Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 128 of 163
Found at i:35146196 original size:58 final size:57
Alignment explanation
Indices: 35145804--35146205 Score: 328
Period size: 58 Copynumber: 6.9 Consensus size: 57
35145794 TTAAACCCCC
** * * *
35145804 AAACTTTTTAAAAATTA-CATTATTACCCCTAAATTTTCCAAAATTCCAATTTTGACCCT
1 AAACTTTCCAAAAATTACCATT-TTACCCC-GAATGTT-CAAAATTCCATTTTTGACCCT
* * * *
35145863 AAACTTTCCAAAAATTA-CATTTTACCTC-AATATTTCCCAAAATTCCA-TTTTAACCTT
1 AAACTTTCCAAAAATTACCATTTTACCCCGAAT-GTT--CAAAATTCCATTTTTGACCCT
* * * *
35145920 GAACCTTCCAAAAATTACCATTTTACCCCTGAATGTCTAAAAATTCCATTTTTGACCTT
1 AAACTTTCCAAAAATTACCATTTTACCCC-GAATGT-TCAAAATTCCATTTTTGACCCT
* *
35145979 AAACTTTCCAAAAATTACCATTTTACCCTCGAATGTTTAAAATTCCATCTTTGACCCT
1 AAACTTTCCAAAAATTACCATTTTACCC-CGAATGTTCAAAATTCCATTTTTGACCCT
* * * * * * * * *
35146037 GAACCTTCCAAAAATTACCACTTTACCCCTAAATATATAAAAACTCCATTTTTTACCCC
1 AAACTTTCCAAAAATTACCATTTTACCCC-GAATGT-TCAAAATTCCATTTTTGACCCT
* * * * * * *
35146096 AAAATTT-TAGAAATTACCCTTTTACCCCTAAATATCCAAAAATTCCATTTTTGACCCT
1 AAACTTTCCAAAAATTACCATTTTACCCC-GAATGTTC-AAAATTCCATTTTTGACCCT
* * *
35146154 AAAATTTCTAAAAATTACCATTTTACCTCGAAGTGTTCAAAATTACCATTTT
1 AAACTTTCCAAAAATTACCATTTTACCCCGAA-TGTTCAAAATT-CCATTTT
35146206 ACCCTCGAGC
Statistics
Matches: 285, Mismatches: 44, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
56 3 0.01
57 27 0.09
58 140 0.49
59 110 0.39
60 5 0.02
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.36
Consensus pattern (57 bp):
AAACTTTCCAAAAATTACCATTTTACCCCGAATGTTCAAAATTCCATTTTTGACCCT
Found at i:35146222 original size:28 final size:28
Alignment explanation
Indices: 35146164--35146223 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
35146154 AAAATTTCTA
** *
35146164 AAAATTACCATTTTACCTCGAAGTGTTC
1 AAAATTACCATTTTACCTCGAAGCATCC
35146192 AAAATTACCATTTTACCCTCG-AGCATCC
1 AAAATTACCATTTTA-CCTCGAAGCATCC
35146220 AAAA
1 AAAA
35146224 ATCGCGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 23 0.82
29 5 0.18
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.30
Consensus pattern (28 bp):
AAAATTACCATTTTACCTCGAAGCATCC
Found at i:35146305 original size:22 final size:23
Alignment explanation
Indices: 35146280--35146328 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
35146270 TTATATTTAG
35146280 TTTTA-ATTATCATT-ATTTTGTA
1 TTTTATATTAT-ATTAATTTTGTA
* *
35146302 TTTTATATTCTATTAATTTTTTA
1 TTTTATATTATATTAATTTTGTA
35146325 TTTT
1 TTTT
35146329 TGCGTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTATATTATATTAATTTTGTA
Found at i:35151416 original size:16 final size:16
Alignment explanation
Indices: 35151385--35151422 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
35151375 TAAGTACCAA
35151385 TTAATT-AGTATTAGC
1 TTAATTGAGTATTAGC
*
35151400 TTAATTGAGTCTTAGC
1 TTAATTGAGTATTAGC
35151416 TTAATTG
1 TTAATTG
35151423 GCATGAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (16 bp):
TTAATTGAGTATTAGC
Found at i:35154192 original size:59 final size:59
Alignment explanation
Indices: 35154043--35154466 Score: 547
Period size: 59 Copynumber: 7.3 Consensus size: 59
35154033 ACCCGGGGGC
* *
35154043 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGAAATTTTTGAGAA-TTCG-GGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGA-AAGTTCGAGGGT
* ** *
35154100 AAAATGGTAA-TTTTGGTGACATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * * * * *
35154158 AAAATGGTATTTTTTGGTGAAATCAGGGTTAAAAATAGAATTTTAGAAGGTTTGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * * *
35154217 AAAATGATAATTTTTGGTGAAATCGGGTTTAAAATTGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * *
35154276 AAAATGGTAATTTTTGATAAAATCGGGGTT--AAATGGAATTTTGGAAAGTTCAAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
* *
35154333 AAAATGATAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * * * * *
35154392 AAAATGGTAATTTTCGATGAAATCGGGGTT-AAAATGGAATTTTAGAAGGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
35154450 AAAATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
35154467 AAGTCTCGGG
Statistics
Matches: 318, Mismatches: 44, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
56 2 0.01
57 94 0.30
58 52 0.16
59 170 0.53
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
Found at i:35154312 original size:175 final size:175
Alignment explanation
Indices: 35154043--35154465 Score: 559
Period size: 175 Copynumber: 2.4 Consensus size: 175
35154033 ACCCGGGGGC
* *
35154043 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGAAATTTTTGAGAA-TTC-GGGGTAAAAT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTAGA-AAGTTCGGGGGTAAAAT
* * * * ** * *
35154105 GGTAA-TTTTGGTGACATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTATT
64 GGTAATTTTTGATAAAATCAGGGTT-AAAATGGAATTTTGGAAAGTTCAAGGGTAAAATGATAAT
* *
35154169 TTTTGGTGAAATCAGGGTTAAAAATAGAATTTTAGAAGGTTTGAGGGT
128 TTTTGGTGAAATCAGGGTTAAAAATAGAATTTTAGAAAGTTCGAGGGT
* * *
35154217 AAAATGATAATTTTTGGTGAAATCGGGTTTAAAATTGGAATTTTGGAAAGTTCGGGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAA-TGGAATTTTAGAAAGTTCGGGGGTAAAATG
*
35154282 GTAATTTTTGATAAAATCGGGGTT-AAATGGAATTTTGGAAAGTTCAAGGGTAAAATGATAATTT
65 GTAATTTTTGATAAAATCAGGGTTAAAATGGAATTTTGGAAAGTTCAAGGGTAAAATGATAATTT
** * *
35154346 TTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
130 TTGGTGAAATCAGGGTTAAAAATAGAATTTTAGAAAGTTCGAGGGT
* * * *
35154392 AAAATGGTAATTTTCGATGAAATCGGGGTTAAAATGGAATTTTAGAAGGTTTGGGGGTAAAATGG
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTAGAAAGTTCGGGGGTAAAATGG
35154457 TAATTTTTG
66 TAATTTTTG
35154466 GAAGTCTCGG
Statistics
Matches: 218, Mismatches: 26, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
174 52 0.24
175 137 0.63
176 15 0.07
177 14 0.06
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.35
Consensus pattern (175 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTAGAAAGTTCGGGGGTAAAATGG
TAATTTTTGATAAAATCAGGGTTAAAATGGAATTTTGGAAAGTTCAAGGGTAAAATGATAATTTT
TGGTGAAATCAGGGTTAAAAATAGAATTTTAGAAAGTTCGAGGGT
Found at i:35154375 original size:116 final size:117
Alignment explanation
Indices: 35154043--35154466 Score: 561
Period size: 116 Copynumber: 3.6 Consensus size: 117
35154033 ACCCGGGGGC
* * *
35154043 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGAAATTTTTGAGAA-TTCG-GGGTAAAAT
1 AAAATGGTAATTTTTGATGAAATCGGGGTT-AAAATGGAATTTTAGA-AAGTTCGAGGGTAAAAT
* * * *
35154105 GGTAA-TTTTGGTGACATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT
64 GATAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * * * * *
35154158 AAAATGGTATTTTTTGGTGAAATCAGGGTTAAAAATAGAATTTTAGAAGGTTTGAGGGTAAAATG
1 AAAATGGTAATTTTTGATGAAATCGGGGTT-AAAATGGAATTTTAGAAAGTTCGAGGGTAAAATG
* * * *
35154223 ATAATTTTTGGTGAAATCGGGTTTAAAATTGGAATTTTGGAAAGTTCGGGGGT
65 ATAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * *
35154276 AAAATGGTAATTTTTGATAAAATCGGGGTT-AAATGGAATTTTGGAAAGTTCAAGGGTAAAATGA
1 AAAATGGTAATTTTTGATGAAATCGGGGTTAAAATGGAATTTTAGAAAGTTCGAGGGTAAAATGA
35154340 TAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
66 TAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * * * *
35154392 AAAATGGTAATTTTCGATGAAATCGGGGTTAAAATGGAATTTTAGAAGGTTTGGGGGTAAAATGG
1 AAAATGGTAATTTTTGATGAAATCGGGGTTAAAATGGAATTTTAGAAAGTTCGAGGGTAAAATGA
35154457 TAATTTTTGG
66 TAATTTTTGG
35154467 AAGTCTCGGG
Statistics
Matches: 268, Mismatches: 36, Indels: 8
0.86 0.12 0.03
Matches are distributed among these distances:
115 10 0.04
116 140 0.52
117 51 0.19
118 67 0.25
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (117 bp):
AAAATGGTAATTTTTGATGAAATCGGGGTTAAAATGGAATTTTAGAAAGTTCGAGGGTAAAATGA
TAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
Found at i:35154477 original size:29 final size:28
Alignment explanation
Indices: 35154038--35154491 Score: 167
Period size: 29 Copynumber: 15.6 Consensus size: 28
35154028 TGGACACCCG
* * *
35154038 GGGGCAAAATGGTAATTTTGGTGAA-ATC
1 GGGGTAAAATGGTAATTTTTG-GAAGTTC
*
35154066 GGGGTTAAAAAT-GAAATTTTTGAGAA-TTC
1 GGGG-T-AAAATGGTAATTTTTG-GAAGTTC
* *
35154095 GGGGTAAAATGGTAATTTTGGTGACA-TTA
1 GGGGTAAAATGGTAATTTTTG-GA-AGTTC
* *
35154124 GGGTTAAAAATGG-AA-TTTTGGAAAGTTT
1 GGGGT-AAAATGGTAATTTTTGG-AAGTTC
* *
35154152 GAGGGTAAAATGGTATTTTTTGGTGAA-ATC
1 G-GGGTAAAATGGTAATTTTT-G-GAAGTTC
* * * *
35154182 AGGGTTAAAAATAG-AA-TTTTAGAAGGTTT
1 -GGGGT-AAAATGGTAATTTTTGGAA-GTTC
* *
35154211 GAGGGTAAAATGATAATTTTTGGTGAA-ATC
1 G-GGGTAAAATGGTAATTTTT-G-GAAGTTC
*
35154241 GGGTTTAAAATTGG-AA-TTTTGGAAAGTTC
1 GGG-GTAAAA-TGGTAATTTTTGG-AAGTTC
* **
35154270 GGGGGTAAAATGGTAATTTTTGATAAAATC
1 -GGGGTAAAATGGTAATTTTTG-GAAGTTC
*
35154300 GGGGTTAAATGG-AA-TTTTGGAAAGTTC
1 GGGGTAAAATGGTAATTTTTGG-AAGTTC
* * *
35154327 AAGGGTAAAATGATAATTTTTGGTGAAATT-
1 -GGGGTAAAATGGTAATTTTT-G-GAAGTTC
35154357 GGGGTTAAAAATGG-AA-TTTTGGAAAGTTC
1 GGGG-T-AAAATGGTAATTTTTGG-AAGTTC
* *
35154386 GAGGGTAAAATGGTAATTTTCGATGAA-ATC
1 G-GGGTAAAATGGTAATTTTTG--GAAGTTC
* *
35154416 GGGGTTAAAATGG-AA-TTTTAGAAGGTTTG
1 GGGG-TAAAATGGTAATTTTTGGAA-G-TTC
35154445 GGGGTAAAATGGTAATTTTTGGAAGTCTC
1 GGGGTAAAATGGTAATTTTTGGAAGT-TC
*
35154474 GGGGTCAGAAT-GTAATTT
1 GGGGT-AAAATGGTAATTT
35154492 CCTAAAATTT
Statistics
Matches: 319, Mismatches: 55, Indels: 103
0.67 0.12 0.22
Matches are distributed among these distances:
26 3 0.01
27 21 0.07
28 77 0.24
29 105 0.33
30 82 0.26
31 25 0.08
32 6 0.02
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTTGGAAGTTC
Found at i:35154522 original size:175 final size:169
Alignment explanation
Indices: 35154043--35154524 Score: 473
Period size: 175 Copynumber: 2.8 Consensus size: 169
35154033 ACCCGGGGGC
* * ** *
35154043 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGAAATTTTTG-AGAATTCGGGGTAAAATGG
1 AAAATGGTAATTTTGGTGAAATCGGGGTT-AAAATGGAATTTTAGAAGGTTTGGGGGTAAAATGG
* * * * * *
35154107 TAATTTTGGTGACATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTATTTTT
65 TAATTTTTG-GACATTCGGGGT-AAAATGGAATTTT-AAAATTTTG-GGGTAAAAT-GTAATTTT
* *
35154172 TGGTGAAATCAGGGTTAAAAATAGAATTTTAGAAGGTTTGAGGGT
125 TGGTGAAATCAGGGTTAAAAATAGAATTTTAGAAAGTTCGAGGGT
* * * * *
35154217 AAAATGATAATTTTTGGTGAAATCGGGTTTAAAATTGGAATTTTGGAAAGTTCGGGGGTAAAATG
1 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAA-TGGAATTTTAGAAGGTTTGGGGGTAAAATG
* * * * * ***
35154282 GTAATTTTTGATAAAATCGGGGTTAAATGGAATTTTGGAAAGTTCAAGGGTAAAATGATAATTTT
64 GTAATTTTTG-GACATTCGGGGTAAAATGGAATTTT--AAAATTTTGGGGTAAAATG-TAATTTT
** * *
35154347 TGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
125 TGGTGAAATCAGGGTTAAAAATAGAATTTTAGAAAGTTCGAGGGT
*
35154392 AAAATGGTAATTTTCGATGAAATCGGGGTTAAAATGGAATTTTAGAAGGTTTGGGGGTAAAATGG
1 AAAATGGTAATTTT-GGTGAAATCGGGGTTAAAATGGAATTTTAGAAGGTTTGGGGGTAAAATGG
* * *
35154457 TAATTTTTGGA-AGTCTCGGGGTCAGAATGTAATTTCCTAAAATTTTGGGGTCAAAATGCAATTT
65 TAATTTTTGGACA-T-TCGGGGT-AAAATGGAATTT--TAAAATTTTGGGGT-AAAATGTAATTT
35154521 TTGG
124 TTGG
35154525 ACTGTTTGGG
Statistics
Matches: 250, Mismatches: 46, Indels: 23
0.78 0.14 0.07
Matches are distributed among these distances:
172 1 0.00
173 1 0.00
174 62 0.25
175 146 0.58
176 39 0.16
177 1 0.00
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (169 bp):
AAAATGGTAATTTTGGTGAAATCGGGGTTAAAATGGAATTTTAGAAGGTTTGGGGGTAAAATGGT
AATTTTTGGACATTCGGGGTAAAATGGAATTTTAAAATTTTGGGGTAAAATGTAATTTTTGGTGA
AATCAGGGTTAAAAATAGAATTTTAGAAAGTTCGAGGGT
Found at i:35155266 original size:15 final size:16
Alignment explanation
Indices: 35155246--35155277 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
35155236 TTTAAAACCG
35155246 AACCAGATCTGG-GAA
1 AACCAGATCTGGAGAA
35155261 AACCAGATCTGGAGAA
1 AACCAGATCTGGAGAA
35155277 A
1 A
35155278 TTTCGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (16 bp):
AACCAGATCTGGAGAA
Found at i:35156339 original size:6 final size:6
Alignment explanation
Indices: 35156324--35156412 Score: 78
Period size: 6 Copynumber: 15.0 Consensus size: 6
35156314 TAAATTTGTT
* **
35156324 TTTATAA TTTTAA TTTAAA TTTAAA TTT-AA GGTAAA TTTAAA TAATTAAA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
**
35156374 TTTAAA TTT-AA GGTAAA TTTAAA TTTAAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
35156413 ATCAATTTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
4 4 0.06
5 6 0.09
6 47 0.71
7 3 0.05
8 6 0.09
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:35156359 original size:11 final size:11
Alignment explanation
Indices: 35156345--35156395 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
35156335 AATTTAAATT
35156345 TAAATTTAAGG
1 TAAATTTAAGG
*
35156356 TAAATTTAA-A
1 TAAATTTAAGG
* **
35156366 T-AATTAAATT
1 TAAATTTAAGG
35156376 TAAATTTAAGG
1 TAAATTTAAGG
35156387 TAAATTTAA
1 TAAATTTAA
35156396 ATTTAAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 24 0.75
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (11 bp):
TAAATTTAAGG
Found at i:35156373 original size:31 final size:32
Alignment explanation
Indices: 35156333--35156412 Score: 126
Period size: 31 Copynumber: 2.5 Consensus size: 32
35156323 TTTTATAATT
35156333 TTAATTTAAATTTAAATTTAAGGTAAATTTAAA
1 TTAA-TTAAATTTAAATTTAAGGTAAATTTAAA
35156366 -TAATTAAATTTAAATTTAAGGTAAATTTAAA
1 TTAATTAAATTTAAATTTAAGGTAAATTTAAA
*
35156397 TTTAAATAAATTTAAA
1 -TTAATTAAATTTAAA
35156413 ATCAATTTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
31 28 0.64
32 3 0.07
33 13 0.30
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (32 bp):
TTAATTAAATTTAAATTTAAGGTAAATTTAAA
Found at i:35156414 original size:17 final size:17
Alignment explanation
Indices: 35156339--35156412 Score: 102
Period size: 17 Copynumber: 4.6 Consensus size: 17
35156329 AATTTTAATT
35156339 TAAATTTAAATTTAAGG
1 TAAATTTAAATTTAAGG
*
35156356 TAAATTTAAA--TAA-T
1 TAAATTTAAATTTAAGG
35156370 TAAATTTAAATTTAAGG
1 TAAATTTAAATTTAAGG
*
35156387 TAAATTTAAATTTAA-A
1 TAAATTTAAATTTAAGG
35156403 TAAATTTAAA
1 TAAATTTAAA
35156413 ATCAATTTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
14 10 0.20
15 3 0.06
16 13 0.25
17 25 0.49
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAGG
Found at i:35160503 original size:2 final size:2
Alignment explanation
Indices: 35160498--35160527 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35160488 TTGATTTAGC
35160498 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
35160528 GCGCTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35164154 original size:23 final size:23
Alignment explanation
Indices: 35164085--35164173 Score: 81
Period size: 23 Copynumber: 3.8 Consensus size: 23
35164075 TCATTAACAT
* * *
35164085 TGTTCGTGAACGTGTTCAATTATA
1 TGTTCATGAACATGTTCGATTA-A
* * *
35164109 TGTTCATTAACATGTTTGTTTAA
1 TGTTCATGAACATGTTCGATTAA
*
35164132 TGTTCGTGAACATGTTCGATTAA
1 TGTTCATGAACATGTTCGATTAA
*
35164155 -GTTAAATGAACATGTTCGA
1 TGTT-CATGAACATGTTCGA
35164174 GAACATTAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
22 3 0.06
23 33 0.63
24 16 0.31
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (23 bp):
TGTTCATGAACATGTTCGATTAA
Found at i:35164182 original size:23 final size:23
Alignment explanation
Indices: 35164138--35164183 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
35164128 TTAATGTTCG
* *
35164138 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
35164161 TGAACATGTTCGA-GAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
35164184 CAAACGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.30
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:35166667 original size:160 final size:160
Alignment explanation
Indices: 35166401--35166725 Score: 535
Period size: 160 Copynumber: 2.0 Consensus size: 160
35166391 TGTGCCCGCT
* *
35166401 CGTGTTCTTACTCGAAATAACTCTATTAACTTACATCACATGCTCGTGTGTGAGACAGTGTGTTA
1 CGTGTTCCTACTCGAAATAACTCTATTAACTTACATCACATGCCCGTGTGTGAGACAGTGTGTTA
* * * *
35166466 GACCGTGTGTCTATACGAAAATGGGCCACGCGACTGTGTCCTAGCTTC-TGTACCCTGCACTGTA
66 GACCGTGTGTCTATACGAAAATGGGCCACACGACCGTGTCCTAGC-CCACGTACCCTGCACTGTA
*
35166530 TCTCAAAATAGCACACGACCGTGTGATTACC
130 TCTCAAAATAGCACACGACCGTGTGACTACC
* *
35166561 CGTGTTCCTACTCGAAATAACTCTATTGACTTACATCACATGCCCGTGTGTGATACAGTGTGTTA
1 CGTGTTCCTACTCGAAATAACTCTATTAACTTACATCACATGCCCGTGTGTGAGACAGTGTGTTA
* *
35166626 GAGCGTGTGTCTATACGAAAATGGGCCACACGGCCGTGTCCTAGCCCACGTACCCTGCACTGTAT
66 GACCGTGTGTCTATACGAAAATGGGCCACACGACCGTGTCCTAGCCCACGTACCCTGCACTGTAT
35166691 CTCAAAATAGCACACGACCGTGTGACTACC
131 CTCAAAATAGCACACGACCGTGTGACTACC
35166721 CGTGT
1 CGTGT
35166726 CATAGGTCGC
Statistics
Matches: 153, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
159 1 0.01
160 152 0.99
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (160 bp):
CGTGTTCCTACTCGAAATAACTCTATTAACTTACATCACATGCCCGTGTGTGAGACAGTGTGTTA
GACCGTGTGTCTATACGAAAATGGGCCACACGACCGTGTCCTAGCCCACGTACCCTGCACTGTAT
CTCAAAATAGCACACGACCGTGTGACTACC
Found at i:35169148 original size:26 final size:26
Alignment explanation
Indices: 35169119--35169171 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
35169109 CATAAGGTTG
*
35169119 TTGCATTTCATAGTTTCAAAAACCTA
1 TTGCATTCCATAGTTTCAAAAACCTA
35169145 TTGCATTCCATAGTTTCAAAAACCTA
1 TTGCATTCCATAGTTTCAAAAACCTA
35169171 T
1 T
35169172 CATACTTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.38
Consensus pattern (26 bp):
TTGCATTCCATAGTTTCAAAAACCTA
Found at i:35170725 original size:21 final size:20
Alignment explanation
Indices: 35170701--35170747 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
35170691 CCATTAAGCT
* *
35170701 TTAATTAACCCTTTTTAAATC
1 TTAATTAAACCTATTTAAA-C
*
35170722 TTAATTAAACCTATTTATAC
1 TTAATTAAACCTATTTAAAC
35170742 TTAATT
1 TTAATT
35170748 TAACTCATGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAATTAAACCTATTTAAAC
Found at i:35172189 original size:2 final size:2
Alignment explanation
Indices: 35172182--35172207 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35172172 TTAGTTCAAT
35172182 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
35172208 ACTATTGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35175379 original size:82 final size:84
Alignment explanation
Indices: 35175228--35175448 Score: 218
Period size: 84 Copynumber: 2.6 Consensus size: 84
35175218 TCTAAATGTA
** * * * *
35175228 TAAATGGAAGACTCATGTCTCGGGTTGAGCATGAGAAATTATATAAAAGGAAGACTCGTGACTCG
1 TAAATGGAAGACTCATGTCTCAAGATGAGAATGAG-AATTATATAAAAGGAAGACTCATGACTCA
35175293 GAATGAGCATGAGAATATTT
65 GAATGAGCATGAGAATATTT
* * * *
35175313 TAAA-GGAAGACTCGTGTCTCAAGATGAGAATGAG-ATTATGTTAAAGGAAGACTCATGCCTCAG
1 TAAATGGAAGACTCATGTCTCAAGATGAGAATGAGAATTATATAAAAGGAAGACTCATGACTCAG
*
35175376 AATGAGCGTGAGAATATGTT
66 AATGAGCATGAGAATAT-TT
* * * * * *
35175396 CAAAAAGGAAGACTTATGACTCAATA-GAGAATAAG-ATTAT-TAAAAAGGAAGAC
1 -TAAATGGAAGACTCATGTCTCAAGATGAGAATGAGAATTATAT-AAAAGGAAGAC
35175449 ATATGAACCT
Statistics
Matches: 114, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
82 40 0.35
83 3 0.03
84 51 0.45
85 20 0.18
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.24
Consensus pattern (84 bp):
TAAATGGAAGACTCATGTCTCAAGATGAGAATGAGAATTATATAAAAGGAAGACTCATGACTCAG
AATGAGCATGAGAATATTT
Found at i:35175394 original size:41 final size:41
Alignment explanation
Indices: 35175223--35175418 Score: 169
Period size: 41 Copynumber: 4.6 Consensus size: 41
35175213 GAAAATCTAA
* * **
35175223 ATGTATAAATGGAAGACTCATGTCTCGGGTTGAGCATGAGAAATT
1 ATGT-TAAA-GGAAGACTCATGACTCAGAATGAGCATGAG-AA-T
* * * *
35175268 ATATAAAAGGAAGACTCGTGACTCGGAATGAGCATGAGAAT
1 ATGTTAAAGGAAGACTCATGACTCAGAATGAGCATGAGAAT
* * * * *
35175309 ATTTTAAAGGAAGACTCGTGTCTCA-AGATGAGAATGAGATT
1 ATGTTAAAGGAAGACTCATGACTCAGA-ATGAGCATGAGAAT
* *
35175350 ATGTTAAAGGAAGACTCATGCCTCAGAATGAGCGTGAGAAT
1 ATGTTAAAGGAAGACTCATGACTCAGAATGAGCATGAGAAT
*
35175391 ATGTTCAAAAAGGAAGACTTATGACTCA
1 ATGTT---AAAGGAAGACTCATGACTCA
35175419 ATAGAGAATA
Statistics
Matches: 126, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
40 1 0.01
41 72 0.57
42 3 0.02
43 26 0.21
44 21 0.17
45 3 0.02
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (41 bp):
ATGTTAAAGGAAGACTCATGACTCAGAATGAGCATGAGAAT
Found at i:35175448 original size:84 final size:82
Alignment explanation
Indices: 35175265--35175448 Score: 210
Period size: 82 Copynumber: 2.2 Consensus size: 82
35175255 AGCATGAGAA
* * * * * *
35175265 ATTATATAAAAGGAAGACTCGTGACTCGGAATGAGCATGAGAATATTTTAAAGGAAGACTCGTGT
1 ATTATGTAAAAGGAAGACTCATGACTCAGAATGAGCATGAGAATATTTAAAAGGAAGACTCATGA
*
35175330 CTCAAGATGAGAATGAG
66 CTCAAGATGAGAATAAG
* * * *
35175347 ATTATGTTAAAGGAAGACTCATGCCTCAGAATGAGCGTGAGAATATGTTCAAAAAGGAAGACTTA
1 ATTATGTAAAAGGAAGACTCATGACTCAGAATGAGCATGAGAATAT-TT--AAAAGGAAGACTCA
*
35175412 TGACTCAATA-GAGAATAAG
63 TGACTCAAGATGAGAATAAG
35175431 ATTAT-TAAAAAGGAAGAC
1 ATTATGT-AAAAGGAAGAC
35175449 ATATGAACCT
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
82 40 0.47
83 3 0.04
84 23 0.27
85 19 0.22
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.24
Consensus pattern (82 bp):
ATTATGTAAAAGGAAGACTCATGACTCAGAATGAGCATGAGAATATTTAAAAGGAAGACTCATGA
CTCAAGATGAGAATAAG
Found at i:35176158 original size:21 final size:21
Alignment explanation
Indices: 35176134--35176177 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
35176124 TAGAAGGATG
35176134 ACTTGT-TTCGGTAGAAGTTAC
1 ACTTGTATT-GGTAGAAGTTAC
35176155 ACTTGTATTGGTAGAAGTTAC
1 ACTTGTATTGGTAGAAGTTAC
35176176 AC
1 AC
35176178 AAGTATCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (21 bp):
ACTTGTATTGGTAGAAGTTAC
Found at i:35176183 original size:21 final size:21
Alignment explanation
Indices: 35176141--35176190 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
35176131 ATGACTTGTT
**
35176141 TCGGTAGAAGTTACACTTGTA
1 TCGGTAGAAGTTACACAAGTA
*
35176162 TTGGTAGAAGTTACACAAGTA
1 TCGGTAGAAGTTACACAAGTA
35176183 TCGGTAGA
1 TCGGTAGA
35176191 CATCTGCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (21 bp):
TCGGTAGAAGTTACACAAGTA
Found at i:35179779 original size:160 final size:159
Alignment explanation
Indices: 35179490--35179812 Score: 574
Period size: 160 Copynumber: 2.0 Consensus size: 159
35179480 ATTAGTGAAT
*
35179490 CTTCTTCTACTCTGCCCGTGGTTTTTTCCCGAAATGGTTTCCACATAAAATCTGTGTGTGTTTTT
1 CTTCTTCTACTCTGCCAGTGGTTTTTTCCCGAAATGGTTTCCACATAAAATCTGTGTGTGTTTTT
* *
35179555 TTCTGTTTTCTTTGCTATATTTCTTCATTGTCGAAATTTAATGTTATCAGACCACACTAATATTG
66 TTCTGTTTTCTTTGCAATATTTCTTCATTGTCGAAATTTAATGTTATCAGACCACACCAATATTG
35179620 TTACCCAGATCAAAAAACAAATTACTAAA
131 TTACCCAGATCAAAAAACAAATTACTAAA
* * *
35179649 CTTCTTCTACTCTGCCAGTGGTTTTTTCTCGAAATGGTTTCCTCGTAAAATCTGTGTGTGTTTTT
1 CTTCTTCTACTCTGCCAGTGGTTTTTTCCCGAAATGGTTTCCACATAAAATCTGTGTGTG-TTTT
*
35179714 TTTCTGTTTTCTTTGCAATATTTCTTCATTGTCGAAATTTAATTTTATCAGACCACACCAATATT
65 TTTCTGTTTTCTTTGCAATATTTCTTCATTGTCGAAATTTAATGTTATCAGACCACACCAATATT
35179779 GTTACCCAGATCAAAAAACAAATTACTAAA
130 GTTACCCAGATCAAAAAACAAATTACTAAA
35179809 CTTC
1 CTTC
35179813 CCTATTTACA
Statistics
Matches: 156, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
159 56 0.36
160 100 0.64
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (159 bp):
CTTCTTCTACTCTGCCAGTGGTTTTTTCCCGAAATGGTTTCCACATAAAATCTGTGTGTGTTTTT
TTCTGTTTTCTTTGCAATATTTCTTCATTGTCGAAATTTAATGTTATCAGACCACACCAATATTG
TTACCCAGATCAAAAAACAAATTACTAAA
Found at i:35189355 original size:3 final size:3
Alignment explanation
Indices: 35189347--35189384 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
35189337 CCATAGATAC
35189347 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
35189385 ATCAAAATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:35195448 original size:29 final size:29
Alignment explanation
Indices: 35195400--35195456 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
35195390 ATATAAACAC
*
35195400 AAATATGACATAATTATATA-AACATATAA
1 AAATATGACAAAATTATATATAA-ATATAA
35195429 AAATATGACAAAAATT-TATATAAATATA
1 AAATATGAC-AAAATTATATATAAATATA
35195457 TAACATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.32
Consensus pattern (29 bp):
AAATATGACAAAATTATATATAAATATAA
Found at i:35195451 original size:31 final size:29
Alignment explanation
Indices: 35195400--35195459 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
35195390 ATATAAACAC
*
35195400 AAATATGACATAATTATATAAACATATAA
1 AAATATGACAAAATTATATAAACATATAA
*
35195429 AAATATGACAAAAATTTATATAAATATATAA
1 AAATATGAC-AAAA-TTATATAAACATATAA
35195460 CATTTTAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 9 0.33
30 3 0.11
31 15 0.56
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (29 bp):
AAATATGACAAAATTATATAAACATATAA
Found at i:35197138 original size:23 final size:23
Alignment explanation
Indices: 35197094--35197169 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 23
35197084 AGTTTTTACA
*
35197094 ATTTTATGT-TATATATCGTTTATT
1 ATTTTATGTATAT-TAT-TTTTATT
35197118 ATTTTATGTATATTATTTTTA-T
1 ATTTTATGTATATTATTTTTATT
*
35197140 ATTTTAT-TATAAATTATTTATTTTT
1 ATTTTATGTAT--ATTATTT-TTATT
35197165 ATTTT
1 ATTTT
35197170 TATTTTTATG
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
21 3 0.07
22 8 0.18
23 11 0.24
24 14 0.31
25 9 0.20
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.67
Consensus pattern (23 bp):
ATTTTATGTATATTATTTTTATT
Found at i:35197167 original size:6 final size:6
Alignment explanation
Indices: 35197130--35197178 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
35197120 TTTATGTATA
**
35197130 TTATTT TTATATT TTATTAT AAATTAT TTATTT TTATTT TTATTT TTAT
1 TTATTT TTAT-TT TTATT-T TTATT-T TTATTT TTATTT TTATTT TTAT
35197179 GTTATTAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 22 0.59
7 15 0.41
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (6 bp):
TTATTT
Found at i:35197183 original size:27 final size:27
Alignment explanation
Indices: 35197116--35197184 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
35197106 ATATCGTTTA
35197116 TTATTTTATG-TATATTATTTTTATATT
1 TTATTTTATGTTAT-TTATTTTTATATT
* **
35197143 TTATTATAAATTATTTATTTTTAT-TT
1 TTATTTTATGTTATTTATTTTTATATT
35197169 TTATTTTTATGTTATT
1 TTA-TTTTATGTTATT
35197185 AATGTGTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
26 5 0.15
27 26 0.76
28 3 0.09
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (27 bp):
TTATTTTATGTTATTTATTTTTATATT
Found at i:35209006 original size:24 final size:24
Alignment explanation
Indices: 35208971--35209021 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
35208961 ATATACTAGT
*
35208971 TAACCATTTTGGGCTCGTAAGAGC
1 TAACCATCTTGGGCTCGTAAGAGC
*
35208995 TAACCATCTTGGGCTCGTGAGAGC
1 TAACCATCTTGGGCTCGTAAGAGC
35209019 TAA
1 TAA
35209022 ATTTGTTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.27
Consensus pattern (24 bp):
TAACCATCTTGGGCTCGTAAGAGC
Found at i:35209036 original size:25 final size:26
Alignment explanation
Indices: 35209003--35209052 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
35208993 GCTAACCATC
35209003 TTGGGCTCGTGA-GAGCT-AAATTTGT
1 TTGGGCTCGT-ATGAGCTAAAATTTGT
35209028 TTGGGCTCGTATGAGCTAAAATTTG
1 TTGGGCTCGTATGAGCTAAAATTTG
35209053 GAAGACTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 1 0.04
25 15 0.65
26 7 0.30
ACGTcount: A:0.22, C:0.12, G:0.30, T:0.36
Consensus pattern (26 bp):
TTGGGCTCGTATGAGCTAAAATTTGT
Found at i:35209814 original size:21 final size:21
Alignment explanation
Indices: 35209764--35209803 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
35209754 CGATAGATGA
*
35209764 GTCACTTGTATCGGTAGAACT
1 GTCACTTATATCGGTAGAACT
35209785 GTCACTTATATCGGTAGAA
1 GTCACTTATATCGGTAGAA
35209804 GTCTGTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (21 bp):
GTCACTTATATCGGTAGAACT
Found at i:35211914 original size:47 final size:47
Alignment explanation
Indices: 35211860--35211954 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
35211850 AAGGACCTAC
35211860 TATGTCGAGTGCACAATCTCCAATGGTCTTCTAACTCATTGAGATTT
1 TATGTCGAGTGCACAATCTCCAATGGTCTTCTAACTCATTGAGATTT
35211907 TATGTCGAGTGCACAATCTCCAATGGTCTTCTAACTCATTGAGATTT
1 TATGTCGAGTGCACAATCTCCAATGGTCTTCTAACTCATTGAGATTT
35211954 T
1 T
35211955 CCAACTTCAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (47 bp):
TATGTCGAGTGCACAATCTCCAATGGTCTTCTAACTCATTGAGATTT
Found at i:35218031 original size:130 final size:128
Alignment explanation
Indices: 35217887--35218159 Score: 467
Period size: 130 Copynumber: 2.1 Consensus size: 128
35217877 ATTGATGTTG
*
35217887 TTGTTGTTGTTGTTGTGACCATTTTATAACTTTTTAAAGTTCGATAACCAAAAAAGAAACTTACC
1 TTGTTGTTGTTGTTGTGACCATTTTACAACTTTTTAAAGTTCGATAACCAAAAAAGAAACTTACC
*
35217952 AATATAGTTGGGCAACTTCCAATGTAATTTACCTTCTATTTTTT-GGGTTGAAGTTGGTTTTAAT
66 -A-ATAGTTGGGCAACTACCAATGTAA-TTACCTTCTATTTTTTGGGGTTGAAGTTGGTTTTAAT
35218016 T
128 T
*
35218017 TTGTTGTTGTTGTTGTGACCATTTTACAACTTTTTAGAGTTCGATAACCAAAAAAGAAACTTACC
1 TTGTTGTTGTTGTTGTGACCATTTTACAACTTTTTAAAGTTCGATAACCAAAAAAGAAACTTACC
**
35218082 AATAGTTGGGTGACTACCAATGTAATTACCTTCTATTTTTTGGGGTTGAAGTTGGTTTTAATT
66 AATAGTTGGGCAACTACCAATGTAATTACCTTCTATTTTTTGGGGTTGAAGTTGGTTTTAATT
35218145 TTGTTGTTGTTGTTG
1 TTGTTGTTGTTGTTG
35218160 CTGCTGCTGC
Statistics
Matches: 137, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
127 16 0.12
128 57 0.42
129 1 0.01
130 63 0.46
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (128 bp):
TTGTTGTTGTTGTTGTGACCATTTTACAACTTTTTAAAGTTCGATAACCAAAAAAGAAACTTACC
AATAGTTGGGCAACTACCAATGTAATTACCTTCTATTTTTTGGGGTTGAAGTTGGTTTTAATT
Found at i:35218203 original size:24 final size:24
Alignment explanation
Indices: 35218176--35218239 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 24
35218166 CTGCTGCTGC
35218176 AAGAAGAAAAAAATAAATTGCTCA
1 AAGAAGAAAAAAATAAATTGCTCA
* *
35218200 AAGAACATAAAAAAAAAAATTGCTCA
1 AAG-A-AGAAAAAAATAAATTGCTCA
*
35218226 AA-ACGAAAAAAATA
1 AAGAAGAAAAAAATA
35218240 TGAGGATTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
23 8 0.24
24 4 0.12
25 1 0.03
26 20 0.61
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.14
Consensus pattern (24 bp):
AAGAAGAAAAAAATAAATTGCTCA
Found at i:35219070 original size:30 final size:30
Alignment explanation
Indices: 35219036--35219092 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
35219026 TTTTATAATT
* *
35219036 TTTAT-AATGTTTTACAAAATTTTAATACTA
1 TTTATCAAT-TTTTAAAAAAATTTAATACTA
*
35219066 TTTATCTATTTTTAAAAAAATTTAATA
1 TTTATCAATTTTTAAAAAAATTTAATA
35219093 TATAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 21 0.91
31 2 0.09
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (30 bp):
TTTATCAATTTTTAAAAAAATTTAATACTA
Found at i:35220946 original size:42 final size:42
Alignment explanation
Indices: 35220887--35221008 Score: 208
Period size: 42 Copynumber: 2.9 Consensus size: 42
35220877 GATTTTAGAG
*
35220887 TATGATTCGAACTCATACCATATCTGAAGTAATGAATACCAA
1 TATGATTCGAACTCATACCATATCTGAAGTAATGAACACCAA
* * *
35220929 TATGATTTGAACCCATACTATATCTGAAGTAATGAACACCAA
1 TATGATTCGAACTCATACCATATCTGAAGTAATGAACACCAA
35220971 TATGATTCGAACTCATACCATATCTGAAGTAATGAACA
1 TATGATTCGAACTCATACCATATCTGAAGTAATGAACA
35221009 TCCTAACTAT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (42 bp):
TATGATTCGAACTCATACCATATCTGAAGTAATGAACACCAA
Found at i:35221873 original size:30 final size:30
Alignment explanation
Indices: 35221808--35221885 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
35221798 TTTAAACTTT
* * * *
35221808 AATATGAGAACAATTGTTAAGTTCAAGTTTC
1 AATATGAGGACAATT-ATCAGTTCAAGTCTC
* *
35221839 AATATGAGGATAATTATCAGTTTAAGTCTC
1 AATATGAGGACAATTATCAGTTCAAGTCTC
35221869 AATATGAGGACAATTAT
1 AATATGAGGACAATTAT
35221886 TAAATTTAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 27 0.68
31 13 0.32
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.35
Consensus pattern (30 bp):
AATATGAGGACAATTATCAGTTCAAGTCTC
Found at i:35238531 original size:24 final size:23
Alignment explanation
Indices: 35238491--35238536 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
35238481 TCCCTTCAAA
*
35238491 TTTATAAAAAATATATATATATT
1 TTTATAAAAAATATATACATATT
35238514 TTTA-AAAAAATAAGTATACATAT
1 TTTATAAAAAAT-A-TATACATAT
35238537 GTCAAACATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 5 0.25
24 8 0.40
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TTTATAAAAAATATATACATATT
Found at i:35269775 original size:22 final size:25
Alignment explanation
Indices: 35269741--35269786 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
35269731 TATAATATAC
35269741 TTTTTGATCATAA-TTT-TAAAATT
1 TTTTTGATCATAACTTTATAAAATT
*
35269764 TTTTTG-TTATAACTTTATAAAAT
1 TTTTTGATCATAACTTTATAAAAT
35269787 ACACAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (25 bp):
TTTTTGATCATAACTTTATAAAATT
Found at i:35270145 original size:20 final size:19
Alignment explanation
Indices: 35270120--35270216 Score: 79
Period size: 20 Copynumber: 4.9 Consensus size: 19
35270110 AAATGGTACA
35270120 TCATAATTTTTGGTATTGCC
1 TCATAATTTTTGGTATT-CC
** *
35270140 TCATAATAATTGGTATATAC
1 TCATAATTTTTGGTAT-TCC
* * *
35270160 TTATAATTATTGGTATCCC
1 TCATAATTTTTGGTATTCC
*
35270179 TACA-AATTTTTTAGTACTTCC
1 T-CATAA-TTTTTGGTA-TTCC
35270200 TCATAATTTTTGGTATT
1 TCATAATTTTTGGTATT
35270217 GTTTCAAAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 11
0.72 0.14 0.13
Matches are distributed among these distances:
19 6 0.10
20 47 0.78
21 7 0.12
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.48
Consensus pattern (19 bp):
TCATAATTTTTGGTATTCC
Found at i:35270330 original size:14 final size:14
Alignment explanation
Indices: 35270313--35270342 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
35270303 TGTAACGAAA
*
35270313 AAATTGTAATTTTT
1 AAATTATAATTTTT
35270327 AAATTATAATTTTT
1 AAATTATAATTTTT
35270341 AA
1 AA
35270343 TGCTAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
AAATTATAATTTTT
Found at i:35270697 original size:18 final size:18
Alignment explanation
Indices: 35270659--35270697 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
35270649 TGTGTTTTAT
*
35270659 TTTTGGTATTCTCCCATA
1 TTTTGGTATTCTCCCAAA
* *
35270677 TTTTGGTATTTTCTCAAA
1 TTTTGGTATTCTCCCAAA
35270695 TTT
1 TTT
35270698 ATTGGTACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.15, G:0.10, T:0.56
Consensus pattern (18 bp):
TTTTGGTATTCTCCCAAA
Found at i:35270807 original size:19 final size:21
Alignment explanation
Indices: 35270772--35270817 Score: 69
Period size: 19 Copynumber: 2.3 Consensus size: 21
35270762 ACTTTCTAAT
35270772 ATTTTTTAGTATCCCCTCATA
1 ATTTTTTAGTATCCCCTCATA
35270793 ATTTTTTA-TAT-CCCTCATA
1 ATTTTTTAGTATCCCCTCATA
*
35270812 ACTTTT
1 ATTTTT
35270818 GGTATTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 13 0.54
20 3 0.12
21 8 0.33
ACGTcount: A:0.24, C:0.22, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTTTTTAGTATCCCCTCATA
Found at i:35270850 original size:20 final size:19
Alignment explanation
Indices: 35270747--35270850 Score: 68
Period size: 20 Copynumber: 5.3 Consensus size: 19
35270737 ATGGTGTTCT
* *
35270747 CTCATAATTTTTTGTACTTT
1 CTCATAATTTTTTATA-TTC
* *
35270767 CTAAT-ATTTTTTAGTATCCC
1 CTCATAATTTTTTA-TAT-TC
*
35270787 CTCATAATTTTTTATATCC
1 CTCATAATTTTTTATATTC
* *
35270806 CTCATAACTTTTGGTAT-TTG
1 CTCATAA-TTTT-TTATATTC
*
35270826 ATCATAATTTTTTATACTTC
1 CTCATAATTTTTTATA-TTC
35270846 CTCAT
1 CTCAT
35270851 GTTTTTTAGG
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.05
19 21 0.32
20 30 0.46
21 11 0.17
ACGTcount: A:0.24, C:0.18, G:0.05, T:0.53
Consensus pattern (19 bp):
CTCATAATTTTTTATATTC
Found at i:35270876 original size:40 final size:40
Alignment explanation
Indices: 35270714--35270878 Score: 138
Period size: 40 Copynumber: 4.2 Consensus size: 40
35270704 ACATCCTTAT
* * * *
35270714 TTTTTTATACTTCTTCA-AGTTTTATGGTGTTCTCTCATAA
1 TTTTTTATACTTCCTCATA-TTTTTTGGTATTCCCTCATAA
* * * * *
35270754 TTTTTTGTACTTTCTAATATTTTTTAGTATCCCCTCATAA
1 TTTTTTATACTTCCTCATATTTTTTGGTATTCCCTCATAA
* ** ***
35270794 TTTTTTATA-TCCCTCATAACTTTTGGTATTTGATCATAA
1 TTTTTTATACTTCCTCATATTTTTTGGTATTCCCTCATAA
* *
35270833 TTTTTTATACTTCCTCATGTTTTTTAGGCATTCCCTCAT-A
1 TTTTTTATACTTCCTCATATTTTTT-GGTATTCCCTCATAA
35270873 TTTTTT
1 TTTTTT
35270879 GGAATTCATA
Statistics
Matches: 94, Mismatches: 28, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
39 29 0.31
40 55 0.59
41 10 0.11
ACGTcount: A:0.21, C:0.17, G:0.07, T:0.55
Consensus pattern (40 bp):
TTTTTTATACTTCCTCATATTTTTTGGTATTCCCTCATAA
Found at i:35270885 original size:20 final size:21
Alignment explanation
Indices: 35270845--35270885 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
35270835 TTTTATACTT
* *
35270845 CCTCATGTTTTTTAGGCATTC
1 CCTCATATTTTTTAGGAATTC
35270866 CCTCATATTTTTT-GGAATTC
1 CCTCATATTTTTTAGGAATTC
35270886 ATAATTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.17, C:0.22, G:0.12, T:0.49
Consensus pattern (21 bp):
CCTCATATTTTTTAGGAATTC
Found at i:35271278 original size:21 final size:20
Alignment explanation
Indices: 35271252--35271317 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
35271242 TTCCTCAAAA
35271252 TTTTTGATATTCTCTCATAAT
1 TTTTTGATATT-TCTCATAAT
*
35271273 TTTTTG-TATTTCCTCA-AGTT
1 TTTTTGATATTT-CTCATA-AT
*
35271293 TTTTTTATATTTTCTCATAAT
1 TTTTTGATA-TTTCTCATAAT
35271314 TTTT
1 TTTT
35271318 CGTAGTTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
19 2 0.05
20 14 0.38
21 17 0.46
22 4 0.11
ACGTcount: A:0.20, C:0.12, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTTTGATATTTCTCATAAT
Found at i:35271426 original size:21 final size:21
Alignment explanation
Indices: 35271376--35271427 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
35271366 TATACTTAGA
* * *
35271376 TTTTTTGGTGATTCCTTATAT
1 TTTTTTTGTAATTCCTCATAT
*
35271397 TTCTTTTTGTAATTCCTCATGT
1 TT-TTTTTGTAATTCCTCATAT
35271419 TTTTTTTGT
1 TTTTTTTGT
35271428 GGTTGCTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.65
Consensus pattern (21 bp):
TTTTTTTGTAATTCCTCATAT
Found at i:35271627 original size:21 final size:20
Alignment explanation
Indices: 35271577--35271627 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
35271567 ACTTTCTTTT
*
35271577 ATTTTTA-TATTTTCTCATA
1 ATTTTTAGTATTTTCTCAAA
*
35271596 ATTTTTGGTATTTTCTCAAA
1 ATTTTTAGTATTTTCTCAAA
35271616 ATTTTTTAGTAT
1 A-TTTTTAGTAT
35271628 ATCCTCAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 6 0.22
20 12 0.44
21 9 0.33
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.61
Consensus pattern (20 bp):
ATTTTTAGTATTTTCTCAAA
Found at i:35271999 original size:21 final size:20
Alignment explanation
Indices: 35271956--35272002 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
35271946 TTAGGGTATT
*
35271956 AAAAAATATGAGAGAATATC
1 AAAAAATATGAGAGAATACC
* *
35271976 AAAAAATATGATGTGAGTACC
1 AAAAAATATGA-GAGAATACC
35271997 AAAAAA
1 AAAAAA
35272003 CATAACGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.60, C:0.06, G:0.15, T:0.19
Consensus pattern (20 bp):
AAAAAATATGAGAGAATACC
Found at i:35274691 original size:18 final size:18
Alignment explanation
Indices: 35274654--35274702 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
35274644 TAATTTTAAA
35274654 AAATATTTTTATACTTTTT
1 AAATATTTTTA-ACTTTTT
35274673 AAATGATTTTTAA-TTTTT
1 AAAT-ATTTTTAACTTTTT
*
35274691 AAAAATTTTTAA
1 AAATATTTTTAA
35274703 AAATCAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 8 0.29
18 8 0.29
19 5 0.18
20 7 0.25
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
AAATATTTTTAACTTTTT
Found at i:35274696 original size:20 final size:19
Alignment explanation
Indices: 35274644--35274700 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 19
35274634 CTTTTTAAAA
*
35274644 TAATTTTAAAAAATATTTT
1 TAATTTTTAAAAATATTTT
35274663 TATACTTTTT--AAATGATTTT
1 TA-A-TTTTTAAAAAT-ATTTT
35274683 TAATTTTTAAAAAT-TTTT
1 TAATTTTTAAAAATATTTT
35274701 AAAAATCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
18 9 0.28
19 7 0.22
20 12 0.38
21 4 0.12
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TAATTTTTAAAAATATTTT
Found at i:35276134 original size:26 final size:28
Alignment explanation
Indices: 35276087--35276147 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 28
35276077 TACCTCATTA
35276087 AAATATTT--TAATCGAAATTAATGTTT
1 AAATATTTAATAATCGAAATTAATGTTT
*
35276113 AAATATTTAATAAT-GAAA-TAATTTTT
1 AAATATTTAATAATCGAAATTAATGTTT
*
35276139 TAAT-TTTAA
1 AAATATTTAA
35276148 CAAAATGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 5 0.16
26 18 0.58
27 4 0.13
28 4 0.13
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (28 bp):
AAATATTTAATAATCGAAATTAATGTTT
Found at i:35289385 original size:17 final size:17
Alignment explanation
Indices: 35289365--35289403 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
35289355 AATTTTTAGT
*
35289365 ATATTAA-AATATTATTC
1 ATATTAATAAT-TTATAC
35289382 ATATTAATAATTTATAC
1 ATATTAATAATTTATAC
35289399 ATATT
1 ATATT
35289404 TTTATCAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATTAATAATTTATAC
Found at i:35299745 original size:20 final size:20
Alignment explanation
Indices: 35299700--35299753 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
35299690 TTATTAAAAT
35299700 AATAAAATTATAATTAGTTA
1 AATAAAATTATAATTAGTTA
35299720 TAA-AAATATT-TAATTA-TTA
1 -AATAAA-ATTATAATTAGTTA
35299739 AATAAAATTATAATT
1 AATAAAATTATAATT
35299754 TGCATTATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
18 5 0.17
19 11 0.37
20 9 0.30
21 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
AATAAAATTATAATTAGTTA
Found at i:35302723 original size:18 final size:18
Alignment explanation
Indices: 35302700--35302745 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
35302690 GTTTAAATTG
**
35302700 ATTTAAATTTATTTTTAA
1 ATTTAAATTTAGCTTTAA
35302718 ATTTAAATTT-GCTTTAA
1 ATTTAAATTTAGCTTTAA
*
35302735 ATTTGAATTTA
1 ATTTAAATTTA
35302746 ATTAAATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (18 bp):
ATTTAAATTTAGCTTTAA
Found at i:35302766 original size:16 final size:16
Alignment explanation
Indices: 35302695--35302767 Score: 73
Period size: 16 Copynumber: 4.8 Consensus size: 16
35302685 ATTAGGTTTA
35302695 AATTGATTTAAATTT-
1 AATTGATTTAAATTTG
*
35302710 -ATT--TTTAAATTTA
1 AATTGATTTAAATTTG
*
35302723 AATTTGCTTTAAATTTG
1 AA-TTGATTTAAATTTG
* *
35302740 AATTTAATTAAATTTG
1 AATTGATTTAAATTTG
35302756 AATTGATTTAAA
1 AATTGATTTAAA
35302768 ACTTAATATT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
12 9 0.19
14 4 0.09
15 2 0.04
16 21 0.45
17 11 0.23
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.52
Consensus pattern (16 bp):
AATTGATTTAAATTTG
Found at i:35303505 original size:3 final size:3
Alignment explanation
Indices: 35303497--35303544 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
35303487 TGAAATGAAT
** * * *
35303497 TAA TAA TAA TAA TAA TTT TAA TAA TAA AAA TAT TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35303545 ATATTTATAA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:35303517 original size:18 final size:18
Alignment explanation
Indices: 35303495--35303549 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
35303485 CATGAAATGA
35303495 ATTAATAATAATAATAATT
1 ATTAATAATAATAAT-ATT
*
35303514 -TTAATAATAAAAATATT
1 ATTAATAATAATAATATT
*
35303531 AGTAATAATAATAAATATT
1 ATTAATAATAAT-AATATT
35303550 TATAAGATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 3 0.10
18 22 0.71
19 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATTAATAATAATAATATT
Found at i:35303520 original size:15 final size:15
Alignment explanation
Indices: 35303500--35303543 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
35303490 AATGAATTAA
*
35303500 TAATAATAATAATTT
1 TAATAATAATAATAT
*
35303515 TAATAATAAAAATAT
1 TAATAATAATAATAT
*
35303530 TAGTAATAATAATA
1 TAATAATAATAATA
35303544 AATATTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (15 bp):
TAATAATAATAATAT
Found at i:35304776 original size:29 final size:28
Alignment explanation
Indices: 35304733--35304883 Score: 90
Period size: 29 Copynumber: 5.2 Consensus size: 28
35304723 CTAAACTTCT
*
35304733 AAAAATTCTACTTTTAACCTCGATTTTCC
1 AAAAATTCCA-TTTTAACCTCGATTTTCC
* * *
35304762 AAAAATTACCATTTTACCCTCAAACTTT-C
1 AAAAATT-CCATTTTAACCTC-GATTTTCC
* *
35304791 TAAAATTCCATTTTGA-CTCTGATTTTTCC
1 AAAAATTCCATTTTAACCTC-GA-TTTTCC
** * ** *
35304820 AAAAATTAATATTTTACCCTCGAACTTCT
1 AAAAATT-CCATTTTAACCTCGATTTTCC
* *
35304849 AAAAATTCCATTTTTGACCTCAATTTTTCC
1 AAAAATTCCA-TTTTAACCTCGA-TTTTCC
35304879 AAAAA
1 AAAAA
35304884 ATATCATTGT
Statistics
Matches: 88, Mismatches: 26, Indels: 15
0.68 0.20 0.12
Matches are distributed among these distances:
27 4 0.05
28 11 0.12
29 49 0.56
30 21 0.24
31 3 0.03
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (28 bp):
AAAAATTCCATTTTAACCTCGATTTTCC
Found at i:35304796 original size:58 final size:58
Alignment explanation
Indices: 35304715--35304883 Score: 211
Period size: 58 Copynumber: 2.9 Consensus size: 58
35304705 AATTATATTT
* * *
35304715 TTTTACCC-CTAAACTTCTAAAAATTCTACTTTTAACCTCGA-TTTTCCAAAAATTACCA
1 TTTTACCCTC-AAACTTCTAAAAATTCCA-TTTTGACCTCGATTTTTCCAAAAATTAACA
*
35304773 TTTTACCCTCAAACTTTCT-AAAATTCCATTTTGA-CTCTGATTTTTCCAAAAATTAATA
1 TTTTACCCTCAAAC-TTCTAAAAATTCCATTTTGACCTC-GATTTTTCCAAAAATTAACA
* *
35304831 TTTTACCCTCGAACTTCTAAAAATTCCATTTTTGACCTCAATTTTTCCAAAAA
1 TTTTACCCTCAAACTTCTAAAAATTCCA-TTTTGACCTCGATTTTTCCAAAAA
35304884 ATATCATTGT
Statistics
Matches: 98, Mismatches: 6, Indels: 13
0.84 0.05 0.11
Matches are distributed among these distances:
56 3 0.03
57 11 0.11
58 57 0.58
59 24 0.24
60 3 0.03
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (58 bp):
TTTTACCCTCAAACTTCTAAAAATTCCATTTTGACCTCGATTTTTCCAAAAATTAACA
Found at i:35306127 original size:12 final size:12
Alignment explanation
Indices: 35306110--35306135 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35306100 TGAAGTTTTC
35306110 ACTTTCGTGCAA
1 ACTTTCGTGCAA
35306122 ACTTTCGTGCAA
1 ACTTTCGTGCAA
35306134 AC
1 AC
35306136 ATGTGGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (12 bp):
ACTTTCGTGCAA
Found at i:35316484 original size:49 final size:50
Alignment explanation
Indices: 35316428--35316848 Score: 259
Period size: 49 Copynumber: 8.6 Consensus size: 50
35316418 CGAAACATGA
* * *
35316428 AGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACC-AAGAAGATATAG
1 AGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCTAAGAAGACATAG
* *
35316477 AGGGAAAGGTTTAAGTCGCAACGGCG-ATCCTAGTACCTCAGAAG-CAT-G
1 AGGGAAAGATTTAAGTCGCAACGGCGAATCC-AGTACCTAAGAAGACATAG
* * * *
35316525 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACC-AAGAAGATATGG
1 -AGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCTAAGAAGACATAG
* * * * * * *
35316575 AGAGAAAGGTTTATGTCACAACGGCGAA-CCGTGTACCTCAGAA-ACATAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAATCC-AGTACCTAAGAAGACATAG
** *
35316624 AGGGAAAGATTTAAGTCGCAACGGTAAATCTAGTACC-ATAG-AGACAT-G
1 AGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCTA-AGAAGACATAG
* * * * * * *
35316672 AAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCGCAA-AGATACA-AA
1 -AGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACC-TAAGA-AGACATAG
* * *
35316723 AGGGAAAGGTTTAAGTCGCAACGACGAA-CCTAAG-ACCTCAG-AGACAT-G
1 AGGGAAAGATTTAAGTCGCAACGGCGAATCC--AGTACCTAAGAAGACATAG
* * * * * * *
35316771 AAGGGAAGGATTTAAGCCACAATGGCAAATCCAGTA-C-AGCGAAGACA-CG
1 -AGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCTA-AGAAGACATAG
* *
35316820 AGGGGAAAGGTTTAAGTCGCAATGGCGAA
1 A-GGGAAAGATTTAAGTCGCAACGGCGAA
35316849 CCCTATACCT
Statistics
Matches: 280, Mismatches: 64, Indels: 56
0.70 0.16 0.14
Matches are distributed among these distances:
48 21 0.08
49 210 0.75
50 42 0.15
51 7 0.03
ACGTcount: A:0.39, C:0.19, G:0.27, T:0.16
Consensus pattern (50 bp):
AGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCTAAGAAGACATAG
Found at i:35316597 original size:98 final size:98
Alignment explanation
Indices: 35316419--35316661 Score: 362
Period size: 98 Copynumber: 2.5 Consensus size: 98
35316409 TCAGTACCAC
* * *
35316419 GAAACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCAAGAAGATATAGAGGGAAA
1 GAAACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCAAGAAGATATAGAGAGAAA
* *
35316484 GGTTTAAGTCGCAACGGCGATCC-TAGTACCTCA
66 GGTTTAAGTCACAACGGCGAACCGT-GTACCTCA
* *
35316517 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCAAGAAGATATGGAGAGAAA
1 GAAACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCAAGAAGATATAGAGAGAAA
*
35316582 GGTTTATGTCACAACGGCGAACCGTGTACCTCA
66 GGTTTAAGTCACAACGGCGAACCGTGTACCTCA
* * **
35316615 GAAACATAAAGGGAAAGATTTAAGTCGCAACGGTAAATCTAGTACCA
1 GAAACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCA
35316662 TAGAGACATG
Statistics
Matches: 131, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
98 130 0.99
99 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.26, T:0.17
Consensus pattern (98 bp):
GAAACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCAAGAAGATATAGAGAGAAA
GGTTTAAGTCACAACGGCGAACCGTGTACCTCA
Found at i:35316709 original size:98 final size:97
Alignment explanation
Indices: 35316410--35316807 Score: 358
Period size: 98 Copynumber: 4.1 Consensus size: 97
35316400 CTATAGGTCT
* * * *
35316410 CAGTACCAC-GAAACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCAAGAAGATA
1 CAGTACCTCAGAAACATAAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAAGAAGACA
* * *
35316474 T-AGAGGGAAAGGTTTAAGTCGCAACGGCGATC
66 TGA-AGGGAAAGATTTAAGCCACAACGGCGATC
* * * *
35316506 CTAGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCAAGAAGAT
1 C-AGTACCTCAGAAACATAAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAAGAAGAC
* * * * * *
35316571 ATGGAGAGAAAGGTTTATGTCACAACGGCGAAC
65 ATGAAGGGAAAGATTTAAGCCACAACGGCGATC
* * ***
35316604 CGTGTACCTCAGAAACATAAAGGGAAAGATTTAAGTCGCAACGGTAAATCTAGTACCATAG-AGA
1 C-AGTACCTCAGAAACATAAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCA-AGAAGA
* * *
35316668 CATGAAGGGAAAGATCTAAGCCGCAATGGCGGATC
64 CATGAAGGGAAAGATTTAAGCCACAACGGC-GATC
* * * * * *
35316703 CAGTACCGCAAAGATACA-AAAGGGAAAGGTTTAAGTCGCAACGACGAACCTAAG-ACCTCAG-A
1 CAGTACCTC--AGAAACATAAAGGGAAAGATTTAAGCCGCAACGACGAATCT-AGTACC-AAGAA
* * *
35316765 GACATGAAGGGAAGGATTTAAGCCACAATGGCAAATC
62 GACATGAAGGGAAAGATTTAAGCCACAACGGC-GATC
35316802 CAGTAC
1 CAGTAC
35316808 AGCGAAGACA
Statistics
Matches: 253, Mismatches: 40, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
96 1 0.00
97 7 0.03
98 159 0.63
99 78 0.31
100 8 0.03
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.16
Consensus pattern (97 bp):
CAGTACCTCAGAAACATAAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAAGAAGACA
TGAAGGGAAAGATTTAAGCCACAACGGCGATC
Found at i:35316717 original size:147 final size:147
Alignment explanation
Indices: 35316477--35316786 Score: 353
Period size: 147 Copynumber: 2.1 Consensus size: 147
35316467 GAAGATATAG
* ** *
35316477 AGGGAAAGGTTTAAGTCGCAACGGCGATCCTAGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
1 AGGGAAAGATTTAAGTCGCAACGGAAATCCTAGTACCTCAGAAGCATGAAGGGAAAGATCTAAGC
* *** * *
35316542 CGCAACGGCGAATCTAGTACCAAGAAGATA-TGGAGAGAAAGGTTTATGTCACAACGGCGAACCG
66 CGCAACGGCGAATCCAGTACCAAGAAGATACAAAAGAGAAAGGTTTAAGTCACAACGACGAACC-
35316606 T-GTACCTCAGAAACATAA
130 TAG-ACCTCAGAAACATAA
35316624 AGGGAAAGATTTAAGTCGCAACGGTAAAT-CTAGTACCAT-AG-AGACATGAAGGGAAAGATCTA
1 AGGGAAAGATTTAAGTCGCAACGG-AAATCCTAGTACC-TCAGAAG-CATGAAGGGAAAGATCTA
* * * * *
35316686 AGCCGCAATGGCGGATCCAGTACCGCA-AAGATACAAAAGGGAAAGGTTTAAGTCGCAACGACGA
63 AGCCGCAACGGCGAATCCAGTACC-AAGAAGATACAAAAGAGAAAGGTTTAAGTCACAACGACGA
* *
35316750 ACCTAAGACCTCAGAGACATGA
127 ACCT-AGACCTCAGAAACATAA
*
35316772 AGGGAAGGATTTAAG
1 AGGGAAAGATTTAAG
35316787 CCACAATGGC
Statistics
Matches: 138, Mismatches: 18, Indels: 13
0.82 0.11 0.08
Matches are distributed among these distances:
146 2 0.01
147 78 0.57
148 57 0.41
149 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.17
Consensus pattern (147 bp):
AGGGAAAGATTTAAGTCGCAACGGAAATCCTAGTACCTCAGAAGCATGAAGGGAAAGATCTAAGC
CGCAACGGCGAATCCAGTACCAAGAAGATACAAAAGAGAAAGGTTTAAGTCACAACGACGAACCT
AGACCTCAGAAACATAA
Found at i:35316745 original size:99 final size:98
Alignment explanation
Indices: 35316622--35316841 Score: 264
Period size: 99 Copynumber: 2.2 Consensus size: 98
35316612 TCAGAAACAT
* ** *
35316622 AAAGGGAAAGATTTAAGTCGCAACGGTAAATCT-AGTACCAT-AGAGACATGAAGGGAAAGATCT
1 AAAGGGAAAGGTTTAAGTCGCAACGACAAACCTAAG-ACC-TCAGAGACATGAAGGGAAAGATCT
* ** * *
35316685 AAGCCGCAATGGCGGATCCAGTACCGCAAAGATAC
64 AAGCCACAATGGCAAATCCAGTACAGCAAAGACAC
* * *
35316720 AAAAGGGAAAGGTTTAAGTCGCAACGACGAACCTAAGACCTCAGAGACATGAAGGGAAGGATTTA
1 -AAAGGGAAAGGTTTAAGTCGCAACGACAAACCTAAGACCTCAGAGACATGAAGGGAAAGATCTA
*
35316785 AGCCACAATGGCAAATCCAGTACAGCGAAGACAC
65 AGCCACAATGGCAAATCCAGTACAGCAAAGACAC
* *
35316819 GAGGGGAAAGGTTTAAGTCGCAA
1 AAAGGGAAAGGTTTAAGTCGCAA
35316842 TGGCGAACCC
Statistics
Matches: 104, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
98 22 0.21
99 80 0.77
100 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.27, T:0.15
Consensus pattern (98 bp):
AAAGGGAAAGGTTTAAGTCGCAACGACAAACCTAAGACCTCAGAGACATGAAGGGAAAGATCTAA
GCCACAATGGCAAATCCAGTACAGCAAAGACAC
Found at i:35316817 original size:148 final size:148
Alignment explanation
Indices: 35316477--35316848 Score: 362
Period size: 148 Copynumber: 2.5 Consensus size: 148
35316467 GAAGATATAG
* * * * **
35316477 AGGGAAAGGTTTAAGTCGCAACGGC-GATCCTAGTACCTCAGAAG-CATGAAGGGAAAGATTTAA
1 AGGGAAAGATTTAAGCCACAACGGCAAATCC-AGTACCAGAGAAGACATGAAGGGAAAGATTTAA
* * *** * *
35316540 GCCGCAACGGCGAATCTAGTACCAAGAAGATATGGAGAGAAAGGTTTATGTCACAACGGCGAACC
65 GCCGCAATGGCGAATCCAGTACCAAGAAGATAAAAAGAGAAAGGTTTAAGTCACAACGACGAACC
35316605 GTGTACCTCAGAAACATAA
130 GTGTACCTCAGAAACATAA
* * * * * *
35316624 AGGGAAAGATTTAAGTCGCAACGGTAAATCTAGTACCATAG-AGACATGAAGGGAAAGATCTAAG
1 AGGGAAAGATTTAAGCCACAACGGCAAATCCAGTACCAGAGAAGACATGAAGGGAAAGATTTAAG
* * * *
35316688 CCGCAATGGCGGATCCAGTACCGCA-AAGATACAAAAGGGAAAGGTTTAAGTCGCAACGACGAAC
66 CCGCAATGGCGAATCCAGTACC-AAGAAGATA-AAAAGAGAAAGGTTTAAGTCACAACGACGAAC
* *
35316752 C-TAAG-ACCTCAGAGACATGA
129 CGT--GTACCTCAGAAACATAA
* * * * * *
35316772 AGGGAAGGATTTAAGCCACAATGGCAAATCCAGTA-CAGCGAAGACACGAGGGGAAAGGTTTAAG
1 AGGGAAAGATTTAAGCCACAACGGCAAATCCAGTACCAGAGAAGACATGAAGGGAAAGATTTAAG
*
35316836 TCGCAATGGCGAA
66 CCGCAATGGCGAA
35316849 CCCTATACCT
Statistics
Matches: 184, Mismatches: 34, Indels: 13
0.80 0.15 0.06
Matches are distributed among these distances:
146 2 0.01
147 79 0.43
148 102 0.55
149 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.16
Consensus pattern (148 bp):
AGGGAAAGATTTAAGCCACAACGGCAAATCCAGTACCAGAGAAGACATGAAGGGAAAGATTTAAG
CCGCAATGGCGAATCCAGTACCAAGAAGATAAAAAGAGAAAGGTTTAAGTCACAACGACGAACCG
TGTACCTCAGAAACATAA
Found at i:35317379 original size:29 final size:28
Alignment explanation
Indices: 35317325--35317380 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
35317315 TCAAATTAGG
* *
35317325 TTTAAATTGGTTTAAATTTATTTTTAAA
1 TTTAAATTGCTTTAAATTTATATTTAAA
35317353 TTTAAATTTGCTTTAAATTTGA-ATTTAA
1 TTTAAA-TTGCTTTAAATTT-ATATTTAA
35317381 TTGAATTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.25
29 17 0.71
30 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (28 bp):
TTTAAATTGCTTTAAATTTATATTTAAA
Found at i:35318137 original size:3 final size:3
Alignment explanation
Indices: 35318129--35318179 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
35318119 TTAAATGAAT
** * * *
35318129 TAA TAA TAA TAA TAA TAA TTT TAA TAA TAA AAA TAC TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35318177 TAA
1 TAA
35318180 ATATTTATAA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:35319431 original size:59 final size:58
Alignment explanation
Indices: 35319349--35319535 Score: 232
Period size: 59 Copynumber: 3.2 Consensus size: 58
35319339 AAAATTATAT
* * *
35319349 TTTTACCCCCAAAC-TTCCAAAAATTCCACTTTTAACCTGATTTTTTGTAAAAATTACCA
1 TTTTACCCTCGAACTTTCC-AAAATTCCATTTTTAACCTGATTTTTT-TAAAAATTACCA
** * *
35319408 TTTTATGCTCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTTCAAAAATTACCA
1 TTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCT-GATTTTTTTAAAAATTACCA
* * *
35319467 TTTTACCCTTGAACTTTCCAAAATTCCATTTTTGAACCCGATTTTTTTAAAAATTATCA
1 TTTTACCCTCGAACTTTCCAAAATTCCATTTTT-AACCTGATTTTTTTAAAAATTACCA
*
35319526 TTGTACCCTC
1 TTTTACCCTC
35319536 AAGTGTCTAA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
59 94 0.86
60 15 0.14
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (58 bp):
TTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTGATTTTTTTAAAAATTACCA
Found at i:35319499 original size:29 final size:29
Alignment explanation
Indices: 35319398--35319501 Score: 99
Period size: 29 Copynumber: 3.6 Consensus size: 29
35319388 ATTTTTTGTA
35319398 AAAATTACCATTTTATG--CTCGAACTTTCC
1 AAAATT-CCATTTT-TGACCTCGAACTTTCC
** *
35319427 AAAATTCCATTTTTGACCTCGATTTTTTCA
1 AAAATTCCATTTTTGACCTCGA-ACTTTCC
*
35319457 AAAATTACCA-TTTT-ACCCTTGAACTTTCC
1 AAAATT-CCATTTTTGA-CCTCGAACTTTCC
35319486 AAAATTCCATTTTTGA
1 AAAATTCCATTTTTGA
35319502 ACCCGATTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
27 2 0.03
28 10 0.16
29 26 0.43
30 20 0.33
31 3 0.05
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (29 bp):
AAAATTCCATTTTTGACCTCGAACTTTCC
Found at i:35319549 original size:59 final size:58
Alignment explanation
Indices: 35319349--35319588 Score: 225
Period size: 59 Copynumber: 4.1 Consensus size: 58
35319339 AAAATTATAT
* * * *
35319349 TTTTACCCCCAAACTTCCAAAAATTCCACTTTT-AACCTGATTTTTTGTAAAAATTACCA
1 TTTTACCCTC-AACTTTCAAAAATTCCATTTTTGAACCCGATTTTTT-TAAAAATTACCA
** * *
35319408 TTTTATGCTCGAACTTTCCAAAATTCCATTTTTG-ACCTCGATTTTTTCAAAAATTACCA
1 TTTTACCCTC-AACTTTCAAAAATTCCATTTTTGAACC-CGATTTTTTTAAAAATTACCA
* * *
35319467 TTTTACCCTTGAACTTTCCAAAATTCCATTTTTGAACCCGATTTTTTTAAAAATTATCA
1 TTTTACCC-TCAACTTTCAAAAATTCCATTTTTGAACCCGATTTTTTTAAAAATTACCA
* * * * * * ** *
35319526 TTGTACCCTCAAGTGTCTAAAAATTCTATTTTTG-ACCCCAATTTTTCCAAAATTACTA
1 TTTTACCCTCAACTTTC-AAAAATTCCATTTTTGAACCCGATTTTTTTAAAAATTACCA
35319584 TTTTA
1 TTTTA
35319589 TTTCCGAATG
Statistics
Matches: 149, Mismatches: 27, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
58 28 0.19
59 109 0.73
60 12 0.08
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.42
Consensus pattern (58 bp):
TTTTACCCTCAACTTTCAAAAATTCCATTTTTGAACCCGATTTTTTTAAAAATTACCA
Found at i:35322375 original size:18 final size:19
Alignment explanation
Indices: 35322340--35322375 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35322330 TAATATGATT
*
35322340 AAATGTTAATTAACTTAAG
1 AAATCTTAATTAACTTAAG
35322359 AAATCTTAATT-ACTTAA
1 AAATCTTAATTAACTTAA
35322376 CATAATTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (19 bp):
AAATCTTAATTAACTTAAG
Found at i:35331936 original size:10 final size:10
Alignment explanation
Indices: 35331923--35331957 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
35331913 GAAAAATATC
35331923 AAAAAAAAGA
1 AAAAAAAAGA
35331933 AAAAAAAAGA
1 AAAAAAAAGA
35331943 AAAAAAAAGA
1 AAAAAAAAGA
35331953 AAAAA
1 AAAAA
35331958 GAAGGCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:35332090 original size:20 final size:20
Alignment explanation
Indices: 35332065--35332123 Score: 118
Period size: 20 Copynumber: 3.0 Consensus size: 20
35332055 TTGTTTAGCA
35332065 ATTCATATCAATTAGAGTTT
1 ATTCATATCAATTAGAGTTT
35332085 ATTCATATCAATTAGAGTTT
1 ATTCATATCAATTAGAGTTT
35332105 ATTCATATCAATTAGAGTT
1 ATTCATATCAATTAGAGTT
35332124 ATTAGACCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (20 bp):
ATTCATATCAATTAGAGTTT
Found at i:35337051 original size:22 final size:22
Alignment explanation
Indices: 35337009--35337051 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
35336999 GTGGGATTAT
**
35337009 TAAAATATAATTAAATTAAAAA
1 TAAAATATAATTAAAACAAAAA
*
35337031 TAAAATATATTTAAAACAAAA
1 TAAAATATAATTAAAACAAAA
35337052 GTTAAAAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAATATAATTAAAACAAAAA
Found at i:35338913 original size:158 final size:158
Alignment explanation
Indices: 35338619--35338953 Score: 419
Period size: 158 Copynumber: 2.1 Consensus size: 158
35338609 TTACATGTTA
*
35338619 CATTT-ACAGCTCGTGTGAGCATTACAGGTTATATGAGTGCTGGCCTTGGATTTCCTACCGATGG
1 CATTTCACAGCTCGTGTGAGCATTACAGGTTATATGAGTGCTGGCCTTAGATTTCCTACCGATGG
** * * * *
35338683 CTGAGGTCTTGCATTGGTTGCGGATTCTTCACAACTCGTGTGAGCAGCATCGCGTAGCCTAACAT
66 CTGAGGTCTAACATTGATTGCGGATTCTCCACAACTCGTGTGAGCAACATCGCGTAGCCCAACAT
*
35338748 CTCGACCCACAGCTCATGTGAGC-AGATC
131 CTCGACCCACAACTCATGTGAGCAAG-TC
* * *
35338776 CATTTCACAGCTCGTGTGAGCATTATAGGTTATAT-AGGTGTTGGTCTTAG-TTGTCCTACCGAT
1 CATTTCACAGCTCGTGTGAGCATTACAGGTTATATGA-GTGCTGGCCTTAGATT-TCCTACCGAT
* * * * *
35338839 GGCTGAGGT-TCAACATTTATTGCGGATTCTCCACAGCTTGTGTGAGCAACATCGTGTAGCCCCA
64 GGCTGAGGTCT-AACATTGATTGCGGATTCTCCACAACTCGTGTGAGCAACATCGCGTAGCCCAA
* * *
35338903 CATCTTGACCCATAACTCGTGTGAGCAAGTC
128 CATCTCGACCCACAACTCATGTGAGCAAGTC
*
35338934 CATTTCACAGCTAGTGTGAG
1 CATTTCACAGCTCGTGTGAG
35338954 TACATATGGT
Statistics
Matches: 153, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
157 9 0.06
158 142 0.93
159 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (158 bp):
CATTTCACAGCTCGTGTGAGCATTACAGGTTATATGAGTGCTGGCCTTAGATTTCCTACCGATGG
CTGAGGTCTAACATTGATTGCGGATTCTCCACAACTCGTGTGAGCAACATCGCGTAGCCCAACAT
CTCGACCCACAACTCATGTGAGCAAGTC
Found at i:35340288 original size:24 final size:23
Alignment explanation
Indices: 35340244--35340290 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
35340234 AAGTAGGTCT
** *
35340244 TAATTACGTTTCTGCTTGTCAGC
1 TAATTACGTTTAAGCTCGTCAGC
35340267 TAATATACGTTTAAGCTCGTCAGC
1 TAAT-TACGTTTAAGCTCGTCAGC
35340291 CACTTTACGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (23 bp):
TAATTACGTTTAAGCTCGTCAGC
Found at i:35341886 original size:28 final size:28
Alignment explanation
Indices: 35341823--35341887 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
35341813 GGCAGGGCCA
*
35341823 GCCATATATTATTCAAGCAGTAGAGCCG
1 GCCATATATCATTCAAGCAGTAGAGCCG
* * * * * *
35341851 ACCGTATATCATTTAAGCGGTTGAGCTG
1 GCCATATATCATTCAAGCAGTAGAGCCG
35341879 GCCATATAT
1 GCCATATAT
35341888 AAAAGCTAAC
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (28 bp):
GCCATATATCATTCAAGCAGTAGAGCCG
Found at i:35345163 original size:17 final size:17
Alignment explanation
Indices: 35345141--35345183 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
35345131 AAGTCAATTG
*
35345141 AATTAAAATTATAAATA
1 AATTAAAATTATAAACA
* *
35345158 AATTAATATTGTAAACA
1 AATTAAAATTATAAACA
*
35345175 AATTCAAAT
1 AATTAAAAT
35345184 ATTGGCAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (17 bp):
AATTAAAATTATAAACA
Found at i:35355647 original size:17 final size:16
Alignment explanation
Indices: 35355615--35355653 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
35355605 TAATATAACA
35355615 AATAAAAATGTGTTTG
1 AATAAAAATGTGTTTG
35355631 AATAAAAAT-TGCTTTTG
1 AATAAAAATGTG--TTTG
35355648 AATAAA
1 AATAAA
35355654 GAAATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.10
16 9 0.43
17 10 0.48
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.36
Consensus pattern (16 bp):
AATAAAAATGTGTTTG
Found at i:35359788 original size:3 final size:3
Alignment explanation
Indices: 35359780--35359847 Score: 65
Period size: 3 Copynumber: 24.3 Consensus size: 3
35359770 TCTGGGCAGT
* * * *
35359780 AGA AGA AGA AG- AGA AAA AGA AGT ATA AG- AGA AGA AGA AGA AAA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
35359826 A-A AGA A-A AGA AGA AG- AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
35359848 ATAGAGATAC
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
2 10 0.19
3 42 0.81
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:35359811 original size:25 final size:24
Alignment explanation
Indices: 35359782--35359844 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 24
35359772 TGGGCAGTAG
* *
35359782 AAGAAGAAGAGAAAAAGAAGTATAA
1 AAGAAGAAGAGAAAAAGAA-AAGAA
*
35359807 GAGAAGAAGAAGAAAAAGAAAAGAA
1 AAGAAGAAG-AGAAAAAGAAAAGAA
35359832 AAGAAGAAGAGAA
1 AAGAAGAAGAGAA
35359845 GAAATAGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 4 0.12
25 19 0.58
26 10 0.30
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (24 bp):
AAGAAGAAGAGAAAAAGAAAAGAA
Found at i:35359830 original size:22 final size:22
Alignment explanation
Indices: 35359783--35359854 Score: 67
Period size: 22 Copynumber: 3.1 Consensus size: 22
35359773 GGGCAGTAGA
35359783 AGAAGAAG-AGAAAAAGAAGTATAAG
1 AGAAGAAGAAGAAAAAG-A--A-AAG
35359808 AGAAGAAGAAGAAAAAGAAAAG
1 AGAAGAAGAAGAAAAAGAAAAG
* *
35359830 AAAAGAAGAAG-AGAAGAAATAG
1 AGAAGAAGAAGAAAAAGAAA-AG
35359852 AGA
1 AGA
35359855 TACTGTCCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
21 7 0.17
22 17 0.40
23 1 0.02
25 9 0.21
26 8 0.19
ACGTcount: A:0.68, C:0.00, G:0.28, T:0.04
Consensus pattern (22 bp):
AGAAGAAGAAGAAAAAGAAAAG
Found at i:35359846 original size:11 final size:11
Alignment explanation
Indices: 35359780--35359847 Score: 58
Period size: 11 Copynumber: 6.6 Consensus size: 11
35359770 TCTGGGCAGT
35359780 AGAAGAAGAAG
1 AGAAGAAGAAG
*
35359791 AGAAAAAGAAG
1 AGAAGAAGAAG
*
35359802 TATAAG-AG-A-
1 -AGAAGAAGAAG
35359811 AGAAGAAGAA-
1 AGAAGAAGAAG
35359821 A-AAGAA-AAG
1 AGAAGAAGAAG
*
35359830 AAAAGAAGAAG
1 AGAAGAAGAAG
35359841 AGAAGAA
1 AGAAGAA
35359848 ATAGAGATAC
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
8 6 0.13
9 8 0.17
10 8 0.17
11 21 0.46
12 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (11 bp):
AGAAGAAGAAG
Found at i:35360531 original size:21 final size:22
Alignment explanation
Indices: 35360489--35360531 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
35360479 CAACAAATAA
* * *
35360489 TTTTAAAAGTATTACAATTATT
1 TTTTAAAAATATTAAAAATATT
35360511 TTTTAAAAATA-TAAAAATATT
1 TTTTAAAAATATTAAAAATATT
35360532 AAATTTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTTAAAAATATTAAAAATATT
Found at i:35360569 original size:12 final size:11
Alignment explanation
Indices: 35360530--35360564 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
35360520 TATAAAAATA
35360530 TTAAATTTATT
1 TTAAATTTATT
35360541 TTAAATTTAATT
1 TTAAATTT-ATT
35360553 TTAAA-TTATT
1 TTAAATTTATT
35360563 TT
1 TT
35360565 TTAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.22
11 10 0.43
12 8 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTAAATTTATT
Found at i:35361567 original size:30 final size:29
Alignment explanation
Indices: 35361492--35361569 Score: 95
Period size: 30 Copynumber: 2.7 Consensus size: 29
35361482 AAAATTATTT
*
35361492 AATAAATTTAATAATTTTATATTTAAAAA
1 AATAATTTTAATAATTTTATATTTAAAAA
* *
35361521 AAT-ATTTAAAAGAATTTTATATTTTAAAAA
1 AATAATTT-TAATAATTTTATA-TTTAAAAA
*
35361551 TATAATTTTAATAATTTTA
1 AATAATTTTAATAATTTTA
35361570 AAATCATTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 3 0.08
29 14 0.35
30 19 0.47
31 4 0.10
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (29 bp):
AATAATTTTAATAATTTTATATTTAAAAA
Found at i:35362151 original size:3 final size:3
Alignment explanation
Indices: 35362143--35362171 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
35362133 ATGATTAGCT
35362143 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
35362172 CCCTTTCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:35362708 original size:25 final size:25
Alignment explanation
Indices: 35362680--35362733 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
35362670 TCTTCCTTTC
35362680 ATTTCT-GAAAATATTTTTTATTTTT
1 ATTTCTAGAAAATA-TTTTTATTTTT
* *
35362705 ATTTTTAGATAATATTTTTATTTTT
1 ATTTCTAGAAAATATTTTTATTTTT
35362730 ATTT
1 ATTT
35362734 TTTAAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 20 0.77
26 6 0.23
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (25 bp):
ATTTCTAGAAAATATTTTTATTTTT
Found at i:35364651 original size:33 final size:30
Alignment explanation
Indices: 35364591--35364651 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 30
35364581 ATGAAAAAAA
35364591 TTGAATTTTGAATTAATCGAATCGAGTTAT
1 TTGAATTTTGAATTAATCGAATCGAGTTAT
* *
35364621 TTGAATTATTGTAGTTAACTCGATTCGAGTT
1 TTGAATT-TTG-AATTAA-TCGAATCGAGTT
35364652 TCGAGTTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 7 0.27
31 3 0.12
32 5 0.19
33 11 0.42
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (30 bp):
TTGAATTTTGAATTAATCGAATCGAGTTAT
Found at i:35364673 original size:150 final size:149
Alignment explanation
Indices: 35364393--35364682 Score: 456
Period size: 150 Copynumber: 1.9 Consensus size: 149
35364383 TTATAGAACT
* * *
35364393 TTAATTAGGAGTGAGCGAAACTCGATTATATTCAAAAAATAAAAAAAATTGAATTTAGAATTAAT
1 TTAACTAGGAGTGAGCAAAACTCGATTAGATTCAAAAAATAAAAAAAATTGAATTTAGAATTAAT
*
35364458 CGAATCGAGTTATTCAAATTATTGTAGTTAACTTGATTCCGGTTTCGAGTTCGAGTCGAGTTGAA
66 CGAATCGAGTTATTCAAATTATTGTAGTTAACTCGATTCCGGTTTCGAGTTCGAGTCGAGTTGAA
35364523 TTTTACAATTCGAACAACC
131 TTTTACAATTCGAACAACC
* * * *
35364542 TTAACTAGGGGTGAGCAAAACTCGATTCGATTCGAAAAAATGAAAAAAATTGAATTTTGAATTAA
1 TTAACTAGGAGTGAGCAAAACTCGATTAGATTC-AAAAAATAAAAAAAATTGAATTTAGAATTAA
** *
35364607 TCGAATCGAGTTATTTGAATTATTGTAGTTAACTCGATT-CGAGTTTCGAGTTCGAGTTGAGTTG
65 TCGAATCGAGTTATTCAAATTATTGTAGTTAACTCGATTCCG-GTTTCGAGTTCGAGTCGAGTTG
35364671 AATTTTACAATT
129 AATTTTACAATT
35364683 GAAATAACAG
Statistics
Matches: 128, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
149 30 0.23
150 98 0.77
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.34
Consensus pattern (149 bp):
TTAACTAGGAGTGAGCAAAACTCGATTAGATTCAAAAAATAAAAAAAATTGAATTTAGAATTAAT
CGAATCGAGTTATTCAAATTATTGTAGTTAACTCGATTCCGGTTTCGAGTTCGAGTCGAGTTGAA
TTTTACAATTCGAACAACC
Found at i:35366849 original size:20 final size:20
Alignment explanation
Indices: 35366824--35366863 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
35366814 AAAAAGCGCC
35366824 GCTAAAGAACATGTTCTTTA
1 GCTAAAGAACATGTTCTTTA
**
35366844 GCTAAAGGCCATGTTCTTTA
1 GCTAAAGAACATGTTCTTTA
35366864 ACGGCGCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (20 bp):
GCTAAAGAACATGTTCTTTA
Found at i:35366953 original size:42 final size:43
Alignment explanation
Indices: 35366844--35367017 Score: 282
Period size: 43 Copynumber: 4.1 Consensus size: 43
35366834 ATGTTCTTTA
35366844 GCTAAAGGCCATGTTCTTTAACGGCGC-TTC-CCACAAGCGCC
1 GCTAAAGGCCATGTTCTTTAACGGCGCTTTCTCCACAAGCGCC
35366885 GCTAAAGGCCATGTTCTTTAACGGCGCTTTCTCCACAAGCGCC
1 GCTAAAGGCCATGTTCTTTAACGGCGCTTTCTCCACAAGCGCC
* * *
35366928 GCTAAAGG-CATGTTTTTTAGCGGCGCTTTCTCCACAAGTGCC
1 GCTAAAGGCCATGTTCTTTAACGGCGCTTTCTCCACAAGCGCC
* *
35366970 GCTAAAGCCCATGTTCTTTAGCGGCGCTTTCTCCACAAGCGCC
1 GCTAAAGGCCATGTTCTTTAACGGCGCTTTCTCCACAAGCGCC
35367013 GCTAA
1 GCTAA
35367018 TATAACAGAT
Statistics
Matches: 124, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
41 27 0.22
42 41 0.33
43 56 0.45
ACGTcount: A:0.21, C:0.32, G:0.22, T:0.26
Consensus pattern (43 bp):
GCTAAAGGCCATGTTCTTTAACGGCGCTTTCTCCACAAGCGCC
Found at i:35366986 original size:85 final size:84
Alignment explanation
Indices: 35366844--35367017 Score: 278
Period size: 85 Copynumber: 2.1 Consensus size: 84
35366834 ATGTTCTTTA
*
35366844 GCTAAAGGCCATGTTCTTTAACGGCGCTTCCCACAAGCGCCGCTAAAGGCCATGTTCTTTAACGG
1 GCTAAAGGCCATGTTCTTTAACGGCGCTTCCCACAAGCGCCGCTAAAGCCCATGTTCTTTAACGG
35366909 CGCTTTCTCCACAAGCGCC
66 CGCTTTCTCCACAAGCGCC
* * * *
35366928 GCTAAAGG-CATGTTTTTTAGCGGCGCTTTCTCCACAAGTGCCGCTAAAGCCCATGTTCTTTAGC
1 GCTAAAGGCCATGTTCTTTAACGGCGC-TTC-CCACAAGCGCCGCTAAAGCCCATGTTCTTTAAC
35366992 GGCGCTTTCTCCACAAGCGCC
64 GGCGCTTTCTCCACAAGCGCC
35367013 GCTAA
1 GCTAA
35367018 TATAACAGAT
Statistics
Matches: 83, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
83 16 0.19
84 11 0.13
85 56 0.67
ACGTcount: A:0.21, C:0.32, G:0.22, T:0.26
Consensus pattern (84 bp):
GCTAAAGGCCATGTTCTTTAACGGCGCTTCCCACAAGCGCCGCTAAAGCCCATGTTCTTTAACGG
CGCTTTCTCCACAAGCGCC
Found at i:35367106 original size:15 final size:15
Alignment explanation
Indices: 35367086--35367114 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35367076 CCTGTAAATT
35367086 CAAATCCAACCAATG
1 CAAATCCAACCAATG
35367101 CAAATCCAACCAAT
1 CAAATCCAACCAAT
35367115 AACTTCAAAT
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:0.48, C:0.34, G:0.03, T:0.14
Consensus pattern (15 bp):
CAAATCCAACCAATG
Found at i:35367447 original size:66 final size:66
Alignment explanation
Indices: 35367341--35367489 Score: 253
Period size: 66 Copynumber: 2.3 Consensus size: 66
35367331 CCTCGCTGTT
* *
35367341 GCCTCCACTTTAAGTTGTAGATGGAGTTCTTCATATTTTTTTTGAAACTCTGCTTCTCTCACTGC
1 GCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAAACTCTGCTTCTCTCACTGC
35367406 A
66 A
* **
35367407 GCCTCCTCTTTAAGTTTTAGATGGAGTTCATCATATTTTTTTTGAGCCTCTGCTTCTCTCACTGC
1 GCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAAACTCTGCTTCTCTCACTGC
35367472 A
66 A
35367473 GCCTCCTCTTTAAGTTG
1 GCCTCCTCTTTAAGTTG
35367490 AGCAAATTGC
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 77 1.00
ACGTcount: A:0.17, C:0.24, G:0.15, T:0.43
Consensus pattern (66 bp):
GCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAAACTCTGCTTCTCTCACTGC
A
Found at i:35370134 original size:31 final size:33
Alignment explanation
Indices: 35370095--35370161 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
35370085 TTGATTTAAA
35370095 TTTAAAA-ATATATATTAGTGACAACATTTTAC
1 TTTAAAATATATATATTAGTGACAACATTTTAC
35370127 TTTAAAATATATATATTAGTGACAACATTTTAC
1 TTTAAAATATATATATTAGTGACAACATTTTAC
35370160 TT
1 TT
35370162 AAATATTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 7 0.21
33 27 0.79
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (33 bp):
TTTAAAATATATATATTAGTGACAACATTTTAC
Found at i:35370196 original size:8 final size:8
Alignment explanation
Indices: 35370183--35370262 Score: 67
Period size: 8 Copynumber: 9.8 Consensus size: 8
35370173 TTGTTTTCAT
35370183 TAATTAAA
1 TAATTAAA
35370191 TAATTAAA
1 TAATTAAA
*
35370199 T-ATTTAA
1 TAATTAAA
*
35370206 T--TTAGTA
1 TAATTA-AA
35370213 TAATTAAA
1 TAATTAAA
35370221 TAATTAAA
1 TAATTAAA
35370229 TAATTAATTA
1 TAATTAA--A
*
35370239 AAATTAAA
1 TAATTAAA
35370247 TAATTATATA
1 TAATTA-A-A
35370257 TAATTA
1 TAATTA
35370263 TTTACGAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
6 2 0.03
7 8 0.14
8 31 0.53
9 4 0.07
10 14 0.24
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (8 bp):
TAATTAAA
Found at i:35370219 original size:30 final size:27
Alignment explanation
Indices: 35370183--35370257 Score: 98
Period size: 30 Copynumber: 2.7 Consensus size: 27
35370173 TTGTTTTCAT
35370183 TAATTAAATAATTAAATATTTAATTTAGTA
1 TAATTAAATAATTAAATATTTAA-TTA--A
*
35370213 TAATTAAATAATTAAATAATTAATTAA
1 TAATTAAATAATTAAATATTTAATTAA
*
35370240 -AATTAAATAATTATATAT
1 TAATTAAATAATTAAATAT
35370258 AATTATTTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 16 0.38
27 1 0.02
29 3 0.07
30 22 0.52
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (27 bp):
TAATTAAATAATTAAATATTTAATTAA
Found at i:35370238 original size:4 final size:4
Alignment explanation
Indices: 35370181--35370262 Score: 51
Period size: 4 Copynumber: 20.0 Consensus size: 4
35370171 GGTTGTTTTC
* * * * * *
35370181 ATTA ATTA AATA ATTA AATA TTTA ATTTA GTATA ATTA AATA ATTA AATA
1 ATTA ATTA ATTA ATTA ATTA ATTA A-TTA AT-TA ATTA ATTA ATTA ATTA
*
35370231 ATTA ATTA A--A ATTA AATA ATTA TATATA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA -AT-TA ATTA
35370263 TTTACGAAAA
Statistics
Matches: 58, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
2 2 0.03
4 44 0.76
5 10 0.17
6 2 0.03
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (4 bp):
ATTA
Found at i:35370243 original size:26 final size:29
Alignment explanation
Indices: 35370213--35370266 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 29
35370203 TAATTTAGTA
35370213 TAATTAAATAATTAAATAATTAA-TTA-A
1 TAATTAAATAATTAAATAATTAATTTAGA
35370240 -AATTAAATAATTATATATAATT-ATTTA
1 TAATTAAATAATTA-A-ATAATTAATTTA
35370267 CGAAAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 13 0.54
27 2 0.08
28 9 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
TAATTAAATAATTAAATAATTAATTTAGA
Found at i:35370303 original size:18 final size:18
Alignment explanation
Indices: 35370183--35370702 Score: 104
Period size: 18 Copynumber: 28.1 Consensus size: 18
35370173 TTGTTTTCAT
35370183 TAATTAAATAATTAAATA
1 TAATTAAATAATTAAATA
*
35370201 TTTAATTTAGTATAATT-AA-A
1 --TAA-TTA-AATAATTAAATA
*
35370221 TAATTAAATAATTAATTA
1 TAATTAAATAATTAAATA
* *
35370239 AAATTAAATAATTATATA
1 TAATTAAATAATTAAATA
* * **
35370257 TAATT-ATTTACGAAA-A
1 TAATTAAATAATTAAATA
**
35370273 T-ATTTTA-AATTAAATA
1 TAATTAAATAATTAAATA
*
35370289 TAATTAAATAATTAATTGA
1 TAATTAAATAATTAAAT-A
* ** *
35370308 TACTGTTTACAATTAAATACA
1 TAAT-TAAATAATTAAAT--A
*
35370329 TAATTAAATAATTTAATA
1 TAATTAAATAATTAAATA
** * *
35370347 TAATTATTTACTTTAATA
1 TAATTAAATAATTAAATA
*
35370365 TAAATTAAATAATTAAATCTTT
1 T-AATTAAATAATTAAA---TA
*
35370387 TAATTAAAT-ATTTAAT-
1 TAATTAAATAATTAAATA
* **
35370403 TAATTGATACTGTTTACAAT-
1 TAATT-A-AATAATTA-AATA
* * *
35370423 TAAATACATAATTAAACA
1 TAATTAAATAATTAAATA
* *
35370441 TAATTAATTGATGT-AATA
1 TAATTAAATAAT-TAAATA
* * *
35370459 TAATT-ATTGACTTTAATA
1 TAATTAAAT-AATTAAATA
35370477 TAATTAAATAATTAAATA
1 TAATTAAATAATTAAATA
*
35370495 TTTTAAATTAATTATTTAATTAATTGA
1 ---T-AATTAA--A--TAATTAAAT-A
* **
35370522 TACTGTTTATAATTAAATACA
1 TAAT-TAAATAATTAAAT--A
*
35370543 TAATTAAATAATTTAATA
1 TAATTAAATAATTAAATA
** * *
35370561 TAATTATTTAGTTTAATA
1 TAATTAAATAATTAAATA
*
35370579 TAATTAAATATTTTAAAT-
1 TAATTAAATA-ATTAAATA
** * *
35370597 TAATTATTTAATTAATTGG
1 TAATTAAATAATTAAAT-A
* **
35370616 TACTGTTTAT-ATT---T-
1 TAAT-TAAATAATTAAATA
* *
35370630 TAA-TACATAATTAAACA
1 TAATTAAATAATTAAATA
*
35370647 TAATTAAATAATTTAATA
1 TAATTAAATAATTAAATA
** * *
35370665 TAATTATTTACTTTAATA
1 TAATTAAATAATTAAATA
35370683 TAAATTAAATAATTAAATA
1 T-AATTAAATAATTAAATA
35370702 T
1 T
35370703 TTTAAATTAA
Statistics
Matches: 357, Mismatches: 97, Indels: 93
0.65 0.18 0.17
Matches are distributed among these distances:
12 3 0.01
13 3 0.01
14 2 0.01
15 7 0.02
16 16 0.04
17 29 0.08
18 145 0.41
19 46 0.13
20 55 0.15
21 22 0.06
22 15 0.04
23 2 0.01
24 3 0.01
26 8 0.02
27 1 0.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (18 bp):
TAATTAAATAATTAAATA
Found at i:35370390 original size:13 final size:12
Alignment explanation
Indices: 35370191--35370405 Score: 61
Period size: 12 Copynumber: 17.6 Consensus size: 12
35370181 ATTAATTAAA
35370191 TAATTAAATATT
1 TAATTAAATATT
* *
35370203 TAATTTAGTA--
1 TAATTAAATATT
*
35370213 TAATTAAATAAT
1 TAATTAAATATT
* *
35370225 TAAATAATTAATT
1 TAATTAAAT-ATT
* *
35370238 AAAATTAAATAAT
1 -TAATTAAATATT
*
35370251 TATATATAATTATT
1 TA-AT-TAAATATT
***
35370265 TACGAAAATATTT
1 TAATTAAATA-TT
35370278 TAAATTAAATA--
1 T-AATTAAATATT
*
35370289 TAATTAAATAAT
1 TAATTAAATATT
* *
35370301 TAATTGATACTGTT
1 TAATT-A-AATATT
**
35370315 TACAATTAAATACA
1 T--AATTAAATATT
35370329 TAATTAAATAATT
1 TAATTAAAT-ATT
*
35370342 TAATATAATTATT
1 TAAT-TAAATATT
* *
35370355 TACTTTAATA-T
1 TAATTAAATATT
*
35370366 AAATT-AA-A--
1 TAATTAAATATT
*
35370374 TAATTAAATCTTT
1 TAATTAAAT-ATT
35370387 TAATTAAATATT
1 TAATTAAATATT
35370399 TAATTAA
1 TAATTAA
35370406 TTGATACTGT
Statistics
Matches: 143, Mismatches: 39, Indels: 42
0.64 0.17 0.19
Matches are distributed among these distances:
8 4 0.03
9 3 0.02
10 19 0.13
11 5 0.03
12 46 0.32
13 30 0.21
14 31 0.22
15 1 0.01
16 4 0.03
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (12 bp):
TAATTAAATATT
Found at i:35370461 original size:94 final size:94
Alignment explanation
Indices: 35370336--35370667 Score: 294
Period size: 94 Copynumber: 3.3 Consensus size: 94
35370326 ACATAATTAA
* * * * *
35370336 ATAATTTAATATAATTATTTACTTTAATATAAATTAA-ATAATTAAATCTTTTAATTAAATATTT
1 ATAATTAAACATAATTAATTA-ATTAATATAAATTAATATAATTAAATATTTTAATTAAATATTT
*
35370400 AATTAATTGATACTGTTTACAATTAAATAC
65 AATTAATTGATACTGTTTATAATTAAATAC
35370430 ATAATTAAACATAATTAATTGATGTAATATAATTATTGACTTTAATATAATTAAATAATTAAATA
1 ATAATTAAACATAATT-A---AT-TAAT-TAA-TA-T-A----AAT-TAA-T--ATAATTAAATA
*
35370495 TTTTAAATTAATTATTTAATTAATTGATACTGTTTATAATTAAATAC
49 TTTT-AATTAAATATTTAATTAATTGATACTGTTTATAATTAAATAC
* ** *
35370542 ATAATT-AA-ATAATTTAATATAATT-ATTTAGTTTAATATAATTAAATATTTTAAATTAATTAT
1 ATAATTAAACATAA-TTAAT-TAATTAATATAAATTAATATAATTAAATATTTT-AATTAAATAT
* * *
35370604 TTAATTAATTGGTACTGTTTATATTTTAATAC
63 TTAATTAATTGATACTGTTTATAATTAAATAC
*
35370636 ATAATTAAACATAATTAAATAATTTAATATAA
1 ATAATTAAACATAATTAATTAA-TTAATATAA
35370668 TTATTTACTT
Statistics
Matches: 197, Mismatches: 17, Indels: 46
0.76 0.07 0.18
Matches are distributed among these distances:
94 78 0.40
95 9 0.05
96 9 0.05
97 3 0.02
98 3 0.02
99 5 0.03
100 2 0.01
101 1 0.01
102 2 0.01
103 1 0.01
104 1 0.01
105 1 0.01
106 4 0.02
107 9 0.05
110 5 0.03
111 18 0.09
112 46 0.23
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (94 bp):
ATAATTAAACATAATTAATTAATTAATATAAATTAATATAATTAAATATTTTAATTAAATATTTA
ATTAATTGATACTGTTTATAATTAAATAC
Found at i:35370567 original size:58 final size:57
Alignment explanation
Indices: 35370373--35370570 Score: 203
Period size: 58 Copynumber: 3.5 Consensus size: 57
35370363 TATAAATTAA
** * *
35370373 ATAATTAAATCTTTTAATTAAATATTTAATTAATTGATACTGTTTACAATTAAATAC
1 ATAATTAAATAATTTAATTAATTATTTAATTAATTGATACTGTTTATAATTAAATAC
* * * * *
35370430 ATAATTAAA-CA--TAATTAATTGATGTAATATAATT-AT--TGACTT-TAATATAATTAA
1 ATAATTAAATAATTTAATTAATT-ATTTAAT-TAATTGATACTG-TTTATAAT-TAAATAC
*
35370484 ATAATTAAATATTTTAAATTAATTATTTAATTAATTGATACTGTTTATAATTAAATAC
1 ATAATTAAATAATTT-AATTAATTATTTAATTAATTGATACTGTTTATAATTAAATAC
35370542 ATAATTAAATAATTTAATATAATTATTTA
1 ATAATTAAATAATTTAAT-TAATTATTTA
35370571 GTTTAATATA
Statistics
Matches: 114, Mismatches: 14, Indels: 25
0.75 0.09 0.16
Matches are distributed among these distances:
53 5 0.04
54 24 0.21
55 8 0.07
56 11 0.10
57 21 0.18
58 39 0.34
59 6 0.05
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (57 bp):
ATAATTAAATAATTTAATTAATTATTTAATTAATTGATACTGTTTATAATTAAATAC
Found at i:35370582 original size:36 final size:35
Alignment explanation
Indices: 35370542--35370702 Score: 118
Period size: 36 Copynumber: 4.6 Consensus size: 35
35370532 AATTAAATAC
35370542 ATAATTAAATAATTTAATATAATTATTTAGTTTAAT
1 ATAATTAAATAATTTAATATAATTATTTA-TTTAAT
* *
35370578 ATAATTAAATATTTTAA-ATTAATTATTTAATTAATT
1 ATAATTAAATAATTTAATA-TAATTATTTATTTAA-T
* * ** * * * *
35370614 GGTACTGTTTATATTTTAATA-CA-TA---ATTAAAC
1 -ATAAT-TAAATAATTTAATATAATTATTTATTTAAT
35370646 ATAATTAAATAATTTAATATAATTATTTACTTTAAT
1 ATAATTAAATAATTTAATATAATTATTTA-TTTAAT
*
35370682 ATAAATTAAATAATTAAATAT
1 AT-AATTAAATAATTTAATAT
35370703 TTTAAATTAA
Statistics
Matches: 94, Mismatches: 19, Indels: 23
0.69 0.14 0.17
Matches are distributed among these distances:
30 11 0.12
31 4 0.04
32 2 0.02
33 4 0.04
35 6 0.06
36 35 0.37
37 21 0.22
38 10 0.11
39 1 0.01
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (35 bp):
ATAATTAAATAATTTAATATAATTATTTATTTAAT
Found at i:35370708 original size:113 final size:113
Alignment explanation
Indices: 35370573--35371038 Score: 622
Period size: 113 Copynumber: 4.1 Consensus size: 113
35370563 ATTATTTAGT
* * * * *
35370573 TTAATATAATTAAATATTTTAAATTAATTATTTAATTAATTGGTACTGTTTATATTTTAATACAT
1 TTAA-ATAATTAAATATTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTAAATACAT
35370638 AATTAAACATAATTAAATAATTTAATATAATTATTTACTTTAATATAAA
65 AATTAAACATAATTAAATAATTTAATATAATTATTTACTTTAATATAAA
35370687 TTAAATAATTAAATATTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTAAATACATA
1 TTAAATAATTAAATATTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTAAATACATA
* * *
35370752 ATTAAACATAATTAATTGATTTAATATAATTATTTATTTTAATATAAA
66 ATTAAACATAATTAAATAATTTAATATAATTATTTACTTTAATATAAA
* * *
35370800 TTAAATAAATAAATCTTTTAAATTAAATATTTAATTAATTGATACGGTTTACAATTAAATACATA
1 TTAAATAATTAAATATTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTAAATACATA
* * *
35370865 ATTAAACATAATTAATTGATTTAATATAATTATTTAGTTT-A-AT--A
66 ATTAAACATAATTAAATAATTTAATATAATTATTTACTTTAATATAAA
* * * * * * *
35370909 TT---TAATTAAATCTTTCAAATTAAATATTTAATTAAGTAATAATGTTTATAATTAAATATATA
1 TTAAATAATTAAATATTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTAAATACATA
* *
35370971 ATTAAACATAGTTAAATAATTAAATATAATTATTTACTTTAATATTTTAAA
66 ATTAAACATAATTAAATAATTTAATATAATTATTTACTTTAATA---TAAA
35371022 TTAAATATAATTAAATA
1 TT-AA-ATAATTAAATA
35371039 ATAATTTCCT
Statistics
Matches: 314, Mismatches: 26, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
106 87 0.28
107 1 0.00
108 1 0.00
109 3 0.01
111 3 0.01
112 1 0.00
113 205 0.65
114 4 0.01
118 9 0.03
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (113 bp):
TTAAATAATTAAATATTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTAAATACATA
ATTAAACATAATTAAATAATTTAATATAATTATTTACTTTAATATAAA
Found at i:35370718 original size:45 final size:48
Alignment explanation
Indices: 35370628--35370719 Score: 120
Period size: 45 Copynumber: 2.0 Consensus size: 48
35370618 CTGTTTATAT
*
35370628 TTTAATACATAATTAAACATAATTAAATAATTTAATATAATTATTTAC
1 TTTAATACATAATTAAACATAATTAAATAATTTAATATAAATATTTAC
* *
35370676 TTTAATATA-AATT-AA-ATAATTAAATATTTTAA-ATTAAATATTTA
1 TTTAATACATAATTAAACATAATTAAATAATTTAATA-TAAATATTTA
35370720 ATTAATTGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
44 1 0.03
45 25 0.62
46 2 0.05
47 4 0.10
48 8 0.20
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (48 bp):
TTTAATACATAATTAAACATAATTAAATAATTTAATATAAATATTTAC
Found at i:35370782 original size:18 final size:19
Alignment explanation
Indices: 35370759--35370803 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
35370749 ATAATTAAAC
35370759 ATAATTAATTGA-TTTAAT
1 ATAATTAATTGATTTTAAT
*
35370777 ATAATT-ATTTATTTTAAT
1 ATAATTAATTGATTTTAAT
35370795 ATAAATTAA
1 AT-AATTAA
35370804 ATAAATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 4 0.17
18 14 0.61
19 4 0.17
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
ATAATTAATTGATTTTAAT
Found at i:35370895 original size:18 final size:18
Alignment explanation
Indices: 35370872--35370909 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
35370862 ATAATTAAAC
35370872 ATAATTAATTGA-TTTAAT
1 ATAATT-ATTGAGTTTAAT
*
35370890 ATAATTATTTAGTTTAAT
1 ATAATTATTGAGTTTAAT
35370908 AT
1 AT
35370910 TTAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (18 bp):
ATAATTATTGAGTTTAAT
Found at i:35370899 original size:13 final size:12
Alignment explanation
Indices: 35370873--35370943 Score: 54
Period size: 14 Copynumber: 5.6 Consensus size: 12
35370863 TAATTAAACA
35370873 TAATTAATTGATT
1 TAATTAATT-ATT
35370886 TAATATAATTATT
1 TAAT-TAATTATT
*
35370899 TAGTTTAA-TATT
1 TA-ATTAATTATT
* *
35370911 TAATTAAATCTT
1 TAATTAATTATT
*
35370923 TCAAATTAAATATT
1 T--AATTAATTATT
35370937 TAATTAA
1 TAATTAA
35370944 GTAATAATGT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
11 4 0.08
12 16 0.33
13 12 0.24
14 17 0.35
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (12 bp):
TAATTAATTATT
Found at i:35372225 original size:15 final size:17
Alignment explanation
Indices: 35372193--35372225 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
35372183 TTATTTGTTT
35372193 TTTTCTTTTAAATCTAA
1 TTTTCTTTTAAATCTAA
35372210 TTTT-TTTTAAAT-TAA
1 TTTTCTTTTAAATCTAA
35372225 T
1 T
35372226 CAAACTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTCTTTTAAATCTAA
Done.