Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008091.1 Hibiscus syriacus cultivar Beakdansim tig00110602_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: 2471235
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1556934 original size:42 final size:42
Alignment explanation
Indices: 1556856--1556955 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
1556846 GGCAGGACCA
* * * * * * * *
1556856 CTTGAACGATGACAGAGACCTCTTGAACGGTGGGAGGGGCTT
1 CTTGAATGATGATAGGGGCCTCTTGAACGATAGGAGGCGCCT
1556898 CTTTG-ATGATGATAGGGGCCTCTTGAACGATAGGAGGCGCCT
1 C-TTGAATGATGATAGGGGCCTCTTGAACGATAGGAGGCGCCT
1556940 CTTGAATGATGATAGG
1 CTTGAATGATGATAGG
1556956 TGCATCGGGC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
41 3 0.06
42 42 0.88
43 3 0.06
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.25
Consensus pattern (42 bp):
CTTGAATGATGATAGGGGCCTCTTGAACGATAGGAGGCGCCT
Found at i:1559155 original size:20 final size:19
Alignment explanation
Indices: 1559120--1559185 Score: 89
Period size: 19 Copynumber: 3.4 Consensus size: 19
1559110 AATTCGCAAC
1559120 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
1559139 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
*
1559159 GCGATTTTCATTTCGTGTT
1 GCGATTTTCATTTCGCGTT
*
1559178 GTGATTTT
1 GCGATTTT
1559186 GGTGTTGCGA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 23 0.53
20 20 0.47
ACGTcount: A:0.11, C:0.15, G:0.23, T:0.52
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:1559228 original size:13 final size:13
Alignment explanation
Indices: 1559210--1559241 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1559200 GGGTTTCTTC
1559210 AACAAAAAGACAA
1 AACAAAAAGACAA
1559223 AACAAAAAGACAA
1 AACAAAAAGACAA
1559236 AACAAA
1 AACAAA
1559242 GACAAATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.78, C:0.16, G:0.06, T:0.00
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:1559244 original size:11 final size:12
Alignment explanation
Indices: 1559214--1559247 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
1559204 TTCTTCAACA
1559214 AAAAGACAAAAC
1 AAAAGACAAAAC
1559226 AAAAAGACAAAAC
1 -AAAAGACAAAAC
1559239 -AAAGACAAA
1 AAAAGACAAA
1559248 TACTAACTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
13 12 0.57
ACGTcount: A:0.76, C:0.15, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAGACAAAAC
Found at i:1559483 original size:22 final size:22
Alignment explanation
Indices: 1559455--1559505 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1559445 GATGGAGATA
*
1559455 GACGGATTTCGTCGGAAATGAG
1 GACGGATTTCGTCAGAAATGAG
* *
1559477 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGTCAGAAATGAG
1559499 GACGGAT
1 GACGGAT
1559506 GTCGCCGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.14, G:0.39, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCAGAAATGAG
Found at i:1559696 original size:21 final size:21
Alignment explanation
Indices: 1559672--1559734 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1559662 ATGTGTTGGG
1559672 ATTTACAAATTCGCGTTGCGA
1 ATTTACAAATTCGCGTTGCGA
** * **
1559693 ATTTGGAAAATCGCAATGCG-
1 ATTTACAAATTCGCGTTGCGA
*
1559713 ATTTACATATTCGCGTTGCGA
1 ATTTACAAATTCGCGTTGCGA
1559734 A
1 A
1559735 ATTGGAAACT
Statistics
Matches: 30, Mismatches: 11, Indels: 2
0.70 0.26 0.05
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (21 bp):
ATTTACAAATTCGCGTTGCGA
Found at i:1559732 original size:20 final size:20
Alignment explanation
Indices: 1559666--1559733 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
1559656 TGACTTATGT
*
1559666 GTTGGGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
** *
1559686 GTTGCGAATTTGGAAAATCGC
1 GTTGCG-ATTTACAAATTCGC
** *
1559707 AATGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
1559727 GTTGCGA
1 GTTGCGA
1559734 AATTGGAAAC
Statistics
Matches: 35, Mismatches: 12, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.32
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:1559770 original size:20 final size:19
Alignment explanation
Indices: 1559723--1559774 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1559713 ATTTACATAT
1559723 TCGCGTTGCGAAATTGGAA
1 TCGCGTTGCGAAATTGGAA
* * *
1559742 ACTGAGTTGCGAAATTTGAGA
1 TC-GCGTTGCGAAATTGGA-A
1559763 TCGCGTTGCGAA
1 TCGCGTTGCGAA
1559775 TTTATTGGTC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 1 0.04
20 23 0.88
21 2 0.08
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (19 bp):
TCGCGTTGCGAAATTGGAA
Found at i:1563079 original size:32 final size:34
Alignment explanation
Indices: 1563012--1563096 Score: 98
Period size: 38 Copynumber: 2.4 Consensus size: 34
1563002 TCGGACCGGA
1563012 TATATATATATATTTAAATTAAATATATAAATAT
1 TATATATATATATTTAAATTAAATATATAAATAT
* * * *
1563046 TATATATATTTTTTAATTTAAATTAAATTTATTAATGT
1 TATATATA---TAT-ATTTAAATTAAATATATAAATAT
1563084 TATATATATATAT
1 TATATATATATAT
1563097 ATATATATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
34 10 0.24
35 2 0.05
37 2 0.05
38 28 0.67
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (34 bp):
TATATATATATATTTAAATTAAATATATAAATAT
Found at i:1563234 original size:36 final size:36
Alignment explanation
Indices: 1563180--1563265 Score: 129
Period size: 36 Copynumber: 2.4 Consensus size: 36
1563170 ACCAAACCCA
* *
1563180 TCCCCGTCCCCATCCCCGTTTAGCATAAACGA-TTT
1 TCCCCGTCCCCGTTCCCGTTTAGCATAAACGATTTT
*
1563215 TCTCCCGTCCCCGTTCCCGTTTAGCATAAACGGTTTT
1 TC-CCCGTCCCCGTTCCCGTTTAGCATAAACGATTTT
1563252 TCCCCGTCCCCGTT
1 TCCCCGTCCCCGTT
1563266 TAATTCGGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 2 0.04
36 39 0.85
37 5 0.11
ACGTcount: A:0.14, C:0.41, G:0.14, T:0.31
Consensus pattern (36 bp):
TCCCCGTCCCCGTTCCCGTTTAGCATAAACGATTTT
Found at i:1566971 original size:18 final size:18
Alignment explanation
Indices: 1566948--1566982 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1566938 TTCCATCCGG
*
1566948 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1566966 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1566983 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1568320 original size:18 final size:18
Alignment explanation
Indices: 1568299--1568344 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
1568289 GTCGAGTCAA
1568299 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
1568317 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
1568335 CGGGTCGGGT
1 CGGGTCGGGT
1568345 TGTGACCGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.13, C:0.17, G:0.52, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:1568339 original size:13 final size:13
Alignment explanation
Indices: 1568278--1568322 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
1568268 CGACGATCAA
1568278 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
1568291 CGAGTCAACGGGT
1 CGGGTCAACGGGT
*
1568304 CGGGTAAACGGGT
1 CGGGTCAACGGGT
1568317 CGGGTC
1 CGGGTC
1568323 GGGTAAACGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.18, C:0.22, G:0.44, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:1572145 original size:18 final size:18
Alignment explanation
Indices: 1572122--1572156 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1572112 TTCCATCCGG
*
1572122 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1572140 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1572157 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1573468 original size:18 final size:18
Alignment explanation
Indices: 1573447--1573519 Score: 80
Period size: 18 Copynumber: 4.1 Consensus size: 18
1573437 TCAACGACGA
1573447 TCAACGGGTCGGGTCGGG
1 TCAACGGGTCGGGTCGGG
1573465 TCAACGGGTCGGGTAAACGGG
1 TCAACGGGTCGGGT---CGGG
1573486 T---CGGGTCGGGTCGGG
1 TCAACGGGTCGGGTCGGG
* *
1573501 TAAACGGGTCTGGTCGGG
1 TCAACGGGTCGGGTCGGG
1573519 T
1 T
1573520 TGTGACCGGT
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
15 5 0.10
18 38 0.79
21 5 0.10
ACGTcount: A:0.14, C:0.19, G:0.48, T:0.19
Consensus pattern (18 bp):
TCAACGGGTCGGGTCGGG
Found at i:1573474 original size:13 final size:13
Alignment explanation
Indices: 1573456--1573510 Score: 80
Period size: 13 Copynumber: 4.5 Consensus size: 13
1573446 ATCAACGGGT
*
1573456 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
1573469 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
1573482 CGGGTCGGGT---
1 CGGGTCGGGTAAA
1573492 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
1573505 CGGGTC
1 CGGGTC
1573511 TGGTCGGGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
10 10 0.26
13 28 0.74
ACGTcount: A:0.15, C:0.20, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:1573495 original size:23 final size:23
Alignment explanation
Indices: 1573469--1573519 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
1573459 GTCGGGTCAA
1573469 CGGGTCGGGTAAACGGGTCGGGT
1 CGGGTCGGGTAAACGGGTCGGGT
*
1573492 CGGGTCGGGTAAACGGGTCTGGT
1 CGGGTCGGGTAAACGGGTCGGGT
1573515 CGGGT
1 CGGGT
1573520 TGTGACCGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.12, C:0.18, G:0.51, T:0.20
Consensus pattern (23 bp):
CGGGTCGGGTAAACGGGTCGGGT
Found at i:1577318 original size:18 final size:18
Alignment explanation
Indices: 1577295--1577329 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1577285 TTCCATCCGG
*
1577295 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1577313 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1577330 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1578646 original size:13 final size:13
Alignment explanation
Indices: 1578628--1578652 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1578618 CGGTCAACGG
1578628 GTCAACGGGTCGA
1 GTCAACGGGTCGA
1578641 GTCAACGGGTCG
1 GTCAACGGGTCG
1578653 GGTCGGGTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:1578656 original size:18 final size:18
Alignment explanation
Indices: 1578633--1578706 Score: 86
Period size: 18 Copynumber: 4.4 Consensus size: 18
1578623 AACGGGTCAA
1578633 CGGGTCGAGTCAACGGGT
1 CGGGTCGAGTCAACGGGT
*
1578651 CGGGTCGGGTCAACGGGT
1 CGGGTCGAGTCAACGGGT
1578669 CGGGT--A---AACGGGT
1 CGGGTCGAGTCAACGGGT
* *
1578682 CGGGTCGGGTAAACGGGT
1 CGGGTCGAGTCAACGGGT
1578700 CGGGTCG
1 CGGGTCG
1578707 GGTTGTGACC
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
13 12 0.25
18 36 0.75
ACGTcount: A:0.15, C:0.20, G:0.49, T:0.16
Consensus pattern (18 bp):
CGGGTCGAGTCAACGGGT
Found at i:1578667 original size:13 final size:13
Alignment explanation
Indices: 1578651--1578687 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1578641 GTCAACGGGT
1578651 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
1578664 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
1578677 CGGGTCGGGTC
1 CGGGTCGGGTC
1578688 GGGTAAACGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.22, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:1578702 original size:31 final size:31
Alignment explanation
Indices: 1578625--1578704 Score: 133
Period size: 31 Copynumber: 2.6 Consensus size: 31
1578615 CGACGGTCAA
* *
1578625 CGGGTCAACGGGTCGAGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
1578656 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
*
1578687 CGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
1578705 CGGGTTGTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.16, C:0.20, G:0.47, T:0.16
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
Found at i:1578707 original size:18 final size:18
Alignment explanation
Indices: 1578664--1578709 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
1578654 GTCGGGTCAA
1578664 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
1578682 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
1578700 CGGGTCGGGT
1 CGGGTCGGGT
1578710 TGTGACCGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.13, C:0.17, G:0.52, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:1585018 original size:29 final size:29
Alignment explanation
Indices: 1584984--1585042 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1584974 CCTAAATTAA
1584984 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1585013 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1585042 T
1 T
1585043 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1589702 original size:29 final size:29
Alignment explanation
Indices: 1589668--1589726 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1589658 CCTAAATTAA
1589668 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1589697 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1589726 T
1 T
1589727 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1591422 original size:16 final size:16
Alignment explanation
Indices: 1591401--1591431 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1591391 AGAAGCTCAC
1591401 CAAGTATAGGATGAAT
1 CAAGTATAGGATGAAT
1591417 CAAGTATAGGATGAA
1 CAAGTATAGGATGAA
1591432 GGATATTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.26, T:0.23
Consensus pattern (16 bp):
CAAGTATAGGATGAAT
Found at i:1591848 original size:2 final size:2
Alignment explanation
Indices: 1591843--1591906 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
1591833 ATTTCACCAA
1591843 AT AT AT 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 AT AT AT
1591885 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
1591907 TTTTGATAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1593742 original size:5 final size:5
Alignment explanation
Indices: 1593732--1593784 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
1593722 AACGGTCAAC
* *
1593732 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAT GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
1593781 GGTC
1 GGTC
1593785 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.21, G:0.51, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:1593747 original size:17 final size:17
Alignment explanation
Indices: 1593725--1593762 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1593715 AACGGTCAAC
1593725 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1593742 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1593759 GGTC
1 GGTC
1593763 GGGTCAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:1593760 original size:22 final size:22
Alignment explanation
Indices: 1593718--1593784 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
1593708 GAAAGTCAAC
*
1593718 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
1593742 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
1593764 GGTCAATGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
1593785 AGACCGGTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
22 30 0.73
24 11 0.27
ACGTcount: A:0.12, C:0.22, G:0.46, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:1593774 original size:17 final size:17
Alignment explanation
Indices: 1593725--1593785 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 17
1593715 AACGGTCAAC
*
1593725 GGTCAACGGTCGGGTCG
1 GGTCAATGGTCGGGTCG
1593742 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA---T--GGTCGGGTCG
1593764 GGTCAATGGTCGGGTCG
1 GGTCAATGGTCGGGTCG
1593781 GGTCA
1 GGTCA
1593786 GACCGGTCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 21 0.55
19 1 0.03
22 16 0.42
ACGTcount: A:0.11, C:0.21, G:0.48, T:0.20
Consensus pattern (17 bp):
GGTCAATGGTCGGGTCG
Found at i:1593799 original size:9 final size:9
Alignment explanation
Indices: 1593781--1593851 Score: 52
Period size: 10 Copynumber: 7.3 Consensus size: 9
1593771 GGTCGGGTCG
*
1593781 GGTCAGACC
1 GGTCAAACC
1593790 GGTCAAACC
1 GGTCAAACC
*
1593799 GGTTCGAACC
1 GG-TCAAACC
* *
1593809 GGTTGAAATC
1 GG-TCAAACC
1593819 GGTCAGAACC
1 GGTCA-AACC
*
1593829 GGTTGAAAACC
1 GG-T-CAAACC
1593840 GGTCAAACC
1 GGTCAAACC
1593849 GGT
1 GGT
1593852 TTCCAGCAGC
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
9 20 0.41
10 21 0.43
11 7 0.14
12 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.30, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1593827 original size:20 final size:21
Alignment explanation
Indices: 1593794--1593852 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
1593784 CAGACCGGTC
1593794 AAACCGGTTC-GAACCGGTTG-
1 AAACCGG-TCAGAACCGGTTGA
*
1593814 AAATCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
1593835 AAACCGGTCA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
1593853 TCCAGCAGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.06
20 24 0.69
21 9 0.26
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.19
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:1600054 original size:32 final size:31
Alignment explanation
Indices: 1600016--1600092 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
1600006 CGGGGCCGTG
* *
1600016 GGGCCTACCTAAGAACACATCTTAGGGCTGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
1600048 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
1600079 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
1600093 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 23 0.62
32 14 0.38
ACGTcount: A:0.29, C:0.30, G:0.26, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:1600075 original size:63 final size:63
Alignment explanation
Indices: 1599969--1600092 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
1599959 CCCTAAGGGA
* * ** *
1599969 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
1600032 ACATCTTAGGG-CTGCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
1600093 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 3 0.06
63 46 0.88
64 3 0.06
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:1601014 original size:17 final size:17
Alignment explanation
Indices: 1600992--1601029 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1600982 AACGGTTAAC
1600992 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1601009 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1601026 GGTC
1 GGTC
1601030 GGGGTCAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:1601019 original size:7 final size:7
Alignment explanation
Indices: 1600965--1601002 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
1600955 GTCAAAGAAA
1600965 GTCAACG
1 GTCAACG
1600972 GTCAACG
1 GTCAACG
1600979 GTCAACG
1 GTCAACG
*
1600986 GTTAACG
1 GTCAACG
1600993 GTCAACG
1 GTCAACG
1601000 GTC
1 GTC
1601003 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:1601019 original size:12 final size:12
Alignment explanation
Indices: 1601004--1601047 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1600994 TCAACGGTCG
1601004 GGTCGGGTCAAC
1 GGTCGGGTCAAC
*
1601016 GGTCGGGTC--G
1 GGTCGGGTCAAC
1601026 GGTCGGGGTCAAC
1 GGTC-GGGTCAAC
1601039 GGTCGGGTC
1 GGTCGGGTC
1601048 GGGTTAGACC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
10 4 0.15
11 5 0.19
12 14 0.52
13 4 0.15
ACGTcount: A:0.09, C:0.23, G:0.50, T:0.18
Consensus pattern (12 bp):
GGTCGGGTCAAC
Found at i:1601038 original size:23 final size:22
Alignment explanation
Indices: 1600999--1601051 Score: 97
Period size: 23 Copynumber: 2.4 Consensus size: 22
1600989 AACGGTCAAC
1600999 GGTCGGGTCGGGTCAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
1601021 GGTCGGGTCGGGGTCAACGGTCG
1 GGTCGGGTC-GGGTCAACGGTCG
1601044 GGTCGGGT
1 GGTCGGGT
1601052 TAGACCGGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 9 0.30
23 21 0.70
ACGTcount: A:0.08, C:0.21, G:0.53, T:0.19
Consensus pattern (22 bp):
GGTCGGGTCGGGTCAACGGTCG
Found at i:1602023 original size:13 final size:13
Alignment explanation
Indices: 1602007--1602053 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 13
1601997 AGTTTTTTCA
1602007 AAAATATTTTTTT
1 AAAATATTTTTTT
**
1602020 -AAA-ATTTTTCA
1 AAAATATTTTTTT
1602031 AAAATATTTTTTT
1 AAAATATTTTTTT
1602044 AAAAT-TTTTT
1 AAAATATTTTT
1602054 AAAAATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
11 6 0.21
12 11 0.39
13 11 0.39
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
AAAATATTTTTTT
Found at i:1602028 original size:11 final size:11
Alignment explanation
Indices: 1602007--1602059 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
1601997 AGTTTTTTCA
1602007 AAAATATTTTTT
1 AAAA-ATTTTTT
* *
1602019 TAAAATTTTTCA
1 AAAAATTTTT-T
1602031 AAAATATTTTTT
1 AAAA-ATTTTTT
*
1602043 TAAAATTTTTT
1 AAAAATTTTTT
1602054 AAAAAT
1 AAAAAT
1602060 AAATTTACAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
11 18 0.55
12 9 0.27
13 6 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
AAAAATTTTTT
Found at i:1602032 original size:24 final size:24
Alignment explanation
Indices: 1602000--1602060 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
1601990 AAAATGGAGT
1602000 TTTTTCAAAAATATTTTTTTAAAA
1 TTTTTCAAAAATATTTTTTTAAAA
1602024 TTTTTCAAAAATATTTTTTTAAAA
1 TTTTTCAAAAATATTTTTTTAAAA
*
1602048 TTTTTTAAAAATA
1 TTTTTCAAAAATA
1602061 AATTTACAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTTCAAAAATATTTTTTTAAAA
Found at i:1602071 original size:24 final size:24
Alignment explanation
Indices: 1602000--1602073 Score: 67
Period size: 24 Copynumber: 3.1 Consensus size: 24
1601990 AAAATGGAGT
** **
1602000 TTTTTCAAAAATATTTTTTTAAAA
1 TTTTTCAAAAATAAATTTACAAAA
** **
1602024 TTTTTCAAAAATATTTTTTTAAAA
1 TTTTTCAAAAATAAATTTACAAAA
*
1602048 TTTTTTAAAAATAAATTTACAAAA
1 TTTTTCAAAAATAAATTTACAAAA
1602072 TT
1 TT
1602074 ACCATTTCAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTTTCAAAAATAAATTTACAAAA
Found at i:1606647 original size:19 final size:19
Alignment explanation
Indices: 1606623--1606672 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
1606613 AATCTGAAGG
1606623 TTTAAAATTTAAGGATCAA
1 TTTAAAATTTAAGGATCAA
1606642 TTTAAAATTTAAGGATCAA
1 TTTAAAATTTAAGGATCAA
*
1606661 TTTGAAATTTAA
1 TTTAAAATTTAA
1606673 ATCAGAGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (19 bp):
TTTAAAATTTAAGGATCAA
Found at i:1612252 original size:2 final size:2
Alignment explanation
Indices: 1612239--1612290 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
1612229 TTCAAATAAC
*
1612239 AT AT AT AA 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 AT AT AT
1612281 AT AT AT AT AT
1 AT AT AT AT AT
1612291 TTAAACATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1620754 original size:9 final size:9
Alignment explanation
Indices: 1620740--1620765 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1620730 GAAATCGATT
1620740 AATTAACCG
1 AATTAACCG
1620749 AATTAACCG
1 AATTAACCG
1620758 AATTAACC
1 AATTAACC
1620766 TTTAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:1620902 original size:17 final size:17
Alignment explanation
Indices: 1620880--1620918 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1620870 TGAATCAAAT
1620880 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1620897 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1620914 -AATTA
1 TAATTA
1620919 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:1628165 original size:33 final size:32
Alignment explanation
Indices: 1628091--1628270 Score: 193
Period size: 33 Copynumber: 5.5 Consensus size: 32
1628081 ACAATAAACC
*
1628091 CCAACCCGACCCGAATATCACGCTTAAAAAAA
1 CCAACCCGACCCGAATATCACACTTAAAAAAA
* *
1628123 -CAAGACCGACCCGAATATCAAACTTAAAAAAA
1 CCAA-CCCGACCCGAATATCACACTTAAAAAAA
* *
1628155 TCCAACCCGACCTGAATACCACACTTAAAAAAA
1 -CCAACCCGACCCGAATATCACACTTAAAAAAA
* *
1628188 CCCGACCCCGACCCGAATATCACACTTAAAAAAC
1 -CC-AACCCGACCCGAATATCACACTTAAAAAAA
* * *
1628222 CTCGACCCTAACCGAATATC-CAACTTAAAAAAA
1 C-CAACCCGACCCGAATATCAC-ACTTAAAAAAA
1628255 CCTAACCCGACCCGAA
1 CC-AACCCGACCCGAA
1628271 GCCGATTTTT
Statistics
Matches: 121, Mismatches: 20, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
31 3 0.02
32 27 0.22
33 61 0.50
34 30 0.25
ACGTcount: A:0.44, C:0.34, G:0.08, T:0.13
Consensus pattern (32 bp):
CCAACCCGACCCGAATATCACACTTAAAAAAA
Found at i:1628217 original size:67 final size:64
Alignment explanation
Indices: 1628090--1628270 Score: 195
Period size: 67 Copynumber: 2.8 Consensus size: 64
1628080 CACAATAAAC
* * **
1628090 CCCAACCCGACCCGAATATCACGCTTAAAAAAACAAGA-CCGACCCGAATATCAAACTTAAAAAA
1 CCCAACCCGA-CCGAATACCACACTTAAAAAAACCCGACCCGACCCGAATATCAAACTT-AAAAA
1628154 A
64 A
* *
1628155 TCCAACCCGACCTGAATACCACACTTAAAAAAACCCGACCCCGACCCGAATATCACACTTAAAAA
1 CCCAACCCGACC-GAATACCACACTTAAAAAAACCCGA-CCCGACCCGAATATCAAACTTAAAAA
1628220 A
64 A
* * **
1628221 CCTCGACCCTAACCGAATATCCA-ACTTAAAAAAACCTAACCCGACCCGAA
1 CC-CAACCC-GACCGAATA-CCACACTTAAAAAAACCCGACCCGACCCGAA
1628271 GCCGATTTTT
Statistics
Matches: 99, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
64 2 0.02
65 30 0.30
66 18 0.18
67 43 0.43
68 6 0.06
ACGTcount: A:0.44, C:0.35, G:0.08, T:0.13
Consensus pattern (64 bp):
CCCAACCCGACCGAATACCACACTTAAAAAAACCCGACCCGACCCGAATATCAAACTTAAAAAA
Found at i:1643870 original size:10 final size:10
Alignment explanation
Indices: 1643855--1643884 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1643845 TTCTCATTGA
1643855 TTGATACTTT
1 TTGATACTTT
1643865 TTGATACTTT
1 TTGATACTTT
*
1643875 TTAATACTTT
1 TTGATACTTT
1643885 CACAAATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (10 bp):
TTGATACTTT
Found at i:1645846 original size:21 final size:21
Alignment explanation
Indices: 1645807--1645846 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1645797 ATGCAACAGG
*
1645807 GCCAGATTTTGCTAAGTACAT
1 GCCAGATTTTGATAAGTACAT
* *
1645828 GCCAGATTTTTATAGGTAC
1 GCCAGATTTTGATAAGTAC
1645847 CTGGAAGTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (21 bp):
GCCAGATTTTGATAAGTACAT
Found at i:1648556 original size:22 final size:23
Alignment explanation
Indices: 1648510--1648561 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
1648500 GGTGAACTTT
1648510 TAAAATTCTAGAGGTAGAATTTA
1 TAAAATTCTAGAGGTAGAATTTA
*
1648533 TAAAATT-TA-AGGCTAGCATTTA
1 TAAAATTCTAGAGG-TAGAATTTA
1648555 TAAAATT
1 TAAAATT
1648562 ATCAAAAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 3 0.11
22 17 0.63
23 7 0.26
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (23 bp):
TAAAATTCTAGAGGTAGAATTTA
Found at i:1651432 original size:34 final size:32
Alignment explanation
Indices: 1651379--1651448 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1651369 CCTTACAAAC
* *
1651379 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
*
1651411 TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
1651445 TCCC
1 TCCC
1651449 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:1651688 original size:20 final size:22
Alignment explanation
Indices: 1651663--1651702 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1651653 AGTCGTATAT
1651663 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1651683 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1651703 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1651754 original size:21 final size:21
Alignment explanation
Indices: 1651730--1651772 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1651720 CCCAGAATAG
*
1651730 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
1651751 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
1651772 A
1 A
1651773 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:1651850 original size:21 final size:20
Alignment explanation
Indices: 1651808--1651846 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1651798 CTGTTGAACA
1651808 GGGGGGGAATCGGTACCCCT
1 GGGGGGGAATCGGTACCCCT
1651828 GGGGGGGAATCGGTACCCC
1 GGGGGGGAATCGGTACCCC
1651847 CTGGACATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.26, G:0.46, T:0.13
Consensus pattern (20 bp):
GGGGGGGAATCGGTACCCCT
Found at i:1651909 original size:21 final size:21
Alignment explanation
Indices: 1651884--1651962 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
1651874 AAAACCTGCA
1651884 GGGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
1651905 GGGGGTATCTGTA--CCC---
1 GGGGGTATCTGTACCCCCTGG
1651921 -GGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
* *
1651941 GGGGGAATCTATACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
1651962 G
1 G
1651963 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
21 32 0.64
ACGTcount: A:0.13, C:0.28, G:0.37, T:0.23
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:1651925 original size:36 final size:36
Alignment explanation
Indices: 1651885--1651956 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
1651875 AAACCTGCAG
* *
1651885 GGGGTATCTGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
1651921 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
1651957 CCTGGGCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.14, C:0.28, G:0.35, T:0.24
Consensus pattern (36 bp):
GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
Found at i:1651926 original size:15 final size:15
Alignment explanation
Indices: 1651906--1651935 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1651896 ACCCCCTGGG
1651906 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
1651921 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
1651936 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:1652084 original size:29 final size:31
Alignment explanation
Indices: 1652052--1652111 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
1652042 AAACTTTGAA
1652052 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1652081 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1652112 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1654322 original size:34 final size:32
Alignment explanation
Indices: 1654269--1654338 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1654259 CCTTACAAAC
*
1654269 TCCCTAGTTTTTCCGGGCTAAACTAGAACATT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
* *
1654301 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
1654335 TCCC
1 TCCC
1654339 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:1654578 original size:20 final size:22
Alignment explanation
Indices: 1654553--1654592 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1654543 AGTCGTATAT
1654553 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1654573 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1654593 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1654644 original size:21 final size:21
Alignment explanation
Indices: 1654620--1654662 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1654610 CCCAGAATAG
*
1654620 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
1654641 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
1654662 A
1 A
1654663 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:1654740 original size:21 final size:20
Alignment explanation
Indices: 1654698--1654736 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1654688 CTGTTGAACA
1654698 GGGGGGGAATCGGTACCCCT
1 GGGGGGGAATCGGTACCCCT
1654718 GGGGGGGAATCGGTACCCC
1 GGGGGGGAATCGGTACCCC
1654737 CTGGACATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.26, G:0.46, T:0.13
Consensus pattern (20 bp):
GGGGGGGAATCGGTACCCCT
Found at i:1654799 original size:21 final size:20
Alignment explanation
Indices: 1654774--1654851 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 20
1654764 AAAACCTGCA
1654774 GGGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTA-CCCCTGG
1654795 GGGGGTATCTGTA-CCC---
1 GGGGGTATCTGTACCCCTGG
*
1654811 -GGGGTATCTGTACCCCCTTG
1 GGGGGTATCTGTA-CCCCTGG
* *
1654831 GGGGGAATCTATACCCCTGG
1 GGGGGTATCTGTACCCCTGG
1654851 G
1 G
1654852 CAATCTTGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
15 12 0.25
17 3 0.06
19 3 0.06
20 7 0.15
21 23 0.48
ACGTcount: A:0.13, C:0.27, G:0.36, T:0.24
Consensus pattern (20 bp):
GGGGGTATCTGTACCCCTGG
Found at i:1654815 original size:36 final size:36
Alignment explanation
Indices: 1654775--1654846 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
1654765 AAACCTGCAG
* *
1654775 GGGGTATCTGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
*
1654811 GGGGTATCTGTACCCCCTTGGGGGGAATCTATACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
1654847 CTGGGCAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.14, C:0.28, G:0.33, T:0.25
Consensus pattern (36 bp):
GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
Found at i:1654816 original size:15 final size:15
Alignment explanation
Indices: 1654796--1654825 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1654786 ACCCCCTGGG
1654796 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
1654811 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
1654826 CCTTGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:1654973 original size:29 final size:31
Alignment explanation
Indices: 1654941--1655000 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
1654931 AAACTTTGAA
1654941 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1654970 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1655001 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1655426 original size:102 final size:103
Alignment explanation
Indices: 1655250--1655655 Score: 458
Period size: 102 Copynumber: 3.8 Consensus size: 103
1655240 AAGCGCTACT
* * * * *
1655250 GGATATATTGAAAGTGTCGATACATTATAAAAATATATTGATCCATAACAATATAACAGGTAAAA
1 GGATATATTAAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAA
* *
1655315 AAATGACAAAATCGGTCTATAAATAACAAAACA-TGTC
66 AAATGACAAAACCGGTCTATAAATGACAAAACATTGTC
1655352 GGATATATTAAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAA
1 GGATATATTAAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAA
*
1655417 AAATGACAAAACCGGTCTATAAATGACAAAACAGGTAAATTTCTATC
66 AAATGACAAAACCGGTCTATAAATGACAAAAC------A--T-TGTC
* * * *
1655464 GGATATATTGAAAGTGTCAATATTTTATAAAAATGTATCGATCCATAACCATATAACAAGT-AAA
1 GGATATATTAAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAA
* * *
1655528 AGATGACAAAACCGATCTATAAATGACAAAACAGGTAAAGCGCTACC
66 AAATGACAAAACCGGTCTATAAATGACAAAACA--T----TG-T--C
* *
1655575 GGATATATTGAAAA-TGTCGATACTTTATAAAAATGTATAGATTCATAACAATATAACAAGTAAA
1 GGATATATT-AAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAA
*
1655639 AATATGACAAAACCGGT
65 AAAATGACAAAACCGGT
1655656 AAAGAGCTAC
Statistics
Matches: 259, Mismatches: 27, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
102 90 0.35
105 2 0.01
108 1 0.00
109 1 0.00
111 85 0.33
112 80 0.31
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (103 bp):
GGATATATTAAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAA
AAATGACAAAACCGGTCTATAAATGACAAAACATTGTC
Found at i:1655586 original size:111 final size:112
Alignment explanation
Indices: 1655351--1655653 Score: 473
Period size: 111 Copynumber: 2.7 Consensus size: 112
1655341 CAAAACATGT
*
1655351 CGGATATATTAAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAA
1 CGGATATATTGAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAA
* *** *
1655416 AAAATGACAAAACCGGTCTATAAATGACAAAACAGGTAAATTTCTAT
66 AAAATGACAAAACCGATCTATAAATGACAAAACAGGTAAAGCGCTAC
* * *
1655463 CGGATATATTGAAAGTGTCAATATTTTATAAAAATGTATCGATCCATAACCATATAACAAGT-AA
1 CGGATATATTGAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAA
*
1655527 AAGATGACAAAACCGATCTATAAATGACAAAACAGGTAAAGCGCTAC
66 AAAATGACAAAACCGATCTATAAATGACAAAACAGGTAAAGCGCTAC
* * *
1655574 CGGATATATTGAAAATGTCGATACTTTATAAAAATGTATAGATTCATAACAATATAACAAGTAAA
1 CGGATATATTGAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAA
*
1655639 AATATGACAAAACCG
66 AAAATGACAAAACCG
1655654 GTAAAGAGCT
Statistics
Matches: 173, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
111 99 0.57
112 74 0.43
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.26
Consensus pattern (112 bp):
CGGATATATTGAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAA
AAAATGACAAAACCGATCTATAAATGACAAAACAGGTAAAGCGCTAC
Found at i:1664515 original size:2 final size:2
Alignment explanation
Indices: 1664508--1664543 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1664498 ACTGAAAGAA
1664508 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1664544 CTAATTAGCT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1668900 original size:16 final size:17
Alignment explanation
Indices: 1668879--1668935 Score: 71
Period size: 18 Copynumber: 3.4 Consensus size: 17
1668869 CAAGAGCCCC
*
1668879 AGGGGTGGCACTT-TGG
1 AGGGGTGACACTTGTGG
**
1668895 AGGGGTGACACTTGTATT
1 AGGGGTGACACTTGT-GG
1668913 AGGGGTGACACTTGTGG
1 AGGGGTGACACTTGTGG
1668930 AGGGGT
1 AGGGGT
1668936 TGCCTGGGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
16 12 0.35
17 7 0.21
18 15 0.44
ACGTcount: A:0.18, C:0.11, G:0.46, T:0.26
Consensus pattern (17 bp):
AGGGGTGACACTTGTGG
Found at i:1669891 original size:21 final size:22
Alignment explanation
Indices: 1669867--1669937 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 22
1669857 ACCGAATTCG
1669867 AATATATTAATATT-TTAAAAT
1 AATATATTAATATTATTAAAAT
* *
1669888 AATATATTTATAATTATT--TAT
1 AATATATTAAT-ATTATTAAAAT
* *
1669909 TATATTTTAA-ATTATTAAAAT
1 AATATATTAATATTATTAAAAT
1669930 AATATATT
1 AATATATT
1669938 GTTTTATATT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 6 0.16
21 27 0.71
22 3 0.08
23 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATATTAATATTATTAAAAT
Found at i:1669967 original size:32 final size:33
Alignment explanation
Indices: 1669908--1669969 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
1669898 TAATTATTTA
*
1669908 TTATATTTTAAATTATTAAAATAATATATTGTT
1 TTATATTTTAAATAATTAAAATAATATATTGTT
*
1669941 TTATATTTTTAATAATT-AAATAATATATT
1 TTATATTTTAAATAATTAAAATAATATATT
1669970 TTAATAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (33 bp):
TTATATTTTAAATAATTAAAATAATATATTGTT
Found at i:1672004 original size:24 final size:24
Alignment explanation
Indices: 1671965--1672010 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1671955 TTTCCAAAGT
1671965 ATCGATACTTTTCCAAAAGTATAA
1 ATCGATACTTTTCCAAAAGTATAA
1671989 ATCGATA-TTTTCCCAAAAGTAT
1 ATCGATACTTTT-CCAAAAGTAT
1672011 TCATACTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (24 bp):
ATCGATACTTTTCCAAAAGTATAA
Found at i:1672191 original size:40 final size:40
Alignment explanation
Indices: 1672143--1672274 Score: 137
Period size: 40 Copynumber: 3.3 Consensus size: 40
1672133 TTTTTGGCGT
1672143 AACCTATTTTATTAATAAAAATATTAACATAACATATCAC
1 AACCTATTTTATTAATAAAAATATTAACATAACATATCAC
* * * * * * * *
1672183 AACATA-TTTA-TATTCAAAATCA-TGACATTA-TTGAGCGC
1 AACCTATTTTATTAATAAAAAT-ATTAACATAACAT-ATCAC
1672221 AACCTATTTTATTAATAAAAATATTAACATAACATATCAC
1 AACCTATTTTATTAATAAAAATATTAACATAACATATCAC
1672261 AACCTATTTCTATT
1 AACCTATTT-TATT
1672275 CAAAATTATG
Statistics
Matches: 69, Mismatches: 16, Indels: 13
0.70 0.16 0.13
Matches are distributed among these distances:
37 1 0.01
38 22 0.32
39 10 0.14
40 31 0.45
41 5 0.07
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.36
Consensus pattern (40 bp):
AACCTATTTTATTAATAAAAATATTAACATAACATATCAC
Found at i:1672202 original size:38 final size:38
Alignment explanation
Indices: 1672160--1672280 Score: 111
Period size: 38 Copynumber: 3.1 Consensus size: 38
1672150 TTTATTAATA
*
1672160 AAAATATTAACATAACATATCACAACATATTTATATTC
1 AAAATATTAACATAACATATCACAACCTATTTATATTC
* * * * * * *
1672198 AAAATCA-TGACATTA-TTGAGCGCAACCTATTTTATTAATA
1 AAAAT-ATTAACATAACAT-ATCACAACCTA-TTTA-TATTC
*
1672238 AAAATATTAACATAACATATCACAACCTATTTCTATTC
1 AAAATATTAACATAACATATCACAACCTATTTATATTC
1672276 AAAAT
1 AAAAT
1672281 TATGACATTA
Statistics
Matches: 61, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
37 1 0.02
38 27 0.44
39 9 0.15
40 23 0.38
41 1 0.02
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (38 bp):
AAAATATTAACATAACATATCACAACCTATTTATATTC
Found at i:1672275 original size:78 final size:78
Alignment explanation
Indices: 1672143--1672320 Score: 304
Period size: 78 Copynumber: 2.3 Consensus size: 78
1672133 TTTTTGGCGT
1672143 AACCTATTTTATTAATAAAAATATTAACATAACATATCACAACATATTTATATTCAAAATCATGA
1 AACCTATTTTATTAATAAAAATATTAACATAACATATCACAACATATTTATATTCAAAATCATGA
1672208 CATTATTGAGCGC
66 CATTATTGAGCGC
* * *
1672221 AACCTATTTTATTAATAAAAATATTAACATAACATATCACAACCTATTTCTATTCAAAATTATGA
1 AACCTATTTTATTAATAAAAATATTAACATAACATATCACAACATATTTATATTCAAAATCATGA
*
1672286 CATTATTGGGCGC
66 CATTATTGAGCGC
1672299 AACCTATTTTTATTAA-AAAAAT
1 AACCTA-TTTTATTAATAAAAAT
1672321 TAACATTCTA
Statistics
Matches: 95, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
78 86 0.91
79 9 0.09
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (78 bp):
AACCTATTTTATTAATAAAAATATTAACATAACATATCACAACATATTTATATTCAAAATCATGA
CATTATTGAGCGC
Found at i:1672327 original size:38 final size:38
Alignment explanation
Indices: 1672207--1672327 Score: 97
Period size: 38 Copynumber: 3.1 Consensus size: 38
1672197 CAAAATCATG
1672207 ACATTATTGAGCGCAACCTA-TTTTATTAATAAAAATATTA
1 ACATTATTGAGCGCAACCTATTTTTATT-A-AAAAA-ATTA
* * * * * *
1672247 ACATAACAT-ATCACAACCTATTTCTATT--CAAAATTA
1 ACATTA-TTGAGCGCAACCTATTTTTATTAAAAAAATTA
*
1672283 TGACATTATTGGGCGCAACCTATTTTTATTAAAAAAATTA
1 --ACATTATTGAGCGCAACCTATTTTTATTAAAAAAATTA
1672323 ACATT
1 ACATT
1672328 CTAGATCGCA
Statistics
Matches: 61, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
36 4 0.07
37 4 0.07
38 25 0.41
40 21 0.34
41 7 0.11
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (38 bp):
ACATTATTGAGCGCAACCTATTTTTATTAAAAAAATTA
Found at i:1673490 original size:31 final size:31
Alignment explanation
Indices: 1673455--1673522 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1673445 TTTAATTAAA
* * *
1673455 AAAATTTAA-CATTTAAATTGATATTTTATTT
1 AAAATTTAATCA-TAAAATTAATATTTTATCT
*
1673486 AAAATTTAATGATAAAATTAATATTTTATCT
1 AAAATTTAATCATAAAATTAATATTTTATCT
1673517 AAAATT
1 AAAATT
1673523 CGTGAATCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (31 bp):
AAAATTTAATCATAAAATTAATATTTTATCT
Found at i:1673663 original size:38 final size:38
Alignment explanation
Indices: 1673603--1673688 Score: 109
Period size: 38 Copynumber: 2.3 Consensus size: 38
1673593 GATCAAGCAG
* * *
1673603 ACCCGACCCAAAATTTATACACCCTCTATCCGACCCGA
1 ACCCGATCCAAAAATTAAACACCCTCTATCCGACCCGA
* * **
1673641 ACCCGATCGAAAAATTAAACACCCTTTATCCGACTTGA
1 ACCCGATCCAAAAATTAAACACCCTCTATCCGACCCGA
1673679 ACCCGATCCA
1 ACCCGATCCA
1673689 CCCTTTTGAG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.34, C:0.37, G:0.09, T:0.20
Consensus pattern (38 bp):
ACCCGATCCAAAAATTAAACACCCTCTATCCGACCCGA
Found at i:1675180 original size:31 final size:30
Alignment explanation
Indices: 1675145--1675229 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 30
1675135 CCTAACATTG
*
1675145 ACTTTTTGTTTTATTTTAATACCAGGTGTTT-
1 ACTTTTTATTTTATTTTAATACCA--TGTTTA
* * *
1675176 ACTTTTCATTTTATTTTATTACCCATTTTTA
1 ACTTTTTATTTTATTTTAATA-CCATGTTTA
*
1675207 ACTTTTTATTTTATTTTAGTACC
1 ACTTTTTATTTTATTTTAATACC
1675230 TAAATTTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
30 6 0.13
31 37 0.80
32 3 0.07
ACGTcount: A:0.21, C:0.13, G:0.06, T:0.60
Consensus pattern (30 bp):
ACTTTTTATTTTATTTTAATACCATGTTTA
Found at i:1680185 original size:37 final size:36
Alignment explanation
Indices: 1680139--1680214 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 36
1680129 TGGGTCATCA
* * *
1680139 AAATTAAACTTAAATAAAATGTTAGGCATAATTTTG
1 AAATTAAACTTAAACAAAATGATAGACATAATTTTG
*
1680175 AAATTGAAACTTAAACCAAATGATAGACATAATTTTG
1 AAATT-AAACTTAAACAAAATGATAGACATAATTTTG
1680212 AAA
1 AAA
1680215 AAAATGTGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
36 5 0.14
37 30 0.86
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.32
Consensus pattern (36 bp):
AAATTAAACTTAAACAAAATGATAGACATAATTTTG
Found at i:1685608 original size:129 final size:127
Alignment explanation
Indices: 1685475--1685798 Score: 437
Period size: 111 Copynumber: 2.7 Consensus size: 127
1685465 AAATTATACT
1685475 AAAATTTAATATCATTGAAATCAATAATATATACTAAAATACCTAATTGAACAGGAAAAAAAATA
1 AAAATTTAATATCATTGAAATCAATAATATATACTAAAATACCTAATTGAACAGGAAAAAAAATA
1685540 CCAAATTGAACCTTAAAATTGCATATTAAAGTTAAGTTTATATACTAAAATATATATCAAACCA
66 CCAAATTGAACCTTAAAA-T-CATATTAAAGTTAAGTTTATATACTAAAATATATATCAAACCA
* **
1685604 AAAATTTAATATCATTGAAATCAATAATATATACTAAAATA--T-A-T-ATC----AAAAATTTA
1 AAAATTTAATATCATTGAAATCAATAATATATACTAAAATACCTAATTGAACAGGAAAAAAAATA
*** * * *
1685660 --TGTTTTAA-ATT----GCATATTAAAGTTAAGTTTATATACTAAAATATATATCAAACCA
66 CCAAATTGAACCTTAAAATCATATTAAAGTTAAGTTTATATACTAAAATATATATCAAACCA
1685715 AAAATTTAATATCATTGAAATCAATAATATATACTAAAATACCTAATTGAACAGGAAAAAAAATA
1 AAAATTTAATATCATTGAAATCAATAATATATACTAAAATACCTAATTGAACAGGAAAAAAAATA
1685780 CCAAATTGAACCTTAAAAT
66 CCAAATTGAACCTTAAAAT
1685799 ATCTAAATAT
Statistics
Matches: 161, Mismatches: 18, Indels: 34
0.76 0.08 0.16
Matches are distributed among these distances:
111 84 0.52
113 1 0.01
114 1 0.01
115 1 0.01
116 2 0.01
117 2 0.01
118 4 0.02
120 14 0.09
122 4 0.02
123 2 0.01
124 2 0.01
125 1 0.01
126 1 0.01
127 1 0.01
129 41 0.25
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (127 bp):
AAAATTTAATATCATTGAAATCAATAATATATACTAAAATACCTAATTGAACAGGAAAAAAAATA
CCAAATTGAACCTTAAAATCATATTAAAGTTAAGTTTATATACTAAAATATATATCAAACCA
Found at i:1685636 original size:53 final size:53
Alignment explanation
Indices: 1685578--1685755 Score: 202
Period size: 53 Copynumber: 3.3 Consensus size: 53
1685568 AAGTTAAGTT
1685578 TATATACTAAAATATATATCAAACCAAAAATTTAATATCATTGAAATCAATAA
1 TATATACTAAAATATATATCAAACCAAAAATTTAATATCATTGAAATCAATAA
** * * *
1685631 TATATACTAAAATATATATCAAA--AATTTATGTTTTAA-ATTGCATATTAAAGTTAAGT-T
1 TATATACTAAAATATATATCAAACCAA---A-AATTTAATA-T-CAT-TGAAA-TCAA-TAA
1685689 TATATACTAAAATATATATCAAACCAAAAATTTAATATCATTGAAATCAATAA
1 TATATACTAAAATATATATCAAACCAAAAATTTAATATCATTGAAATCAATAA
1685742 TATATACTAAAATA
1 TATATACTAAAATA
1685756 CCTAATTGAA
Statistics
Matches: 102, Mismatches: 10, Indels: 26
0.74 0.07 0.19
Matches are distributed among these distances:
51 2 0.02
52 1 0.01
53 40 0.39
54 6 0.06
55 9 0.09
56 9 0.09
57 6 0.06
58 26 0.25
59 1 0.01
60 2 0.02
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (53 bp):
TATATACTAAAATATATATCAAACCAAAAATTTAATATCATTGAAATCAATAA
Found at i:1694011 original size:23 final size:23
Alignment explanation
Indices: 1693993--1694053 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1693983 TTCGTATAAA
1693993 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1694016 TGCACCAAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
1694039 TGCACTGTAGTGCCA
1 TGCACCGAAGTGCCA
1694054 TATAATATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1694403 original size:2 final size:2
Alignment explanation
Indices: 1694384--1694427 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
1694374 TTATGGTTAC
*
1694384 AT AT AT CAT AT A- AC 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 AT AT AT
1694426 AT
1 AT
1694428 TCACACATCA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1698034 original size:4 final size:4
Alignment explanation
Indices: 1698025--1698050 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1698015 AACCTTTCAA
1698025 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
1698051 TATTTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1699142 original size:26 final size:26
Alignment explanation
Indices: 1699113--1699164 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1699103 ATATATTCTT
*
1699113 ATTTTTTATTGTTAATCTTAACTATC
1 ATTTTCTATTGTTAATCTTAACTATC
1699139 ATTTTCTATTGTTAATCTTAACTATC
1 ATTTTCTATTGTTAATCTTAACTATC
1699165 TCTTTTCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.13, G:0.04, T:0.56
Consensus pattern (26 bp):
ATTTTCTATTGTTAATCTTAACTATC
Found at i:1701188 original size:12 final size:12
Alignment explanation
Indices: 1701171--1701203 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1701161 AACATACGAA
1701171 GAGAAGCATAAG
1 GAGAAGCATAAG
1701183 GAGAAGCATAAG
1 GAGAAGCATAAG
*
1701195 AAGAAGCAT
1 GAGAAGCAT
1701204 GAGTTTACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.52, C:0.09, G:0.30, T:0.09
Consensus pattern (12 bp):
GAGAAGCATAAG
Found at i:1707492 original size:2 final size:2
Alignment explanation
Indices: 1707485--1707509 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1707475 TTTTAATGTG
1707485 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 T
1707510 TTATTTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1714732 original size:11 final size:11
Alignment explanation
Indices: 1714716--1714740 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1714706 ATATAACCCT
1714716 CTATTTATAGG
1 CTATTTATAGG
1714727 CTATTTATAGG
1 CTATTTATAGG
1714738 CTA
1 CTA
1714741 GAAATAGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (11 bp):
CTATTTATAGG
Found at i:1715183 original size:6 final size:6
Alignment explanation
Indices: 1715172--1715214 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
1715162 GACACGTATT
1715172 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1715215 GTCGAGACGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1716468 original size:14 final size:14
Alignment explanation
Indices: 1716449--1716504 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
1716439 CGTTTGTGAA
1716449 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1716463 CGTTCGGTTA--TT
1 CGTTCGGTTATGTT
**
1716475 --TTCATTTATGTT
1 CGTTCGGTTATGTT
*
1716487 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
1716501 CGTT
1 CGTT
1716505 TATGTTCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 6 0.18
12 4 0.12
14 24 0.71
ACGTcount: A:0.11, C:0.14, G:0.21, T:0.54
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:1716483 original size:24 final size:24
Alignment explanation
Indices: 1716456--1716524 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
1716446 GAACGTTCGG
* *
1716456 TTATGTTCGTTCGGTTATTTTCAT
1 TTATGTTCGTTCGATTATGTTCAT
*
1716480 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTCAT
*
1716504 TTATGTTCTTTC-ATTTATGTT
1 TTATGTTCGTTCGA-TTATGTT
1716525 TAACCCAATC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.03
24 39 0.98
ACGTcount: A:0.13, C:0.12, G:0.16, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTCAT
Found at i:1717531 original size:16 final size:16
Alignment explanation
Indices: 1717510--1717557 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
1717500 TCCAACGTTG
1717510 ATGTTCGTGTTCATTT
1 ATGTTCGTGTTCATTT
* *
1717526 ATGTTCATGTTCGTTT
1 ATGTTCGTGTTCATTT
1717542 ATGTTCGT-TT-ATTT
1 ATGTTCGTGTTCATTT
1717556 AT
1 AT
1717558 TAAATGAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 5 0.18
15 2 0.07
16 21 0.75
ACGTcount: A:0.15, C:0.10, G:0.17, T:0.58
Consensus pattern (16 bp):
ATGTTCGTGTTCATTT
Found at i:1717640 original size:16 final size:16
Alignment explanation
Indices: 1717619--1717651 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1717609 AAAAAATTTT
1717619 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1717635 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1717651 T
1 T
1717652 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1719436 original size:6 final size:6
Alignment explanation
Indices: 1719425--1719456 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1719415 CTCACTGTCC
1719425 TCACCA TCACCA TCACCA TCACCA TCACCA TC
1 TCACCA TCACCA TCACCA TCACCA TCACCA TC
1719457 CCAAACCCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.50, G:0.00, T:0.19
Consensus pattern (6 bp):
TCACCA
Found at i:1721886 original size:32 final size:32
Alignment explanation
Indices: 1721845--1721909 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1721835 TATAAGCTTC
*
1721845 ACCTGAATTTGTAATGTTTTATGTATGCTTTT
1 ACCTGAATTTATAATGTTTTATGTATGCTTTT
1721877 ACCTGAATTTATAATGTTTTATGTATGCTTTT
1 ACCTGAATTTATAATGTTTTATGTATGCTTTT
1721909 A
1 A
1721910 ACGTTTTACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.52
Consensus pattern (32 bp):
ACCTGAATTTATAATGTTTTATGTATGCTTTT
Found at i:1722757 original size:19 final size:20
Alignment explanation
Indices: 1722729--1722773 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1722719 TTTGCATTAT
* * *
1722729 AATATTATTTAATA-TATCA
1 AATATAATTTAAAATTATAA
1722748 AATATAATTTAAAATTATAA
1 AATATAATTTAAAATTATAA
1722768 AATATA
1 AATATA
1722774 TTCATAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AATATAATTTAAAATTATAA
Found at i:1725411 original size:34 final size:34
Alignment explanation
Indices: 1725368--1725438 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
1725358 GATAGCACAC
* * *
1725368 AGGGTCGAGGCCTGTGCACAACGAGGGTGCACCG
1 AGGGTCGAGGCCCGTACACAACGAGAGTGCACCG
* *
1725402 AGGGTCGAGGCCCGTACACACCGATAGTGCACCG
1 AGGGTCGAGGCCCGTACACAACGAGAGTGCACCG
1725436 AGG
1 AGG
1725439 AATGAGGCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.23, C:0.28, G:0.38, T:0.11
Consensus pattern (34 bp):
AGGGTCGAGGCCCGTACACAACGAGAGTGCACCG
Found at i:1727694 original size:14 final size:15
Alignment explanation
Indices: 1727670--1727699 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1727660 TTTTCCGAAT
1727670 ATTATAAATAAATAA
1 ATTATAAATAAATAA
1727685 ATTA-AAATAAATAA
1 ATTATAAATAAATAA
1727699 A
1 A
1727700 CATATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTATAAATAAATAA
Found at i:1728159 original size:5 final size:4
Alignment explanation
Indices: 1728137--1728221 Score: 64
Period size: 4 Copynumber: 19.8 Consensus size: 4
1728127 ATACCCATTC
* * *
1728137 AAAT AAAT AAAT AAAT AAAAT AAAAT AATT AAAT AAAT AAAT TATT CAAAAT
1 AAAT AAAT AAAT AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT AAAT --AAAT
*
1728189 AATT AAA- AAATT CAAAGT AAAT AAAT AAAT AAA
1 AAAT AAAT AAA-T -AAA-T AAAT AAAT AAAT AAA
1728222 AATTACTGCC
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
3 3 0.05
4 45 0.68
5 12 0.18
6 6 0.09
ACGTcount: A:0.69, C:0.02, G:0.01, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:1728176 original size:26 final size:26
Alignment explanation
Indices: 1728140--1728199 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
1728130 CCCATTCAAA
1728140 TAAATAAATAAATAAAAT-AAAATAAT
1 TAAATAAATAAAT-AAATCAAAATAAT
* *
1728166 TAAATAAATAAATTATTCAAAATAAT
1 TAAATAAATAAATAAATCAAAATAAT
1728192 TAAA-AAAT
1 TAAATAAAT
1728200 TCAAAGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 6 0.19
26 25 0.81
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (26 bp):
TAAATAAATAAATAAATCAAAATAAT
Found at i:1728188 original size:18 final size:18
Alignment explanation
Indices: 1728133--1728216 Score: 74
Period size: 18 Copynumber: 5.1 Consensus size: 18
1728123 GTTCATACCC
1728133 ATTC-AAATAAATAAATA
1 ATTCAAAATAAATAAATA
*
1728150 AAT-AAAAT--A-AAATA
1 ATTCAAAATAAATAAATA
*
1728164 ATT--AAATAAATAAATT
1 ATTCAAAATAAATAAATA
* *
1728180 ATTCAAAATAATTAAAAA
1 ATTCAAAATAAATAAATA
*
1728198 ATTCAAAGTAAATAAATA
1 ATTCAAAATAAATAAATA
1728216 A
1 A
1728217 ATAAAAATTA
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
13 4 0.08
14 7 0.13
15 2 0.04
16 7 0.13
17 6 0.12
18 26 0.50
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.29
Consensus pattern (18 bp):
ATTCAAAATAAATAAATA
Found at i:1730122 original size:27 final size:27
Alignment explanation
Indices: 1730055--1730128 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 27
1730045 TGTTTAGAGG
* * *
1730055 TTTCTTTTGTT-AAAATGATTTAAGGA
1 TTTCTTCTGTTAAAAATGGTATAAGGA
* *
1730081 TTT-TTCTATTAAAAATGGTATAATGA
1 TTTCTTCTGTTAAAAATGGTATAAGGA
1730107 TTTCTTCTGTTAAAAA-GGTATA
1 TTTCTTCTGTTAAAAATGGTATA
1730129 GTATATATGA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 5 0.12
26 24 0.60
27 11 0.28
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (27 bp):
TTTCTTCTGTTAAAAATGGTATAAGGA
Found at i:1730166 original size:25 final size:25
Alignment explanation
Indices: 1730132--1730215 Score: 132
Period size: 25 Copynumber: 3.4 Consensus size: 25
1730122 AGGTATAGTA
* *
1730132 TATATGAATAGATTTATTTATTGAT
1 TATATGAATAGATTTGTTTACTGAT
* *
1730157 TATATGAATAAATTTGTTTACGGAT
1 TATATGAATAGATTTGTTTACTGAT
1730182 TATATGAATAGATTTGTTTACTGAT
1 TATATGAATAGATTTGTTTACTGAT
1730207 TATATGAAT
1 TATATGAAT
1730216 TTGATCTATT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (25 bp):
TATATGAATAGATTTGTTTACTGAT
Found at i:1730272 original size:28 final size:29
Alignment explanation
Indices: 1730234--1730303 Score: 90
Period size: 27 Copynumber: 2.5 Consensus size: 29
1730224 TTAAAACCCT
*
1730234 AAATTTGTTTATGAGGTTTCTTCTGTTAA
1 AAATTGGTTTATGAGGTTTCTTCTGTTAA
* *
1730263 AAA-TGGTTTA-GGGGTTTCTTTTGTTAA
1 AAATTGGTTTATGAGGTTTCTTCTGTTAA
*
1730290 AAATTTGTTTATGA
1 AAATTGGTTTATGA
1730304 TAATATATGT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 18 0.53
28 12 0.35
29 4 0.12
ACGTcount: A:0.26, C:0.04, G:0.20, T:0.50
Consensus pattern (29 bp):
AAATTGGTTTATGAGGTTTCTTCTGTTAA
Found at i:1732590 original size:23 final size:23
Alignment explanation
Indices: 1732564--1732608 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1732554 TGCTTATATG
* *
1732564 TTCTTTTTGTTATACTAATGTTT
1 TTCTTTATGTTATACAAATGTTT
1732587 TTCTTTATGTTATACAAATGTT
1 TTCTTTATGTTATACAAATGTT
1732609 GGCCCATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.60
Consensus pattern (23 bp):
TTCTTTATGTTATACAAATGTTT
Found at i:1735808 original size:2 final size:2
Alignment explanation
Indices: 1735801--1735837 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1735791 TACCAGTAAG
1735801 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1735838 AGTTGCATGA
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1739060 original size:21 final size:20
Alignment explanation
Indices: 1738974--1739131 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
1738964 AAATGACCAA
**
1738974 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1738993 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1739013 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1739033 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1739054 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* * **
1739075 CAAATTCACATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1739095 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
1739116 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1739132 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1739160 original size:20 final size:20
Alignment explanation
Indices: 1739099--1739327 Score: 221
Period size: 20 Copynumber: 11.4 Consensus size: 20
1739089 GATTTTCAAG
* ** *
1739099 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1739119 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1739139 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
1739159 AACCGCAACGTGTATTCGTA
1 AATCGCAACGCGTATCCGTA
*
1739179 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1739199 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1739219 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1739239 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1739259 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1739279 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1739299 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1739319 AATCACAAC
1 AATCGCAAC
1739328 ACTGAAATTT
Statistics
Matches: 173, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 169 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1740059 original size:24 final size:24
Alignment explanation
Indices: 1740020--1740066 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1740010 AAATTTGGTC
1740020 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1740044 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1740067 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1740258 original size:12 final size:12
Alignment explanation
Indices: 1740241--1740265 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1740231 ATATAATCCT
1740241 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1740253 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1740265 G
1 G
1740266 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1742657 original size:72 final size:72
Alignment explanation
Indices: 1742564--1742797 Score: 297
Period size: 72 Copynumber: 3.3 Consensus size: 72
1742554 GCAACGAGAG
1742564 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1742629 AAATGAA
66 AAATGAA
* *
1742636 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
1742700 GAAATGAA
65 GAAATGAA
* * * * *
1742708 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCAA--
1 AATCGCAATGCGA-AAT-GAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATG
*
1742768 CG--A-GAG
64 CGAAATGAA
1742774 AATCGCAATGCGGAAATGAAAATC
1 AATCGCAATGC-GAAATGAAAATC
1742798 GCAATGCGAA
Statistics
Matches: 142, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
65 1 0.01
66 17 0.12
67 3 0.02
69 2 0.01
71 17 0.12
72 92 0.65
73 9 0.06
74 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:1742685 original size:53 final size:52
Alignment explanation
Indices: 1742550--1742819 Score: 415
Period size: 53 Copynumber: 5.1 Consensus size: 52
1742540 CGGAAATTAC
*
1742550 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
1742597 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1742655 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
1742708 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1742760 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
1742813 AATCGCA
1 AATCGCA
1742820 TTGCGATTCT
Statistics
Matches: 207, Mismatches: 3, Indels: 20
0.90 0.01 0.09
Matches are distributed among these distances:
47 8 0.04
49 1 0.00
50 1 0.00
52 66 0.32
53 115 0.56
55 2 0.01
56 1 0.00
58 13 0.06
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1742825 original size:72 final size:68
Alignment explanation
Indices: 1742531--1742824 Score: 276
Period size: 72 Copynumber: 4.2 Consensus size: 68
1742521 GCATTTGACT
** * * *
1742531 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAC-ATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGATG
1742595 AAA
66 AAA
*
1742598 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA
*
1742663 CGA-GAGA
61 CGATGAAA
* * * * *
1742670 ATCGCAATGCGGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAA--
1742732 CGAAATGAAA
61 CG--ATGAAA
1742742 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAA--CG
1742806 AAATGAAA
63 --ATGAAA
*
1742814 ATCGCATTGCG
1 ATCGCAATGCG
1742825 ATTCTCTCGT
Statistics
Matches: 189, Mismatches: 19, Indels: 32
0.79 0.08 0.13
Matches are distributed among these distances:
65 7 0.04
66 7 0.04
67 33 0.17
69 4 0.02
70 1 0.01
71 21 0.11
72 107 0.57
73 4 0.02
74 5 0.03
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.14
Consensus pattern (68 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGATG
AAA
Found at i:1742839 original size:105 final size:105
Alignment explanation
Indices: 1742550--1742819 Score: 426
Period size: 105 Copynumber: 2.6 Consensus size: 105
1742540 CGGAAATTAC
*
1742550 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--C-
*
1742609 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
63 G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1742655 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
1742720 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1742760 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1742820 TTGCGATTCT
Statistics
Matches: 157, Mismatches: 2, Indels: 12
0.92 0.01 0.07
Matches are distributed among these distances:
105 125 0.80
106 16 0.10
108 2 0.01
109 1 0.01
111 13 0.08
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (105 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1742859 original size:53 final size:52
Alignment explanation
Indices: 1742796--1742911 Score: 151
Period size: 53 Copynumber: 2.2 Consensus size: 52
1742786 GAAATGAAAA
* *
1742796 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTACGATTCTCTCGTTGCGATTTTCATT
** ** **
1742848 TCCGCATTGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTACGATTCTCTCGTTGCGATTTTCATT
1742901 TCGCATTGCGA
1 TCGCATTGCGA
1742912 TTTTCATTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 11 0.20
53 44 0.80
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTACGATTCTCTCGTTGCGATTTTCATT
Found at i:1742939 original size:19 final size:19
Alignment explanation
Indices: 1742834--1742931 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
1742824 GATTCTCTCG
1742834 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1742854 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
1742873 TTACGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1742887 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1742906 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1742925 TTGCGAT
1 TTGCGAT
1742932 AGTCATTTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 5 0.07
16 7 0.10
17 7 0.10
19 35 0.51
20 15 0.22
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Done.