Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 13 of 356
Found at i:4515454 original size:20 final size:17
Alignment explanation
Indices: 4515429--4515498 Score: 50
Period size: 18 Copynumber: 3.7 Consensus size: 17
4515419 AATATTAATT
4515429 AAAAACAAAACGAAATAGAA
1 AAAAACAAAA-G--ATAGAA
4515449 AAAAACAGAAAGATAGAA
1 AAAAACA-AAAGATAGAA
* *
4515467 CAAAACAAAGAAGAAAGAA
1 AAAAAC-AA-AAGATAGAA
*
4515486 AGAAAAAAAAAGA
1 A-AAAACAAAAGA
4515499 AAAGAAAAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 16 0.38
19 11 0.26
20 12 0.29
21 3 0.07
ACGTcount: A:0.76, C:0.07, G:0.14, T:0.03
Consensus pattern (17 bp):
AAAAACAAAAGATAGAA
Found at i:4515476 original size:16 final size:16
Alignment explanation
Indices: 4515432--4515481 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
4515422 ATTAATTAAA
*
4515432 AACAAAACGAA-ATAG
1 AACAAAACAAAGATAG
*
4515447 AAAAAAACAGAAAGATAG
1 AACAAAAC--AAAGATAG
4515465 AACAAAACAAAGA-AG
1 AACAAAACAAAGATAG
4515480 AA
1 AA
4515482 AGAAAGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 11 0.38
16 5 0.17
17 2 0.07
18 11 0.38
ACGTcount: A:0.72, C:0.10, G:0.14, T:0.04
Consensus pattern (16 bp):
AACAAAACAAAGATAG
Found at i:4515489 original size:23 final size:21
Alignment explanation
Indices: 4515447--4515499 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 21
4515437 AACGAAATAG
* *
4515447 AAAAAAA-CAGAAAGATAGAA
1 AAAAAAAGAAGAAAGAAAGAA
4515467 CAAAACAAAGAAGAAAGAAAGAA
1 -AAAA-AAAGAAGAAAGAAAGAA
4515490 AAAAAAAGAA
1 AAAAAAAGAA
4515500 AAGAAAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 10 0.36
22 7 0.25
23 11 0.39
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.02
Consensus pattern (21 bp):
AAAAAAAGAAGAAAGAAAGAA
Found at i:4515502 original size:19 final size:19
Alignment explanation
Indices: 4515445--4515505 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
4515435 AAAACGAAAT
* *
4515445 AGAAAAAAACAG-AAAGAT
1 AGAAAAAAAAAGAAAAGAA
4515463 AGAACAAAACAAAGAAGAAAGAA
1 AGAA-AAAA-AAAG-A-AAAGAA
4515486 AGAAAAAAAAAGAAAAGAA
1 AGAAAAAAAAAGAAAAGAA
4515505 A
1 A
4515506 AGAGAAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 4 0.11
19 11 0.31
20 4 0.11
21 4 0.11
22 4 0.11
23 9 0.25
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (19 bp):
AGAAAAAAAAAGAAAAGAA
Found at i:4515503 original size:23 final size:23
Alignment explanation
Indices: 4515447--4515513 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
4515437 AACGAAATAG
* *
4515447 AAAAA-AACAGAAAGATAGAACAA
1 AAAAAGAAAAGAAAGAAAGAA-AA
4515470 AACAAAG--AAGAAAGAAAGAAAA
1 AA-AAAGAAAAGAAAGAAAGAAAA
*
4515492 AAAAAGAAAAGAAA-AGAGAAAA
1 AAAAAGAAAAGAAAGAAAGAAAA
4515514 GAAGGAGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
21 4 0.11
22 11 0.30
23 19 0.51
24 3 0.08
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.01
Consensus pattern (23 bp):
AAAAAGAAAAGAAAGAAAGAAAA
Found at i:4515507 original size:20 final size:20
Alignment explanation
Indices: 4515429--4515513 Score: 59
Period size: 21 Copynumber: 4.0 Consensus size: 20
4515419 AATATTAATT
*
4515429 AAAAACAAAACGAAATAGAAAA
1 AAAAAGAAAA-GAAA-AGAAAA
* *
4515451 AAACAG-AAAG-ATAGAACAA
1 AAAAAGAAAAGAAAAGAA-AA
4515470 AACAAAGAAGAA-AGAAAGAAAA
1 AA-AAAGAA-AAGA-AAAGAAAA
4515492 AAAAAGAAAAGAAAAGAGAAA
1 AAAAAGAAAAGAAAAGA-AAA
4515513 A
1 A
4515514 GAAGGAGAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
18 4 0.08
19 5 0.10
20 11 0.22
21 15 0.30
22 10 0.20
23 5 0.10
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAAGAAAAGAAAA
Found at i:4515511 original size:12 final size:11
Alignment explanation
Indices: 4515484--4515516 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
4515474 AAGAAGAAAG
4515484 AAAGAAAA-AA
1 AAAGAAAAGAA
4515494 AAAGAAAAGAA
1 AAAGAAAAGAA
4515505 AAGAGAAAAGAA
1 AA-AGAAAAGAA
4515517 GGAGAATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.38
11 4 0.19
12 9 0.43
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:4516639 original size:38 final size:39
Alignment explanation
Indices: 4516555--4516689 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
4516545 ACCAATATGG
*
4516555 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
4516594 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
4516632 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
4516673 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
4516690 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:4518263 original size:5 final size:5
Alignment explanation
Indices: 4518253--4518287 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
4518243 TTTCTTTTAT
4518253 ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA
4518288 CTTAATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:4522332 original size:47 final size:47
Alignment explanation
Indices: 4522254--4522662 Score: 647
Period size: 47 Copynumber: 8.6 Consensus size: 47
4522244 CCCTTCGGGA
* * * * * *
4522254 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
4522301 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
4522348 CTTATCACATATATACACTTTCACATTCTTCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4522395 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
4522442 CTTATCACATATATACACTTTCACATTCATCATATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
4522489 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
4522538 CTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4522585 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4522636 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
4522663 TATTCAAATA
Statistics
Matches: 336, Mismatches: 20, Indels: 12
0.91 0.05 0.03
Matches are distributed among these distances:
47 246 0.73
49 44 0.13
51 46 0.14
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:4526327 original size:40 final size:40
Alignment explanation
Indices: 4526301--4526628 Score: 539
Period size: 40 Copynumber: 8.2 Consensus size: 40
4526291 TGATTACTCT
* * * *
4526301 TCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
* ** * *
4526341 TTGGGGTTTAGCACGGATATATCACTAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
* *
4526381 TCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
4526421 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
*
4526461 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCA
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
*
4526501 TCGGGACTTAGCCCAGATATATCACTAGCACGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
4526541 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
4526581 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
4526621 TCGGGACT
1 TCGGGACT
4526629 AGCACGAATG
Statistics
Matches: 268, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 268 1.00
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
Found at i:4528198 original size:47 final size:47
Alignment explanation
Indices: 4528120--4528722 Score: 918
Period size: 47 Copynumber: 12.6 Consensus size: 47
4528110 CCCTTCGGGA
* * * * * *
4528120 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
4528167 CCTGTCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
4528214 CTTATCACATATATACACTTTCACATTCCTCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
4528261 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4528308 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
4528355 CTTATCACATATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4528406 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
4528453 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
4528502 CTTATCACATATATACACTTTCACATTCATCATATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
4528549 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
4528598 CTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
4528645 CTTATCACATATATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4528696 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
4528723 TATTCAAATA
Statistics
Matches: 511, Mismatches: 33, Indels: 24
0.90 0.06 0.04
Matches are distributed among these distances:
47 332 0.65
49 89 0.17
51 90 0.18
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:4528492 original size:96 final size:96
Alignment explanation
Indices: 4528120--4528722 Score: 962
Period size: 96 Copynumber: 6.3 Consensus size: 96
4528110 CCCTTCGGGA
* * * * * * * *
4528120 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
4528183 ACTTTCATATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
4528214 CTTATCACATATATACACTTTCACATTCCTCACATCGGCCATTAGGCCTTATCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
4528277 ACTTTCACATTCATCACATCGGCTATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
4528308 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAT
* *
4528373 ACACTTTCACATTCATCACATTGGCCATTCGGC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
4528406 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
* *
4528471 ACTTTCACATTCATCACATTGGCCATTCGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
4528502 CTTATCACATATATACACTTTCACATTCATCATATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
* *
4528567 ACTTTCACATTCATCACATTGGCCATTCGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
4528598 CTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAT
*
4528663 ACACTTTCACATTCATCACATCAGCCATTAGGC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
4528696 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
4528723 TATTCAAATA
Statistics
Matches: 481, Mismatches: 22, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
94 137 0.28
96 189 0.39
98 155 0.32
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:4534401 original size:38 final size:39
Alignment explanation
Indices: 4534317--4534451 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
4534307 ACCAATATGG
*
4534317 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
4534356 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
4534394 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
4534435 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
4534452 ACTCGAGGTT
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:4536023 original size:5 final size:5
Alignment explanation
Indices: 4536013--4536047 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
4536003 TTTCTTTTAT
4536013 ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA
4536048 CTTAATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:4536772 original size:40 final size:39
Alignment explanation
Indices: 4536651--4536782 Score: 110
Period size: 40 Copynumber: 3.4 Consensus size: 39
4536641 CCTCGAGTCG
*
4536651 ATGAGACACTAGGTGTCAATCTATTACTTC-AGATTAAT-TCA
1 ATGAGACACTGGGTGTCAAT-TATTACTTCGA-ATT-ATCT-A
* * ** * *
4536692 ATGAGGCACTGGGTGCCAA-T-TTACTTCGGTTTAGCCA
1 ATGAGACACTGGGTGTCAATTATTACTTCGAATTATCTA
4536729 ATGAGACACTGGGTGTCAACTTATTACTTCGAATTATCTA
1 ATGAGACACTGGGTGTCAA-TTATTACTTCGAATTATCTA
**
4536769 ATGAGGTACTGGGT
1 ATGAGACACTGGGT
4536783 ACCAAACTGG
Statistics
Matches: 71, Mismatches: 15, Indels: 11
0.73 0.15 0.11
Matches are distributed among these distances:
37 19 0.27
38 9 0.13
39 2 0.03
40 25 0.35
41 16 0.23
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (39 bp):
ATGAGACACTGGGTGTCAATTATTACTTCGAATTATCTA
Found at i:4537546 original size:24 final size:24
Alignment explanation
Indices: 4537511--4537557 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4537501 TAAAGGTATT
*
4537511 TGAATGTGTTTTGAATTGGTTGAA
1 TGAATGTGTTTTGAATTGCTTGAA
*
4537535 TGAATG-GTTTTTGAGTTGCTTGA
1 TGAATGTG-TTTTGAATTGCTTGA
4537558 TGTCTAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.21, C:0.02, G:0.30, T:0.47
Consensus pattern (24 bp):
TGAATGTGTTTTGAATTGCTTGAA
Found at i:4538162 original size:8 final size:8
Alignment explanation
Indices: 4538149--4538192 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
4538139 ACTTAAGTAT
4538149 ATAATATA
1 ATAATATA
4538157 ATAATATA
1 ATAATATA
*
4538165 TTAATATA
1 ATAATATA
*
4538173 ATAATTTA
1 ATAATATA
4538181 ATAATATA
1 ATAATATA
4538189 ATAA
1 ATAA
4538193 AACATAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATAATATA
Found at i:4538242 original size:17 final size:16
Alignment explanation
Indices: 4538198--4538243 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
4538188 AATAAAACAT
*
4538198 AAAAGAAATAAAAAGA
1 AAAAGAAAGAAAAAGA
*
4538214 ATAAACAAAGAAAAAGA
1 A-AAAGAAAGAAAAAGA
4538231 AAAAGAATAGAAA
1 AAAAGAA-AGAAA
4538244 CGAGATAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (16 bp):
AAAAGAAAGAAAAAGA
Found at i:4540646 original size:47 final size:47
Alignment explanation
Indices: 4540539--4540729 Score: 186
Period size: 47 Copynumber: 3.9 Consensus size: 47
4540529 AATGTGATTT
* * * *
4540539 CCGTATAAGACCATAGCTGGGCTATGGCTTCGGACAAATGTGATATGTGCTT
1 CCGTATAAGACCATATCTGGGATATGGCATCGG-----TGTGATATGTGCTA
*
4540591 CCGTATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTA
1 CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
* * * *
4540638 CTGTATAAGACCATATTTGGGATATGGCATCAGTGTGATATGTGAT-
1 CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
* ** * *
4540684 CCGTGTAAGACCATGGCTGGGTTATGGCCTCGGTATGTGATATGTG
1 CCGTATAAGACCATATCTGGGATATGGCATCGG--TGTGATATGTG
4540730 ACTATGTGCA
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
46 25 0.21
47 54 0.45
48 11 0.09
52 29 0.24
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (47 bp):
CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
Found at i:4540762 original size:95 final size:93
Alignment explanation
Indices: 4540577--4540747 Score: 211
Period size: 93 Copynumber: 1.8 Consensus size: 93
4540567 TTCGGACAAA
* *
4540577 TGTGATATGTGCTTCCGTATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTACTGT
1 TGTGATATGTGCATCCGTATAAGACCATAGCCGGGATATGGCATCGGTGTGATATGTGCTACTGT
*
4540642 ATAAGACCATATTTGGGATATGGCATCAG
66 ACAAGACCATATTT-GGATATGGCATCAG
* * * * *
4540671 TGTGATATGTG-ATCCGTGTAAGACCATGGCTGGGTTATGGCCTCGGTATGTGATATGTGACTA-
1 TGTGATATGTGCATCCGTATAAGACCATAGCCGGGATATGGCATCGG--TGTGATATGTG-CTAC
*
4540734 TGTGCAAGACCATA
63 TGTACAAGACCATA
4540748 GTTTTACTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
93 28 0.43
94 11 0.17
95 23 0.35
96 3 0.05
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.32
Consensus pattern (93 bp):
TGTGATATGTGCATCCGTATAAGACCATAGCCGGGATATGGCATCGGTGTGATATGTGCTACTGT
ACAAGACCATATTTGGATATGGCATCAG
Found at i:4545395 original size:14 final size:14
Alignment explanation
Indices: 4545378--4545425 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
4545368 AATTTAAAAA
4545378 TAAAAAAATCAAAT
1 TAAAAAAATCAAAT
*
4545392 TAAAAAAAT-TAA-
1 TAAAAAAATCAAAT
4545404 -AAAAAAATCAAAT
1 TAAAAAAATCAAAT
4545417 TAAAAAAAT
1 TAAAAAAAT
4545426 TAAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 8 0.28
12 2 0.07
13 2 0.07
14 17 0.59
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAAAAAATCAAAT
Found at i:4545407 original size:11 final size:11
Alignment explanation
Indices: 4545393--4545438 Score: 56
Period size: 11 Copynumber: 3.9 Consensus size: 11
4545383 AAATCAAATT
4545393 AAAAAAATTAA
1 AAAAAAATTAA
*
4545404 AAAAAAATCAAA
1 AAAAAAAT-TAA
4545416 TTAAAAAAATTAA
1 --AAAAAAATTAA
4545429 AAAAAAATTA
1 AAAAAAATTA
4545439 CATACCATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 18 0.60
12 2 0.07
13 2 0.07
14 8 0.27
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAAAAATTAA
Found at i:4545413 original size:25 final size:25
Alignment explanation
Indices: 4545379--4545436 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
4545369 ATTTAAAAAT
4545379 AAAAAAATCAAATTAAAAAAATTAA
1 AAAAAAATCAAATTAAAAAAATTAA
4545404 AAAAAAATCAAATTAAAAAAATTAA
1 AAAAAAATCAAATTAAAAAAATTAA
4545429 AAAAAAAT
1 AAAAAAAT
4545437 TACATACCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (25 bp):
AAAAAAATCAAATTAAAAAAATTAA
Found at i:4545434 original size:10 final size:9
Alignment explanation
Indices: 4545388--4545433 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
4545378 TAAAAAAATC
4545388 AAATTAAAA
1 AAATTAAAA
4545397 AAATTAAAA
1 AAATTAAAA
**
4545406 AAA--AATC
1 AAATTAAAA
4545413 AAATTAAAA
1 AAATTAAAA
4545422 AAATTAAAA
1 AAATTAAAA
4545431 AAA
1 AAA
4545434 AATTACATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
7 5 0.16
9 26 0.84
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATTAAAA
Found at i:4548786 original size:30 final size:32
Alignment explanation
Indices: 4548735--4548804 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 32
4548725 TTAAATTAAT
** *
4548735 AATGA-AAAAATTATACTTTTAA-CCTTCAAA
1 AATGATAAAAATTATAAATTTAATCATTCAAA
*
4548765 AATGATAAAAATT-TAAATTTAATCATTTAAA
1 AATGATAAAAATTATAAATTTAATCATTCAAA
*
4548796 AATTATAAA
1 AATGATAAA
4548805 GATATAGATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 12 0.36
31 21 0.64
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (32 bp):
AATGATAAAAATTATAAATTTAATCATTCAAA
Found at i:4548849 original size:22 final size:22
Alignment explanation
Indices: 4548794--4548857 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
4548784 TAATCATTTA
*
4548794 AAAATTATAAAGATATAGATTATT
1 AAAATTATAAA-AT-TATATTATT
* *
4548818 AAAATAATAAAATTATATTTTT
1 AAAATTATAAAATTATATTATT
* *
4548840 AATATTATAAAAATATAT
1 AAAATTATAAAATTATAT
4548858 AATTTAGTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 22 0.65
23 2 0.06
24 10 0.29
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (22 bp):
AAAATTATAAAATTATATTATT
Found at i:4553538 original size:84 final size:84
Alignment explanation
Indices: 4553385--4553540 Score: 233
Period size: 84 Copynumber: 1.9 Consensus size: 84
4553375 AACCCTAAAT
* * *
4553385 TCAAACCCCTTTGTCTCCATGGTCAAAGGCATTGGATTGAAGTTGTCTATCATGCTAATAATTTT
1 TCAAACCCCTATGTCTCCATGGTCAAAGACATTGGATTGAAGTTCTCTATCATGCTAATAATTTT
4553450 TTTTTTTAATTTTCAAAAA
66 TTTTTTTAATTTTCAAAAA
* * * *
4553469 TCAAACCCCTATGTCTCTATGGTCAAAGACATT-GTTTGAAGTTCTGTATTATGCTAATAATTTT
1 TCAAACCCCTATGTCTCCATGGTCAAAGACATTGGATTGAAGTTCTCTATCATGCTAATAATTTT
4553533 ATTTTTTT
66 -TTTTTTT
4553541 TCAAAATTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
83 27 0.42
84 37 0.58
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.44
Consensus pattern (84 bp):
TCAAACCCCTATGTCTCCATGGTCAAAGACATTGGATTGAAGTTCTCTATCATGCTAATAATTTT
TTTTTTTAATTTTCAAAAA
Found at i:4573296 original size:19 final size:20
Alignment explanation
Indices: 4573250--4573296 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
4573240 AATTATAAAA
4573250 AATATTATCTAAAAATTATG
1 AATATTATCTAAAAATTATG
* *
4573270 AAGTTATTAT-TAAATATTATT
1 AA--TATTATCTAAAAATTATG
4573291 AATATT
1 AATATT
4573297 TAATTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 4 0.17
20 2 0.09
21 11 0.48
22 6 0.26
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (20 bp):
AATATTATCTAAAAATTATG
Found at i:4573594 original size:11 final size:11
Alignment explanation
Indices: 4573578--4573609 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
4573568 TTTTATTAAA
4573578 ATTATAAAAAT
1 ATTATAAAAAT
4573589 ATTATAAAAAT
1 ATTATAAAAAT
4573600 ATTATAAAAA
1 ATTATAAAAA
4573610 GAGGGTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
ATTATAAAAAT
Found at i:4573944 original size:16 final size:17
Alignment explanation
Indices: 4573923--4573956 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4573913 CATTTGTATA
4573923 TATTTTTATAAT-ATTT
1 TATTTTTATAATAATTT
*
4573939 TATTTTTTTAATAATTT
1 TATTTTTATAATAATTT
4573956 T
1 T
4573957 TAATAATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTTTATAATAATTT
Found at i:4581735 original size:18 final size:18
Alignment explanation
Indices: 4581712--4581800 Score: 106
Period size: 18 Copynumber: 4.9 Consensus size: 18
4581702 CCAACTACTG
* *
4581712 TATACGTGAACAGTATCA
1 TATACGTGAATAGTACCA
*
4581730 TATACGTGAATAGTACCG
1 TATACGTGAATAGTACCA
* *
4581748 TATACATAAATAGTACCA
1 TATACGTGAATAGTACCA
* **
4581766 TATACGTGAATAGTGCTG
1 TATACGTGAATAGTACCA
4581784 TATACGTGAATAGTACC
1 TATACGTGAATAGTACC
4581801 GTAAACGATC
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 58 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (18 bp):
TATACGTGAATAGTACCA
Found at i:4594604 original size:16 final size:16
Alignment explanation
Indices: 4594583--4594625 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
4594573 GTGAAATTTA
* *
4594583 AATATTTTATTGAGAT
1 AATATTTTATTAAAAT
4594599 AATATTTTAATTAAAAT
1 AATATTTT-ATTAAAAT
4594616 AAT-TTTTATT
1 AATATTTTATT
4594626 TAATAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 3 0.12
16 12 0.50
17 9 0.38
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
AATATTTTATTAAAAT
Found at i:4612082 original size:3 final size:3
Alignment explanation
Indices: 4612069--4612105 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
4612059 AAATATAAGA
4612069 AAT ACAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4612106 CCGCGTAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4612329 original size:20 final size:22
Alignment explanation
Indices: 4612284--4612331 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
4612274 GCAAAAAGAG
4612284 AAAAAAATAATAATAAATAAAT
1 AAAAAAATAATAATAAATAAAT
4612306 --AAAAATAATAA-AAA-AAAT
1 AAAAAAATAATAATAAATAAAT
4612324 AAAAAAAT
1 AAAAAAAT
4612332 TGAATGAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 4 0.17
19 3 0.12
20 17 0.71
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (22 bp):
AAAAAAATAATAATAAATAAAT
Found at i:4615922 original size:33 final size:33
Alignment explanation
Indices: 4615880--4615948 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
4615870 GATTGTCAGG
4615880 TTTGAGTGTATTATGTAAGCCTCTTACTTTTTC
1 TTTGAGTGTATTATGTAAGCCTCTTACTTTTTC
4615913 TTTGAGTGTATTATGTAAGCCTCTTACTTTTTC
1 TTTGAGTGTATTATGTAAGCCTCTTACTTTTTC
4615946 TTT
1 TTT
4615949 CTCTGATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.54
Consensus pattern (33 bp):
TTTGAGTGTATTATGTAAGCCTCTTACTTTTTC
Found at i:4632743 original size:16 final size:16
Alignment explanation
Indices: 4632709--4632744 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4632699 GTATCATGGA
* *
4632709 TTAATTAGATATTAGT
1 TTAATTAGATAGTAAT
4632725 TTAATTAGATAGTAAT
1 TTAATTAGATAGTAAT
4632741 TTAA
1 TTAA
4632745 ATATTATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (16 bp):
TTAATTAGATAGTAAT
Found at i:4635247 original size:30 final size:30
Alignment explanation
Indices: 4635211--4635269 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
4635201 AGAAGCATTA
4635211 TAAACACCCCTATTAATTAATAAAAATACG
1 TAAACACCCCTATTAATTAATAAAAATACG
* *
4635241 TAAACACCCCTATTGATTGATAAAAATAC
1 TAAACACCCCTATTAATTAATAAAAATAC
4635270 ATATTCTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.27
Consensus pattern (30 bp):
TAAACACCCCTATTAATTAATAAAAATACG
Found at i:4635748 original size:5 final size:5
Alignment explanation
Indices: 4635738--4635817 Score: 160
Period size: 5 Copynumber: 16.0 Consensus size: 5
4635728 AATAATTAAG
4635738 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
4635788 TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT
4635818 ATAAAAGAAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 75 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:4635887 original size:31 final size:30
Alignment explanation
Indices: 4635852--4635912 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
4635842 GAAACAGAAT
*
4635852 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
4635883 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
4635913 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:4639628 original size:131 final size:131
Alignment explanation
Indices: 4639323--4639709 Score: 456
Period size: 131 Copynumber: 2.9 Consensus size: 131
4639313 AAAACACGAG
* * * * * * * *
4639323 TGAAATTCCGAAGAGATATTCAATTATTTTGAACAAACGGGAGATTGCAACCCAGCACGATAGGG
1 TGAAATTTCGAAGAGATATTCGATTATTTTGAGCAAACGCGAAATTGTAACCCAACACGTTAGGG
* * * * * * *
4639388 CACTATTCCCCGAATTGCCAAACATCGAA-CAT-TTCTTTCGTTTTAAAGAGTTTTTAGAAGATA
66 CACGATTCCGCGAATTGCCAAACATCGAATC-TCGTC-TTCGTTTTGAAGA-ATTTTAAAAGACA
4639451 TGAA
128 TGAA
* *
4639455 TGAAATCTT-GAAGGGATACTCGATTATTTTGAGCAAACGCGAAATTGTAACCCAACACGTTAGG
1 TGAAAT-TTCGAAGAGATATTCGATTATTTTGAGCAAACGCGAAATTGTAACCCAACACGTTAGG
* * * * * * *
4639519 GCACGATTCCGTGAATTACTAAATATCGAATGTCGTCCTCGTTTGGAAGAATTTTAAAAGACATG
65 GCACGATTCCGCGAATTGCCAAACATCGAATCTCGTCTTCGTTTTGAAGAATTTTAAAAGACATG
4639584 AA
130 AA
* *
4639586 TGAAATTTCGAAGCGATATTCGGTTATTTTGAGCAAACGCGAAATTGTAACCCAACACGTTAGGG
1 TGAAATTTCGAAGAGATATTCGATTATTTTGAGCAAACGCGAAATTGTAACCCAACACGTTAGGG
* * *
4639651 CACGATTCCGCGAATTGCCAAACATCAAATCTTGTCTTCGTTTTGAAGAATTTTTAAAG
66 CACGATTCCGCGAATTGCCAAACATCGAATCTCGTCTTCGTTTTGAAGAATTTTAAAAG
4639710 GAATACTTAT
Statistics
Matches: 214, Mismatches: 37, Indels: 9
0.82 0.14 0.03
Matches are distributed among these distances:
130 2 0.01
131 122 0.57
132 87 0.41
133 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (131 bp):
TGAAATTTCGAAGAGATATTCGATTATTTTGAGCAAACGCGAAATTGTAACCCAACACGTTAGGG
CACGATTCCGCGAATTGCCAAACATCGAATCTCGTCTTCGTTTTGAAGAATTTTAAAAGACATGA
A
Found at i:4646085 original size:39 final size:40
Alignment explanation
Indices: 4646033--4646117 Score: 118
Period size: 39 Copynumber: 2.1 Consensus size: 40
4646023 ATTTATATTA
*
4646033 TATATATATATATATATATGTGTGTTTTAAATATTAT-GT
1 TATATATATATATATATATGTGTATTTTAAATATTATAGT
* * *
4646072 TATATATATATATATGTGTGTGTATTTTTAATATTATCAGT
1 TATATATATATATATATATGTGTATTTTAAATATTAT-AGT
4646113 TATAT
1 TATAT
4646118 TTTCTTATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 33 0.82
41 7 0.17
ACGTcount: A:0.34, C:0.01, G:0.11, T:0.54
Consensus pattern (40 bp):
TATATATATATATATATATGTGTATTTTAAATATTATAGT
Found at i:4647684 original size:41 final size:40
Alignment explanation
Indices: 4647605--4647688 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 40
4647595 TAATATACAT
* *
4647605 ATATTAGTAATTATTATATATTTACTTATAATTTAAGTAA
1 ATATTAGTAATTATTATATATTTAATTATAATTAAAGTAA
*
4647645 ATATTATTATATTATTATATTATATTAATTA-AA-TAAAGTAA
1 ATATTAGTA-ATTATTATA-TAT-TTAATTATAATTAAAGTAA
4647686 ATA
1 ATA
4647689 AATTAAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
40 8 0.21
41 19 0.50
42 5 0.13
43 6 0.16
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (40 bp):
ATATTAGTAATTATTATATATTTAATTATAATTAAAGTAA
Found at i:4647908 original size:17 final size:15
Alignment explanation
Indices: 4647886--4647919 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
4647876 AGGGGAGAAA
4647886 GAAAGAAAGGAAAAAGG
1 GAAAGAAA-G-AAAAGG
4647903 GAAAGAAAGAAAAGG
1 GAAAGAAAGAAAAGG
4647918 GA
1 GA
4647920 GAAATTGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 1 0.06
17 8 0.47
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
GAAAGAAAGAAAAGG
Found at i:4647923 original size:17 final size:18
Alignment explanation
Indices: 4647885--4647923 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
4647875 CAGGGGAGAA
4647885 AGAAAGAAAGGAAAAAGG
1 AGAAAGAAAGGAAAAAGG
*
4647903 -GAAAGAAA-GAAAAGGG
1 AGAAAGAAAGGAAAAAGG
4647919 AGAAA
1 AGAAA
4647924 TTGGGGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AGAAAGAAAGGAAAAAGG
Found at i:4648643 original size:25 final size:26
Alignment explanation
Indices: 4648611--4648659 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
4648601 ATATAGATGT
4648611 GAAATGAAAG-AATGATACATGTTAA
1 GAAATGAAAGAAATGATACATGTTAA
4648636 GAAATGAAAGAAATGATACATGTT
1 GAAATGAAAGAAATGATACATGTT
4648660 TGGAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.51, C:0.04, G:0.20, T:0.24
Consensus pattern (26 bp):
GAAATGAAAGAAATGATACATGTTAA
Found at i:4648858 original size:39 final size:39
Alignment explanation
Indices: 4648803--4648910 Score: 146
Period size: 39 Copynumber: 2.7 Consensus size: 39
4648793 CCTTCTCGAG
4648803 AATTAAAAGTGAATAGGATTTATTCCTGATTCACTA-AAGA
1 AATT-AAAGTGAATAGGATTTATTCCTGATTCACTAGAA-A
4648843 AATTAAAGTGAATAGGATTTATTCCTGATTCACTAGAAA
1 AATTAAAGTGAATAGGATTTATTCCTGATTCACTAGAAA
* * * *
4648882 TATATAAAATGGATAGGATTTGTTCCTGA
1 AAT-TAAAGTGAATAGGATTTATTCCTGA
4648911 AATGGTAACT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
39 34 0.55
40 28 0.45
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (39 bp):
AATTAAAGTGAATAGGATTTATTCCTGATTCACTAGAAA
Found at i:4648909 original size:40 final size:39
Alignment explanation
Indices: 4648803--4648910 Score: 146
Period size: 40 Copynumber: 2.7 Consensus size: 39
4648793 CCTTCTCGAG
4648803 AATTAAAAGTGAATAGGATTTATTCCTGATTCACTAAAGA
1 AATTAAAA-TGAATAGGATTTATTCCTGATTCACTAAAGA
*
4648843 AATTAAAGTGAATAGGATTTATTCCTGATTCACTAGAA-A
1 AATTAAAATGAATAGGATTTATTCCTGATTCACTA-AAGA
* * *
4648882 TATATAAAATGGATAGGATTTGTTCCTGA
1 AAT-TAAAATGAATAGGATTTATTCCTGA
4648911 AATGGTAACT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
39 30 0.49
40 31 0.51
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (39 bp):
AATTAAAATGAATAGGATTTATTCCTGATTCACTAAAGA
Found at i:4658404 original size:41 final size:43
Alignment explanation
Indices: 4658321--4658418 Score: 110
Period size: 41 Copynumber: 2.3 Consensus size: 43
4658311 ATCGGGTACC
* * * **
4658321 TAGTACCTCATCGGATTTAATCCGAAGCAATAAAACGGCAC-A
1 TAGTGCCTCATTGGAATTAATCCGAAGCAATAAAACAACACAA
**
4658363 TAGTGCCTCATTGGAATT-ATCCGAAGCAATATTACAACACATA
1 TAGTGCCTCATTGGAATTAATCCGAAGCAATAAAACAACACA-A
4658406 TAGTGCCTCATTG
1 TAGTGCCTCATTG
4658419 ACTCAAGGCC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
41 18 0.38
42 15 0.32
43 14 0.30
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (43 bp):
TAGTGCCTCATTGGAATTAATCCGAAGCAATAAAACAACACAA
Found at i:4666596 original size:13 final size:12
Alignment explanation
Indices: 4666564--4666601 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
4666554 CCTTTCCCCC
4666564 TCCCTTCTCTC-
1 TCCCTTCTCTCT
4666575 TCCCTTCTCTCT
1 TCCCTTCTCTCT
4666587 TCCCTCTCTCTCT
1 TCCCT-TCTCTCT
4666600 TC
1 TC
4666602 TTTTTTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.44
12 5 0.20
13 9 0.36
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (12 bp):
TCCCTTCTCTCT
Found at i:4667147 original size:23 final size:23
Alignment explanation
Indices: 4667103--4667148 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4667093 GTATCACTAT
*
4667103 TATTATTATTATGTATTAGTATA
1 TATTATTATTATGTAGTAGTATA
*
4667126 TATTTTTATTATGTACGT-GTATA
1 TATTATTATTATGTA-GTAGTATA
4667149 CATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (23 bp):
TATTATTATTATGTAGTAGTATA
Found at i:4669346 original size:33 final size:33
Alignment explanation
Indices: 4669291--4669406 Score: 121
Period size: 33 Copynumber: 3.5 Consensus size: 33
4669281 TGCATATTTT
* ** *
4669291 CACAGCTCACACATTA-CATAGCTTGCACATTA
1 CACAGCTCACACATCATTGTAGCTCGCACATTA
* * *
4669323 CACAACTCGCACATCATTGTAGCTCACACATTA
1 CACAGCTCACACATCATTGTAGCTCGCACATTA
*
4669356 CACAGCTCACACATCACTATG-A-CTCGCAAATTA
1 CACAGCTCACACATCA-T-TGTAGCTCGCACATTA
4669389 CACAGCTCACACATCATT
1 CACAGCTCACACATCATT
4669407 ACGACTCGCA
Statistics
Matches: 70, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
31 1 0.01
32 14 0.20
33 51 0.73
34 2 0.03
35 2 0.03
ACGTcount: A:0.34, C:0.34, G:0.09, T:0.23
Consensus pattern (33 bp):
CACAGCTCACACATCATTGTAGCTCGCACATTA
Found at i:4669364 original size:16 final size:16
Alignment explanation
Indices: 4669291--4669402 Score: 75
Period size: 16 Copynumber: 6.9 Consensus size: 16
4669281 TGCATATTTT
4669291 CACAGCTCACACATTA
1 CACAGCTCACACATTA
* **
4669307 CATAGCTTGCACATTA
1 CACAGCTCACACATTA
* * *
4669323 CACAACTCGCACATCA
1 CACAGCTCACACATTA
***
4669339 TTGTAGCTCACACATTA
1 -CACAGCTCACACATTA
4669356 CACAGCTCACACA-T-
1 CACAGCTCACACATTA
* *
4669370 CACTATGACTCGCAAATTA
1 CAC-A-G-CTCACACATTA
4669389 CACAGCTCACACAT
1 CACAGCTCACACAT
4669403 CATTACGACT
Statistics
Matches: 70, Mismatches: 20, Indels: 12
0.69 0.20 0.12
Matches are distributed among these distances:
14 3 0.04
15 2 0.03
16 43 0.61
17 17 0.24
18 2 0.03
19 3 0.04
ACGTcount: A:0.35, C:0.34, G:0.09, T:0.22
Consensus pattern (16 bp):
CACAGCTCACACATTA
Found at i:4669413 original size:33 final size:33
Alignment explanation
Indices: 4669352--4669416 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
4669342 TAGCTCACAC
*
4669352 ATTACACAGCTCACACATCACTATGACTCGCAA
1 ATTACACAGCTCACACATCACTACGACTCGCAA
*
4669385 ATTACACAGCTCACACATCATTACGACTCGCA
1 ATTACACAGCTCACACATCACTACGACTCGCA
4669417 CATTGATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.34, G:0.09, T:0.22
Consensus pattern (33 bp):
ATTACACAGCTCACACATCACTACGACTCGCAA
Found at i:4671595 original size:43 final size:44
Alignment explanation
Indices: 4671520--4671606 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 44
4671510 ATTGATACTT
* * *
4671520 TTATGTGGTGTAATATTTAGTTATGCACTTGGACAATGTTATTA
1 TTATGTGGTGTAATATCTAATTATGCACTTGGACAATATTATTA
* * *
4671564 TTATGTGGTGTACTA-CTAATTATGCATTTGGATAATATTATTA
1 TTATGTGGTGTAATATCTAATTATGCACTTGGACAATATTATTA
4671607 ATTTCTAGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 23 0.62
44 14 0.38
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.46
Consensus pattern (44 bp):
TTATGTGGTGTAATATCTAATTATGCACTTGGACAATATTATTA
Found at i:4671871 original size:22 final size:20
Alignment explanation
Indices: 4671828--4671866 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4671818 CAATTTAAAA
4671828 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
4671848 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
4671867 ATGTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:4673952 original size:14 final size:14
Alignment explanation
Indices: 4673928--4673960 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
4673918 TCCCTGCTTC
4673928 GTTTCTGTTTCTTTT
1 GTTTCTGTTTC-TTT
4673943 GTTT-TGTTTCTTT
1 GTTTCTGTTTCTTT
4673956 GTTTC
1 GTTTC
4673961 CTTAATTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.41
14 6 0.35
15 4 0.24
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.73
Consensus pattern (14 bp):
GTTTCTGTTTCTTT
Found at i:4674007 original size:16 final size:16
Alignment explanation
Indices: 4673988--4674018 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4673978 TTTATTATTT
4673988 TATTAACATAATATAA
1 TATTAACATAATATAA
*
4674004 TATTAATATAATATA
1 TATTAACATAATATA
4674019 TTAAAATATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAACATAATATAA
Found at i:4674293 original size:15 final size:14
Alignment explanation
Indices: 4674275--4674305 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
4674265 TTAATTTATT
4674275 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
4674290 TAATAATAATCTAA
1 TAATAATAATCTAA
4674304 TA
1 TA
4674306 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:4674316 original size:21 final size:20
Alignment explanation
Indices: 4674292--4674360 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
4674282 AATGCTAATA
4674292 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
4674313 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
4674332 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
4674353 ATAATAAT
1 ATAATAAT
4674361 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:4689288 original size:20 final size:21
Alignment explanation
Indices: 4689259--4689297 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
4689249 TTGAAACCTT
*
4689259 AAAATCATTTATGATTCACGA
1 AAAATCATTTATGACTCACGA
4689280 AAAAT-ATTTATGACTCAC
1 AAAATCATTTATGACTCAC
4689298 ATAGAGAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (21 bp):
AAAATCATTTATGACTCACGA
Found at i:4689605 original size:19 final size:19
Alignment explanation
Indices: 4689582--4689624 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
4689572 TATAATTTTT
4689582 ATTTTTTA-AAAAAATAAG
1 ATTTTTTATAAAAAATAAG
**
4689600 ATTTTTTATTTAAAATAAG
1 ATTTTTTATAAAAAATAAG
4689619 ATTTTT
1 ATTTTT
4689625 AGTTTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
ATTTTTTATAAAAAATAAG
Found at i:4690388 original size:20 final size:20
Alignment explanation
Indices: 4690352--4690389 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4690342 AAGTTATAAC
*
4690352 AATATTTATATTAATTTATT
1 AATATTTATAATAATTTATT
4690372 AATATTTTATAAT-ATTTA
1 AATA-TTTATAATAATTTA
4690390 AAATTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATATTTATAATAATTTATT
Found at i:4694721 original size:14 final size:14
Alignment explanation
Indices: 4694698--4694728 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4694688 CATATTATAT
*
4694698 ATACATACACACAC
1 ATACACACACACAC
4694712 ATACACACACACAC
1 ATACACACACACAC
4694726 ATA
1 ATA
4694729 TATATAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.35, G:0.00, T:0.13
Consensus pattern (14 bp):
ATACACACACACAC
Found at i:4706810 original size:15 final size:17
Alignment explanation
Indices: 4706770--4706811 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
4706760 ATTTTAGAAG
4706770 TATTTTTAAGATAAAAA
1 TATTTTTAAGATAAAAA
* *
4706787 TATTATTAA-AT-AATA
1 TATTTTTAAGATAAAAA
4706802 TATTTTTAAG
1 TATTTTTAAG
4706812 TTTTTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 11 0.52
16 2 0.10
17 8 0.38
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (17 bp):
TATTTTTAAGATAAAAA
Found at i:4711921 original size:32 final size:31
Alignment explanation
Indices: 4711885--4711948 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 31
4711875 ATAAAAGTGA
4711885 AAGT-AAAAGTAAAAGTGAAAGTAAAAAGTAAA
1 AAGTAAAAAGTAAAAGT-AAAGT-AAAAGTAAA
4711917 AAGTAAAAAGTAAAAGTAAAGTAAAAGTAAA
1 AAGTAAAAAGTAAAAGTAAAGTAAAAGTAAA
4711948 A
1 A
4711949 GAAGAACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 10 0.32
32 9 0.29
33 12 0.39
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.16
Consensus pattern (31 bp):
AAGTAAAAAGTAAAAGTAAAGTAAAAGTAAA
Found at i:4711939 original size:5 final size:6
Alignment explanation
Indices: 4711871--4711949 Score: 97
Period size: 6 Copynumber: 12.8 Consensus size: 6
4711861 AACAAATAAG
* * *
4711871 AAAAAT AAAAGT GAAAGT AAAAGT AAAAGT GAAAGT AAAAAGT AAAAAGT
1 AAAAGT AAAAGT AAAAGT AAAAGT AAAAGT AAAAGT -AAAAGT -AAAAGT
4711921 AAAAAGT AAAAGT -AAAGT AAAAGT AAAAG
1 -AAAAGT AAAAGT AAAAGT AAAAGT AAAAG
4711950 AAGAACAAAC
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
5 5 0.08
6 42 0.64
7 19 0.29
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (6 bp):
AAAAGT
Found at i:4723118 original size:22 final size:21
Alignment explanation
Indices: 4723093--4723138 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4723083 GATTTTTCCG
*
4723093 ATTTCTAGTTGAATAAATTAAA
1 ATTTC-AGTTAAATAAATTAAA
* *
4723115 ATTTCAGTTAAATTAGTTAAA
1 ATTTCAGTTAAATAAATTAAA
4723136 ATT
1 ATT
4723139 AATATCCGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (21 bp):
ATTTCAGTTAAATAAATTAAA
Found at i:4724706 original size:20 final size:20
Alignment explanation
Indices: 4724681--4724730 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
4724671 TGGCTTAAAA
4724681 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
4724701 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
4724718 GTGGTAGTGGATT
1 TTGGTAGTGGATT
4724731 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:4729343 original size:20 final size:20
Alignment explanation
Indices: 4729318--4729367 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
4729308 TGGCTTAAAA
4729318 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
4729338 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
4729355 GTGGTAGTGGATT
1 TTGGTAGTGGATT
4729368 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:4745538 original size:23 final size:23
Alignment explanation
Indices: 4745481--4745541 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
4745471 AATTGAACCT
* *
4745481 AAAAAAACTTAAATACTAAATTA
1 AAAAAAAATTAAGTACTAAATTA
* ***
4745504 ACAAATTGTTAAGTACTAAATTA
1 AAAAAAAATTAAGTACTAAATTA
4745527 AAAAAAAATTAAGTA
1 AAAAAAAATTAAGTA
4745542 TATTAGTGTA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.28
Consensus pattern (23 bp):
AAAAAAAATTAAGTACTAAATTA
Found at i:4745633 original size:18 final size:19
Alignment explanation
Indices: 4745593--4745633 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
4745583 TTAAATATAT
4745593 TTAAATATTAAATAAGAAA
1 TTAAATATTAAATAAGAAA
4745612 -TAAATATTATAA-AA-AAA
1 TTAAATATTA-AATAAGAAA
4745629 TTAAA
1 TTAAA
4745634 AGTATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.15
18 15 0.75
19 2 0.10
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
TTAAATATTAAATAAGAAA
Found at i:4748578 original size:46 final size:44
Alignment explanation
Indices: 4748474--4748581 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
4748464 TGTCTTTGAC
** * * *
4748474 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
4748518 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
4748564 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
4748582 TTTCCGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:4757692 original size:22 final size:22
Alignment explanation
Indices: 4757652--4757693 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4757642 CTATATATTT
*
4757652 ATTATTTTTTTAATTTTTTATA
1 ATTATTTTTTTAATATTTTATA
4757674 ATTATATTTTTTAA-ATTTTA
1 ATTAT-TTTTTTAATATTTTA
4757694 GAAGAATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
ATTATTTTTTTAATATTTTATA
Found at i:4758886 original size:29 final size:28
Alignment explanation
Indices: 4758823--4758885 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 28
4758813 CAAATACTTA
4758823 TTTTTGTAATTAATTTATTTTTCATATAT
1 TTTTTGTAATTAATTTATTTTT-ATATAT
*
4758852 TTTTTGTAATTAATTATTACTTTTATATTAT
1 TTTTTGTAATTAA-T-TTATTTTTATA-TAT
4758883 TTT
1 TTT
4758886 GATAAAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 13 0.43
30 4 0.13
31 13 0.43
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (28 bp):
TTTTTGTAATTAATTTATTTTTATATAT
Found at i:4758996 original size:19 final size:20
Alignment explanation
Indices: 4758972--4759013 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
4758962 AAATATATCA
4758972 TAATCATTAT-AAACAAAAT
1 TAATCATTATAAAACAAAAT
*
4758991 TAATCATTATAAAACATAAT
1 TAATCATTATAAAACAAAAT
4759011 TAA
1 TAA
4759014 ATATCTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (20 bp):
TAATCATTATAAAACAAAAT
Found at i:4762267 original size:45 final size:44
Alignment explanation
Indices: 4762201--4762287 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 44
4762191 TGGCTAGATC
4762201 TAAAGAAAAATTTTACATTTCAAAATTAGT-GCAAAGCATAACAAA
1 TAAAGAAAAATTTTACATTTCAAAA-TAGTAG-AAAGCATAACAAA
* *
4762246 TAAAGTAAAAA-TTTACTTTTCAAAATAGTAGAAATCATAACA
1 TAAAG-AAAAATTTTACATTTCAAAATAGTAGAAAGCATAACA
4762288 TTTAATCTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
44 14 0.37
45 19 0.50
46 5 0.13
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (44 bp):
TAAAGAAAAATTTTACATTTCAAAATAGTAGAAAGCATAACAAA
Found at i:4763426 original size:16 final size:17
Alignment explanation
Indices: 4763405--4763437 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4763395 TAAAAGGCTT
4763405 TAATTAT-ATTATTAAA
1 TAATTATAATTATTAAA
4763421 TAATTATAATTATTAAA
1 TAATTATAATTATTAAA
4763438 ATGAAATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATTATAATTATTAAA
Found at i:4765597 original size:2 final size:2
Alignment explanation
Indices: 4765592--4765627 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4765582 ATATATACAT
4765592 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4765628 CAAAGCAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4768897 original size:17 final size:18
Alignment explanation
Indices: 4768862--4768904 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
4768852 AACTAAAATT
*
4768862 TAATTTACTAAAATCCAAA
1 TAATTTAC-AAAATACAAA
4768881 TAATTTAC-AAATACAAA
1 TAATTTACAAAATACAAA
4768898 T-ATTTAC
1 TAATTTAC
4768905 CGATTGCACC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 6 0.26
17 9 0.39
19 8 0.35
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATTTACAAAATACAAA
Found at i:4771274 original size:27 final size:26
Alignment explanation
Indices: 4771194--4771279 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 26
4771184 ATCGTCGTCG
*
4771194 TCATCTGCAGCAGCACCAACACAATCA
1 TCATCTGCAACAG-ACCAACACAATCA
* * * *
4771221 GCAGCTGCAAC-GACACCACTACCATCA
1 TCATCTGCAACAGAC-CAAC-ACAATCA
*
4771248 TCATCTGCACCAGTACCAACACAATCA
1 TCATCTGCAACAG-ACCAACACAATCA
*
4771275 CCATC
1 TCATC
4771280 ACAATCAGCA
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
25 2 0.05
26 4 0.09
27 32 0.73
28 4 0.09
29 2 0.05
ACGTcount: A:0.35, C:0.40, G:0.10, T:0.15
Consensus pattern (26 bp):
TCATCTGCAACAGACCAACACAATCA
Found at i:4771313 original size:27 final size:29
Alignment explanation
Indices: 4771235--4771313 Score: 74
Period size: 33 Copynumber: 2.6 Consensus size: 29
4771225 CTGCAACGAC
*
4771235 ACCACTACCATCATCATCTGCACCAGTACCA
1 ACCA-TACCATCATCATCAGCACCA-TACCA
4771266 ACACAATCACCATCA-CAATCAGCACC-TA-CA
1 AC-C-AT-ACCATCATC-ATCAGCACCATACCA
4771296 ACCATACCATCATCATCA
1 ACCATACCATCATCATCA
4771314 TCTGCAACAA
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
27 11 0.26
28 3 0.07
29 1 0.02
30 4 0.10
31 4 0.10
32 3 0.07
33 16 0.38
ACGTcount: A:0.38, C:0.41, G:0.04, T:0.18
Consensus pattern (29 bp):
ACCATACCATCATCATCAGCACCATACCA
Found at i:4771357 original size:30 final size:29
Alignment explanation
Indices: 4771276--4771358 Score: 71
Period size: 30 Copynumber: 2.8 Consensus size: 29
4771266 ACACAATCAC
* * *
4771276 CATCACAATCAGCACCTACAACCATACCAT
1 CATCACAATCATCAACTACAA-CATAACAT
*
4771306 CATCATC-ATC-TGCAACAACAACATCAACAT
1 CATCA-CAATCAT-CAACTACAACAT-AACAT
*
4771336 CATCACAATCATCATCTACAACA
1 CATCACAATCATCAACTACAACA
4771359 GCAATACCAG
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
29 4 0.10
30 36 0.86
31 2 0.05
ACGTcount: A:0.42, C:0.36, G:0.02, T:0.19
Consensus pattern (29 bp):
CATCACAATCATCAACTACAACATAACAT
Found at i:4771680 original size:15 final size:15
Alignment explanation
Indices: 4771660--4771691 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4771650 TCACCGTCGC
4771660 CATCACCAGCACCAG
1 CATCACCAGCACCAG
*
4771675 CATCACCAGTACCAG
1 CATCACCAGCACCAG
4771690 CA
1 CA
4771692 ACGACAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.44, G:0.12, T:0.09
Consensus pattern (15 bp):
CATCACCAGCACCAG
Found at i:4773090 original size:16 final size:16
Alignment explanation
Indices: 4773069--4773103 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4773059 TAAATAAATT
4773069 ATTAAAAAT-TTATAAA
1 ATTAAAAATATTA-AAA
4773085 ATTAAAAATATTAAAA
1 ATTAAAAATATTAAAA
4773101 ATT
1 ATT
4773104 CGATTCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTAAAAATATTAAAA
Found at i:4773613 original size:16 final size:15
Alignment explanation
Indices: 4773578--4773642 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 15
4773568 TTTGATTTCG
4773578 ATAAAATAAAATAAT
1 ATAAAATAAAATAAT
* *
4773593 TTAAAATCAAATTAAT
1 ATAAAAT-AAAATAAT
4773609 ATAAATCATAAAAGGTAAT
1 ATAAA--ATAAAA--TAAT
*
4773628 A-AATATAAAATAAT
1 ATAAAATAAAATAAT
4773642 A
1 A
4773643 GACAAAACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
14 5 0.12
15 6 0.15
16 17 0.43
17 3 0.08
18 4 0.10
19 5 0.12
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (15 bp):
ATAAAATAAAATAAT
Found at i:4773949 original size:18 final size:19
Alignment explanation
Indices: 4773914--4773953 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
4773904 AAAATTAAGA
4773914 AAAAATATATTATAAAAAT
1 AAAAATATATTATAAAAAT
4773933 AAAAATAT-TTA-ATAAAAT
1 AAAAATATATTATA-AAAAT
4773951 AAA
1 AAA
4773954 TTTTGAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 1 0.05
18 11 0.55
19 8 0.40
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAATATATTATAAAAAT
Found at i:4774945 original size:59 final size:59
Alignment explanation
Indices: 4774786--4774954 Score: 161
Period size: 59 Copynumber: 2.9 Consensus size: 59
4774776 TACTATAACA
* * * * *
4774786 TTTGGTAATTGAA-TT-TCACATTTTTTTAATTTAGTACCTAA-TTTTTTTTTTCTAAT
1 TTTGATAATTGAACTTGACACAATTTTCTAATCTAGTACCTAAGTTTTTTTTTTCTAAT
* * *
4774842 TTTGATACTTGAACTTGACACAATTTTCTAATCTAGTGCTTAAGTTTTTTTTTGTCTAA-
1 TTTGATAATTGAACTTGACACAATTTTCTAATCTAGTACCTAAGTTTTTTTTT-TCTAAT
* * * *
4774901 TTTGATAATTGAACTTGGCAC-TTTTTCCT-ATTTTGATACCTAAGTTTTTTTTTT
1 TTTGATAATTGAACTTGACACAATTTT-CTAATCTAG-TACCTAAGTTTTTTTTTT
4774955 TCAAATTACT
Statistics
Matches: 92, Mismatches: 15, Indels: 10
0.79 0.13 0.09
Matches are distributed among these distances:
56 11 0.12
57 2 0.02
58 29 0.32
59 45 0.49
60 5 0.05
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.54
Consensus pattern (59 bp):
TTTGATAATTGAACTTGACACAATTTTCTAATCTAGTACCTAAGTTTTTTTTTTCTAAT
Found at i:4774949 original size:58 final size:59
Alignment explanation
Indices: 4774786--4774952 Score: 148
Period size: 58 Copynumber: 2.9 Consensus size: 59
4774776 TACTATAACA
* * * * * *
4774786 TTTGGTAATTGAA-TT-TCACATTTTTTTAATTTAGTACCTAA-TTTTTTTTTTCTAAT
1 TTTGATAATTGAACTTGACACAATTTTCTAATCTAGTACCTAAGTTTTTTTTGTCTAAT
* * *
4774842 TTTGATACTTGAACTTGACACAATTTTCTAATCTAGTGCTTAAGTTTTTTTTTGTCTAA-
1 TTTGATAATTGAACTTGACACAATTTTCTAATCTAGTACCTAAG-TTTTTTTTGTCTAAT
* * * *
4774901 TTTGATAATTGAACTTGGCAC-TTTTTCCT-ATTTTGATACCTAAGTTTTTTTT
1 TTTGATAATTGAACTTGACACAATTTT-CTAATCTAG-TACCTAAGTTTTTTTT
4774953 TTTCAAATTA
Statistics
Matches: 89, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
56 11 0.12
57 2 0.02
58 36 0.40
59 27 0.30
60 13 0.15
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.54
Consensus pattern (59 bp):
TTTGATAATTGAACTTGACACAATTTTCTAATCTAGTACCTAAGTTTTTTTTGTCTAAT
Found at i:4775561 original size:30 final size:29
Alignment explanation
Indices: 4775495--4775603 Score: 84
Period size: 27 Copynumber: 3.9 Consensus size: 29
4775485 AAAAGTGTCC
**
4775495 AGTTCA-AGTACCAAATTAGACTAAA--TA
1 AGTTCAGA-TACCAAATTAGAAAAAATTTA
*
4775522 AGTTCAGATATCAAATTAAGAAAAAATTTA
1 AGTTCAGATACCAAATT-AGAAAAAATTTA
* * *
4775552 AGTTTAGATACCAAATTGGAAAAAA-TAA
1 AGTTCAGATACCAAATTAGAAAAAATTTA
* * *
4775580 ACTTAAG-TACCAAATTAGGAAAAA
1 AGTTCAGATACCAAATTAGAAAAAA
4775604 GTATCATGTT
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
27 29 0.43
28 14 0.21
29 7 0.10
30 17 0.25
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.26
Consensus pattern (29 bp):
AGTTCAGATACCAAATTAGAAAAAATTTA
Found at i:4780916 original size:23 final size:20
Alignment explanation
Indices: 4780890--4780938 Score: 53
Period size: 23 Copynumber: 2.3 Consensus size: 20
4780880 AATATTTTTT
*
4780890 ATTTATTTTTATGAATTTAATTA
1 ATTTATTTTT-TGAAATTAA--A
*
4780913 ATTTACTTTTTGAAATTAAA
1 ATTTATTTTTTGAAATTAAA
4780933 ATTTAT
1 ATTTAT
4780939 GTCTATTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 6 0.26
22 8 0.35
23 9 0.39
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (20 bp):
ATTTATTTTTTGAAATTAAA
Found at i:4790230 original size:20 final size:21
Alignment explanation
Indices: 4790200--4790246 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
4790190 TTATAGAAAA
*
4790200 TTATATTTTTACAAAGATTTT
1 TTATATTTTTAAAAAGATTTT
*
4790221 TTAT-TTTTTAAAAATATTTT
1 TTATATTTTTAAAAAGATTTT
4790241 TATATA
1 T-TATA
4790247 AAAATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TTATATTTTTAAAAAGATTTT
Found at i:4790240 original size:19 final size:21
Alignment explanation
Indices: 4790200--4790245 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
4790190 TTATAGAAAA
4790200 TTATATTTTTACAAAGATTTT
1 TTATATTTTTACAAAGATTTT
4790221 TTAT-TTTTTA-AAA-ATATTT
1 TTATATTTTTACAAAGAT-TTT
4790240 TTATAT
1 TTATAT
4790246 AAAAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.09
19 10 0.43
20 7 0.30
21 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
TTATATTTTTACAAAGATTTT
Found at i:4791640 original size:24 final size:24
Alignment explanation
Indices: 4791613--4791693 Score: 67
Period size: 24 Copynumber: 3.5 Consensus size: 24
4791603 AATACAAATC
4791613 AATATAATTTTATTAATATATACT
1 AATATAATTTTATTAATATATACT
* * * * * **
4791637 AATA-AA-ATAATAAACAAATTTT
1 AATATAATTTTATTAATATATACT
*
4791659 AAGATAATTTTATTAATATATACT
1 AATATAATTTTATTAATATATACT
*
4791683 AATAGAATTTT
1 AATATAATTTT
4791694 TATGAGAATA
Statistics
Matches: 38, Mismatches: 17, Indels: 4
0.64 0.29 0.07
Matches are distributed among these distances:
22 12 0.32
23 4 0.11
24 22 0.58
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (24 bp):
AATATAATTTTATTAATATATACT
Found at i:4791989 original size:15 final size:17
Alignment explanation
Indices: 4791969--4792005 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
4791959 GATAACAATA
*
4791969 TTAATATT-AATTGAG-
1 TTAATATTCAATCGAGC
4791984 TTAATATTCAATCGAGC
1 TTAATATTCAATCGAGC
4792001 TTAAT
1 TTAAT
4792006 TATTGTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 6 0.32
17 5 0.26
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (17 bp):
TTAATATTCAATCGAGC
Found at i:4804146 original size:25 final size:26
Alignment explanation
Indices: 4804109--4804162 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
4804099 TAAAAAACAA
* *
4804109 ATATATACTTAAGG-TGGAATGATAT
1 ATATATACTTAAGGATGAAATGAAAT
4804134 ATATATA-TATAAGGATGAAATGAAAT
1 ATATATACT-TAAGGATGAAATGAAAT
4804160 ATA
1 ATA
4804163 ATGTAGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 1 0.04
25 12 0.48
26 12 0.48
ACGTcount: A:0.48, C:0.02, G:0.17, T:0.33
Consensus pattern (26 bp):
ATATATACTTAAGGATGAAATGAAAT
Found at i:4809443 original size:19 final size:18
Alignment explanation
Indices: 4809420--4809474 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
4809410 ATTTTAAATG
4809420 ATTTAAACACTTTTTAAT
1 ATTTAAACACTTTTTAAT
* *
4809438 ATTTTAATATA-TATTTTATT
1 A-TTTAA-ACACT-TTTTAAT
4809458 ATTTAAACACTTTTTAA
1 ATTTAAACACTTTTTAA
4809475 CATTCACACA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
18 8 0.28
19 12 0.41
20 9 0.31
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTAAACACTTTTTAAT
Found at i:4810051 original size:19 final size:19
Alignment explanation
Indices: 4810029--4810083 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
4810019 AAATTTATGA
4810029 TAATTATTTATTATTATTT
1 TAATTATTTATTATTATTT
**
4810048 TAATTA-AAATTCATTATTT
1 TAATTATTTATT-ATTATTT
*
4810067 TTATTATTTGATTATTA
1 TAATTATTT-ATTATTA
4810084 ATATATATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 3 0.11
19 18 0.64
20 4 0.14
21 3 0.11
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TAATTATTTATTATTATTT
Found at i:4812846 original size:16 final size:16
Alignment explanation
Indices: 4812825--4812858 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
4812815 ATTCTAATCT
4812825 GAAAAGGAAAAAA-AAA
1 GAAAA-GAAAAAAGAAA
4812841 GAAAAGAAAAAAGAAA
1 GAAAAGAAAAAAGAAA
4812857 GA
1 GA
4812859 GGGTAGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
GAAAAGAAAAAAGAAA
Found at i:4821234 original size:19 final size:23
Alignment explanation
Indices: 4821177--4821224 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
4821167 GTGTAAGGTG
* *
4821177 ATAATA-ATATACAAATGTAATA
1 ATAATATATATATAATTGTAATA
4821199 ATAATATATATATAATTGTAA-A
1 ATAATATATATATAATTGTAATA
4821221 ATAA
1 ATAA
4821225 ATAATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (23 bp):
ATAATATATATATAATTGTAATA
Found at i:4821274 original size:27 final size:27
Alignment explanation
Indices: 4821222--4821279 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
4821212 AATTGTAAAA
* *
4821222 TAAATAATTAATTACTTTGTATTTAAG
1 TAAATAATTAATTACTTTGAAATTAAG
*
4821249 TAAATAATTATTTA-TTTGAAAATTAAG
1 TAAATAATTAATTACTTTG-AAATTAAG
4821276 TAAA
1 TAAA
4821280 ATATAATTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (27 bp):
TAAATAATTAATTACTTTGAAATTAAG
Found at i:4823706 original size:18 final size:17
Alignment explanation
Indices: 4823680--4823733 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
4823670 AAAAATTCAA
*
4823680 TTTTTATTCAAAAATAC
1 TTTTAATTCAAAAATAC
*
4823697 TTTATAATTCAAAAATAA
1 TTT-TAATTCAAAAATAC
4823715 TTTTAA-T-AAACAATAC
1 TTTTAATTCAAA-AATAC
4823731 TTT
1 TTT
4823734 CAAATAACGC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 3 0.09
16 8 0.25
17 6 0.19
18 15 0.47
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTTAATTCAAAAATAC
Found at i:4823721 original size:17 final size:17
Alignment explanation
Indices: 4823678--4823721 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
4823668 AGAAAAATTC
*
4823678 AATTTTTATTCAAAAAT
1 AATTTTAATTCAAAAAT
*
4823695 ACTTTATAATTCAAAAAT
1 AATTT-TAATTCAAAAAT
4823713 AATTTTAAT
1 AATTTTAAT
4823722 AAACAATACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTTAATTCAAAAAT
Found at i:4828474 original size:23 final size:23
Alignment explanation
Indices: 4828432--4828494 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
4828422 AAAAATAATG
* *
4828432 AAATTATAAATT-AATATAT-AAT
1 AAATTAT-AATTAAATTTATAAAA
*
4828454 AAATCTATATTTAAATTTATAAAA
1 AAAT-TATAATTAAATTTATAAAA
4828478 AAATTATAATTAAATTT
1 AAATTATAATTAAATTT
4828495 TCACTTTCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
22 7 0.21
23 21 0.62
24 6 0.18
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATTATAATTAAATTTATAAAA
Found at i:4828492 original size:11 final size:11
Alignment explanation
Indices: 4828426--4828493 Score: 50
Period size: 11 Copynumber: 6.0 Consensus size: 11
4828416 CCCTTTAAAA
*
4828426 ATAATGAAATT
1 ATAATTAAATT
4828437 ATAAATT-AATAT
1 AT-AATTAAAT-T
4828449 ATAA-TAAATCT
1 ATAATTAAAT-T
*
4828460 ATATTTAAATTT
1 ATAATTAAA-TT
**
4828472 ATAAAAAAATT
1 ATAATTAAATT
4828483 ATAATTAAATT
1 ATAATTAAATT
4828494 TTCACTTTCC
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
10 1 0.02
11 25 0.57
12 17 0.39
13 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (11 bp):
ATAATTAAATT
Found at i:4836518 original size:21 final size:21
Alignment explanation
Indices: 4836492--4836532 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4836482 AGACGAGCAA
* *
4836492 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
4836513 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
4836533 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:4843466 original size:29 final size:28
Alignment explanation
Indices: 4843433--4843487 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 28
4843423 ATTTAATTAA
4843433 TATTTTAAAATTTAGAAAT-ATATAAAAAC
1 TATTTTAAAATTTA-AAATCAT-TAAAAAC
4843462 TATTTTAAAATTTAAAATCATTAAAA
1 TATTTTAAAATTTAAAATCATTAAAA
4843488 TTATAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (28 bp):
TATTTTAAAATTTAAAATCATTAAAAAC
Found at i:4847274 original size:21 final size:21
Alignment explanation
Indices: 4847228--4847274 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
4847218 TACTTTCTTT
*
4847228 TTAATTATATATTTCTTTTTC
1 TTAATTATATATTTCTTTGTC
* *
4847249 ATAATTTTATATTT-TGTTGTC
1 TTAATTATATATTTCT-TTGTC
4847270 TTAAT
1 TTAAT
4847275 AATTTAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (21 bp):
TTAATTATATATTTCTTTGTC
Found at i:4847815 original size:23 final size:22
Alignment explanation
Indices: 4847782--4847838 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
4847772 TTTTATGAAA
*
4847782 TAAAAAT-TAAA-TTATGAAAAC
1 TAAAAATATAAAGTCAT-AAAAC
4847803 TATAAAATATAAAGTCATAAAAC
1 TA-AAAATATAAAGTCATAAAAC
4847826 TAAAATATATAAA
1 TAAAA-ATATAAA
4847839 ATTAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 2 0.06
22 8 0.26
23 18 0.58
24 3 0.10
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (22 bp):
TAAAAATATAAAGTCATAAAAC
Found at i:4847844 original size:21 final size:22
Alignment explanation
Indices: 4847784--4847845 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
4847774 TTATGAAATA
*
4847784 AAAAT-TAAATTATGAAAACTAT
1 AAAATATAAAATAT-AAAACTAT
*
4847806 AAAATATAAAGTCATAAAACTA-
1 AAAATATAAAAT-ATAAAACTAT
4847828 AAATATATAAAAT-TAAAA
1 AAA-ATATAAAATATAAAA
4847846 AAAATAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
21 5 0.14
22 8 0.23
23 20 0.57
24 2 0.06
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (22 bp):
AAAATATAAAATATAAAACTAT
Found at i:4847937 original size:15 final size:16
Alignment explanation
Indices: 4847901--4847945 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 16
4847891 CCTTTTTTGA
*
4847901 ATTAAAATATTATTTT
1 ATTAAAATATAATTTT
4847917 -TT-AAAT-TAATTTT
1 ATTAAAATATAATTTT
*
4847930 ATTAAAATATTATTTT
1 ATTAAAATATAATTTT
4847946 TATAGGTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
13 6 0.25
14 6 0.25
15 6 0.25
16 6 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTAAAATATAATTTT
Found at i:4851902 original size:5 final size:5
Alignment explanation
Indices: 4851894--4851926 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
4851884 TCCTCTCCAT
4851894 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT
4851927 GGTATGCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:4852448 original size:3 final size:3
Alignment explanation
Indices: 4852440--4852465 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4852430 ACAATTTAAG
4852440 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
4852466 CAGAAAACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:4853996 original size:14 final size:14
Alignment explanation
Indices: 4853962--4853994 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
4853952 AACTATTAAT
4853962 AAATTTAATTTTTA
1 AAATTTAATTTTTA
*
4853976 CAATTTAA-TTTTA
1 AAATTTAATTTTTA
4853989 AAATTT
1 AAATTT
4853995 TACAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
AAATTTAATTTTTA
Found at i:4854903 original size:28 final size:30
Alignment explanation
Indices: 4854864--4854930 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 30
4854854 TAGTAAAGAT
*
4854864 AAAAT-TACATTTTACCCCCT-AAAATTATA
1 AAAATATA-ATTTAACCCCCTAAAAATTATA
* **
4854893 AAAA-ATAATTTAATCCTTTAAAAATTATA
1 AAAATATAATTTAACCCCCTAAAAATTATA
4854922 AAAATATAA
1 AAAATATAA
4854931 ACTATTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
28 8 0.26
29 19 0.61
30 4 0.13
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (30 bp):
AAAATATAATTTAACCCCCTAAAAATTATA
Found at i:4859178 original size:14 final size:14
Alignment explanation
Indices: 4859159--4859204 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
4859149 ATTCTAAAGT
4859159 AAAATTAATTATAA
1 AAAATTAATTATAA
* *
4859173 AAAATTTATTTTAAA
1 AAAATTAATTAT-AA
*
4859188 AAAATTATTTATAA
1 AAAATTAATTATAA
4859202 AAA
1 AAA
4859205 TATATTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAATTAATTATAA
Found at i:4859191 original size:15 final size:15
Alignment explanation
Indices: 4859171--4859226 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
4859161 AATTAATTAT
4859171 AAAAAATTTATTTTA
1 AAAAAATTTATTTTA
4859186 AAAAAA-TTA-TTTA
1 AAAAAATTTATTTTA
* *
4859199 TAAAAATATATTTTA
1 AAAAAATTTATTTTA
4859214 ATAAAATATTTAT
1 A-AAAA-ATTTAT
4859227 CTTTGAGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 9 0.27
14 5 0.15
15 10 0.30
16 4 0.12
17 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAAAATTTATTTTA
Found at i:4859204 original size:28 final size:29
Alignment explanation
Indices: 4859159--4859226 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 29
4859149 ATTCTAAAGT
* *
4859159 AAAATTAATTATAAAAAATTTATTTTAAA
1 AAAATTATTTATAAAAAATATATTTTAAA
*
4859188 AAAATTATTTAT-AAAAATATATTTTAAT
1 AAAATTATTTATAAAAAATATATTTTAAA
4859216 AAAA-TATTTAT
1 AAAATTATTTAT
4859227 CTTTGAGATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 7 0.19
28 18 0.50
29 11 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
AAAATTATTTATAAAAAATATATTTTAAA
Found at i:4859210 original size:14 final size:14
Alignment explanation
Indices: 4859167--4859226 Score: 54
Period size: 14 Copynumber: 4.3 Consensus size: 14
4859157 GTAAAATTAA
*
4859167 TTATAAAAAATTTAT
1 TTAT-AAAAATATAT
*
4859182 TT-TAAAAAAATTAT
1 TTATAAAAATA-TAT
4859196 TTATAAAAATATAT
1 TTATAAAAATATAT
4859210 TT-TAATAAA-ATAT
1 TTATAA-AAATATAT
4859223 TTAT
1 TTAT
4859227 CTTTGAGATA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 14 0.37
14 15 0.39
15 9 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTATAAAAATATAT
Found at i:4868564 original size:7 final size:7
Alignment explanation
Indices: 4868554--4868579 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4868544 AATCAGGGAT
4868554 CAAGGTC
1 CAAGGTC
4868561 CAAGGTC
1 CAAGGTC
4868568 CAAGGTC
1 CAAGGTC
4868575 CAAGG
1 CAAGG
4868580 ATAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.27, G:0.31, T:0.12
Consensus pattern (7 bp):
CAAGGTC
Done.