Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008624.1 Hibiscus syriacus cultivar Beakdansim tig00111587_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: 642794
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:11591 original size:8 final size:8
Alignment explanation
Indices: 11578--11639 Score: 51
Period size: 8 Copynumber: 7.8 Consensus size: 8
11568 AAAATGAGTG
11578 AAATGAAA
1 AAATGAAA
11586 AAATG-AA
1 AAATGAAA
11593 AAAT-AAA
1 AAATGAAA
11600 AAAT--AA
1 AAATGAAA
*
11606 AAATAAAA
1 AAATGAAA
11614 ATGAATGAAAAA
1 A--AATG--AAA
11626 AAATGAAA
1 AAATGAAA
11634 AAATGA
1 AAATGA
11640 GGGTTCAAGA
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
6 6 0.13
7 12 0.26
8 17 0.37
10 7 0.15
12 4 0.09
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.15
Consensus pattern (8 bp):
AAATGAAA
Found at i:11596 original size:7 final size:7
Alignment explanation
Indices: 11578--11635 Score: 52
Period size: 7 Copynumber: 8.4 Consensus size: 7
11568 AAAATGAGTG
11578 AAATGAAA
1 AAATG-AA
11586 AAATGAA
1 AAATGAA
*
11593 AAATAAA
1 AAATGAA
11600 AAAT-AA
1 AAATGAA
11606 AAAT-AA
1 AAATGAA
11612 AAATGAA
1 AAATGAA
11619 TGAAA--AA
1 --AAATGAA
11626 AAATGAA
1 AAATGAA
11633 AAA
1 AAA
11636 ATGAGGGTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
5 3 0.07
6 12 0.27
7 21 0.48
8 5 0.11
9 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.14
Consensus pattern (7 bp):
AAATGAA
Found at i:11602 original size:14 final size:14
Alignment explanation
Indices: 11578--11635 Score: 68
Period size: 14 Copynumber: 4.2 Consensus size: 14
11568 AAAATGAGTG
11578 AAATGAAAAAATGAA
1 AAAT-AAAAAATGAA
11593 AAATAAAAAAT-AA
1 AAATAAAAAATGAA
11606 AAAT-AAAAATGAA
1 AAATAAAAAATGAA
*
11619 TGAA-AAAAAATGAA
1 -AAATAAAAAATGAA
11633 AAA
1 AAA
11636 ATGAGGGTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
12 6 0.16
13 10 0.26
14 18 0.47
15 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.14
Consensus pattern (14 bp):
AAATAAAAAATGAA
Found at i:11613 original size:26 final size:27
Alignment explanation
Indices: 11584--11635 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
11574 AGTGAAATGA
11584 AAAAATGAA-AAATAAAAAAT-AAAAAT
1 AAAAATGAATAAA-AAAAAATGAAAAAT
*
11610 AAAAATGAATGAAAAAAAATGAAAAA
1 AAAAATGAATAAAAAAAAATGAAAAA
11636 ATGAGGGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (27 bp):
AAAAATGAATAAAAAAAAATGAAAAAT
Found at i:12699 original size:54 final size:54
Alignment explanation
Indices: 12617--12912 Score: 423
Period size: 54 Copynumber: 5.4 Consensus size: 54
12607 GGTTTCCCAA
* *
12617 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGAAGAGG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGCAGACG
*
12671 CGATCGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGGGCAGACG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATA-GGGGCAGACG
*
12726 CGATCGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGCAGACG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGCAGACG
* * *
12780 CGATCATTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG-GCAGACG
* * * * *
12835 AGATTTGTTGAAGATTGTTTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACA
1 CGA-TCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG-GCAGACG
* *
12891 CGATTGTTGAAGA-TATTCGAGT
1 CGATCGTTGAAGATTGTTCGAGT
12913 TCTATTCTCC
Statistics
Matches: 220, Mismatches: 19, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
54 103 0.47
55 68 0.31
56 49 0.22
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.29
Consensus pattern (54 bp):
CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGCAGACG
Found at i:12808 original size:109 final size:109
Alignment explanation
Indices: 12616--12912 Score: 443
Period size: 109 Copynumber: 2.7 Consensus size: 109
12606 AGGTTTCCCA
* * *
12616 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGAAGAGGCGATCGTTGA
1 ACGATCGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGCAGACGCGATCGTTGA
*
12681 AGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGGGCAGAC
66 AGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCAGAC
* *
12725 GCGATCGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGCAGACGCGATCATTGA
1 ACGATCGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGCAGACGCGATCGTTGA
* *
12790 AGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGAC
66 AGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCAGAC
* * * * *
12834 AAGATTTGTTGAAGATTGTTTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
1 ACGA-TCGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGG-GCAGACGCGATCGTT
*
12899 GAAGA-TATTCGAGT
64 GAAGATTGTTCGAGT
12913 TCTATTCTCC
Statistics
Matches: 170, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
109 103 0.61
110 50 0.29
111 17 0.10
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (109 bp):
ACGATCGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGCAGACGCGATCGTTGA
AGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCAGAC
Found at i:13016 original size:54 final size:54
Alignment explanation
Indices: 12899--13160 Score: 300
Period size: 54 Copynumber: 4.9 Consensus size: 54
12889 CACGATTGTT
* * *
12899 GAAGATATTCGAGTTCTATTCTCCCT--AGAGAGAGGGAGCAAACCCGTTTGAA
1 GAAGATATTCGAGTTCTATTCTCCCTGAAGAAAGAGGGAGCGAACCCGTTAGAA
* * *
12951 GAAGATATTCGAGTTCTATTCTCCCTGAAGAAAGAGGGAGCGAACTCATTTGAA
1 GAAGATATTCGAGTTCTATTCTCCCTGAAGAAAGAGGGAGCGAACCCGTTAGAA
* * * *
13005 GAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCGGTTAGCA
1 GAAGATATTCGAGTTCTATTCTCCCTGAAGAAAGAGGGAGCGAACCCGTTAGAA
* * * *
13059 GAAGAT-TCTTGAGTTCTATACTCCCTGAA-ACAATAGGGAGCGAACCCGTTAGCA
1 GAAGATAT-TCGAGTTCTATTCTCCCTGAAGA-AAGAGGGAGCGAACCCGTTAGAA
* ** *
13113 GAAGATTTTCGAGTTCTATGT-TCCCTGAAGCGATAGGGAGCGAACCCG
1 GAAGATATTCGAGTTCTAT-TCTCCCTGAAGAAAGAGGGAGCGAACCCG
13161 ATGTTGAAAA
Statistics
Matches: 185, Mismatches: 18, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
52 26 0.14
53 2 0.01
54 156 0.84
55 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (54 bp):
GAAGATATTCGAGTTCTATTCTCCCTGAAGAAAGAGGGAGCGAACCCGTTAGAA
Found at i:14164 original size:19 final size:16
Alignment explanation
Indices: 14116--14155 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
14106 ATAACGACGA
14116 AACCAGAGAAATCCAC
1 AACCAGAGAAATCCAC
14132 AACCAGAGAAATCCAC
1 AACCAGAGAAATCCAC
14148 AACCAGAG
1 AACCAGAG
14156 TCTAAATCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.50, C:0.30, G:0.15, T:0.05
Consensus pattern (16 bp):
AACCAGAGAAATCCAC
Found at i:18336 original size:16 final size:16
Alignment explanation
Indices: 18315--18345 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18305 ACCAAATTTC
18315 ACTATTCATGAAAATT
1 ACTATTCATGAAAATT
*
18331 ACTATTCATGCAAAT
1 ACTATTCATGAAAAT
18346 AGTAACCTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (16 bp):
ACTATTCATGAAAATT
Found at i:21423 original size:18 final size:18
Alignment explanation
Indices: 21375--21425 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
21365 TACATCACCG
* *
21375 GCAGGCGGTTCCATAGTT
1 GCAGGCGGATCCGTAGTT
*
21393 GTAGGCGGATCCGTAGTT
1 GCAGGCGGATCCGTAGTT
*
21411 GCAGGTGGATCCGTA
1 GCAGGCGGATCCGTA
21426 CTTGGTGATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.18, C:0.20, G:0.37, T:0.25
Consensus pattern (18 bp):
GCAGGCGGATCCGTAGTT
Found at i:22719 original size:21 final size:20
Alignment explanation
Indices: 22639--22720 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 20
22629 CGCAAATCAG
22639 TTTCCAGATTCGCAATGCGAT
1 TTTCCA-ATTCGCAATGCGAT
* * *
22660 TAT-GACTATCGCAATGCGAT
1 TTTCCAAT-TCGCAATGCGAT
**
22680 TTTCCAATTTCGCGTTGCGAT
1 TTTCCAA-TTCGCAATGCGAT
22701 TTTCCCAATTCGCAATGCGA
1 TTT-CCAATTCGCAATGCGA
22721 ATAAGTAAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
19 1 0.02
20 15 0.32
21 26 0.55
22 5 0.11
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.34
Consensus pattern (20 bp):
TTTCCAATTCGCAATGCGAT
Found at i:22753 original size:21 final size:20
Alignment explanation
Indices: 22710--22760 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
22700 TTTTCCCAAT
*
22710 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
22730 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
22751 TCGCAATGCG
1 TCGCAATGCG
22761 CTACTGACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:22774 original size:41 final size:42
Alignment explanation
Indices: 22747--22924 Score: 147
Period size: 40 Copynumber: 4.4 Consensus size: 42
22737 GCGAATTTGG
* *
22747 AAAATCGCAATGCGCTACTGACTATCGCAACGCG-ATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGAATAATAC
* *
22788 AAAATCGCAACGCGATACTGACTTTCGCAACGCG-ATACTGAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGAATAAT-AC
** * *
22830 --TTTCGCAACGCGATACTGACTTTCGCAACGCG-ATACTGAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGAATAAT-AC
** * * *
22870 --TTTCGCAACGCAATACTGACTTTCGCAACGAG-ATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGAATAATAC
* *
22909 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
22925 TTTCAAAGCG
Statistics
Matches: 121, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
39 2 0.02
40 72 0.60
41 45 0.37
42 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (42 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGAATAATAC
Found at i:22775 original size:20 final size:20
Alignment explanation
Indices: 22751--22904 Score: 211
Period size: 20 Copynumber: 7.7 Consensus size: 20
22741 ATTTGGAAAA
* * *
22751 TCGCAATGCGCTACTGACTA
1 TCGCAACGCGATACTGACTT
* **
22771 TCGCAACGCGATAAT-ACAAAA
1 TCGCAACGCGATACTGAC--TT
22792 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
22812 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
22832 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
22852 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
22872 TCGCAACGCAATACTGACTT
1 TCGCAACGCGATACTGACTT
*
22892 TCGCAACGAGATA
1 TCGCAACGCGATA
22905 ATACATAATC
Statistics
Matches: 121, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
19 2 0.02
20 102 0.84
21 15 0.12
22 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:22878 original size:60 final size:60
Alignment explanation
Indices: 22751--22924 Score: 233
Period size: 60 Copynumber: 2.9 Consensus size: 60
22741 ATTTGGAAAA
* * *
22751 TCGCAATGCGCTACTGACTATCGCAACGCGATAATACAAAATCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTTTCGCAACGCGATAATAC-AAATCGCAACGCGATACTGACTT
* **
22812 TCGCAACGCGATACTGACTTTCGCAACGCGATACTGAC-TTTCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTTTCGCAACGCGATAAT-ACAAATCGCAACGCGATACTGACTT
* * *
22872 TCGCAACGCAATACTGACTTTCGCAACGAGATAATACATAATCGCAATGCGAT
1 TCGCAACGCGATACTGACTTTCGCAACGCGATAATACA-AATCGCAACGCGAT
22925 TTTCAAAGCG
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
59 2 0.02
60 52 0.53
61 42 0.43
62 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (60 bp):
TCGCAACGCGATACTGACTTTCGCAACGCGATAATACAAATCGCAACGCGATACTGACTT
Found at i:23119 original size:22 final size:22
Alignment explanation
Indices: 23091--23134 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
23081 CACTCTCTCA
*
23091 CCCATCTCCGACGAGATCCGTC
1 CCCATCTCCGACGAAATCCGTC
* *
23113 CCCATCTCTGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
23135 TATCTCCATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.18, C:0.43, G:0.18, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:23193 original size:23 final size:23
Alignment explanation
Indices: 23163--23213 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
23153 CCACCCTCAC
23163 AATCAGAAATGGAAAATCAACCA
1 AATCAGAAATGGAAAATCAACCA
23186 AATCAGAAATGGAAAATCAACCA
1 AATCAGAAATGGAAAATCAACCA
23209 AATCA
1 AATCA
23214 ACCACCGAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.57, C:0.18, G:0.12, T:0.14
Consensus pattern (23 bp):
AATCAGAAATGGAAAATCAACCA
Found at i:23468 original size:20 final size:20
Alignment explanation
Indices: 23416--23453 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
23406 CGATTTTAGT
23416 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
23436 TTCGCGTTGCGATAGTCA
1 TTCGCGTTGCGATAGTCA
23454 TTTTTGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:23669 original size:25 final size:24
Alignment explanation
Indices: 23615--23669 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
23605 TGTTTATTAT
* *
23615 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
23639 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
23665 TGTTT
1 TGTTT
23670 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:25392 original size:20 final size:20
Alignment explanation
Indices: 25367--25408 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
25357 TAGTTTACTT
25367 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
25387 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
25407 TC
1 TC
25409 ACAATGCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:25421 original size:19 final size:20
Alignment explanation
Indices: 25378--25422 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
25368 CGCAACACGA
*
25378 AAATGACTATCGCAACGCGG
1 AAATGACTATCACAACGCGG
* *
25398 AAATGGCTATCACAATGC-G
1 AAATGACTATCACAACGCGG
25417 AAATGA
1 AAATGA
25423 AAATCGCAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AAATGACTATCACAACGCGG
Found at i:25441 original size:14 final size:14
Alignment explanation
Indices: 25422--25480 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
25412 ATGCGAAATG
25422 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
25436 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
25455 AAAATCGCAACGAC
1 AAAATCGCAACGAC
25469 AAAATCGCAACG
1 AAAATCGCAACG
25481 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:25452 original size:33 final size:33
Alignment explanation
Indices: 25410--25494 Score: 161
Period size: 33 Copynumber: 2.6 Consensus size: 33
25400 ATGGCTATCA
25410 CAATGCGAAATGAAAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCG
25443 CAATGCGAAATGAAAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCG
*
25476 CAACGCGAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
25495 TAATGCGATT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGACAAAATCG
Found at i:25460 original size:19 final size:19
Alignment explanation
Indices: 25410--25502 Score: 80
Period size: 19 Copynumber: 5.4 Consensus size: 19
25400 ATGGCTATCA
25410 CAATGCGAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
*
25429 CAA--CG--A-CAAAATCG
1 CAATGCGAAATGAAAATCG
25443 CAATGCGAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
*
25462 CAA--CG--A-CAAAATCG
1 CAATGCGAAATGAAAATCG
*
25476 CAACGCGAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
*
25495 TAATGCGA
1 CAATGCGA
25503 TTTGTGTTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.34
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 26 0.45
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.13
Consensus pattern (19 bp):
CAATGCGAAATGAAAATCG
Found at i:25533 original size:14 final size:14
Alignment explanation
Indices: 25514--25572 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
25504 TTGTGTTTCG
25514 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
25528 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
25545 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
25561 CGTTGCGATTTT
1 CGTTGCGATTTT
25573 TATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:25546 original size:33 final size:33
Alignment explanation
Indices: 25509--25591 Score: 139
Period size: 33 Copynumber: 2.5 Consensus size: 33
25499 GCGATTTGTG
*
25509 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
25542 TTTCGCATTGCGATTTTGTCGTTGCGATTTTTA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
25575 TTTCGCATTGCAATTTT
1 TTTCGCATTGCGATTTT
25592 CATTTTGCGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.12, C:0.17, G:0.20, T:0.51
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:25554 original size:19 final size:19
Alignment explanation
Indices: 25530--25607 Score: 76
Period size: 19 Copynumber: 4.4 Consensus size: 19
25520 GATTTTGTCG
25530 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
25549 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
*
25563 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
* * *
25582 TTGCAATTTTCATTTTGCG
1 TTGCGATTTTCATTTCGCA
25601 TTGCGAT
1 TTGCGAT
25608 AGCCATTTCC
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
14 6 0.13
15 3 0.06
16 4 0.09
17 4 0.09
18 3 0.06
19 27 0.57
ACGTcount: A:0.14, C:0.17, G:0.19, T:0.50
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:26080 original size:41 final size:42
Alignment explanation
Indices: 25990--26080 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 42
25980 CCCGACTCAC
* * *
25990 CTGTCATCCCTCAAGAGTTCCCTCCAATCGTTCAAGAGGCCT
1 CTGTCATCCCTCAAGAGTTCCCCCCAACCGTTCAAGAGGCCA
* * *
26032 CTATCATCTCTCAAGAG-TCCCCCCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTTCCCCCCAACCGTTCAAGAGGCCA
26073 CTGTCATC
1 CTGTCATC
26081 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 27 0.64
42 15 0.36
ACGTcount: A:0.22, C:0.38, G:0.15, T:0.24
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTTCCCCCCAACCGTTCAAGAGGCCA
Found at i:26089 original size:41 final size:42
Alignment explanation
Indices: 25993--26110 Score: 114
Period size: 41 Copynumber: 2.8 Consensus size: 42
25983 GACTCACCTG
* * * * * *
25993 TCATCCCTCAAGAGTTCCCTCCAATCGTTCAAGAGGCCTCTA
1 TCATCTCTCAAGAGGTCCCCCCCACCGTTCAAGAGGCCACTA
*
26035 TCATCTCTCAAGA-GTCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCTCTCAAGAGGTCCCCCCCACCGTTCAAGAGGCCACTA
* * * *
26076 TCATCGT-TGAAGAGGTCCCTCCCACCATTCCAGAG
1 TCATC-TCTCAAGAGGTCCCCCCCACCGTTCAAGAG
26111 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 32 0.51
42 31 0.49
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATCTCTCAAGAGGTCCCCCCCACCGTTCAAGAGGCCACTA
Found at i:27524 original size:14 final size:14
Alignment explanation
Indices: 27490--27528 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
27480 TTGATTGTTT
27490 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
27504 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
27518 TGTTGATTTGT
1 AATTGATTTGT
27529 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:27725 original size:20 final size:19
Alignment explanation
Indices: 27668--27714 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
27658 GCAACGAGAG
27668 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
27687 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
27706 AATCGCAAT
1 AATCGCAAT
27715 ATTCAAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:27943 original size:12 final size:12
Alignment explanation
Indices: 27926--27950 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27916 TCTTCGGGGA
27926 CTTTTTCTTCTT
1 CTTTTTCTTCTT
27938 CTTTTTCTTCTT
1 CTTTTTCTTCTT
27950 C
1 C
27951 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:28202 original size:20 final size:20
Alignment explanation
Indices: 28181--28268 Score: 131
Period size: 20 Copynumber: 4.4 Consensus size: 20
28171 TGTATTATCT
* *
28181 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
28201 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
28221 CGTTGCGAAAGTCAAAATCG
1 CGTTGCGAAAGTCAGAATCG
* *
28241 CGTTACGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
28261 CGTTGCGA
1 CGTTGCGA
28269 TTTTGTATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:28302 original size:20 final size:20
Alignment explanation
Indices: 28176--28310 Score: 128
Period size: 20 Copynumber: 6.7 Consensus size: 20
28166 GATTCTGTAT
*
28176 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
28196 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
28216 AATCGCGTTGCGAAAGTCAA
1 TATCGCGTTGCGATAGTCAG
* * *
28236 AATCGCGTTACGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
28256 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
28277 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
28297 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
28311 TTTCCAAATT
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 3 0.03
20 79 0.81
21 14 0.14
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:28348 original size:21 final size:20
Alignment explanation
Indices: 28298--28351 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
28288 GATAGTCAGT
*
28298 ATCGCATTGCGATTTTCCAA
1 ATCGCATTGCGATTTACCAA
* *
28318 ATTCGTATTGCGATTTACTTAA
1 A-TCGCATTGCGATTTAC-CAA
28340 ATCGCATTGCGA
1 ATCGCATTGCGA
28352 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.86
22 3 0.11
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (20 bp):
ATCGCATTGCGATTTACCAA
Found at i:28362 original size:21 final size:20
Alignment explanation
Indices: 28338--28393 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
28328 CGATTTACTT
*
28338 AAATCGCATTGCGAATTGGGA
1 AAATCGCATTGCGAATT-AGA
**
28359 AAATCGCAACGCGAAATTAGA
1 AAATCGCATTGCG-AATTAGA
28380 AAATCGCATTGCGA
1 AAATCGCATTGCGA
28394 TAGTCATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.03
21 24 0.83
22 4 0.14
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (20 bp):
AAATCGCATTGCGAATTAGA
Found at i:30475 original size:60 final size:60
Alignment explanation
Indices: 30406--30541 Score: 193
Period size: 60 Copynumber: 2.3 Consensus size: 60
30396 TAGTCGGGGA
* * * *
30406 ACTCAACAAAGTAACATCCGATAATCAAAGGACTATTTTGTAACTTTTGATAGAT-AGAGG
1 ACTCAACAAAGAAACATCAGATAATCAAAGGACTATTTTATAACTTTTAATAGATAAG-GG
* *
30466 ACTCAACAAAGAAACATCATATAATCAAAGGATTATTTTATAACTTTTAATAGATAAGGG
1 ACTCAACAAAGAAACATCAGATAATCAAAGGACTATTTTATAACTTTTAATAGATAAGGG
*
30526 ACTCAACAAAGCAACA
1 ACTCAACAAAGAAACA
30542 CTTTATAGTT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
60 66 0.97
61 2 0.03
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.26
Consensus pattern (60 bp):
ACTCAACAAAGAAACATCAGATAATCAAAGGACTATTTTATAACTTTTAATAGATAAGGG
Found at i:30572 original size:60 final size:60
Alignment explanation
Indices: 30406--30572 Score: 162
Period size: 60 Copynumber: 2.8 Consensus size: 60
30396 TAGTCGGGGA
* ** * *
30406 ACTCAACAAAGTAACATCCGATAATCAAAGGACTATTTTGTA-ACTTTTGATAGATAGAGG
1 ACTCAACAAAGAAACATCATATAATCAAAGGACCA-TTTGTATACTTTTAATAGATAGAGG
**
30466 ACTCAACAAAGAAACATCATATAATCAAAGGATTATTT-TATAACTTTTAATAGATA-AGGG
1 ACTCAACAAAGAAACATCATATAATCAAAGGACCATTTGTAT-ACTTTTAATAGATAGA-GG
* * * * *
30526 ACTCAACAAAGCAACA-CTTTATAGTTAGAGGACCATTTGTATACTTT
1 ACTCAACAAAGAAACATC-ATATAATCAAAGGACCATTTGTATACTTT
30573 ACCCTATTAT
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
58 2 0.02
59 5 0.06
60 80 0.89
61 3 0.03
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (60 bp):
ACTCAACAAAGAAACATCATATAATCAAAGGACCATTTGTATACTTTTAATAGATAGAGG
Found at i:40622 original size:2 final size:2
Alignment explanation
Indices: 40615--40650 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40605 ACTCCCATGA
40615 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40651 GTTTTCATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41352 original size:11 final size:11
Alignment explanation
Indices: 41336--41375 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
41326 CTCCAAAACA
41336 TTTCAAAATCT
1 TTTCAAAATCT
**
41347 TTTCAAAA-GA
1 TTTCAAAATCT
41357 TTTCAAAATCT
1 TTTCAAAATCT
41368 TTTCAAAA
1 TTTCAAAA
41376 GAAAACCCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (11 bp):
TTTCAAAATCT
Found at i:41359 original size:21 final size:21
Alignment explanation
Indices: 41329--41377 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
41319 ATGGTGACTC
*
41329 CAAAACATTTCAAAATCTTTT
1 CAAAAGATTTCAAAATCTTTT
41350 CAAAAGATTTCAAAATCTTTT
1 CAAAAGATTTCAAAATCTTTT
41371 CAAAAGA
1 CAAAAGA
41378 AAACCCCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (21 bp):
CAAAAGATTTCAAAATCTTTT
Found at i:43020 original size:20 final size:20
Alignment explanation
Indices: 42995--43060 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
42985 AATTCCTTTG
42995 TTGCATTTACA-TTTTGCATT
1 TTGCATTTACATTTTTGCA-T
*
43015 TTGCATTTCCATTTTTGCAT
1 TTGCATTTACATTTTTGCAT
* *
43035 TTGCA-TGAGCATCTTTGCAT
1 TTGCATTTA-CATTTTTGCAT
43055 TTGCAT
1 TTGCAT
43061 GAGCATCTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.79
21 7 0.18
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.50
Consensus pattern (20 bp):
TTGCATTTACATTTTTGCAT
Found at i:43060 original size:14 final size:13
Alignment explanation
Indices: 43007--43040 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
42997 GCATTTACAT
43007 TTTGCATTTTGCA
1 TTTGCATTTTGCA
*
43020 TTTCCATTTTTGCA
1 TTTGCA-TTTTGCA
43034 TTTGCAT
1 TTTGCAT
43041 GAGCATCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.15, C:0.18, G:0.12, T:0.56
Consensus pattern (13 bp):
TTTGCATTTTGCA
Found at i:43061 original size:20 final size:20
Alignment explanation
Indices: 43028--43080 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
43018 CATTTCCATT
43028 TTTGCATTTGCATGAGCATC
1 TTTGCATTTGCATGAGCATC
43048 TTTGCATTTGCATGAGCATC
1 TTTGCATTTGCATGAGCATC
*
43068 TTTGCATTAGCAT
1 TTTGCATTTGCAT
43081 ATATACAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (20 bp):
TTTGCATTTGCATGAGCATC
Found at i:44421 original size:11 final size:11
Alignment explanation
Indices: 44407--44434 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
44397 AACACACAAA
44407 AAGAAAGAAAG
1 AAGAAAGAAAG
44418 AAGAAAGAAAG
1 AAGAAAGAAAG
44429 AAGAAA
1 AAGAAA
44435 AAAAATGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (11 bp):
AAGAAAGAAAG
Found at i:44446 original size:11 final size:10
Alignment explanation
Indices: 44432--44479 Score: 53
Period size: 11 Copynumber: 4.6 Consensus size: 10
44422 AAGAAAGAAG
44432 AAAAAAAATGA
1 AAAAAAAAT-A
*
44443 AAAAATAAA-G
1 AAAAA-AAATA
44453 AAAAAAAATA
1 AAAAAAAATA
44463 GAAAAAAAATA
1 -AAAAAAAATA
44474 AAAAAA
1 AAAAAA
44480 GGTAAAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 3 0.09
10 11 0.34
11 15 0.47
12 3 0.09
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.08
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:44453 original size:21 final size:22
Alignment explanation
Indices: 44429--44469 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
44419 AGAAAGAAAG
44429 AAGAAAAAAAAT-GAAAAAATA
1 AAGAAAAAAAATAGAAAAAATA
44450 AAGAAAAAAAATAGAAAAAA
1 AAGAAAAAAAATAGAAAAAA
44470 AATAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (22 bp):
AAGAAAAAAAATAGAAAAAATA
Found at i:44485 original size:10 final size:9
Alignment explanation
Indices: 44444--44525 Score: 67
Period size: 9 Copynumber: 8.8 Consensus size: 9
44434 AAAAAATGAA
*
44444 AAAATAAAGA
1 AAAA-AAAGG
*
44454 AAAAAAATAG
1 AAAAAAA-GG
**
44464 AAAAAAAAT
1 AAAAAAAGG
44473 AAAAAAAGG
1 AAAAAAAGG
44482 TAAAAGAAAGG
1 -AAAA-AAAGG
*
44493 AAAAATAGG
1 AAAAAAAGG
*
44502 AAAAATAGG
1 AAAAAAAGG
44511 -AAAAAAGG
1 AAAAAAAGG
44519 AAAAAAA
1 AAAAAAA
44526 AGAAGATATA
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
8 7 0.11
9 30 0.49
10 19 0.31
11 5 0.08
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:44496 original size:26 final size:25
Alignment explanation
Indices: 44467--44523 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
44457 AAAATAGAAA
44467 AAAAATA-AAAAA-AGGTAAAAGAAAGG
1 AAAAATAGAAAAATAGG--AAA-AAAGG
44493 AAAAATAGGAAAAATAGGAAAAAAGG
1 AAAAATA-GAAAAATAGGAAAAAAGG
44519 AAAAA
1 AAAAA
44524 AAAGAAGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
26 17 0.61
27 3 0.11
28 5 0.18
29 3 0.11
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (25 bp):
AAAAATAGAAAAATAGGAAAAAAGG
Found at i:45012 original size:1 final size:1
Alignment explanation
Indices: 45008--45041 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
44998 GGGAAAATGG
*
45008 AAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
45042 GAAGATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:45022 original size:18 final size:17
Alignment explanation
Indices: 45007--45040 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
44997 TGGGAAAATG
45007 GAAAAAAAAAAAAAAAA
1 GAAAAAAAAAAAAAAAA
45024 GAAAAAAAAAAAAAAAA
1 GAAAAAAAAAAAAAAAA
45041 AGAAGATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (17 bp):
GAAAAAAAAAAAAAAAA
Found at i:45053 original size:18 final size:18
Alignment explanation
Indices: 45008--45044 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
44998 GGGAAAATGG
45008 AAAAAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAAAGA
45026 AAAAAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAAAGA
45044 A
1 A
45045 GATATAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.95, C:0.00, G:0.05, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAAGA
Found at i:46810 original size:4 final size:4
Alignment explanation
Indices: 46801--46837 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
46791 TAAGTGTATT
*
46801 CATA CATA CATA CATA CAT- -ATA CATA CATA TATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
46838 TTCTTACAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.07
4 27 0.93
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (4 bp):
CATA
Found at i:46825 original size:18 final size:18
Alignment explanation
Indices: 46802--46837 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
46792 AAGTGTATTC
46802 ATACATACATACATACAT
1 ATACATACATACATACAT
*
46820 ATACATACATATATACAT
1 ATACATACATACATACAT
46838 TTCTTACAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (18 bp):
ATACATACATACATACAT
Found at i:47092 original size:50 final size:50
Alignment explanation
Indices: 47003--47229 Score: 156
Period size: 50 Copynumber: 4.5 Consensus size: 50
46993 GCTAATGAGT
* * *** *
47003 TTTTAAATAAACTAAGTCT-AATTTT-GAAGTTTGACGATTTTTAAATGA
1 TTTTAAAGAAACTAAGTCTGATTTTTAGAAGTTTCTTGATTTTCAAATGA
* * *
47051 TTTTTAAGAAACTAAGTCTGATTTTTAGAAGTTTCTTGATTTTTAAAAGAA
1 TTTTAAAGAAACTAAGTCTGATTTTTAGAAGTTTCTTGATTTTCAAATG-A
* * * * **
47102 CTTTAAAGAAATTAAGCCTAATTTTTAGGGGTTTCTTGACGTTTTCAAATGAA
1 TTTTAAAGAAACTAAGTCTGATTTTTAGAAGTTTCTTGA--TTTTCAAATG-A
* * * * *
47155 TTTAAAAGAAGCTAAGACTG-TTTTCAGGAGTTT-TTGATGTTTCAAATGAA
1 TTTTAAAGAAACTAAGTCTGATTTTTAGAAGTTTCTTGAT-TTTCAAATG-A
* * * *
47205 TTTCAAAGAAATTAAGCCTAATTTT
1 TTTTAAAGAAACTAAGTCTGATTTT
47230 AATGATAACT
Statistics
Matches: 143, Mismatches: 29, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
48 17 0.12
49 6 0.04
50 44 0.31
51 41 0.29
52 11 0.08
53 24 0.17
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.41
Consensus pattern (50 bp):
TTTTAAAGAAACTAAGTCTGATTTTTAGAAGTTTCTTGATTTTCAAATGA
Found at i:47136 original size:51 final size:51
Alignment explanation
Indices: 47038--47229 Score: 176
Period size: 51 Copynumber: 3.8 Consensus size: 51
47028 GAAGTTTGAC
* ** * * *
47038 GATTTTTAAATG-ATTTTTAAGAAACTAAGTCTGATTTTTAGAAGTTTCTT
1 GATTTTCAAATGAATTTAAAAGAAACTAAGCCTAATTTTTAGGAGTTTCTT
* * * *
47088 GATTTTTAAAAGAACTTT-AAAGAAATTAAGCCTAATTTTTAGGGGTTTCTT
1 GATTTTCAAATGAA-TTTAAAAGAAACTAAGCCTAATTTTTAGGAGTTTCTT
* * * *
47139 GACGTTTTCAAATGAATTTAAAAGAAGCTAAGACT-GTTTTCAGGAGTTT-TT
1 GA--TTTTCAAATGAATTTAAAAGAAACTAAGCCTAATTTTTAGGAGTTTCTT
* *
47190 GATGTTTCAAATGAATTTCAAAGAAATTAAGCCTAATTTT
1 GAT-TTTCAAATGAATTTAAAAGAAACTAAGCCTAATTTT
47230 AATGATAACT
Statistics
Matches: 115, Mismatches: 20, Indels: 13
0.78 0.14 0.09
Matches are distributed among these distances:
49 1 0.01
50 37 0.32
51 38 0.33
52 17 0.15
53 22 0.19
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (51 bp):
GATTTTCAAATGAATTTAAAAGAAACTAAGCCTAATTTTTAGGAGTTTCTT
Found at i:47213 original size:103 final size:104
Alignment explanation
Indices: 47033--47229 Score: 258
Period size: 103 Copynumber: 1.9 Consensus size: 104
47023 ATTTTGAAGT
* ** * * *
47033 TTGACGATTTTTAAATGATTTTTAAGAAACTAAGTCTGATTTTTAGAAGTTTCTTGATTTTTAAA
1 TTGACGATTTTCAAATGATTTAAAAGAAACTAAGACTGATTTTCAGAAGTTTCTTGATTTTCAAA
47098 AGAACTTTAAAGAAATTAAGCCTAATTTTTAGGGGTTTC
66 AGAACTTTAAAGAAATTAAGCCTAATTTTTAGGGGTTTC
* *
47137 TTGACG-TTTTCAAATGAATTTAAAAGAAGCTAAGACTG-TTTTCAGGAGTTT-TTGATGTTTCA
1 TTGACGATTTTCAAATG-ATTTAAAAGAAACTAAGACTGATTTTCAGAAGTTTCTTGAT-TTTCA
*
47199 AATGAA-TTTCAAAGAAATTAAGCCTAATTTT
64 AAAGAACTTT-AAAGAAATTAAGCCTAATTTT
47230 AATGATAACT
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
102 8 0.10
103 50 0.62
104 23 0.28
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.41
Consensus pattern (104 bp):
TTGACGATTTTCAAATGATTTAAAAGAAACTAAGACTGATTTTCAGAAGTTTCTTGATTTTCAAA
AGAACTTTAAAGAAATTAAGCCTAATTTTTAGGGGTTTC
Found at i:47345 original size:42 final size:41
Alignment explanation
Indices: 47286--47415 Score: 143
Period size: 42 Copynumber: 3.1 Consensus size: 41
47276 AAGGGTTTCT
*
47286 TGATGAGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCA
1 TGATGA-TAAATCCTTCGGGCCATCAATAAGTCTTTCGAGCA
* * *
47328 TGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCA
1 TGATG-ATAAATCCTTCGGGCCATCAATAAGTCTTTCGAGCA
* * * * * * *
47370 AGATGATAAGTCTTTCGGGCCATCCATAAGACCTTCGGGCA
1 TGATGATAAATCCTTCGGGCCATCAATAAGTCTTTCGAGCA
47411 TGATG
1 TGATG
47416 TTTTCAACAT
Statistics
Matches: 73, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
41 32 0.44
42 41 0.56
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (41 bp):
TGATGATAAATCCTTCGGGCCATCAATAAGTCTTTCGAGCA
Found at i:48681 original size:136 final size:136
Alignment explanation
Indices: 48382--48878 Score: 445
Period size: 136 Copynumber: 3.6 Consensus size: 136
48372 TAAACCAATC
* * * * ** *
48382 AACATTTCCAATGGAGAGTTCAAAATGAGAATAACTCATCCGATAAGATAGAAGAAGTTCATAAT
1 AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAGGGAGAAAAAGTTCATAAT
* * * * *
48447 GAGAAGAACTTGTTC-A-ATCTT-AGCTCGATTAATCACATATGGAGTT-GAATCAGCAACACCT
66 GAGAAGAACTTGTTCGACCTATTCA-CTCGA-T--TCACA-A--CACTTCGAATCAGTAACACCT
** *
48508 CAATCGAGGG-AT
124 CGCTTGAGGGAAT
*
48520 CAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAAAAGATCATA
1 -AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGA-AAAGGGAGAAAAAGTTCATA
* *** * * *
48585 ATGAGAAGAACTTGTTCGACCTA-TCACTTGATTCACGGTATTTCGAATCAGTGACGCCTCGCTT
64 ATGAGAAGAACTTGTTCGACCTATTCACTCGATTCACAACACTTCGAATCAGTAACACCTCGCTT
48649 GAGGGAAT
129 GAGGGAAT
* * * * * *
48657 GACATTT-CAGATGAAGAGATCATAATGAGAAGAACTCATCTGAAAGAGTGAG-AAGAGTTTCAT
1 AACATTTCCAG-TGGAGAGTTCATAATGAGAAGAACTCATCCGAAA-AGGGAGAAAAAG-TTCAT
** ** * *
48720 AATGAGAAGAGTTTGTTCGACCTATTTGCTCGATTCACAACACTTCGAATTAGTAACACCTGGCT
63 AATGAGAAGAACTTGTTCGACCTATTCACTCGATTCACAACACTTCGAATCAGTAACACCTCGCT
*
48785 TGAGGGATT
128 TGAGGGAAT
* * * *
48794 AACATTTCCAGTGGAGAGTTCTTAATGAGAAGATCTTATCCGATAAA-GGAGAAGAAGTTCATAA
1 AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGA-AAAGGGAGAAAAAGTTCATAA
*
48858 TGAGAAGAACTTGTTCAACCT
65 TGAGAAGAACTTGTTCGACCT
48879 TAGCTTGTTT
Statistics
Matches: 290, Mismatches: 55, Indels: 29
0.78 0.15 0.08
Matches are distributed among these distances:
135 12 0.04
136 113 0.39
137 75 0.26
138 9 0.03
139 40 0.14
140 33 0.11
141 6 0.02
142 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.26
Consensus pattern (136 bp):
AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAGGGAGAAAAAGTTCATAAT
GAGAAGAACTTGTTCGACCTATTCACTCGATTCACAACACTTCGAATCAGTAACACCTCGCTTGA
GGGAAT
Found at i:54609 original size:74 final size:71
Alignment explanation
Indices: 54492--54742 Score: 189
Period size: 74 Copynumber: 3.5 Consensus size: 71
54482 GAAAAATACG
* **
54492 TATATAATATATGATTTTTAAAA-ATACATTTTGAAAATGTATATAATATAGT-TTTTAAAAAT-
1 TATATAATATAT-AATTTTAAAACAT---TTTTGAAAAAATATATAATATA-TATTTT-AAAATC
54554 ACCTTTGAAAA-C
60 A-CTTTGAAAAGC
*
54566 TATATAATATATAATATTTCAAAACATTTTTAGAAAAAATATATAATATATAATTTTAAAATCAT
1 TATATAATATATAAT-TTT-AAAACATTTTT-GAAAAAATATATAATATAT-ATTTTAAAATCAC
*
54631 TTTGAAAAGT
62 TTTGAAAAGC
* ** * * *
54641 TATATAATATATAGTTTTAAAATCA-TTTTG-AAATCTATATAATATATAGTTTAAAAAACATTT
1 TATATAATATATAATTTTAAAA-CATTTTTGAAAAAATATATAATATATA-TTTTAAAATCA-CT
54704 TTGAAAA-C
63 TTGAAAAGC
* *
54712 -ATAT-A-ATATAGTTTTAAAACGTTTTTGAAAA
1 TATATAATATATAATTTTAAAACATTTTTGAAAA
54743 CTATAATCTA
Statistics
Matches: 152, Mismatches: 12, Indels: 31
0.78 0.06 0.16
Matches are distributed among these distances:
67 1 0.01
68 19 0.12
69 4 0.03
70 5 0.03
71 24 0.16
72 10 0.07
73 15 0.10
74 49 0.32
75 23 0.15
76 2 0.01
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (71 bp):
TATATAATATATAATTTTAAAACATTTTTGAAAAAATATATAATATATATTTTAAAATCACTTTG
AAAAGC
Found at i:54687 original size:35 final size:35
Alignment explanation
Indices: 54492--54833 Score: 235
Period size: 36 Copynumber: 9.6 Consensus size: 35
54482 GAAAAATACG
* *
54492 TATATAATATATGATTTTTAAAAATACATTTTGAAAATG
1 TATATAATATAT-AGTTTT-AAAAT-CATTTTG-AAATC
* *
54531 TATAT-A-ATATAGTTTTTAAAAAT-ACCTTTGAAAAC
1 TATATAATATATAG-TTTT-AAAATCA-TTTTGAAATC
* **
54566 TATATAATATATAATATTTCAAAA-CATTTTTAGAAAAAA
1 TATATAATATATAGT-TTT-AAAATCA-TTTT-G-AAATC
*
54605 TATATAATATATAATTTTAAAATCATTTTGAAAAGT-
1 TATATAATATATAGTTTTAAAATCATTTTG-AAA-TC
54641 TATATAATATATAGTTTTAAAATCATTTTGAAATC
1 TATATAATATATAGTTTTAAAATCATTTTGAAATC
* * *
54676 TATATAATATATAGTTTAAAAAACATTTTTGAAAAC
1 TATATAATATATAGTTTTAAAATCA-TTTTGAAATC
* *
54712 -ATAT-A-ATATAGTTTTAAAA-CGTTTTTGAAAAC
1 TATATAATATATAGTTTTAAAATC-ATTTTGAAATC
* * *
54744 --TATAATCTATAGTTTGAAAA-CATTTTTAAAAT-
1 TATATAATATATAGTTTTAAAATCA-TTTTGAAATC
* * *
54776 TATATAATATATGGTTTCGAAAAT-ATCTTTGAAATA
1 TATATAATATATAGTTT-TAAAATCAT-TTTGAAATC
*
54812 TATATTATATATAGTTTTAAAA
1 TATATAATATATAGTTTTAAAA
54834 CAATTTTTTT
Statistics
Matches: 254, Mismatches: 27, Indels: 48
0.77 0.08 0.15
Matches are distributed among these distances:
31 3 0.01
32 12 0.05
33 33 0.13
34 16 0.06
35 56 0.22
36 65 0.26
37 38 0.15
38 7 0.03
39 24 0.09
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.42
Consensus pattern (35 bp):
TATATAATATATAGTTTTAAAATCATTTTGAAATC
Found at i:54755 original size:33 final size:34
Alignment explanation
Indices: 54557--54841 Score: 240
Period size: 36 Copynumber: 8.1 Consensus size: 34
54547 TAAAAATACC
*
54557 TTTGAAAACTATATAATATATAATATTTCAAAACATT
1 TTTGAAAAC-ATATAATATATAGT-TTT-AAAACATT
* *
54594 TTTAGAAAAAATATATAATATATAATTTTAAAATCA-T
1 TTT-G--AAAACATATAATATATAGTTTTAAAA-CATT
*
54631 TTTGAAAAGTTATATAATATATAGTTTTAAAATCA-T
1 TTTGAAAA--CATATAATATATAGTTTTAAAA-CATT
* *
54667 TTTGAAATCTATATAATATATAGTTTAAAAAACATT
1 TTTGAAAAC-ATATAATATATAGTTT-TAAAACATT
*
54703 TTTGAAAACATAT-A-ATATAGTTTTAAAACGTT
1 TTTGAAAACATATAATATATAGTTTTAAAACATT
* *
54735 TTTGAAAAC-TATAATCTATAGTTTGAAAACATT
1 TTTGAAAACATATAATATATAGTTTTAAAACATT
* * * * *
54768 TTT-AAAATTATATAATATATGGTTTCGAAAATATC
1 TTTGAAAA-CATATAATATATAGTTT-TAAAACATT
* *
54803 TTTGAAATATATATTATATATAGTTTTAAAACAATT
1 TTTGAAA-ACATATAATATATAGTTTTAAAAC-ATT
54839 TTT
1 TTT
54842 TTATATTATA
Statistics
Matches: 210, Mismatches: 21, Indels: 35
0.79 0.08 0.13
Matches are distributed among these distances:
31 3 0.01
32 21 0.10
33 27 0.13
34 18 0.09
35 36 0.17
36 69 0.33
37 12 0.06
38 6 0.03
39 14 0.07
40 4 0.02
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (34 bp):
TTTGAAAACATATAATATATAGTTTTAAAACATT
Found at i:54823 original size:36 final size:34
Alignment explanation
Indices: 54600--54835 Score: 162
Period size: 35 Copynumber: 6.9 Consensus size: 34
54590 CATTTTTAGA
* * *
54600 AAAAATATATAATATATAATTTTAAAATCAT-TTT
1 AAAATTATATAATATATAGTTTGAAAA-CATCTTT
*
54634 GAAAAGTTATATAATATATAGTTTTAAAATCAT-TTT
1 -AAAA-TTATATAATATATAGTTTGAAAA-CATCTTT
* * *
54670 GAAATCTATATAATATATAGTTTAAAAAACATTTTT
1 AAAAT-TATATAATATATAGTTT-GAAAACATCTTT
* * * *
54706 GAAAA-CATAT-A-ATATAGTTTTAAAACGTTTTT
1 -AAAATTATATAATATATAGTTTGAAAACATCTTT
* * *
54738 GAAAA--CTATAATCTATAGTTTGAAAACATTTTT
1 -AAAATTATATAATATATAGTTTGAAAACATCTTT
* *
54771 AAAATTATATAATATATGGTTTCGAAAATATCTTT
1 AAAATTATATAATATATAGTTT-GAAAACATCTTT
* * *
54806 GAAATATATATTATATATAGTTTTAAAACA
1 AAAAT-TATATAATATATAGTTTGAAAACA
54836 ATTTTTTTAT
Statistics
Matches: 168, Mismatches: 22, Indels: 22
0.79 0.10 0.10
Matches are distributed among these distances:
31 3 0.02
32 20 0.12
33 27 0.16
34 15 0.09
35 50 0.30
36 50 0.30
37 3 0.02
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (34 bp):
AAAATTATATAATATATAGTTTGAAAACATCTTT
Found at i:55956 original size:3 final size:3
Alignment explanation
Indices: 55941--56015 Score: 57
Period size: 3 Copynumber: 25.0 Consensus size: 3
55931 TATATATATA
* * * *
55941 TAT TAT AAT TAT TAT TAT TAT TAT T-T CAT TAT TAAA CAT ATATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT -TA-T TAT
*
55988 T-T TA- TAT TTT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
56016 CATTGTATAT
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
2 5 0.09
3 46 0.82
4 4 0.07
5 1 0.02
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:55999 original size:13 final size:14
Alignment explanation
Indices: 55920--56015 Score: 55
Period size: 12 Copynumber: 7.1 Consensus size: 14
55910 AGTCACTAGT
*
55920 TTATATATATA-TA
1 TTATATATTTATTA
*
55933 -TATATATATATTA
1 TTATATATTTATTA
*
55946 TAAT-TA-TTATTA
1 TTATATATTTATTA
55958 TTAT-TATTTCATTA
1 TTATATATTT-ATTA
55972 TTAAACATATATTTATT-
1 TT----ATATATTTATTA
*
55989 TTATATTTTTATTA
1 TTATATATTTATTA
56003 TTAT-TA-TTATTA
1 TTATATATTTATTA
56015 T
1 T
56016 CATTGTATAT
Statistics
Matches: 68, Mismatches: 5, Indels: 21
0.72 0.05 0.22
Matches are distributed among these distances:
12 27 0.40
13 17 0.25
14 12 0.18
17 2 0.03
18 5 0.07
19 5 0.07
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATATATTTATTA
Found at i:56071 original size:32 final size:30
Alignment explanation
Indices: 56035--56108 Score: 76
Period size: 32 Copynumber: 2.4 Consensus size: 30
56025 TACTTTTTTA
**
56035 ATTTTTTTATTTCCTTTTTTTATATTTATTGT
1 ATTTTTTTATTTCCTAGTTTT-TATTTATT-T
* *
56067 ATTTTTTCTCTTTTCTAGTTTTTATTTATTT
1 ATTTTTT-TATTTCCTAGTTTTTATTTATTT
*
56098 ATTTATTTATT
1 ATTTTTTTATT
56109 ATATGGTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
30 3 0.09
31 7 0.20
32 15 0.43
33 10 0.29
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.74
Consensus pattern (30 bp):
ATTTTTTTATTTCCTAGTTTTTATTTATTT
Found at i:56119 original size:47 final size:47
Alignment explanation
Indices: 56069--56159 Score: 114
Period size: 47 Copynumber: 2.0 Consensus size: 47
56059 TTTATTGTAT
* *
56069 TTTTTCTCTTTTC-TAGTTTTTA-TTTATTTATTTATTTATTATATGG
1 TTTTTCCCTTTGCTTAGTTTTTATTTTATTTATTTA-TTATTATATGG
** *
56115 TTTTTCCCTTTGCTTCTTTTTTATTTTATTTTTTTATTATTATAT
1 TTTTTCCCTTTGCTTAGTTTTTATTTTATTTATTTATTATTATAT
56160 TTATCCTATC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
46 11 0.29
47 16 0.42
48 11 0.29
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.71
Consensus pattern (47 bp):
TTTTTCCCTTTGCTTAGTTTTTATTTTATTTATTTATTATTATATGG
Found at i:56830 original size:16 final size:17
Alignment explanation
Indices: 56785--56830 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
56775 TCGTTTTCAT
56785 AATCATTT-TTTTTAAA
1 AATCATTTATTTTTAAA
* * *
56801 AATAATTAAATTTTAAA
1 AATCATTTATTTTTAAA
56818 AA-CATTTATTTTT
1 AATCATTTATTTTT
56831 TGATTTAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (17 bp):
AATCATTTATTTTTAAA
Found at i:59896 original size:64 final size:65
Alignment explanation
Indices: 59766--60087 Score: 318
Period size: 64 Copynumber: 4.9 Consensus size: 65
59756 TTAGGGATAA
* *
59766 ATGTTTCAAGAGAAACTGTCTCGAA-AGAGACAAAATTCGTTTAAAGGGAAACGATCTCAAAGAT
1 ATGTTTCAAGAGAAACTGTCTC-AAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAATAT
59830 G
65 G
* * *
59831 ATGTTTCAAGAGAAACTGTTTCAAGAGAGAC-AAATTCGTTTCAAGGGAAATGATATCAAATATG
1 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAATATG
* * * * * * *
59895 ATGTTTCAAGAGAAATTGTCTAAAAAGAGACTAATTTTGTTTCAAGGGAAACAATCTCAAAGT-T
1 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAA-TAT
59959 G
65 G
* * * * *
59960 TTGTGTTTCAAGAGAAACTGTATCAAGGGAGACAAAACTAGTTTCAAGGGAAAC-AGTCTCAAAG
1 --ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGA-TCTCAAA-
60024 T-TG
62 TATG
* * *
60027 TATGTTTCAAGGGAAACAT-TCTCAAAAGAGACAAAACTT-GTTTTAAGGGAAACTG-TCTCAA
1 -ATGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAA-TTCGTTTCAAGGGAAAC-GATCTCAA
60088 GAGAGACAAA
Statistics
Matches: 216, Mismatches: 31, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
64 58 0.27
65 53 0.25
66 50 0.23
67 55 0.25
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (65 bp):
ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAATATG
Found at i:59952 original size:129 final size:131
Alignment explanation
Indices: 59766--60079 Score: 361
Period size: 129 Copynumber: 2.4 Consensus size: 131
59756 TTAGGGATAA
** *
59766 ATGTTTCAAGAGAAACTGTCTCGAAAGAGACAAAATTCGTTTAAAGGGAAACGATCTCAAAGATG
1 ATGTTTCAAGAGAAACTGTCTAAAAAGAGACAAAATTCGTTTAAAGGGAAACAATCTCAAAGATG
* * *
59831 -ATGTTTCAAGAGAAACTGTTTCAAGAGAGAC-AAATTCGTTTCAAGGGAAATGATATCAAATAT
66 TATGTTTCAAGAGAAACTGTATCAAGAGAGACAAAACTAGTTTCAAGGGAAATGATATCAAATAT
59894 G
131 G
* * * * * *
59895 ATGTTTCAAGAGAAATTGTCTAAAAAGAGACTAATTTTGTTTCAAGGGAAACAATCTCAAAGTTG
1 ATGTTTCAAGAGAAACTGTCTAAAAAGAGACAAAATTCGTTTAAAGGGAAACAATCTCAAAGATG
* * * *
59960 TTGTGTTTCAAGAGAAACTGTATCAAGGGAGACAAAACTAGTTTCAAGGGAAA-CAGTCTCAAAG
66 -TATGTTTCAAGAGAAACTGTATCAAGAGAGACAAAACTAGTTTCAAGGGAAATGA-TATCAAA-
60024 T-TG
128 TATG
* * *
60027 TATGTTTCAAGGGAAACAT-TCTCAAAAGAGACAAAACTT-GTTTTAAGGGAAAC
1 -ATGTTTCAAGAGAAAC-TGTCTAAAAAGAGACAAAA-TTCGTTTAAAGGGAAAC
60080 TGTCTCAAGA
Statistics
Matches: 155, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
129 56 0.36
131 29 0.19
132 25 0.16
133 42 0.27
134 3 0.02
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (131 bp):
ATGTTTCAAGAGAAACTGTCTAAAAAGAGACAAAATTCGTTTAAAGGGAAACAATCTCAAAGATG
TATGTTTCAAGAGAAACTGTATCAAGAGAGACAAAACTAGTTTCAAGGGAAATGATATCAAATAT
G
Found at i:60013 original size:36 final size:36
Alignment explanation
Indices: 59963--60116 Score: 135
Period size: 36 Copynumber: 4.4 Consensus size: 36
59953 AAAGTTGTTG
* * *
59963 TGTTTCAAGAGAAACTGTATCAAGGGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
* * * *
59999 AGTTTCAAGGGAAACAGTCTCAA-AGTTG----TA--
1 TGTTTCAAGGGAAACTGTCTCAAGAG-AGACAAAACT
*
60029 TGTTTCAAGGGAAACAT-TCTCAAAAGAGACAAAACT
1 TGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAACT
*
60065 TGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAACAT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC-T
*
60102 TGTTTCAAGAGAAAC
1 TGTTTCAAGGGAAAC
60117 ATACTCAAAG
Statistics
Matches: 92, Mismatches: 15, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
30 21 0.23
31 2 0.02
32 1 0.01
34 1 0.01
35 2 0.02
36 51 0.55
37 14 0.15
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
Found at i:60140 original size:103 final size:102
Alignment explanation
Indices: 59963--60180 Score: 250
Period size: 103 Copynumber: 2.1 Consensus size: 102
59953 AAAGTTGTTG
* * * *
59963 TGTTTCAAGAGAAACTGTATCAAGGGAGACAAAACTAGTTTCAAGGGAAACAGTCTCAAAGTTGT
1 TGTTTTAAGGGAAACTGTATCAAGAGAGACAAAACTAGTTTCAAGAGAAACAGTCTCAAAGTTGT
* *
60028 ATGTTTCAAGGGAAACAT-TCTCAAAAGAGACAAAACT
66 ATCTTTCAAGAGAAA-ATGTCTCAAAAGAGACAAAACT
* *
60065 TGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAACATTGTTTCAAGAGAAACA-TACTCAAAGAC
1 TGTTTTAAGGGAAACTGTATCAAGAGAGACAAAAC-TAGTTTCAAGAGAAACAGT-CTCAAAG--
* *
60129 TT-T-TCTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACT
62 TTGTATCTTTCAAGAGAAAATGTCTCAAAAGAGACAAAACT
*
60168 T-TGTTAA-GGAAAC
1 TGTTTTAAGGGAAAC
60181 ATACTCAATG
Statistics
Matches: 100, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
101 6 0.06
102 38 0.38
103 53 0.53
104 1 0.01
105 2 0.02
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (102 bp):
TGTTTTAAGGGAAACTGTATCAAGAGAGACAAAACTAGTTTCAAGAGAAACAGTCTCAAAGTTGT
ATCTTTCAAGAGAAAATGTCTCAAAAGAGACAAAACT
Found at i:60209 original size:64 final size:67
Alignment explanation
Indices: 60064--60232 Score: 254
Period size: 64 Copynumber: 2.6 Consensus size: 67
60054 GAGACAAAAC
* * * *
60064 TTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAACATTGTTTCAAGAGAAACATACTCAAAGAC
1 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACATACTCAAAGAC
60129 TT
66 TT
* * *
60131 TTCTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTG-TT-AAG-GAAACATACTCAATGAT
1 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACATACTCAAAGAC
60193 TT
66 TT
60195 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
60233 GCTTTGAAAT
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
64 54 0.57
65 3 0.03
66 2 0.02
67 35 0.37
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (67 bp):
TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACATACTCAAAGAC
TT
Found at i:60738 original size:16 final size:16
Alignment explanation
Indices: 60717--60756 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
60707 TTCATGTATC
*
60717 ATGTATGTATGTGTTG
1 ATGTATGTATGTATTG
60733 ATGTATGTATGTATTG
1 ATGTATGTATGTATTG
60749 ATGTATGT
1 ATGTATGT
60757 TTTCTTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.50
Consensus pattern (16 bp):
ATGTATGTATGTATTG
Found at i:63779 original size:74 final size:71
Alignment explanation
Indices: 63662--63912 Score: 189
Period size: 74 Copynumber: 3.5 Consensus size: 71
63652 GAAAAATACG
* **
63662 TATATAATATATGATTTTTAAAA-ATACATTTTGAAAATGTATATAATATAGT-TTTTAAAAAT-
1 TATATAATATAT-AATTTTAAAACAT---TTTTGAAAAAATATATAATATA-TATTTT-AAAATC
63724 ACCTTTGAAAA-C
60 A-CTTTGAAAAGC
*
63736 TATATAATATATAATATTTCAAAACATTTTTAGAAAAAATATATAATATATAATTTTAAAATCAT
1 TATATAATATATAAT-TTT-AAAACATTTTT-GAAAAAATATATAATATAT-ATTTTAAAATCAC
*
63801 TTTGAAAAGT
62 TTTGAAAAGC
* ** * * *
63811 TATATAATATATAGTTTTAAAATCA-TTTTG-AAATCTATATAATATATAGTTTAAAAAACATTT
1 TATATAATATATAATTTTAAAA-CATTTTTGAAAAAATATATAATATATA-TTTTAAAATCA-CT
63874 TTGAAAA-C
63 TTGAAAAGC
* *
63882 -ATAT-A-ATATAGTTTTAAAACGTTTTTGAAAA
1 TATATAATATATAATTTTAAAACATTTTTGAAAA
63913 CTATAATCTA
Statistics
Matches: 152, Mismatches: 12, Indels: 31
0.78 0.06 0.16
Matches are distributed among these distances:
67 1 0.01
68 19 0.12
69 4 0.03
70 5 0.03
71 24 0.16
72 10 0.07
73 15 0.10
74 49 0.32
75 23 0.15
76 2 0.01
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (71 bp):
TATATAATATATAATTTTAAAACATTTTTGAAAAAATATATAATATATATTTTAAAATCACTTTG
AAAAGC
Found at i:63857 original size:35 final size:35
Alignment explanation
Indices: 63662--64003 Score: 235
Period size: 36 Copynumber: 9.6 Consensus size: 35
63652 GAAAAATACG
* *
63662 TATATAATATATGATTTTTAAAAATACATTTTGAAAATG
1 TATATAATATAT-AGTTTT-AAAAT-CATTTTG-AAATC
* *
63701 TATAT-A-ATATAGTTTTTAAAAAT-ACCTTTGAAAAC
1 TATATAATATATAG-TTTT-AAAATCA-TTTTGAAATC
* **
63736 TATATAATATATAATATTTCAAAA-CATTTTTAGAAAAAA
1 TATATAATATATAGT-TTT-AAAATCA-TTTT-G-AAATC
*
63775 TATATAATATATAATTTTAAAATCATTTTGAAAAGT-
1 TATATAATATATAGTTTTAAAATCATTTTG-AAA-TC
63811 TATATAATATATAGTTTTAAAATCATTTTGAAATC
1 TATATAATATATAGTTTTAAAATCATTTTGAAATC
* * *
63846 TATATAATATATAGTTTAAAAAACATTTTTGAAAAC
1 TATATAATATATAGTTTTAAAATCA-TTTTGAAATC
* *
63882 -ATAT-A-ATATAGTTTTAAAA-CGTTTTTGAAAAC
1 TATATAATATATAGTTTTAAAATC-ATTTTGAAATC
* * *
63914 --TATAATCTATAGTTTGAAAA-CATTTTTAAAAT-
1 TATATAATATATAGTTTTAAAATCA-TTTTGAAATC
* * *
63946 TATATAATATATGGTTTCGAAAAT-ATCTTTGAAATA
1 TATATAATATATAGTTT-TAAAATCAT-TTTGAAATC
*
63982 TATATTATATATAGTTTTAAAA
1 TATATAATATATAGTTTTAAAA
64004 CAATTTTTTT
Statistics
Matches: 254, Mismatches: 27, Indels: 48
0.77 0.08 0.15
Matches are distributed among these distances:
31 3 0.01
32 12 0.05
33 33 0.13
34 16 0.06
35 56 0.22
36 65 0.26
37 38 0.15
38 7 0.03
39 24 0.09
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.42
Consensus pattern (35 bp):
TATATAATATATAGTTTTAAAATCATTTTGAAATC
Found at i:63925 original size:33 final size:34
Alignment explanation
Indices: 63727--64011 Score: 240
Period size: 36 Copynumber: 8.1 Consensus size: 34
63717 TAAAAATACC
*
63727 TTTGAAAACTATATAATATATAATATTTCAAAACATT
1 TTTGAAAAC-ATATAATATATAGT-TTT-AAAACATT
* *
63764 TTTAGAAAAAATATATAATATATAATTTTAAAATCA-T
1 TTT-G--AAAACATATAATATATAGTTTTAAAA-CATT
*
63801 TTTGAAAAGTTATATAATATATAGTTTTAAAATCA-T
1 TTTGAAAA--CATATAATATATAGTTTTAAAA-CATT
* *
63837 TTTGAAATCTATATAATATATAGTTTAAAAAACATT
1 TTTGAAAAC-ATATAATATATAGTTT-TAAAACATT
*
63873 TTTGAAAACATAT-A-ATATAGTTTTAAAACGTT
1 TTTGAAAACATATAATATATAGTTTTAAAACATT
* *
63905 TTTGAAAAC-TATAATCTATAGTTTGAAAACATT
1 TTTGAAAACATATAATATATAGTTTTAAAACATT
* * * * *
63938 TTT-AAAATTATATAATATATGGTTTCGAAAATATC
1 TTTGAAAA-CATATAATATATAGTTT-TAAAACATT
* *
63973 TTTGAAATATATATTATATATAGTTTTAAAACAATT
1 TTTGAAA-ACATATAATATATAGTTTTAAAAC-ATT
64009 TTT
1 TTT
64012 TTATATTATA
Statistics
Matches: 210, Mismatches: 21, Indels: 35
0.79 0.08 0.13
Matches are distributed among these distances:
31 3 0.01
32 21 0.10
33 27 0.13
34 18 0.09
35 36 0.17
36 69 0.33
37 12 0.06
38 6 0.03
39 14 0.07
40 4 0.02
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (34 bp):
TTTGAAAACATATAATATATAGTTTTAAAACATT
Found at i:63993 original size:36 final size:34
Alignment explanation
Indices: 63770--64005 Score: 162
Period size: 35 Copynumber: 6.9 Consensus size: 34
63760 CATTTTTAGA
* * *
63770 AAAAATATATAATATATAATTTTAAAATCAT-TTT
1 AAAATTATATAATATATAGTTTGAAAA-CATCTTT
*
63804 GAAAAGTTATATAATATATAGTTTTAAAATCAT-TTT
1 -AAAA-TTATATAATATATAGTTTGAAAA-CATCTTT
* * *
63840 GAAATCTATATAATATATAGTTTAAAAAACATTTTT
1 AAAAT-TATATAATATATAGTTT-GAAAACATCTTT
* * * *
63876 GAAAA-CATAT-A-ATATAGTTTTAAAACGTTTTT
1 -AAAATTATATAATATATAGTTTGAAAACATCTTT
* * *
63908 GAAAA--CTATAATCTATAGTTTGAAAACATTTTT
1 -AAAATTATATAATATATAGTTTGAAAACATCTTT
* *
63941 AAAATTATATAATATATGGTTTCGAAAATATCTTT
1 AAAATTATATAATATATAGTTT-GAAAACATCTTT
* * *
63976 GAAATATATATTATATATAGTTTTAAAACA
1 AAAAT-TATATAATATATAGTTTGAAAACA
64006 ATTTTTTTAT
Statistics
Matches: 168, Mismatches: 22, Indels: 22
0.79 0.10 0.10
Matches are distributed among these distances:
31 3 0.02
32 20 0.12
33 27 0.16
34 15 0.09
35 50 0.30
36 50 0.30
37 3 0.02
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (34 bp):
AAAATTATATAATATATAGTTTGAAAACATCTTT
Found at i:64053 original size:25 final size:25
Alignment explanation
Indices: 64025--64079 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
64015 TATTATATAG
*
64025 TATTTT-TATTTTATTCTTTTTTATT
1 TATTTTGTATTTTATT-TTTATTATT
* *
64050 TATTTTGTTTTTTGTTTTTATTATT
1 TATTTTGTATTTTATTTTTATTATT
64075 TATTT
1 TATTT
64080 AATCATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.15, C:0.02, G:0.04, T:0.80
Consensus pattern (25 bp):
TATTTTGTATTTTATTTTTATTATT
Found at i:64060 original size:16 final size:16
Alignment explanation
Indices: 64008--64062 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
63998 TTAAAACAAT
*
64008 TTTTTTATATTATATAG
1 TTTTTTAT-TTATATTG
*
64025 TATTTTTATTT-TATTC
1 T-TTTTTATTTATATTG
*
64041 TTTTTTATTTATTTTG
1 TTTTTTATTTATATTG
64057 TTTTTT
1 TTTTTT
64063 GTTTTTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
15 9 0.28
16 13 0.41
17 3 0.09
18 7 0.22
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (16 bp):
TTTTTTATTTATATTG
Found at i:65089 original size:2 final size:2
Alignment explanation
Indices: 65082--65130 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
65072 GTCACTAGTT
65082 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
65124 TA TA TA T
1 TA TA TA T
65131 TATTATTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:65136 original size:3 final size:3
Alignment explanation
Indices: 65128--65203 Score: 79
Period size: 3 Copynumber: 26.0 Consensus size: 3
65118 TATATATATA
* *
65128 TAT TAT TAT TAT TAT TAT TAT TCAT TAT TAT TAA CA- TAT ATAT T-T
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT -TAT TAT
*
65173 TAT T-T TA- TAT TTT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
65204 CATTGTATAT
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
2 7 0.11
3 49 0.79
4 6 0.10
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:65241 original size:21 final size:23
Alignment explanation
Indices: 65205--65257 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
65195 TATTATTATC
* *
65205 ATTGTATATACTTTTTTA-ATTT
1 ATTGTATTTCCTTTTTTATATTT
*
65227 -TTTTATTTCCTTTTTTATATTT
1 ATTGTATTTCCTTTTTTATATTT
65249 ATTGTATTT
1 ATTGTATTT
65258 TTTCTCTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 14 0.56
22 4 0.16
23 7 0.28
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.70
Consensus pattern (23 bp):
ATTGTATTTCCTTTTTTATATTT
Found at i:65288 original size:4 final size:4
Alignment explanation
Indices: 65274--65307 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
65264 TTTTCTAGTT
* *
65274 TTTA ATTA TTTA TTTA TTTA TTTA TTTA ATTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
65308 ATATGGTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:65294 original size:12 final size:12
Alignment explanation
Indices: 65274--65307 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
65264 TTTTCTAGTT
65274 TTTAATTATTTA
1 TTTAATTATTTA
*
65286 TTTATTTATTTA
1 TTTAATTATTTA
65298 TTTAATTATT
1 TTTAATTATT
65308 ATATGGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTAATTATTTA
Found at i:68797 original size:135 final size:134
Alignment explanation
Indices: 68578--68964 Score: 395
Period size: 135 Copynumber: 2.9 Consensus size: 134
68568 TAAAATTGGA
* * *
68578 GATAACACAG-TCTCTACGTGATGAGAACGACTAGTTATCTAAGAG-TGACATGGCTCCTACGTG
1 GATAACACAGCTC-CTACGTGATGAGAACGACTGGTTATCTAAG-GTTGACGTGGCTCCTACATG
* * * * * *
68641 ATGAAGAGAT-ATAGTCGGTGGATAACACATTTCCTACGTAATGAGGACAACTGGTCATCTTTAG
64 ATGAGGAGATCA-GGTCGGTGGATGACACAGTTCCTACGTGATGAGGACGACTGGTCATCTTTAG
68705 GGATAATT
128 GGATAA-T
* ** * * * *
68713 TATAACATGGCTCCTACGTGATGAGGACGACTGGTTATCTAAGGTTGACGCGACTCTTACATGAT
1 GATAACACAGCTCCTACGTGATGAGAACGACTGGTTATCTAAGGTTGACGTGGCTCCTACATGAT
** * ** **
68778 GAGGAGATCAGGTTAGTGGATGACATAGTTCCTACGTGATGAGGGA-GGTTGACCATCTTTAGGG
66 GAGGAGATCAGGTCGGTGGATGACACAGTTCCTACGTGATGA-GGACGACTGGTCATCTTTAGGG
*
68842 ATGAT
130 ATAAT
* * * * ** * *
68847 GCTAACACAGTTCCTACGCGATGAGAATGGTTGATTATCTAAGGTTGATGTGGCTCCTACATGAT
1 GATAACACAGCTCCTACGTGATGAGAACGACTGGTTATCTAAGGTTGACGTGGCTCCTACATGAT
* *
68912 AAGGAGATCTGGTCGGTGGATGACACAGTTCCTACGTGATGAGGACGACTGGT
66 GAGGAGATCAGGTCGGTGGATGACACAGTTCCTACGTGATGAGGACGACTGGT
68965 TAGGGATAAA
Statistics
Matches: 199, Mismatches: 48, Indels: 11
0.77 0.19 0.04
Matches are distributed among these distances:
133 3 0.02
134 92 0.46
135 98 0.49
136 6 0.03
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (134 bp):
GATAACACAGCTCCTACGTGATGAGAACGACTGGTTATCTAAGGTTGACGTGGCTCCTACATGAT
GAGGAGATCAGGTCGGTGGATGACACAGTTCCTACGTGATGAGGACGACTGGTCATCTTTAGGGA
TAAT
Found at i:69184 original size:67 final size:65
Alignment explanation
Indices: 68974--69288 Score: 353
Period size: 65 Copynumber: 4.8 Consensus size: 65
68964 TTAGGGATAA
* * * * *
68974 ATGTTTCAAGAGAAACTGTCTCGAAAGAGACAAAATTCGTTTAAAGGGAAACGATCTCAAAGATG
1 ATGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGTTG
* * * ** *
69039 ATGTTTCAAGAGAAACTGTTTCAAGAGAGACAAAATTCGTTTCAAGGGAAATGATATCAAA-TAT
1 ATGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGT-T
69103 G
65 G
* * * * *
69104 ATGTTTCAAGAGAAATTGTCTAAAAAGAGACTAATTTTGTTTCAAGGGAAACAATCTTAAAGTTG
1 ATGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGTTG
* * ** * *
69169 TTGTGTTTCAAGAGAAACTGTATCAAGGGAGACAAAACTTGTTTCAAGGGAAACAGTCTCAAAGT
1 --ATGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGT
69234 TG
64 TG
* * * *
69236 TATGTTTCAAGGGAAACAGTCTCAAAAGAGACAAAACTTGTTTTAAGGGAAAC
1 -ATGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAATTTGTTTCAAGGGAAAC
69289 TGTCTCAAGA
Statistics
Matches: 210, Mismatches: 36, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
65 109 0.52
66 47 0.22
67 54 0.26
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (65 bp):
ATGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGTTG
Found at i:69222 original size:36 final size:36
Alignment explanation
Indices: 69172--69326 Score: 153
Period size: 36 Copynumber: 4.4 Consensus size: 36
69162 AAAGTTGTTG
* * * *
69172 TGTTTCAAGAGAAACTGTATCAAGGGAGACAAAACT
1 TGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAACT
* *
69208 TGTTTCAAGGGAAACAGTCTCAA-AGTTG----TA--
1 TGTTTCAAGGGAAACAGTCTCAAGAG-AGACAAAACT
*
69238 TGTTTCAAGGGAAACAGTCTCAAAAGAGACAAAACT
1 TGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAACT
* *
69274 TGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAACAT
1 TGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAAC-T
*
69311 TGTTTCAAGAGAAACA
1 TGTTTCAAGGGAAACA
69327 TACTCAAAGA
Statistics
Matches: 96, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
30 24 0.25
31 2 0.02
32 1 0.01
34 1 0.01
35 1 0.01
36 53 0.55
37 14 0.15
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (36 bp):
TGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAACT
Found at i:69347 original size:103 final size:103
Alignment explanation
Indices: 69172--69391 Score: 279
Period size: 103 Copynumber: 2.1 Consensus size: 103
69162 AAAGTTGTTG
* * * *
69172 TGTTTCAAGAGAAACTGTATCAAGGGAGACAAAACTTGTTTCAAGGGAAACAGTCTCAAAGTTGT
1 TGTTTTAAGGGAAACTGTATCAAGAGAGACAAAACTTGTTTCAAGAGAAACAGTCTCAAAGTTGT
* *
69237 ATGTTTCAAGGGAAACAGTCTCAAAAGAGACAAAAC-T
66 ATCTTTCAAGAGAAACAGTCTCAAAAGAGACAAAACTT
*
69274 TGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAACATTGTTTCAAGAGAAACA-TACTCAAAGAC
1 TGTTTTAAGGGAAACTGTATCAAGAGAGACAAAAC-TTGTTTCAAGAGAAACAGT-CTCAAAG--
** *
69338 TT-T-TCTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
62 TTGTATCTTTCAAGAGAAACAGTCTCAAAAGAGACAAAACTT
69378 TGTTTTAA-GGAAAC
1 TGTTTTAAGGGAAAC
69392 ATACTCAATG
Statistics
Matches: 103, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
102 32 0.31
103 59 0.57
104 10 0.10
105 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.26
Consensus pattern (103 bp):
TGTTTTAAGGGAAACTGTATCAAGAGAGACAAAACTTGTTTCAAGAGAAACAGTCTCAAAGTTGT
ATCTTTCAAGAGAAACAGTCTCAAAAGAGACAAAACTT
Found at i:69421 original size:66 final size:67
Alignment explanation
Indices: 69273--69443 Score: 263
Period size: 66 Copynumber: 2.6 Consensus size: 67
69263 GAGACAAAAC
* * * *
69273 TTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAACATTGTTTCAAGAGAAACATACTCAAAGAC
1 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACATACTCAAAGAC
69338 TT
66 TT
* * * *
69340 TTCTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTTAAG-GAAACATACTCAATGAT
1 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACATACTCAAAGAC
69404 TT
66 TT
69406 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
69444 GCTTTGAAAT
Statistics
Matches: 95, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
66 54 0.57
67 41 0.43
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (67 bp):
TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACATACTCAAAGAC
TT
Found at i:69465 original size:66 final size:66
Alignment explanation
Indices: 69273--69470 Score: 222
Period size: 66 Copynumber: 3.0 Consensus size: 66
69263 GAGACAAAAC
* * * * * * *
69273 TTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAACATTGTTTCAAGAGAAACATACTCAAAGAC
1 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACATTGTTTAAAGAGACA-ATACTCAATGAT
69338 TT
65 TT
* * * *
69340 TTCTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTTAAG-GAAACATACTCAATGAT
1 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACATTGTTTAAAGAGACA-ATACTCAATGAT
69404 TT
65 TT
*
69406 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAAC-TTGCTTTGAAATAGACAAT-CTCAAGTG
1 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACATTG-TTT-AAAGAGACAATACTCAA-TG
69469 AT
63 AT
69471 ATCAATTAGT
Statistics
Matches: 115, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
65 3 0.03
66 60 0.52
67 49 0.43
68 3 0.03
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (66 bp):
TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACATTGTTTAAAGAGACAATACTCAATGATT
T
Found at i:69949 original size:16 final size:16
Alignment explanation
Indices: 69928--69967 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
69918 TTCATGTATC
*
69928 ATGTATGTATGTGTTG
1 ATGTATGTATGTATTG
69944 ATGTATGTATGTATTG
1 ATGTATGTATGTATTG
69960 ATGTATGT
1 ATGTATGT
69968 TTTCTTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.50
Consensus pattern (16 bp):
ATGTATGTATGTATTG
Found at i:77359 original size:11 final size:11
Alignment explanation
Indices: 77343--77384 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
77333 CATGCGCCGA
77343 GTATGGATCGG
1 GTATGGATCGG
*
77354 GTATGGATCGA
1 GTATGGATCGG
*
77365 GTCTGGATCGG
1 GTATGGATCGG
*
77376 ATATGGATC
1 GTATGGATC
77385 CTGGGTCGGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.21, C:0.12, G:0.38, T:0.29
Consensus pattern (11 bp):
GTATGGATCGG
Found at i:77371 original size:22 final size:22
Alignment explanation
Indices: 77340--77384 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
77330 GGGCATGCGC
*
77340 CGAGTATGGATCGGGTATGGAT
1 CGAGTATGGATCGGATATGGAT
*
77362 CGAGTCTGGATCGGATATGGAT
1 CGAGTATGGATCGGATATGGAT
77384 C
1 C
77385 CTGGGTCGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.22, C:0.13, G:0.38, T:0.27
Consensus pattern (22 bp):
CGAGTATGGATCGGATATGGAT
Found at i:77504 original size:3 final size:3
Alignment explanation
Indices: 77496--77530 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
77486 AAAATATGTA
77496 AAT AAT AAT AAT AAT AAT AAT AAT AAT AATT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT A
77531 TTTTTTAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:77623 original size:16 final size:16
Alignment explanation
Indices: 77602--77643 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
77592 GTTGGTTTCA
77602 TTGCTTTAGGAATGGT
1 TTGCTTTAGGAATGGT
**
77618 TTGCTTTAAAAATGGT
1 TTGCTTTAGGAATGGT
*
77634 TTGTTTTAGG
1 TTGCTTTAGG
77644 GGTAGTTGTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.48
Consensus pattern (16 bp):
TTGCTTTAGGAATGGT
Found at i:79052 original size:24 final size:24
Alignment explanation
Indices: 79020--79072 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
79010 GTCTAGCCGT
79020 TATTCTTATTAAAAAAAGTGAAAA
1 TATTCTTATTAAAAAAAGTGAAAA
79044 TATTCTTATTAAAAAAAGTGAAAA
1 TATTCTTATTAAAAAAAGTGAAAA
79068 TATTC
1 TATTC
79073 AAAATTCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.36
Consensus pattern (24 bp):
TATTCTTATTAAAAAAAGTGAAAA
Found at i:90487 original size:59 final size:57
Alignment explanation
Indices: 90341--90488 Score: 140
Period size: 59 Copynumber: 2.6 Consensus size: 57
90331 TATGTTTTAG
* * * * *
90341 CCCTTGAC-TT-ATATTTGATTTACAATTTGGCCCCTTGCCTTTTTTCATGCTATTTGG
1 CCCTTGACTTTGA-ATTTGATTTATAATTT-GTCCCTTGCCTTTTTTAATGCAATTTGA
** *
90398 CCCTTGACTTTGGCTTT-ATATTGTAATTTGTCCCTTGACCTTTTGTTAATGCAATTTGA
1 CCCTTGACTTTGAATTTGAT-TTATAATTTGTCCCTTG-CCTTTT-TTAATGCAATTTGA
* *
90457 CCCTTGATTTTGAATTTGATTTATAGTTTGTC
1 CCCTTGACTTTGAATTTGATTTATAATTTGTC
90489 TGTAACATCC
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
57 17 0.24
58 18 0.25
59 35 0.49
60 2 0.03
ACGTcount: A:0.18, C:0.19, G:0.15, T:0.49
Consensus pattern (57 bp):
CCCTTGACTTTGAATTTGATTTATAATTTGTCCCTTGCCTTTTTTAATGCAATTTGA
Found at i:92525 original size:37 final size:37
Alignment explanation
Indices: 92449--92525 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
92439 TTTTTATATT
*
92449 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
92486 TTTAATTTTTTAAATAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
92523 TTT
1 TTT
92526 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:92954 original size:19 final size:16
Alignment explanation
Indices: 92920--92980 Score: 68
Period size: 16 Copynumber: 3.6 Consensus size: 16
92910 TATGCACTAT
*
92920 TTATATGATCTATGTG
1 TTATATGATTTATGTG
92936 TTATATGTCATCTTATGTG
1 TTATATG--AT-TTATGTG
*
92955 TTACATGATTTATGTG
1 TTATATGATTTATGTG
92971 ATTATATGAT
1 -TTATATGAT
92981 AATATGATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 14 0.37
17 10 0.26
18 2 0.05
19 12 0.32
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.51
Consensus pattern (16 bp):
TTATATGATTTATGTG
Found at i:93015 original size:45 final size:45
Alignment explanation
Indices: 92965--93091 Score: 173
Period size: 45 Copynumber: 2.8 Consensus size: 45
92955 TTACATGATT
* * *
92965 TATGTGATTATATGATAATATGATATAAGCTATGTGACATTGACC
1 TATGTGATTATATGAAAATGTGATATAAGCTATGTGACATTGAAC
* ** * *
93010 TATGTGATTAAATGAAAATGTGATATAATATATGTAATATTGAAC
1 TATGTGATTATATGAAAATGTGATATAAGCTATGTGACATTGAAC
*
93055 TACGTGATTATATGAAAATGTGATATAAGCTATGTGA
1 TATGTGATTATATGAAAATGTGATATAAGCTATGTGA
93092 AATGATCTAT
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (45 bp):
TATGTGATTATATGAAAATGTGATATAAGCTATGTGACATTGAAC
Found at i:93237 original size:23 final size:23
Alignment explanation
Indices: 93210--93311 Score: 123
Period size: 23 Copynumber: 4.4 Consensus size: 23
93200 GAGTCGAGGG
* *
93210 TTCTACGCGGTCCTTCGAGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* *
93233 TTCTACGTAGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
*
93256 TTCTACGTGGTCCTTTGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* * *
93279 TACTATGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
*
93302 TTCTATGTGG
1 TTCTACGTGG
93312 CACTTTAATG
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 67 1.00
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.34
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:93278 original size:46 final size:46
Alignment explanation
Indices: 93210--93311 Score: 141
Period size: 46 Copynumber: 2.2 Consensus size: 46
93200 GAGTCGAGGG
* *
93210 TTCTACGCGGTCCTTCGAGACAATTCTACGTAGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGAGACAATACTACGTAGTCCTTCGGGACAT
* * * *
93256 TTCTACGTGGTCCTTTGGGACAATACTATGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGAGACAATACTACGTAGTCCTTCGGGACAT
*
93302 TTCTATGTGG
1 TTCTACGTGG
93312 CACTTTAATG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.34
Consensus pattern (46 bp):
TTCTACGTGGTCCTTCGAGACAATACTACGTAGTCCTTCGGGACAT
Found at i:96399 original size:2 final size:2
Alignment explanation
Indices: 96392--96428 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
96382 ATTATATCAT
96392 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
96429 TAATGATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:98542 original size:27 final size:27
Alignment explanation
Indices: 98509--98599 Score: 93
Period size: 27 Copynumber: 3.4 Consensus size: 27
98499 TTTATATTTT
98509 TAATAAAATATTTTTAAATTAAGTTAA
1 TAATAAAATATTTTTAAATTAAGTTAA
*
98536 TAATAAAATATATTT-AA-TAAGTTAATA
1 TAATAAAATATTTTTAAATTAAGTT-A-A
* *
98563 TAAAAAAATATTTTTTAAGTTAA--TAA
1 TAATAAAATA-TTTTTAAATTAAGTTAA
98589 T-ATAAAATATT
1 TAATAAAATATT
98600 ATGAATTTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
24 2 0.04
25 13 0.24
26 5 0.09
27 25 0.46
28 5 0.09
29 1 0.02
30 3 0.06
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (27 bp):
TAATAAAATATTTTTAAATTAAGTTAA
Found at i:98562 original size:25 final size:25
Alignment explanation
Indices: 98509--98599 Score: 96
Period size: 25 Copynumber: 3.6 Consensus size: 25
98499 TTTATATTTT
*
98509 TAATAAAATATTTTTAAATTAAGTTAA
1 TAATAAAATATATTT-AA-TAAGTTAA
98536 TAATAAAATATATTTAATAAGTTAA
1 TAATAAAATATATTTAATAAGTTAA
* **
98561 T-ATAAAAAAATATTTTTTAAGTTAA
1 TAAT-AAAATATATTTAATAAGTTAA
98586 TAATATAAA-ATATT
1 TAATA-AAATATATT
98600 ATGAATTTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
24 2 0.04
25 34 0.60
26 7 0.12
27 14 0.25
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (25 bp):
TAATAAAATATATTTAATAAGTTAA
Found at i:99014 original size:32 final size:32
Alignment explanation
Indices: 98978--99042 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
98968 GCTTAATGAT
98978 TATGTCTCGGAAGAGAACATGCAAGAAGATCC
1 TATGTCTCGGAAGAGAACATGCAAGAAGATCC
99010 TATGTCTCGGAAGAGAACATGCAAGAAGATCC
1 TATGTCTCGGAAGAGAACATGCAAGAAGATCC
99042 T
1 T
99043 TCTTTCCATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (32 bp):
TATGTCTCGGAAGAGAACATGCAAGAAGATCC
Found at i:99673 original size:22 final size:23
Alignment explanation
Indices: 99648--99692 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
99638 TTAATAGTCT
*
99648 TTTATTTCTGAAA-AAA-TCTTAA
1 TTTATGTCT-AAATAAATTCTTAA
99670 TTTATGTCTAAATAAATTCTTAA
1 TTTATGTCTAAATAAATTCTTAA
99693 AACAACTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 3 0.15
22 11 0.55
23 6 0.30
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (23 bp):
TTTATGTCTAAATAAATTCTTAA
Found at i:106510 original size:2 final size:2
Alignment explanation
Indices: 106503--106528 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
106493 GGTATGTTTC
106503 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
106529 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:109630 original size:20 final size:21
Alignment explanation
Indices: 109589--109630 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
109579 AAAGCTCAGG
*
109589 AGAAAGGAGAGACAAAGGAAA
1 AGAAAGGAGAGACAAAGAAAA
109610 AGAAA-GAGAGA-AAGAGAAAA
1 AGAAAGGAGAGACAA-AGAAAA
109630 A
1 A
109631 ATGTGCAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 2 0.11
20 12 0.63
21 5 0.26
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (21 bp):
AGAAAGGAGAGACAAAGAAAA
Found at i:113638 original size:16 final size:17
Alignment explanation
Indices: 113601--113639 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
113591 TATTAGCCCA
*
113601 TATACATATGTGAGAAC
1 TATAGATATGTGAGAAC
*
113618 TATAGATATGTGA-ATC
1 TATAGATATGTGAGAAC
113634 TATAGA
1 TATAGA
113640 GGTTGTGCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (17 bp):
TATAGATATGTGAGAAC
Found at i:113695 original size:23 final size:23
Alignment explanation
Indices: 113669--113733 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
113659 CACCACAGCT
* *
113669 CGTATAAATGCACCGAAGTGTCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
113692 CGTAGAATTGCACCTAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
113715 CGTAGAAATGCACCGAAGT
1 CGTAGAAATGCACCGAAGT
113734 TCCATATAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:115351 original size:24 final size:20
Alignment explanation
Indices: 115298--115355 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
115288 TCCCCTTTGA
*
115298 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
115318 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
115341 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
115356 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:115434 original size:64 final size:63
Alignment explanation
Indices: 115343--115504 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
115333 TCTTTAACAT
* * *
115343 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAA-GGG
* * * ** *
115407 GTGCATCGATGCACTCCTTATGTATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCC-TATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
*
115471 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
115505 CTGAACAATT
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 2 0.02
64 71 0.87
65 9 0.11
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:125004 original size:16 final size:17
Alignment explanation
Indices: 124985--125019 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
124975 AAGTAATTAA
*
124985 TTATTTTATTA-TTATT
1 TTATTTTAGTATTTATT
125001 TTATTTTAGTATTTATT
1 TTATTTTAGTATTTATT
125018 TT
1 TT
125020 TTTATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTATTTTAGTATTTATT
Found at i:125033 original size:20 final size:20
Alignment explanation
Indices: 124993--125034 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
124983 AATTATTTTA
* *
124993 TTATTATTTTATTTTAGTAT
1 TTATTATTTTATTTAAATAT
*
125013 TTATTTTTTTATTTAAATAT
1 TTATTATTTTATTTAAATAT
125033 TT
1 TT
125035 GAATATTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
TTATTATTTTATTTAAATAT
Found at i:126872 original size:21 final size:21
Alignment explanation
Indices: 126848--126898 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
126838 CAGCCGGTTC
126848 AGATGCCACATCCA-CAAGTCT
1 AGATGCCACATCCATC-AGTCT
* * *
126869 AGATGACATATCCATCAGTTT
1 AGATGCCACATCCATCAGTCT
126890 AGATGCCAC
1 AGATGCCAC
126899 TACCGTTTGG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (21 bp):
AGATGCCACATCCATCAGTCT
Found at i:128522 original size:20 final size:20
Alignment explanation
Indices: 128497--128541 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
128487 ATGATGAATA
** *
128497 GTATCAATACTGATATGAAG
1 GTATCAATACCAATAGGAAG
128517 GTATCAATACCAATAGGAAG
1 GTATCAATACCAATAGGAAG
128537 GTATC
1 GTATC
128542 GATATTGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (20 bp):
GTATCAATACCAATAGGAAG
Found at i:129435 original size:23 final size:23
Alignment explanation
Indices: 129403--129485 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
129393 TCGAGGGTTA
*
129403 TATGTAGTCCTTCGGGACAAACC
1 TATGTGGTCCTTCGGGACAAACC
*
129426 TATGTGGTCCTTTGGGACAAACC
1 TATGTGGTCCTTCGGGACAAACC
129449 TATGTGGTCCTTCGGGGACAAA--
1 TATGTGGTCCTTC-GGGACAAACC
129471 TATGTGG-CACTTCGG
1 TATGTGGTC-CTTCGG
129486 TGCAAATTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.05
22 11 0.20
23 33 0.60
24 8 0.15
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGACAAACC
Found at i:129477 original size:22 final size:23
Alignment explanation
Indices: 129403--129498 Score: 94
Period size: 23 Copynumber: 4.3 Consensus size: 23
129393 TCGAGGGTTA
*
129403 TATGTAGTCCTTC-GGGACAAACC
1 TATGTGGTCCTTCGGGGACAAA-C
*
129426 TATGTGGTCCTT-TGGGACAAACC
1 TATGTGGTCCTTCGGGGACAAA-C
129449 TATGTGGTCCTTCGGGGACAAA-
1 TATGTGGTCCTTCGGGGACAAAC
* *
129471 TATGTGG-CACTTCGGTG-CAAAT
1 TATGTGGTC-CTTCGGGGACAAAC
129493 TATGTG
1 TATGTG
129499 AGCAGTGGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 9
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.08
22 20 0.30
23 33 0.50
24 8 0.12
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGGACAAAC
Done.