Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008001.1 Hibiscus syriacus cultivar Beakdansim tig00110458_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3902382
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 18
Found at i:1267440 original size:14 final size:14
Alignment explanation
Indices: 1267421--1267485 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 14
1267411 AACGAGAAAT
1267421 GAAAATCGCAACGA
1 GAAAATCGCAACGA
1267435 GAAAATCGCAACACGAAA
1 GAAAATCGC-A-ACG--A
1267453 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
1267468 CAAAATCGCAACGT
1 GAAAATCGCAACGA
1267482 GAAA
1 GAAA
1267486 CCAAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
14 24 0.56
15 2 0.05
16 3 0.07
17 3 0.07
18 2 0.05
19 9 0.21
ACGTcount: A:0.51, C:0.22, G:0.18, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:1267453 original size:33 final size:33
Alignment explanation
Indices: 1267375--1267504 Score: 140
Period size: 33 Copynumber: 4.0 Consensus size: 33
1267365 AAAAATGACT
* * *
1267375 ATCGCAACGCGAAATG--AATGGCAACGAGAGA
1 ATCGCAACACGAAATGAAAATCGCAACGAGAAA
*
1267406 ATCACAACGA-GAAATGAAAATCGCAACGAGAAA
1 ATCGCAAC-ACGAAATGAAAATCGCAACGAGAAA
*
1267439 ATCGCAACACGAAATGAAAATCGCAACGACAAA
1 ATCGCAACACGAAATGAAAATCGCAACGAGAAA
** ** *
1267472 ATCGCAACGTGAAACCAAAATCGCAACGCGAAA
1 ATCGCAACACGAAATGAAAATCGCAACGAGAAA
1267505 CCAAAATCGC
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
31 13 0.16
32 1 0.01
33 69 0.83
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.09
Consensus pattern (33 bp):
ATCGCAACACGAAATGAAAATCGCAACGAGAAA
Found at i:1267551 original size:19 final size:19
Alignment explanation
Indices: 1267436--1267543 Score: 136
Period size: 19 Copynumber: 5.9 Consensus size: 19
1267426 TCGCAACGAG
* **
1267436 AAAATCGCAACACGAAATG
1 AAAATCGCAACGCGAAACC
1267455 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
1267469 AAAATCGCAACGTGAAACC
1 AAAATCGCAACGCGAAACC
1267488 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
1267507 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
*
1267526 AAAATCGTAACGCGAAAC
1 AAAATCGCAACGCGAAAC
1267544 TATAATCGCG
Statistics
Matches: 80, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 1 0.01
17 2 0.03
18 1 0.01
19 65 0.81
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.08
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:1267639 original size:20 final size:20
Alignment explanation
Indices: 1267587--1267644 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
1267577 AATTCTCTCG
**
1267587 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1267607 TTACGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1267627 TTGCGATAGTCATTTTCG
1 TTGCGATAGTCATTTTCG
1267645 TGTTACGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1269398 original size:149 final size:149
Alignment explanation
Indices: 1269154--1269459 Score: 533
Period size: 149 Copynumber: 2.1 Consensus size: 149
1269144 ACCAAAGTGT
* *
1269154 CGCGTAGAATTGCACCGTAGTTCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGA
1 CGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAAAATTCCTTAAGA
** *
1269219 ATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAGAATA
66 ATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAATA
1269284 TATATATATCCCGAAGGAC
131 TATATATATCCCGAAGGAC
*
1269303 CGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAAAATTCCTTAAGA
1 CGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAAAATTCCTTAAGA
*
1269368 ATCATATACATATGCTAGGGATCATA-TATGTGTCTCACCAGACTTCACACATGTTCCAAAGAAT
66 ATCATATACATATGCTAGGGATCA-AGTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAAT
1269432 ATATATATATCCCGAAGGAC
130 ATATATATATCCCGAAGGAC
1269452 CGCGTAGA
1 CGCGTAGA
1269460 CCCTCGACTC
Statistics
Matches: 149, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
149 148 0.99
150 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAAAATTCCTTAAGA
ATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAATA
TATATATATCCCGAAGGAC
Found at i:1270379 original size:18 final size:18
Alignment explanation
Indices: 1270358--1270392 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1270348 TCCCATCTAG
1270358 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
1270376 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
1270393 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:1270982 original size:64 final size:64
Alignment explanation
Indices: 1270884--1271044 Score: 209
Period size: 64 Copynumber: 2.5 Consensus size: 64
1270874 TAATGAAGGT
* *
1270884 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACTACA-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
*
1270947 GG
63 GC
* * *
1270949 ATGCATCGATGCACTTCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
1271013 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTACATATGCATCGATGCA
1271045 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 58 0.68
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:1274440 original size:23 final size:23
Alignment explanation
Indices: 1274414--1274458 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1274404 CACCACAGCT
*
1274414 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
1274437 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
1274459 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:1274679 original size:149 final size:149
Alignment explanation
Indices: 1274426--1274740 Score: 517
Period size: 149 Copynumber: 2.1 Consensus size: 149
1274416 TATAATTGCA
* *
1274426 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCATAGTGCCATATAATAATGTCCATAAGGACCACATAAAA
* **
1274490 TTCCTTAAGAATCATATGCATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTT
*
1274555 CCACAGAATATATATATATC
130 CCAAAGAATATATATATATC
*
1274575 CCGAAGGACCGCGTAGAATTGCACCATAGTGCCATATAATGATGTCCATAAGGACCACATAAAAT
1 CCGAAGGACCGCGTAGAATTGCACCATAGTGCCATATAATAATGTCCATAAGGACCACATAAAAT
*
1274640 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTCACCAGACTTCACACATGTT
66 TCCTTAAGAATCATATACATATGCTAGGGATCA-AGTATGTGTCTCACAAGACTTCACACATGTT
*
1274704 CCAAAGAATATATATATATT
130 CCAAAGAATATATATATATC
1274724 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
1274741 CCCTCGACTC
Statistics
Matches: 155, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
148 1 0.01
149 153 0.99
150 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCATAGTGCCATATAATAATGTCCATAAGGACCACATAAAAT
TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTC
CAAAGAATATATATATATC
Found at i:1275662 original size:18 final size:18
Alignment explanation
Indices: 1275641--1275675 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1275631 TCCCATCTAG
1275641 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
1275659 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
1275676 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:1276265 original size:64 final size:63
Alignment explanation
Indices: 1276167--1276327 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
1276157 TAATGAAGGT
* *
1276167 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
*
1276230 GG
62 GC
*
1276232 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
1276296 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
1276328 CCTTAAACAA
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.67
65 24 0.28
66 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:1278256 original size:14 final size:14
Alignment explanation
Indices: 1278237--1278272 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1278227 ATTGTTTAAT
1278237 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1278251 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1278265 TGATTTGT
1 TGATTTGT
1278273 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1278462 original size:34 final size:33
Alignment explanation
Indices: 1278385--1278469 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
1278375 TCGCAACTTG
**
1278385 GAAATGACTATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
*
1278418 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1278451 GAAAATGAAAATCGCAACG
1 G-AAATGAAAATCGCAACG
1278470 CGAAATTAGT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 31 0.65
34 17 0.35
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.14
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:1278465 original size:20 final size:19
Alignment explanation
Indices: 1278407--1278475 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
1278397 GCAACGAGAG
1278407 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1278426 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
1278440 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
1278460 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
1278476 TAGTTTCGCG
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.07
19 12 0.29
20 11 0.27
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1278541 original size:33 final size:33
Alignment explanation
Indices: 1278484--1278568 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
1278474 ATTAGTTTCG
1278484 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
1278518 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
* **
1278551 CATTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
1278569 CGCGTTACGA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 33 0.70
34 14 0.30
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:1278581 original size:20 final size:20
Alignment explanation
Indices: 1278553--1278639 Score: 104
Period size: 20 Copynumber: 4.3 Consensus size: 20
1278543 GATTCTCTCA
1278553 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGCG
* * *
1278573 TTACGATAGTCAATTCCGCA
1 TTGCGATAGTCATTTCCGCG
* **
1278593 TTGTGATAGTCATTTCCTTG
1 TTGCGATAGTCATTTCCGCG
1278613 TTGCGATAGTCATATT-CGCG
1 TTGCGATAGTCAT-TTCCGCG
1278633 TTGCGAT
1 TTGCGAT
1278640 TTCCGCGTTG
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 52 0.96
21 2 0.04
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCG
Found at i:1278606 original size:40 final size:41
Alignment explanation
Indices: 1278551--1278639 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 41
1278541 GCGATTCTCT
1278551 CATTGCGATAGTCATTTCCGCGTTACGATAGTCA-ATTCCG
1 CATTGCGATAGTCATTTCCGCGTTACGATAGTCATATTCCG
* ** *
1278591 CATTGTGATAGTCATTTCCTTGTTGCGATAGTCATATT-CG
1 CATTGCGATAGTCATTTCCGCGTTACGATAGTCATATTCCG
*
1278631 CGTTGCGAT
1 CATTGCGAT
1278640 TTCCGCGTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 39 0.93
41 3 0.07
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (41 bp):
CATTGCGATAGTCATTTCCGCGTTACGATAGTCATATTCCG
Found at i:1281103 original size:24 final size:24
Alignment explanation
Indices: 1281069--1281122 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1281059 CTGAAAAATC
1281069 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
1281093 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
1281117 ATCAAA
1 ATCAAA
1281123 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:1281998 original size:20 final size:19
Alignment explanation
Indices: 1281977--1282210 Score: 100
Period size: 20 Copynumber: 11.7 Consensus size: 19
1281967 GCGATAGTCA
1281977 GAATCTCGTTGCGATTTAC
1 GAATCTCGTTGCGATTTAC
* * * *
1281996 AGATTCACATTGTGATTTAC
1 -GAATCTCGTTGCGATTTAC
* * *
1282016 AGATTCGCATTGCGATTTAC
1 -GAATCTCGTTGCGATTTAC
*
1282036 GTAT-TCGCATTGCGATTTAC
1 GAATCTCG--TTGCGATTTAC
*
1282056 GTAT-TCGCATTGCGATTTAC
1 GAATCTCG--TTGCGATTTAC
* * *
1282076 AGATTCGCATTGCGATTTAC
1 -GAATCTCGTTGCGATTTAC
*
1282096 GTAT-TCGCATTGCGATTTAC
1 GAATCTCG--TTGCGATTTAC
*
1282116 GTAT-TCGCATTGCGATTTAC
1 GAATCTCG--TTGCGATTTAC
* * *
1282136 AGATTCGCATTGCGATTTAC
1 -GAATCTCGTTGCGATTTAC
*
1282156 GTAT-TCGCATTGCGATTTAC
1 GAATCTCG--TTGCGATTTAC
*
1282176 GTAATCGCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
* *
1282196 GTATTCGCGTTGCGA
1 G-AATCTCGTTGCGA
1282211 ATTATGAAAA
Statistics
Matches: 173, Mismatches: 29, Indels: 24
0.77 0.13 0.11
Matches are distributed among these distances:
18 3 0.02
19 6 0.03
20 154 0.89
21 6 0.03
22 4 0.02
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (19 bp):
GAATCTCGTTGCGATTTAC
Found at i:1282031 original size:40 final size:40
Alignment explanation
Indices: 1281985--1282210 Score: 343
Period size: 40 Copynumber: 5.7 Consensus size: 40
1281975 CAGAATCTCG
* *
1281985 TTGCGATTTACAG-ATTCACATTGTGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCATTGCGATTTAC-GTATTCGCA
1282025 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
1282065 TTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTAC-GTATTCGCATTGCGATTTACGTATTCGCA
1282105 TTGCGATTTACGTATTCGCATTGCGATTTACAG-ATTCGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTAC-GTATTCGCA
* *
1282145 TTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCG
1 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
*
1282185 TTGCGATTTACGTATTCGCGTTGCGA
1 TTGCGATTTACGTATTCGCATTGCGA
1282211 ATTATGAAAA
Statistics
Matches: 175, Mismatches: 5, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
39 4 0.02
40 169 0.97
41 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (40 bp):
TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
Found at i:1282049 original size:60 final size:60
Alignment explanation
Indices: 1281985--1282210 Score: 375
Period size: 60 Copynumber: 3.8 Consensus size: 60
1281975 CAGAATCTCG
* *
1281985 TTGCGATTTACAG-ATTCACATTGTGATTTACAGATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTAC-GTATTCGCATTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCA
1282045 TTGCGATTTACGTATTCGCATTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCA
1282105 TTGCGATTTACGTATTCGCATTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCA
* * *
1282165 TTGCGATTTACGTAATCGCGTTGCGATTTAC-GTATTCGCGTTGCGA
1 TTGCGATTTACGTATTCGCATTGCGATTTACAG-ATTCGCATTGCGA
1282211 ATTATGAAAA
Statistics
Matches: 159, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
59 2 0.01
60 157 0.99
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (60 bp):
TTGCGATTTACGTATTCGCATTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCA
Found at i:1282231 original size:21 final size:21
Alignment explanation
Indices: 1282207--1282252 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1282197 TATTCGCGTT
1282207 GCGAATTAT-GAAAATCGCAAC
1 GCGAATT-TGGAAAATCGCAAC
* *
1282228 GCGAATTTGGGAAATCGCAAT
1 GCGAATTTGGAAAATCGCAAC
1282249 GCGA
1 GCGA
1282253 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (21 bp):
GCGAATTTGGAAAATCGCAAC
Found at i:1282347 original size:20 final size:20
Alignment explanation
Indices: 1282303--1282495 Score: 185
Period size: 20 Copynumber: 9.6 Consensus size: 20
1282293 TACCGGAGAT
*
1282303 CGCGTTGCGAATTATC-GAT-
1 CGCGTTGCGATTTA-CGGATA
1282322 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1282342 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
1282362 TGTCGTTGCAATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
1282383 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
1282403 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
1282423 CGCGTTGCAATTTTACGTATT
1 CGCGTTGCGA-TTTACGGATA
*
1282444 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1282464 CGCGTTACGATTTTACAGATA
1 CGCGTTGCGA-TTTACGGATA
*
1282485 CTCGTTGCGAT
1 CGCGTTGCGAT
1282496 AGTCAGAATC
Statistics
Matches: 140, Mismatches: 27, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
18 1 0.01
19 16 0.11
20 74 0.53
21 49 0.35
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1282376 original size:41 final size:41
Alignment explanation
Indices: 1282324--1282495 Score: 267
Period size: 41 Copynumber: 4.2 Consensus size: 41
1282314 TTATCGATCG
*
1282324 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
1282365 CGTTGCAATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
1282405 CGTTGCGATTTACGGATACGCGTTGCAATTTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
1282446 CGTTGCGATTTACGGATACGCGTTACGATTTTACAG-ATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTAC-GTATTCT
1282487 CGTTGCGAT
1 CGTTGCGAT
1282496 AGTCAGAATC
Statistics
Matches: 120, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
40 36 0.30
41 83 0.69
42 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:1282417 original size:81 final size:82
Alignment explanation
Indices: 1282324--1282495 Score: 267
Period size: 81 Copynumber: 2.1 Consensus size: 82
1282314 TTATCGATCG
* *
1282324 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCAATTTACGGATACGCATT
1 CGTTGCGATTTACGGATACGCGTTGCAATTTTACGTATTCTCGTTGCAATTTACGGATACGCATT
* *
1282389 GCGA-TTTAC-GTATTCT
66 ACGATTTTACAG-ATACT
* *
1282405 CGTTGCGATTTACGGATACGCGTTGCAATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTT
1 CGTTGCGATTTACGGATACGCGTTGCAATTTTACGTATTCTCGTTGCAATTTACGGATACGCATT
1282470 ACGATTTTACAGATACT
66 ACGATTTTACAGATACT
1282487 CGTTGCGAT
1 CGTTGCGAT
1282496 AGTCAGAATC
Statistics
Matches: 83, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
81 64 0.77
82 18 0.22
83 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.37
Consensus pattern (82 bp):
CGTTGCGATTTACGGATACGCGTTGCAATTTTACGTATTCTCGTTGCAATTTACGGATACGCATT
ACGATTTTACAGATACT
Found at i:1282527 original size:20 final size:20
Alignment explanation
Indices: 1282321--1282556 Score: 107
Period size: 20 Copynumber: 11.7 Consensus size: 20
1282311 GAATTATCGA
* **
1282321 TCGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTTCATAT
* *
1282341 ACGCGTTGCGATTTTACGTAT
1 TCGCGTTGCGATTTT-CATAT
* * **
1282362 T-GTCGTTGCAATTTACGGAT
1 TCG-CGTTGCGATTTTCATAT
* * * *
1282382 ACGCATTGCGATTTACGTAT
1 TCGCGTTGCGATTTTCATAT
* * **
1282402 TCTCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTTCATAT
* * *
1282422 ACGCGTTGCAATTTTACGTAT
1 TCGCGTTGCGATTTT-CATAT
* * **
1282443 TCTCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTTCATAT
* * *
1282463 ACGCGTTACGATTTTACAGAT
1 TCGCGTTGCGATTTT-CATAT
* * ** * *
1282484 ACTCGTTGCGATAGTCAGAA
1 TCGCGTTGCGATTTTCATAT
*
1282504 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
1282524 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
1282544 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1282557 CTGGAAAATC
Statistics
Matches: 166, Mismatches: 43, Indels: 14
0.74 0.19 0.06
Matches are distributed among these distances:
19 1 0.01
20 119 0.72
21 46 0.28
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:1282531 original size:81 final size:79
Alignment explanation
Indices: 1282324--1282537 Score: 209
Period size: 81 Copynumber: 2.6 Consensus size: 79
1282314 TTATCGATCG
* * * * *
1282324 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCAATTTACGGATACGCATT
1 CGTTGCGATTCACGAATACGCGTTGCGATTTTATGT-TCG-CGTTGCGATTTACGGATACGCATT
* *
1282389 GCGATTTACGTATTCT
64 ACGATTTACGTATACT
* * * * * *
1282405 CGTTGCGATTTACGGATACGCGTTGCAATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTT
1 CGTTGCGATTCACGAATACGCGTTGCGATTTTA--TGTTCGCGTTGCGATTTACGGATACGCATT
1282470 ACGATTTTACAG-ATACT
64 ACGA-TTTAC-GTATACT
1282487 CGTTGCGATAGTCA-GAAT-CGCGTTGCGATTTATATGTTCGCGTTGCGATTT
1 CGTTGCGAT--TCACGAATACGCGTTGCGATTT-TATGTTCGCGTTGCGATTT
1282538 TCATATTCGC
Statistics
Matches: 112, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
81 72 0.64
82 31 0.28
83 7 0.06
84 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (79 bp):
CGTTGCGATTCACGAATACGCGTTGCGATTTTATGTTCGCGTTGCGATTTACGGATACGCATTAC
GATTTACGTATACT
Found at i:1290203 original size:156 final size:156
Alignment explanation
Indices: 1289976--1290325 Score: 475
Period size: 156 Copynumber: 2.2 Consensus size: 156
1289966 GTATATGAGT
* * * * *
1289976 ATGTGGTTTAAATTTGGTAAAACACGAACTTAAAATAAATGACAAATTGAAGGAATAAGGAGATT
1 ATGTGGTTCAAATTTGGTAAAA-ATGGACTTAAAATAAATGACAAATTGAAGAAATAAAGAGATT
* * * * *
1290041 ATGAAAATTTGAAAGACTAAATTGAAAAATACAAATTTATTATCAAAAATAGGAATTGAAAGTAC
65 ATGAAAAATTGAAAGACTAAATTAAAAAATAAAAATTTATTATAAAAAATAGGAATTGAAAGTAA
* *
1290106 ACATTTATTATACTATGATTTAGAATC
130 ACATGTATTATACTATGATTTAGAAGC
* * *
1290133 ATGTGGCTCAAATTTGGTAAAAATGGACTTAAAATAAATGACGAATTGAATAAATAAAGAGATTA
1 ATGTGGTTCAAATTTGGTAAAAATGGACTTAAAATAAATGACAAATTGAAGAAATAAAGAGATTA
* * *
1290198 TGAAAAATTGAAGGACTAAATTAAAAAATAAAAATTTGTTATAAAAAATATGAATTGAAAGTAAA
66 TGAAAAATTGAAAGACTAAATTAAAAAATAAAAATTTATTATAAAAAATAGGAATTGAAAGTAAA
* * *
1290263 CATGTATTCTACTATGGTTTAGGAGC
131 CATGTATTATACTATGATTTAGAAGC
*
1290289 ATGTGGTTCAAATTTGGTAAAAAAATAGACTTAAAAT
1 ATGTGGTTCAAATTTGGT--AAAAATGGACTTAAAAT
1290326 GAAAGAGTTG
Statistics
Matches: 168, Mismatches: 23, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
156 132 0.79
157 20 0.12
158 16 0.10
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.30
Consensus pattern (156 bp):
ATGTGGTTCAAATTTGGTAAAAATGGACTTAAAATAAATGACAAATTGAAGAAATAAAGAGATTA
TGAAAAATTGAAAGACTAAATTAAAAAATAAAAATTTATTATAAAAAATAGGAATTGAAAGTAAA
CATGTATTATACTATGATTTAGAAGC
Found at i:1292398 original size:20 final size:20
Alignment explanation
Indices: 1292364--1292408 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1292354 AACAAGTGAG
*
1292364 TATCGATACTCAAGGTTCAA
1 TATCGATACTCAAGGGTCAA
* * *
1292384 TATCGATATTGAAGGGTCAG
1 TATCGATACTCAAGGGTCAA
1292404 TATCG
1 TATCG
1292409 GTACCCATAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGATACTCAAGGGTCAA
Found at i:1294485 original size:2 final size:2
Alignment explanation
Indices: 1294478--1294525 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
1294468 ATTAAATTTA
1294478 AT AT AT AT -T AT AT -T AT AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1294517 AT AT AT AT A
1 AT AT AT AT A
1294526 AATGAATTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1294492 original size:21 final size:24
Alignment explanation
Indices: 1294463--1294514 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 24
1294453 TTTCACATGG
1294463 ATATA-ATTAAATT-TA-ATATAT
1 ATATATATTAAATTATATATATAT
*
1294484 AT-TATATTATATTATATATATAT
1 ATATATATTAAATTATATATATAT
1294507 ATATATAT
1 ATATATAT
1294515 ATATATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 2 0.08
21 9 0.35
22 2 0.08
23 8 0.31
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATATATATTAAATTATATATATAT
Found at i:1295460 original size:47 final size:48
Alignment explanation
Indices: 1295401--1295523 Score: 142
Period size: 48 Copynumber: 2.6 Consensus size: 48
1295391 GAACATATCA
* * * *
1295401 TAACATATAACTTTCT-TGATAGGAACTTGCATCATCAATTCATAATT
1 TAACATATAACTTTCTATAACAAGAACTTGCATCATAAATTCATAATT
* * *
1295448 TAACGTATAACTTTTTATAACAAGAACTTGCATCATAAATTCATAGTT
1 TAACATATAACTTTCTATAACAAGAACTTGCATCATAAATTCATAATT
* **
1295496 TAACATATAGCTTTC-ATGGCAAGAACTT
1 TAACATATAACTTTCTATAACAAGAACTT
1295524 TTATCATATA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
47 25 0.40
48 38 0.60
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (48 bp):
TAACATATAACTTTCTATAACAAGAACTTGCATCATAAATTCATAATT
Found at i:1306343 original size:17 final size:17
Alignment explanation
Indices: 1306316--1306350 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1306306 AATATATTAA
1306316 TTTAAATTAAATTCAAAT
1 TTTAAATTAAA-TCAAAT
1306334 TTTAAA-TAAATCAAAT
1 TTTAAATTAAATCAAAT
1306350 T
1 T
1306351 AAAAATTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAAATTAAATCAAAT
Found at i:1306358 original size:23 final size:22
Alignment explanation
Indices: 1306286--1306354 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
1306276 TTTATTTGAT
*
1306286 ATTTT-AATAGAATCAAATTGAAT
1 ATTTTAAATA-AATCAAATT-AAA
* * * *
1306309 ATATTAATTTAAATTAAATTCAA
1 ATTTTAA-ATAAATCAAATTAAA
1306332 ATTTTAAATAAATCAAATTAAA
1 ATTTTAAATAAATCAAATTAAA
1306354 A
1 A
1306355 ATTTGCATTG
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
22 13 0.37
23 11 0.31
24 9 0.26
25 2 0.06
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (22 bp):
ATTTTAAATAAATCAAATTAAA
Found at i:1309556 original size:26 final size:26
Alignment explanation
Indices: 1309527--1309585 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
1309517 ACTACGGTTT
1309527 CGAAATAGAAAAGGTCTAGCAGTAAG
1 CGAAATAGAAAAGGTCTAGCAGTAAG
1309553 CGAAATAGAAAAGGTCTAGCAGTAAG
1 CGAAATAGAAAAGGTCTAGCAGTAAG
1309579 CGAAATA
1 CGAAATA
1309586 CAGTTAGAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.47, C:0.12, G:0.25, T:0.15
Consensus pattern (26 bp):
CGAAATAGAAAAGGTCTAGCAGTAAG
Found at i:1310456 original size:154 final size:154
Alignment explanation
Indices: 1310201--1310508 Score: 607
Period size: 154 Copynumber: 2.0 Consensus size: 154
1310191 GAATGGCATA
1310201 ATCATGACCTGCACGAAGGGCAAACAATCCAGCCTCCGTACAAACATTTCGTAGATCGGCACCAT
1 ATCATGACCTGCACGAAGGGCAAACAATCCAGCCTCCGTACAAACATTTCGTAGATCGGCACCAT
*
1310266 TAAACCCTCAGAGAGTTTAGCTACAGCTTCATAGTCGATTCCACCACGCTACTCCATAGCCGTAT
66 TAAACCCTCAGAGAGTTTAGCTACAGCTTCATAGTCGATTCCACCACGCCACTCCATAGCCGTAT
1310331 CATGAATCTTGAGGATCTCCAATC
131 CATGAATCTTGAGGATCTCCAATC
1310355 ATCATGACCTGCACGAAGGGCAAACAATCCAGCCTCCGTACAAACATTTCGTAGATCGGCACCAT
1 ATCATGACCTGCACGAAGGGCAAACAATCCAGCCTCCGTACAAACATTTCGTAGATCGGCACCAT
1310420 TAAACCCTCAGAGAGTTTAGCTACAGCTTCATAGTCGATTCCACCACGCCACTCCATAGCCGTAT
66 TAAACCCTCAGAGAGTTTAGCTACAGCTTCATAGTCGATTCCACCACGCCACTCCATAGCCGTAT
1310485 CATGAATCTTGAGGATCTCCAATC
131 CATGAATCTTGAGGATCTCCAATC
1310509 TCGAGTGCTC
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 153 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (154 bp):
ATCATGACCTGCACGAAGGGCAAACAATCCAGCCTCCGTACAAACATTTCGTAGATCGGCACCAT
TAAACCCTCAGAGAGTTTAGCTACAGCTTCATAGTCGATTCCACCACGCCACTCCATAGCCGTAT
CATGAATCTTGAGGATCTCCAATC
Found at i:1310645 original size:18 final size:18
Alignment explanation
Indices: 1310622--1310660 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1310612 CTTAACCTTG
*
1310622 TCAAGCTTATGAAATCCA
1 TCAAGCTAATGAAATCCA
* *
1310640 TCAAGCTAATTAACTCCA
1 TCAAGCTAATGAAATCCA
1310658 TCA
1 TCA
1310661 TTGTTCTTTC
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:0.38, C:0.26, G:0.08, T:0.28
Consensus pattern (18 bp):
TCAAGCTAATGAAATCCA
Found at i:1313403 original size:2 final size:2
Alignment explanation
Indices: 1313396--1313441 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1313386 TGTAAAATTA
1313396 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1313438 AT AT
1 AT AT
1313442 TAAAATGATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1314151 original size:19 final size:20
Alignment explanation
Indices: 1314124--1314171 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
1314114 CCGTCGACCC
* *
1314124 TTAATATTTTTATTT-TAAA
1 TTAAAATTTTCATTTATAAA
*
1314143 TTAAAATTTTCATTTATAAT
1 TTAAAATTTTCATTTATAAA
1314163 TTCAAAATT
1 TT-AAAATT
1314172 ATTTTTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 13 0.54
20 5 0.21
21 6 0.25
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAAAATTTTCATTTATAAA
Found at i:1314246 original size:21 final size:20
Alignment explanation
Indices: 1314220--1314272 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
1314210 TTCACATTAA
*
1314220 TATTTAAATTATTTCTTAAAT
1 TATTTAAATTA-ATCTTAAAT
**
1314241 TATTTATTTTAATCTTAAAT
1 TATTTAAATTAATCTTAAAT
*
1314261 CATTTTAAATTA
1 TA-TTTAAATTA
1314273 GTTGTAATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTTAAATTAATCTTAAAT
Found at i:1314297 original size:13 final size:13
Alignment explanation
Indices: 1314279--1314313 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1314269 ATTAGTTGTA
1314279 ATTTTATAATTTT
1 ATTTTATAATTTT
*
1314292 ATTTTATATTTTT
1 ATTTTATAATTTT
1314305 ATTTGTATA
1 ATTT-TATA
1314314 TTATATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
ATTTTATAATTTT
Found at i:1322940 original size:25 final size:25
Alignment explanation
Indices: 1322912--1322963 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
1322902 CCTACGGTGT
*
1322912 AATTCTATGAGGCATTTTCGAGTGC
1 AATTCTACGAGGCATTTTCGAGTGC
1322937 AATTCTACGAGGCATTTTCGAGTGC
1 AATTCTACGAGGCATTTTCGAGTGC
1322962 AA
1 AA
1322964 ATATATCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (25 bp):
AATTCTACGAGGCATTTTCGAGTGC
Found at i:1324956 original size:2 final size:2
Alignment explanation
Indices: 1324949--1324990 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1324939 AGTACTTGTT
1324949 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
1324991 CTTCATTACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1325178 original size:12 final size:12
Alignment explanation
Indices: 1325161--1325185 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1325151 TATCTAAAGT
1325161 TAATATATACAA
1 TAATATATACAA
1325173 TAATATATACAA
1 TAATATATACAA
1325185 T
1 T
1325186 TCTGTCCTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (12 bp):
TAATATATACAA
Found at i:1326990 original size:22 final size:23
Alignment explanation
Indices: 1326962--1327023 Score: 99
Period size: 22 Copynumber: 2.7 Consensus size: 23
1326952 CGTTCTTGAG
1326962 TAAATGATATGAACATGA-ATTT
1 TAAATGATATGAACATGATATTT
*
1326984 TAAATGATATGAACATGATTTTT
1 TAAATGATATGAACATGATATTT
1327007 TAAAATGATATGAACAT
1 T-AAATGATATGAACAT
1327024 AAAAATATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
22 18 0.49
23 4 0.11
24 15 0.41
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (23 bp):
TAAATGATATGAACATGATATTT
Found at i:1332230 original size:40 final size:40
Alignment explanation
Indices: 1332174--1332252 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
1332164 ATAAAGTTTG
* *
1332174 GACCCCTTTGCCAAATATTATGGTACGAGGTGGTTGTTCT
1 GACCCCTTTGCAAAATACTATGGTACGAGGTGGTTGTTCT
1332214 GACCCCTTTGCAAAATACTATGGTACGAGGTGGTTGTTC
1 GACCCCTTTGCAAAATACTATGGTACGAGGTGGTTGTTC
1332253 AAACTTATGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (40 bp):
GACCCCTTTGCAAAATACTATGGTACGAGGTGGTTGTTCT
Found at i:1333934 original size:31 final size:30
Alignment explanation
Indices: 1333894--1333955 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
1333884 TTATGTATAT
1333894 TTTTATTA-TTAGTT-TTATTTATTATAAATA
1 TTTTATTATTTA-TTATTA-TTATTATAAATA
*
1333924 TTTTATTTATTTATTATTATTATTATTAATA
1 TTTTA-TTATTTATTATTATTATTATAAATA
1333955 T
1 T
1333956 AATAAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 5 0.18
31 17 0.61
32 6 0.21
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (30 bp):
TTTTATTATTTATTATTATTATTATAAATA
Found at i:1334129 original size:29 final size:29
Alignment explanation
Indices: 1334087--1334143 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
1334077 CTAGCTCCAG
1334087 CCGCTGCCTCAAGCTTCCAGAAGCCACAA
1 CCGCTGCCTCAAGCTTCCAGAAGCCACAA
1334116 CCGCTGCCTCAAGCTTCCAGAAGCCACA
1 CCGCTGCCTCAAGCTTCCAGAAGCCACA
1334144 GTCGCCGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.42, G:0.18, T:0.14
Consensus pattern (29 bp):
CCGCTGCCTCAAGCTTCCAGAAGCCACAA
Found at i:1335412 original size:4 final size:4
Alignment explanation
Indices: 1335405--1335431 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1335395 TAATAAATAA
1335405 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
1335432 ATCAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:1336323 original size:24 final size:23
Alignment explanation
Indices: 1336296--1336354 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
1336286 TATATATACT
1336296 TATTATTTTCA-TAATATTTATATA
1 TATTATTTTCATTAATATTT-T-TA
*
1336320 TATTATTTTTTATTAATATTTTTA
1 TATTA-TTTTCATTAATATTTTTA
*
1336344 TTTTATTTTCA
1 TATTATTTTCA
1336355 AGTATTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 5 0.17
24 11 0.37
25 6 0.20
26 8 0.27
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTATTTTCATTAATATTTTTA
Found at i:1336330 original size:26 final size:26
Alignment explanation
Indices: 1336284--1336352 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
1336274 TTTTAAAATT
1336284 TTTATATATACTTATTATTTTCA-TAATA
1 TTTATATATA-TTATT-TTTT-ATTAATA
1336312 TTTATATATATTATTTTTTATTAATA
1 TTTATATATATTATTTTTTATTAATA
*
1336338 TTT-T-TATTTTATTTT
1 TTTATATATATTATTTT
1336353 CAAGTATTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
24 10 0.26
25 2 0.05
26 12 0.31
27 5 0.13
28 10 0.26
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTATATATATTATTTTTTATTAATA
Found at i:1338802 original size:35 final size:35
Alignment explanation
Indices: 1338757--1338835 Score: 149
Period size: 35 Copynumber: 2.3 Consensus size: 35
1338747 TTTATGTGAA
*
1338757 TATGTGATACGATATGAGATTCATAAATATATGTT
1 TATGAGATACGATATGAGATTCATAAATATATGTT
1338792 TATGAGATACGATATGAGATTCATAAATATATGTT
1 TATGAGATACGATATGAGATTCATAAATATATGTT
1338827 TATGAGATA
1 TATGAGATA
1338836 TATGTTTACA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.38
Consensus pattern (35 bp):
TATGAGATACGATATGAGATTCATAAATATATGTT
Found at i:1339345 original size:30 final size:30
Alignment explanation
Indices: 1339305--1339407 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
1339295 GGTTCTTCGG
* *
1339305 GACCTATGGATAGTTATTGAGGATCTTTAT
1 GACCTCTGGATAGTTATCGAGGATCTTTAT
1339335 GACCTCTGGATAGTTATCGAGGATCTTTAT
1 GACCTCTGGATAGTTATCGAGGATCTTTAT
*
1339365 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTATCGAGGATCTTTAT
*
1339395 GACCTTTGGATAG
1 GACCTCTGGATAG
1339408 GTCCTTCGGG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 69 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (30 bp):
GACCTCTGGATAGTTATCGAGGATCTTTAT
Found at i:1342411 original size:15 final size:15
Alignment explanation
Indices: 1342393--1342423 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1342383 GATCAATACC
1342393 TTTGCATACATTCAT
1 TTTGCATACATTCAT
1342408 TTTGCATACATTCAT
1 TTTGCATACATTCAT
1342423 T
1 T
1342424 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.48
Consensus pattern (15 bp):
TTTGCATACATTCAT
Found at i:1347852 original size:14 final size:15
Alignment explanation
Indices: 1347832--1347866 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1347822 TTTTTTATTA
*
1347832 GGTTTGGGCCGGTCT
1 GGTTTGGGCCAGTCT
1347847 -GTTTGGGCCAGTCT
1 GGTTTGGGCCAGTCT
1347861 GGTTTG
1 GGTTTG
1347867 TAATCTGGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.03, C:0.17, G:0.43, T:0.37
Consensus pattern (15 bp):
GGTTTGGGCCAGTCT
Found at i:1347935 original size:3 final size:3
Alignment explanation
Indices: 1347927--1347986 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
1347917 TTTAATAAAT
* *
1347927 ATA ATA AT- ATA A-C ATA ATA AT- ATA A-C ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1347971 ATA ATA ATA ATTA ATA
1 ATA ATA ATA A-TA ATA
1347987 TAAGCAAATG
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
2 6 0.12
3 39 0.81
4 3 0.06
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1347945 original size:13 final size:13
Alignment explanation
Indices: 1347927--1347976 Score: 73
Period size: 13 Copynumber: 3.7 Consensus size: 13
1347917 TTTAATAAAT
1347927 ATAATAATATAAC
1 ATAATAATATAAC
1347940 ATAATAATATAAC
1 ATAATAATATAAC
*
1347953 ATAATAATAATAATA
1 ATAATAAT-ATAA-C
1347968 ATAATAATA
1 ATAATAATA
1347977 ATAATTAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
13 21 0.62
14 5 0.15
15 8 0.24
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAATAATATAAC
Found at i:1348515 original size:112 final size:113
Alignment explanation
Indices: 1348303--1348954 Score: 857
Period size: 112 Copynumber: 5.8 Consensus size: 113
1348293 TTCGTGATAG
* *
1348303 ATTCATGCAAAAGGCTGAACAAATTCTTCTCATTATGAACTTCTTC-TCC-TCTTCAGATGAGTT
1 ATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT
* * * **
1348366 CTTCTTATTATGAACTCTTCCTGGCAATATTGATCCATTGAGTGATGA
66 CTTCTCATTATGAACTCTTCCTGGAAATGTTGATCCATCAAGTGATGA
* * *
1348414 ATTCAGGCAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATAAGTT
1 ATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT
1348478 CTTCTCATTATGAACT-TTCTCTGGAAATGTTGATCCATCAAGTGATGA
66 CTTCTCATTATGAACTCTTC-CTGGAAATGTTGATCCATCAAGTGATGA
* *
1348526 ATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTATTCTTCC-TCTTCAGATGAGTT
1 ATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT
**
1348590 CTTCTCATTATGAACTCTT-CTGGAAATACTGATCCATCGAA-TGATGA
66 CTTCTCATTATGAACTCTTCCTGGAAATGTTGATCCATC-AAGTGATGA
* * *
1348637 ATTCAAGCAAAAAGTTGAAC-AATTCCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGT
1 ATTCAGGCAAAAGGTTGAACAAATT-CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
* *
1348701 TCTTCTCATTATGAA-TTTTCTCTGGAAATGTTGAT-C--C-AGTGATGG
65 TCTTCTCATTATGAACTCTTC-CTGGAAATGTTGATCCATCAAGTGATGA
* * * *
1348746 ATTC-GAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGT
1 ATTCAG-GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
* * *
1348810 TCTTTTCATTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGG
65 TCTTCTCATTATGAACTCTTCCTGGAAATGTTGATCCATCAAGTGATGA
* * * * *
1348859 ATT-TGAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGT
1 ATTCAG-GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
*
1348923 TCTTCTCATTATGAACTCTACCTGGAAATGTT
65 TCTTCTCATTATGAACTCTTCCTGGAAATGTT
1348955 TTAAGAAAGA
Statistics
Matches: 489, Mismatches: 35, Indels: 32
0.88 0.06 0.06
Matches are distributed among these distances:
108 1 0.00
109 85 0.17
110 12 0.02
111 112 0.23
112 163 0.33
113 116 0.24
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
ATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT
CTTCTCATTATGAACTCTTCCTGGAAATGTTGATCCATCAAGTGATGA
Found at i:1348560 original size:223 final size:221
Alignment explanation
Indices: 1348303--1348954 Score: 897
Period size: 223 Copynumber: 2.9 Consensus size: 221
1348293 TTCGTGATAG
* *
1348303 ATTCATGCAAAAGGCTGAACAAATTCTTCTCATTATGAACTTCTTC-TCCTCTTCAGATGAGTTC
1 ATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTC
* *
1348367 TTCTTATTATGAACTCTTCCTGGCAATATTGATCCATTGAGTGATGAATTCAGGCAAAAAGTTGA
66 TTCTTATTATGAACTCTTCCTGGAAATATTGATCCATCGAGTGATGAATTCAGGCAAAAAGTTGA
*
1348432 ACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTT
131 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTT
1348496 CTCTGGAAATGTTGATCCATCAAGTGATGA
196 CTCTGGAAATGTTGAT-C--C-AGTGATGA
* *
1348526 ATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTATTCTTCCTCTTCAGATGAGTTC
1 ATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTC
* * * *
1348591 TTCTCATTATGAACTCTT-CTGGAAATACTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGA
66 TTCTTATTATGAACTCTTCCTGGAAATATTGATCCATCGAGTGATGAATTCAGGCAAAAAGTTGA
*
1348655 AC-AATTCCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAATTT
131 ACAAATT-CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTT
*
1348719 TCTCTGGAAATGTTGATCCAGTGATGG
195 TCTCTGGAAATGTTGATCCAGTGATGA
* * * *
1348746 ATTC-GAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGT
1 ATTCAG-GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGT
* * * * * * *
1348810 TCTT-TTCATTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGGATT-TGAACAAAAGG
64 TCTTCTT-ATTATGAACTCTTCCTGGAAATATTGATCCATCGAGTGATGAATTCAG-GCAAAAAG
* * * *
1348873 TTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
127 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAA
*
1348938 CTCTAC-CTGGAAATGTT
192 CT-TTCTCTGGAAATGTT
1348955 TTAAGAAAGA
Statistics
Matches: 383, Mismatches: 36, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
219 1 0.00
220 50 0.13
221 30 0.08
222 105 0.27
223 115 0.30
224 82 0.21
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (221 bp):
ATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTC
TTCTTATTATGAACTCTTCCTGGAAATATTGATCCATCGAGTGATGAATTCAGGCAAAAAGTTGA
ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTT
CTCTGGAAATGTTGATCCAGTGATGA
Found at i:1349105 original size:76 final size:75
Alignment explanation
Indices: 1348976--1349148 Score: 274
Period size: 76 Copynumber: 2.3 Consensus size: 75
1348966 AAAAAAATTC
* * * *
1348976 TGCACTGTAGGGCTTACAGCTGACTCGAAGGTTTTGAAACATCAAAAAGCTCCCGAAGGCTTTTT
1 TGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAACATCAAAAAGCTCCCGAAGGCTTTTT
1349041 GGAAACATCA
66 GGAAACATCA
* * *
1349051 TGCACTGTAGGACTTATAGATGGCCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTT
1 TGCACTGTAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCTCCCGAAGGCTTTT
1349116 TGGAAACATCA
65 TGGAAACATCA
1349127 TGCACTGTAGGACTTACAGATG
1 TGCACTGTAGGACTTACAGATG
1349149 TGGGAAATAG
Statistics
Matches: 89, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
75 29 0.33
76 60 0.67
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (75 bp):
TGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAACATCAAAAAGCTCCCGAAGGCTTTTT
GGAAACATCA
Found at i:1350274 original size:50 final size:50
Alignment explanation
Indices: 1350214--1350308 Score: 163
Period size: 50 Copynumber: 1.9 Consensus size: 50
1350204 TAACTGGTTC
* * *
1350214 GTAAATCATTTGACAACACATTCATTATTTCCTGTGGTTTCTGCCCATAT
1 GTAAACCATTTGACAACACATTCATCATTTCCTATGGTTTCTGCCCATAT
1350264 GTAAACCATTTGACAACACATTCATCATTTCCTATGGTTTCTGCC
1 GTAAACCATTTGACAACACATTCATCATTTCCTATGGTTTCTGCC
1350309 AAGATTTCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (50 bp):
GTAAACCATTTGACAACACATTCATCATTTCCTATGGTTTCTGCCCATAT
Found at i:1354749 original size:10 final size:11
Alignment explanation
Indices: 1354729--1354753 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1354719 CTTGATTCAA
1354729 TTTTCCTTTTT
1 TTTTCCTTTTT
1354740 TTTTCCTTTTT
1 TTTTCCTTTTT
1354751 TTT
1 TTT
1354754 ATGAGTATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCCTTTTT
Found at i:1359105 original size:11 final size:12
Alignment explanation
Indices: 1359088--1359120 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1359078 TAATACTTGA
1359088 AAAAATAATAAT
1 AAAAATAATAAT
1359100 -AAAATAAT-AT
1 AAAAATAATAAT
1359110 AAAAATAATAA
1 AAAAATAATAA
1359121 GTAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.11
11 16 0.84
12 1 0.05
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:1361393 original size:3 final size:3
Alignment explanation
Indices: 1361385--1361431 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
1361375 TTTAATAAAT
*
1361385 ATA ATA AT- ATA A-C ATA ATA ATA ATA ATA ATA ATA ATA ATA ATTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
1361429 ATA
1 ATA
1361432 TAAGCAAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 3 0.08
3 33 0.85
4 3 0.08
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1364044 original size:20 final size:20
Alignment explanation
Indices: 1364019--1364057 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1364009 AATTTGTAAA
1364019 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
1364039 TCGCAACACAGAAGTCAAA
1 TCGCAACACAGAAGTCAAA
1364058 GCACGTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.13
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:1364606 original size:20 final size:19
Alignment explanation
Indices: 1364553--1364607 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
1364543 AAATCGCAAC
* *
1364553 GCGAATTTAGTTTCGCGTT
1 GCGAATTTAGTTTCACATT
* *
1364572 GCGATTTTCATTTTCACATT
1 GCGAATTT-AGTTTCACATT
1364592 GCGAATTTAAGTTTCA
1 GCGAATTT-AGTTTCA
1364608 GAAACTACTT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (19 bp):
GCGAATTTAGTTTCACATT
Found at i:1366752 original size:21 final size:20
Alignment explanation
Indices: 1366726--1366821 Score: 93
Period size: 21 Copynumber: 4.6 Consensus size: 20
1366716 TGCACTTCCT
1366726 ATCGTTCAAGAGGCCCCCCTC
1 ATCGTTCAAGAGGCCCCCC-C
*
1366747 ATCGTTCAAGAGGCCTCTCCC
1 ATCGTTCAAGAGGCC-CCCCC
* * *
1366768 ACCATTCAAGAGGCCCCTGCC
1 ATCGTTCAAGAGGCCCC-CCC
* *
1366789 ATCGTTCAAGAGGTCTCTCCC
1 ATCGTTCAAGAGG-CCCCCCC
*
1366810 ACCGTTCAAGAG
1 ATCGTTCAAGAG
1366822 CCCGATTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.02
21 55 0.90
22 5 0.08
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.21
Consensus pattern (20 bp):
ATCGTTCAAGAGGCCCCCCC
Found at i:1366792 original size:42 final size:42
Alignment explanation
Indices: 1366730--1366821 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
1366720 CTTCCTATCG
1366730 TTCAAGAGGCCCCCCTCATCGTTCAAGAGGCCTCTCCCACCA
1 TTCAAGAGGCCCCCCTCATCGTTCAAGAGGCCTCTCCCACCA
* * *
1366772 TTCAAGAGGCCCCTGC-CATCGTTCAAGAGGTCTCTCCCACCG
1 TTCAAGAGGCCCC-CCTCATCGTTCAAGAGGCCTCTCCCACCA
1366814 TTCAAGAG
1 TTCAAGAG
1366822 CCCGATTCAC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.21
Consensus pattern (42 bp):
TTCAAGAGGCCCCCCTCATCGTTCAAGAGGCCTCTCCCACCA
Found at i:1368235 original size:63 final size:66
Alignment explanation
Indices: 1368167--1368338 Score: 252
Period size: 65 Copynumber: 2.7 Consensus size: 66
1368157 CTGGGGTACA
*
1368167 ATTTTTTTGCTTGTTTAATTGAATTT-T-ACA-TTGATTTGTTTAATTGATGAGGAAATAAGAAT
1 ATTTTTTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAAT
1368229 T
66 T
* *
1368230 A--TTTTTGCTTGTTTAATTG-ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAAGAAT
1 ATTTTTTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAAT
1368292 T
66 T
*
1368293 ATTTTTTTGCTTGTTTAATTG-ATTTGTAAAAGTTTATTT-TTTAATT
1 ATTTTTTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTTTAATT
1368339 TATTCAATCT
Statistics
Matches: 100, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
60 4 0.04
61 19 0.19
62 2 0.02
63 33 0.33
64 7 0.07
65 35 0.35
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.54
Consensus pattern (66 bp):
ATTTTTTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAAT
T
Found at i:1368587 original size:42 final size:43
Alignment explanation
Indices: 1368525--1368605 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 43
1368515 GAATTTGACT
* * * *
1368525 ATCGCAACGCAAAAATCGCAATGCAAATTTGACTTTCGCATTA
1 ATCGCAACGAAAAAAGCGCAACGCAAATATGACTTTCGCATTA
**
1368568 ATCGCAAC-AAAAAAGCGCAACGTGAATATGACTTTCGC
1 ATCGCAACGAAAAAAGCGCAACGCAAATATGACTTTCGC
1368606 GTTGCGAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
42 24 0.75
43 8 0.25
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.22
Consensus pattern (43 bp):
ATCGCAACGAAAAAAGCGCAACGCAAATATGACTTTCGCATTA
Found at i:1368840 original size:18 final size:18
Alignment explanation
Indices: 1368817--1368852 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1368807 AAGCCGGTTG
*
1368817 TGATTGGGATTTTAATTT
1 TGATTGCGATTTTAATTT
*
1368835 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTAATTT
1368853 CCTTTTGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTAATTT
Found at i:1371922 original size:16 final size:15
Alignment explanation
Indices: 1371900--1371938 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1371890 GAAATCATTG
1371900 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
1371916 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
1371931 AAAAATTA
1 AAAAATTA
1371939 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:1372139 original size:20 final size:20
Alignment explanation
Indices: 1372114--1372187 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 20
1372104 TTAAATTCAT
1372114 GTTGCGAATTTGAAAATCGA
1 GTTGCGAATTTGAAAATCGA
*
1372134 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAAATCGA
* *
1372153 GTTTTGCGAATTTGGTAAA-CGC
1 G--TTGCGAATTT-GAAAATCGA
1372175 GTTGCGAATTTGA
1 GTTGCGAATTTGA
1372188 CTTCTTTGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
19 3 0.07
20 27 0.60
21 11 0.24
22 4 0.09
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATCGA
Found at i:1372161 original size:21 final size:20
Alignment explanation
Indices: 1372096--1372166 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
1372086 CTAAAACCTG
*
1372096 TTGCGAAATT-AAATTCA-T
1 TTGCGAATTTGAAATTCAGT
*
1372114 GTTGCGAATTTGAAAATCGAG-
1 -TTGCGAATTTGAAATTC-AGT
1372135 TTGCGAATTTGAAATTCAGTT
1 TTGCGAATTTGAAATTCAG-T
1372156 TTGCGAATTTG
1 TTGCGAATTTG
1372167 GTAAACGCGT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
19 11 0.25
20 21 0.48
21 12 0.27
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGAATTTGAAATTCAGT
Found at i:1372163 original size:41 final size:40
Alignment explanation
Indices: 1372095--1372187 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 40
1372085 ACTAAAACCT
*
1372095 GTTGCGAAATT-AAATTCATGTTGCGAATTT-GAAAATCGA
1 GTTGCGAATTTGAAATTCATGTTGCGAATTTGGAAAA-CGA
* * *
1372134 GTTGCGAATTTGAAATTCAGTTTTGCGAATTTGGTAAACGC
1 GTTGCGAATTTGAAATTCA-TGTTGCGAATTTGGAAAACGA
1372175 GTTGCGAATTTGA
1 GTTGCGAATTTGA
1372188 CTTCTTTGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
39 10 0.21
40 7 0.15
41 26 0.55
42 4 0.09
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (40 bp):
GTTGCGAATTTGAAATTCATGTTGCGAATTTGGAAAACGA
Found at i:1372283 original size:19 final size:19
Alignment explanation
Indices: 1372211--1372285 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 19
1372201 ATTCGCATAT
1372211 TCGCGTTGCGAATTTG-GAA
1 TCGCGTTGCGAATTTGAG-A
* * * *
1372230 ACTGGGTTGCGAAATTGGAGT
1 TC-GCGTTGCG-AATTTGAGA
* *
1372251 TCGCGTTACAAATTTGAGA
1 TCGCGTTGCGAATTTGAGA
1372270 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
1372286 TTGGTCATTT
Statistics
Matches: 41, Mismatches: 12, Indels: 6
0.69 0.20 0.10
Matches are distributed among these distances:
19 22 0.54
20 12 0.29
21 6 0.15
22 1 0.02
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.32
Consensus pattern (19 bp):
TCGCGTTGCGAATTTGAGA
Found at i:1376689 original size:3 final size:3
Alignment explanation
Indices: 1376676--1376748 Score: 51
Period size: 3 Copynumber: 24.0 Consensus size: 3
1376666 TTTATATTTA
* * * * * *
1376676 TAT TTT TAT TAT TAGT T-T TATT TAT TAT AAA CAT TAT TAT AAA TAT
1 TAT TAT TAT TAT TA-T TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
1376722 T-T TATT TAT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT
1376749 AATAAATTTA
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
2 4 0.07
3 42 0.78
4 8 0.15
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1378000 original size:11 final size:11
Alignment explanation
Indices: 1377965--1378044 Score: 56
Period size: 12 Copynumber: 6.9 Consensus size: 11
1377955 TAGTCACTAT
1377965 TTATTTATATT-
1 TTATTTA-ATTA
1377976 TTAATTTAATTTA
1 TT-ATTTAA-TTA
*
1377989 TTATTTCATTA
1 TTATTTAATTA
*
1378000 -TGTTTAATTCA
1 TTATTTAATT-A
*
1378011 ATATTCTAATTA
1 TTATT-TAATTA
*
1378023 TTATTTTATTA
1 TTATTTAATTA
1378034 TTATTTTAATT
1 TTA-TTTAATT
1378045 TATTCATATA
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
10 7 0.13
11 15 0.27
12 26 0.47
13 7 0.13
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (11 bp):
TTATTTAATTA
Found at i:1378440 original size:2 final size:2
Alignment explanation
Indices: 1378433--1378458 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1378423 ATAAATATCT
1378433 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
1378459 ATTATATTAA
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:1383199 original size:19 final size:18
Alignment explanation
Indices: 1383173--1383228 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
1383163 CGATAAATCG
1383173 AACCGAACCGAACCGAAA
1 AACCGAACCGAACCGAAA
1383191 AACCCGAACCGTTAA---AAA
1 AA-CCGAACCG--AACCGAAA
1383209 AACCGAACCGAACCGAAA
1 AACCGAACCGAACCGAAA
1383227 AA
1 AA
1383229 ATCGGTTTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
15 2 0.06
17 8 0.25
18 12 0.38
19 8 0.25
21 2 0.06
ACGTcount: A:0.52, C:0.30, G:0.14, T:0.04
Consensus pattern (18 bp):
AACCGAACCGAACCGAAA
Found at i:1388567 original size:20 final size:20
Alignment explanation
Indices: 1388523--1388567 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1388513 ACAGACTTTG
*
1388523 TAACTAACCATTAACAACCT
1 TAACTAAACATTAACAACCT
* *
1388543 CAACTAAACATTAACAGCCT
1 TAACTAAACATTAACAACCT
1388563 TAACT
1 TAACT
1388568 GCTAACAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.29, G:0.02, T:0.24
Consensus pattern (20 bp):
TAACTAAACATTAACAACCT
Found at i:1388798 original size:36 final size:36
Alignment explanation
Indices: 1388746--1388883 Score: 181
Period size: 36 Copynumber: 3.8 Consensus size: 36
1388736 TGAATAATTG
1388746 AATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTTT
1 AATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTTT
* *
1388782 AATCGAAAGTGTCGATGCTTCCTTTCGTT--CTTCTT
1 AATCGAAAGTGCCGATGCTTCCTTCCGTTCACTT-TT
* *
1388817 GAATCGAAAGTGCCGATGCTTTCTTCCGTTCACTTTG
1 -AATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTTT
* * *
1388854 AATCGAAAGTGTCAATGCTTCCTTTCGTTC
1 AATCGAAAGTGCCGATGCTTCCTTCCGTTC
1388884 TTCTTCCTCA
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
34 3 0.03
35 2 0.02
36 79 0.90
37 1 0.01
38 3 0.03
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.38
Consensus pattern (36 bp):
AATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTTT
Found at i:1388860 original size:72 final size:72
Alignment explanation
Indices: 1388743--1388888 Score: 265
Period size: 72 Copynumber: 2.0 Consensus size: 72
1388733 AGATGAATAA
* *
1388743 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTTTAATCGAAAGTGTCGATGCTTCCTTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGTCAATGCTTCCTTTC
1388808 GTTCTTC
66 GTTCTTC
*
1388815 TTGAATCGAAAGTGCCGATGCTTTCTTCCGTTCACTTTGAATCGAAAGTGTCAATGCTTCCTTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGTCAATGCTTCCTTTC
1388880 GTTCTTC
66 GTTCTTC
1388887 TT
1 TT
1388889 CCTCACCTTC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (72 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGTCAATGCTTCCTTTC
GTTCTTC
Found at i:1390263 original size:20 final size:20
Alignment explanation
Indices: 1390219--1390263 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1390209 ACAGACTTTG
*
1390219 TAACTAACCATTAACAACCT
1 TAACTAAACATTAACAACCT
* *
1390239 CAACTAAACATTAACAGCCT
1 TAACTAAACATTAACAACCT
1390259 TAACT
1 TAACT
1390264 GCTAACAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.29, G:0.02, T:0.24
Consensus pattern (20 bp):
TAACTAAACATTAACAACCT
Found at i:1391309 original size:22 final size:21
Alignment explanation
Indices: 1391265--1391309 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
1391255 AAAATATACA
*
1391265 ATATATATAGCTTTTGAAGAT
1 ATATATATAGCTTTTGAAAAT
* *
1391286 ATATAGTATAGTTTTTTAAAAT
1 ATATA-TATAGCTTTTGAAAAT
1391308 AT
1 AT
1391310 TTTTGAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (21 bp):
ATATATATAGCTTTTGAAAAT
Found at i:1391353 original size:39 final size:40
Alignment explanation
Indices: 1391310--1391455 Score: 154
Period size: 39 Copynumber: 3.7 Consensus size: 40
1391300 TTTAAAATAT
* *
1391310 TTTTGAAAACAAATAATAAATAGTTTTTTTTAAAAACGG-
1 TTTTGAAAACATATAATAAATAGTTTTTTTTAAAAATGGA
* * ** *
1391349 TTTTGAAAACCTATAATATATAGTTTTTTAAAAAAATGGT
1 TTTTGAAAACATATAATAAATAGTTTTTTTTAAAAATGGA
* * **
1391389 TTTTGAAAATATATAATATATA-TAATTTTTAAAAATGGA
1 TTTTGAAAACATATAATAAATAGTTTTTTTTAAAAATGGA
*
1391428 TTTTGAAAACGTAT-ATAATATAGTTTTT
1 TTTTGAAAACATATAATAA-ATAGTTTTT
1391456 GAAAACATAT
Statistics
Matches: 86, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
38 3 0.03
39 60 0.70
40 23 0.27
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (40 bp):
TTTTGAAAACATATAATAAATAGTTTTTTTTAAAAATGGA
Found at i:1391395 original size:79 final size:79
Alignment explanation
Indices: 1391309--1391460 Score: 200
Period size: 79 Copynumber: 1.9 Consensus size: 79
1391299 TTTTAAAATA
**
1391309 TTTTTGAAAACAAATAATAAATAGTTTTTTTTAAAAACGG-TTTTGAAAACCTATA-ATATATAG
1 TTTTTGAAAACAAATAATAAATA-TAATTTTTAAAAACGGATTTTGAAAACCTATATA-ATATAG
*
1391372 TTTTTTAAAAAAATGG
64 TTTTTGAAAAAAATGG
* * * * *
1391388 TTTTTGAAAATATATAATATATATAATTTTTAAAAATGGATTTTGAAAACGTATATAATATAGTT
1 TTTTTGAAAACAAATAATAAATATAATTTTTAAAAACGGATTTTGAAAACCTATATAATATAGTT
1391453 TTTGAAAA
66 TTTGAAAA
1391461 CATATATATA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
78 13 0.21
79 49 0.78
80 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (79 bp):
TTTTTGAAAACAAATAATAAATATAATTTTTAAAAACGGATTTTGAAAACCTATATAATATAGTT
TTTGAAAAAAATGG
Found at i:1391471 original size:21 final size:23
Alignment explanation
Indices: 1391428--1391482 Score: 80
Period size: 21 Copynumber: 2.5 Consensus size: 23
1391418 TAAAAATGGA
1391428 TTTTGAAAACGTATATAATATAGT
1 TTTTGAAAACG-ATATAATATAGT
1391452 TTTTGAAAAC-ATAT-ATATAGT
1 TTTTGAAAACGATATAATATAGT
1391473 TTTT-AAAACG
1 TTTTGAAAACG
1391483 GGTTTTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.17
21 11 0.37
22 4 0.13
24 10 0.33
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (23 bp):
TTTTGAAAACGATATAATATAGT
Found at i:1391504 original size:57 final size:61
Alignment explanation
Indices: 1391404--1391538 Score: 161
Period size: 57 Copynumber: 2.2 Consensus size: 61
1391394 AAAATATATA
* * ** *
1391404 ATATATATAATTTTTAAAAATGGATTTTGAAAACGTATATAATATA-GT-T-TTTGAAAAC
1 ATATATATAGTTTTTAAAAACGGATTTTGAAAAAATATATAATATATATATCTTTGAAAAC
*
1391462 ATATATATAGTTTTT-AAAACGGGTTTTGAAAAAATATATAATATATATAATCTTTGAAAAC
1 ATATATATAGTTTTTAAAAACGGATTTTGAAAAAATATATAATATATAT-ATCTTTGAAAAC
*
1391523 ATATTATATTGTTTTT
1 ATA-TATATAGTTTTT
1391539 GAAATATGAT
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
57 26 0.40
58 15 0.23
60 1 0.02
61 12 0.18
62 11 0.17
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.44
Consensus pattern (61 bp):
ATATATATAGTTTTTAAAAACGGATTTTGAAAAAATATATAATATATATATCTTTGAAAAC
Found at i:1391568 original size:5 final size:5
Alignment explanation
Indices: 1391558--1391631 Score: 50
Period size: 5 Copynumber: 15.2 Consensus size: 5
1391548 TACATACATA
* * *
1391558 TTATT TTATT TT-TCA TT-TT TTATCT TTCTT TTCTT TTCATT TTATT
1 TTATT TTATT TTAT-T TTATT TTAT-T TTATT TTATT TT-ATT TTATT
*
1391604 TTATT TTA-T TTA-T TCATT TTA-T TTATT T
1 TTATT TTATT TTATT TTATT TTATT TTATT T
1391632 AATTATTTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
4 14 0.25
5 35 0.61
6 8 0.14
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:1391641 original size:13 final size:13
Alignment explanation
Indices: 1391593--1391630 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
1391583 TTCTTTTCTT
1391593 TTCATTTTA-TT-
1 TTCATTTTATTTA
1391604 TT-ATTTTATTTA
1 TTCATTTTATTTA
1391616 TTCATTTTATTTA
1 TTCATTTTATTTA
1391629 TT
1 TT
1391631 TAATTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 6 0.25
11 4 0.17
12 2 0.08
13 12 0.50
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (13 bp):
TTCATTTTATTTA
Found at i:1392098 original size:42 final size:42
Alignment explanation
Indices: 1392022--1392105 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
1392012 CCAAATCAGT
* * * ** *
1392022 GGTCGAATTTCAAGGAAACAAACCACAATTAAATCTAAGCAA
1 GGTCGAATCTCAAAGAAACAAACAACAACCAAATCAAAGCAA
*
1392064 GGTCGAATCTCAAAGAAACAAGCAACAACCAAATCAAAGCAA
1 GGTCGAATCTCAAAGAAACAAACAACAACCAAATCAAAGCAA
1392106 ATCACGACAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.50, C:0.21, G:0.14, T:0.14
Consensus pattern (42 bp):
GGTCGAATCTCAAAGAAACAAACAACAACCAAATCAAAGCAA
Found at i:1395382 original size:38 final size:39
Alignment explanation
Indices: 1395335--1395421 Score: 149
Period size: 38 Copynumber: 2.3 Consensus size: 39
1395325 TTAGAAAACC
1395335 TATATATATAATCTTTAAAACATTTTGAAAACATATATA
1 TATATATATAATCTTTAAAACATTTTGAAAACATATATA
* *
1395374 TA-ATATATAGTTTTTAAAACATTTTGAAAACATATATA
1 TATATATATAATCTTTAAAACATTTTGAAAACATATATA
1395412 TATATATATA
1 TATATATATA
1395422 TATATATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
38 36 0.80
39 9 0.20
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (39 bp):
TATATATATAATCTTTAAAACATTTTGAAAACATATATA
Found at i:1395412 original size:2 final size:2
Alignment explanation
Indices: 1395405--1395438 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1395395 TTTTGAAAAC
1395405 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1395439 CTTTTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1395465 original size:54 final size:55
Alignment explanation
Indices: 1395367--1395480 Score: 178
Period size: 56 Copynumber: 2.1 Consensus size: 55
1395357 TTTTGAAAAC
*
1395367 ATATATATAATATATAGTTTTTAAAACATTTTGAAAACATATATATATATATATAT
1 ATATATATAATATATACTTTTTAAAACATTTTGAAAACATATATATATATATAT-T
* *
1395423 ATATATATATTATATACTTTTTAAAATATTTT-AAAA-ATATATATATATATATT
1 ATATATATAATATATACTTTTTAAAACATTTTGAAAACATATATATATATATATT
1395476 ATATA
1 ATATA
1395481 GTTTTTAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
53 6 0.11
54 16 0.29
55 4 0.07
56 29 0.53
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (55 bp):
ATATATATAATATATACTTTTTAAAACATTTTGAAAACATATATATATATATATT
Found at i:1395471 original size:44 final size:43
Alignment explanation
Indices: 1395415--1395516 Score: 163
Period size: 42 Copynumber: 2.4 Consensus size: 43
1395405 ATATATATAT
*
1395415 ATATATATATATATATATTATATACTTTTTAAAATATTTTAAA
1 ATATATATATATATATATTATATACTTTTTAAAACATTTTAAA
*
1395458 A-ATATATATATATATATTATATAGTTTTTAAAACATTTTAAA
1 ATATATATATATATATATTATATACTTTTTAAAACATTTTAAA
1395500 A-ATATATATAATATATA
1 ATATATATAT-ATATATA
1395517 GTTTTTAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
42 48 0.86
43 8 0.14
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (43 bp):
ATATATATATATATATATTATATACTTTTTAAAACATTTTAAA
Found at i:1395505 original size:38 final size:38
Alignment explanation
Indices: 1395421--1395603 Score: 185
Period size: 39 Copynumber: 4.7 Consensus size: 38
1395411 ATATATATAT
* *
1395421 ATATATATATATTATATACTTTTTAAAATATTTTAAAAATA
1 ATATATATATATTATATAGTTTTTAAAACATTTT--AAA-A
1395462 TATATATATATATTATATAGTTTTTAAAACATTTTAAAA
1 -ATATATATATATTATATAGTTTTTAAAACATTTTAAAA
**
1395501 ATATATATA-A-TATATAGTTTTTAAAACAATTTTTGAA
1 ATATATATATATTATATAGTTTTTAAAAC-ATTTTAAAA
* * * *
1395538 A-ATATATATACTATATAGTTTTGAAAATTATTTTTGAAA
1 ATATATATATATTATATAGTTTTTAAAA-CA-TTTTAAAA
* *
1395577 A-ATATATGTATTATATAGTTTTGAAAA
1 ATATATATATATTATATAGTTTTTAAAA
1395604 TTATTTTTAA
Statistics
Matches: 126, Mismatches: 10, Indels: 13
0.85 0.07 0.09
Matches are distributed among these distances:
36 24 0.19
37 10 0.08
38 25 0.20
39 32 0.25
40 3 0.02
42 32 0.25
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (38 bp):
ATATATATATATTATATAGTTTTTAAAACATTTTAAAA
Found at i:1395592 original size:39 final size:38
Alignment explanation
Indices: 1395423--1395615 Score: 203
Period size: 38 Copynumber: 5.0 Consensus size: 38
1395413 ATATATATAT
* * *
1395423 ATATATATATTATATACTTTTTAAAA-TATTTTAAAAATATA
1 ATATATATATTATATAGTTTTGAAAATTATTTT--TAA-A-A
* *
1395464 TATATATATATTATATAGTTTTTAAAA-CA-TTTTAAAA
1 -ATATATATATTATATAGTTTTGAAAATTATTTTTAAAA
* * ** *
1395501 ATATATATAATATATAGTTTTTAAAACAATTTTTGAAA
1 ATATATATATTATATAGTTTTGAAAATTATTTTTAAAA
*
1395539 ATATATATACTATATAGTTTTGAAAATTATTTTTGAAAA
1 ATATATATATTATATAGTTTTGAAAATTATTTTT-AAAA
*
1395578 ATATATGTATTATATAGTTTTGAAAATTATTTTTAAAA
1 ATATATATATTATATAGTTTTGAAAATTATTTTTAAAA
1395616 GAGAAAATAA
Statistics
Matches: 135, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
36 25 0.19
37 2 0.01
38 42 0.31
39 37 0.27
41 3 0.02
42 26 0.19
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (38 bp):
ATATATATATTATATAGTTTTGAAAATTATTTTTAAAA
Found at i:1395791 original size:21 final size:21
Alignment explanation
Indices: 1395762--1395808 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1395752 AATATGTAAA
1395762 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
1395783 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
1395804 TCGCA
1 TCGCA
1395809 ACGCGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1395814 original size:21 final size:21
Alignment explanation
Indices: 1395697--1395814 Score: 80
Period size: 20 Copynumber: 5.8 Consensus size: 21
1395687 AAATGACCAA
*
1395697 CAAATTCGCAACGCGA-ATTC
1 CAAATTCGCAACGCGATTTTC
* * * *
1395717 CAATTTCGTAAC-CCAGTTTC
1 CAAATTCGCAACGCGATTTTC
* * * *
1395737 CAATTTCGCAACGCGAATATG
1 CAAATTCGCAACGCGATTTTC
* **
1395758 TAAA-TCGCATTGCGATTTTC
1 CAAATTCGCAACGCGATTTTC
***
1395778 CAAATTCGCGTTGCGATTTTC
1 CAAATTCGCAACGCGATTTTC
1395799 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
1395815 ATTTGTAAAT
Statistics
Matches: 74, Mismatches: 21, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
19 2 0.03
20 38 0.51
21 34 0.46
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (21 bp):
CAAATTCGCAACGCGATTTTC
Found at i:1395824 original size:21 final size:21
Alignment explanation
Indices: 1395741--1395855 Score: 58
Period size: 21 Copynumber: 5.6 Consensus size: 21
1395731 AGTTTCCAAT
*
1395741 TTCGCAACGCGAATATGTAAA
1 TTCGCAACGCGAATTTGTAAA
** * **
1395762 -TCGCATTGCGATTTTCCAAA
1 TTCGCAACGCGAATTTGTAAA
*** * **
1395782 TTCGCGTTGCGATTTTCCAAA
1 TTCGCAACGCGAATTTGTAAA
1395803 TTCGCAACGCGAATTTGTAAA
1 TTCGCAACGCGAATTTGTAAA
* **
1395824 -TCGCAACAC--ATAAGTCAAA
1 TTCGCAACGCGAATTTGT-AAA
1395843 TTCGCAACGCGAA
1 TTCGCAACGCGAA
1395856 AGTCAAATGT
Statistics
Matches: 72, Mismatches: 17, Indels: 9
0.73 0.17 0.09
Matches are distributed among these distances:
18 4 0.06
19 3 0.04
20 30 0.42
21 34 0.47
22 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (21 bp):
TTCGCAACGCGAATTTGTAAA
Found at i:1395847 original size:20 final size:20
Alignment explanation
Indices: 1395824--1395863 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1395814 AATTTGTAAA
1395824 TCGCAACAC-ATAAGTCAAAT
1 TCGCAACACGA-AAGTCAAAT
*
1395844 TCGCAACGCGAAAGTCAAAT
1 TCGCAACACGAAAGTCAAAT
1395864 GTTTTTACGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAGTCAAAT
Found at i:1396010 original size:22 final size:22
Alignment explanation
Indices: 1395985--1396057 Score: 119
Period size: 22 Copynumber: 3.3 Consensus size: 22
1395975 CTACGGCGAC
* *
1395985 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATTTCTGACGAA
1396007 ATCCGTCCCCATTTCTGACGAA
1 ATCCGTCCCCATTTCTGACGAA
*
1396029 ATCCATCCCCATTTCTGACGAA
1 ATCCGTCCCCATTTCTGACGAA
1396051 ATCCGTC
1 ATCCGTC
1396058 TATCTCCATC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.23, C:0.40, G:0.12, T:0.25
Consensus pattern (22 bp):
ATCCGTCCCCATTTCTGACGAA
Found at i:1396528 original size:24 final size:24
Alignment explanation
Indices: 1396494--1396547 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1396484 CCATCACATC
1396494 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1396518 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1396542 ATCAAA
1 ATCAAA
1396548 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1396561 original size:24 final size:24
Alignment explanation
Indices: 1396494--1396561 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1396484 CCATCACATC
* * *
1396494 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1396518 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1396542 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1396562 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1397464 original size:19 final size:19
Alignment explanation
Indices: 1397440--1397568 Score: 82
Period size: 20 Copynumber: 6.6 Consensus size: 19
1397430 ACTAAAACCT
*
1397440 GTTGCGAAATTAAATTTGC
1 GTTGCGAATTTAAATTTGC
1397459 GTTGCGAATTTGAAA-TT-C
1 GTTGCGAATTT-AAATTTGC
* *
1397477 AGTTGCGAATTTGACTTTCGC
1 -GTTGCGAATTTAAATTT-GC
* * **
1397498 GTTGCGAATTTGACTATCAC
1 GTTGCGAATTTAAAT-TTGC
* *
1397518 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTAAATTT-GC
* * *
1397538 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTAAAT-TTGC
1397558 GTTGCGAATTT
1 GTTGCGAATTT
1397569 GGAAAATCGC
Statistics
Matches: 94, Mismatches: 8, Indels: 15
0.80 0.07 0.13
Matches are distributed among these distances:
18 2 0.02
19 26 0.28
20 63 0.67
21 3 0.03
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.38
Consensus pattern (19 bp):
GTTGCGAATTTAAATTTGC
Found at i:1397503 original size:20 final size:20
Alignment explanation
Indices: 1397457--1397569 Score: 165
Period size: 20 Copynumber: 5.7 Consensus size: 20
1397447 AATTAAATTT
**
1397457 GCGTTGCGAATTTGAAATTC
1 GCGTTGCGAATTTGACTTTC
*
1397477 -AGTTGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTTTC
*
1397496 GCGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTTTC
*
1397516 ACGTTGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTTTC
*
1397536 GCGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTTTC
1397556 GCGTTGCGAATTTG
1 GCGTTGCGAATTTG
1397570 GAAAATCGCA
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
19 16 0.19
20 67 0.81
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTTTC
Found at i:1397532 original size:40 final size:40
Alignment explanation
Indices: 1397440--1397569 Score: 185
Period size: 40 Copynumber: 3.3 Consensus size: 40
1397430 ACTAAAACCT
* * * *
1397440 GTTGCGAAATTAAATTT-GCGTTGCGAATTTGA-AATTCA-
1 GTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTA-TCAC
1397478 GTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCAC
1 GTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCAC
*
1397518 GTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCAC
1397558 GTTGCGAATTTG
1 GTTGCGAATTTG
1397570 GAAAATCGCA
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
38 14 0.17
39 18 0.21
40 52 0.62
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (40 bp):
GTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCAC
Found at i:1397642 original size:20 final size:20
Alignment explanation
Indices: 1397440--1397646 Score: 79
Period size: 20 Copynumber: 10.4 Consensus size: 20
1397430 ACTAAAACCT
* *
1397440 GTTGCGAAATT-AAATTTGC
1 GTTGCGAAATTGGAATTCGC
* * *
1397459 GTTGCGAATTTGAAATTC-A
1 GTTGCGAAATTGGAATTCGC
* *
1397478 GTTGCG-AATTTGACTTTCGC
1 GTTGCGAAATTGGA-ATTCGC
* * *
1397498 GTTGCG-AATTTGACTATCAC
1 GTTGCGAAATTGGAAT-TCGC
* *
1397518 GTTGCG-AATTTGACTTTCGC
1 GTTGCGAAATTGGA-ATTCGC
* *
1397538 GTTGCG-AATTTGACTATCGC
1 GTTGCGAAATTGGAAT-TCGC
* *
1397558 GTTGCGAATTTGGAAAATCGC
1 GTTGCGAAATTGG-AATTCGC
** * ** *
1397579 AATGCG-ATTTACATATTCGT
1 GTTGCGAAATTGGA-ATTCGC
* *
1397599 GTTGCGAAATTGGAA-ACTGG
1 GTTGCGAAATTGGAATTC-GC
1397619 GTTGCGAAATTGGAATTCGC
1 GTTGCGAAATTGGAATTCGC
1397639 GTTGCGAA
1 GTTGCGAA
1397647 TTTGTTGGTC
Statistics
Matches: 144, Mismatches: 32, Indels: 23
0.72 0.16 0.12
Matches are distributed among these distances:
18 4 0.03
19 23 0.16
20 98 0.68
21 18 0.12
22 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (20 bp):
GTTGCGAAATTGGAATTCGC
Found at i:1397792 original size:36 final size:39
Alignment explanation
Indices: 1397732--1397852 Score: 169
Period size: 36 Copynumber: 3.1 Consensus size: 39
1397722 TTATTTTCTC
*
1397732 TTTTTAAAAATATATATATATTATATAGTTTTGAAAATTA
1 TTTTT-AAAACATATATATATTATATAGTTTTGAAAATTA
1397772 TTTTT-AAA-A-ATATATATTATATAGTTTTGAAAATTA
1 TTTTTAAAACATATATATATTATATAGTTTTGAAAATTA
*
1397808 TTTTTTAAAACATATATATTATTATATAGTTTT-AAAAATA
1 -TTTTTAAAACATATATA-TATTATATAGTTTTGAAAATTA
1397848 TTTTT
1 TTTTT
1397853 TATTATATTT
Statistics
Matches: 75, Mismatches: 1, Indels: 11
0.86 0.01 0.13
Matches are distributed among these distances:
36 27 0.36
37 6 0.08
38 6 0.08
39 6 0.08
40 16 0.21
41 14 0.19
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (39 bp):
TTTTTAAAACATATATATATTATATAGTTTTGAAAATTA
Found at i:1397853 original size:40 final size:39
Alignment explanation
Indices: 1397732--1397854 Score: 164
Period size: 40 Copynumber: 3.2 Consensus size: 39
1397722 TTATTTTCTC
*
1397732 TTTTTAAAAATATATATATATTATATAGTTTTGAAAAT-T
1 TTTTTAAAAATATATAT-TATTATATAGTTTTAAAAATAT
*
1397771 ATTTTT-AAAA-ATATA-TATTATATAGTTTTGAAAATTAT
1 -TTTTTAAAAATATATATTATTATATAGTTTT-AAAAATAT
1397809 TTTTTAAAACATATATATTATTATATAGTTTTAAAAATAT
1 TTTTTAAAA-ATATATATTATTATATAGTTTTAAAAATAT
1397849 TTTTTA
1 TTTTTA
1397855 TTATATTTTT
Statistics
Matches: 74, Mismatches: 3, Indels: 12
0.83 0.03 0.13
Matches are distributed among these distances:
36 14 0.19
37 9 0.12
38 9 0.12
39 5 0.07
40 23 0.31
41 14 0.19
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (39 bp):
TTTTTAAAAATATATATTATTATATAGTTTTAAAAATAT
Found at i:1397866 original size:26 final size:27
Alignment explanation
Indices: 1397808--1397867 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
1397798 TTGAAAATTA
1397808 TTTTTTAAAACATATATATTATTATAT
1 TTTTTTAAAACATATATATTATTATAT
** * *
1397835 AGTTTTAAAA-ATATTTTTTATTATAT
1 TTTTTTAAAACATATATATTATTATAT
1397861 TTTTTTA
1 TTTTTTA
1397868 TTTATTATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 19 0.70
27 8 0.30
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTTTAAAACATATATATTATTATAT
Found at i:1397875 original size:7 final size:7
Alignment explanation
Indices: 1397846--1397924 Score: 56
Period size: 7 Copynumber: 11.1 Consensus size: 7
1397836 GTTTTAAAAA
*
1397846 TATTTTT
1 TATTTAT
1397853 TATTATAT
1 TATT-TAT
1397861 T-TTT-T
1 TATTTAT
1397866 TATTTAT
1 TATTTAT
*
1397873 TATTTTT
1 TATTTAT
*
1397880 CTACTTTTT
1 -TA-TTTAT
1397889 TATTTAT
1 TATTTAT
*
1397896 T-TTATTT
1 TATT-TAT
1397903 TATTTAT
1 TATTTAT
1397910 TATTTAT
1 TATTTAT
*
1397917 TGTTTAT
1 TATTTAT
1397924 T
1 T
1397925 TCTCGTTTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
5 2 0.03
6 6 0.10
7 37 0.63
8 9 0.15
9 5 0.08
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (7 bp):
TATTTAT
Found at i:1402289 original size:24 final size:24
Alignment explanation
Indices: 1402262--1402375 Score: 149
Period size: 24 Copynumber: 4.8 Consensus size: 24
1402252 TCGATTTGAT
* *
1402262 TTCTGATCTGATACTTGACATGAA
1 TTCTGATATGATACTTGACATGGA
*
1402286 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
* *
1402310 TTATGATATGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
*
1402334 TTCTGATATGATACTTGACCTGGA
1 TTCTGATATGATACTTGACATGGA
*
1402358 TTTTGATATGATACTTGA
1 TTCTGATATGATACTTGA
1402376 ATTATGATTT
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.01
24 79 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.40
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:1404006 original size:22 final size:22
Alignment explanation
Indices: 1403973--1404015 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1403963 TTTTAAAAAT
1403973 ATACAATATATAGCTTTTGAAG
1 ATACAATATATAGCTTTTGAAG
*
1403995 ATAC-ATAGTATAGTTTTTGAA
1 ATACAATA-TATAGCTTTTGAA
1404016 AATATTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.40
Consensus pattern (22 bp):
ATACAATATATAGCTTTTGAAG
Found at i:1404062 original size:37 final size:38
Alignment explanation
Indices: 1404020--1404166 Score: 183
Period size: 37 Copynumber: 3.9 Consensus size: 38
1404010 TTTGAAAATA
*
1404020 TTTTTGAAAACATATAATAAATAGTTTTTTTAAAACGG
1 TTTTTGAAAACATATAATAAATAGTTTTTTAAAAACGG
* * *
1404058 -TTTTGAAAACATATAATATATAGTTTTTAAAAAAATGG
1 TTTTTGAAAACATATAATAAATAGTTTTT-TAAAAACGG
* *
1404096 TTTTTGAAAATATATAATATATAG-TTTTTAAAAACGG
1 TTTTTGAAAACATATAATAAATAGTTTTTTAAAAACGG
* *
1404133 TTTTTGAAAACGTAT-ATAATATAGTTTTTGAAAA
1 TTTTTGAAAACATATAATAA-ATAGTTTTTTAAAA
1404167 CATATATATA
Statistics
Matches: 94, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
36 3 0.03
37 51 0.54
38 18 0.19
39 22 0.23
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.42
Consensus pattern (38 bp):
TTTTTGAAAACATATAATAAATAGTTTTTTAAAAACGG
Found at i:1404105 original size:76 final size:76
Alignment explanation
Indices: 1404020--1404166 Score: 217
Period size: 76 Copynumber: 1.9 Consensus size: 76
1404010 TTTGAAAATA
*
1404020 TTTTTGAAAACATATAATAAATAGTTTTTTTAAAACGG-TTTTGAAAACATATA-ATATATAGTT
1 TTTTTGAAAACATATAATAAATAG-TTTTTAAAAACGGTTTTTGAAAACATATATA-ATATAGTT
1404083 TTTAAAAAAATGG
64 TTTAAAAAAATGG
* * *
1404096 TTTTTGAAAATATATAATATATAGTTTTTAAAAACGGTTTTTGAAAACGTATATAATATAGTTTT
1 TTTTTGAAAACATATAATAAATAGTTTTTAAAAACGGTTTTTGAAAACATATATAATATAGTTTT
*
1404161 TGAAAA
66 TAAAAA
1404167 CATATATATA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
75 12 0.19
76 51 0.80
77 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.42
Consensus pattern (76 bp):
TTTTTGAAAACATATAATAAATAGTTTTTAAAAACGGTTTTTGAAAACATATATAATATAGTTTT
TAAAAAAATGG
Found at i:1404177 original size:21 final size:23
Alignment explanation
Indices: 1404132--1404188 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 23
1404122 TTTAAAAACG
1404132 GTTTTTGAAAACGTATATAATATA
1 GTTTTTGAAAACG-ATATAATATA
1404156 GTTTTTGAAAAC-ATAT-ATATA
1 GTTTTTGAAAACGATATAATATA
1404177 GTTTTT-AAAACG
1 GTTTTTGAAAACG
1404189 GGTTTTGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.16
21 11 0.34
22 4 0.12
24 12 0.38
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.42
Consensus pattern (23 bp):
GTTTTTGAAAACGATATAATATA
Found at i:1404207 original size:57 final size:61
Alignment explanation
Indices: 1404112--1404244 Score: 184
Period size: 57 Copynumber: 2.2 Consensus size: 61
1404102 AAAATATATA
* * *
1404112 ATATATAGTTTTTAAAAACGGTTTTTGAAAACGTATATAATATA-GT-T-TTTGAAAACAT
1 ATATATAGTTTTTAAAAACGGGTTTTGAAAACATATATAATATATATATCTTTGAAAACAT
1404170 ATATATAGTTTTT-AAAACGGGTTTTGAAAACATATATAATATATATAATCTTTGAAAACAT
1 ATATATAGTTTTTAAAAACGGGTTTTGAAAACATATATAATATATAT-ATCTTTGAAAACAT
*
1404231 ATTATATTGTTTTT
1 A-TATATAGTTTTT
1404245 GAAATATGAT
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
57 28 0.42
58 14 0.21
60 1 0.02
61 12 0.18
62 11 0.17
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.44
Consensus pattern (61 bp):
ATATATAGTTTTTAAAAACGGGTTTTGAAAACATATATAATATATATATCTTTGAAAACAT
Found at i:1404303 original size:5 final size:5
Alignment explanation
Indices: 1404293--1404337 Score: 60
Period size: 5 Copynumber: 9.6 Consensus size: 5
1404283 CTTTCTTTCT
*
1404293 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTA -TTCA TTTTA -TTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1404338 AATTATTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
4 11 0.31
5 25 0.69
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Done.