATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCAATTTTGTCGTTGCGATTTTCA
9490 TTTCGCATTGCAATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCAATTTTGTCGTTGCGATTTTCA
9523 TTTCGCATTGC
1 TTTCGCATTGC
9534 GATAGCCATT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (33 bp):
TTTCGCATTGCAATTTTGTCGTTGCGATTTTCA
Found at i:9505 original size:19 final size:19
Alignment explanation
Indices: 9478--9536 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
9468 AATTTTGTCG
9478 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
9497 TTGC-AATTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
9511 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
9530 TTGCGAT
1 TTGCGAT
9537 AGCCATTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 4 0.13
15 4 0.13
16 4 0.13
17 4 0.13
18 4 0.13
19 11 0.35
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:9566 original size:20 final size:20
Alignment explanation
Indices: 9543--9581 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
9533 CGATAGCCAT
9543 TTTCGCGTTGCGAAAGTAAG
1 TTTCGCGTTGCGAAAGTAAG
*
9563 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCGAAAGTAA
9582 ACTATTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (20 bp):
TTTCGCGTTGCGAAAGTAAG
Found at i:9957 original size:21 final size:21
Alignment explanation
Indices: 9931--9998 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
9921 CTGTCATCCC
9931 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCCAATCGT
* * * *
9952 TCAAGAGGCCCCTATCATTC-C
1 TCAAGAGTCCCCT-CCAATCGT
*
9973 TCAAGAGTCCCC-CC-ACCGT
1 TCAAGAGTCCCCTCCAATCGT
9992 TCAAGAG
1 TCAAGAG
9999 GCCACTGTCA
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
18 1 0.03
19 8 0.22
21 23 0.64
22 4 0.11
ACGTcount: A:0.25, C:0.38, G:0.16, T:0.21
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCAATCGT
Found at i:10019 original size:40 final size:40
Alignment explanation
Indices: 9924--10009 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
9914 GACTCACCTG
* * *
9924 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATTCCTCAAGAGTCCCC-CC-ACCGTTCAAGAGGCCACTA
*
9966 TCATTCCTCAAGAGTCCCCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCAAGAGTCCCCCCACCGTTCAAGAGGCCACTA
10006 TCAT
1 TCAT
10010 CGTTGAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 20 0.50
41 2 0.05
42 18 0.45
ACGTcount: A:0.23, C:0.40, G:0.15, T:0.22
Consensus pattern (40 bp):
TCATTCCTCAAGAGTCCCCCCACCGTTCAAGAGGCCACTA
Found at i:11654 original size:19 final size:20
Alignment explanation
Indices: 11632--11680 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
11622 AAAATCGCAA
*
11632 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTCCATTTTCGCGT
**
11651 TGCGATAGCCATTTTCGCGT
1 TGCGATTTCCATTTTCGCGT
11671 TGCGATTTCC
1 TGCGATTTCC
11681 CCGTTGCGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.41
Consensus pattern (20 bp):
TGCGATTTCCATTTTCGCGT
Found at i:11969 original size:21 final size:21
Alignment explanation
Indices: 11943--12018 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
11933 CGAAAGTCAG
11943 TATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATTTTGTAT
* *
11964 TATCGCGTTGCGA--TAGTCAG
1 TATCGCGTTGCGATTTTGT-AT
11984 TATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATTTTGTAT
12005 TATCGCGTTGCGAT
1 TATCGCGTTGCGAT
12019 AGTCAGTATC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.06
20 14 0.29
21 28 0.58
22 3 0.06
ACGTcount: A:0.16, C:0.17, G:0.26, T:0.41
Consensus pattern (21 bp):
TATCGCGTTGCGATTTTGTAT
Found at i:11997 original size:20 final size:20
Alignment explanation
Indices: 11908--12038 Score: 131
Period size: 20 Copynumber: 6.5 Consensus size: 20
11898 TTCAGAATTT
* *
11908 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGATAGTCAGTATCG
* *
11928 CGTTTCGAAAGTCAGTATCG
1 CGTTGCGATAGTCAGTATCG
* *
11948 CGTTGCGATTTTGT-ATTATCG
1 CGTTGCGA--TAGTCAGTATCG
11969 CGTTGCGATAGTCAGTATCG
1 CGTTGCGATAGTCAGTATCG
* *
11989 CGTTGCGATTTTGT-ATTATCG
1 CGTTGCGA--TAGTCAGTATCG
12010 CGTTGCGATAGTCAGTATCG
1 CGTTGCGATAGTCAGTATCG
*
12030 CATTGCGAT
1 CGTTGCGAT
12039 TTTCCAAATT
Statistics
Matches: 92, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
19 6 0.07
20 53 0.58
21 28 0.30
22 5 0.05
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAGTATCG
Found at i:12059 original size:41 final size:41
Alignment explanation
Indices: 11924--12041 Score: 209
Period size: 41 Copynumber: 2.9 Consensus size: 41
11914 GAAAGTCAGA
* *
11924 ATCGCGTTTCGAAAGTCAGTATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTGTATT
11965 ATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTGTATT
*
12006 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTT
12042 CCAAATTCGC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 74 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTGTATT
Found at i:12071 original size:20 final size:21
Alignment explanation
Indices: 12027--12078 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
12017 ATAGTCAGTA
*
12027 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
12048 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
12068 TCGCATTGCGA
1 TCGCATTGCGA
12079 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:12120 original size:21 final size:22
Alignment explanation
Indices: 12068--12120 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
12058 ATTTACTTAT
12068 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
** *
12089 TCGCAACGCGAAATT-GTAAAA
1 TCGCATTGCGAAATTGGGAAAA
12110 TCGCATTGCGA
1 TCGCATTGCGA
12121 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:13613 original size:130 final size:128
Alignment explanation
Indices: 13401--13647 Score: 343
Period size: 130 Copynumber: 1.9 Consensus size: 128
13391 GAATAGCAAT
* * * *
13401 GAATGTTCATCATATTTTAAAAGTGTCAAGTCTTAGCTTGAATTTGCTGTCCCTAGTAAGAATAG
1 GAATATTCATCATATTTTAAAAATGTCAAGGCGTAGCTTGAATTTGCTGTCCCTAGTAAGAATAG
* *
13466 CACAGCACTGATTAGAGCCTTGAATC-CGGTTTACGGTATATACACATATCAACATTCGAACCG
66 CAAAGCACTGATTAGAGCCTTGAATCAC-GTTTACAGTATATACACATATCAACATTCGAACCG
* *
13529 GAATATTCATCATATTTATAAAAATGTTACAGGCGTAGCTTGAATTTGCTGTCCTTAGTAAGAAT
1 GAATATTCATCATATTT-TAAAAATGTCA-AGGCGTAGCTTGAATTTGCTGTCCCTAGTAAGAAT
* * * **
13594 TGCAAAGCATTGATTAGAGCCTTGGATCACGTTTACAGTATATATGCATATCAA
64 AGCAAAGCACTGATTAGAGCCTTGAATCACGTTTACAGTATATACACATATCAA
13648 GGTTCGATAC
Statistics
Matches: 103, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
128 16 0.16
129 9 0.09
130 77 0.75
131 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (128 bp):
GAATATTCATCATATTTTAAAAATGTCAAGGCGTAGCTTGAATTTGCTGTCCCTAGTAAGAATAG
CAAAGCACTGATTAGAGCCTTGAATCACGTTTACAGTATATACACATATCAACATTCGAACCG
Found at i:14893 original size:75 final size:75
Alignment explanation
Indices: 14797--14946 Score: 255
Period size: 75 Copynumber: 2.0 Consensus size: 75
14787 TTAGAAATTC
* *
14797 AAAATACAAATCAAACACTATAATTTTATATTTTTATTAAATAAATCAAATAAGATATATAACAT
1 AAAATACAAATAAAACACTATAATTTTATATTTTTATTAAACAAATCAAATAAGATATATAACAT
14862 TTGCACTATT
66 TTGCACTATT
* * *
14872 AAAATATAAATAAAACACTATAATTTTATTTTTTTATTAAACAAATCAAATAAGGTATATAACAT
1 AAAATACAAATAAAACACTATAATTTTATATTTTTATTAAACAAATCAAATAAGATATATAACAT
14937 TTGCACTATT
66 TTGCACTATT
14947 GTATCTCGTA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (75 bp):
AAAATACAAATAAAACACTATAATTTTATATTTTTATTAAACAAATCAAATAAGATATATAACAT
TTGCACTATT
Found at i:15478 original size:6 final size:6
Alignment explanation
Indices: 15460--15495 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
15450 AAACTACCTA
* *
15460 TTCATC TTTATC TTCATC TTCTTC TTCATC TTCATC
1 TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC
15496 GTAGTTGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.14, C:0.31, G:0.00, T:0.56
Consensus pattern (6 bp):
TTCATC
Found at i:21787 original size:60 final size:59
Alignment explanation
Indices: 21689--21875 Score: 198
Period size: 60 Copynumber: 3.1 Consensus size: 59
21679 TTTGGATGAA
* * * *
21689 TTTGTGGATGAAATTGGAA-GATCTAAAAGTTTAAGGACTAATTTAGAATGAGACTCATAG
1 TTTGGGGATGAAATT-GAATGTTC-AAAAGTTTAAGGACTAATTTAAAATGAGAATCATAG
* * *
21749 TTTGGGGATGAAATTAGAATGTTCAAAAGTTTAAGGACTAA-TTATAATGAGAATCACAA
1 TTTGGGGATGAAATT-GAATGTTCAAAAGTTTAAGGACTAATTTAAAATGAGAATCATAG
* * * * * **
21808 TTTGTGGATGAAATTGTAATTTTTAAAAATTTAAGGAGTAATTTAAAATGAGTGTCATAG
1 TTTGGGGATGAAATTG-AATGTTCAAAAGTTTAAGGACTAATTTAAAATGAGAATCATAG
21868 TTTGGGGA
1 TTTGGGGA
21876 CACAATGCAA
Statistics
Matches: 106, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
58 1 0.01
59 48 0.45
60 54 0.51
61 3 0.03
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (59 bp):
TTTGGGGATGAAATTGAATGTTCAAAAGTTTAAGGACTAATTTAAAATGAGAATCATAG
Found at i:21841 original size:59 final size:59
Alignment explanation
Indices: 21687--21859 Score: 195
Period size: 59 Copynumber: 2.9 Consensus size: 59
21677 TATTTGGATG
* * * * *
21687 AATTTGTGGATGAAATTGGAAGATCTAAAAGTTTAAGGACTAATTTAGAATGAGACTCAT
1 AATTTGTGGATGAAATT-GAATATTTAAAAGTTTAAGGACTAATTTAAAATGAGAATCAC
* * * * *
21747 AGTTTGGGGATGAAATTAGAATGTTCAAAAGTTTAAGGACTAA-TTATAATGAGAATCAC
1 AATTTGTGGATGAAATT-GAATATTTAAAAGTTTAAGGACTAATTTAAAATGAGAATCAC
* * *
21806 AATTTGTGGATGAAATTGTAATTTTTAAAAATTTAAGGAGTAATTTAAAATGAG
1 AATTTGTGGATGAAATTG-AATATTTAAAAGTTTAAGGACTAATTTAAAATGAG
21860 TGTCATAGTT
Statistics
Matches: 94, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
58 1 0.01
59 48 0.51
60 45 0.48
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.34
Consensus pattern (59 bp):
AATTTGTGGATGAAATTGAATATTTAAAAGTTTAAGGACTAATTTAAAATGAGAATCAC
Found at i:24731 original size:4 final size:4
Alignment explanation
Indices: 24714--24748 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
24704 TGATTATGCA
**
24714 TATG TATG CGTG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
24749 ACCTTGTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.03, G:0.26, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:26966 original size:31 final size:30
Alignment explanation
Indices: 26911--26979 Score: 102
Period size: 31 Copynumber: 2.3 Consensus size: 30
26901 CCCAAAAGCC
* * *
26911 TAACAAATGGTCACTAATATTATCGATTTG
1 TAACAAATAGTCAATAACATTATCGATTTG
26941 TAACAAAGTAGTCAATAACATTATCGATTTG
1 TAACAAA-TAGTCAATAACATTATCGATTTG
26972 TAACAAAT
1 TAACAAAT
26980 TAGTTGCTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 8 0.23
31 27 0.77
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (30 bp):
TAACAAATAGTCAATAACATTATCGATTTG
Found at i:27889 original size:31 final size:31
Alignment explanation
Indices: 27851--27925 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
27841 GAACGACGAG
*
27851 TGACTAATTTGTTATAAATCGATAACATTAA
1 TGACTAATTTGTTACAAATCGATAACATTAA
*
27882 TGACTAATTTGTTACAAATCGATAACATTAG
1 TGACTAATTTGTTACAAATCGATAACATTAA
*
27913 TGAC-CATTTGTTA
1 TGACTAATTTGTTA
27926 GGCTTTTGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 8 0.20
31 33 0.80
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (31 bp):
TGACTAATTTGTTACAAATCGATAACATTAA
Found at i:34267 original size:26 final size:26
Alignment explanation
Indices: 34209--34270 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
34199 AACATTTGTC
*
34209 AAAGAGATATAACTCTGAAAGCATTA
1 AAAGAGCTATAACTCTGAAAGCATTA
34235 AAAGAGCTATAACTCTGAAAGCATTA
1 AAAGAGCTATAACTCTGAAAGCATTA
34261 AAAGAGCTAT
1 AAAGAGCTAT
34271 TGATTCCTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (26 bp):
AAAGAGCTATAACTCTGAAAGCATTA
Found at i:35174 original size:81 final size:81
Alignment explanation
Indices: 35026--35496 Score: 466
Period size: 81 Copynumber: 5.7 Consensus size: 81
35016 CTCAAGGTTG
* * * * *
35026 GAAGGGTTATCTGTGACCAAAAGACCTTCAAGTTTGACTACGCTCAGC-TCCAAGGCACATCATT
1 GAAGGGTTATC--TG-CC-AAAGACCTTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATT
35090 TGCAGCATAGCTTAAGTCGA
62 TGCAGCATAGCTTAAGTCGA
* * *
35110 GAAGGGTTATATGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCA
1 GAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTGCA
* *
35175 ACATAACTTAAGTCGA
66 GCATAGCTTAAGTCGA
* * * *
35191 GAAGGGTTATCTGCCAATAAAATACCTTCGAGTTTGACTACGCTCAGCTTC-AAGGCACATCATT
1 GAAGGGTTATCTGCC----AAAGACCTTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATT
* *
35255 TTCAGCATAAGCTCAAGTCGA
62 TGCAGCAT-AGCTTAAGTCGA
** * * * *
35276 GAAGGGCAATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGTTTCG-AGAACACATCATTTAC
1 GAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAAG-GCACATCATTTGC
** * *
35340 AGCATAATTTAAGGCTA
65 AGCATAGCTTAAGTCGA
* * *
35357 GAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTT
1 GAAGGGTTATCTG---CCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTT
35421 GCAGCATAGCTTAAGTCGA
63 GCAGCATAGCTTAAGTCGA
* * *
35440 GAAGGGTTATTTGCCAACCGAAGACCTTCGAGTTCAATTACACTCAGC-TCAAAGGCA
1 GAAGGGTTATCTGCC-A---AAGACCTTCGAGTTCGATTACACTCAGCTTCGAAGGCA
35497 AACCAAATCT
Statistics
Matches: 317, Mismatches: 54, Indels: 32
0.79 0.13 0.08
Matches are distributed among these distances:
80 26 0.08
81 95 0.30
82 18 0.06
83 38 0.12
84 90 0.28
85 50 0.16
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (81 bp):
GAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTGCA
GCATAGCTTAAGTCGA
Found at i:35362 original size:166 final size:165
Alignment explanation
Indices: 35002--35488 Score: 670
Period size: 165 Copynumber: 2.9 Consensus size: 165
34992 TTAAAGACAA
* * * * * *
35002 CATTTACAGCATAACTCAAGGTTGGAAGGGTTATCTGTGACCAAAAGACCTTCAAGTTTGACTAC
1 CATTTACAGCATAACTTAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTTGACTAC
35067 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATATGCCAAAGACC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATATGCCAAAGACC
**
35132 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
131 CTCGAGTTCGATTACACTCAGCTTCGAGAACACAT
* * * * * * *
35167 CATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAATAAAATACCTTCGAGTTTGACTAC
1 CATTTACAGCATAACTTAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTTGACTAC
* * * ** *
35232 GCTCAGCTTCAAGGCACATCATTTTCAGCATAAGCTCAAGTCGAGAAGGGCAATCTGCCAAAGAC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCAT-AGCTTAAGTCGAGAAGGGTTATATGCCAAAGAC
*
35297 CCTCGAGTTCGATTACACTCAGTTTCGAGAACACAT
130 CCTCGAGTTCGATTACACTCAGCTTCGAGAACACAT
* * *
35333 CATTTACAGCATAATTTAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTAC
1 CATTTACAGCATAACTTAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTTGACTAC
*
35397 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATTTGCCAACCGAA
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATATGCC-A---AA
* *
35462 GACCTTCGAGTTCAATTACACTCAGCT
127 GACCCTCGAGTTCGATTACACTCAGCT
35489 CAAAGGCAAA
Statistics
Matches: 276, Mismatches: 41, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
164 23 0.08
165 132 0.48
166 95 0.34
168 26 0.09
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (165 bp):
CATTTACAGCATAACTTAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTTGACTAC
GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATATGCCAAAGACC
CTCGAGTTCGATTACACTCAGCTTCGAGAACACAT
Found at i:35391 original size:84 final size:82
Alignment explanation
Indices: 35002--35496 Score: 489
Period size: 84 Copynumber: 6.0 Consensus size: 82
34992 TTAAAGACAA
* * * * * *
35002 CATTTACAGCATAACTCAAGGTTG-GAAGGGTTATCTGTGACCAAAAGACCTTCAAGTTTGACTA
1 CATTTGCAGCATAACTTAA-GTCGAGAAGGGTTATCTG-CACC-AAAGACCTTCGAGTTCGACTA
* *
35066 CGCTCAGCTCCAAGGCACAT
63 CACTCAGCTTCAAGGCACAT
* * * *
35086 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATATG--CCAAAGACCCTCGAGTTCGATTACAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACAC
*
35149 TCAGCTTCGAGGGCACAT
66 TCAGCTTC-AAGGCACAT
* ** * *
35167 CATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAATAAAATACCTTCGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTAC
*
35232 GCTCAGCTTCAAGGCACAT
64 ACTCAGCTTCAAGGCACAT
* * ** * *
35251 CATTTTCAGCATAAGCTCAAGTCGAGAAGGGCAATCTG--CCAAAGACCCTCGAGTTCGATTACA
1 CATTTGCAGCATAA-CTTAAGTCGAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACA
* * *
35314 CTCAGTTTCGAGAACACAT
65 CTCAGCTTCAAG-GCACAT
* * * * *
35333 CATTTACAGCATAATTTAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CACCAAAGACCTTCGAGTTCGACTACA
*
35398 CTCAGCTCCAAGGCACAT
65 CTCAGCTTCAAGGCACAT
* * * * *
35416 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATTTGCCAACCGAAGACCTTCGAGTTCAATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTAC
35481 ACTCAGC-TCAAAGGCA
64 ACTCAGCTTC-AAGGCA
35497 AACCAAATCT
Statistics
Matches: 334, Mismatches: 64, Indels: 26
0.79 0.15 0.06
Matches are distributed among these distances:
80 26 0.08
81 89 0.27
82 18 0.05
83 41 0.12
84 113 0.34
85 47 0.14
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (82 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACAC
TCAGCTTCAAGGCACAT
Found at i:36774 original size:21 final size:21
Alignment explanation
Indices: 36748--36792 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
36738 GATTTCTGGG
* *
36748 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
36769 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
36790 CAA
1 CAA
36793 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:37376 original size:18 final size:18
Alignment explanation
Indices: 37353--37387 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
37343 CTAGGAGATT
37353 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
37371 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
37388 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:37473 original size:21 final size:22
Alignment explanation
Indices: 37444--37487 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
37434 GTTGTATGAT
37444 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
37465 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
37487 A
1 A
37488 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:39026 original size:149 final size:149
Alignment explanation
Indices: 38266--39016 Score: 1466
Period size: 149 Copynumber: 5.0 Consensus size: 149
38256 GAGTCGAGGG
*
38266 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGAAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
38331 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
38396 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
38415 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
38480 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
38545 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
38564 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
38629 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
38694 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
38713 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
38778 ACTTGATCTCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
38843 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
38862 TCTACGCGGTTCTTCGAGATATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
38927 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
38992 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
39011 TCTACG
1 TCTACG
39017 GGGCACTTCG
Statistics
Matches: 597, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 597 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:39039 original size:23 final size:23
Alignment explanation
Indices: 38995--39039 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
38985 ATTATTATAT
*
38995 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
39018 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
39040 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:41982 original size:21 final size:21
Alignment explanation
Indices: 41956--42000 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
41946 GATTTCTGGG
* *
41956 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
41977 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
41998 CAA
1 CAA
42001 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:42609 original size:18 final size:18
Alignment explanation
Indices: 42586--42620 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
42576 CTAGGAGATT
42586 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
42604 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
42621 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:42706 original size:21 final size:22
Alignment explanation
Indices: 42677--42720 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
42667 GTTGTATGAT
42677 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
42698 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
42720 A
1 A
42721 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:44256 original size:149 final size:149
Alignment explanation
Indices: 43495--44245 Score: 1475
Period size: 149 Copynumber: 5.0 Consensus size: 149
43485 GAGTCGAGGG
43495 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
43560 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACGTTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
43625 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
43644 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACATAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
43709 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
43774 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
43793 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
43858 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
43923 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
43942 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
44007 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
44072 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
44091 TCTACGCAGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
44156 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
44221 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
44240 TCTACG
1 TCTACG
44246 GGGCACTTCG
Statistics
Matches: 598, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 598 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:44268 original size:23 final size:23
Alignment explanation
Indices: 44224--44268 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
44214 ATTATTATAT
*
44224 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
44247 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
44269 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:44919 original size:10 final size:10
Alignment explanation
Indices: 44904--44940 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
44894 CATCTTTTTT
44904 TATATATACA
1 TATATATACA
44914 TATATAT-CTA
1 TATATATAC-A
44924 TATATATACA
1 TATATATACA
44934 T-TATATA
1 TATATATA
44941 GTTTGCAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 7 0.28
10 17 0.68
11 1 0.04
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (10 bp):
TATATATACA
Found at i:44995 original size:37 final size:35
Alignment explanation
Indices: 44967--45224 Score: 180
Period size: 37 Copynumber: 7.2 Consensus size: 35
44957 TGAAACTACG
*
44967 TATATAATATATA-ATTTTAAAACATTTTGAAAATA
1 TATATAATATATAGATTTTAAAACATTTTGAAAA-C
* *
45002 TATATAATATATAGTTTTTTTTAAAAAAAACTTTTTGAAAAC
1 TATATAATATATAG---ATTTT----AAAACATTTTGAAAAC
* * *
45044 TATATAGTATATAGTTTTTAAAACATTTGGAATATA-
1 TATATAATATATAGATTTTAAAACATTTTGAA-A-AC
*
45080 TATATAATATATAGTTTTTAAAAACATTTTTGAAAAC
1 TATATAATATATAGATTTT-AAAACA-TTTTGAAAAC
*
45117 TATATAATATATA-ATTTTTAAAATTATTTTTGAAAAC
1 TATATAATATATAGA-TTTTAAAA-CA-TTTTGAAAAC
45154 TTATATAATATATA-ATTTTAAAAACA---T----A-
1 -TATATAATATATAGATTTT-AAAACATTTTGAAAAC
*
45182 TATATAATATATAGTTTTTAAAATCATTTTGAAAAC
1 TATATAATATATAGATTTTAAAA-CATTTTGAAAAC
45218 TTATATA
1 -TATATA
45225 GTTTTTTTAA
Statistics
Matches: 183, Mismatches: 12, Indels: 54
0.73 0.05 0.22
Matches are distributed among these distances:
27 17 0.09
28 6 0.03
29 1 0.01
31 1 0.01
33 1 0.01
35 25 0.14
36 24 0.13
37 48 0.26
38 24 0.13
39 9 0.05
42 13 0.07
43 14 0.08
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.45
Consensus pattern (35 bp):
TATATAATATATAGATTTTAAAACATTTTGAAAAC
Found at i:45168 original size:38 final size:37
Alignment explanation
Indices: 44952--45180 Score: 211
Period size: 37 Copynumber: 6.1 Consensus size: 37
44942 TTTGCAAATG
*
44952 ATTTTTGAAACTACGTATATAATATATAA-TTTTAAAAC
1 ATTTTTGAAA--ACTTATATAATATATAATTTTTAAAAC
* *
44990 A-TTTTGAAAA-TATATATAATATATAGTTTTTTTTAAAAAAA
1 ATTTTTGAAAACT-TATATAATATATA---ATTTTT--AAAAC
* *
45031 ACTTTTTGAAAAC-TATATAGTATATAGTTTTTAAAAC
1 A-TTTTTGAAAACTTATATAATATATAATTTTTAAAAC
* * *
45068 A-TTTGGAATA-TATATATAATATATAGTTTTTAAAAAC
1 ATTTTTGAAAACT-TATATAATATATAATTTTT-AAAAC
*
45105 ATTTTTGAAAAC-TATATAATATATAATTTTTAAAATT
1 ATTTTTGAAAACTTATATAATATATAATTTTTAAAA-C
*
45142 ATTTTTGAAAACTTATATAATATATAATTTTAAAAAC
1 ATTTTTGAAAACTTATATAATATATAATTTTTAAAAC
45179 AT
1 AT
45181 ATATATAATA
Statistics
Matches: 159, Mismatches: 15, Indels: 35
0.76 0.07 0.17
Matches are distributed among these distances:
35 21 0.13
36 22 0.14
37 51 0.32
38 30 0.19
39 9 0.06
41 5 0.03
42 12 0.08
43 9 0.06
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (37 bp):
ATTTTTGAAAACTTATATAATATATAATTTTTAAAAC
Found at i:45192 original size:111 final size:110
Alignment explanation
Indices: 44967--45224 Score: 261
Period size: 111 Copynumber: 2.4 Consensus size: 110
44957 TGAAACTACG
*
44967 TATATAATATATAATTTTAAAACATTTTGAAAATATATATAATATATAGTTTTTTTTAAAAAAAA
1 TATATAATATATAATTTTAAAACATTTTGAAAATATATATAATATATA--TATTTTTAAAAAAAA
* * * *
45032 CTTTTTGAAAACTATATAGTATATAGTTTTTAAAACATTTGGAATATA
64 CTTTTTGAAAACTATATAATATATAATTTTAAAAACATAT-GAATATA
* * **
45080 TATATAATATATAGTTTTTAAAAACATTTTTGAAAA-CTATATAATATATA-ATTTTT-AAAATT
1 TATATAATATATA-ATTTT-AAAACA-TTTTGAAAATATATATAATATATATATTTTTAAAAAAA
45142 A-TTTTTGAAAACTTATATAATATATAATTTTAAAAACATAT--ATATA
63 ACTTTTTGAAAAC-TATATAATATATAATTTTAAAAACATATGAATATA
*
45188 -ATAT-ATA-GT--TTTTAAAATCATTTTGAAAACT-TATATA
1 TATATAATATATAATTTTAAAA-CATTTTGAAAA-TATATATA
45225 GTTTTTTTAA
Statistics
Matches: 128, Mismatches: 10, Indels: 25
0.79 0.06 0.15
Matches are distributed among these distances:
101 13 0.10
102 12 0.09
105 1 0.01
106 3 0.02
107 4 0.03
108 5 0.04
110 11 0.09
111 29 0.23
112 5 0.04
113 13 0.10
114 4 0.03
115 19 0.15
116 9 0.07
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.45
Consensus pattern (110 bp):
TATATAATATATAATTTTAAAACATTTTGAAAATATATATAATATATATATTTTTAAAAAAAACT
TTTTGAAAACTATATAATATATAATTTTAAAAACATATGAATATA
Found at i:45281 original size:55 final size:58
Alignment explanation
Indices: 45219--45344 Score: 138
Period size: 55 Copynumber: 2.3 Consensus size: 58
45209 TTTGAAAACT
* * *
45219 TATATAGTTTTTTTAAAAT-ATTTT-AGATTTTGAAAACATTTTT-TAATATGTATAA
1 TATATAGTTTTTTTAAAATGATTTTGAAATTTTGAAAACATTTTTAAAATATATATAA
* * *
45274 TATATAG---TCTGAAAATGTTTTTGAAATTTTGAAAACATTTTTAAAATATATATAA
1 TATATAGTTTTTTTAAAATGATTTTGAAATTTTGAAAACATTTTTAAAATATATATAA
*
45329 TATATATTTGTTTTTA
1 TATATAGTT-TTTTTA
45345 TTATTTATTT
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
52 7 0.13
53 4 0.07
54 18 0.33
55 23 0.42
59 3 0.05
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (58 bp):
TATATAGTTTTTTTAAAATGATTTTGAAATTTTGAAAACATTTTTAAAATATATATAA
Found at i:45349 original size:13 final size:13
Alignment explanation
Indices: 45333--45394 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
45323 ATATAATATA
*
45333 TATTTGTTTTTAT
1 TATTTATTTTTAT
45346 TATTTATTTTTAT
1 TATTTATTTTTAT
**
45359 T-TTTATTATTCGT
1 TATTTATT-TTTAT
*
45372 TTTTTA-TTTTATT
1 TATTTATTTTTA-T
45385 TATTTATTTT
1 TATTTATTTT
45395 CTCTCTCTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
12 8 0.21
13 24 0.62
14 7 0.18
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (13 bp):
TATTTATTTTTAT
Found at i:45375 original size:20 final size:19
Alignment explanation
Indices: 45339--45394 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
45329 TATATATTTG
45339 TTTTTATTATTTATTTTTA
1 TTTTTATTATTTATTTTTA
45358 TTTTTATTATTCGT-TTTTTA
1 TTTTTATTATT--TATTTTTA
45378 -TTTTATTTATTTATTTT
1 TTTTTA-TTATTTATTTT
45395 CTCTCTCTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 1 0.03
19 20 0.61
20 11 0.33
21 1 0.03
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTTATTATTTATTTTTA
Found at i:46693 original size:13 final size:13
Alignment explanation
Indices: 46675--46703 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
46665 AAATTGTATT
46675 TTTTGTTTCTTTA
1 TTTTGTTTCTTTA
46688 TTTTGTTTCTTTA
1 TTTTGTTTCTTTA
46701 TTT
1 TTT
46704 CTTTAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTGTTTCTTTA
Found at i:53040 original size:21 final size:21
Alignment explanation
Indices: 53016--53084 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
53006 GAATCGATAC
*
53016 CCCCTTGAAGGGGAACCGATT
1 CCCCTTGTAGGGGAACCGATT
53037 CCCCCTTTGTAGGGGAACCGATT
1 -CCCC-TTGTAGGGGAACCGATT
* * *
53060 CCCCCTGTAGGGGAATCGATA
1 CCCCTTGTAGGGGAACCGATT
53081 CCCC
1 CCCC
53085 CTGGGGTTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 18 0.43
22 8 0.19
23 16 0.38
ACGTcount: A:0.20, C:0.33, G:0.26, T:0.20
Consensus pattern (21 bp):
CCCCTTGTAGGGGAACCGATT
Found at i:53087 original size:21 final size:22
Alignment explanation
Indices: 53004--53086 Score: 105
Period size: 23 Copynumber: 3.8 Consensus size: 22
52994 TTAGTGCAGA
* *
53004 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGTAG
*
53026 GGGAACCGATTCCCCCTTTGTAG
1 GGGAACCGATACCCCC-TTGTAG
*
53049 GGGAACCGATTCCCCC-TGTAG
1 GGGAACCGATACCCCCTTGTAG
*
53070 GGGAATCGATACCCCCT
1 GGGAACCGATACCCCCT
53087 GGGGTTCTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
21 19 0.35
22 14 0.26
23 21 0.39
ACGTcount: A:0.22, C:0.31, G:0.27, T:0.20
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGTAG
Found at i:54688 original size:18 final size:18
Alignment explanation
Indices: 54650--54690 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
54640 AGAACAACAC
*
54650 GAGGAACAAGCACGAGTA
1 GAGGAACAAGCACGAGCA
54668 GAGGAACAAGCAC-AGCCA
1 GAGGAACAAGCACGAG-CA
54686 GAGGA
1 GAGGA
54691 TCAAATGCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.44, C:0.20, G:0.34, T:0.02
Consensus pattern (18 bp):
GAGGAACAAGCACGAGCA
Found at i:59819 original size:22 final size:22
Alignment explanation
Indices: 59791--59839 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
59781 GAAAAAGGGT
59791 GTACCCATTCGGCTATCTCCAA
1 GTACCCATTCGGCTATCTCCAA
*
59813 GTACCCATTTGGCTATCTCCAA
1 GTACCCATTCGGCTATCTCCAA
59835 GTACC
1 GTACC
59840 GAGAGATAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.22, C:0.35, G:0.14, T:0.29
Consensus pattern (22 bp):
GTACCCATTCGGCTATCTCCAA
Found at i:65136 original size:22 final size:21
Alignment explanation
Indices: 65082--65145 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
65072 AGTCGAGGGT
65082 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
* *
65103 CTCATAGGTCCTTCAGGACATA
1 TTCATAGGTCCTTCGGGACA-A
*
65125 TTCACAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
65146 ATTTCATATG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 19 0.51
22 18 0.49
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.27
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:65963 original size:25 final size:23
Alignment explanation
Indices: 65922--65970 Score: 55
Period size: 25 Copynumber: 2.0 Consensus size: 23
65912 CTGGTATGGT
*
65922 AATGAGTATGTTGTTTTGCTAATAG
1 AATGAGTATGTTATTTT--TAATAG
65947 AATGA-TATGTTTATTTTTAATAG
1 AATGAGTATG-TTATTTTTAATAG
65970 A
1 A
65971 TGTCCGGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 7 0.32
24 4 0.18
25 11 0.50
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (23 bp):
AATGAGTATGTTATTTTTAATAG
Found at i:70790 original size:19 final size:20
Alignment explanation
Indices: 70768--70805 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
70758 TTCTCTCATC
*
70768 TCTTCTTCATTCTT-TCTTA
1 TCTTCTTCACTCTTCTCTTA
70787 TCTTCTTCACTCTTCTCTT
1 TCTTCTTCACTCTTCTCTT
70806 CTTCCAAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.08, C:0.32, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTTCTTCACTCTTCTCTTA
Found at i:71761 original size:21 final size:21
Alignment explanation
Indices: 71735--71775 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
71725 GTCGAGGGTT
71735 TCATAGGTCCTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
71756 TCATAGGTCCTTCGGGACAA
1 TCATAGGTCCTTCGGGACAA
71776 ATTTCATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:75413 original size:18 final size:19
Alignment explanation
Indices: 75390--75433 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
75380 TTATCAAATC
75390 ATTATAAAAT-AATTTTAA
1 ATTATAAAATGAATTTTAA
*
75408 ATTAT-AAATGCATTTTAA
1 ATTATAAAATGAATTTTAA
*
75426 AATATAAA
1 ATTATAAA
75434 TAAATTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 16 0.73
19 2 0.09
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
ATTATAAAATGAATTTTAA
Found at i:75444 original size:18 final size:17
Alignment explanation
Indices: 75396--75446 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
75386 AATCATTATA
*
75396 AAATAATTTTAAATTAT
1 AAATAATTTTAAAATAT
*
75413 AAATGCATTTTAAAATAT
1 AAAT-AATTTTAAAATAT
*
75431 AAATAAATTATAAAAT
1 AAAT-AATTTTAAAAT
75447 CATTTTATGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 4 0.14
18 24 0.86
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
AAATAATTTTAAAATAT
Found at i:77304 original size:60 final size:60
Alignment explanation
Indices: 77181--77308 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 60
77171 AACATAATGA
* * * * * *
77181 ATAGTCGGGTGATCATTTTGTATCTTTTAATAATAGATGGACTGAATAAAGTAACATTCT
1 ATAGTTGGATGATCATTTTGTAACTTTTAATAATAGACGGACTGAATAAAGCAACATCCT
* * * *
77241 ATAGTTGGATGATCATTTTGTAACTTTTAATAGTCGACGGACTTAATAAAGCAATA-CCAT
1 ATAGTTGGATGATCATTTTGTAACTTTTAATAATAGACGGACTGAATAAAGCAACATCC-T
77301 ATAGTTGG
1 ATAGTTGG
77309 GGGACCATTT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 1 0.02
60 56 0.98
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.37
Consensus pattern (60 bp):
ATAGTTGGATGATCATTTTGTAACTTTTAATAATAGACGGACTGAATAAAGCAACATCCT
Found at i:77318 original size:60 final size:60
Alignment explanation
Indices: 77194--77327 Score: 137
Period size: 60 Copynumber: 2.2 Consensus size: 60
77184 GTCGGGTGAT
* * * * * *
77194 CATTTTGTATCTTTTAATAATAGATGGACTGAATAAAGTAACATTCTATAGTTGGATGAT
1 CATTTTGTAACTTTTAATAATAGACGGACTGAATAAAGCAACATCCTATAGTTGGAGGAC
* * * * *
77254 CATTTTGTAACTTTTAATAGTCGACGGACTTAATAAAGCAATA-CCATATAGTTGGGGGAC
1 CATTTTGTAACTTTTAATAATAGACGGACTGAATAAAGCAACATCC-TATAGTTGGAGGAC
77314 CATTTGTGT-ACTTT
1 CATTT-TGTAACTTT
77328 ACCCTATAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
59 1 0.02
60 57 0.93
61 3 0.05
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAATAGACGGACTGAATAAAGCAACATCCTATAGTTGGAGGAC
Found at i:79099 original size:18 final size:18
Alignment explanation
Indices: 79076--79110 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
79066 ATGATAAAAT
79076 ATGACCA-CATAATCTCAA
1 ATGACCATCAT-ATCTCAA
79094 ATGACCATCATATCTCA
1 ATGACCATCATATCTCA
79111 CTCACCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.40, C:0.29, G:0.06, T:0.26
Consensus pattern (18 bp):
ATGACCATCATATCTCAA
Found at i:80165 original size:2 final size:2
Alignment explanation
Indices: 80158--80188 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
80148 TTGACCGACT
80158 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
80189 TATTCTTGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.