Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008821.1 Hibiscus syriacus cultivar Beakdansim tig00111989_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: 1271541
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:313116 original size:46 final size:48
Alignment explanation
Indices: 313009--313122 Score: 135
Period size: 46 Copynumber: 2.4 Consensus size: 48
312999 TTTTATCCCA
*
313009 TAAGCTCATAAGCTTA-TTTTTACCAAAATACTTACCATTTAAAATTCCT
1 TAAGCTCATAAGCTTATTTTTTACCAAAATACTTACCATTT--AATTCCG
* ** * *
313058 TAAGCTCGTAAGCTTATTTTTTTTCAATATACTTGCCA-TT-ATTCCG
1 TAAGCTCATAAGCTTATTTTTTACCAAAATACTTACCATTTAATTCCG
313104 TAAGCTCATAAGCTTATTT
1 TAAGCTCATAAGCTTATTT
313123 GCATGGTTAC
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
46 23 0.40
49 17 0.30
50 17 0.30
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (48 bp):
TAAGCTCATAAGCTTATTTTTTACCAAAATACTTACCATTTAATTCCG
Found at i:318313 original size:6 final size:6
Alignment explanation
Indices: 318278--318312 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
318268 CCTTGTATCA
*
318278 TGACCG TGACCG TGACCG TGACCG TGACCT TGACC
1 TGACCG TGACCG TGACCG TGACCG TGACCG TGACC
318313 TATGAGTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.34, G:0.29, T:0.20
Consensus pattern (6 bp):
TGACCG
Found at i:322311 original size:13 final size:13
Alignment explanation
Indices: 322295--322342 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
322285 TTTATTTATG
322295 TTTTTTAATTTTA
1 TTTTTTAATTTTA
322308 TTTTTTAATAATATTA
1 TTTTTTAAT--T-TTA
*
322324 TTTTTAAATTTTA
1 TTTTTTAATTTTA
322337 TTTTTT
1 TTTTTT
322343 TCATTACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 17 0.57
14 1 0.03
15 1 0.03
16 11 0.37
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTTTAATTTTA
Found at i:322324 original size:16 final size:16
Alignment explanation
Indices: 322300--322363 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 16
322290 TTATGTTTTT
* *
322300 TAATTTTATTTTTTAA
1 TAATATTATTTTTAAA
322316 TAATATTATTTTTAAA
1 TAATATTATTTTTAAA
** * *
322332 TTTTATT-TTTTTCAT
1 TAATATTATTTTTAAA
*
322347 TACTATTATTTTTAAA
1 TAATATTATTTTTAAA
322363 T
1 T
322364 TATCCCATTG
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
15 11 0.30
16 26 0.70
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TAATATTATTTTTAAA
Found at i:322354 original size:31 final size:29
Alignment explanation
Indices: 322295--322364 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 29
322285 TTTATTTATG
*
322295 TTTTTTAATTTTATTTTTTAATAATATTA
1 TTTTTAAATTTTATTTTTTAATAATATTA
* *
322324 TTTTTAAATTTTATTTTTTTCATTACTATTA
1 TTTTTAAATTTTA-TTTTTT-AATAATATTA
322355 TTTTTAAATT
1 TTTTTAAATT
322365 ATCCCATTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 12 0.33
30 6 0.17
31 18 0.50
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (29 bp):
TTTTTAAATTTTATTTTTTAATAATATTA
Found at i:326316 original size:28 final size:28
Alignment explanation
Indices: 326278--326357 Score: 117
Period size: 28 Copynumber: 2.9 Consensus size: 28
326268 TCTGGACCTT
*
326278 TGGAAATGGATGTGTATTGGACCTTTGC
1 TGGACATGGATGTGTATTGGACCTTTGC
*
326306 TGGACATGGATGTGTATTGGACCTTTGT
1 TGGACATGGATGTGTATTGGACCTTTGC
* *
326334 TGGAC-TGGATTTGTATTTGACCTT
1 TGGACATGGATGTGTATTGGACCTT
326358 GACTATTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
27 17 0.35
28 31 0.65
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.40
Consensus pattern (28 bp):
TGGACATGGATGTGTATTGGACCTTTGC
Found at i:326428 original size:9 final size:9
Alignment explanation
Indices: 326414--326467 Score: 62
Period size: 9 Copynumber: 6.3 Consensus size: 9
326404 GTATTTAAAA
326414 ATAATATAT
1 ATAATATAT
326423 ATAATATAT
1 ATAATATAT
326432 ATAATATAT
1 ATAATATAT
326441 AT--T-T-T
1 ATAATATAT
*
326446 CAAAATATAT
1 -ATAATATAT
326456 ATAATATAT
1 ATAATATAT
326465 ATA
1 ATA
326468 TATTTTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
5 1 0.03
6 2 0.05
7 1 0.03
8 1 0.03
9 32 0.84
10 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
ATAATATAT
Found at i:326433 original size:11 final size:11
Alignment explanation
Indices: 326417--326469 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
326407 TTTAAAAATA
326417 ATATATAT-A-
1 ATATATATAAT
326426 ATATATATAAT
1 ATATATATAAT
* *
326437 ATATATTTTCAAA
1 ATATA-TAT-AAT
326450 ATATATATAAT
1 ATATATATAAT
326461 ATATATATA
1 ATATATATA
326470 TTTTAAAACT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 8 0.22
10 1 0.03
11 16 0.44
12 4 0.11
13 7 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (11 bp):
ATATATATAAT
Found at i:326436 original size:33 final size:33
Alignment explanation
Indices: 326392--326467 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
326382 AAATTAAAAC
*
326392 ATAAT-TA-ATAATGTAT-TTAAAAATAATATAT
1 ATAATATATATAATATATATTAAAAA-AATATAT
***
326423 ATAATATATATAATATATATTTTCAAAATATAT
1 ATAATATATATAATATATATTAAAAAAATATAT
326456 ATAATATATATA
1 ATAATATATATA
326468 TATTTTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 5 0.13
32 2 0.05
33 27 0.71
34 4 0.11
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (33 bp):
ATAATATATATAATATATATTAAAAAAATATAT
Found at i:326454 original size:15 final size:14
Alignment explanation
Indices: 326434--326488 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
326424 TAATATATAT
326434 AATATATATTTTCAA
1 AATATATATTTT-AA
**
326449 AATATATATAAT-A
1 AATATATATTTTAA
*
326462 TATATATATTTTAA
1 AATATATATTTTAA
326476 AACTATATATTTT
1 AA-TATATATTTT
326489 CATAAGTTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 10 0.31
14 2 0.06
15 20 0.62
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (14 bp):
AATATATATTTTAA
Found at i:326482 original size:26 final size:29
Alignment explanation
Indices: 326419--326485 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 29
326409 TAAAAATAAT
326419 ATATATAATATATATAATATATATTTTCAAA
1 ATATAT-ATA-ATATAATATATATTTTCAAA
326450 ATATATATAATAT-ATATATATTTT-AAA
1 ATATATATAATATAATATATATTTTCAAA
326477 ACTATATAT
1 A-TATATAT
326486 TTTCATAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
27 4 0.11
28 18 0.51
29 4 0.11
30 3 0.09
31 6 0.17
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (29 bp):
ATATATATAATATAATATATATTTTCAAA
Found at i:326490 original size:43 final size:43
Alignment explanation
Indices: 326414--326648 Score: 190
Period size: 42 Copynumber: 5.7 Consensus size: 43
326404 GTATTTAAAA
* *
326414 ATAATATATATA-ATATATATAA-TATATATTTTCAAAATATAT
1 ATAATATATATATAT-TTTAAAACTATATATTTTCAAAATATAT
*
326456 ATAATATATATATATTTTAAAACTATATATTTTCATAAGT-TAT
1 ATAATATATATATATTTTAAAACTATATATTTTCA-AAATATAT
** * ** *
326499 ATAATATATATAT-TTAGAAAACTATATGTTTTGTAAA-ACAT
1 ATAATATATATATATTTTAAAACTATATATTTTCAAAATATAT
* * * *
326540 ATAATATATATAGATTTCAAAACTATATGTTTTCAAAACATAT
1 ATAATATATATATATTTTAAAACTATATATTTTCAAAATATAT
* * * *
326583 AT-A-ATATATGT-TTTTAAAAC-CTATATTAT--ATATATAT
1 ATAATATATATATATTTTAAAACTATATATTTTCAAAATATAT
*
326620 AT-ATATATACT-TATTTTAAAATTATATAT
1 ATAATATATA-TATATTTTAAAACTATATAT
326649 GATATATCTA
Statistics
Matches: 157, Mismatches: 26, Indels: 22
0.77 0.13 0.11
Matches are distributed among these distances:
37 9 0.06
38 6 0.04
39 15 0.10
40 13 0.08
41 22 0.14
42 54 0.34
43 35 0.22
44 3 0.02
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (43 bp):
ATAATATATATATATTTTAAAACTATATATTTTCAAAATATAT
Found at i:326542 original size:41 final size:39
Alignment explanation
Indices: 326461--326591 Score: 131
Period size: 41 Copynumber: 3.3 Consensus size: 39
326451 TATATATAAT
* * ***
326461 ATATATATATTTTAAAACTATATATTTTCATAAGTTATATA
1 ATATATATATTTCAAAACTATATGTTTT--TAAAACATATA
*
326502 ATATATATATTTAGAAAACTATATGTTTTGTAAAACATATA
1 ATATATATATTT-CAAAACTATATGTTTT-TAAAACATATA
*
326543 ATATATATAGATTTCAAAACTATATGTTTTCAAAACATAT-
1 ATATATAT--ATTTCAAAACTATATGTTTTTAAAACATATA
326583 ATA-ATATAT
1 ATATATATAT
326592 GTTTTTAAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
37 2 0.03
39 4 0.05
40 3 0.04
41 37 0.47
42 29 0.37
43 4 0.05
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.44
Consensus pattern (39 bp):
ATATATATATTTCAAAACTATATGTTTTTAAAACATATA
Found at i:326565 original size:84 final size:83
Alignment explanation
Indices: 326454--326608 Score: 220
Period size: 84 Copynumber: 1.9 Consensus size: 83
326444 TTCAAAATAT
* * * **
326454 ATATAATATATATATATTTTAAAACTATATATTTTCATAAGTTATATAATATATATATTTAGAAA
1 ATATAATATATATAGATTTCAAAACTATATATTTTCAAAACATATATAATATATATATTTA-AAA
326519 ACTATATGTTTTGTAAAAC
65 ACTATATGTTTTGTAAAAC
* * * *
326538 ATATAATATATATAGATTTCAAAACTATATGTTTTCAAAACATATATAATATATGTTTTTAAAAC
1 ATATAATATATATAGATTTCAAAACTATATATTTTCAAAACATATATAATATATATATTTAAAAA
326603 CTATAT
66 CTATAT
326609 TATATATATA
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
83 9 0.15
84 53 0.85
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (83 bp):
ATATAATATATATAGATTTCAAAACTATATATTTTCAAAACATATATAATATATATATTTAAAAA
CTATATGTTTTGTAAAAC
Found at i:326607 original size:41 final size:41
Alignment explanation
Indices: 326436--326608 Score: 170
Period size: 43 Copynumber: 4.1 Consensus size: 41
326426 ATATATATAA
*
326436 TATATATTTTCAAAATATATATAATATATATATATTTTAAAAC
1 TATATATTTTCAAAACATATAT-ATATATATAT-TTTTAAAAC
* ** **
326479 TATATATTTTCATAAGTTATATAATATATATATTTAGAAAAC
1 TATATATTTTCAAAACATATAT-ATATATATATTTTTAAAAC
* * * *
326521 TATATGTTTTGTAAAACATATA-ATATATATAGATTTCAAAAC
1 TATATATTTT-CAAAACATATATATATATATA-TTTTTAAAAC
* *
326563 TATATGTTTTCAAAACATATATA-ATATATGTTTTTAAAACC
1 TATATATTTTCAAAACATATATATATATATATTTTTAAAA-C
326604 TATAT
1 TATAT
326609 TATATATATA
Statistics
Matches: 109, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
40 7 0.06
41 31 0.28
42 34 0.31
43 37 0.34
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (41 bp):
TATATATTTTCAAAACATATATATATATATATTTTTAAAAC
Found at i:326617 original size:26 final size:24
Alignment explanation
Indices: 326563--326615 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
326553 ATTTCAAAAC
326563 TATATGTTTTCAAAACATATATAA
1 TATATGTTTTCAAAACATATATAA
* * *
326587 TATATGTTTTTAAAACCTATATTA
1 TATATGTTTTCAAAACATATATAA
326611 TATAT
1 TATAT
326616 ATATATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.47
Consensus pattern (24 bp):
TATATGTTTTCAAAACATATATAA
Found at i:326646 original size:38 final size:37
Alignment explanation
Indices: 326579--326655 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 37
326569 TTTTCAAAAC
326579 ATATATAATATATGTTTTTAAAACCTATATTAT-ATAT
1 ATATATAATATATGTTTTTAAAACCTATA-TATGATAT
*
326616 ATATATATATATACT-TATTTTAAAA-TTATATATGATAT
1 ATATATA-ATATA-TGT-TTTTAAAACCTATATATGATAT
326654 AT
1 AT
326656 CTACAAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
37 10 0.29
38 16 0.46
39 9 0.26
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (37 bp):
ATATATAATATATGTTTTTAAAACCTATATATGATAT
Found at i:335417 original size:2 final size:2
Alignment explanation
Indices: 335406--335434 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
335396 AATAATAATA
335406 AT AT AT -T 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
335435 GTTGGATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:336792 original size:23 final size:23
Alignment explanation
Indices: 336701--336784 Score: 141
Period size: 23 Copynumber: 3.7 Consensus size: 23
336691 ACATCTTATA
*
336701 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
336724 TGGCACTTAGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
336747 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
336770 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
336785 TTTATACGAG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.17, C:0.24, G:0.27, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:338548 original size:23 final size:23
Alignment explanation
Indices: 338522--338581 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
338512 ATGGCATTTT
338522 GGTGAATTTCTACGCGGCACTTA
1 GGTGAATTTCTACGCGGCACTTA
* *
338545 GGTGCAA-TTCTACGTGGCACTTC
1 GGTG-AATTTCTACGCGGCACTTA
* *
338568 GGTGCATTTATACG
1 GGTGAATTTCTACG
338582 AGCTGTGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 1 0.03
23 28 0.90
24 2 0.06
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.32
Consensus pattern (23 bp):
GGTGAATTTCTACGCGGCACTTA
Found at i:343538 original size:30 final size:29
Alignment explanation
Indices: 343499--343557 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
343489 GAGAATTTAC
* *
343499 ATGAACTACGTGATTAAATGTATATGTGA
1 ATGAACTACGAGATTAAATGAATATGTGA
* *
343528 ATGAAGCTACGAGTTTATATGAATATGTGA
1 ATGAA-CTACGAGATTAAATGAATATGTGA
343558 TATGTTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (29 bp):
ATGAACTACGAGATTAAATGAATATGTGA
Found at i:343809 original size:23 final size:23
Alignment explanation
Indices: 343783--343844 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
343773 ATCTTATATG
*
343783 GCACTTCGGTGCATTTCTATGCA
1 GCACTTCGGTGCATTTCTACGCA
* * **
343806 GCACTTAGGTGCAATTCTACGTG
1 GCACTTCGGTGCATTTCTACGCA
343829 GCACTTCGGTGCATTT
1 GCACTTCGGTGCATTT
343845 ATGGTGACAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACGCA
Found at i:349399 original size:68 final size:68
Alignment explanation
Indices: 349316--349444 Score: 213
Period size: 68 Copynumber: 1.9 Consensus size: 68
349306 TAGTCTTTTA
* * * *
349316 CTCAAAGGCATTTAGCGTTTCATCTAACTGACATAATTGACATCTTTCTGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTATCAAATGCACAGTTA
349381 GGC
66 GGC
*
349384 CTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTGACACCTTTTTATCAAATGCACA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTATCAAATGCACA
349445 ACTAGGCCAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (68 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTATCAAATGCACAGTTA
GGC
Found at i:349799 original size:55 final size:55
Alignment explanation
Indices: 349662--350334 Score: 893
Period size: 55 Copynumber: 12.3 Consensus size: 55
349652 TTTATTAAGA
* * * * *
349662 TGCACACATAGTGCCTATACGG-TAGTTCATCAACTCATAATGAATTTCGTGG-GT
1 TGCACACATAGTGCTTGTACGGTTA-TTCATCAACTCATGATGAATTCCGTGGATT
* * * * *
349716 TGCACACATCGTGCATGTACGGTTATTCATCAACTCGTAATGAATTCCGTGAATT
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * **
349771 TGGACACATAGTGCTTGTACGGTTATTCATCAACTCGTAATGAATTCTATGGATT
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* ** *
349826 TGCACACATAGTG-TATGTATGGTTATTCATCAACTCATGATGAATTCTATTGATT
1 TGCACACATAGTGCT-TGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* *
349881 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATAAATTTCGTGGATT
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * *
349936 TGTACACATAGTGCCTGTATGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * * **
349991 TGCATACATAGTGCCTCTACGGTTATTCATCCACTCATGATGAATTCATTGGATT
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
*
350046 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * **
350101 TGTACACATAGTGCATGTACGGTTATTCATCAATTCATGATGAATTTTGTGGATT
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * *
350156 TGCACACATAGTGCCTGTAAGGTTATTCATCAACTCATGATGAATTTCGTGGATT
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * *
350211 TTCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCTGCGGATT
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * *
350266 TGCACACTTAGTGTTTGTACGGTTATTCATCAACTCAAGATGAATTCCATGGATT
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
350321 TGCACACATAGTGC
1 TGCACACATAGTGC
350335 CTATTTGGTA
Statistics
Matches: 549, Mismatches: 66, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
54 44 0.08
55 504 0.92
56 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (55 bp):
TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
Found at i:350774 original size:20 final size:20
Alignment explanation
Indices: 350751--350822 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
350741 CATCTTTATA
*
350751 GTATCGACACTCCCCTCTTG
1 GTATCGATACTCCCCTCTTG
* * * *
350771 GTATCGATAC-CACTTGAATCG
1 GTATCGATACTCCCCT--CTTG
350792 GTATCGATACTCCCCTCTTG
1 GTATCGATACTCCCCTCTTG
350812 GTATCGATACT
1 GTATCGATACT
350823 ACTTGAATCG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
19 3 0.08
20 22 0.55
21 12 0.30
22 3 0.08
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.32
Consensus pattern (20 bp):
GTATCGATACTCCCCTCTTG
Found at i:350806 original size:41 final size:41
Alignment explanation
Indices: 350729--350843 Score: 171
Period size: 41 Copynumber: 2.8 Consensus size: 41
350719 TTTTTAACAA
* * *
350729 TGGTATCGATACCATCTT-TAT-AGTATCGACACTCCCCTCT
1 TGGTATCGATACCA-CTTGAATCGGTATCGATACTCCCCTCT
350769 TGGTATCGATACCACTTGAATCGGTATCGATACTCCCCTCT
1 TGGTATCGATACCACTTGAATCGGTATCGATACTCCCCTCT
*
350810 TGGTATCGATACTACTTGAATCGGTATCGATACT
1 TGGTATCGATACCACTTGAATCGGTATCGATACT
350844 ACTGAGCAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
39 3 0.04
40 16 0.23
41 50 0.72
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (41 bp):
TGGTATCGATACCACTTGAATCGGTATCGATACTCCCCTCT
Found at i:350843 original size:21 final size:21
Alignment explanation
Indices: 350770--350846 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
350760 CTCCCCTCTT
*
350770 GGTATCGATACCACTTGAATC
1 GGTATCGATACTACTTGAATC
* * * *
350791 GGTATCGATACTCCCCT--CTT
1 GGTATCGATACT-ACTTGAATC
350811 GGTATCGATACTACTTGAATC
1 GGTATCGATACTACTTGAATC
350832 GGTATCGATACTACT
1 GGTATCGATACTACT
350847 GAGCAAATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 27 0.61
22 2 0.05
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (21 bp):
GGTATCGATACTACTTGAATC
Found at i:352178 original size:26 final size:26
Alignment explanation
Indices: 352142--352204 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
352132 CTAGTGGTCA
352142 TGAAAAGATTACTAAGGCACATAATC
1 TGAAAAGATTACTAAGGCACATAATC
352168 TGAAAAGATTACTAAGGCACATAATC
1 TGAAAAGATTACTAAGGCACATAATC
352194 TGAAAAGATTA
1 TGAAAAGATTA
352205 TCAAGATCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.24
Consensus pattern (26 bp):
TGAAAAGATTACTAAGGCACATAATC
Found at i:360304 original size:155 final size:157
Alignment explanation
Indices: 360023--360380 Score: 431
Period size: 155 Copynumber: 2.3 Consensus size: 157
360013 AAGTCCATTT
* * * * *
360023 TTTTACCAAATTTGAACCACAAGCTCCTAAACCATAGTAGAATACGTGTATTTTTAATTCATCTT
1 TTTTACCAAATTTGAATCACATGCTCCTAAATCATAGTAGAATACGTGTACTTTCAATTCATCTT
** * * * *
360088 TTTTATAACAAATATTTTATATTTTTCAATTTAGTCCTTCAGTTTTTCATAATCTCTTTATTTCA
66 TTCGATAAC-AATATTTTATATTTTTCAAATTAGTCCTTCAATTTTTCATAATCTCCTTATTCCA
360153 TAAATTCGTCATTTATTTTAAGTAC-GG
130 TAAATTCGTCATTTATTTTAAGTACTGG
* *
360180 TTTTACCAAATTTGAGTCACATGCTCCTAAATCATAGTAGAATACATGTGTACTTTCAATTCCTC
1 TTTTACCAAATTTGAATCACATGCTCCTAAATCATAGTAGAATAC--GTGTACTTTCAATTCATC
360245 TTTTCGATAAC-AT-TTTT-TATTTTTCAAATTAGTCCTTCAATTTTTCATAA-CATCCTTATTC
64 TTTTCGATAACAATATTTTATATTTTTCAAATTAGTCCTTCAATTTTTCATAATC-TCCTTATTC
* * * * **
360306 CTTCAATTTGTCATTTATTTTAAGTTCTTT
128 CATAAATTCGTCATTTATTTTAAGTACTGG
* * *
360336 TTTTACCAAATTT-AATCCACATGCTCATATATCATAATAGAATAC
1 TTTTACCAAATTTGAAT-CACATGCTCCTAAATCATAGTAGAATAC
360381 CTATAAAACT
Statistics
Matches: 173, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
154 1 0.01
155 63 0.36
156 42 0.24
157 43 0.25
159 24 0.14
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (157 bp):
TTTTACCAAATTTGAATCACATGCTCCTAAATCATAGTAGAATACGTGTACTTTCAATTCATCTT
TTCGATAACAATATTTTATATTTTTCAAATTAGTCCTTCAATTTTTCATAATCTCCTTATTCCAT
AAATTCGTCATTTATTTTAAGTACTGG
Found at i:361328 original size:13 final size:13
Alignment explanation
Indices: 361324--361380 Score: 96
Period size: 13 Copynumber: 4.4 Consensus size: 13
361314 CCCGTTGACC
361324 TGACCCGACCCGT
1 TGACCCGACCCGT
*
361337 TTACCCGACCCGT
1 TGACCCGACCCGT
361350 TGACCCGACCCGT
1 TGACCCGACCCGT
*
361363 TGACTCGACCCGT
1 TGACCCGACCCGT
361376 TGACC
1 TGACC
361381 GTTGACCGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.16, C:0.44, G:0.21, T:0.19
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:361361 original size:18 final size:18
Alignment explanation
Indices: 361303--361348 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
361293 ACCGGTCACA
361303 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
361321 ACCTGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
361339 ACCCGACCCG
1 ACCCGACCCG
361349 TTGACCCGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.17, C:0.50, G:0.20, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:361374 original size:31 final size:28
Alignment explanation
Indices: 361303--361361 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 28
361293 ACCGGTCACA
*
361303 ACCCGACCCGACCCGTTGACCTGACCCG
1 ACCCGACCCGACCCGTTGACCCGACCCG
361331 ACCCGTTTACCCGACCCGTTGACCCGACCCG
1 ACCCG---ACCCGACCCGTTGACCCGACCCG
361362 TTGACTCGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 5 0.19
31 22 0.81
ACGTcount: A:0.17, C:0.49, G:0.20, T:0.14
Consensus pattern (28 bp):
ACCCGACCCGACCCGTTGACCCGACCCG
Found at i:361384 original size:7 final size:7
Alignment explanation
Indices: 361372--361410 Score: 69
Period size: 7 Copynumber: 5.4 Consensus size: 7
361362 TTGACTCGAC
361372 CCGTTGA
1 CCGTTGA
361379 CCGTTGA
1 CCGTTGA
361386 CCGTTGA
1 CCGTTGA
361393 CCCGTTGA
1 -CCGTTGA
361401 CCGTTGA
1 CCGTTGA
361408 CCG
1 CCG
361411 ACGTTGACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 24 0.77
8 7 0.23
ACGTcount: A:0.13, C:0.33, G:0.28, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:361397 original size:15 final size:15
Alignment explanation
Indices: 361372--361409 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
361362 TTGACTCGAC
361372 CCGTTGA-CCGTTGA
1 CCGTTGACCCGTTGA
361386 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
361401 CCGTTGACC
1 CCGTTGACC
361410 GACGTTGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:361397 original size:22 final size:22
Alignment explanation
Indices: 361369--361410 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
361359 CCGTTGACTC
361369 GACCCGTTGACCGTTGACCGTT
1 GACCCGTTGACCGTTGACCGTT
361391 GACCCGTTGACCGTTGACCG
1 GACCCGTTGACCGTTGACCG
361411 ACGTTGACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.33, G:0.29, T:0.24
Consensus pattern (22 bp):
GACCCGTTGACCGTTGACCGTT
Found at i:366139 original size:13 final size:13
Alignment explanation
Indices: 366121--366145 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
366111 CAACCCGACC
366121 CGACCCGTTGACT
1 CGACCCGTTGACT
366134 CGACCCGTTGAC
1 CGACCCGTTGAC
366146 CGTTGACCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.24, T:0.20
Consensus pattern (13 bp):
CGACCCGTTGACT
Found at i:368745 original size:24 final size:24
Alignment explanation
Indices: 368639--368745 Score: 81
Period size: 24 Copynumber: 4.5 Consensus size: 24
368629 ATATTTTATC
* *
368639 TGATTTCTGATTTGAATTTTGTTT
1 TGATTTCTGATCTGAATTCTGTTT
* * *
368663 TGACATT-TGATCTGAAATCTGTTC
1 TGA-TTTCTGATCTGAATTCTGTTT
* * * * *
368687 TGATTCCTAACCTGGATTCTGTTA
1 TGATTTCTGATCTGAATTCTGTTT
* *
368711 TGATATCTGATCTGAATTATGTTT
1 TGATTTCTGATCTGAATTCTGTTT
*
368735 TGATTTTTGAT
1 TGATTTCTGAT
368746 ATCTCCGTTT
Statistics
Matches: 60, Mismatches: 21, Indels: 4
0.71 0.25 0.05
Matches are distributed among these distances:
23 1 0.02
24 57 0.95
25 2 0.03
ACGTcount: A:0.21, C:0.11, G:0.17, T:0.50
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTCTGTTT
Found at i:369592 original size:2 final size:2
Alignment explanation
Indices: 369585--369654 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
369575 ATATGAAAGA
369585 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
369627 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
369655 GGTTAGTTAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:370381 original size:21 final size:21
Alignment explanation
Indices: 370333--370384 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
370323 TTAAAGGTGC
* *
370333 TGCAAATTGAGTTATAACTAT
1 TGCAAATTGAGTCACAACTAT
** *
370354 TATAAATTGAGTCACAACTCT
1 TGCAAATTGAGTCACAACTAT
370375 TGCAAATTGA
1 TGCAAATTGA
370385 TTACAAGTGC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (21 bp):
TGCAAATTGAGTCACAACTAT
Found at i:381990 original size:31 final size:30
Alignment explanation
Indices: 381954--382038 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 30
381944 GGAGTACCTT
* *
381954 GGGGCCTGAGAGCCTACCCAAGACAATTCTC
1 GGGGCC-GAGAGCCTACCCAAGAAAAATCTC
* *
381985 TGGGCC-ACGAAGGCTTACCCAAGAAAAATCTC
1 GGGGCCGA-G-A-GCCTACCCAAGAAAAATCTC
382017 GGGGCCGTAGAGCCTACCCAAG
1 GGGGCCG-AGAGCCTACCCAAG
382039 GGTCGCTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
29 1 0.02
30 1 0.02
31 16 0.37
32 23 0.53
33 1 0.02
34 1 0.02
ACGTcount: A:0.28, C:0.31, G:0.27, T:0.14
Consensus pattern (30 bp):
GGGGCCGAGAGCCTACCCAAGAAAAATCTC
Found at i:382842 original size:17 final size:17
Alignment explanation
Indices: 382812--382845 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
382802 CGAAAAACAT
*
382812 AAAATATGACTTTTCAA
1 AAAATATGAATTTTCAA
*
382829 AAAATTTGAATTTTCAA
1 AAAATATGAATTTTCAA
382846 TTCAAAGTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (17 bp):
AAAATATGAATTTTCAA
Found at i:382890 original size:24 final size:24
Alignment explanation
Indices: 382863--382915 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
382853 TCAACTCTGA
*
382863 TCAAGGTCAACGGGTC-GAGTCGGG
1 TCAAAGTCAACGGGTCAG-GTCGGG
*
382887 TCAAAGTCAACGTGTCAGGTCGGG
1 TCAAAGTCAACGGGTCAGGTCGGG
382911 TCAAA
1 TCAAA
382916 CAGTTCGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.26, C:0.21, G:0.34, T:0.19
Consensus pattern (24 bp):
TCAAAGTCAACGGGTCAGGTCGGG
Found at i:393439 original size:17 final size:18
Alignment explanation
Indices: 393406--393439 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
393396 CCGTTACTAG
393406 TGAACCGGTCAGAACCGT
1 TGAACCGGTCAGAACCGT
*
393424 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
393440 GATCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGT
Found at i:394193 original size:22 final size:22
Alignment explanation
Indices: 394150--394190 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
394140 AAAAAATTAT
394150 TTTTTATTAAATATTTTTAATA
1 TTTTTATTAAATATTTTTAATA
*
394172 TTTTTATTTAAT-TTTTTAA
1 TTTTTATTAAATATTTTTAA
394191 ATAATTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTATTAAATATTTTTAATA
Found at i:397502 original size:45 final size:45
Alignment explanation
Indices: 397448--397567 Score: 159
Period size: 45 Copynumber: 2.7 Consensus size: 45
397438 TTCAAACATA
*
397448 TTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
1 TTTTCTGTTGATAATGCACCCATATGCATTTCAACCATAGTATAC
* * * *
397493 TTTTATGTTGATAATGTACCCATATACATCTCAACCATAGTATAC
1 TTTTCTGTTGATAATGCACCCATATGCATTTCAACCATAGTATAC
*** *
397538 TTTTCTGCCAATAATGCACTCATATGCATT
1 TTTTCTGTTGATAATGCACCCATATGCATT
397568 ATTCTGTTAT
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (45 bp):
TTTTCTGTTGATAATGCACCCATATGCATTTCAACCATAGTATAC
Found at i:397641 original size:21 final size:21
Alignment explanation
Indices: 397611--397666 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
397601 ATCAGTTAAG
*
397611 GCATCTTTTCATGCCACTAAT
1 GCATCATTTCATGCCACTAAT
*
397632 GCATCCTTTCATGCCACTAAT
1 GCATCATTTCATGCCACTAAT
*
397653 GCATTATTTCATGC
1 GCATCATTTCATGC
397667 ATTTTCAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.23, C:0.29, G:0.11, T:0.38
Consensus pattern (21 bp):
GCATCATTTCATGCCACTAAT
Found at i:397691 original size:27 final size:27
Alignment explanation
Indices: 397660--397787 Score: 113
Period size: 27 Copynumber: 5.3 Consensus size: 27
397650 AATGCATTAT
397660 TTCATGCATTTTCAATTATGGCATCCG
1 TTCATGCATTTTCAATTATGGCATCCG
* *
397687 TTCATGC-----C-TTTAT-GCATCCT
1 TTCATGCATTTTCAATTATGGCATCCG
*
397707 TTCATGCATTTTCAATTATGGCATTCG
1 TTCATGCATTTTCAATTATGGCATCCG
* *
397734 TTCATGC-----C-TTTAT-GCATCCT
1 TTCATGCATTTTCAATTATGGCATCCG
397754 TTCATGCATTTTCAATTATGGCATCCG
1 TTCATGCATTTTCAATTATGGCATCCG
397781 TTCATGC
1 TTCATGC
397788 CATTATGCAT
Statistics
Matches: 77, Mismatches: 10, Indels: 28
0.67 0.09 0.24
Matches are distributed among these distances:
20 25 0.32
21 8 0.10
22 2 0.03
25 2 0.03
26 8 0.10
27 32 0.42
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.43
Consensus pattern (27 bp):
TTCATGCATTTTCAATTATGGCATCCG
Found at i:397705 original size:20 final size:21
Alignment explanation
Indices: 397675--397760 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 21
397665 GCATTTTCAA
397675 TTATGGCATCCGTTCATGCCT
1 TTATGGCATCCGTTCATGCCT
* *
397696 TTAT-GCATCCTTTCATGCATTTTCAA
1 TTATGGCATCCGTTCATGC-----C-T
*
397722 TTATGGCATTCGTTCATGCCT
1 TTATGGCATCCGTTCATGCCT
*
397743 TTAT-GCATCCTTTCATGC
1 TTATGGCATCCGTTCATGC
397761 ATTTTCAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 15
0.70 0.10 0.21
Matches are distributed among these distances:
20 25 0.49
21 8 0.16
22 1 0.02
25 1 0.02
26 4 0.08
27 12 0.24
ACGTcount: A:0.17, C:0.26, G:0.14, T:0.43
Consensus pattern (21 bp):
TTATGGCATCCGTTCATGCCT
Found at i:397713 original size:47 final size:47
Alignment explanation
Indices: 397632--397820 Score: 297
Period size: 47 Copynumber: 4.0 Consensus size: 47
397622 TGCCACTAAT
* * * **
397632 GCATCCTTTCATGCCACTAATGCATTATTTCATGCATTTTCAATTATG
1 GCATCCGTTCATGCC-TTTATGCATCCTTTCATGCATTTTCAATTATG
397680 GCATCCGTTCATGCCTTTATGCATCCTTTCATGCATTTTCAATTATG
1 GCATCCGTTCATGCCTTTATGCATCCTTTCATGCATTTTCAATTATG
*
397727 GCATTCGTTCATGCCTTTATGCATCCTTTCATGCATTTTCAATTATG
1 GCATCCGTTCATGCCTTTATGCATCCTTTCATGCATTTTCAATTATG
* *
397774 GCATCCGTTCATGCCATTATGCATCTTTTCATGCATTTTCAATTATG
1 GCATCCGTTCATGCCTTTATGCATCCTTTCATGCATTTTCAATTATG
397821 AAATTGATTT
Statistics
Matches: 132, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
47 118 0.89
48 14 0.11
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.43
Consensus pattern (47 bp):
GCATCCGTTCATGCCTTTATGCATCCTTTCATGCATTTTCAATTATG
Found at i:397880 original size:2 final size:2
Alignment explanation
Indices: 397873--397897 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
397863 TAATATTATA
397873 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
397898 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:398372 original size:95 final size:92
Alignment explanation
Indices: 398201--398405 Score: 236
Period size: 95 Copynumber: 2.2 Consensus size: 92
398191 ATACCCTTAC
* * *
398201 CTTGGTATCGATACCCCCCTTCCAGTATCAATACCAAAATTAGCTTCGATGTAGTTTGGTATCGA
1 CTTGGTACCGATA-CCCCCTT-CAGTATCAATACCAAAATTAGATTCGATGTA-TTAGGTATCGA
*
398266 TACCCTCACCATGGTATCGATACCAC-TATG
63 TACCCTCACCATGGTATCAATACCACAT-TG
*
398296 CTATGGTACCGATACCCCCTT-AGGTATCGATACCAAAATTAGATTCAGATGT-TTACAGGTATC
1 CT-TGGTACCGATACCCCCTTCA-GTATCAATACCAAAATTAGATTC-GATGTATT--AGGTATC
* *
398359 GATACCCTTACCATGGTATCAATGCCACATTG
61 GATACCCTCACCATGGTATCAATACCACATTG
398391 CTTGGGTACCGATAC
1 CTT-GGTACCGATAC
398406 TGATTGAATC
Statistics
Matches: 96, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
93 3 0.03
94 22 0.23
95 60 0.62
96 11 0.11
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (92 bp):
CTTGGTACCGATACCCCCTTCAGTATCAATACCAAAATTAGATTCGATGTATTAGGTATCGATAC
CCTCACCATGGTATCAATACCACATTG
Found at i:399200 original size:312 final size:313
Alignment explanation
Indices: 398636--399265 Score: 1201
Period size: 312 Copynumber: 2.0 Consensus size: 313
398626 CATACCAAAA
* *
398636 TTTCCAACTTGTTTTTAAACTCATTTTAGACTTCTAATCTTTCATTTACCTCATTGATAAGTCAA
1 TTTCCAACTTGTTTTTAAACTCATTCTAGACTTCTAATCTTTCATTTACCTCATTGACAAGTCAA
398701 TTTTACCAATAACCATCCATAAACCCTCCTATTTCAACATATCATTATAAAACCCATTTTTAAAT
66 TTTTACCAATAACCATCCATAAACCCTCCTATTTCAACATATCATTATAAAACCCATTTTTAAAT
*
398766 TCTCTTTTATTTCCTTTATCTCATTGTTTTAATCCCATTTAAACCTTCATTAAGCTTCTATCATG
131 TCTCTTTTATTTCCTTTATCTCATTGTTTTAATCCAATTTAAACCTTCATTAAGCTTCTATCATG
398831 CTCAAGATTTCAATAACCAACCAAAATCTAAATAATCAACTAACAATTTGAAAACTCACCTTTGC
196 CTCAAGATTTCAATAACCAACCAAAATCTAAATAATCAACTAACAATTTGAAAACTCACCTTTGC
*
398896 TATGGGGAATAGCCTTTCCACGGGGAAGAAGA-AAAA-AGGGAGATAGCTTAC
261 TAAGGGGAATAGCCTTTCCACGGGGAAGAAGAGAAAAGAGGGAGATAGCTTAC
398947 TTTCCAACTTGTTTTTAAACTCATTCTAGACTTCTAATCTTTCATTTACCTCATTGACAAGTCAA
1 TTTCCAACTTGTTTTTAAACTCATTCTAGACTTCTAATCTTTCATTTACCTCATTGACAAGTCAA
399012 TTTTACCAATAACCATCCATAAACCCTCCTATTTCAACATATCATTATAAAACCCATTTTTTAAA
66 TTTTACCAATAACCATCCATAAACCCTCCTATTTCAACATATCATTATAAAACCCA-TTTTTAAA
399077 TTCTCTTTTATTTCCTTTATCTCATTGTTTTAATCCAATTTAAACCTTCATTAAGCTTCTATCAT
130 TTCTCTTTTATTTCCTTTATCTCATTGTTTTAATCCAATTTAAACCTTCATTAAGCTTCTATCAT
399142 GCTCAAGATTTCAATAACCAACCAAAATCTAAATAATCAACTAACAATTTGAAAACTCACCTTTG
195 GCTCAAGATTTCAATAACCAACCAAAATCTAAATAATCAACTAACAATTTGAAAACTCACCTTTG
399207 CTAAGGGGAATAGCCTTTCCACGGGGAAGAAGAGAAAAGAGGGAGATAGCTTAC
260 CTAAGGGGAATAGCCTTTCCACGGGGAAGAAGAGAAAAGAGGGAGATAGCTTAC
399261 TTTCC
1 TTTCC
399266 TCTCTTTTCC
Statistics
Matches: 312, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
311 119 0.38
312 169 0.54
313 4 0.01
314 20 0.06
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.36
Consensus pattern (313 bp):
TTTCCAACTTGTTTTTAAACTCATTCTAGACTTCTAATCTTTCATTTACCTCATTGACAAGTCAA
TTTTACCAATAACCATCCATAAACCCTCCTATTTCAACATATCATTATAAAACCCATTTTTAAAT
TCTCTTTTATTTCCTTTATCTCATTGTTTTAATCCAATTTAAACCTTCATTAAGCTTCTATCATG
CTCAAGATTTCAATAACCAACCAAAATCTAAATAATCAACTAACAATTTGAAAACTCACCTTTGC
TAAGGGGAATAGCCTTTCCACGGGGAAGAAGAGAAAAGAGGGAGATAGCTTAC
Found at i:399646 original size:18 final size:20
Alignment explanation
Indices: 399604--399651 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
399594 CTTACTAAGG
* *
399604 GTATCGATACTCCACTCTTA
1 GTATCGATACTCCACTATGA
399624 GTATCGATACTCC-C-ATGA
1 GTATCGATACTCCACTATGA
*
399642 GTATCAATAC
1 GTATCGATAC
399652 CTAAATTGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 11 0.44
19 1 0.04
20 13 0.52
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (20 bp):
GTATCGATACTCCACTATGA
Found at i:399693 original size:83 final size:83
Alignment explanation
Indices: 399605--399780 Score: 230
Period size: 83 Copynumber: 2.1 Consensus size: 83
399595 TTACTAAGGG
* * * *
399605 TATCGATACTCCACT-CTTAGTATCGATACTCCCATGAGTATCAATACCTAAATTG-GCTACTGG
1 TATCGATACTCCA-TGCTCAGTATCAATACTCCCATAAGTACCAATACCTAAA-TGAGCTACTGG
399668 AATCTACAAACCAAACATGA
64 AATCTACAAACCAAACATGA
* **
399688 TATCGATACTCCATGCTCAGTATTAATACTCCCATAAGTACCGGTACCTAAATGAGCTACTGGAA
1 TATCGATACTCCATGCTCAGTATCAATACTCCCATAAGTACCAATACCTAAATGAGCTACTGGAA
** *
399753 TCTGTAAACCAAACATGG
66 TCTACAAACCAAACATGA
399771 TATCGATACT
1 TATCGATACT
399781 ACATCTTTGA
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
82 3 0.04
83 78 0.96
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (83 bp):
TATCGATACTCCATGCTCAGTATCAATACTCCCATAAGTACCAATACCTAAATGAGCTACTGGAA
TCTACAAACCAAACATGA
Found at i:402304 original size:85 final size:85
Alignment explanation
Indices: 402180--402391 Score: 239
Period size: 85 Copynumber: 2.5 Consensus size: 85
402170 TCCCAAGTTG
* * * * * *
402180 TAATCAATAGTTGATATGCT-TTTTCTATGAAGGATGCCAAATTGAAGAATAATCTTACTCCTTT
1 TAATCAATGGTTGATATGCTCCTTTCTCTAAAGGACGCCAAATTGAAGAACAATCTTACTCCTTT
* *
402244 ATCTAAAGGA-AGTCAATTCA
66 ATCTAAA-GATAGTAAAGTCA
* ** *
402264 TAATCAATGGTTGATTTGCTCCTTTCTCTAAAGGACGCCAAATTGAAGAACGGTCTTACTCTTTT
1 TAATCAATGGTTGATATGCTCCTTTCTCTAAAGGACGCCAAATTGAAGAACAATCTTACTCCTTT
* * *
402329 CTCTAAAGATTGTAAAGTCG
66 ATCTAAAGATAGTAAAGTCA
* * *
402349 TAATCAATGGTTGATCTGCTCCTTTCTCTAATGGACTCCAAAT
1 TAATCAATGGTTGATATGCTCCTTTCTCTAAAGGACGCCAAAT
402392 CAGAGAATGA
Statistics
Matches: 108, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
84 20 0.19
85 88 0.81
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (85 bp):
TAATCAATGGTTGATATGCTCCTTTCTCTAAAGGACGCCAAATTGAAGAACAATCTTACTCCTTT
ATCTAAAGATAGTAAAGTCA
Found at i:408477 original size:19 final size:20
Alignment explanation
Indices: 408443--408490 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
408433 TCTAAATCAT
*
408443 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTTCATTTTAG
408463 TTTTCAAAA-TTCATTTTAG
1 TTTTCAAAATTTCATTTTAG
*
408482 CTTTCAAAA
1 TTTTCAAAA
408491 GAAAATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATTTCATTTTAG
Found at i:409765 original size:21 final size:21
Alignment explanation
Indices: 409736--409783 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
409726 ATAATATTGA
*
409736 TACTATTCACGGTATCGATAC
1 TACTGTTCACGGTATCGATAC
*
409757 TACTGTTCATGGTATCGATAC
1 TACTGTTCACGGTATCGATAC
409778 TACTGT
1 TACTGT
409784 AGCAGTATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (21 bp):
TACTGTTCACGGTATCGATAC
Found at i:411336 original size:25 final size:24
Alignment explanation
Indices: 411275--411341 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
411265 ATTATCTCTT
*
411275 TATTTTTG-TTTTAACTTATTAAA
1 TATTTTTGTTTTTAATTTATTAAA
411298 TATTTTT-TTGTTTAATTTATTAAA
1 TATTTTTGTT-TTTAATTTATTAAA
*
411322 TATATTTTGTTTTTATTTTA
1 TAT-TTTTGTTTTTAATTTA
411342 ATGTAAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.21
24 16 0.42
25 12 0.32
26 2 0.05
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.67
Consensus pattern (24 bp):
TATTTTTGTTTTTAATTTATTAAA
Found at i:411356 original size:31 final size:31
Alignment explanation
Indices: 411321--411391 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
411311 AATTTATTAA
* * * *
411321 ATATATTTTGTTTTTATTTTAA-TGTAAAATT
1 ATATATTTTATCTTTATTATAACT-TAAAAAT
411352 ATATATTTTATCTTTATTATAACTTAAAAAT
1 ATATATTTTATCTTTATTATAACTTAAAAAT
411383 ATAT-TTTTA
1 ATATATTTTA
411392 AATATATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.14
31 29 0.83
32 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (31 bp):
ATATATTTTATCTTTATTATAACTTAAAAAT
Found at i:411680 original size:25 final size:26
Alignment explanation
Indices: 411647--411708 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
411637 TAAGTGATGA
* *
411647 TAAAGATAAAATATATATTTT-TACAT
1 TAAAGATAAAA-AAATATTTTATAAAT
411673 TAAA-ATAAAAAAATATTTTATAAAT
1 TAAAGATAAAAAAATATTTTATAAAT
*
411698 T-AAGACAAAAA
1 TAAAGATAAAAA
411709 TAAGTTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 10 0.32
25 17 0.55
26 4 0.13
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (26 bp):
TAAAGATAAAAAAATATTTTATAAAT
Found at i:416741 original size:10 final size:11
Alignment explanation
Indices: 416726--416759 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
416716 TAATTAATCT
416726 TATTAAATT-A
1 TATTAAATTGA
416736 TATTAAATTGA
1 TATTAAATTGA
*
416747 TACTAAATTGA
1 TATTAAATTGA
416758 TA
1 TA
416760 CAATATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (11 bp):
TATTAAATTGA
Found at i:418974 original size:22 final size:22
Alignment explanation
Indices: 418949--418991 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
418939 CATTGAATGA
418949 ATGTTTCAAGTTTCAACACAAC
1 ATGTTTCAAGTTTCAACACAAC
418971 ATGTTTCAAGTTTCAACACAA
1 ATGTTTCAAGTTTCAACACAA
418992 TATAGAGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (22 bp):
ATGTTTCAAGTTTCAACACAAC
Found at i:420656 original size:20 final size:19
Alignment explanation
Indices: 420624--420661 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 19
420614 TACTTTTTTT
420624 AATATTTGATAAT-TAATA
1 AATATTTGATAATATAATA
420642 AATATATTGATTAATATAAT
1 AATAT-TTGA-TAATATAAT
420662 TTATTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 4 0.24
21 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
AATATTTGATAATATAATA
Found at i:422039 original size:35 final size:35
Alignment explanation
Indices: 421997--422067 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
421987 AAGAAATAAG
*
421997 TTTATGGGCCCTGCTTTTAATTTAGTTTATTAATA
1 TTTATGGGCCCTGCTTTTAATTTAGTATATTAATA
422032 TTTATGGGCCCTGCTTTTAATTTAGTATATTAATA
1 TTTATGGGCCCTGCTTTTAATTTAGTATATTAATA
422067 T
1 T
422068 AGCTTTTAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.24, C:0.11, G:0.14, T:0.51
Consensus pattern (35 bp):
TTTATGGGCCCTGCTTTTAATTTAGTATATTAATA
Found at i:430394 original size:54 final size:54
Alignment explanation
Indices: 430335--430558 Score: 358
Period size: 54 Copynumber: 4.1 Consensus size: 54
430325 TTACCAAATA
* * *
430335 GGCACTAAGTGTGTATTTCACGGAATTCATCCTAAGTGGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTAAGTGGATGAATAACCGTTTC
* * *
430389 GGCACTAAGTGTGCATTTCACGGAATTCATACTAAGTGGATGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTAAGTGGATGAATAACCGTTTC
* * *
430443 GGCACTAAGTGTGCATTTCACAAAATTCATCCTAAGTGAATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTAAGTGGATGAATAACCGTTTC
*
430497 GACACTAAGTGTGCATTTCACGAAATTCATCCTAAGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTAAGTGGATGAATAACCGTTTC
430551 GGCACTAA
1 GGCACTAA
430559 TAACCGTTTC
Statistics
Matches: 155, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 155 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGAAATTCATCCTAAGTGGATGAATAACCGTTTC
Found at i:430562 original size:18 final size:18
Alignment explanation
Indices: 430539--430576 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
430529 TAAGTGGATG
*
430539 AATAACCGTTTCGGCACT
1 AATAACCGTTTCGACACT
430557 AATAACCGTTTCGACACT
1 AATAACCGTTTCGACACT
430575 AA
1 AA
430577 GTGTGCAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.26
Consensus pattern (18 bp):
AATAACCGTTTCGACACT
Found at i:434228 original size:22 final size:22
Alignment explanation
Indices: 434161--434230 Score: 104
Period size: 22 Copynumber: 3.2 Consensus size: 22
434151 GTATTTATCT
*
434161 CGAAGGACCACTGGATACGTCC
1 CGAAAGACCACTGGATACGTCC
* *
434183 CAAAAAACCACTGGATACGTCC
1 CGAAAGACCACTGGATACGTCC
*
434205 CGAAAGACCACTGGATACATCC
1 CGAAAGACCACTGGATACGTCC
434227 CGAA
1 CGAA
434231 GGACTAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.36, C:0.31, G:0.20, T:0.13
Consensus pattern (22 bp):
CGAAAGACCACTGGATACGTCC
Found at i:437028 original size:11 final size:12
Alignment explanation
Indices: 437009--437039 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
436999 CTACTTAAGG
437009 CATTCGCTACCA
1 CATTCGCTACCA
437021 CA-TCGCTACCA
1 CATTCGCTACCA
437032 CATTCGCT
1 CATTCGCT
437040 TTCCCTGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.23, C:0.42, G:0.10, T:0.26
Consensus pattern (12 bp):
CATTCGCTACCA
Found at i:440847 original size:22 final size:22
Alignment explanation
Indices: 440819--440871 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
440809 TTCAGTATTT
*
440819 GTCCCGAAGGACCATTGGATAC
1 GTCCCGAAGGACCACTGGATAC
440841 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
440863 GTCCCGAAG
1 GTCCCGAAG
440872 ACTAATATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.15
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:445317 original size:108 final size:108
Alignment explanation
Indices: 445077--445321 Score: 316
Period size: 108 Copynumber: 2.3 Consensus size: 108
445067 TACCAAATAG
***
445077 GCACTAAGTGTGCATTTCACGGAATTCATCCTAAGTGGATGAATAACCATTTCGACACTAAGTGT
1 GCACTAAGTGTGCAAACCACGGAATTCATCCTAAGTGGATGAATAACCATTTCGACACTAAGTGT
*
445142 ACATTTCACAGAATTCATACTAAGTGGATGAATAACCGTTTCA
66 ACATTTCACAGAATTCATACTAAGTAGATGAATAACCGTTTCA
*** *
445185 GCACTAAGTGTGCATTTCACGGAATTCATCCTAAGTGGATGAATAACTATTTC-AGCACTAAGTG
1 GCACTAAGTGTGCAAACCACGGAATTCATCCTAAGTGGATGAATAACCATTTCGA-CACTAAGTG
* * * *
445249 TGCTTTTCACGGAATTCAT-CTTAAGTAGATGAATAACCGTTT-T
65 TACATTTCACAGAATTCATAC-TAAGTAGATGAATAACCGTTTCA
* *
445292 GCCAGTAAGTGTGCAAACCATGGAATTCAT
1 G-CACTAAGTGTGCAAACCACGGAATTCAT
445322 AATATGTTTA
Statistics
Matches: 123, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
107 3 0.02
108 120 0.98
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (108 bp):
GCACTAAGTGTGCAAACCACGGAATTCATCCTAAGTGGATGAATAACCATTTCGACACTAAGTGT
ACATTTCACAGAATTCATACTAAGTAGATGAATAACCGTTTCA
Found at i:445321 original size:54 final size:54
Alignment explanation
Indices: 445077--445286 Score: 332
Period size: 54 Copynumber: 3.9 Consensus size: 54
445067 TACCAAATAG
445077 GCACTAAGTGTGCATTTCACGGAATTCATCCTAAGTGGATGAATAACCATTTC-
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTAAGTGGATGAATAACCATTTCA
* * * *
445130 GACACTAAGTGTACATTTCACAGAATTCATACTAAGTGGATGAATAACCGTTTCA
1 G-CACTAAGTGTGCATTTCACGGAATTCATCCTAAGTGGATGAATAACCATTTCA
*
445185 GCACTAAGTGTGCATTTCACGGAATTCATCCTAAGTGGATGAATAACTATTTCA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTAAGTGGATGAATAACCATTTCA
* * *
445239 GCACTAAGTGTGCTTTTCACGGAATTCATCTTAAGTAGATGAATAACC
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTAAGTGGATGAATAACC
445287 GTTTTGCCAG
Statistics
Matches: 142, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
53 1 0.01
54 140 0.99
55 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (54 bp):
GCACTAAGTGTGCATTTCACGGAATTCATCCTAAGTGGATGAATAACCATTTCA
Found at i:453509 original size:13 final size:13
Alignment explanation
Indices: 453493--453523 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
453483 ATTCTTTTAA
*
453493 TCATTTCTCATTT
1 TCATTTCTAATTT
453506 TCATTTCTAATTT
1 TCATTTCTAATTT
453519 TCATT
1 TCATT
453524 AACCATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (13 bp):
TCATTTCTAATTT
Found at i:453708 original size:14 final size:16
Alignment explanation
Indices: 453679--453722 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
453669 GATTATTTCA
453679 TCTCATT-TTCTC-TTT
1 TCTCATTATT-TCATTT
453694 TCTC-TT-TTTCATTT
1 TCTCATTATTTCATTT
453708 TCTCATTATTTCATT
1 TCTCATTATTTCATT
453723 GGTGTTGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.08
14 11 0.42
15 6 0.23
16 7 0.27
ACGTcount: A:0.11, C:0.23, G:0.00, T:0.66
Consensus pattern (16 bp):
TCTCATTATTTCATTT
Found at i:453713 original size:8 final size:8
Alignment explanation
Indices: 453679--453714 Score: 51
Period size: 7 Copynumber: 4.9 Consensus size: 8
453669 GATTATTTCA
453679 TCTCATTT
1 TCTCATTT
453687 TCTC-TTT
1 TCTCATTT
453694 TCTC-TTT
1 TCTCATTT
453701 T-TCATTT
1 TCTCATTT
453708 TCTCATT
1 TCTCATT
453715 ATTTCATTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 2 0.08
7 15 0.58
8 9 0.35
ACGTcount: A:0.08, C:0.25, G:0.00, T:0.67
Consensus pattern (8 bp):
TCTCATTT
Found at i:458328 original size:20 final size:20
Alignment explanation
Indices: 458280--458354 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
458270 TATAATGTAT
*
458280 AGATACAAATGCAAAGATTCG-
1 AGATGCAAATGCAAAGA-T-GA
458301 A-ATGCAAATGCAAAGATGA
1 AGATGCAAATGCAAAGATGA
* *
458320 AGATTCAAATGAAAAGATGA
1 AGATGCAAATGCAAAGATGA
*
458340 GGATGCAAATGCAAA
1 AGATGCAAATGCAAA
458355 AAAATGTATG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
18 1 0.02
19 2 0.04
20 42 0.91
21 1 0.02
ACGTcount: A:0.51, C:0.11, G:0.21, T:0.17
Consensus pattern (20 bp):
AGATGCAAATGCAAAGATGA
Found at i:460302 original size:142 final size:142
Alignment explanation
Indices: 460123--460391 Score: 371
Period size: 142 Copynumber: 1.9 Consensus size: 142
460113 CCTAGAGGAC
* * * * * *
460123 TAAACCTAAACATGAAGGCTTTAATATTAATCCTAATTTATTTTAACAAATTATTGATTTGAATA
1 TAAACCTAAACATGAAGGCTCTAATAGTAATCATAATTTATTTTAACAAATTATTGAGTCGAACA
* * * *
460188 ATCAAAATGGACTCTTGGGGCATTTTAATGCA-AGGGTCATATCAAAATATTCCCTAAATTAAGG
66 ATCAAAATGGAC-CCTCGGGCATTTTAATG-AGAGGGTAAAATCAAAATATTCCCTAAATTAAGG
460252 GACTAAAATGAAAA
129 GACTAAAATGAAAA
* *
460266 TAAACCTAAA-GTGAAGGCTCTAATAGTAATCATAATTTATTTTAACCAATTATTGAGTCGAACA
1 TAAACCTAAACATGAAGGCTCTAATAGTAATCATAATTTATTTTAACAAATTATTGAGTCGAACA
* * *
460330 ATCAAAATGGACCCTCGTGCGTTTTAATGAGAGGGTAAAATCAAATTATTCCCTAAATTAAG
66 ATCAAAATGGACCCTCGGGCATTTTAATGAGAGGGTAAAATCAAAATATTCCCTAAATTAAG
460392 TAGTTTAGGG
Statistics
Matches: 110, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
140 1 0.01
141 41 0.37
142 58 0.53
143 10 0.09
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (142 bp):
TAAACCTAAACATGAAGGCTCTAATAGTAATCATAATTTATTTTAACAAATTATTGAGTCGAACA
ATCAAAATGGACCCTCGGGCATTTTAATGAGAGGGTAAAATCAAAATATTCCCTAAATTAAGGGA
CTAAAATGAAAA
Found at i:465063 original size:2 final size:2
Alignment explanation
Indices: 465056--465090 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
465046 TACATTCTTT
* *
465056 TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
465091 TAATGACCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:471645 original size:18 final size:18
Alignment explanation
Indices: 471622--471666 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
471612 AACATTCCCA
*
471622 GTAATCTTATTCCCGCCG
1 GTAATCTTATTCCCACCG
471640 GTAATCTTATTCCCACCG
1 GTAATCTTATTCCCACCG
*
471658 ATAATCTTA
1 GTAATCTTA
471667 CATTCTGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.36
Consensus pattern (18 bp):
GTAATCTTATTCCCACCG
Found at i:472212 original size:4 final size:4
Alignment explanation
Indices: 472203--472235 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
472193 ATAAAAGGAA
472203 AAAT AAAT AAAT -AA- AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
472236 ATATTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 4 0.15
4 23 0.85
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:472218 original size:14 final size:14
Alignment explanation
Indices: 472150--472231 Score: 68
Period size: 14 Copynumber: 6.1 Consensus size: 14
472140 TGTTAGAGGG
*
472150 AAAATGAATAAATGA
1 AAAATAAATAAAT-A
472165 AAAA-AAA-AGAATA
1 AAAATAAATA-AATA
*
472178 AAAATAAGT-AA-A
1 AAAATAAATAAATA
**
472190 AAAAT-AA-AAGGA
1 AAAATAAATAAATA
472202 AAAATAAATAAATA
1 AAAATAAATAAATA
472216 AAAATAAATAAATA
1 AAAATAAATAAATA
472230 AA
1 AA
472232 TAAAATATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
11 2 0.04
12 12 0.22
13 10 0.19
14 26 0.48
15 4 0.07
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (14 bp):
AAAATAAATAAATA
Found at i:473129 original size:37 final size:37
Alignment explanation
Indices: 473088--473192 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
473078 GTGCTTGTGG
* * *
473088 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
473125 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
473162 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
473193 GACGAAAAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:474248 original size:106 final size:106
Alignment explanation
Indices: 473923--475403 Score: 2136
Period size: 106 Copynumber: 14.0 Consensus size: 106
473913 GCATTGTTCT
* ** * ** * * *
473923 GAGTCCAATATCCTCCATTGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
473988 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
474029 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * * *
474088 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGCCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * *
474130 G-GTTCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
474194 CCAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
474235 GATTCCAATATCCTACGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
474300 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
474341 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAG-AGATTTTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAG-TTGTTTATTGACA
* *
474405 ACCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTATG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
474447 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
474512 CCAGCGGTCCTTTCTTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
474553 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
474618 CCAGCGGTTCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** * * *
474659 AAGTCCAATATCCTTCATTATGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
474724 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
474765 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
474830 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
474871 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
474936 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
474977 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
475042 CCAGCGGTCCCTTCTTCATGAAGTCGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
475083 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAAATTGGAAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
475148 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
475189 GAGTCCAATATCTTTCGCTGTGAAGTTGAGATTGGATCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
475254 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
475295 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATTG-TTGTTGACTA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
475359 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
475400 GAGT
1 GAGT
475404 GGCACGATAT
Statistics
Matches: 1243, Mismatches: 121, Indels: 23
0.90 0.09 0.02
Matches are distributed among these distances:
99 1 0.00
100 75 0.06
101 5 0.00
102 4 0.00
104 3 0.00
105 55 0.04
106 1098 0.88
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:476255 original size:22 final size:22
Alignment explanation
Indices: 476229--476305 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
476219 TTATGTTTGG
476229 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
476251 TCAAAGGTTTGGCATTTGATAC
1 TCAAAGGTTTGGCATTTGATGC
*
476273 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
476295 TCAACGGTTTG
1 TCAAAGGTTTG
476306 ATGGGGTAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:476928 original size:22 final size:22
Alignment explanation
Indices: 476900--476941 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
476890 TTGCATGTGC
476900 TTTTTGTCCATTT-TTTTTTTGA
1 TTTTTGTCC-TTTCTTTTTTTGA
*
476922 TTTTTGTTCTTTCTTTTTTT
1 TTTTTGTCCTTTCTTTTTTT
476942 CTTTTGTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.05, C:0.10, G:0.07, T:0.79
Consensus pattern (22 bp):
TTTTTGTCCTTTCTTTTTTTGA
Found at i:476960 original size:9 final size:8
Alignment explanation
Indices: 476931--476993 Score: 63
Period size: 8 Copynumber: 7.2 Consensus size: 8
476921 ATTTTTGTTC
476931 TTTCTTTT
1 TTTCTTTT
476939 TTTCTTTT
1 TTTCTTTT
476947 GTTTCTCTTT
1 -TTTCT-TTT
476957 TTTCTTTTTT
1 TTTC--TTTT
476967 TTTCTTCTT
1 TTTCTT-TT
* *
476976 TTGCTTCT
1 TTTCTTTT
476984 TTTCTTTT
1 TTTCTTTT
476992 TT
1 TT
476994 GTTCTTGATT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
8 19 0.41
9 16 0.35
10 10 0.22
11 1 0.02
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (8 bp):
TTTCTTTT
Found at i:476960 original size:26 final size:27
Alignment explanation
Indices: 476931--476999 Score: 81
Period size: 26 Copynumber: 2.6 Consensus size: 27
476921 ATTTTTGTTC
*
476931 TTTCTTTTTTTCTT-TTGTTTCT-CTT-T
1 TTTCTTTTTTT-TTCTTCTTT-TGCTTCT
476957 TTTCTTTTTTTTTCTTCTTTTGCTTCT
1 TTTCTTTTTTTTTCTTCTTTTGCTTCT
*
476984 TTTCTTTTTTGTTCTT
1 TTTCTTTTTTTTTCTT
477000 GATTGGATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
25 3 0.08
26 19 0.50
27 16 0.42
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (27 bp):
TTTCTTTTTTTTTCTTCTTTTGCTTCT
Found at i:476968 original size:27 final size:26
Alignment explanation
Indices: 476923--476999 Score: 72
Period size: 28 Copynumber: 3.0 Consensus size: 26
476913 TTTTTTTGAT
476923 TTTTG-TTC-TTTC-TTTTTTTCTT-
1 TTTTGCTTCTTTTCTTTTTTTTCTTC
* *
476945 TTGTTTCTCTTTTTTCTTTTTTTTTCTTC
1 TT-TTGCT-TCTTTTC-TTTTTTTTCTTC
476974 TTTTGCTTCTTTTCTTTTTTGTTCTT
1 TTTTGCTTCTTTTCTTTTTT-TTCTT
477000 GATTGGATCT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
22 2 0.05
23 2 0.05
24 1 0.02
25 1 0.02
26 10 0.23
27 11 0.26
28 14 0.33
29 2 0.05
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (26 bp):
TTTTGCTTCTTTTCTTTTTTTTCTTC
Found at i:476978 original size:31 final size:31
Alignment explanation
Indices: 476923--476983 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
476913 TTTTTTTGAT
*
476923 TTTTGTTCTTTCTTTTTTTCTTTTGTTTCTC
1 TTTTGTTCTTTCTTTTTTTCTTTTGCTTCTC
*
476954 TTTT-TTCTTTTTTTTTCTTCTTTTGCTTCT
1 TTTTGTTCTTTCTTTTT-TTCTTTTGCTTCT
476984 TTTCTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (31 bp):
TTTTGTTCTTTCTTTTTTTCTTTTGCTTCTC
Found at i:481479 original size:12 final size:12
Alignment explanation
Indices: 481441--481519 Score: 63
Period size: 12 Copynumber: 6.3 Consensus size: 12
481431 GGAAAAAATG
481441 AATAAATGAAAAA
1 AATAAAT-AAAAA
*
481454 AA-AGAAGAATAAA
1 AATA-AATAA-AAA
*
481467 AATAAGTAAAAA
1 AATAAATAAAAA
*
481479 AATAAA-AGGAAA
1 AATAAATA-AAAA
*
481491 AATAAATAAATA
1 AATAAATAAAAA
481503 AATAAATAAATAA
1 AATAAATAAA-AA
481516 AATA
1 AATA
481520 TTAAAATATA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
11 1 0.02
12 32 0.62
13 18 0.35
14 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AATAAATAAAAA
Found at i:481499 original size:4 final size:4
Alignment explanation
Indices: 481490--481516 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
481480 ATAAAAGGAA
481490 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
481517 ATATTAAAAT
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:481532 original size:2 final size:2
Alignment explanation
Indices: 481525--481559 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
481515 AAATATTAAA
481525 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
481560 AATGAGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:481836 original size:2 final size:2
Alignment explanation
Indices: 481831--481869 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
481821 ATTAAAAAAG
481831 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
481870 TAAAAAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:483622 original size:18 final size:18
Alignment explanation
Indices: 483599--483633 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
483589 ATGTGTAATA
483599 TCCCTTAAGTAAAATTAG
1 TCCCTTAAGTAAAATTAG
483617 TCCCTTAAGTAAAATTA
1 TCCCTTAAGTAAAATTA
483634 TCTCATACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (18 bp):
TCCCTTAAGTAAAATTAG
Found at i:491085 original size:15 final size:15
Alignment explanation
Indices: 491067--491099 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
491057 TACTATGGTT
491067 ATATGTTATATGTGA
1 ATATGTTATATGTGA
*
491082 ATATGTTTTATGTGA
1 ATATGTTATATGTGA
491097 ATA
1 ATA
491100 AATGATAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (15 bp):
ATATGTTATATGTGA
Found at i:491245 original size:23 final size:23
Alignment explanation
Indices: 491210--491265 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
491200 GGTTCTACAC
** *
491210 GGTCCTTTAGGACAATTCAATGT
1 GGTCCTTCGGGACAAATCAATGT
*
491233 GGTCCTTCGGGACAAATCTATGT
1 GGTCCTTCGGGACAAATCAATGT
491256 GG-CACTTCGG
1 GGTC-CTTCGG
491266 TGCATATTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (23 bp):
GGTCCTTCGGGACAAATCAATGT
Found at i:491287 original size:24 final size:24
Alignment explanation
Indices: 491237--491304 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
491227 CAATGTGGTC
* *
491237 CTTCGG-GACAAA-TCTATGTGGCA
1 CTTCGGTG-CAAATTCTACGTGACA
* *
491260 CTTCGGTGCATATTCTGCGTGACA
1 CTTCGGTGCAAATTCTACGTGACA
491284 CTTCGGTGCAAATTCTACGTG
1 CTTCGGTGCAAATTCTACGTG
491305 GGAGTTTCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
23 9 0.24
24 28 0.76
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.31
Consensus pattern (24 bp):
CTTCGGTGCAAATTCTACGTGACA
Found at i:494407 original size:22 final size:21
Alignment explanation
Indices: 494382--494438 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
494372 GAGTTAGCAC
494382 CTTCTAGAATGAACAGTCAG-T
1 CTTCTAGAA-GAACAGTCAGCT
*
494403 GCTTCTAGAAGGACCAGTCAGCT
1 -CTTCTAGAA-GAACAGTCAGCT
494426 CTTCTAGAAGAAC
1 CTTCTAGAAGAAC
494439 GAATGGATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.10
22 27 0.87
23 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (21 bp):
CTTCTAGAAGAACAGTCAGCT
Found at i:494763 original size:18 final size:18
Alignment explanation
Indices: 494737--494771 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
494727 ATTTTCAAAG
*
494737 TTCACGTTTTATTTTTAT
1 TTCAAGTTTTATTTTTAT
494755 TTCAAGTTTTATTTTTA
1 TTCAAGTTTTATTTTTA
494772 AAATATGCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.09, G:0.06, T:0.66
Consensus pattern (18 bp):
TTCAAGTTTTATTTTTAT
Found at i:502163 original size:22 final size:22
Alignment explanation
Indices: 502135--502180 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
502125 TAATATATAT
502135 ATATATATATTTGAGATCCCTG
1 ATATATATATTTGAGATCCCTG
502157 ATATATATATTTGAGATCCCTG
1 ATATATATATTTGAGATCCCTG
502179 AT
1 AT
502181 GTTAGTCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (22 bp):
ATATATATATTTGAGATCCCTG
Found at i:503860 original size:52 final size:52
Alignment explanation
Indices: 503793--503922 Score: 172
Period size: 52 Copynumber: 2.5 Consensus size: 52
503783 GACAACCGGT
* *
503793 AATCTTTCGGCGCTCTTACATTGTCAAGACA-TGTTTCACCAAGACCCCAGCC
1 AATCTCTCGACGCTCTTACATTGTCAAGA-AGTGTTTCACCAAGACCCCAGCC
* * *
503845 AATCTCTCGTCGCTCTTACATTGTTAAGAAGTGTTTCACCAAGACCCCAGGC
1 AATCTCTCGACGCTCTTACATTGTCAAGAAGTGTTTCACCAAGACCCCAGCC
* * *
503897 AATATCTCGAAGCTCTTACAGTGTCA
1 AATCTCTCGACGCTCTTACATTGTCA
503923 GGGAAAATGT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 1 0.01
52 67 0.99
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.28
Consensus pattern (52 bp):
AATCTCTCGACGCTCTTACATTGTCAAGAAGTGTTTCACCAAGACCCCAGCC
Found at i:510798 original size:21 final size:21
Alignment explanation
Indices: 510773--510815 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
510763 GCATAAAGTC
*
510773 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCATGAAATCT
* *
510794 TTTGTCGAGGCCATGAATTCT
1 TTTGTCGAAGCCATGAAATCT
510815 T
1 T
510816 GCAGTGAAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (21 bp):
TTTGTCGAAGCCATGAAATCT
Found at i:520376 original size:12 final size:12
Alignment explanation
Indices: 520361--520410 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
520351 CTTGTCATCC
520361 TTCTTTTCGTCT
1 TTCTTTTCGTCT
*
520373 TTCTTTTCATCT
1 TTCTTTTCGTCT
* *
520385 TTCTTGTCGTCC
1 TTCTTTTCGTCT
*
520397 TTCTTTTCTTCT
1 TTCTTTTCGTCT
520409 TT
1 TT
520411 AGCAGGTCCC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.02, C:0.26, G:0.06, T:0.66
Consensus pattern (12 bp):
TTCTTTTCGTCT
Found at i:520409 original size:24 final size:24
Alignment explanation
Indices: 520349--520410 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
520339 AAACGATCAT
* * * *
520349 TTCTTGTCATCCTTCTTTTCGTCT
1 TTCTTTTCATCTTTCTTGTCGTCC
520373 TTCTTTTCATCTTTCTTGTCGTCC
1 TTCTTTTCATCTTTCTTGTCGTCC
*
520397 TTCTTTTCTTCTTT
1 TTCTTTTCATCTTT
520411 AGCAGGTCCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.03, C:0.27, G:0.06, T:0.63
Consensus pattern (24 bp):
TTCTTTTCATCTTTCTTGTCGTCC
Found at i:522629 original size:31 final size:32
Alignment explanation
Indices: 522569--522640 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
522559 TGGTATGTAT
*
522569 ACATCATCACTTTGGATGACACAATATATGTC
1 ACATCATCACTTTAGATGACACAATATATGTC
* *
522601 GCATCATCACTTTAG-TGACA-AGTCATATGTC
1 ACATCATCACTTTAGATGACACAAT-ATATGTC
*
522632 ACAACATCA
1 ACATCATCA
522641 ATTAAATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 2 0.06
31 19 0.56
32 13 0.38
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (32 bp):
ACATCATCACTTTAGATGACACAATATATGTC
Found at i:525421 original size:20 final size:20
Alignment explanation
Indices: 525387--525424 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
525377 ATTTTATAGA
**
525387 AAATTATCCCCAACGGCTCC
1 AAATTATCCAAAACGGCTCC
525407 AAATTATCCAAAACGGCT
1 AAATTATCCAAAACGGCT
525425 AGAAACAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.32, G:0.11, T:0.21
Consensus pattern (20 bp):
AAATTATCCAAAACGGCTCC
Found at i:527209 original size:19 final size:19
Alignment explanation
Indices: 527165--527209 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
527155 TGATTTTCTC
* *
527165 TTGAAAACAAAATTAGATT
1 TTGAAAACAAAATGAAATT
527184 TTGAAAAGCAAAATGAAATT
1 TTGAAAA-CAAAATGAAATT
527204 TT-AAAA
1 TTGAAAA
527210 ATAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.29
Consensus pattern (19 bp):
TTGAAAACAAAATGAAATT
Found at i:528736 original size:20 final size:20
Alignment explanation
Indices: 528671--528742 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 20
528661 GTAAAATAGG
528671 TATCGATACCATGATCATAA
1 TATCGATACCATGATCATAA
* * * *
528691 TATAGATACTACTTTACACAATAA
1 TATCGATAC--CATGA-TC-ATAA
528715 TATCGATACCATGATCATAA
1 TATCGATACCATGATCATAA
528735 TATCGATA
1 TATCGATA
528743 TTGGTAAGAC
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
20 20 0.50
21 1 0.03
22 6 0.15
23 1 0.03
24 12 0.30
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (20 bp):
TATCGATACCATGATCATAA
Found at i:528815 original size:21 final size:22
Alignment explanation
Indices: 528779--528819 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
528769 TTAAATATTA
*
528779 TAAAGGAAGTATCGATACTCAT
1 TAAAGGAAGTAACGATACTCAT
528801 TAAAGG-AGTAACGATACTC
1 TAAAGGAAGTAACGATACTC
528820 TCTGTTCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (22 bp):
TAAAGGAAGTAACGATACTCAT
Found at i:542426 original size:27 final size:27
Alignment explanation
Indices: 542395--542449 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
542385 TTAATTCATT
* *
542395 TTAAA-TTAAGGATCTAATTGAAGAGAA
1 TTAAAGTTAAGGACCTAACTGAA-AGAA
*
542422 TTAAAGTTCAGGACCTAACTGAAAGAA
1 TTAAAGTTAAGGACCTAACTGAAAGAA
542449 T
1 T
542450 CAAAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.27
Consensus pattern (27 bp):
TTAAAGTTAAGGACCTAACTGAAAGAA
Found at i:543086 original size:245 final size:242
Alignment explanation
Indices: 542643--543092 Score: 857
Period size: 245 Copynumber: 1.8 Consensus size: 242
542633 CTTAACAGGA
542643 TCATCCACACATTCTCTTCCTAATCGAAAATCTCTTCAGGAAAGCTACAGAAAGTTGCTCCATTG
1 TCATCCACACATTCTCTTCCTAATCGAAAATCTCTTCAGGAAAGCTACAGAAAGTTGCTCCATTG
542708 ATGCAGAAATGCCGACACTTAATTACTTCAATGTCGACAGATAGCCTTGATTTATCAGACGTGTA
66 ATGCAGAAATGCCGACACTTAATTACTTCAATGTCGACAGATAGCCTTGATTTATCAGACGTGTA
542773 AAGAGCTGAAAACTCCACGTGTAAATACCATATTCATTATCCTACAAAGCTGACCCGATTTTTTT
131 AAGAGCTGAAAACTCCACGTGTAAATACCATATTCATTATCCTACAAAGCTGACCCGATTTTTTT
542838 CACAGGGCTCCAAACAAAAGGTTCCTGGCTTTACTTGAAAATGCTCT
196 CACAGGGCTCCAAACAAAAGGTTCCTGGCTTTACTTGAAAATGCTCT
542885 TCATCCACACATTTCTTCTTCCTAATCGAAAATCTCTTCAGGAAAGCTACAGAAAGTTGCTCCAT
1 TCATCCACACA-TTC-TCTTCCTAATCGAAAATCTCTTCAGGAAAGCTACAGAAAGTTGCTCCAT
542950 TGATGCAAGAAATGCCGACACTTAATTACTTCAATGTCGACAGATAGCCTTGATTTATCAGACGT
64 TGATGC-AGAAATGCCGACACTTAATTACTTCAATGTCGACAGATAGCCTTGATTTATCAGACGT
543015 GTAAAGAGCTGAAAACTCCACGTGTAAATACCATATTCATTATCCTACAAAGCTGACCCCGA-TT
128 GTAAAGAGCTGAAAACTCCACGTGTAAATACCATATTCATTATCCTACAAAGCTGA-CCCGATTT
543079 TTTTCACAGGGCTC
192 TTTTCACAGGGCTC
543093 TAGCACAATT
Statistics
Matches: 204, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
242 11 0.05
243 3 0.01
244 55 0.27
245 130 0.64
246 5 0.02
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (242 bp):
TCATCCACACATTCTCTTCCTAATCGAAAATCTCTTCAGGAAAGCTACAGAAAGTTGCTCCATTG
ATGCAGAAATGCCGACACTTAATTACTTCAATGTCGACAGATAGCCTTGATTTATCAGACGTGTA
AAGAGCTGAAAACTCCACGTGTAAATACCATATTCATTATCCTACAAAGCTGACCCGATTTTTTT
CACAGGGCTCCAAACAAAAGGTTCCTGGCTTTACTTGAAAATGCTCT
Found at i:545032 original size:29 final size:30
Alignment explanation
Indices: 544978--545034 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
544968 GTGTCTATAT
544978 TATCAATAACTAAAAAAATATTTAAAAAAA
1 TATCAATAACTAAAAAAATATTTAAAAAAA
*
545008 TATCAATAACT-AGAAAATATTTAAAAA
1 TATCAATAACTAAAAAAATATTTAAAAA
545035 TTAAATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (30 bp):
TATCAATAACTAAAAAAATATTTAAAAAAA
Found at i:545495 original size:43 final size:43
Alignment explanation
Indices: 545402--545496 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 43
545392 CTCATCACAA
* *
545402 TCTGATGCTAGTATTAGTAATTAATATTGTTTTGTATATTAAT
1 TCTGATGTTAGGATTAGTAATTAATATTGTTTTGTATATTAAT
* * *
545445 TCTGATGTTAGGATTAGTAGTTGATATTGTTTTGTTTATTAAT
1 TCTGATGTTAGGATTAGTAATTAATATTGTTTTGTATATTAAT
545488 T-TCGATGTT
1 TCT-GATGTT
545497 CAAGTTCTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 1 0.02
43 45 0.98
ACGTcount: A:0.25, C:0.04, G:0.18, T:0.53
Consensus pattern (43 bp):
TCTGATGTTAGGATTAGTAATTAATATTGTTTTGTATATTAAT
Found at i:546240 original size:32 final size:32
Alignment explanation
Indices: 546195--546264 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
546185 AGAACCAAAT
* *
546195 TCCTAACCTTATTCTCAAATTTATAATTTTCA
1 TCCTAACCCTATTCTAAAATTTATAATTTTCA
546227 TCCTAACCCTATTCTAAAATTTATAATTTTCA
1 TCCTAACCCTATTCTAAAATTTATAATTTTCA
546259 TCCTAA
1 TCCTAA
546265 ATTAACTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (32 bp):
TCCTAACCCTATTCTAAAATTTATAATTTTCA
Found at i:546689 original size:32 final size:33
Alignment explanation
Indices: 546643--546744 Score: 156
Period size: 33 Copynumber: 3.2 Consensus size: 33
546633 ACAAAGTTTA
* *
546643 CGAT-AATTAAAATACTT-AATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
*
546674 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
546707 CGATAAATTCAAATACTTAAAAACTTCC-AGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
546739 CGATAA
1 CGATAA
546745 TTGAAACAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
31 4 0.06
32 22 0.34
33 39 0.60
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:546763 original size:21 final size:21
Alignment explanation
Indices: 546739--546780 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
546729 ACTTCCAGTT
546739 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
546760 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
546781 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:549324 original size:30 final size:31
Alignment explanation
Indices: 549290--549353 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
549280 TATAATTAAC
**
549290 CATTTA-TTTTATATTAAATTAAAATATAAA
1 CATTTATTTTTATATTAAACAAAAATATAAA
549320 CATTTATTTTTATATTAAACAAAAATATAAA
1 CATTTATTTTTATATTAAACAAAAATATAAA
549351 CAT
1 CAT
549354 AACACATGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 6 0.19
31 25 0.81
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (31 bp):
CATTTATTTTTATATTAAACAAAAATATAAA
Found at i:549513 original size:38 final size:38
Alignment explanation
Indices: 549431--549518 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 38
549421 ATTAATCAAC
* * *
549431 TAAAAGTATAACGGTAAAAGTATTTTTCGTTAAATATT
1 TAAAAGTGTAACGGTAAAAGTATTTTCCGTTAAACATT
* * *
549469 TAAAAGTGTAATGGTAAAAGTGTTTTCCGTTAAGCATCT
1 TAAAAGTGTAACGGTAAAAGTATTTTCCGTTAAACAT-T
549508 T-AAAGTGTAAC
1 TAAAAGTGTAAC
549519 AAAAAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 40 0.95
39 2 0.05
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (38 bp):
TAAAAGTGTAACGGTAAAAGTATTTTCCGTTAAACATT
Found at i:561370 original size:20 final size:21
Alignment explanation
Indices: 561326--561383 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
561316 TGCATGGTAG
561326 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T-AAGAA
561350 TGCATCGATGCACTG-AAGAA
1 TGCATCGATGCACTGTAAGAA
* *
561370 TGCACCGATCCACT
1 TGCATCGATGCACT
561384 TCAATGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
23 2 0.06
24 13 0.41
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (21 bp):
TGCATCGATGCACTGTAAGAA
Found at i:562215 original size:21 final size:21
Alignment explanation
Indices: 562189--562272 Score: 141
Period size: 21 Copynumber: 4.0 Consensus size: 21
562179 GAGTCGAGGG
562189 TCTATGTGGTCCTTCGGGACA
1 TCTATGTGGTCCTTCGGGACA
562210 TCTATGTGGTCCTTCGGGACA
1 TCTATGTGGTCCTTCGGGACA
**
562231 TCTATGTGGTCCTTTAGGACA
1 TCTATGTGGTCCTTCGGGACA
*
562252 TCTATGTGGTCATTCGGGACA
1 TCTATGTGGTCCTTCGGGACA
562273 AATTCTACGC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (21 bp):
TCTATGTGGTCCTTCGGGACA
Found at i:564195 original size:24 final size:24
Alignment explanation
Indices: 564168--564219 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
564158 CAGGGGTATG
564168 TAGAGTAATCTCCGGAGCTTGTTT
1 TAGAGTAATCTCCGGAGCTTGTTT
*
564192 TAGAGTAATCTCTGGAGCTTGTTT
1 TAGAGTAATCTCCGGAGCTTGTTT
564216 TAGA
1 TAGA
564220 TGTGGGGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.38
Consensus pattern (24 bp):
TAGAGTAATCTCCGGAGCTTGTTT
Done.