Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 12 of 193
Found at i:4328940 original size:12 final size:11
Alignment explanation
Indices: 4328904--4328946 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
4328894 AATGTATTTA
*
4328904 AATTT-AAATA
1 AATTTAAAATT
4328914 AATTTAAAATT
1 AATTTAAAATT
*
4328925 AATTTCAAACTT
1 AATTT-AAAATT
4328937 AATTTAAAAT
1 AATTTAAAAT
4328947 CCAAGTTGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 10 0.36
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:4330065 original size:201 final size:200
Alignment explanation
Indices: 4329291--4330220 Score: 1590
Period size: 200 Copynumber: 4.6 Consensus size: 200
4329281 GGTCTTCTTC
* * * *
4329291 CCTTTATATTGCTTCGACTTGCTTCTCAGTGTCTCATCTGGAAGTTGGGTTCGAAGATTTGCTCG
1 CCTTTTTATTGCTTCGATTTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCG
*
4329356 TGTTGAGCGCTAAGTTGATGTTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTT
66 TGTTGAGCGCTAAGTTGGTGTTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTT
4329421 GATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTGTCTCATCAGGAA
131 GATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTGTCTCATCAGGAA
4329486 GCTAA
196 GCTAA
* * *
4329491 CCTTTTTATTGCTTTGATTTGCTTCTTAGTGTCTCATCAGGAAGCTGGATTCGAAGATTTGCTCG
1 CCTTTTTATTGCTTCGATTTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCG
**
4329556 TGTAAAGCGCTAAGTTGGTGTTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTT
66 TGTTGAGCGCTAAGTTGGTGTTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTT
* *
4329621 GATTCGCTTCTCTGGATCTCCTCAAGAAGACGAATCTGGTCTACTTCTCTGTGTCTCATCAGGAA
131 GATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTGTCTCATCAGGAA
4329686 GCTAA
196 GCTAA
* *
4329691 CCTTTTTATTGCTTTGATTTGCTTCTCAGTGTCTCATCAGGAAGCTGGATTCGAAGATTTGCTCG
1 CCTTTTTATTGCTTCGATTTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCG
* *
4329756 TGTTGAGCGCTAAGTTGGTGTTCTTCTCTGTATCTCATCAAGAAGATGATCGCCTCGCTTGTTTT
66 TGTTGAGCGCTAAGTTGGTGTTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTT
4329821 GATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTGTCTCATCAGGAA
131 GATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTGTCTCATCAGGAA
4329886 GCTAA
196 GCTAA
*
4329891 CCTTTTTATTGCTTCGATTTGCTTCTCAATGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCG
1 CCTTTTTATTGCTTCGATTTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCG
* * * * *
4329956 TGTTTGAGCGCTGAGTTGATGTTCTTCTCTGTATCTCATCAAGAAGTTGAACGCCTCGCTTGTTT
66 TG-TTGAGCGCTAAGTTGGTGTTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTT
* *
4330021 TGATTCGCTTCTCTGGATTTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTGTCTCATTAGGA
130 TGATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTGTCTCATCAGGA
4330086 AGCTAA
195 AGCTAA
* *
4330092 CCTTTTTATTGCTTCGACTTGCTTCTCGGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCG
1 CCTTTTTATTGCTTCGATTTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCG
* *
4330157 TGTTTGAGCGCTGATTTGGTGTTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTT
66 TG-TTGAGCGCTAAGTTGGTGTTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTT
4330221 GAACTACTCC
Statistics
Matches: 693, Mismatches: 36, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
200 445 0.64
201 248 0.36
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.37
Consensus pattern (200 bp):
CCTTTTTATTGCTTCGATTTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCG
TGTTGAGCGCTAAGTTGGTGTTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTT
GATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTGTCTCATCAGGAA
GCTAA
Found at i:4342234 original size:29 final size:28
Alignment explanation
Indices: 4342198--4342508 Score: 151
Period size: 28 Copynumber: 10.7 Consensus size: 28
4342188 TTGACTTTCG
* *
4342198 AGGGTAAAAATGGAATTTTGGTGAAATC
1 AGGGTTAAAATGGAATTTTGGTGAAATT
* *
4342226 AGGGTTAAAATGGGATTTT-G-AAAAGTTT
1 AGGGTTAAAATGGAATTTTGGTGAAA--TT
* *
4342254 AGAGCTAAAATGGTAATTTTTGGTGAAATT
1 AGGGTTAAAATGG-AA-TTTTGGTGAAATT
*
4342284 AGGGTTAAAAATAGAATTTT-G-GAAAGTTT
1 AGGGTT-AAAATGGAATTTTGGTGAAA--TT
*
4342313 AGGAG-TAAAATGGTAATTTTTGGTGAAA-C
1 AGG-GTTAAAATGG-AA-TTTTGGTGAAATT
* *
4342342 CGAGGTCAAAAATGGAATTTT-G-GAAAGTTT
1 AG-GGT-TAAAATGGAATTTTGGTGAAA--TT
* *
4342372 AGGGGTAAAATGGTAATTTTTGGTGAAATC
1 AGGGTTAAAATGG-AA-TTTTGGTGAAATT
* * *
4342402 GGGGTCAAAAATGGAATTTTGG-GAAGTTT
1 AGGGT-TAAAATGGAATTTTGGTGAA-ATT
*
4342431 AGGGGTAAAATGGTAATTTT--TGAAAGTTTT
1 AGGGTTAAAATGG-AATTTTGGTGAAA---TT
*
4342461 AGGGTTAAAAATGGAATTTTGG-GAAGTTT
1 AGGGTT-AAAATGGAATTTTGGTGAA-ATT
* *
4342490 AGGGGTAAAATGGTATTTT
1 AGGGTTAAAATGGAATTTT
4342509 TTTATGAAAT
Statistics
Matches: 215, Mismatches: 33, Indels: 70
0.68 0.10 0.22
Matches are distributed among these distances:
26 3 0.01
27 9 0.04
28 69 0.32
29 46 0.21
30 44 0.20
31 33 0.15
32 11 0.05
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (28 bp):
AGGGTTAAAATGGAATTTTGGTGAAATT
Found at i:4342322 original size:59 final size:59
Alignment explanation
Indices: 4342199--4342551 Score: 420
Period size: 59 Copynumber: 6.1 Consensus size: 59
4342189 TGACTTTCGA
* *
4342199 GGGTAAAAATGG-AA-TTTTGGTGAAATCAGGGTT-AAAATGGGATTTTGAAAAGTTTAG
1 GGGT-AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTAG
* * * *
4342256 AGCTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATAGAATTTTGGAAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTAG
* * *
4342315 GAGTAAAATGGTAATTTTTGGTGAAA-CCGAGGTCAAAAATGGAATTTTGGAAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGTGAAATCAG-GGTTAAAAATGGAATTTTGGAAAGTTTAG
* * *
4342374 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGGAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTAG
* *
4342433 GGGTAAAATGGTAA-TTTT--TGAAAGTTTTAGGGTTAAAAATGGAATTTTGGGAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGTGAAA---TCAGGGTTAAAAATGGAATTTTGGAAAGTTTAG
* ** *
4342492 GGGTAAAATGGTATTTTTTTATGAAATC-GATGTT-AAAATGGAATTTTGGAAAGTTT-G
1 GGGTAAAATGGTAATTTTTGGTGAAATCAG-GGTTAAAAATGGAATTTTGGAAAGTTTAG
4342549 GGG
1 GGG
4342552 ACTAGAGAGC
Statistics
Matches: 261, Mismatches: 23, Indels: 24
0.85 0.07 0.08
Matches are distributed among these distances:
56 12 0.05
57 8 0.03
58 45 0.17
59 185 0.71
60 6 0.02
62 5 0.02
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.34
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTAG
Found at i:4344500 original size:6 final size:6
Alignment explanation
Indices: 4344489--4344551 Score: 55
Period size: 6 Copynumber: 11.2 Consensus size: 6
4344479 TTTCAAATGT
* *
4344489 ATTTAA ATTTAA A-ATAA ATTTAA ATTTAA A--TAA ATTTAA AATT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
4344533 ATTTCAA ACTT-A ATTTAA A
1 ATTT-AA ATTTAA ATTTAA A
4344552 ATCCAAGTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
4 4 0.09
5 12 0.27
6 25 0.56
7 4 0.09
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:4344513 original size:27 final size:28
Alignment explanation
Indices: 4344478--4344540 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
4344468 GTTTAAAGTT
**
4344478 ATTTCAAATGTATTTAAATTTAAAATAA
1 ATTTCAAATGTAAATAAATTTAAAATAA
* *
4344506 ATTT-AAATTTAAATAAATTTAAAATTA
1 ATTTCAAATGTAAATAAATTTAAAATAA
4344533 ATTTCAAA
1 ATTTCAAA
4344541 CTTAATTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 23 0.77
28 7 0.23
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (28 bp):
ATTTCAAATGTAAATAAATTTAAAATAA
Found at i:4344521 original size:16 final size:16
Alignment explanation
Indices: 4344489--4344533 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
4344479 TTTCAAATGT
4344489 ATTTAAATTTAAAATAA
1 ATTTAAATTT-AAATAA
4344506 ATTTAAATTTAAATAA
1 ATTTAAATTTAAATAA
*
4344522 ATTTAAAATTAA
1 ATTTAAATTTAA
4344534 TTTCAAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:4344530 original size:23 final size:24
Alignment explanation
Indices: 4344504--4344553 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
4344494 AATTTAAAAT
4344504 AAATTTAAATTT-AAA-TAAATTTA
1 AAATTT-AATTTCAAACTAAATTTA
*
4344527 AAA-TTAATTTCAAACTTAATTTA
1 AAATTTAATTTCAAACTAAATTTA
4344550 AAAT
1 AAAT
4344554 CCAAGTTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 5 0.22
22 5 0.22
23 13 0.57
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATTTAATTTCAAACTAAATTTA
Found at i:4344547 original size:12 final size:11
Alignment explanation
Indices: 4344511--4344553 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
4344501 AATAAATTTA
*
4344511 AATTT-AAATA
1 AATTTAAAATT
4344521 AATTTAAAATT
1 AATTTAAAATT
*
4344532 AATTTCAAACTT
1 AATTT-AAAATT
4344544 AATTTAAAAT
1 AATTTAAAAT
4344554 CCAAGTTGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 10 0.36
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:4345507 original size:54 final size:54
Alignment explanation
Indices: 4345443--4345550 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
4345433 CTAAAACGCT
4345443 CATCTAAATACACCCCAAGGGTTTGTCTAACAAAAGAGCAAAGTTCAAGAGAAA
1 CATCTAAATACACCCCAAGGGTTTGTCTAACAAAAGAGCAAAGTTCAAGAGAAA
4345497 CATCTAAATACACCCCAAGGGTTTGTCTAACAAAAGAGCAAAGTTCAAGAGAAA
1 CATCTAAATACACCCCAAGGGTTTGTCTAACAAAAGAGCAAAGTTCAAGAGAAA
4345551 AATCAATTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.19
Consensus pattern (54 bp):
CATCTAAATACACCCCAAGGGTTTGTCTAACAAAAGAGCAAAGTTCAAGAGAAA
Found at i:4348019 original size:30 final size:30
Alignment explanation
Indices: 4347985--4348062 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
4347975 AATAGTTTAT
*
4347985 ATTTTTA-TAATTTTTAAAATATTAAATTAA
1 ATTTTTATTAA-TTTTAAAAAATTAAATTAA
*
4348015 ATTTTTATTAATTTTAAAAAATTAATTTAA
1 ATTTTTATTAATTTTAAAAAATTAAATTAA
* **
4348045 AATTTTAAGAATTTTAAA
1 ATTTTTATTAATTTTAAA
4348063 TGAAAAATCC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 39 0.93
31 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
ATTTTTATTAATTTTAAAAAATTAAATTAA
Found at i:4354390 original size:18 final size:18
Alignment explanation
Indices: 4354367--4354411 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
4354357 TAATTTTATA
4354367 TGGATTCTATTTTACCAT
1 TGGATTCTATTTTACCAT
* **
4354385 TGGATTCTGTTTTTTCAT
1 TGGATTCTATTTTACCAT
4354403 TGGATTCTA
1 TGGATTCTA
4354412 AATTTCCCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.13, G:0.16, T:0.53
Consensus pattern (18 bp):
TGGATTCTATTTTACCAT
Found at i:4357207 original size:58 final size:58
Alignment explanation
Indices: 4357141--4357568 Score: 636
Period size: 58 Copynumber: 7.4 Consensus size: 58
4357131 TGGATACCCG
*
4357141 GGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
* * * *
4357198 GGGGATAAAATGGTAATTTTTGGTGGAATCAGGGTTAAAAATGGAATTTTAG-AAGTTTA
1 GGGG-TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTC
*
4357257 GGGGTAAAACGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGG-AAGTTC
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
* *
4357314 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTC
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
4357373 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTGG-AAGTTC
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
* *
4357430 AGGGGTAAAATGGTAATTTTTAGTGAAATCGAGGTT-AAAATGGAATTTTGGAAAGTTC
1 -GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
* *
4357488 GGGGGTAAAATGGTAATTTTTGATGAAATCGAGGTT-AAAATGGAATTTTGGAAAGTTC
1 -GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
4357546 AGGGGTAAAATGGTAATTTTTGG
1 -GGGGTAAAATGGTAATTTTTGG
4357569 ACTGTTTGGG
Statistics
Matches: 343, Mismatches: 21, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
57 59 0.17
58 205 0.60
59 79 0.23
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
Found at i:4357928 original size:162 final size:161
Alignment explanation
Indices: 4357657--4357974 Score: 557
Period size: 162 Copynumber: 2.0 Consensus size: 161
4357647 GATTAAATTG
* * *
4357657 TAAATCTTGAAAACTTTTTGGGCCAATTTCGTAATTAAATAAAAGTTGATTTAGGATTAAATTAA
1 TAAACCTTGAAAAATTATTGGGCCAATTTCGTAATTAAATAAAAGTTGATTTAGGATTAAATTAA
4357722 AACAAATTAAAAATAAAAAGGACTAAATGCATAAATAAGCCAAAAAGTGACATGTGGCAGCCTCT
66 AACAAATTAAAAATAAAAAGGACTAAATGCATAAATAAGCCAAAAAGTGACATGTGGCAGCCTCT
4357787 GGTACAGTCAAACAGTCAAAGGACTAGTTTA
131 GGTACAGTCAAACAGTCAAAGGACTAGTTTA
*
4357818 TAAACCTTGAAAAATTATTGGGCCAATTTCGTAATTAAA-ATAAAGTTGATTTGGGGATTAAATT
1 TAAACCTTGAAAAATTATTGGGCCAATTTCGTAATTAAATA-AAAGTTGATTT-AGGATTAAATT
*
4357882 AAAACAAATTAAAAATAAAAATGACTAAATGCATAAATAAGCCAAAAAGTGACATGTGGCAGCCT
64 AAAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAAGCCAAAAAGTGACATGTGGCAGCCT
*
4357947 CTGGTATAGTCAAACAGTCAAAGGACTA
129 CTGGTACAGTCAAACAGTCAAAGGACTA
4357975 AATTGAAAGC
Statistics
Matches: 149, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
160 1 0.01
161 47 0.32
162 101 0.68
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (161 bp):
TAAACCTTGAAAAATTATTGGGCCAATTTCGTAATTAAATAAAAGTTGATTTAGGATTAAATTAA
AACAAATTAAAAATAAAAAGGACTAAATGCATAAATAAGCCAAAAAGTGACATGTGGCAGCCTCT
GGTACAGTCAAACAGTCAAAGGACTAGTTTA
Found at i:4359331 original size:6 final size:6
Alignment explanation
Indices: 4359311--4359395 Score: 81
Period size: 6 Copynumber: 15.0 Consensus size: 6
4359301 TAATATTATT
* *
4359311 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
4359356 -ATAAA TTTAAA TTTAAA -TAAAA TTTAAA ATTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
4359396 ATGAACAAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
4 2 0.03
5 16 0.25
6 45 0.71
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:4359343 original size:11 final size:11
Alignment explanation
Indices: 4359329--4359397 Score: 52
Period size: 11 Copynumber: 6.1 Consensus size: 11
4359319 TAATTAAATT
4359329 TAAATTTAAAA
1 TAAATTTAAAA
*
4359340 TAAATTTAAACT
1 TAAATTTAAA-A
* *
4359352 TAAA-ATAAATT
1 TAAATTTAAA-A
4359363 TAAATTT-AAA
1 TAAATTTAAAA
4359373 TAAAATTTAAAA
1 T-AAATTTAAAA
*
4359385 TTAATTTTAAAA
1 -TAAATTTAAAA
4359397 T
1 T
4359398 GAACAAAATC
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
10 1 0.02
11 28 0.60
12 17 0.36
13 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:4359345 original size:17 final size:17
Alignment explanation
Indices: 4359311--4359388 Score: 106
Period size: 17 Copynumber: 4.6 Consensus size: 17
4359301 TAATATTATT
*
4359311 TTTAAATTT-AATTAAA
1 TTTAAATTTAAAATAAA
4359327 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
4359344 TTTAAACTTAAAATAAA
1 TTTAAATTTAAAATAAA
4359361 TTTAAATTT-AAATAAAA
1 TTTAAATTTAAAAT-AAA
*
4359378 TTTAAAATTAA
1 TTTAAATTTAA
4359389 TTTTAAAATG
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
16 13 0.24
17 41 0.75
18 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:4374959 original size:121 final size:120
Alignment explanation
Indices: 4374787--4375018 Score: 374
Period size: 121 Copynumber: 1.9 Consensus size: 120
4374777 CCCCGATTCC
** * * *
4374787 CCCAAGTAATGTGGGTTCACAAACACATTTGACACGTTATTAGCAGCATGTTTCTTTCTATCCCC
1 CCCAAGTAACATGGATTCACAAACACATTTGACACATTATTAGCAACATGTTTCTTTCTATCCCC
4374852 ACCAACCAAGCAGGGGATTTTGAGATAAGTCAAAGCAACTACTGTTTGTTACCAT
66 ACCAACCAAGCAGGGGATTTTGAGATAAGTCAAAGCAACTACTGTTTGTTACCAT
* *
4374907 CCCAAGTAACATGGATTCACAAAATACATTTTACACATTATTAGCAACATGTTTCTTTCTATCCC
1 CCCAAGTAACATGGATTCAC-AAACACATTTGACACATTATTAGCAACATGTTTCTTTCTATCCC
* *
4374972 CACCAACCAAGCAGGGGATTTTGGGATAGGTCAAAGCAACTACTGTT
65 CACCAACCAAGCAGGGGATTTTGAGATAAGTCAAAGCAACTACTGTT
4375019 ACTATCATGA
Statistics
Matches: 102, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
120 17 0.17
121 85 0.83
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.29
Consensus pattern (120 bp):
CCCAAGTAACATGGATTCACAAACACATTTGACACATTATTAGCAACATGTTTCTTTCTATCCCC
ACCAACCAAGCAGGGGATTTTGAGATAAGTCAAAGCAACTACTGTTTGTTACCAT
Found at i:4377213 original size:32 final size:32
Alignment explanation
Indices: 4377151--4377213 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
4377141 GATAGGGCTA
*
4377151 CAATTAAAGAAGGTAGAAATTTAAAAGTTAAT
1 CAATTAAAGAAGGTACAAATTTAAAAGTTAAT
4377183 CAATTAAA-AA-GTACAAATTTATAAATGTTAA
1 CAATTAAAGAAGGTACAAATTTA-AAA-GTTAA
4377214 CAAACCATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 10 0.36
31 5 0.18
32 13 0.46
ACGTcount: A:0.54, C:0.05, G:0.11, T:0.30
Consensus pattern (32 bp):
CAATTAAAGAAGGTACAAATTTAAAAGTTAAT
Found at i:4381662 original size:24 final size:25
Alignment explanation
Indices: 4381635--4381693 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 25
4381625 AAAATATGTG
*
4381635 TATTGTTTTTATTTA-ATAATTTTA
1 TATTGTTTTTATTTATAAAATTTTA
*
4381659 TATTTTTTTTATTTATTAAAATTTTA
1 TATTGTTTTTATTTA-TAAAATTTTA
*
4381685 TATAGTTTT
1 TATTGTTTT
4381694 ATGTGTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 14 0.48
26 15 0.52
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (25 bp):
TATTGTTTTTATTTATAAAATTTTA
Found at i:4381687 original size:26 final size:24
Alignment explanation
Indices: 4381616--4381693 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 24
4381606 ATTTTTGTAA
* * *
4381616 TTTTATTAAAAAATATGTGTATTGT
1 TTTTATTTAAAAAT-TTTATATTGT
* *
4381641 TTTTATTTAATAATTTTATATTTT
1 TTTTATTTAAAAATTTTATATTGT
*
4381665 TTTTATTTATTAAAATTTTATATAGT
1 TTTTATTTA--AAAATTTTATATTGT
4381691 TTT
1 TTT
4381694 ATGTGTTTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
24 16 0.37
25 12 0.28
26 15 0.35
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (24 bp):
TTTTATTTAAAAATTTTATATTGT
Found at i:4382434 original size:20 final size:21
Alignment explanation
Indices: 4382394--4382434 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4382384 GACTGTTTCT
4382394 AATTGTTATATTAATAACAAA
1 AATTGTTATATTAATAACAAA
4382415 AATTGTT-TATATAA-AACAAA
1 AATTGTTATAT-TAATAACAAA
4382435 TGAATGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (21 bp):
AATTGTTATATTAATAACAAA
Found at i:4393736 original size:19 final size:19
Alignment explanation
Indices: 4393712--4393755 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
4393702 TTAGAAATGA
*
4393712 TTTTTATCATAA-AAATAAT
1 TTTTTATAATAATAAAT-AT
*
4393731 TTTTTATAATAATTAATAT
1 TTTTTATAATAATAAATAT
4393750 TTTTTA
1 TTTTTA
4393756 AAAATATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTTATAATAATAAATAT
Found at i:4396719 original size:61 final size:61
Alignment explanation
Indices: 4396597--4396874 Score: 346
Period size: 62 Copynumber: 4.5 Consensus size: 61
4396587 TCTTTTTGCA
* *** * * *
4396597 TTTTTGGGTGTTGGCCATTGCATGGCCGACGCCTCCTGTT-T-GAGAAAAAAAATTCAAAAT
1 TTTTTTGGTGTTGGCCATCAAATGGCCGACACCTCCTTTTCTCGAGAAAAAAATTTC-AAAT
* * *
4396657 TTTTTTTGTGTTGGTCATCAAATAGCCGACACCTCCTTTTCTCGAGAAAAAAATTTCAAAT
1 TTTTTTGGTGTTGGCCATCAAATGGCCGACACCTCCTTTTCTCGAGAAAAAAATTTCAAAT
* *
4396718 TTTTTTTGTGTTGGCCATCAAATGGCCGACACCTCCCTTTTCTCGAG-AAAAAATCTTTAAAT
1 TTTTTTGGTGTTGGCCATCAAATGGCCGACACCT-CCTTTTCTCGAGAAAAAAAT-TTCAAAT
* * *
4396780 TTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTTGGATAAAAAAATTTCAAAT
1 TTTTTTGGTGTTGGCCATCAAATGGCCGACACCTCCTTTTC-TCGAGAAAAAAATTTCAAAT
* *
4396842 TTTTTTGGTATTGGCCATCAAATGGCTGACACC
1 TTTTTTGGTGTTGGCCATCAAATGGCCGACACC
4396875 AACTTCTCCT
Statistics
Matches: 192, Mismatches: 20, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
60 31 0.16
61 51 0.27
62 103 0.54
63 7 0.04
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.36
Consensus pattern (61 bp):
TTTTTTGGTGTTGGCCATCAAATGGCCGACACCTCCTTTTCTCGAGAAAAAAATTTCAAAT
Found at i:4397752 original size:30 final size:30
Alignment explanation
Indices: 4397692--4397783 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 30
4397682 TAATAATTAG
* * ** *
4397692 AATATACAGGAAATTAGAAAGAAAAATTAA
1 AATATACAAGAAATTCGAAATTAAATTTAA
4397722 AATATACAAGAAATTCGAAATTAAATTTAA
1 AATATACAAGAAATTCGAAATTAAATTTAA
*
4397752 AATA-AAAACGAAATTAC-AAATTAAATTTAA
1 AATATACAA-GAAATT-CGAAATTAAATTTAA
4397782 AA
1 AA
4397784 AGTAAAGGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
29 3 0.06
30 50 0.93
31 1 0.02
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.25
Consensus pattern (30 bp):
AATATACAAGAAATTCGAAATTAAATTTAA
Found at i:4398325 original size:24 final size:24
Alignment explanation
Indices: 4398289--4398335 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
4398279 ATCGGCCTTA
* *
4398289 TCTGCGGGGTCGTCTGCGGGCTCT
1 TCTGCGGGATCGTCCGCGGGCTCT
*
4398313 TCTGCGGGATCGTCCGCTGGCTC
1 TCTGCGGGATCGTCCGCGGGCTC
4398336 GTCATTGGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.02, C:0.32, G:0.38, T:0.28
Consensus pattern (24 bp):
TCTGCGGGATCGTCCGCGGGCTCT
Found at i:4399199 original size:14 final size:15
Alignment explanation
Indices: 4399167--4399199 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
4399157 TCTGAAAAAT
4399167 TAAAAAATAATTAGA
1 TAAAAAATAATTAGA
4399182 -AAAAAATAATTA-A
1 TAAAAAATAATTAGA
4399195 TAAAA
1 TAAAA
4399200 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.06
14 16 0.94
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
TAAAAAATAATTAGA
Found at i:4400348 original size:86 final size:86
Alignment explanation
Indices: 4400206--4400489 Score: 484
Period size: 86 Copynumber: 3.3 Consensus size: 86
4400196 TAAATTTAAA
4400206 ATATGATAAAAATTGT-A-AT-ATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAAT
1 ATATGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAAT
* * *
4400268 GTATTGTAAAATCCACACGTT
66 GTATTGTCAAATCAACACATT
4400289 ATATGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAAT
1 ATATGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAAT
4400354 GTATTGTCAAATCAACACATT
66 GTATTGTCAAATCAACACATT
*
4400375 ATATGATAAAAATTGTAATATAATAATAATAAAAATTTTATTTAAAGATATAAAATTAATAAATA
1 ATATGATAAAAATTGTAATATAATAATAAT--AATTTTTATTTAAAGATATAAAATTAATAAATA
4400440 ATGTATTGTCAAATCAACACATT
64 ATGTATTGTCAAATCAACACATT
4400463 ATATGATAAAAATTGTAATATCAATAA
1 ATATGATAAAAATTGTAATAT-AATAA
4400490 AATTTGATGG
Statistics
Matches: 191, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
83 16 0.08
84 1 0.01
85 2 0.01
86 91 0.48
88 76 0.40
89 5 0.03
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.37
Consensus pattern (86 bp):
ATATGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAAT
GTATTGTCAAATCAACACATT
Found at i:4400558 original size:55 final size:58
Alignment explanation
Indices: 4400491--4400605 Score: 164
Period size: 55 Copynumber: 2.0 Consensus size: 58
4400481 TATCAATAAA
* *
4400491 ATTTGATGGCCAACACCTAAAAA-TATAATTTTTT-TGA-GAAAAAGGGGTGTCGACC
1 ATTTGATGGCCAACACCAAAAAATTATAATTTTTTCTGACAAAAAAGGGGTGTCGACC
* * *
4400546 ATTTGATGGCCAACACCAAAAAATTTTATTTTTTTCTGACAAAAAAGGGGTGTCGGCC
1 ATTTGATGGCCAACACCAAAAAATTATAATTTTTTCTGACAAAAAAGGGGTGTCGACC
4400604 AT
1 AT
4400606 GCAATTTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
55 22 0.42
56 9 0.17
57 3 0.06
58 18 0.35
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (58 bp):
ATTTGATGGCCAACACCAAAAAATTATAATTTTTTCTGACAAAAAAGGGGTGTCGACC
Found at i:4403432 original size:59 final size:59
Alignment explanation
Indices: 4403330--4403590 Score: 249
Period size: 59 Copynumber: 4.4 Consensus size: 59
4403320 ACTTTTGATT
* ** * *
4403330 TTCGGGGGTAAAAAT-GTAA-TTTTGGGAAAATTTAGGGTTAAAAATGGGATTTT-TAAAG
1 TTCGGGGGT-AAAATGGTAATTTTTGGTAAAATCGA-GGTCAAAAATGGGATTTTGGAAAG
* *
4403388 ATTCGGGGGTAAAATGGTAATTTTCGATAAAATCGAGGTCAAAAATGGGATTTTGGAAAG
1 -TTCGGGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAATGGGATTTTGGAAAG
*** * * *
4403448 TTCTACGATAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAATGGGATTTTGGAAAG
** * * * * * *
4403507 TTTAGGGGTGAAATGGTAATTTTTTGTGAAATCGAGGTTAAAAATGAGATTTTGAAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAATGGGATTTTGGAAAG
* * **
4403566 CTCGGGTGTAAAAACGTAATTTTTG
1 TTCGGGGGTAAAATGGTAATTTTTG
4403591 AAAAGCTCTA
Statistics
Matches: 165, Mismatches: 34, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
58 5 0.03
59 146 0.88
60 14 0.08
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (59 bp):
TTCGGGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAATGGGATTTTGGAAAG
Found at i:4403552 original size:31 final size:31
Alignment explanation
Indices: 4403457--4403552 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
4403447 GTTCTACGAT
* *
4403457 AAAATGGTAATTTTTGGTGAAATCGAGGTCA
1 AAAATGGTAATTTTTTGTGAAATCGAGGTTA
** *
4403488 AAAATGG-AA--TTTTG-GAAAGTTTAGGGGT-
1 AAAATGGTAATTTTTTGTGAAA-TCGA-GGTTA
*
4403516 GAAATGGTAATTTTTTGTGAAATCGAGGTTA
1 AAAATGGTAATTTTTTGTGAAATCGAGGTTA
4403547 AAAATG
1 AAAATG
4403553 AGATTTTGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
27 4 0.08
28 12 0.25
29 4 0.08
30 5 0.10
31 19 0.40
32 4 0.08
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (31 bp):
AAAATGGTAATTTTTTGTGAAATCGAGGTTA
Found at i:4403638 original size:30 final size:29
Alignment explanation
Indices: 4403538--4403638 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 29
4403528 TTTTGTGAAA
*
4403538 TCGAGGTTAAAAATG-AGATTTTGAAAAGC
1 TCGAGGTTAAAAATGTA-ATTTTTAAAAGC
*
4403567 TCG-GGTGTAAAAACGTAATTTTTGAAAAGC
1 TCGAGGT-TAAAAATGTAATTTTT-AAAAGC
* * * *
4403597 TCTAGGGTAAAAATGTAATTTTTAGAAGTT
1 TCGAGGTTAAAAATGTAATTTTTAAAAG-C
4403627 TCGAGGTTAAAA
1 TCGAGGTTAAAA
4403639 TACAATTTCT
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
28 3 0.05
29 19 0.33
30 34 0.59
31 2 0.03
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.32
Consensus pattern (29 bp):
TCGAGGTTAAAAATGTAATTTTTAAAAGC
Found at i:4405179 original size:26 final size:27
Alignment explanation
Indices: 4405149--4405212 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
4405139 TAGTTGTATT
*
4405149 GATTTCTAAGAAAT-GATT-CGTATTTG
1 GATTTC-AAGAAATGGATTCCGTATTTA
* *
4405175 GATTTCAAGAACTGGGTTCCGTATTTA
1 GATTTCAAGAAATGGATTCCGTATTTA
4405202 GATTTCAAGAA
1 GATTTCAAGAA
4405213 CTGGGTTCGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.18
26 9 0.27
27 18 0.55
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (27 bp):
GATTTCAAGAAATGGATTCCGTATTTA
Found at i:4405199 original size:27 final size:27
Alignment explanation
Indices: 4405167--4405220 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
4405157 AGAAATGATT
*
4405167 CGTATTTGGATTTCAAGAACTGGGTTC
1 CGTATTTAGATTTCAAGAACTGGGTTC
4405194 CGTATTTAGATTTCAAGAACTGGGTTC
1 CGTATTTAGATTTCAAGAACTGGGTTC
4405221 GTAACCCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (27 bp):
CGTATTTAGATTTCAAGAACTGGGTTC
Found at i:4405614 original size:23 final size:23
Alignment explanation
Indices: 4405588--4405633 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4405578 ATTTTCCTTG
*
4405588 TATTTGGACATTT-AATTTATATT
1 TATTT-GAAATTTAAATTTATATT
*
4405611 TATTTTAAATTTAAATTTATATT
1 TATTTGAAATTTAAATTTATATT
4405634 AAGTTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (23 bp):
TATTTGAAATTTAAATTTATATT
Found at i:4405623 original size:17 final size:17
Alignment explanation
Indices: 4405601--4405645 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
4405591 TTGGACATTT
* *
4405601 AATTTATATTTATTTTA
1 AATTTAAATTTATATTA
4405618 AATTTAAATTTATATTA
1 AATTTAAATTTATATTA
*
4405635 AGTTTAAATTT
1 AATTTAAATTT
4405646 TGAAAAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
AATTTAAATTTATATTA
Found at i:4405640 original size:23 final size:22
Alignment explanation
Indices: 4405597--4405645 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
4405587 GTATTTGGAC
* *
4405597 ATTTAATTTATATTTATTTTAA
1 ATTTAATTTATATTAAGTTTAA
4405619 ATTTAAATTTATATTAAGTTTAA
1 ATTT-AATTTATATTAAGTTTAA
4405642 ATTT
1 ATTT
4405646 TGAAAAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
ATTTAATTTATATTAAGTTTAA
Found at i:4407934 original size:25 final size:26
Alignment explanation
Indices: 4407880--4407934 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
4407870 GTGTTTTCCC
*
4407880 AAGTTCATGATGACTTGGTTTTCTTT
1 AAGTTCATGATGACTTCGTTTTCTTT
4407906 -AGTTCATGATGAC-TCGTTCTT-TTT
1 AAGTTCATGATGACTTCGTT-TTCTTT
4407930 AAGTT
1 AAGTT
4407935 TGTGGTCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (26 bp):
AAGTTCATGATGACTTCGTTTTCTTT
Found at i:4409912 original size:15 final size:15
Alignment explanation
Indices: 4409872--4409918 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
4409862 CTCAAAATAT
4409872 TTTG-TTTTAATTTTA
1 TTTGTTTTTAA-TTTA
* *
4409887 TAT-TTTGTAATTTA
1 TTTGTTTTTAATTTA
4409901 TTTGTTTTTAATTTA
1 TTTGTTTTTAATTTA
4409916 TTT
1 TTT
4409919 TTATAATGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 6 0.23
15 20 0.77
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.72
Consensus pattern (15 bp):
TTTGTTTTTAATTTA
Found at i:4410624 original size:12 final size:11
Alignment explanation
Indices: 4410609--4410657 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
4410599 AAATAAAGAA
4410609 AAGAAAGAAAG
1 AAGAAAGAAAG
4410620 CAAGAAAGAAAG
1 -AAGAAAGAAAG
* *
4410632 AAG-AAGGAGG
1 AAGAAAGAAAG
*
4410642 AGGAAAGAAAG
1 AAGAAAGAAAG
4410653 AAGAA
1 AAGAA
4410658 TGAGAGAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
10 7 0.23
11 12 0.40
12 11 0.37
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (11 bp):
AAGAAAGAAAG
Found at i:4410654 original size:4 final size:4
Alignment explanation
Indices: 4410594--4410633 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
4410584 AAATAAACGG
* *
4410594 GAAA GAAA TAAA GAAAA GAAA GAAA GCAA GAAA GAAA GAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAA
4410634 GAAGGAGGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.72, C:0.03, G:0.23, T:0.03
Consensus pattern (4 bp):
GAAA
Found at i:4413987 original size:21 final size:21
Alignment explanation
Indices: 4413963--4414006 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4413953 TAGGATCCAT
4413963 TTGCCCCGGAGGAGTAAAGTA
1 TTGCCCCGGAGGAGTAAAGTA
* * *
4413984 TTGCTCGGGAGGCGTAAAGTA
1 TTGCCCCGGAGGAGTAAAGTA
4414005 TT
1 TT
4414007 ACGGTGGCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.16, G:0.34, T:0.25
Consensus pattern (21 bp):
TTGCCCCGGAGGAGTAAAGTA
Found at i:4414065 original size:45 final size:45
Alignment explanation
Indices: 4414001--4414091 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
4413991 GGAGGCGTAA
*
4414001 AGTATTACGGTGGCTCGTCAAACTGAGCCTGATATCCTTGGCTTG
1 AGTATTACGGTGGCTCGTCAAACTAAGCCTGATATCCTTGGCTTG
* *
4414046 AGTATTGCGGTGGCTCGTCAAACTAAGGCTGATATCCTTGGCTTG
1 AGTATTACGGTGGCTCGTCAAACTAAGCCTGATATCCTTGGCTTG
4414091 A
1 A
4414092 TGAGCTAGGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (45 bp):
AGTATTACGGTGGCTCGTCAAACTAAGCCTGATATCCTTGGCTTG
Found at i:4416855 original size:21 final size:20
Alignment explanation
Indices: 4416826--4416868 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
4416816 TACTTACTAC
4416826 TACTACTAACAAAATAAAAT
1 TACTACTAACAAAATAAAAT
*
4416846 TACTAACTAACAAAATTAAAT
1 TACT-ACTAACAAAATAAAAT
4416867 TA
1 TA
4416869 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (20 bp):
TACTACTAACAAAATAAAAT
Found at i:4416969 original size:23 final size:22
Alignment explanation
Indices: 4416943--4417020 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 22
4416933 CTATAACAAC
4416943 ATTAAATAACAAATCAATTAAAA
1 ATTAAATAACAAATCAA-TAAAA
*
4416966 ATTAAATTAAACAAAACAA-AAAA
1 ATTAAA-T-AACAAATCAATAAAA
* *
4416989 CTTAAAATAATCAAATTAACTAACAA
1 ATT-AAATAA-CAAATCAA-TAA-AA
4417015 ATTAAA
1 ATTAAA
4417021 ATATTTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
22 2 0.05
23 19 0.44
24 4 0.09
25 14 0.33
26 4 0.09
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.24
Consensus pattern (22 bp):
ATTAAATAACAAATCAATAAAA
Found at i:4417225 original size:7 final size:7
Alignment explanation
Indices: 4417201--4417245 Score: 67
Period size: 7 Copynumber: 6.7 Consensus size: 7
4417191 TACATTTTTC
4417201 TCCTTC-
1 TCCTTCT
*
4417207 TCTTTC-
1 TCCTTCT
4417213 TCCTTCT
1 TCCTTCT
4417220 TCCTTCT
1 TCCTTCT
4417227 TCCTTCT
1 TCCTTCT
4417234 TCCTTCT
1 TCCTTCT
4417241 TCCTT
1 TCCTT
4417246 TCTTTCTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
6 10 0.28
7 26 0.72
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (7 bp):
TCCTTCT
Found at i:4418624 original size:29 final size:29
Alignment explanation
Indices: 4418578--4418633 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
4418568 TAGTTTTTGA
* **
4418578 ATTTTAAATTATAAATTATTTACTTAAGT
1 ATTTGAAATTATAAATTAGGTACTTAAGT
4418607 ATTTGAAATT-TAATATTAGGTACTTAA
1 ATTTGAAATTATAA-ATTAGGTACTTAA
4418634 TAAAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.13
29 20 0.87
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (29 bp):
ATTTGAAATTATAAATTAGGTACTTAAGT
Found at i:4421507 original size:27 final size:27
Alignment explanation
Indices: 4421467--4421521 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
4421457 AAAAATACCT
*
4421467 GACACCAATGGAGGAACACCAAGTGGC
1 GACACCAATCGAGGAACACCAAGTGGC
* *
4421494 GACACCAATCGAGGAATATCAAGTGGC
1 GACACCAATCGAGGAACACCAAGTGGC
4421521 G
1 G
4421522 GCATTAAGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.29, T:0.11
Consensus pattern (27 bp):
GACACCAATCGAGGAACACCAAGTGGC
Found at i:4421725 original size:11 final size:11
Alignment explanation
Indices: 4421686--4421726 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
4421676 GGGAGCAAAA
4421686 AAAGAAGAAAG
1 AAAGAAGAAAG
4421697 AAAGAGAGGAAAG
1 AAAGA-A-GAAAG
*
4421710 AAAGAAGAAGG
1 AAAGAAGAAAG
4421721 AAAGAA
1 AAAGAA
4421727 ATGTAATGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 15 0.56
12 2 0.07
13 10 0.37
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (11 bp):
AAAGAAGAAAG
Found at i:4422713 original size:3 final size:3
Alignment explanation
Indices: 4422700--4422733 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
4422690 TCATCCAATG
* *
4422700 CCT CTT CCT CCT CCT CCT CCT CCT CTT CCT CCT C
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT C
4422734 TTCTTGTTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (3 bp):
CCT
Found at i:4424552 original size:29 final size:30
Alignment explanation
Indices: 4424456--4424557 Score: 82
Period size: 30 Copynumber: 3.4 Consensus size: 30
4424446 AAATAATAAT
4424456 TAAATACTTATTTACTAAAATGGTACAAAA
1 TAAATACTTATTTACTAAAATGGTACAAAA
* ** * * * * *
4424486 TATATTTTTATATACCAAAATAGTATCCACA
1 TAAATACTTATTTACTAAAATGGTA-CAAAA
* *
4424517 -CACTA-TTATTTACTAAAATGGTACAAAA
1 TAAATACTTATTTACTAAAATGGTACAAAA
*
4424545 TAAATATTTATTT
1 TAAATACTTATTT
4424558 TGTATTATTT
Statistics
Matches: 50, Mismatches: 19, Indels: 6
0.67 0.25 0.08
Matches are distributed among these distances:
28 3 0.06
29 18 0.36
30 26 0.52
31 3 0.06
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (30 bp):
TAAATACTTATTTACTAAAATGGTACAAAA
Found at i:4424613 original size:16 final size:16
Alignment explanation
Indices: 4424592--4424636 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
4424582 ATGGAAGTAT
4424592 TATTTTGATAATTAAA
1 TATTTTGATAATTAAA
*
4424608 TATTTT-TTATATT--A
1 TATTTTGATA-ATTAAA
4424622 TATTTTGATAATTAA
1 TATTTTGATAATTAA
4424637 TTAGCTAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 8
0.70 0.06 0.24
Matches are distributed among these distances:
14 10 0.43
15 4 0.17
16 9 0.39
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
TATTTTGATAATTAAA
Found at i:4424941 original size:94 final size:94
Alignment explanation
Indices: 4424831--4425093 Score: 420
Period size: 94 Copynumber: 2.8 Consensus size: 94
4424821 TTATATTATT
* *
4424831 TTTTAAAATCAATAAATATGAACAATATTTTTTACTTGCTACTACTACTAACAACAAAATAAAAT
1 TTTT-AAATCAATAAATATAAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAAT
4424896 TACTAACTAATTTTTTTAAACATTATTAAA
65 TACTAACTAATTTTTTTAAACATTATTAAA
4424926 TTTTAAATCAATAAATATAAACAA-AGTTTTTTACTTACTACTACTACTAACAACAAAATAAAAT
1 TTTTAAATCAATAAATATAAACAATA-TTTTTTACTTACTACTACTACTAACAACAAAATAAAAT
* *
4424990 TACTAACTAATTTTTTTAAATATTTTTAAA
65 TACTAACTAATTTTTTTAAACATTATTAAA
* * * *
4425020 TTTTAAATAAATAAATATAAACAATGTTTTTTTACTTATTACTACTACTAACAACAAAATAAACT
1 TTTTAAATCAATAAATATAAACAAT-ATTTTTTACTTACTACTACTACTAACAACAAAATAAAAT
4425085 TACTAACTA
65 TACTAACTA
4425094 CTAACTATTA
Statistics
Matches: 157, Mismatches: 8, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
93 1 0.01
94 107 0.68
95 49 0.31
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.39
Consensus pattern (94 bp):
TTTTAAATCAATAAATATAAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
ACTAACTAATTTTTTTAAACATTATTAAA
Found at i:4425311 original size:4 final size:4
Alignment explanation
Indices: 4425304--4425363 Score: 58
Period size: 4 Copynumber: 16.0 Consensus size: 4
4425294 ACCTTTTTTT
* *
4425304 TTTC TTTC -TTC -TTC TTTC TTTC TTTC TTCCC CTTC TTTC -TTC TTT-
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC TTTC TTTC TTTC TTTC
4425349 TTTC TTTC TTT- TTTC
1 TTTC TTTC TTTC TTTC
4425364 CCTCAATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
3 15 0.32
4 30 0.64
5 2 0.04
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:4425322 original size:7 final size:7
Alignment explanation
Indices: 4425312--4425363 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
4425302 TTTTTCTTTC
4425312 TTCTTCT
1 TTCTTCT
4425319 TTCTTTCT
1 TTC-TTCT
4425327 TTCTTC-
1 TTCTTCT
**
4425333 CCCTTCT
1 TTCTTCT
4425340 TTCTTCT
1 TTCTTCT
*
4425347 TTTTTCT
1 TTCTTCT
*
4425354 TTCTTTT
1 TTCTTCT
4425361 TTC
1 TTC
4425364 CCTCAATTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
6 4 0.11
7 25 0.69
8 7 0.19
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (7 bp):
TTCTTCT
Found at i:4425340 original size:31 final size:31
Alignment explanation
Indices: 4425305--4425365 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
4425295 CCTTTTTTTT
4425305 TTCTTTCTTCTTCTTTCTTTCTTTCTTCCCC
1 TTCTTTCTTCTTCTTTCTTTCTTTCTTCCCC
* *
4425336 TTCTTTCTTCTTTTTTCTTTCTTTTTTCCC
1 TTCTTTCTTCTTCTTTCTTTCTTTCTTCCC
4425366 TCAATTTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (31 bp):
TTCTTTCTTCTTCTTTCTTTCTTTCTTCCCC
Found at i:4426150 original size:15 final size:15
Alignment explanation
Indices: 4426129--4426168 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
4426119 AAAATAGATA
4426129 AAAATTAT-AAAAAT
1 AAAATTATAAAAAAT
4426143 ATAAATTATTAAAAAAT
1 A-AAATTA-TAAAAAAT
4426160 AAAATTATA
1 AAAATTATA
4426169 TTTTTATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 1 0.04
15 8 0.35
16 7 0.30
17 7 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATTATAAAAAAT
Found at i:4426157 original size:16 final size:16
Alignment explanation
Indices: 4426129--4426167 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
4426119 AAAATAGATA
4426129 AAAATTA-T-AAAAAT
1 AAAATTATTAAAAAAT
4426143 ATAAATTATTAAAAAAT
1 A-AAATTATTAAAAAAT
4426160 AAAATTAT
1 AAAATTAT
4426168 ATTTTTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.05
15 6 0.27
16 8 0.36
17 7 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATTATTAAAAAAT
Found at i:4426323 original size:18 final size:17
Alignment explanation
Indices: 4426299--4426338 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
4426289 AAAATAGATA
*
4426299 AAAATTA-TAAAAATAT
1 AAAATTATTAAAAAAAT
4426315 -AAATTATTAAAAAAAT
1 AAAATTATTAAAAAAAT
4426331 AAAATTAT
1 AAAATTAT
4426339 ATTTTTATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 8 0.38
17 7 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTATTAAAAAAAT
Found at i:4426327 original size:17 final size:18
Alignment explanation
Indices: 4426302--4426338 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
4426292 ATAGATAAAA
4426302 ATTAT-AAAAATATAAATT
1 ATTATAAAAAATA-AAATT
4426320 ATTA-AAAAAATAAAATT
1 ATTATAAAAAATAAAATT
4426337 AT
1 AT
4426339 ATTTTTATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTATAAAAAATAAAATT
Found at i:4426396 original size:171 final size:170
Alignment explanation
Indices: 4426112--4426450 Score: 642
Period size: 171 Copynumber: 2.0 Consensus size: 170
4426102 TTATATTTTA
*
4426112 ATATTTAAAAATAGATAAAAATTATAAAAATATAAATTATTAAAAAATAAAATTATATTTTTATT
1 ATATTTAAAAATAGATAAAAATTATAAAAATATAAATTATTAAAAAATAAAATTATATTTTTATC
4426177 CTTATAAAAATATACAATATAATTTCGATCTTTTTAAAAAAATTTCTGATTTTGGCAAGGAAAAT
66 CTTATAAAAATATACAATATAATTTCGATCTTTTTAAAAAAATTTCTGATTTTGGCAAGGAAAAT
4426242 AGGTCGGCGGTGGCTGCTAAAAGCATTGTCCTATTGCTTG
131 AGGTCGGCGGTGGCTGCTAAAAGCATTGTCCTATTGCTTG
4426282 ATATTTAAAAATAGATAAAAATTATAAAAATATAAATTATTAAAAAAATAAAATTATATTTTTAT
1 ATATTTAAAAATAGATAAAAATTATAAAAATATAAATTATT-AAAAAATAAAATTATATTTTTAT
* *
4426347 CCTTATAAAAATATATAATATAATTTCGATCTTTTTAAAAAATTTTCTGATTTTGGCAAGGAAAA
65 CCTTATAAAAATATACAATATAATTTCGATCTTTTTAAAAAAATTTCTGATTTTGGCAAGGAAAA
4426412 TAGGTCGGCGGTGGCTGCTAAAAGCATTGTCCTATTGCT
130 TAGGTCGGCGGTGGCTGCTAAAAGCATTGTCCTATTGCT
4426451 GCGACAAAGT
Statistics
Matches: 165, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
170 41 0.25
171 124 0.75
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (170 bp):
ATATTTAAAAATAGATAAAAATTATAAAAATATAAATTATTAAAAAATAAAATTATATTTTTATC
CTTATAAAAATATACAATATAATTTCGATCTTTTTAAAAAAATTTCTGATTTTGGCAAGGAAAAT
AGGTCGGCGGTGGCTGCTAAAAGCATTGTCCTATTGCTTG
Found at i:4430369 original size:3 final size:3
Alignment explanation
Indices: 4430349--4430466 Score: 56
Period size: 3 Copynumber: 41.7 Consensus size: 3
4430339 ATGTCTCTAA
* * * * *
4430349 AAT AAT AAC AA- AATT AAT AAT AAA AAT AAG AGT TAT -AT AAT -AT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
4430392 CAA- AAT AAT AAT AAT AAT AA- AAT AAT AAC AA- CAT AAT AAT AA-
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
4430434 AAT GAC AAT AA- AAT AAT GAG AA- AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4430467 AACACTGAGA
Statistics
Matches: 86, Mismatches: 18, Indels: 22
0.68 0.14 0.17
Matches are distributed among these distances:
2 17 0.20
3 66 0.77
4 3 0.03
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:4430405 original size:17 final size:17
Alignment explanation
Indices: 4430349--4430450 Score: 68
Period size: 17 Copynumber: 6.0 Consensus size: 17
4430339 ATGTCTCTAA
*
4430349 AATAATAACAAAATTAAT
1 AATAATAATAAAA-TAAT
* * *
4430367 AATAAAAATAAGAGTTAT
1 AATAATAATAA-AATAAT
4430385 -ATAAT-ATCAAAATAAT
1 AATAATAAT-AAAATAAT
4430401 AATAATAATAAAATAAT
1 AATAATAATAAAATAAT
* *
4430418 AACAA-CATAATAATAA-
1 AATAATAATAA-AATAAT
* *
4430434 AATGACAATAAAATAAT
1 AATAATAATAAAATAAT
4430451 GAGAAAATAA
Statistics
Matches: 65, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
16 18 0.28
17 32 0.49
18 14 0.22
19 1 0.02
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (17 bp):
AATAATAATAAAATAAT
Found at i:4430415 original size:11 final size:11
Alignment explanation
Indices: 4430346--4430468 Score: 86
Period size: 11 Copynumber: 10.5 Consensus size: 11
4430336 CATATGTCTC
4430346 TAAAATAATAA
1 TAAAATAATAA
*
4430357 CAAAATTAATAA
1 TAAAA-TAATAA
4430369 TAAAAATAAGAGTTATA
1 T-AAAAT-A-A--TA-A
*
4430386 TAATATCAA-AA
1 TAAAAT-AATAA
4430397 TAATAATAATAA
1 TAA-AATAATAA
4430409 TAAAATAATAA
1 TAAAATAATAA
* *
4430420 CAACATAATAA
1 TAAAATAATAA
* *
4430431 TAAAATGACAA
1 TAAAATAATAA
*
4430442 TAAAATAATGA
1 TAAAATAATAA
*
4430453 GAAAATAATAA
1 TAAAATAATAA
4430464 TAAAA
1 TAAAA
4430469 CACTGAGAAA
Statistics
Matches: 86, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
11 55 0.64
12 15 0.17
13 5 0.06
14 1 0.01
15 1 0.01
16 7 0.08
17 2 0.02
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:4430433 original size:14 final size:14
Alignment explanation
Indices: 4430385--4430433 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
4430375 TAAGAGTTAT
*
4430385 ATAATATCAAAATA
1 ATAATAACAAAATA
*
4430399 ATAATAATAATAA-A
1 ATAATAACAA-AATA
*
4430413 ATAATAACAACATA
1 ATAATAACAAAATA
4430427 ATAATAA
1 ATAATAA
4430434 AATGACAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 1 0.03
14 26 0.90
15 2 0.07
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAATAACAAAATA
Found at i:4430475 original size:22 final size:22
Alignment explanation
Indices: 4430438--4430494 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
4430428 TAATAAAATG
* *
4430438 ACAATAAAATAATGAGAAAATA
1 ACAATAAAACAATGAGAAAACA
* *
4430460 ATAATAAAACACTGAGAAAACA
1 ACAATAAAACAATGAGAAAACA
*
4430482 ACAATAAATCAAT
1 ACAATAAAACAAT
4430495 AATTTTTCTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.65, C:0.11, G:0.07, T:0.18
Consensus pattern (22 bp):
ACAATAAAACAATGAGAAAACA
Found at i:4431514 original size:5 final size:6
Alignment explanation
Indices: 4431488--4431512 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4431478 CTTCCTTCTC
4431488 TTCTTT TTCTTT TTCTTT TTCTTT T
1 TTCTTT TTCTTT TTCTTT TTCTTT T
4431513 CTAATCCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTCTTT
Found at i:4431561 original size:25 final size:25
Alignment explanation
Indices: 4431527--4431576 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
4431517 TCCTTAGATT
* *
4431527 CGTATACTTATACGTAGATATATAC
1 CGTATACTTATACATACATATATAC
4431552 CGTATACTTATACATACATATATAC
1 CGTATACTTATACATACATATATAC
4431577 GTAGACATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (25 bp):
CGTATACTTATACATACATATATAC
Found at i:4444251 original size:15 final size:17
Alignment explanation
Indices: 4444230--4444270 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
4444220 CAATCTTTTA
4444230 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
4444246 -AAATTATTAAAATGAT
1 AAAATTATAAAAATGAT
4444262 AAAATTATA
1 AAAATTATA
4444271 TTTTAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:4444521 original size:18 final size:18
Alignment explanation
Indices: 4444479--4444522 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
4444469 AAAAATATTA
* *
4444479 ATTTCAAAAAATAAATTT
1 ATTTAAAAAAATAAATTC
**
4444497 AAATAAAAAAATAAATTC
1 ATTTAAAAAAATAAATTC
4444515 ATTTAAAA
1 ATTTAAAA
4444523 TATGAGTTTG
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTTAAAAAAATAAATTC
Found at i:4445009 original size:16 final size:18
Alignment explanation
Indices: 4444980--4445012 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
4444970 GGCTTAATTT
4444980 ATTATCATATCAATTAAA
1 ATTATCATATCAATTAAA
4444998 ATTAT-ATA-CAATTAA
1 ATTATCATATCAATTAA
4445013 TAGATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTATCATATCAATTAAA
Found at i:4448176 original size:13 final size:12
Alignment explanation
Indices: 4448134--4448184 Score: 57
Period size: 13 Copynumber: 4.0 Consensus size: 12
4448124 CAAAGCAAAT
*
4448134 AAAAGAAAAGAAA
1 AAAAG-AAAGAGA
4448147 AAAAGAGAAGAGA
1 AAAAGA-AAGAGA
*
4448160 AAAAGACAGAGA
1 AAAAGAAAGAGA
4448172 GAAAAGAAAGAGA
1 -AAAAGAAAGAGA
4448185 TAAGTGGGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 6 0.18
13 27 0.82
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (12 bp):
AAAAGAAAGAGA
Found at i:4454741 original size:16 final size:16
Alignment explanation
Indices: 4454717--4454747 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4454707 AAAAACACAC
4454717 TTGTCTTAAATATAAG
1 TTGTCTTAAATATAAG
*
4454733 TTGTTTTAAATATAA
1 TTGTCTTAAATATAA
4454748 CTATTCCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.48
Consensus pattern (16 bp):
TTGTCTTAAATATAAG
Found at i:4455420 original size:31 final size:31
Alignment explanation
Indices: 4455382--4455462 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
4455372 CATTTAATGG
*
4455382 TGAGTGACCAAAATAGAAACGATCTAAAACA
1 TGAGTGACCAAAATAAAAACGATCTAAAACA
* * *
4455413 TGAGTGACCCAAATAAAAATGATCTAAAACG
1 TGAGTGACCAAAATAAAAACGATCTAAAACA
* * *
4455444 TTAGTGACTAAATTAAAAA
1 TGAGTGACCAAAATAAAAA
4455463 TAGAAACACT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.51, C:0.14, G:0.15, T:0.21
Consensus pattern (31 bp):
TGAGTGACCAAAATAAAAACGATCTAAAACA
Found at i:4462748 original size:13 final size:13
Alignment explanation
Indices: 4462727--4462778 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
4462717 AATGAGATAT
*
4462727 AATTTAATTTTTA
1 AATTAAATTTTTA
4462740 AATTAAATTTATTTTA
1 AATTAAA--T-TTTTA
*
4462756 AATTTAAATTTATA
1 AA-TTAAATTTTTA
4462770 AATTAAATT
1 AATTAAATT
4462779 AATAAAGTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
13 13 0.39
14 6 0.18
15 2 0.06
16 7 0.21
17 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTAAATTTTTA
Found at i:4462762 original size:17 final size:16
Alignment explanation
Indices: 4462735--4462768 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
4462725 ATAATTTAAT
4462735 TTTTAAATTAAATTTA
1 TTTTAAATTAAATTTA
4462751 TTTTAAATTTAAATTTA
1 TTTTAAA-TTAAATTTA
4462768 T
1 T
4462769 AAATTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTAAATTAAATTTA
Found at i:4464626 original size:29 final size:28
Alignment explanation
Indices: 4464589--4464812 Score: 115
Period size: 30 Copynumber: 7.6 Consensus size: 28
4464579 GTCCTTAAAC
*
4464589 TTCCAAAAATTACCATTTTACCCTTGAACT
1 TTCC-AAAATTACCATTTTACCC-CGAACT
*
4464619 TTCCAAAATT-CTATTTTTGACCCCG-A-T
1 TTCCAAAATTACCA-TTTT-ACCCCGAACT
*
4464646 TTCACCAAAAATGACCATTTTACACCCGAACT
1 TT--CC-AAAATTACCATTTTAC-CCCGAACT
* * *
4464678 TTCCAAAATT-CAATTTTTGACCTCG-ATT
1 TTCCAAAATTACCA-TTTT-ACCCCGAACT
*
4464706 TTACCAAAAATTATCATTTTACCCCCGAACT
1 TT-CC-AAAATTACCATTTTA-CCCCGAACT
*
4464737 TTCCAAAATT-CCATTTTTCACCTC-AA-T
1 TTCCAAAATTACCA-TTTT-ACCCCGAACT
* *
4464764 TTCACCAATAATTACCATTTTACCCCTAAAT
1 TT--CCAA-AATTACCATTTTACCCCGAACT
*
4464795 CTTCCAAAA-TCCCATTTT
1 -TTCCAAAATTACCATTTT
4464813 TAACCCTAAA
Statistics
Matches: 153, Mismatches: 16, Indels: 52
0.69 0.07 0.24
Matches are distributed among these distances:
27 6 0.04
28 21 0.14
29 53 0.35
30 56 0.37
31 12 0.08
32 5 0.03
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (28 bp):
TTCCAAAATTACCATTTTACCCCGAACT
Found at i:4464664 original size:59 final size:58
Alignment explanation
Indices: 4464591--4464813 Score: 284
Period size: 59 Copynumber: 3.8 Consensus size: 58
4464581 CCTTAAACTT
* * *
4464591 CCAAAAATTACCATTTTACCCTTGAACTTTCCAAAATTCTATTTTTGACCCCGATTTCA
1 CCAAAAATTACCATTTTACCC-CGAACTTTCCAAAATTCAATTTTTGACCTCGATTTCA
* *
4464650 CCAAAAATGACCATTTTACACCCGAACTTTCCAAAATTCAATTTTTGACCTCGATTTTA
1 CCAAAAATTACCATTTTAC-CCCGAACTTTCCAAAATTCAATTTTTGACCTCGATTTCA
* * * *
4464709 CCAAAAATTATCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTCACCTCAATTTCA
1 CCAAAAATTACCATTTTA-CCCCGAACTTTCCAAAATTCAATTTTTGACCTCGATTTCA
* * * * *
4464768 CCAATAATTACCATTTTACCCCTAAATCTTCCAAAATCCCATTTTT
1 CCAAAAATTACCATTTTACCCCGAACT-TTCCAAAATTCAATTTTT
4464814 AACCCTAAAC
Statistics
Matches: 145, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
58 7 0.05
59 135 0.93
60 3 0.02
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCGAACTTTCCAAAATTCAATTTTTGACCTCGATTTCA
Found at i:4464743 original size:118 final size:118
Alignment explanation
Indices: 4464591--4464813 Score: 313
Period size: 118 Copynumber: 1.9 Consensus size: 118
4464581 CCTTAAACTT
** * * *
4464591 CCAAAAATTACCATTTTACCCTTGAACTTTCCAAAATTCTATTTTTGACCCCGATTTCACCAAAA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTCACCCCAATTTCACCAAAA
* *
4464656 ATGACCATTTTACACCCGAACT-TTCCAAAATTCAATTTTTGACCTCGATTTTA
66 ATGACCATTTTAC-CCCGAAATCTTCCAAAATCCAATTTTTGACCTCGATTTTA
* * *
4464709 CCAAAAATTATCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTCACCTCAATTTCACCAATA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTCACCCCAATTTCACCAAAA
* * *
4464774 ATTACCATTTTACCCCTAAATCTTCCAAAATCCCATTTTT
66 ATGACCATTTTACCCCGAAATCTTCCAAAATCCAATTTTT
4464814 AACCCTAAAC
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
117 6 0.07
118 85 0.93
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (118 bp):
CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTCACCCCAATTTCACCAAAA
ATGACCATTTTACCCCGAAATCTTCCAAAATCCAATTTTTGACCTCGATTTTA
Found at i:4464828 original size:29 final size:28
Alignment explanation
Indices: 4464736--4464828 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 28
4464726 ACCCCCGAAC
* * *
4464736 TTTCCAAAATTCCATTTTTCA-CCTCAA
1 TTTCCAAAATACCATTTTTAACCCTAAA
*
4464763 TTTCACCAATAATTACCA-TTTTACCCCTAAA
1 TTT--CCAA-AA-TACCATTTTTAACCCTAAA
*
4464794 TCTTCCAAAATCCCATTTTTAACCCTAAA
1 T-TTCCAAAATACCATTTTTAACCCTAAA
4464823 CTTTCC
1 -TTTCC
4464829 CGAAATTACA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
27 3 0.06
28 4 0.08
29 22 0.42
30 11 0.21
31 10 0.19
32 2 0.04
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (28 bp):
TTTCCAAAATACCATTTTTAACCCTAAA
Found at i:4464835 original size:118 final size:117
Alignment explanation
Indices: 4464584--4464842 Score: 292
Period size: 118 Copynumber: 2.2 Consensus size: 117
4464574 TATACGTCCT
** * * *
4464584 TAAAC-TT-CCAAAAATTACCATTTTACCCTTGAACTTTCCAAAATTCTATTTTTGACCCCGATT
1 TAAACTTTACCAAAAATTA-CATTTTACCCCCGAACTTTCCAAAATTCCATTTTTCACCCCAATT
* * *
4464647 TCACCAAAAATGACCATTTTACACCCGAACTTTCCAAAATTCAATTTTTGACC
65 TCACCAAAAATGACCATTTTACACCCGAAATTTCCAAAATCCAATTTTTAACC
** * *
4464700 TCGATTTTACCAAAAATTATCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTCACCTCAATT
1 TAAACTTTACCAAAAATTA-CATTTTACCCCCGAACTTTCCAAAATTCCATTTTTCACCCCAATT
* * * *
4464765 TCACCAATAATTACCATTTTAC-CCCTAAATCTTCCAAAATCCCATTTTTAACCC
65 TCACCAAAAATGACCATTTTACACCCGAAAT-TTCCAAAATCCAATTTTTAA-CC
**
4464819 TAAACTTT-CCCGAAATTACATTTT
1 TAAACTTTACCAAAAATTACATTTT
4464843 TGCCCTCGAA
Statistics
Matches: 117, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
116 2 0.02
117 14 0.12
118 94 0.80
119 7 0.06
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (117 bp):
TAAACTTTACCAAAAATTACATTTTACCCCCGAACTTTCCAAAATTCCATTTTTCACCCCAATTT
CACCAAAAATGACCATTTTACACCCGAAATTTCCAAAATCCAATTTTTAACC
Found at i:4464836 original size:59 final size:57
Alignment explanation
Indices: 4464594--4464842 Score: 178
Period size: 59 Copynumber: 4.2 Consensus size: 57
4464584 TAAACTTCCA
*** * * * ***
4464594 AAAATTACCATTTTACCCTTGAACTTTCCAAAATTCTATTTTTGACCCCGATTTCACC
1 AAAATTA-CATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCTAAATTTCACC
* * * * * * ** *
4464652 AAAAATGACCATTTTACACCCGAACTTTCCAAAATTCAATTTTTGACCTCGATTTTACC
1 -AAAATTA-CATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCTAAATTTCACC
* * * *
4464711 AAAAATTATCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTCACCTCAATTTCACC
1 -AAAATTA-CATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCTAAATTTCACC
*
4464770 AATAATTACCATTTTACCCCTAAA-TCTTCCAAAATCCCATTTTTAACCCTAAACTTTC-CC
1 AA-AATTA-CATTTTACCCCCAAACT-TTCCAAAATCCCATTTTTAA-CCTAAA-TTTCACC
*
4464830 GAAATTACATTTT
1 AAAATTACATTTT
4464843 TGCCCTCGAA
Statistics
Matches: 165, Mismatches: 21, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
58 9 0.05
59 144 0.87
60 8 0.05
61 4 0.02
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.36
Consensus pattern (57 bp):
AAAATTACATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCTAAATTTCACC
Found at i:4476687 original size:200 final size:200
Alignment explanation
Indices: 4476344--4477253 Score: 1435
Period size: 200 Copynumber: 4.5 Consensus size: 200
4476334 ACAAAGCAGT
* * *
4476344 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACACTCAACACGAGCCAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACGCGAGCAAAT
* * *
4476409 CTTCGAACCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCT
66 CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
** *
4476474 TGATGAGATACAGAGAAGTGGACCAAATTTATCTTCCTGAGGAGATCCAAAGAAGTGAATTAAAA
131 TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAAAGAAGCGAATTAAAA
*
4476539 CAACC
196 CAAGC
* *
4476544 GAGGCGGTCATCTTCCTGATGAGATATAGAGAAGAATACCAACTCAACGCTCAACGCGAACAAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACGCGAGCAAAT
* *
4476609 CTTCGAACCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTCC
66 CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
*
4476674 TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAA-AAGCGATTTAAA
131 TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCA-AAGAAGCGAATTAAA
*
4476738 ATAAGC
195 ACAAGC
* * *
4476744 GAGGTGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAGCGCTCAACGCGAGCAAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACGCGAGCAAAT
* * * *
4476809 CTTCGAACCAAGCTTCCTGATGAGACACTGAGAAGCAGGTCAAAGTAATAAAATAGTTAGCTTCC
66 CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
* * * * *
4476874 TAATGGGATACAGAGAAGTGGACCAAATTCGTCTTCTTGAGTAGATCCAGAGAAGCGAATTAAAA
131 TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAAAGAAGCGAATTAAAA
4476939 CAAGC
196 CAAGC
* *
4476944 GAAGCGGTCATTTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACGCGAGCAAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACGCGAGCAAAT
* *
4477009 CTTCGAACCCCGCTTCCTGATGAGACACTGAGAAGCAGGTCGACGCAATAAAATGGTTAGCTTCC
66 CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
* * *
4477074 TGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCTAATTAAAA
131 TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAAAGAAGCGAATTAAAA
4477139 CAAGC
196 CAAGC
* **
4477144 GAGGCGGTCATCTTCCTGATGAGACACAGAGAAGAATACCAACTCAACGCTCAACGCGAGCCGAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACGCGAGCAAAT
* * *
4477209 CTTCGAACTCAGCTTCCTGATGAGACATTAAGAAGCAGGTCGAAG
66 CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAG
4477254 TCAGCAAACT
Statistics
Matches: 647, Mismatches: 61, Indels: 4
0.91 0.09 0.01
Matches are distributed among these distances:
199 1 0.00
200 644 1.00
201 2 0.00
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (200 bp):
GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACGCGAGCAAAT
CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAAAGAAGCGAATTAAAA
CAAGC
Found at i:4477629 original size:17 final size:17
Alignment explanation
Indices: 4477602--4477669 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 17
4477592 ATAATTTAAT
4477602 TTTTAAA-TTAAATTTA
1 TTTTAAATTTAAATTTA
4477618 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
** * *
4477635 CATAAAATTTAAGTTTA
1 TTTTAAATTTAAATTTA
* *
4477652 TTATAATTTTAAATTTA
1 TTTTAAATTTAAATTTA
4477669 T
1 T
4477670 AAATTAAATT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
16 7 0.17
17 34 0.83
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:4477733 original size:13 final size:15
Alignment explanation
Indices: 4477705--4477740 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
4477695 ACAAGTGTCC
4477705 AATTACAAAGGCCCA
1 AATTACAAAGGCCCA
4477720 AATTA-AAA-GCCC-
1 AATTACAAAGGCCCA
4477732 AATTACAAA
1 AATTACAAA
4477741 ACTGACCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.25
13 7 0.35
14 3 0.15
15 5 0.25
ACGTcount: A:0.53, C:0.22, G:0.08, T:0.17
Consensus pattern (15 bp):
AATTACAAAGGCCCA
Found at i:4478417 original size:9 final size:9
Alignment explanation
Indices: 4478399--4478505 Score: 58
Period size: 9 Copynumber: 11.6 Consensus size: 9
4478389 CATTAATGAG
*
4478399 TAATAATAA
1 TAATATTAA
4478408 TAATATTAA
1 TAATATTAA
*
4478417 TAATA-AAA
1 TAATATTAA
4478425 TAATATTAA
1 TAATATTAA
***
4478434 GGGTATTAA
1 TAATATTAA
4478443 -ACGAT-TTAA
1 TA--ATATTAA
4478452 TAAATATTAA
1 T-AATATTAA
* *
4478462 TAATGTTTTAG
1 TAA--TATTAA
4478473 TAATAATTAA
1 TAAT-ATTAA
*
4478483 TAATAATAA
1 TAATATTAA
*
4478492 TAATAATAA
1 TAATATTAA
4478501 TAATA
1 TAATA
4478506 ATAAAGAAAG
Statistics
Matches: 76, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
8 7 0.09
9 48 0.63
10 13 0.17
11 8 0.11
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (9 bp):
TAATATTAA
Found at i:4478479 original size:3 final size:3
Alignment explanation
Indices: 4478473--4478509 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
4478463 AATGTTTTAG
4478473 TAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4478510 AGAAAGTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4479539 original size:29 final size:29
Alignment explanation
Indices: 4479506--4479635 Score: 103
Period size: 29 Copynumber: 4.5 Consensus size: 29
4479496 TAAACTTCTA
*
4479506 AAAATTACCATTTTACCCCCAAACTTTCT
1 AAAATTACCATTTTACCCCCAAACTTTCC
* *
4479535 AAAATT-CTATTTT-CACCCC-GA-TTTCACC
1 AAAATTACCATTTTAC-CCCCAAACTTT--CC
4479563 AAAAATTACCATTTTACCCCCAAA-TCTTCC
1 -AAAATTACCATTTTACCCCCAAACT-TTCC
* *
4479593 AAAA-TCCCATTTTTAACCCCAAACTTTCCC
1 AAAATTACCA-TTTTACCCCCAAACTTT-CC
4479623 AAAATTA-CATTTT
1 AAAATTACCATTTT
4479636 TGCCCTCGAA
Statistics
Matches: 81, Mismatches: 8, Indels: 24
0.72 0.07 0.21
Matches are distributed among these distances:
26 3 0.04
27 2 0.02
28 15 0.19
29 34 0.42
30 21 0.26
31 4 0.05
32 2 0.02
ACGTcount: A:0.35, C:0.31, G:0.01, T:0.34
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCAAACTTTCC
Found at i:4479634 original size:58 final size:58
Alignment explanation
Indices: 4479505--4479635 Score: 153
Period size: 58 Copynumber: 2.3 Consensus size: 58
4479495 CTAAACTTCT
* * * * *
4479505 AAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCTATTTTCACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTAACCCCAATTTCACC
4479563 AAAAATTACCATTTTACCCCCAAA-TCTTCCAAAATCCCATTTTTAACCCCAAACTTTC-CC
1 AAAAATTACCATTTTACCCCCAAACT-TTCCAAAATCCCA-TTTTAACCCC-AA-TTTCACC
4479623 -AAAATTA-CATTTT
1 AAAAATTACCATTTT
4479636 TGCCCTCGAA
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
57 1 0.02
58 40 0.62
59 16 0.25
60 3 0.05
61 4 0.06
ACGTcount: A:0.35, C:0.31, G:0.01, T:0.34
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTAACCCCAATTTCACC
Found at i:4481800 original size:39 final size:40
Alignment explanation
Indices: 4481726--4481801 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 40
4481716 AATCTTTTAA
** *
4481726 ATTTAAATTAAAATGTTACTAAATTCCTTTTTTTCTTCCT
1 ATTTAAATTAAAAACTTACTAAATTCCTTTATTTCTTCCT
* *
4481766 ATTTAATTTAAAAACTTA-TAAATTTCTTTATTTCTT
1 ATTTAAATTAAAAACTTACTAAATTCCTTTATTTCTT
4481802 ATTTTTCTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 16 0.52
40 15 0.48
ACGTcount: A:0.33, C:0.12, G:0.01, T:0.54
Consensus pattern (40 bp):
ATTTAAATTAAAAACTTACTAAATTCCTTTATTTCTTCCT
Found at i:4485730 original size:26 final size:26
Alignment explanation
Indices: 4485701--4485751 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
4485691 CCATTCAATT
*
4485701 AATAATATTTTTAATTATTTTAAAAA
1 AATAATATTTTTAATTATTTCAAAAA
* *
4485727 AATAATTTTTTTAATTCTTTCAAAA
1 AATAATATTTTTAATTATTTCAAAA
4485752 CATGATATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
AATAATATTTTTAATTATTTCAAAAA
Found at i:4486118 original size:24 final size:24
Alignment explanation
Indices: 4486089--4486216 Score: 70
Period size: 24 Copynumber: 5.2 Consensus size: 24
4486079 GTTCTAAAAA
4486089 ATTAAAAAA-AGTATATAAA-AATAT
1 ATTAAAAAATA-TATATAAATAA-AT
4486113 ATTAAAAAATATATATAAATAAAT
1 ATTAAAAAATATATATAAATAAAT
*
4486137 ATTTTTTTATAAAATATA-AT-AATAAAT
1 A-----TTAAAAAATATATATAAATAAAT
** *
4486164 -TTAAAATTTATAT-TAATATTAAT
1 ATTAAAAAATATATATAA-ATAAAT
* * *
4486187 ATTAAATAAATATAAATATATTAAT
1 ATTAAA-AAATATATATAAATAAAT
4486212 ATTAA
1 ATTAA
4486217 TATTAAGTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 25
0.71 0.08 0.22
Matches are distributed among these distances:
21 10 0.12
22 1 0.01
23 5 0.06
24 25 0.30
25 19 0.23
26 2 0.02
27 7 0.09
28 2 0.02
29 11 0.13
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.41
Consensus pattern (24 bp):
ATTAAAAAATATATATAAATAAAT
Found at i:4486126 original size:14 final size:13
Alignment explanation
Indices: 4486091--4486138 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
4486081 TCTAAAAAAT
4486091 TAAAAAA-AGTATA
1 TAAAAAATA-TATA
4486104 T-AAAAATATAT-
1 TAAAAAATATATA
4486115 TAAAAAATATATA
1 TAAAAAATATATA
4486128 TAAATAAATAT
1 TAAA-AAATAT
4486139 TTTTTTATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.03
12 18 0.58
13 6 0.19
14 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (13 bp):
TAAAAAATATATA
Found at i:4486182 original size:6 final size:6
Alignment explanation
Indices: 4486173--4486222 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
4486163 TTTAAAATTT
* *
4486173 ATATTA ATATTA ATATTA A-ATAA ATATAAA TATATTA ATATTA ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATAT-TA -ATATTA ATATTA ATATTA
4486222 A
1 A
4486223 GTTTTTTTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 4 0.10
6 28 0.72
7 3 0.08
8 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
ATATTA
Found at i:4486989 original size:15 final size:14
Alignment explanation
Indices: 4486948--4486990 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
4486938 TAATGATAAT
* *
4486948 TTTAATCTTTAATA
1 TTTAATTTTTATTA
4486962 TTTATATTTTTATTAA
1 TTTA-ATTTTTATT-A
4486978 TTTAATTTTTATT
1 TTTAATTTTTATT
4486991 TTGTTCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.16
15 16 0.64
16 5 0.20
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTAATTTTTATTA
Found at i:4491531 original size:6 final size:6
Alignment explanation
Indices: 4491516--4491544 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
4491506 CCTTTTTTTT
4491516 TGGGGG -GGGGG TGGGGG TGGGGG TGGGGG
1 TGGGGG TGGGGG TGGGGG TGGGGG TGGGGG
4491545 GGTTGTATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.00, C:0.00, G:0.86, T:0.14
Consensus pattern (6 bp):
TGGGGG
Found at i:4496106 original size:6 final size:6
Alignment explanation
Indices: 4496095--4496152 Score: 80
Period size: 6 Copynumber: 9.7 Consensus size: 6
4496085 GAGGAAGACT
* * *
4496095 TGGGGC TGGGGC TGGGGC TGGGGC TGGGAC TGGGGC TGGGAC TGGGAC
1 TGGGGC TGGGGC TGGGGC TGGGGC TGGGGC TGGGGC TGGGGC TGGGGC
*
4496143 TGGGAC TGGG
1 TGGGGC TGGG
4496153 ACTCCTTTTG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.07, C:0.16, G:0.60, T:0.17
Consensus pattern (6 bp):
TGGGGC
Found at i:4496118 original size:18 final size:18
Alignment explanation
Indices: 4496095--4496152 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
4496085 GAGGAAGACT
*
4496095 TGGGGCTGGGGCTGGGGC
1 TGGGGCTGGGACTGGGGC
4496113 TGGGGCTGGGACTGGGGC
1 TGGGGCTGGGACTGGGGC
* *
4496131 TGGGACTGGGACTGGGAC
1 TGGGGCTGGGACTGGGGC
4496149 TGGG
1 TGGG
4496153 ACTCCTTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.07, C:0.16, G:0.60, T:0.17
Consensus pattern (18 bp):
TGGGGCTGGGACTGGGGC
Found at i:4496155 original size:12 final size:12
Alignment explanation
Indices: 4496095--4496152 Score: 89
Period size: 12 Copynumber: 4.8 Consensus size: 12
4496085 GAGGAAGACT
*
4496095 TGGGGCTGGGGC
1 TGGGACTGGGGC
*
4496107 TGGGGCTGGGGC
1 TGGGACTGGGGC
4496119 TGGGACTGGGGC
1 TGGGACTGGGGC
*
4496131 TGGGACTGGGAC
1 TGGGACTGGGGC
4496143 TGGGACTGGG
1 TGGGACTGGG
4496153 ACTCCTTTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.07, C:0.16, G:0.60, T:0.17
Consensus pattern (12 bp):
TGGGACTGGGGC
Found at i:4501728 original size:81 final size:81
Alignment explanation
Indices: 4501600--4501762 Score: 283
Period size: 81 Copynumber: 2.0 Consensus size: 81
4501590 AATTGTGTGC
* * *
4501600 GTGTGTGTGTGTTTGTATGATAGAGAGAGATACCAAAACATGCACATATGGGTTATAGAGTGCAC
1 GTGTGCGTGTGTGTGTATGATAGAGAGAGATACCAAAACATGCACATACGGGTTATAGAGTGCAC
4501665 CCTGGACAGTC-CAATT
66 CCTGGACAG-CACAATT
4501681 GTGTGCGTGTGTGTGTATGATAGAGAGAGATACCAAAACATGCACATACGGGTTATAGAGTGCAC
1 GTGTGCGTGTGTGTGTATGATAGAGAGAGATACCAAAACATGCACATACGGGTTATAGAGTGCAC
4501746 CCTGGACAGCACAATT
66 CCTGGACAGCACAATT
4501762 G
1 G
4501763 GGTTAAGATT
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
80 1 0.01
81 77 0.99
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (81 bp):
GTGTGCGTGTGTGTGTATGATAGAGAGAGATACCAAAACATGCACATACGGGTTATAGAGTGCAC
CCTGGACAGCACAATT
Found at i:4516197 original size:15 final size:15
Alignment explanation
Indices: 4516173--4516204 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4516163 ATGTTATTAG
*
4516173 AAAAATGAAATGTTT
1 AAAAAAGAAATGTTT
4516188 AAAAAAGAAATGTTT
1 AAAAAAGAAATGTTT
4516203 AA
1 AA
4516205 GTAAGGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.28
Consensus pattern (15 bp):
AAAAAAGAAATGTTT
Found at i:4517647 original size:31 final size:31
Alignment explanation
Indices: 4517612--4517676 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
4517602 AAGGCCTACA
*
4517612 ACAACCTATAAAAAGTAATAAGATGAAGCTC
1 ACAACCTATAAAAAGCAATAAGATGAAGCTC
*
4517643 ACAACCTATAAAAAGCAATGAGATGAAGCTC
1 ACAACCTATAAAAAGCAATAAGATGAAGCTC
4517674 ACA
1 ACA
4517677 TATATTCAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.51, C:0.18, G:0.14, T:0.17
Consensus pattern (31 bp):
ACAACCTATAAAAAGCAATAAGATGAAGCTC
Found at i:4518601 original size:27 final size:27
Alignment explanation
Indices: 4518571--4518624 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
4518561 TATGGACAAT
4518571 GATTAAGTAACAATGATATTCACTACC
1 GATTAAGTAACAATGATATTCACTACC
4518598 GATTAAGTAACAATGATATTCACTACC
1 GATTAAGTAACAATGATATTCACTACC
4518625 AAGATACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (27 bp):
GATTAAGTAACAATGATATTCACTACC
Found at i:4519012 original size:15 final size:15
Alignment explanation
Indices: 4518992--4519020 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4518982 AAAAGCATAC
4518992 CCCATACTAGTCTTA
1 CCCATACTAGTCTTA
4519007 CCCATACTAGTCTT
1 CCCATACTAGTCTT
4519021 TTGCGTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.34, G:0.07, T:0.34
Consensus pattern (15 bp):
CCCATACTAGTCTTA
Found at i:4519184 original size:14 final size:14
Alignment explanation
Indices: 4519165--4519194 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4519155 TAAAAGGAAT
4519165 TGGGAGAAAAGAAA
1 TGGGAGAAAAGAAA
4519179 TGGGAGAAAAGAAA
1 TGGGAGAAAAGAAA
4519193 TG
1 TG
4519195 TAAGGAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.37, T:0.10
Consensus pattern (14 bp):
TGGGAGAAAAGAAA
Found at i:4519445 original size:66 final size:66
Alignment explanation
Indices: 4519339--4519464 Score: 225
Period size: 66 Copynumber: 1.9 Consensus size: 66
4519329 ACTGTTGAAG
*
4519339 AGAACATAAAATTGTGTCATTCAATCTGATACCAAATAATTCAATTAATAACCATAAAAAACGAA
1 AGAACATAAAATTGTATCATTCAATCTGATACCAAATAATTCAATTAATAACCATAAAAAACGAA
4519404 C
66 C
* *
4519405 AGAACATAAAATTGTATCATTCTATCTGATACCAAATAATTCAATTAATAACCATCAAAA
1 AGAACATAAAATTGTATCATTCAATCTGATACCAAATAATTCAATTAATAACCATAAAAA
4519465 GCTTTGAGCA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (66 bp):
AGAACATAAAATTGTATCATTCAATCTGATACCAAATAATTCAATTAATAACCATAAAAAACGAA
C
Found at i:4519936 original size:29 final size:27
Alignment explanation
Indices: 4519874--4519938 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
4519864 TAACAAATAC
*
4519874 ATGAAAAAGCCTAGAAGATTGAAAAAT
1 ATGAAAAAGCCAAGAAGATTGAAAAAT
4519901 ACATGAAAAAGCCAAGAAGAAAATTGAAAAAT
1 --ATGAAAAAGCCAAGAAG---ATTGAAAAAT
4519933 -TGAAAA
1 ATGAAAA
4519939 TACTCATGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 22 0.69
32 10 0.31
ACGTcount: A:0.60, C:0.08, G:0.17, T:0.15
Consensus pattern (27 bp):
ATGAAAAAGCCAAGAAGATTGAAAAAT
Found at i:4533692 original size:22 final size:22
Alignment explanation
Indices: 4533620--4533705 Score: 101
Period size: 20 Copynumber: 4.1 Consensus size: 22
4533610 TTATACCTAA
4533620 GTAT-TCAGGCTTTATGCC-G-
1 GTATATCAGGCTTTATGCCGGT
* *
4533639 GTAAATCAGGCTTTATGCTGGT
1 GTATATCAGGCTTTATGCCGGT
*
4533661 G-AT-TCAGGCTTTGTGCCGGT
1 GTATATCAGGCTTTATGCCGGT
*
4533681 GTGTATCAGGCTTTATGCCGGT
1 GTATATCAGGCTTTATGCCGGT
4533703 GTA
1 GTA
4533706 ACAGGTTTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
19 3 0.06
20 29 0.54
21 3 0.06
22 19 0.35
ACGTcount: A:0.16, C:0.17, G:0.30, T:0.36
Consensus pattern (22 bp):
GTATATCAGGCTTTATGCCGGT
Found at i:4536356 original size:30 final size:30
Alignment explanation
Indices: 4536322--4536474 Score: 86
Period size: 30 Copynumber: 5.2 Consensus size: 30
4536312 TAAAACGATA
4536322 ATTTTTGGTGAAATCGAGGTTAAAAATGGG
1 ATTTTTGGTGAAATCGAGGTTAAAAATGGG
* ** * * *
4536352 A-TTTT--AGAAAGTTTAGGGGT-AAAACGGTA
1 ATTTTTGGTGAAA-TCGA-GGTTAAAAATGG-G
*
4536381 ATTTTTGGTGAAATCGGGGTTAAAAATGGG
1 ATTTTTGGTGAAATCGAGGTTAAAAATGGG
* * * * *
4536411 A-TTTTGG-AAAATTTGGGGGT-AAAATGGTA
1 ATTTTTGGTGAAA-TCGAGGTTAAAAATGG-G
* *
4536440 ATTTTTGGTGAAATCGAAGTTAAAAAAGGG
1 ATTTTTGGTGAAATCGAGGTTAAAAATGGG
4536470 ATTTT
1 ATTTT
4536475 GGAAAGTTTG
Statistics
Matches: 87, Mismatches: 24, Indels: 24
0.64 0.18 0.18
Matches are distributed among these distances:
27 4 0.05
28 18 0.21
29 21 0.24
30 24 0.28
31 16 0.18
32 4 0.05
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.34
Consensus pattern (30 bp):
ATTTTTGGTGAAATCGAGGTTAAAAATGGG
Found at i:4536399 original size:29 final size:29
Alignment explanation
Indices: 4536367--4536455 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 29
4536357 AGAAAGTTTA
*
4536367 GGGGTAAAACGGTAATTTTTGGTGAAATC
1 GGGGTAAAATGGTAATTTTTGGTGAAATC
* * *
4536396 GGGGTTAAAAATGG-GA-TTTTGG-AAAATTTG
1 GGGG-T-AAAATGGTAATTTTTGGTGAAA--TC
4536426 GGGGTAAAATGGTAATTTTTGGTGAAATC
1 GGGGTAAAATGGTAATTTTTGGTGAAATC
4536455 G
1 G
4536456 AAGTTAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
28 10 0.22
29 14 0.30
30 13 0.28
31 9 0.20
ACGTcount: A:0.31, C:0.03, G:0.33, T:0.33
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATC
Found at i:4536523 original size:59 final size:59
Alignment explanation
Indices: 4536250--4536507 Score: 356
Period size: 59 Copynumber: 4.4 Consensus size: 59
4536240 GGAAAATTTA
** * * *
4536250 GGGTAAAAC-AGTAATTTTCAGTGAAACCGGGGTTAAAAATGAGATTTTAGAAAGTTTGA
1 GGGTAAAACGA-TAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTAGAAAGTTTGG
* *
4536309 GGGTAAAACGATAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTAGAAAGTTTAG
1 GGGTAAAACGATAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTAGAAAGTTTGG
* * *
4536368 GGGTAAAACGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAATTTGG
1 GGGTAAAACGATAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTAGAAAGTTTGG
* * ** * *
4536427 GGGTAAAATGGTAATTTTTGGTGAAATCGAAGTTAAAAAAGGGATTTTGGAAAGTTTGG
1 GGGTAAAACGATAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTAGAAAGTTTGG
4536486 GGGTAAAACGATAATTTTTGGT
1 GGGTAAAACGATAATTTTTGGT
4536508 AGTTTCGGGG
Statistics
Matches: 179, Mismatches: 19, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
59 178 0.99
60 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.32
Consensus pattern (59 bp):
GGGTAAAACGATAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTAGAAAGTTTGG
Found at i:4541259 original size:21 final size:21
Alignment explanation
Indices: 4541229--4541271 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
4541219 TCAAACCCAT
*
4541229 AATAACCCTCGTCTCTGCAGG
1 AATAACCCTCGTATCTGCAGG
*
4541250 AATAATCCTCGTATCTGCAGG
1 AATAACCCTCGTATCTGCAGG
4541271 A
1 A
4541272 GTCGCTGCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (21 bp):
AATAACCCTCGTATCTGCAGG
Found at i:4543023 original size:81 final size:81
Alignment explanation
Indices: 4542895--4543057 Score: 283
Period size: 81 Copynumber: 2.0 Consensus size: 81
4542885 AATTGTGTGC
* * *
4542895 GTGTGTGTGTGTTTGTATGATAGAGAGAGATACCAAAACATGCACATATGGGTTATAGAGTGCAC
1 GTGTGCGTGTGTGTGTATGATAGAGAGAGATACCAAAACATGCACATACGGGTTATAGAGTGCAC
4542960 CCTGGACAGTC-CAATT
66 CCTGGACAG-CACAATT
4542976 GTGTGCGTGTGTGTGTATGATAGAGAGAGATACCAAAACATGCACATACGGGTTATAGAGTGCAC
1 GTGTGCGTGTGTGTGTATGATAGAGAGAGATACCAAAACATGCACATACGGGTTATAGAGTGCAC
4543041 CCTGGACAGCACAATT
66 CCTGGACAGCACAATT
4543057 G
1 G
4543058 GGTTAAGATT
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
80 1 0.01
81 77 0.99
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (81 bp):
GTGTGCGTGTGTGTGTATGATAGAGAGAGATACCAAAACATGCACATACGGGTTATAGAGTGCAC
CCTGGACAGCACAATT
Found at i:4544852 original size:38 final size:38
Alignment explanation
Indices: 4544802--4544927 Score: 112
Period size: 38 Copynumber: 3.1 Consensus size: 38
4544792 TGACATTTCG
4544802 AAATTTTGTTTTTTTAATCTAAAAATCATGTTATTCAA
1 AAATTTTGTTTTTTTAATCTAAAAATCATGTTATTCAA
* * ** *
4544840 AAATTATTTTTTTGGATTTCA-CTAAAATTGATACATGACATTTC-G
1 AAATT-TTGTTTT---TTTAATCTAAAA---AT-CATGTTA-TTCAA
4544885 AAATTTTGTTTTTTTAATCTAAAAATCATGTTATTCAA
1 AAATTTTGTTTTTTTAATCTAAAAATCATGTTATTCAA
4544923 AAATT
1 AAATT
4544928 ATTTTATGCT
Statistics
Matches: 67, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
37 3 0.04
38 15 0.22
39 8 0.12
41 10 0.15
42 10 0.15
44 8 0.12
45 10 0.15
46 3 0.04
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.48
Consensus pattern (38 bp):
AAATTTTGTTTTTTTAATCTAAAAATCATGTTATTCAA
Found at i:4544905 original size:83 final size:83
Alignment explanation
Indices: 4544766--4544932 Score: 334
Period size: 83 Copynumber: 2.0 Consensus size: 83
4544756 TTGTTCATAA
4544766 TTTTGGATTTCACTAAAATTGATACATGACATTTCGAAATTTTGTTTTTTTAATCTAAAAATCAT
1 TTTTGGATTTCACTAAAATTGATACATGACATTTCGAAATTTTGTTTTTTTAATCTAAAAATCAT
4544831 GTTATTCAAAAATTATTT
66 GTTATTCAAAAATTATTT
4544849 TTTTGGATTTCACTAAAATTGATACATGACATTTCGAAATTTTGTTTTTTTAATCTAAAAATCAT
1 TTTTGGATTTCACTAAAATTGATACATGACATTTCGAAATTTTGTTTTTTTAATCTAAAAATCAT
4544914 GTTATTCAAAAATTATTT
66 GTTATTCAAAAATTATTT
4544932 T
1 T
4544933 ATGCTTTTCA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (83 bp):
TTTTGGATTTCACTAAAATTGATACATGACATTTCGAAATTTTGTTTTTTTAATCTAAAAATCAT
GTTATTCAAAAATTATTT
Found at i:4544907 original size:42 final size:42
Alignment explanation
Indices: 4544778--4544908 Score: 130
Period size: 42 Copynumber: 3.1 Consensus size: 42
4544768 TTGGATTTCA
4544778 CTAAAATTGATACATGACATTTCGAAATTTTGTTTTTTTAAT
1 CTAAAATTGATACATGACATTTCGAAATTTTGTTTTTTTAAT
** * * *
4544820 CTAAAA---AT-CATGTTA-TTCAAAAATTATTTTTTTGGATTTCA-
1 CTAAAATTGATACATGACATTTC-GAAATT-TTGTTTT---TTTAAT
4544861 CTAAAATTGATACATGACATTTCGAAATTTTGTTTTTTTAAT
1 CTAAAATTGATACATGACATTTCGAAATTTTGTTTTTTTAAT
4544903 CTAAAA
1 CTAAAA
4544909 ATCATGTTAT
Statistics
Matches: 68, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
37 3 0.04
38 10 0.15
39 8 0.12
41 10 0.15
42 16 0.24
44 8 0.12
45 10 0.15
46 3 0.04
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (42 bp):
CTAAAATTGATACATGACATTTCGAAATTTTGTTTTTTTAAT
Found at i:4546175 original size:31 final size:31
Alignment explanation
Indices: 4546140--4546235 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
4546130 AAGGCCTACA
4546140 ACAACCTATAAAAAGTAATAAGATGAAGCTC
1 ACAACCTATAAAAAGTAATAAGATGAAGCTC
4546171 ACAACCTATAAAAAGTAATAAGATGAAGCTC
1 ACAACCTATAAAAAGTAATAAGATGAAGCTC
* *
4546202 ACAACCTATAAAAGGCAATAAGATGAAGCTC
1 ACAACCTATAAAAAGTAATAAGATGAAGCTC
4546233 ACA
1 ACA
4546236 TATATTCAGT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.51, C:0.18, G:0.14, T:0.18
Consensus pattern (31 bp):
ACAACCTATAAAAAGTAATAAGATGAAGCTC
Found at i:4546731 original size:26 final size:26
Alignment explanation
Indices: 4546702--4546753 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
4546692 CAAAAAAATT
4546702 CATAATTTTATAAGAAAAGTGGGACC
1 CATAATTTTATAAGAAAAGTGGGACC
4546728 CATAATTTTATAAGAAAAGTGGGACC
1 CATAATTTTATAAGAAAAGTGGGACC
4546754 TCACACCTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (26 bp):
CATAATTTTATAAGAAAAGTGGGACC
Found at i:4547208 original size:81 final size:77
Alignment explanation
Indices: 4547077--4547242 Score: 217
Period size: 81 Copynumber: 2.1 Consensus size: 77
4547067 CAAACGCTCC
*** * *
4547077 TCCAATTGTGTGCGTGTGTGTATGATAGAGAGATACCAAAACGTGCACATATGGATTATAGATTG
1 TCCAATTGTGTGCGTGTGTGTATGATAGAGAGATACCAAAAAACGCACATACGGATTATAGAGTG
*
4547142 CACCCTGGACAG
66 CACACTGGACAG
*
4547154 TCCAATTGTGTGCGTGTGTGTGTATGATAGAGAGAGATACCAAAAAACGCACATACGGGTTATAG
1 TCCAATTGTGTGC--GTGTGTGTATGAT--AGAGAGATACCAAAAAACGCACATACGGATTATAG
4547219 AGTGCACACTGGACAG
62 AGTGCACACTGGACAG
4547235 -CACAATTG
1 TC-CAATTG
4547243 GGTTAAGTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
77 13 0.17
79 13 0.17
80 1 0.01
81 50 0.65
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (77 bp):
TCCAATTGTGTGCGTGTGTGTATGATAGAGAGATACCAAAAAACGCACATACGGATTATAGAGTG
CACACTGGACAG
Found at i:4547304 original size:13 final size:13
Alignment explanation
Indices: 4547286--4547337 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
4547276 TGGTAGTGAA
4547286 TATCATTGTCACT
1 TATCATTGTCACT
4547299 TATCATTGTC-C-
1 TATCATTGTCACT
*
4547310 TA-CA--GT-ATT
1 TATCATTGTCACT
4547319 TATCATTGTCACT
1 TATCATTGTCACT
4547332 TATCAT
1 TATCAT
4547338 ACTATAGGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 4 0.13
11 2 0.06
12 3 0.10
13 18 0.58
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (13 bp):
TATCATTGTCACT
Done.