Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 111 of 202
Found at i:34147955 original size:13 final size:13
Alignment explanation
Indices: 34147939--34147971 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
34147929 ACTTTTTTTT
*
34147939 ATTTTTTTTTCAA
1 ATTTTTTTCTCAA
34147952 ATTTTTTTCTCAA
1 ATTTTTTTCTCAA
34147965 ATTTTTT
1 ATTTTTT
34147972 ATTTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (13 bp):
ATTTTTTTCTCAA
Found at i:34149581 original size:20 final size:19
Alignment explanation
Indices: 34149552--34149589 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
34149542 AGCTAATAAC
34149552 GAGCTCAATGAGCTGAATT
1 GAGCTCAATGAGCTGAATT
34149571 GAGCTCGAATGAGCTGAAT
1 GAGCTC-AATGAGCTGAAT
34149590 CAAAAAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:34156473 original size:19 final size:20
Alignment explanation
Indices: 34156449--34156493 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
34156439 CTTTTCATTC
*
34156449 TCTTTTTTTGAATTTTC-TT
1 TCTTTTTTTCAATTTTCTTT
*
34156468 TCTTTTTTTCATTTTTCTTT
1 TCTTTTTTTCAATTTTCTTT
34156488 TCTTTT
1 TCTTTT
34156494 GTATTTTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (20 bp):
TCTTTTTTTCAATTTTCTTT
Found at i:34158691 original size:9 final size:10
Alignment explanation
Indices: 34158676--34158723 Score: 64
Period size: 9 Copynumber: 4.9 Consensus size: 10
34158666 ACCGTATACA
34158676 ATTTTTTTTC
1 ATTTTTTTTC
34158686 -TTTTTTTTC
1 ATTTTTTTTC
*
34158695 AATTTTTTT-
1 ATTTTTTTTC
34158704 ATTTTTTTTC
1 ATTTTTTTTC
34158714 AATTTTTTTT
1 -ATTTTTTTT
34158724 TCAAAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
9 17 0.52
10 7 0.21
11 9 0.27
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (10 bp):
ATTTTTTTTC
Found at i:34158699 original size:20 final size:20
Alignment explanation
Indices: 34158674--34158723 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
34158664 AGACCGTATA
*
34158674 CAATTTTTTTTCTTTTTTTT
1 CAATTTTTTTTATTTTTTTT
34158694 CAA-TTTTTTTATTTTTTTT
1 CAATTTTTTTTATTTTTTTT
34158713 CAATTTTTTTT
1 CAATTTTTTTT
34158724 TCAAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (20 bp):
CAATTTTTTTTATTTTTTTT
Found at i:34158722 original size:14 final size:14
Alignment explanation
Indices: 34158705--34158740 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
34158695 AATTTTTTTA
34158705 TTTTTTTTC--AAT
1 TTTTTTTTCAAAAT
34158717 TTTTTTTTCAAAAT
1 TTTTTTTTCAAAAT
34158731 TTTTTTTTCA
1 TTTTTTTTCA
34158741 CGAGTCTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 9 0.41
14 13 0.59
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTTTTCAAAAT
Found at i:34159071 original size:22 final size:22
Alignment explanation
Indices: 34159041--34159084 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
34159031 TTTGGTATTT
34159041 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
34159063 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
34159085 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:34160293 original size:30 final size:30
Alignment explanation
Indices: 34160235--34160293 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
34160225 TTGAAAATGT
* *
34160235 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
34160265 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
34160294 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:34163060 original size:12 final size:12
Alignment explanation
Indices: 34163027--34163107 Score: 53
Period size: 12 Copynumber: 6.8 Consensus size: 12
34163017 TTTCCACTCG
34163027 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
34163038 AGCTCTCTTTCA
1 ATTTCTTTTTCA
34163050 ATTTCTTTTTCCA
1 ATTTCTTTTT-CA
*
34163063 CTCTTTCTTTTTC-
1 --ATTTCTTTTTCA
*
34163076 --TTCTCTTTCA
1 ATTTCTTTTTCA
34163086 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
34163098 ATCTCTTTTT
1 ATTTCTTTTT
34163108 TCTTTTCACT
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
9 8 0.15
11 3 0.06
12 30 0.57
13 2 0.04
14 1 0.02
15 9 0.17
ACGTcount: A:0.12, C:0.25, G:0.01, T:0.62
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:34163068 original size:21 final size:20
Alignment explanation
Indices: 34163042--34163097 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 20
34163032 TTTTCAAGCT
34163042 CTCTTTCAATTTCTTTTTCCA
1 CTCTTTCAATTTCTTTTT-CA
*
34163063 CTCTTTC--TTT-TTCTT--
1 CTCTTTCAATTTCTTTTTCA
34163078 CTCTTTCAATTTCTTTTTCA
1 CTCTTTCAATTTCTTTTTCA
34163098 ATCTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
15 7 0.25
17 3 0.11
18 8 0.29
19 3 0.11
21 7 0.25
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (20 bp):
CTCTTTCAATTTCTTTTTCA
Found at i:34163115 original size:18 final size:19
Alignment explanation
Indices: 34163087--34163124 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
34163077 TCTCTTTCAA
34163087 TTTCTTTTTCAATCTCTTT
1 TTTCTTTTTCAATCTCTTT
*
34163106 TTTC-TTTTCACTCTCTTT
1 TTTCTTTTTCAATCTCTTT
34163124 T
1 T
34163125 ATTTTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTCTTTTTCAATCTCTTT
Found at i:34163160 original size:15 final size:15
Alignment explanation
Indices: 34163137--34163183 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
34163127 TTTTGAAATC
34163137 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
*
34163152 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
34163167 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
34163183 T
1 T
34163184 ATTCTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:34163178 original size:28 final size:29
Alignment explanation
Indices: 34163137--34163194 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
34163127 TTTTGAAATC
34163137 TCATTTTCATATTTTTCTTT-TTCATTTCTT
1 TCATTTTCA-A-TTTTCTTTATTCATTTCTT
*
34163167 TCATTTTC-ATTTTCTTTATTCTTTTCTT
1 TCATTTTCAATTTTCTTTATTCATTTCTT
34163195 GCTCAAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 8 0.31
28 10 0.38
30 8 0.31
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (29 bp):
TCATTTTCAATTTTCTTTATTCATTTCTT
Found at i:34166756 original size:10 final size:10
Alignment explanation
Indices: 34166741--34166790 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
34166731 ATTGGGTTAA
34166741 AATTGAGCTG
1 AATTGAGCTG
*
34166751 AATTGATCTCG
1 AATTGAGCT-G
34166762 AA-TGAGCTG
1 AATTGAGCTG
*
34166771 AATTGAGCTC
1 AATTGAGCTG
*
34166781 AAGTGAGCTG
1 AATTGAGCTG
34166791 GAAACGAGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 27 0.82
11 3 0.09
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (10 bp):
AATTGAGCTG
Found at i:34166767 original size:20 final size:20
Alignment explanation
Indices: 34166744--34166790 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
34166734 GGGTTAAAAT
*
34166744 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
34166764 TGAGCTGAATTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
34166784 TGAGCTG
1 TGAGCTG
34166791 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:34170315 original size:10 final size:10
Alignment explanation
Indices: 34170300--34170326 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
34170290 ATATTCTCTC
34170300 TTGGTATCAG
1 TTGGTATCAG
34170310 TTGGTATCAG
1 TTGGTATCAG
34170320 TTGGTAT
1 TTGGTAT
34170327 TAGTGAATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.07, G:0.30, T:0.44
Consensus pattern (10 bp):
TTGGTATCAG
Found at i:34170924 original size:63 final size:63
Alignment explanation
Indices: 34170855--34170978 Score: 248
Period size: 63 Copynumber: 2.0 Consensus size: 63
34170845 TCCGAGAAGA
34170855 GAGCTTCGCGACAAAGTACAAGGCGAGAAGGCCAACGAGCACAGGGACCAAGAGATCGAGATC
1 GAGCTTCGCGACAAAGTACAAGGCGAGAAGGCCAACGAGCACAGGGACCAAGAGATCGAGATC
34170918 GAGCTTCGCGACAAAGTACAAGGCGAGAAGGCCAACGAGCACAGGGACCAAGAGATCGAGA
1 GAGCTTCGCGACAAAGTACAAGGCGAGAAGGCCAACGAGCACAGGGACCAAGAGATCGAGA
34170979 GAGGACCGAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.37, C:0.23, G:0.32, T:0.07
Consensus pattern (63 bp):
GAGCTTCGCGACAAAGTACAAGGCGAGAAGGCCAACGAGCACAGGGACCAAGAGATCGAGATC
Found at i:34180490 original size:13 final size:13
Alignment explanation
Indices: 34180472--34180516 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
34180462 TCAAGTTGTG
34180472 AAAAAAAATTTGA
1 AAAAAAAATTTGA
34180485 AAAAAAAA--TG-
1 AAAAAAAATTTGA
34180495 AAAAAAAATTGTGA
1 AAAAAAAATT-TGA
34180509 AAAAAAAA
1 AAAAAAAA
34180517 AGAGAGCTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 8 0.29
11 2 0.07
13 10 0.36
14 8 0.29
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.16
Consensus pattern (13 bp):
AAAAAAAATTTGA
Found at i:34180496 original size:23 final size:24
Alignment explanation
Indices: 34180470--34180516 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
34180460 TATCAAGTTG
34180470 TGAAAAAAAATT-TGAAAAAAAAA
1 TGAAAAAAAATTGTGAAAAAAAAA
34180493 TGAAAAAAAATTGTGAAAAAAAAA
1 TGAAAAAAAATTGTGAAAAAAAAA
34180517 AGAGAGCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (24 bp):
TGAAAAAAAATTGTGAAAAAAAAA
Found at i:34183422 original size:13 final size:12
Alignment explanation
Indices: 34183390--34183421 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
34183380 GTAGTTTCCC
34183390 AAAAAAAATTCA
1 AAAAAAAATTCA
34183402 AAAAAAAATTCA
1 AAAAAAAATTCA
34183414 AAAAAAAA
1 AAAAAAAA
34183422 ACTAGTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:34183482 original size:11 final size:12
Alignment explanation
Indices: 34183463--34183511 Score: 71
Period size: 12 Copynumber: 3.8 Consensus size: 12
34183453 TATCAAGTTG
34183463 TGAAAAAAAATT
1 TGAAAAAAAATT
34183475 TGAAAAAAAATT
1 TGAAAAAAAATT
34183487 TGAAAAAAAAAATT
1 TG--AAAAAAAATT
34183501 GTGAAAAAAAA
1 -TGAAAAAAAA
34183512 GAGCTAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
12 14 0.41
13 8 0.24
14 10 0.29
15 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.20
Consensus pattern (12 bp):
TGAAAAAAAATT
Found at i:34183483 original size:13 final size:13
Alignment explanation
Indices: 34183465--34183511 Score: 69
Period size: 14 Copynumber: 3.5 Consensus size: 13
34183455 TCAAGTTGTG
34183465 AAAAAAAATTTG-
1 AAAAAAAATTTGA
34183477 AAAAAAAATTTGAA
1 AAAAAAAATTTG-A
34183491 AAAAAAAATTGTGA
1 AAAAAAAATT-TGA
34183505 AAAAAAA
1 AAAAAAA
34183512 GAGCTAGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.38
14 18 0.56
15 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (13 bp):
AAAAAAAATTTGA
Found at i:34188416 original size:23 final size:22
Alignment explanation
Indices: 34188392--34188433 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
34188382 CCATTTCCAT
34188392 TTTCGTACCAAATCCATTACTA
1 TTTCGTACCAAATCCATTACTA
** *
34188414 TTTCGTTTCAAATCCCTTAC
1 TTTCGTACCAAATCCATTAC
34188434 CGTTTCATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.05, T:0.40
Consensus pattern (22 bp):
TTTCGTACCAAATCCATTACTA
Found at i:34195878 original size:13 final size:13
Alignment explanation
Indices: 34195860--34195889 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
34195850 GAACTCTTCA
34195860 AGCTTAAGTAATC
1 AGCTTAAGTAATC
*
34195873 AGCTTAATTAATC
1 AGCTTAAGTAATC
34195886 AGCT
1 AGCT
34195890 GAATTGGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
AGCTTAAGTAATC
Found at i:34197229 original size:20 final size:20
Alignment explanation
Indices: 34197195--34197247 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
34197185 TTGAAAAGAA
34197195 AACTC-AAAGAGAATTTATT
1 AACTCAAAAGAGAATTTATT
*
34197214 AACTCAAAAGATAATTTATT
1 AACTCAAAAGAGAATTTATT
*
34197234 AACTCAAAAAAGAA
1 AACTCAAAAGAGAA
34197248 GTTGAATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 5 0.17
20 25 0.83
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.26
Consensus pattern (20 bp):
AACTCAAAAGAGAATTTATT
Found at i:34199290 original size:96 final size:96
Alignment explanation
Indices: 34199171--34199346 Score: 298
Period size: 96 Copynumber: 1.8 Consensus size: 96
34199161 TCTTTTCTCG
** *
34199171 TTGGATATTTAATTGGACATTGGAAACACTTATGATATTTTGAACTACATTAGTAACATTGCACA
1 TTGGATATTTAATTGGACATTGGAAACACTTATGATATTTTGAACTACACCAATAACATTGCACA
*
34199236 AAAGGTGATAGCTCAATCGTATTCTCTCTTT
66 AAAGGTGATAACTCAATCGTATTCTCTCTTT
* *
34199267 TTGGATATTTAATTGGACATTGGAAACTCTTATGATCTTTTGAACTACACCAATAACATTGCACA
1 TTGGATATTTAATTGGACATTGGAAACACTTATGATATTTTGAACTACACCAATAACATTGCACA
34199332 AAAGGTGATAACTCA
66 AAAGGTGATAACTCA
34199347 TAGTCATTAG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
96 74 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (96 bp):
TTGGATATTTAATTGGACATTGGAAACACTTATGATATTTTGAACTACACCAATAACATTGCACA
AAAGGTGATAACTCAATCGTATTCTCTCTTT
Found at i:34199637 original size:21 final size:21
Alignment explanation
Indices: 34199611--34199673 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
34199601 TTGGTATTTG
34199611 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
34199632 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
34199653 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
34199674 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:34205590 original size:25 final size:25
Alignment explanation
Indices: 34205561--34205615 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
34205551 GAAATAAACT
*
34205561 TAAGCCAAGCTCAAACGAGCTAAAG
1 TAAGCCAAACTCAAACGAGCTAAAG
* * * *
34205586 TAAGCTAAATTGAAACGAGCTAAAT
1 TAAGCCAAACTCAAACGAGCTAAAG
34205611 TAAGC
1 TAAGC
34205616 TCATGTGAGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (25 bp):
TAAGCCAAACTCAAACGAGCTAAAG
Found at i:34206706 original size:18 final size:18
Alignment explanation
Indices: 34206680--34206720 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
34206670 AAAGAGTTTG
34206680 AGAATAAAAAAATGTGAAAA
1 AGAA-AAAAAAAT-TGAAAA
34206700 AGAAAAAAAAATTGAAAA
1 AGAAAAAAAAATTGAAAA
34206718 AGA
1 AGA
34206721 GATTGAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.43
19 8 0.38
20 4 0.19
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (18 bp):
AGAAAAAAAAATTGAAAA
Found at i:34209434 original size:26 final size:26
Alignment explanation
Indices: 34209369--34209434 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
34209359 TTGGCCAAAT
34209369 ATACTATT-ACTGGCAGCTTTGCTACG
1 ATACTATTGA-TGGCAGCTTTGCTACG
* **
34209395 ATACTATTGCTGGCAGCTTTGCTGTG
1 ATACTATTGATGGCAGCTTTGCTACG
*
34209421 ATGCTATTGATGGC
1 ATACTATTGATGGC
34209435 TTTGTGCCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (26 bp):
ATACTATTGATGGCAGCTTTGCTACG
Found at i:34209614 original size:32 final size:32
Alignment explanation
Indices: 34209428--34209627 Score: 222
Period size: 32 Copynumber: 6.3 Consensus size: 32
34209418 GTGATGCTAT
* * * *
34209428 TGATGGCTTTGTGCCGTTCAAATTACCATTAG
1 TGATGGCTTTGTGCCGATCATATTACTATTAC
* *
34209460 TGATGGCTATGTGCCGATCATATTACCATTAC
1 TGATGGCTTTGTGCCGATCATATTACTATTAC
* *
34209492 TGATGGCTGTGTGCCGATCATATTACTACTAC
1 TGATGGCTTTGTGCCGATCATATTACTATTAC
* ** *
34209524 TGATGGCTTTGTGTCGGCCATACTACTATTAC
1 TGATGGCTTTGTGCCGATCATATTACTATTAC
* * *
34209556 TAATGGCTGTGTGCCGATCATATTACTACTAC
1 TGATGGCTTTGTGCCGATCATATTACTATTAC
* * *
34209588 TAATGGCTTTGTGCCAATCATATTACT-GTAC
1 TGATGGCTTTGTGCCGATCATATTACTATTAC
*
34209619 TTATGGCTT
1 TGATGGCTT
34209628 GTAGCCATTC
Statistics
Matches: 144, Mismatches: 24, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
31 11 0.08
32 133 0.92
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (32 bp):
TGATGGCTTTGTGCCGATCATATTACTATTAC
Found at i:34209644 original size:22 final size:21
Alignment explanation
Indices: 34209619--34209683 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
34209609 ATTACTGTAC
34209619 TTATGGCTTGTAGCCATTCTGT
1 TTATGGCTT-TAGCCATTCTGT
* *
34209641 TTATAGCTTATAGCTA-TCTTGT
1 TTATGGCTT-TAGCCATTC-TGT
34209663 TTATGGCTCTTAGCCATTCTG
1 TTATGGCT-TTAGCCATTCTG
34209684 GTTACTGGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 2 0.06
22 30 0.86
23 3 0.09
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.46
Consensus pattern (21 bp):
TTATGGCTTTAGCCATTCTGT
Found at i:34212570 original size:19 final size:19
Alignment explanation
Indices: 34212543--34212635 Score: 72
Period size: 19 Copynumber: 5.1 Consensus size: 19
34212533 TTATTCCAGC
*
34212543 AACTAAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
34212562 AACTTAATTAACTAAGATTTG
1 AACTTAATTAACTAAGA--TG
* * *
34212583 TAA-TTTATT--C-CAG--C
1 -AACTTAATTAACTAAGATG
34212597 AACTTAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
*
34212616 AACTCAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
34212635 A
1 A
34212636 GTAATTTATT
Statistics
Matches: 57, Mismatches: 8, Indels: 18
0.69 0.10 0.22
Matches are distributed among these distances:
13 2 0.04
14 5 0.09
16 1 0.02
17 2 0.04
18 2 0.04
19 36 0.63
21 7 0.12
22 2 0.04
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (19 bp):
AACTTAATTAACTAAGATG
Found at i:34212615 original size:54 final size:54
Alignment explanation
Indices: 34212533--34212658 Score: 216
Period size: 54 Copynumber: 2.3 Consensus size: 54
34212523 CAACAATAAA
* **
34212533 TTATTCCAGCAACTAAATTAACTAAGATGAACTTAATTAACTAAGATTTGTAAT
1 TTATTCCAGCAACTAAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAAT
*
34212587 TTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAAT
1 TTATTCCAGCAACTAAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAAT
34212641 TTATTCCAGCAACTAAAT
1 TTATTCCAGCAACTAAAT
34212659 ACTTGTTCTA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (54 bp):
TTATTCCAGCAACTAAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAAT
Found at i:34212762 original size:20 final size:21
Alignment explanation
Indices: 34212733--34212772 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
34212723 AGCTTGAAGA
* *
34212733 AGCTAGAATTGAGC-TCATTG
1 AGCTAAAATTAAGCTTCATTG
34212753 AGCTAAAATTAAGCTTCATT
1 AGCTAAAATTAAGCTTCATT
34212773 TTGCACTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (21 bp):
AGCTAAAATTAAGCTTCATTG
Found at i:34214195 original size:57 final size:55
Alignment explanation
Indices: 34214126--34214248 Score: 128
Period size: 57 Copynumber: 2.2 Consensus size: 55
34214116 TTTTGTAGAC
34214126 TCTTTCTT-ACTTT-TTATTTCATTTTCAATCT-CTTTTTGCATTCTCTTACTATCT-TTT
1 TCTTT-TTCACTTTCTT-TTTCATTTTCAAT-TGCTTTTT-CATTCT-TTACT-TCTCTTT
* * * *
34214183 TCTTTTTCACTTTCTTTTTCTTTTTCAATTGCTTTTTCTTTCTTTTCTTTTCTTT
1 TCTTTTTCACTTTCTTTTTCATTTTCAATTGCTTTTTCATTCTTTACTTCTCTTT
34214238 TCTTTTTCACT
1 TCTTTTTCACT
34214249 AAATTTCTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
54 2 0.03
55 18 0.31
56 8 0.14
57 28 0.48
58 2 0.03
ACGTcount: A:0.10, C:0.21, G:0.02, T:0.67
Consensus pattern (55 bp):
TCTTTTTCACTTTCTTTTTCATTTTCAATTGCTTTTTCATTCTTTACTTCTCTTT
Found at i:34214200 original size:18 final size:18
Alignment explanation
Indices: 34214177--34214248 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
34214167 TCTCTTACTA
34214177 TCTTTTTCTTTTTCACTT
1 TCTTTTTCTTTTTCACTT
*
34214195 TCTTTTTCTTTTTCAATT
1 TCTTTTTCTTTTTCACTT
* **
34214213 GCTTTTTCTTTCTTTTCTT
1 TCTTTTTCTTT-TTCACTT
34214232 T-TCTTTTCTTTTTCACT
1 TCT-TTTTCTTTTTCACT
34214249 AAATTTCTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 32 0.73
19 12 0.27
ACGTcount: A:0.06, C:0.21, G:0.01, T:0.72
Consensus pattern (18 bp):
TCTTTTTCTTTTTCACTT
Found at i:34214262 original size:6 final size:6
Alignment explanation
Indices: 34214177--34214245 Score: 59
Period size: 6 Copynumber: 11.3 Consensus size: 6
34214167 TCTCTTACTA
** ** *
34214177 TCTTTT TCTTTT TCACTT TCTTTT TCTTTT TCAATT GCTTTT TCTTTCT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTT-T
*
34214226 TTTCTTT TC-TTT TCTTTT TC
1 TCT-TTT TCTTTT TCTTTT TC
34214246 ACTAAATTTC
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
5 5 0.10
6 36 0.75
7 5 0.10
8 2 0.04
ACGTcount: A:0.04, C:0.20, G:0.01, T:0.74
Consensus pattern (6 bp):
TCTTTT
Found at i:34214262 original size:37 final size:39
Alignment explanation
Indices: 34214177--34214262 Score: 88
Period size: 37 Copynumber: 2.2 Consensus size: 39
34214167 TCTCTTACTA
***
34214177 TCTTTTTCTTTTTCACTTTCTTTTTCTTTTTCAATTGCTT
1 TCTTTTTC-TTTTCACTTTCTTTTTCTTTTTCAATAAATT
* *
34214217 T-TTCTTTCTTTTC-TTTTC-TTTTCTTTTTCACTAAATT
1 TCTT-TTTCTTTTCACTTTCTTTTTCTTTTTCAATAAATT
34214254 TCTTTTTCT
1 TCTTTTTCT
34214263 CTCTTCCTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
37 21 0.54
38 6 0.15
39 7 0.18
40 5 0.13
ACGTcount: A:0.08, C:0.20, G:0.01, T:0.71
Consensus pattern (39 bp):
TCTTTTTCTTTTCACTTTCTTTTTCTTTTTCAATAAATT
Found at i:34219766 original size:17 final size:16
Alignment explanation
Indices: 34219728--34219769 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
34219718 TTTTTCTTTC
34219728 TCTTTTCTTTCAAGCTT
1 TCTTTTCTTTCAA-CTT
34219745 TCTTTTGCTTTCAA-TT
1 TCTTTT-CTTTCAACTT
34219761 TACTTTTCT
1 T-CTTTTCT
34219770 CTCATTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.22
17 11 0.48
18 7 0.30
ACGTcount: A:0.12, C:0.21, G:0.05, T:0.62
Consensus pattern (16 bp):
TCTTTTCTTTCAACTT
Found at i:34221008 original size:20 final size:20
Alignment explanation
Indices: 34220985--34221039 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
34220975 AGTTCAATTC
34220985 AGCTCAATTTTAGCTCAATG
1 AGCTCAATTTTAGCTCAATG
*
34221005 AGCTC-GTTCTTAGCTCAATG
1 AGCTCAATT-TTAGCTCAATG
*
34221025 AGCTCATTTTTAGCT
1 AGCTCAATTTTAGCT
34221040 TACTTTAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTTAGCTCAATG
Found at i:34228121 original size:25 final size:24
Alignment explanation
Indices: 34228093--34228143 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
34228083 TTAAAACTAC
34228093 TTCTAAAAAAAAACTCAAGAGAGAA
1 TTCTAAAAAAAAACTCAA-AGAGAA
*** *
34228118 TTCTTGGAGAAAACTCAAAGAGAA
1 TTCTAAAAAAAAACTCAAAGAGAA
34228142 TT
1 TT
34228144 TTTTCACTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.22
Consensus pattern (24 bp):
TTCTAAAAAAAAACTCAAAGAGAA
Found at i:34237195 original size:13 final size:12
Alignment explanation
Indices: 34237163--34237205 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
34237153 TATTTTTCTA
34237163 TTTTGTTTGTTTT
1 TTTTGTTT-TTTT
*
34237176 TTGTGTTTTTTT
1 TTTTGTTTTTTT
34237188 GTTTTGTTTTTTAT
1 -TTTTGTTTTTT-T
34237202 TTTT
1 TTTT
34237206 TTTCTTTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 4 0.15
13 21 0.81
14 1 0.04
ACGTcount: A:0.02, C:0.00, G:0.14, T:0.84
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:34237196 original size:22 final size:21
Alignment explanation
Indices: 34237163--34237214 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
34237153 TATTTTTCTA
*
34237163 TTTTG-TTTGTTTTTTGTGTTT
1 TTTTGTTTTGTTTTTTAT-TTT
34237184 TTTTGTTTTGTTTTTTATTTT
1 TTTTGTTTTGTTTTTTATTTT
*
34237205 TTTTCTTTTG
1 TTTTGTTTTG
34237215 GTGTAGAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.83
Consensus pattern (21 bp):
TTTTGTTTTGTTTTTTATTTT
Found at i:34241237 original size:52 final size:51
Alignment explanation
Indices: 34241173--34241304 Score: 167
Period size: 50 Copynumber: 2.6 Consensus size: 51
34241163 ATGAACAAAT
* * *
34241173 GAGTTACTTAATGCATGACTTAATTTAATGATGCAAACTTTAACTACCATGG
1 GAGTTACATAATGCATGACTTAATTTAATGATGCAAAC-TTAACTAACATGA
* *
34241225 GAGTTACATAATGCATGTCATAATTT-ATGATGCAAACTTAACTAACATGA
1 GAGTTACATAATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGA
* * * *
34241275 AAGTTACATAATGCTTGACTTTATTAAATG
1 GAGTTACATAATGCATGACTTAATTTAATG
34241305 CATAACACAT
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
50 31 0.46
51 14 0.21
52 23 0.34
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (51 bp):
GAGTTACATAATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGA
Found at i:34243763 original size:27 final size:27
Alignment explanation
Indices: 34243717--34243893 Score: 201
Period size: 27 Copynumber: 6.6 Consensus size: 27
34243707 AACACGTTAG
* *
34243717 GAAAGAAAAGCCTTTATGGCATAATAT
1 GAAAGAAAAGACTTTGTGGCATAATAT
* *
34243744 GAAAGAAAATAATTTGTGGCATAATAT
1 GAAAGAAAAGACTTTGTGGCATAATAT
* *
34243771 GAAAGAAAAGCCTTTGTGGCGTAATAT
1 GAAAGAAAAGACTTTGTGGCATAATAT
* * *
34243798 GAAAGGAAAGACTTTGTAGCGTAATAT
1 GAAAGAAAAGACTTTGTGGCATAATAT
* *
34243825 AAAAGGAAAGACTTTGTGGCATAATAT
1 GAAAGAAAAGACTTTGTGGCATAATAT
* * *
34243852 GAAAGAAAAGCCTTTGTAGCGTAATAT
1 GAAAGAAAAGACTTTGTGGCATAATAT
* * *
34243879 AAAATAAAAGCCTTT
1 GAAAGAAAAGACTTT
34243894 TAGTGGCGTG
Statistics
Matches: 129, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 129 1.00
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.27
Consensus pattern (27 bp):
GAAAGAAAAGACTTTGTGGCATAATAT
Found at i:34243799 original size:54 final size:54
Alignment explanation
Indices: 34243718--34243893 Score: 244
Period size: 54 Copynumber: 3.3 Consensus size: 54
34243708 ACACGTTAGG
* * * * * *
34243718 AAAGAAAAGCCTTTATGGCATAATATGAAAGAAAATAATTTGTGGCATAATATG
1 AAAGAAAAGCCTTTGTGGCATAATATGAAAGAAAAGACTTTGTAGCGTAATATA
* *
34243772 AAAGAAAAGCCTTTGTGGCGTAATATGAAAGGAAAGACTTTGTAGCGTAATATA
1 AAAGAAAAGCCTTTGTGGCATAATATGAAAGAAAAGACTTTGTAGCGTAATATA
* * *
34243826 AAAGGAAAGACTTTGTGGCATAATATGAAAGAAAAGCCTTTGTAGCGTAATATA
1 AAAGAAAAGCCTTTGTGGCATAATATGAAAGAAAAGACTTTGTAGCGTAATATA
*
34243880 AAATAAAAGCCTTT
1 AAAGAAAAGCCTTT
34243894 TAGTGGCGTG
Statistics
Matches: 106, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 106 1.00
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (54 bp):
AAAGAAAAGCCTTTGTGGCATAATATGAAAGAAAAGACTTTGTAGCGTAATATA
Found at i:34245306 original size:20 final size:21
Alignment explanation
Indices: 34245283--34245323 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
34245273 AGCTCGAATC
34245283 AGCTCACTTGAGCTC-ATTTA
1 AGCTCACTTGAGCTCAATTTA
**
34245303 AGCTCGTTTGAGCTCAATTTA
1 AGCTCACTTGAGCTCAATTTA
34245324 GTTTATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (21 bp):
AGCTCACTTGAGCTCAATTTA
Found at i:34247975 original size:18 final size:17
Alignment explanation
Indices: 34247952--34247985 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
34247942 TTTATATATA
34247952 ATACTTGTTATATCTTTT
1 ATACTTGTTATA-CTTTT
*
34247970 ATACTTTTTATACTTT
1 ATACTTGTTATACTTT
34247986 ACTTTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.12, G:0.03, T:0.62
Consensus pattern (17 bp):
ATACTTGTTATACTTTT
Found at i:34256679 original size:212 final size:212
Alignment explanation
Indices: 34256312--34256740 Score: 858
Period size: 212 Copynumber: 2.0 Consensus size: 212
34256302 TGTTTTATCC
34256312 CTTTTTTGTTGTTTTAGGTCTAAAATTGATAATTGCAATTTAGAAACCAAGCAATTCTACAAGCA
1 CTTTTTTGTTGTTTTAGGTCTAAAATTGATAATTGCAATTTAGAAACCAAGCAATTCTACAAGCA
34256377 GTGCCAACTACTTCAGGCACTCGATATGTTTACTAAGTTCGATTTCCTTACGTCTGTAGGGTTTT
66 GTGCCAACTACTTCAGGCACTCGATATGTTTACTAAGTTCGATTTCCTTACGTCTGTAGGGTTTT
34256442 TCTTAGAGAGATAATCTACTATCTTAGCAAATCGTACAACAAGTGATTACAAGCACTAACACTTA
131 TCTTAGAGAGATAATCTACTATCTTAGCAAATCGTACAACAAGTGATTACAAGCACTAACACTTA
34256507 CGAAATTAGCAACCTCA
196 CGAAATTAGCAACCTCA
34256524 CTTTTTTGTTGTTTTAGGTCTAAAATTGATAATTGCAATTTAGAAACCAAGCAATTCTACAAGCA
1 CTTTTTTGTTGTTTTAGGTCTAAAATTGATAATTGCAATTTAGAAACCAAGCAATTCTACAAGCA
34256589 GTGCCAACTACTTCAGGCACTCGATATGTTTACTAAGTTCGATTTCCTTACGTCTGTAGGGTTTT
66 GTGCCAACTACTTCAGGCACTCGATATGTTTACTAAGTTCGATTTCCTTACGTCTGTAGGGTTTT
34256654 TCTTAGAGAGATAATCTACTATCTTAGCAAATCGTACAACAAGTGATTACAAGCACTAACACTTA
131 TCTTAGAGAGATAATCTACTATCTTAGCAAATCGTACAACAAGTGATTACAAGCACTAACACTTA
34256719 CGAAATTAGCAACCTCA
196 CGAAATTAGCAACCTCA
34256736 CTTTT
1 CTTTT
34256741 GCACCTACGA
Statistics
Matches: 217, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
212 217 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (212 bp):
CTTTTTTGTTGTTTTAGGTCTAAAATTGATAATTGCAATTTAGAAACCAAGCAATTCTACAAGCA
GTGCCAACTACTTCAGGCACTCGATATGTTTACTAAGTTCGATTTCCTTACGTCTGTAGGGTTTT
TCTTAGAGAGATAATCTACTATCTTAGCAAATCGTACAACAAGTGATTACAAGCACTAACACTTA
CGAAATTAGCAACCTCA
Found at i:34258482 original size:25 final size:25
Alignment explanation
Indices: 34258448--34258532 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 25
34258438 CCATACAATA
*
34258448 CGCCACAAAGATGTTTTAGATAATT
1 CGCCATAAAGATGTTTTAGATAATT
**
34258473 CGCCATAAAGACT-TTACAGATAACTT
1 CGCCATAAAGA-TGTTTTAGATAA-TT
34258499 -GCCATAAA-A-GCTTTTCAGATAATT
1 CGCCATAAAGATG-TTTT-AGATAATT
*
34258523 CACCATAAAG
1 CGCCATAAAG
34258533 GCTTTACAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
24 5 0.11
25 39 0.83
26 3 0.06
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (25 bp):
CGCCATAAAGATGTTTTAGATAATT
Found at i:34258536 original size:25 final size:25
Alignment explanation
Indices: 34258465--34258711 Score: 219
Period size: 25 Copynumber: 9.9 Consensus size: 25
34258455 AAGATGTTTT
* * *
34258465 AGATAATTCGCCATAAAGACTTTAC
1 AGATAATTCACCACAAAGGCTTTAC
* * * *
34258490 AGATAACTT-GCCATAAAAGCTTTTC
1 AGATAA-TTCACCACAAAGGCTTTAC
*
34258515 AGATAATTCACCATAAAGGCTTTAC
1 AGATAATTCACCACAAAGGCTTTAC
* **
34258540 AAATAATTTGCCACAAAGGCTTTAC
1 AGATAATTCACCACAAAGGCTTTAC
* *
34258565 AGATAACTCGCCACAAAGGCTTTAC
1 AGATAATTCACCACAAAGGCTTTAC
* * * *
34258590 AAATAATTCACCATAGAGACTTCT-C
1 AGATAATTCACCACAAAGGCTT-TAC
* * *
34258615 AAATAATTCGCCATAAAGGCTTTAC
1 AGATAATTCACCACAAAGGCTTTAC
* **
34258640 AGATAACTCACCACAAAGGCTTTTT
1 AGATAATTCACCACAAAGGCTTTAC
* * *
34258665 AGATAGTTCACCACAAAAGCTTTCC
1 AGATAATTCACCACAAAGGCTTTAC
*
34258690 AGATAACTCACCACAAAGGCTT
1 AGATAATTCACCACAAAGGCTT
34258712 GGTTTGGTTT
Statistics
Matches: 182, Mismatches: 36, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
24 3 0.02
25 176 0.97
26 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.26
Consensus pattern (25 bp):
AGATAATTCACCACAAAGGCTTTAC
Found at i:34258675 original size:75 final size:75
Alignment explanation
Indices: 34258467--34258677 Score: 289
Period size: 75 Copynumber: 2.8 Consensus size: 75
34258457 GATGTTTTAG
* * * *
34258467 ATAATTCGCCATAAAGACTTTACAGATAACTTGCCATAAAAGCTTTTCAGATAATTCACCATAAA
1 ATAATTCGCCATAAAGGCTTTACAGATAACTCGCCACAAAGGCTTTTCAGATAATTCACCATAAA
*
34258532 GGCTTTACAA
66 GACTTTACAA
* * * * *
34258542 ATAATTTGCCACAAAGGCTTTACAGATAACTCGCCACAAAGGCTTTACAAATAATTCACCATAGA
1 ATAATTCGCCATAAAGGCTTTACAGATAACTCGCCACAAAGGCTTTTCAGATAATTCACCATAAA
34258607 GACTTCT-CAA
66 GACTT-TACAA
* * *
34258617 ATAATTCGCCATAAAGGCTTTACAGATAACTCACCACAAAGGCTTTTTAGATAGTTCACCA
1 ATAATTCGCCATAAAGGCTTTACAGATAACTCGCCACAAAGGCTTTTCAGATAATTCACCA
34258678 CAAAAGCTTT
Statistics
Matches: 118, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
75 117 0.99
76 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.27
Consensus pattern (75 bp):
ATAATTCGCCATAAAGGCTTTACAGATAACTCGCCACAAAGGCTTTTCAGATAATTCACCATAAA
GACTTTACAA
Found at i:34258708 original size:75 final size:74
Alignment explanation
Indices: 34258467--34258711 Score: 276
Period size: 75 Copynumber: 3.3 Consensus size: 74
34258457 GATGTTTTAG
* * * * *
34258467 ATAATTCGCCATAAAGACTTTACAGATAACTTGCCATAAAAGCTTTTCAGATAATTCACCATAAA
1 ATAATTCGCCACAAAGGCTTTACAGATAACTCGCCACAAAGGCTTTTCAGATAATTCACCA-AAA
* *
34258532 GGCTTTACAA
65 AGCTTTCCAA
* * * * *
34258542 ATAATTTGCCACAAAGGCTTTACAGATAACTCGCCACAAAGGCTTTACAAATAATTCACCATAGA
1 ATAATTCGCCACAAAGGCTTTACAGATAACTCGCCACAAAGGCTTTTCAGATAATTCACCAAAAA
34258607 GAC-TTCTCAA
66 G-CTTTC-CAA
* * * *
34258617 ATAATTCGCCATAAAGGCTTTACAGATAACTCACCACAAAGGCTTTTTAGATAGTTCACCACAAA
1 ATAATTCGCCACAAAGGCTTTACAGATAACTCGCCACAAAGGCTTTTCAGATAATTCACCA-AAA
*
34258682 AGCTTTCCAG
65 AGCTTTCCAA
* *
34258692 ATAACTCACCACAAAGGCTT
1 ATAATTCGCCACAAAGGCTT
34258712 GGTTTGGTTT
Statistics
Matches: 141, Mismatches: 25, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
74 4 0.03
75 131 0.93
76 6 0.04
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (74 bp):
ATAATTCGCCACAAAGGCTTTACAGATAACTCGCCACAAAGGCTTTTCAGATAATTCACCAAAAA
GCTTTCCAA
Found at i:34270764 original size:20 final size:20
Alignment explanation
Indices: 34270741--34270795 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
34270731 ACTTCAATTC
34270741 AGCTCAATTTTAGCTCAATG
1 AGCTCAATTTTAGCTCAATG
*
34270761 AGCTC-GTTCTTAGCTCAATG
1 AGCTCAATT-TTAGCTCAATG
*
34270781 AGCTCATTTTTAGCT
1 AGCTCAATTTTAGCT
34270796 TACTTTAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTTAGCTCAATG
Found at i:34275401 original size:20 final size:20
Alignment explanation
Indices: 34275374--34275420 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
34275364 ATATTTTCAC
34275374 TTTCTTTTT-TC-ATTTTTCT
1 TTTCTTTTTCTCGA-TTTTCT
34275393 TTTCTTTTTCTCGATTTTCT
1 TTTCTTTTTCTCGATTTTCT
34275413 TTTCTTTT
1 TTTCTTTT
34275421 GAACTCTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.35
20 16 0.62
21 1 0.04
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTCTTTTTCTCGATTTTCT
Found at i:34281954 original size:20 final size:19
Alignment explanation
Indices: 34281889--34281956 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 19
34281879 ATTGCAACTA
34281889 AAATGAGCTAAAATGAGCT
1 AAATGAGCTAAAATGAGCT
* * *
34281908 GAGTGAGCTGGAAATGAGCT
1 AAATGAGCT-AAAATGAGCT
***
34281928 CGTTGAGCTAAAATTGAGCT
1 AAATGAGCTAAAA-TGAGCT
34281948 AAATGAGCT
1 AAATGAGCT
34281957 TGAAGGTAGT
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
19 10 0.27
20 27 0.73
ACGTcount: A:0.37, C:0.12, G:0.28, T:0.24
Consensus pattern (19 bp):
AAATGAGCTAAAATGAGCT
Found at i:34284825 original size:20 final size:19
Alignment explanation
Indices: 34284800--34284839 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
34284790 TGCAAGCTGA
* *
34284800 CTTTAGTTCGATTTTAGCTC
1 CTTTAGCTCG-TTTCAGCTC
34284820 CTTTAGCTCGTTTCAGCTC
1 CTTTAGCTCGTTTCAGCTC
34284839 C
1 C
34284840 AACCAGCTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.12, C:0.28, G:0.15, T:0.45
Consensus pattern (19 bp):
CTTTAGCTCGTTTCAGCTC
Found at i:34284866 original size:20 final size:20
Alignment explanation
Indices: 34284843--34284882 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
34284833 CAGCTCCAAC
* *
34284843 CAGCTCATTTGAGCTTAATT
1 CAGCTCATTCGAGCTCAATT
34284863 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAATT
34284883 TAGTTTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAATT
Found at i:34287191 original size:30 final size:30
Alignment explanation
Indices: 34287151--34287240 Score: 94
Period size: 30 Copynumber: 2.9 Consensus size: 30
34287141 ACATTGTAAT
34287151 AAAAACGAAAAAGAAGAAAAAGAAAAAAGTG
1 AAAAA-GAAAAAGAAGAAAAAGAAAAAAGTG
*
34287182 AAAAAGAAAAAGAA-AAAGAA-AAAGAAATTG
1 AAAAAGAAAAAGAAGAAA-AAGAAA-AAAGTG
*
34287212 CAAAAGAAAAAGAAATCGAAAAAGAAAAA
1 AAAAAGAAAAAG-AA--GAAAAAGAAAAA
34287241 GAAATCGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
29 6 0.12
30 27 0.54
31 7 0.14
33 4 0.08
34 6 0.12
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.04
Consensus pattern (30 bp):
AAAAAGAAAAAGAAGAAAAAGAAAAAAGTG
Found at i:34287239 original size:5 final size:6
Alignment explanation
Indices: 34287164--34287294 Score: 93
Period size: 6 Copynumber: 21.0 Consensus size: 6
34287154 AACGAAAAAG
** *
34287164 AAGAAA AAGAAAA AAGTGAAA AAGAAA AAGAAA AAGAAA AAGAAA TTGCAA
1 AAGAAA AAG-AAA AA--GAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
** ** ** *
34287215 AAGAAA AAGAAA TCGAAA AAGAAA AAGAAA TCGAAA AAGTGA GA-AAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
* *
34287262 AAGAAA ACGAAGAA AAGAAA ATTGAAA AAGAAA
1 AAGAAA AAG-A-AA AAGAAA A-AGAAA AAGAAA
34287295 TTGAGATTGA
Statistics
Matches: 94, Mismatches: 24, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
5 2 0.02
6 70 0.74
7 12 0.13
8 9 0.10
9 1 0.01
ACGTcount: A:0.73, C:0.03, G:0.18, T:0.06
Consensus pattern (6 bp):
AAGAAA
Found at i:34287914 original size:34 final size:33
Alignment explanation
Indices: 34287867--34287976 Score: 184
Period size: 34 Copynumber: 3.2 Consensus size: 33
34287857 GAGTTAGTTT
*
34287867 ATTAACTTTAGTTCAGCTCAAATAAGTGTTAGTA
1 ATTAA-TTTAGTTCAACTCAAATAAGTGTTAGTA
34287901 ATTAATTTCAGTTCAACTCAAATAAGTGTTAGTA
1 ATTAATTT-AGTTCAACTCAAATAAGTGTTAGTA
34287935 ATTAATTTTAGTTCAACTCAAATAAGTGTTAGTA
1 ATTAA-TTTAGTTCAACTCAAATAAGTGTTAGTA
34287969 ATTAATTT
1 ATTAATTT
34287977 GTTTAAATCA
Statistics
Matches: 73, Mismatches: 1, Indels: 5
0.92 0.01 0.06
Matches are distributed among these distances:
33 6 0.08
34 64 0.88
35 3 0.04
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (33 bp):
ATTAATTTAGTTCAACTCAAATAAGTGTTAGTA
Found at i:34297964 original size:30 final size:30
Alignment explanation
Indices: 34297930--34298002 Score: 146
Period size: 30 Copynumber: 2.4 Consensus size: 30
34297920 AGATTCGGTT
34297930 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
1 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
34297960 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
1 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
34297990 TCTTGATTTTCTT
1 TCTTGATTTTCTT
34298003 TTTCCTTCGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (30 bp):
TCTTGATTTTCTTGAAAACAAGAAAGTGAA
Found at i:34299766 original size:18 final size:18
Alignment explanation
Indices: 34299743--34299794 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
34299733 TGAAGAGGAA
34299743 GAAAAGAAATA-AAAAGTG
1 GAAAAGAAATAGAAAA-TG
34299761 GAAAAGAAATAGAAAATG
1 GAAAAGAAATAGAAAATG
* *
34299779 AAAAAGAAAAAGAAAA
1 GAAAAGAAATAGAAAA
34299795 AGAAATTGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 27 0.87
19 4 0.13
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (18 bp):
GAAAAGAAATAGAAAATG
Found at i:34299774 original size:24 final size:24
Alignment explanation
Indices: 34299741--34299823 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
34299731 AATGAAGAGG
*
34299741 AAGAAA-AGAAATAAAAAGTGGAA
1 AAGAAATAGAAATAAAAAGTGAAA
34299764 AAGAAATAGAAAATGAAAAA--GAAA
1 AAGAAATAG-AAAT-AAAAAGTGAAA
* ***
34299788 AAGAAAAAGAAATTGCAAGTGAAA
1 AAGAAATAGAAATAAAAAGTGAAA
*
34299812 AAGAAATCGAAA
1 AAGAAATAGAAA
34299824 AAGTGAGAGA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
22 2 0.04
23 10 0.21
24 27 0.56
25 4 0.08
26 5 0.10
ACGTcount: A:0.69, C:0.02, G:0.19, T:0.10
Consensus pattern (24 bp):
AAGAAATAGAAATAAAAAGTGAAA
Found at i:34299798 original size:30 final size:30
Alignment explanation
Indices: 34299762--34299826 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
34299752 TAAAAAGTGG
34299762 AAAAGAAATAGAAAATGAAAAAGAAAAAGA
1 AAAAGAAATAGAAAATGAAAAAGAAAAAGA
* * * **
34299792 AAAAGAAATTGCAAGTGAAAAAGAAATCGA
1 AAAAGAAATAGAAAATGAAAAAGAAAAAGA
34299822 AAAAG
1 AAAAG
34299827 TGAGAGAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.69, C:0.03, G:0.18, T:0.09
Consensus pattern (30 bp):
AAAAGAAATAGAAAATGAAAAAGAAAAAGA
Found at i:34299799 original size:48 final size:48
Alignment explanation
Indices: 34299744--34299842 Score: 117
Period size: 48 Copynumber: 2.1 Consensus size: 48
34299734 GAAGAGGAAG
* *
34299744 AAAAGAAATAAAAAGTGGAAAAGAAATAGAAAATGAAAAAGAAAAAGA
1 AAAAGAAATAAAAAGTGAAAAAGAAATAGAAAAAGAAAAAGAAAAAGA
*** * ** *
34299792 AAAAGAAATTGCAAGTGAAAAAGAAATCGAAAAAGTGAGAGAAAAAGA
1 AAAAGAAATAAAAAGTGAAAAAGAAATAGAAAAAGAAAAAGAAAAAGA
34299840 AAA
1 AAA
34299843 CAAAGAAAAG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.09
Consensus pattern (48 bp):
AAAAGAAATAAAAAGTGAAAAAGAAATAGAAAAAGAAAAAGAAAAAGA
Found at i:34299817 original size:6 final size:6
Alignment explanation
Indices: 34299762--34299799 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
34299752 TAAAAAGTGG
* *
34299762 AAAAGA AATAGA AAATGA AAAAGA AAAAGA AAAAGA AA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AA
34299800 TTGCAAGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (6 bp):
AAAAGA
Found at i:34301728 original size:34 final size:34
Alignment explanation
Indices: 34301684--34301759 Score: 134
Period size: 34 Copynumber: 2.2 Consensus size: 34
34301674 GAGTTAGTTT
* *
34301684 ATTAAGTTTAGTTTAGCTCAAATAAGTGTTAGTA
1 ATTAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
34301718 ATTAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
1 ATTAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
34301752 ATTAATTT
1 ATTAATTT
34301760 GTTTAAATCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (34 bp):
ATTAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
Found at i:34305542 original size:24 final size:24
Alignment explanation
Indices: 34305518--34305564 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
34305508 AAACTATTTC
34305518 TAAAAAAAACTCAAGAGAGAATTCT
1 TAAAAAAAACTCAA-AGAGAATTCT
* *
34305543 TGAAGAAAACTCAAAGAGAATT
1 TAAAAAAAACTCAAAGAGAATT
34305565 TTTCACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.55, C:0.11, G:0.15, T:0.19
Consensus pattern (24 bp):
TAAAAAAAACTCAAAGAGAATTCT
Found at i:34310775 original size:24 final size:24
Alignment explanation
Indices: 34310751--34310797 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
34310741 AAACTACTTC
34310751 TAAAAAAAACTCAAGAGAGAATTCT
1 TAAAAAAAACTCAA-AGAGAATTCT
** *
34310776 TGGAGAAAACTCAAAGAGAATT
1 TAAAAAAAACTCAAAGAGAATT
34310798 TTTCACTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (24 bp):
TAAAAAAAACTCAAAGAGAATTCT
Found at i:34316027 original size:10 final size:10
Alignment explanation
Indices: 34316012--34316053 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
34316002 TTAATTGCAA
34316012 CTAAAATGAG
1 CTAAAATGAG
34316022 CTAAAATGAG
1 CTAAAATGAG
* *
34316032 CT-CAGTGAG
1 CTAAAATGAG
34316041 CTAGAAATGAG
1 CTA-AAATGAG
34316052 CT
1 CT
34316054 CGTTGAGCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 7 0.27
10 12 0.46
11 7 0.27
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.21
Consensus pattern (10 bp):
CTAAAATGAG
Found at i:34316050 original size:20 final size:19
Alignment explanation
Indices: 34316018--34316073 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 19
34316008 GCAACTAAAA
34316018 TGAGCTAAAATGAGCTCAG-
1 TGAGCTAAAATGAGCTC-GT
34316037 TGAGCTAGAAATGAGCTCGT
1 TGAGCTA-AAATGAGCTCGT
34316057 TGAGCTAAAATTGAGCT
1 TGAGCTAAAA-TGAGCT
34316074 GAATGAGCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 11 0.32
20 23 0.68
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (19 bp):
TGAGCTAAAATGAGCTCGT
Found at i:34316080 original size:20 final size:19
Alignment explanation
Indices: 34316016--34316082 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 19
34316006 TTGCAACTAA
*
34316016 AATGAGCTAAAATGAGCTC
1 AATGAGCTAAAATGAGCTG
*
34316035 AGTGAGCTAGAAATGAGCTCG
1 AATGAGCTA-AAATGAGCT-G
*
34316056 -TTGAGCTAAAATTGAGCTG
1 AATGAGCTAAAA-TGAGCTG
34316075 AATGAGCT
1 AATGAGCT
34316083 TGAAGGCAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 12 0.30
20 28 0.70
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (19 bp):
AATGAGCTAAAATGAGCTG
Found at i:34329900 original size:13 final size:12
Alignment explanation
Indices: 34329882--34329938 Score: 57
Period size: 11 Copynumber: 4.8 Consensus size: 12
34329872 CTTTTCTTCT
34329882 TTTTTTTCATGAA
1 TTTTTTTC-TGAA
*
34329895 TTTTTTT-TCACGA
1 TTTTTTTCTGA--A
34329908 TTTTTTT-TGAA
1 TTTTTTTCTGAA
34329919 TTTTTTT-TGAA
1 TTTTTTTCTGAA
34329930 TTTTTTTCT
1 TTTTTTTCT
34329939 CAAATACTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
11 21 0.54
12 1 0.03
13 17 0.44
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTTTTTCTGAA
Found at i:34329900 original size:14 final size:14
Alignment explanation
Indices: 34329881--34329926 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 14
34329871 ACTTTTCTTC
34329881 TTTTTTTTCATGAA
1 TTTTTTTTCATGAA
*
34329895 TTTTTTTTCACG-A
1 TTTTTTTTCATGAA
34329908 -TTTTTTT--TGAA
1 TTTTTTTTCATGAA
34329919 TTTTTTTT
1 TTTTTTTT
34329927 GAATTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 1 0.04
11 1 0.04
12 14 0.50
13 1 0.04
14 11 0.39
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.72
Consensus pattern (14 bp):
TTTTTTTTCATGAA
Found at i:34329922 original size:10 final size:11
Alignment explanation
Indices: 34329891--34329936 Score: 65
Period size: 11 Copynumber: 4.0 Consensus size: 11
34329881 TTTTTTTTCA
34329891 TGAATTTTTTT
1 TGAATTTTTTT
*
34329902 TCACGATTTTTTT
1 TGA--ATTTTTTT
34329915 TGAATTTTTTT
1 TGAATTTTTTT
34329926 TGAATTTTTTT
1 TGAATTTTTTT
34329937 CTCAAATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 21 0.68
13 10 0.32
ACGTcount: A:0.17, C:0.04, G:0.09, T:0.70
Consensus pattern (11 bp):
TGAATTTTTTT
Found at i:34331245 original size:47 final size:45
Alignment explanation
Indices: 34331153--34331245 Score: 109
Period size: 47 Copynumber: 2.0 Consensus size: 45
34331143 AATATGTTTA
* *
34331153 AATGCATAATTTAATTAAGATGTAAACTAAATGAACAGATGAGTT
1 AATGCATAACTTAATTAAGATGTAAACTAAATGAACAGATAAGTT
*
34331198 AATGCATGACTTAATTTAATGATGTAAACTTAAAT-AACATGA-AAGTT
1 AATGCATAACTTAA-TTAA-GATGTAAAC-TAAATGAACA-GATAAGTT
34331245 A
1 A
34331246 CATAATGCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
45 12 0.29
46 4 0.10
47 18 0.44
48 7 0.17
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (45 bp):
AATGCATAACTTAATTAAGATGTAAACTAAATGAACAGATAAGTT
Found at i:34333890 original size:16 final size:16
Alignment explanation
Indices: 34333869--34333900 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
34333859 GTTTTGTTGC
*
34333869 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
34333885 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
34333901 CTTTCGATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:34334186 original size:51 final size:51
Alignment explanation
Indices: 34334128--34334318 Score: 228
Period size: 51 Copynumber: 3.8 Consensus size: 51
34334118 CCGGTCCACA
* *
34334128 TAGTAGCCTGCACATAGTACTACACATGTGGCCATCACTATCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCTGGTACACG
* * * *
34334179 TAGTAGCCTGCACATAGTACTACACATGTGA--TTGAAGCTATCTGGTACGCC
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAT-CA-CTATCTGGTACACG
* * **
34334230 TAATAGCCTACACATAGTACTACACATGCAACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACC-ATCACTATCTGGTACACG
*
34334280 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACT
34334319 TTCACTTTCA
Statistics
Matches: 115, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
49 5 0.04
50 39 0.34
51 69 0.60
53 1 0.01
54 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCTGGTACACG
Found at i:34334344 original size:101 final size:102
Alignment explanation
Indices: 34334124--34334310 Score: 243
Period size: 101 Copynumber: 1.8 Consensus size: 102
34334114 GATACCGGTC
* ***
34334124 CACATAGTAGCCTGCACATAGTACTACACATGTGGCCATCACTATCTGATACACGTAGTAGCCTG
1 CACATAGTAGCCTACACATAGTACTACACATGCAACCATCACTATCTGATACACGTAGTAGCCTG
* * **
34334189 CACATAGTACTACACATGTGATTGAAGCTATCTGGTA
66 CACATAGTACTACACACGTGAATGAAGCTATCACGTA
* * * *
34334226 CGCCTAATAGCCTACACATAGTACTACACATGCAACCTATCA-T-TCTGGTACACGTAGTAGCCT
1 CACATAGTAGCCTACACATAGTACTACACATGCAACC-ATCACTATCTGATACACGTAGTAGCCT
34334289 GCACATAGTACTACACACGTGA
65 GCACATAGTACTACACACGTGA
34334311 CCATCACTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
101 40 0.53
102 31 0.41
103 4 0.05
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (102 bp):
CACATAGTAGCCTACACATAGTACTACACATGCAACCATCACTATCTGATACACGTAGTAGCCTG
CACATAGTACTACACACGTGAATGAAGCTATCACGTA
Found at i:34337177 original size:47 final size:47
Alignment explanation
Indices: 34337075--34337167 Score: 123
Period size: 47 Copynumber: 2.0 Consensus size: 47
34337065 TTTATATATT
* *
34337075 GATGCCATAGCCCAGCTATGGTCTTACACAGTAGCACATATCACACC
1 GATGCCATAGCCCAGATATGGTCTTACACAGAAGCACATATCACACC
* * * *
34337122 GATGCCATATCCCAGATATGGTCTTATACGGAAATCACATATCACA
1 GATGCCATAGCCCAGATATGGTCTTACACAG-AAGCACATATCACA
34337168 TGTTGCCATA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 27 0.69
48 12 0.31
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (47 bp):
GATGCCATAGCCCAGATATGGTCTTACACAGAAGCACATATCACACC
Found at i:34341422 original size:16 final size:16
Alignment explanation
Indices: 34341401--34341432 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
34341391 GTTTTGTTGC
*
34341401 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
34341417 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
34341433 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:34341719 original size:51 final size:51
Alignment explanation
Indices: 34341650--34341845 Score: 193
Period size: 51 Copynumber: 3.9 Consensus size: 51
34341640 ATTAATGATA
* * *
34341650 CCGGTCCACATAGTAGCCTAAACATAGTACTACACATGTGACCATCACTAT
1 CCGGTACACGTAGTAGCCTACACATAGTACTACACATGTGACCATCACTAT
* * * * *
34341701 CCGATACACGTAGTAGCCTGCACATAGTACTATATATGTGATCGA--AGCTAT
1 CCGGTACACGTAGTAGCCTACACATAGTACTACACATGTGA-CCATCA-CTAT
*** * *
34341752 CCGGTACGTATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-T
1 CCGGTACACGTAGTAGCCTACACATAGTACTACACATGTGACC-ATCACTAT
* * *
34341802 CTGGTACACGTAGTAGCCTACACATAGTACTTCACACGTGACCA
1 CCGGTACACGTAGTAGCCTACACATAGTACTACACATGTGACCA
34341846 CTTTCACTTT
Statistics
Matches: 116, Mismatches: 24, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
49 1 0.01
50 38 0.33
51 74 0.64
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (51 bp):
CCGGTACACGTAGTAGCCTACACATAGTACTACACATGTGACCATCACTAT
Found at i:34358036 original size:72 final size:72
Alignment explanation
Indices: 34357853--34358134 Score: 413
Period size: 72 Copynumber: 3.9 Consensus size: 72
34357843 TTAATTTAGT
* *
34357853 ATAAATAAGTAGAACATAAATTTAATA-CCAAAAAACCAAACATAAACAATTATTGATAAAACTA
1 ATAAATAAGTAGAACATAAATTCAATATCC-AAAAACCAAACATAAACAACTATTGATAAAACTA
** *
34357917 GCCCTAAGC
65 G-ATTAAAC
* * *
34357926 ATAAATAATTAGACCATAAATTCAATATCCAAAGACCAAACATAAACAACTATTGATAAAACTAG
1 ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAG
34357991 ATTAAAC
66 ATTAAAC
* * *
34357998 ATAAATAAGTAAAACATAAATTCAATATCCAAAAACCAAACATAAACAGCCATTGATAAAACTAG
1 ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAG
*
34358063 ATTAGAC
66 ATTAAAC
* *
34358070 ATAAATAAGTAGAACATAAATTCAATACCCAAAAACCAAACATAAATAACTATTGATAAAACTAG
1 ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAG
34358135 TTTAGCATTG
Statistics
Matches: 188, Mismatches: 20, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
72 129 0.69
73 57 0.30
74 2 0.01
ACGTcount: A:0.55, C:0.16, G:0.06, T:0.22
Consensus pattern (72 bp):
ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAG
ATTAAAC
Found at i:34360804 original size:22 final size:22
Alignment explanation
Indices: 34360777--34360857 Score: 117
Period size: 22 Copynumber: 3.7 Consensus size: 22
34360767 GAAAAATTTC
**
34360777 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAAA
* * *
34360799 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAAA
34360821 CATGAGAGCTTAGTACGTTAAA
1 CATGAGAGCTTAGTACGTTAAA
34360843 CATGAGAGCTTAGTA
1 CATGAGAGCTTAGTA
34360858 TGGAATTTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.30
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAAA
Found at i:34365232 original size:52 final size:52
Alignment explanation
Indices: 34365171--34365271 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
34365161 CATGCACATA
* *
34365171 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
*
34365223 TTTGAGCTTCAACCGAGCTAGAAATGAGATTTTAAGCTGCTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
34365272 CGTTTCCTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
Found at i:34376260 original size:20 final size:21
Alignment explanation
Indices: 34376237--34376285 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
34376227 GGGTTGAGGT
34376237 TGAGCTGGA-TTCAACTCGAA
1 TGAGCTGGACTTCAACTCGAA
* * *
34376257 TGAGCT-GACTTGAGCTCGAG
1 TGAGCTGGACTTCAACTCGAA
34376277 TGAGCTGGA
1 TGAGCTGGA
34376286 AATGAGCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.83
21 2 0.08
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.24
Consensus pattern (21 bp):
TGAGCTGGACTTCAACTCGAA
Found at i:34378169 original size:15 final size:15
Alignment explanation
Indices: 34378141--34378180 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
34378131 CAATTTCCTT
34378141 TTCACTTTTCTTTTC
1 TTCACTTTTCTTTTC
34378156 TTCA-TTTTCTTTTTC
1 TTCACTTTTC-TTTTC
34378171 TCTCACTTTT
1 T-TCACTTTT
34378181 TCGATTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.23
15 10 0.45
16 3 0.14
17 4 0.18
ACGTcount: A:0.07, C:0.25, G:0.00, T:0.68
Consensus pattern (15 bp):
TTCACTTTTCTTTTC
Found at i:34378197 original size:18 final size:18
Alignment explanation
Indices: 34378176--34378234 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
34378166 TTTTCTCTCA
34378176 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
34378194 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
34378212 CTTTTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
34378230 GTTTT
1 CTTTT
34378235 CTTTCAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.05, C:0.15, G:0.07, T:0.73
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:34378251 original size:6 final size:6
Alignment explanation
Indices: 34378146--34378238 Score: 62
Period size: 6 Copynumber: 15.3 Consensus size: 6
34378136 TCCTTTTCAC
* * ** * *
34378146 TTTTCTT TTCTTCA TTTTCT TTTTCT CTCACT TTTTCG ATTTCT TTTTCT
1 TTTTC-T TT-TTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
* * * * *
34378196 TTTGCA ATTTCT TTTTCT TTTTCG TTTTCT TTTT-G TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT
34378239 CAATTTCTTT
Statistics
Matches: 62, Mismatches: 22, Indels: 5
0.70 0.25 0.06
Matches are distributed among these distances:
5 4 0.06
6 51 0.82
7 4 0.06
8 3 0.05
ACGTcount: A:0.05, C:0.18, G:0.04, T:0.72
Consensus pattern (6 bp):
TTTTCT
Found at i:34380929 original size:20 final size:21
Alignment explanation
Indices: 34380906--34380954 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
34380896 GGGTTGAGGT
34380906 TGAGCTGGA-TTCAACTCGAA
1 TGAGCTGGACTTCAACTCGAA
* * *
34380926 TGAGCT-GACTTGAGCTCGAG
1 TGAGCTGGACTTCAACTCGAA
34380946 TGAGCTGGA
1 TGAGCTGGA
34380955 AATGAGCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.83
21 2 0.08
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.24
Consensus pattern (21 bp):
TGAGCTGGACTTCAACTCGAA
Found at i:34382822 original size:15 final size:15
Alignment explanation
Indices: 34382794--34382833 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
34382784 CAATTTCCTT
34382794 TTCACTTTTCTTTTC
1 TTCACTTTTCTTTTC
34382809 TTCA-TTTTCTTTTTC
1 TTCACTTTTC-TTTTC
34382824 TCTCACTTTT
1 T-TCACTTTT
34382834 TCGATTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.23
15 10 0.45
16 3 0.14
17 4 0.18
ACGTcount: A:0.07, C:0.25, G:0.00, T:0.68
Consensus pattern (15 bp):
TTCACTTTTCTTTTC
Found at i:34382850 original size:18 final size:18
Alignment explanation
Indices: 34382829--34382921 Score: 84
Period size: 18 Copynumber: 5.3 Consensus size: 18
34382819 TTTTCTCTCA
*
34382829 CTTTTTCGATTTCTTTTT
1 CTTTTTCAATTTCTTTTT
*
34382847 CTTTTGCAATTTCTTTTT
1 CTTTTTCAATTTCTTTTT
**
34382865 CTTTTTCGTTTTCTTTTT
1 CTTTTTCAATTTCTTTTT
* **
34382883 -GTTTTC--TTTCAATTT
1 CTTTTTCAATTTCTTTTT
*
34382898 CTTTTTCAATCTCTTTCTT
1 CTTTTTCAATTTCTTT-TT
34382917 CTTTT
1 CTTTT
34382922 CTCGCTCAAT
Statistics
Matches: 59, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
15 7 0.12
16 5 0.08
17 5 0.08
18 35 0.59
19 7 0.12
ACGTcount: A:0.08, C:0.18, G:0.04, T:0.70
Consensus pattern (18 bp):
CTTTTTCAATTTCTTTTT
Found at i:34382904 original size:6 final size:6
Alignment explanation
Indices: 34382799--34382891 Score: 62
Period size: 6 Copynumber: 15.3 Consensus size: 6
34382789 TCCTTTTCAC
* * ** * *
34382799 TTTTCTT TTCTTCA TTTTCT TTTTCT CTCACT TTTTCG ATTTCT TTTTCT
1 TTTTC-T TT-TTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
* * * * *
34382849 TTTGCA ATTTCT TTTTCT TTTTCG TTTTCT TTTT-G TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT
34382892 CAATTTCTTT
Statistics
Matches: 62, Mismatches: 22, Indels: 5
0.70 0.25 0.06
Matches are distributed among these distances:
5 4 0.06
6 51 0.82
7 4 0.06
8 3 0.05
ACGTcount: A:0.05, C:0.18, G:0.04, T:0.72
Consensus pattern (6 bp):
TTTTCT
Found at i:34385524 original size:20 final size:21
Alignment explanation
Indices: 34385501--34385549 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
34385491 GGGTTGAGGT
34385501 TGAGCTGGA-TTCAACTCGAA
1 TGAGCTGGACTTCAACTCGAA
* * *
34385521 TGAGCT-GACTTGAGCTCGAG
1 TGAGCTGGACTTCAACTCGAA
34385541 TGAGCTGGA
1 TGAGCTGGA
34385550 AACGAGCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.83
21 2 0.08
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.24
Consensus pattern (21 bp):
TGAGCTGGACTTCAACTCGAA
Found at i:34388123 original size:52 final size:52
Alignment explanation
Indices: 34388062--34388162 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
34388052 CATGCACATA
* *
34388062 TTTGAGCTTCAACCGAGCTAAAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAAAAATGAGATCTTAAGCTGCTGTCCATTATTG
* *
34388114 TTTGAGCTTCAACCGAGCTAGAAATGAGATTTTAAGCTGCTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAAAAATGAGATCTTAAGCTGCTGTCCATTA
34388163 CGTTTCCTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAAAAATGAGATCTTAAGCTGCTGTCCATTATTG
Found at i:34392663 original size:21 final size:21
Alignment explanation
Indices: 34392623--34392665 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
34392613 TTTTACCTTA
*
34392623 AATATGAATTGGACTGAATTG
1 AATATGAATTGGACTAAATTG
* *
34392644 AATATGAATTGTATTAAATTG
1 AATATGAATTGGACTAAATTG
34392665 A
1 A
34392666 GTTAAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.37
Consensus pattern (21 bp):
AATATGAATTGGACTAAATTG
Found at i:34395574 original size:34 final size:35
Alignment explanation
Indices: 34395531--34395597 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
34395521 GTATTAAAAA
*
34395531 TTCTATAAAATTTTTGT-AAAATCAAACAATCAAT
1 TTCTATAAAATTTCTGTAAAAATCAAACAATCAAT
34395565 TTCTATAAAATTTCTGTAAAAATCAAACAATCA
1 TTCTATAAAATTTCTGTAAAAATCAAACAATCA
34395598 GAAAACAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 16 0.52
35 15 0.48
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.36
Consensus pattern (35 bp):
TTCTATAAAATTTCTGTAAAAATCAAACAATCAAT
Found at i:34396560 original size:17 final size:17
Alignment explanation
Indices: 34396538--34396571 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
34396528 CACTAACATG
34396538 AAAATGTAATGAAAATA
1 AAAATGTAATGAAAATA
*
34396555 AAAATGTAATGACAATA
1 AAAATGTAATGAAAATA
34396572 TATACTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.24
Consensus pattern (17 bp):
AAAATGTAATGAAAATA
Found at i:34397136 original size:3 final size:3
Alignment explanation
Indices: 34396975--34397113 Score: 170
Period size: 3 Copynumber: 46.3 Consensus size: 3
34396965 CTCAACAAAG
* * *
34396975 TCT TCT TCT TCT TTT TTT TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * * *
34397023 TTT TCT TCT TTT TTT TCT TCT TCT TTT TCT TTT TCT TCT TCT TTT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * *
34397071 TCT TCT TCT TCT TCT TCT TCT TTT TCT TAT TTT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
34397114 TCTCATTTTC
Statistics
Matches: 117, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 117 1.00
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (3 bp):
TCT
Found at i:34399614 original size:22 final size:22
Alignment explanation
Indices: 34399589--34399648 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 22
34399579 TTTGAACCAT
34399589 TACCAATTCGTACCAAATTCC-A
1 TACCAATTCGTACC-AATTCCAA
* *
34399611 TACCATTTTGTACCAATTCCTAAA
1 TACCAATTCGTACCAATTCC--AA
34399635 TACCAATTCGTACC
1 TACCAATTCGTACC
34399649 TAAACCAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 6 0.19
22 12 0.39
24 13 0.42
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (22 bp):
TACCAATTCGTACCAATTCCAA
Found at i:34406959 original size:17 final size:17
Alignment explanation
Indices: 34406937--34406981 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
34406927 AGACAGTATA
*
34406937 CAATTTTTTCTTTTTTT
1 CAATTTTTTATTTTTTT
34406954 CAATTTTTTTTATTTTTTT
1 CAA--TTTTTTATTTTTTT
*
34406973 CGATTTTTT
1 CAATTTTTT
34406982 TTCGATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 9 0.38
19 15 0.62
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.76
Consensus pattern (17 bp):
CAATTTTTTATTTTTTT
Found at i:34406960 original size:10 final size:10
Alignment explanation
Indices: 34406947--34407005 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
34406937 CAATTTTTTC
34406947 TTTTTTTCAA
1 TTTTTTTCAA
*
34406957 TTTTTTT-TA
1 TTTTTTTCAA
*
34406966 TTTTTTTCGAT
1 TTTTTTTC-AA
*
34406977 TTTTTTTCGATT
1 TTTTTTTC-A-A
34406989 TTTTTTTCAA
1 TTTTTTTCAA
34406999 TTTTTTT
1 TTTTTTT
34407006 TTCACGAGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
9 8 0.19
10 14 0.33
11 11 0.26
12 9 0.21
ACGTcount: A:0.12, C:0.07, G:0.03, T:0.78
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:34407009 original size:12 final size:11
Alignment explanation
Indices: 34406947--34407006 Score: 72
Period size: 11 Copynumber: 5.6 Consensus size: 11
34406937 CAATTTTTTC
34406947 TTTTTTTCAAT
1 TTTTTTTCAAT
34406958 TTTTTTT--A-
1 TTTTTTTCAAT
*
34406966 TTTTTTTCGAT
1 TTTTTTTCAAT
*
34406977 TTTTTTTCGATT
1 TTTTTTTC-AAT
34406989 TTTTTTTCAAT
1 TTTTTTTCAAT
34407000 TTTTTTT
1 TTTTTTT
34407007 TCACGAGTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
8 7 0.17
9 1 0.02
10 1 0.02
11 24 0.57
12 9 0.21
ACGTcount: A:0.12, C:0.07, G:0.03, T:0.78
Consensus pattern (11 bp):
TTTTTTTCAAT
Found at i:34408245 original size:29 final size:29
Alignment explanation
Indices: 34408211--34408283 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
34408201 ATGTATTAGT
* *
34408211 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
34408240 TTAGGACATATTTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
34408269 TTAGGACATATTTAA
1 TTAGGACATATTTAA
34408284 TAATATCTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:34422722 original size:3 final size:3
Alignment explanation
Indices: 34422714--34422746 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
34422704 TGATTCACCG
34422714 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
34422747 CTTTCTCCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:34424347 original size:72 final size:73
Alignment explanation
Indices: 34424135--34424379 Score: 291
Period size: 72 Copynumber: 3.4 Consensus size: 73
34424125 AAAATCATAT
* * * * * * *
34424135 ATAAATAACTATTAATAAAATTA-ATT-TAGTATAAATAAGTAGAACATAAATTTAATACCAAAA
1 ATAAACAACTATTGATAAAACTAGATTAGAGCATAAATAAGTAGAACATAAATTCAATACCCAAA
34424198 AACCAAAC
66 AACCAAAC
* * ** * * *
34424206 ATAAACAATTATTGATAAAATTAGCCCTA-AGCATAAATAATTAGACCATAAATTCAATATCCAA
1 ATAAACAACTATTGATAAAACTAG-ATTAGAGCATAAATAAGTAGAACATAAATTCAATACCCAA
34424270 AAACCAAAC
65 AAACCAAAC
* *
34424279 ATAAACAACCATTGATAAAACTAGATTAGA-CATAAATAAGTAGAACACAAATTCAATACCCAAA
1 ATAAACAACTATTGATAAAACTAGATTAGAGCATAAATAAGTAGAACATAAATTCAATACCCAAA
34424343 AACCAAAC
66 AACCAAAC
* *
34424351 ATAAATAACTATTGATAAAACTAGTTTAG
1 ATAAACAACTATTGATAAAACTAGATTAG
34424380 CATTGTTGTT
Statistics
Matches: 147, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
71 20 0.14
72 66 0.45
73 61 0.41
ACGTcount: A:0.54, C:0.15, G:0.06, T:0.25
Consensus pattern (73 bp):
ATAAACAACTATTGATAAAACTAGATTAGAGCATAAATAAGTAGAACATAAATTCAATACCCAAA
AACCAAAC
Found at i:34434480 original size:21 final size:21
Alignment explanation
Indices: 34434440--34434482 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
34434430 TTTTACCTTA
*
34434440 AATATGAATTGGACTGAATTG
1 AATATGAATTGGACTAAATTG
* *
34434461 AATATGAATTGTATTAAATTG
1 AATATGAATTGGACTAAATTG
34434482 A
1 A
34434483 GTTAAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.37
Consensus pattern (21 bp):
AATATGAATTGGACTAAATTG
Found at i:34437430 original size:20 final size:20
Alignment explanation
Indices: 34437407--34437453 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
34437397 GGGTTAAAAT
*
34437407 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
34437427 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
34437447 TGAGCTG
1 TGAGCTG
34437454 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:34438904 original size:34 final size:35
Alignment explanation
Indices: 34438861--34438927 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
34438851 GTATTAAAAA
*
34438861 TTCTATAAAATTTTTGT-AAAATCAAACAATCAAT
1 TTCTATAAAATTTCTGTAAAAATCAAACAATCAAT
34438895 TTCTATAAAATTTCTGTAAAAATCAAACAATCA
1 TTCTATAAAATTTCTGTAAAAATCAAACAATCA
34438928 GAAAACAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 16 0.52
35 15 0.48
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.36
Consensus pattern (35 bp):
TTCTATAAAATTTCTGTAAAAATCAAACAATCAAT
Found at i:34439890 original size:17 final size:17
Alignment explanation
Indices: 34439868--34439901 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
34439858 CACTAACATG
34439868 AAAATGTAATGAAAATA
1 AAAATGTAATGAAAATA
*
34439885 AAAATGTAATGACAATA
1 AAAATGTAATGAAAATA
34439902 TATACTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.24
Consensus pattern (17 bp):
AAAATGTAATGAAAATA
Found at i:34440330 original size:18 final size:18
Alignment explanation
Indices: 34440307--34440410 Score: 165
Period size: 18 Copynumber: 5.7 Consensus size: 18
34440297 TCAACAAAGT
34440307 TTCTTCTTGTTT-TTCTTC
1 TTCTTCTT-TTTCTTCTTC
*
34440325 TTCTTCTTCTTCTTCTTC
1 TTCTTCTTTTTCTTCTTC
34440343 TTCTTCTTTTTCTTCTTC
1 TTCTTCTTTTTCTTCTTC
34440361 TTCTTCTTTTTCTTCTTC
1 TTCTTCTTTTTCTTCTTC
*
34440379 TTCTTCTTTTTCTTCTTT
1 TTCTTCTTTTTCTTCTTC
34440397 TTCTTCTTCTTTCT
1 TTCTTCTT-TTTCT
34440411 CATTTTCAAC
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
17 2 0.02
18 74 0.91
19 5 0.06
ACGTcount: A:0.00, C:0.27, G:0.01, T:0.72
Consensus pattern (18 bp):
TTCTTCTTTTTCTTCTTC
Found at i:34440430 original size:3 final size:3
Alignment explanation
Indices: 34440307--34440407 Score: 148
Period size: 3 Copynumber: 33.7 Consensus size: 3
34440297 TCAACAAAGT
* * *
34440307 TTC TTC TTG TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * *
34440355 TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTT TTC TTC TTT TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
34440403 TTC TT
1 TTC TT
34440408 TCTCATTTTC
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.00, C:0.27, G:0.01, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:34461658 original size:18 final size:18
Alignment explanation
Indices: 34461620--34461653 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
34461610 GTTTAAATTC
34461620 TGAAATAGCAAACATTAT
1 TGAAATAGCAAACATTAT
34461638 TGAAAT-GC-AACATTAT
1 TGAAATAGCAAACATTAT
34461654 GTTGAGTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (18 bp):
TGAAATAGCAAACATTAT
Found at i:34475251 original size:27 final size:27
Alignment explanation
Indices: 34475221--34475300 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 27
34475211 CTCCCCAATT
34475221 TTTATTGTCTTGGCAGACTATCCCATA
1 TTTATTGTCTTGGCAGACTATCCCATA
** * * *
34475248 TTTACCGTCCTGGC-GAACTACCCCACA
1 TTTATTGTCTTGGCAG-ACTATCCCATA
* **
34475275 TTTATTGTCTCGATAGACTATCCCAT
1 TTTATTGTCTTGGCAGACTATCCCAT
34475301 GTTCACCATT
Statistics
Matches: 38, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
26 1 0.03
27 36 0.95
28 1 0.03
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.35
Consensus pattern (27 bp):
TTTATTGTCTTGGCAGACTATCCCATA
Found at i:34478148 original size:24 final size:24
Alignment explanation
Indices: 34478121--34478168 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
34478111 AGGTTTTCTC
*
34478121 TGTTTGATCTCTTGCTATTTTAGG
1 TGTTTGATATCTTGCTATTTTAGG
** *
34478145 TGTTTTTTATCTTTCTATTTTAGG
1 TGTTTGATATCTTGCTATTTTAGG
34478169 CTCATTTGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.60
Consensus pattern (24 bp):
TGTTTGATATCTTGCTATTTTAGG
Found at i:34478642 original size:22 final size:22
Alignment explanation
Indices: 34478590--34478654 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
34478580 TATTTGGGAA
* * *
34478590 TTGGTATGAAACGGTAAGGGAT
1 TTGGTACGAAATGGTAATGGAT
**
34478612 TTGAAACGAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
*
34478634 TTGGTACGAAAATGGAAATGG
1 TTGGTACG-AAATGGTAATGG
34478655 TTCAAAAAGG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 23 0.68
23 11 0.32
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.26
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:34484952 original size:25 final size:25
Alignment explanation
Indices: 34484918--34485012 Score: 109
Period size: 25 Copynumber: 3.8 Consensus size: 25
34484908 GTTGTAAACA
*
34484918 GTAAGCTCCTTCGAGCTGAATAACG
1 GTAAGCTCCTACGAGCTGAATAACG
* * *
34484943 GTAAGATCCTCCGAGCTGAATAATG
1 GTAAGCTCCTACGAGCTGAATAACG
* * *
34484968 GTAAGCTCATACGAGCTGAGTATCG
1 GTAAGCTCCTACGAGCTGAATAACG
* *
34484993 GTAAGCTCATAAGAGCTGAA
1 GTAAGCTCCTACGAGCTGAA
34485013 ATTGGTAACT
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (25 bp):
GTAAGCTCCTACGAGCTGAATAACG
Found at i:34492062 original size:25 final size:25
Alignment explanation
Indices: 34492034--34492093 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
34492024 GCCAAATGGT
* * * *
34492034 ACAGAGCAGAGCATAATTCAATAAA
1 ACAGAGCAGAACAGAATACAACAAA
* *
34492059 ACAGAACAGAACAGAGTACAACAAA
1 ACAGAGCAGAACAGAATACAACAAA
34492084 ACAGAGCAGA
1 ACAGAGCAGA
34492094 CAAAGCATGT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.55, C:0.18, G:0.18, T:0.08
Consensus pattern (25 bp):
ACAGAGCAGAACAGAATACAACAAA
Done.