Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold152
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: 2945013
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 16 of 18
Found at i:2518009 original size:32 final size:32
Alignment explanation
Indices: 2517968--2518051 Score: 132
Period size: 32 Copynumber: 2.6 Consensus size: 32
2517958 AGTAGCTTAA
*
2517968 ATTGTATCGATACAAAACTTATATATAGATAC
1 ATTGTATCGATACAACACTTATATATAGATAC
* * *
2518000 ATTGTATCGATACAACACTTATGTATCGATAT
1 ATTGTATCGATACAACACTTATATATAGATAC
2518032 ATTGTATCGATACAACACTT
1 ATTGTATCGATACAACACTT
2518052 TATGTATCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATATATAGATAC
Found at i:2518144 original size:21 final size:22
Alignment explanation
Indices: 2518097--2518144 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
2518087 TTAACCGTTG
*
2518097 GGACATTGTATCGATACATTCT
1 GGACAATGTATCGATACATTCT
*
2518119 -AACAATGTATCGATACATT-T
1 GGACAATGTATCGATACATTCT
2518139 GGACAA
1 GGACAA
2518145 AAATGTGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (22 bp):
GGACAATGTATCGATACATTCT
Found at i:2518991 original size:17 final size:18
Alignment explanation
Indices: 2518971--2519009 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
2518961 AAAATAAGTA
2518971 AAATAAAATAAT-TAAAT-
1 AAATAAAA-AATATAAATC
2518988 AAATAAAAAATATAAATC
1 AAATAAAAAATATAAATC
2519006 AAAT
1 AAAT
2519010 CAAGTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.15
17 13 0.65
18 4 0.20
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATAAAAAATATAAATC
Found at i:2518996 original size:23 final size:23
Alignment explanation
Indices: 2518953--2518995 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2518943 AATTATACAT
* *
2518953 AAATATTTAAAATAAGTAAAATA
1 AAATAATTAAAATAAATAAAATA
2518976 AAATAATT-AAATAAATAAAA
1 AAATAATTAAAATAAATAAAA
2518996 AATATAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATAATTAAAATAAATAAAATA
Found at i:2519009 original size:22 final size:22
Alignment explanation
Indices: 2518962--2519009 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
2518952 TAAATATTTA
* *
2518962 AAATAAGTAAAATAAAATAATT
1 AAATAAATAAAATAAAATAATC
*
2518984 AAATAAATAAAA-AATATAAATC
1 AAATAAATAAAATAAAAT-AATC
2519006 AAAT
1 AAAT
2519010 CAAGTATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (22 bp):
AAATAAATAAAATAAAATAATC
Found at i:2519247 original size:25 final size:24
Alignment explanation
Indices: 2519219--2519301 Score: 78
Period size: 24 Copynumber: 3.3 Consensus size: 24
2519209 ATTTGAATGG
*
2519219 TTTTAAAAAATAAAATTATATCAAA
1 TTTTAAAAAATAAAATTAAAT-AAA
*
2519244 TTTT-AAAAATAAATTTTAAATTTAAA
1 TTTTAAAAAATAAA-ATTAAA--TAAA
* * *
2519270 TTTTAAAAATTAGAATAAAATAAA
1 TTTTAAAAAATAAAATTAAATAAA
2519294 TTTTAAAA
1 TTTTAAAA
2519302 TTTAATTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
24 21 0.44
25 8 0.17
26 11 0.23
27 8 0.17
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (24 bp):
TTTTAAAAAATAAAATTAAATAAA
Found at i:2519259 original size:13 final size:13
Alignment explanation
Indices: 2519241--2519279 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
2519231 AAATTATATC
2519241 AAATTTTAAAAAT
1 AAATTTTAAAAAT
**
2519254 AAATTTTAAATTT
1 AAATTTTAAAAAT
2519267 AAATTTTAAAAAT
1 AAATTTTAAAAAT
2519280 TAGAATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATTTTAAAAAT
Found at i:2519440 original size:15 final size:15
Alignment explanation
Indices: 2519420--2519450 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2519410 AAATATTAAT
2519420 TATATAATAAATTTA
1 TATATAATAAATTTA
*
2519435 TATATAATATATTTA
1 TATATAATAAATTTA
2519450 T
1 T
2519451 GTACGAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATAATAAATTTA
Found at i:2521469 original size:13 final size:13
Alignment explanation
Indices: 2521451--2521475 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2521441 TATAAAGTGT
2521451 TGTATCGATACAA
1 TGTATCGATACAA
2521464 TGTATCGATACA
1 TGTATCGATACA
2521476 TAAGTGATGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2521487 original size:19 final size:19
Alignment explanation
Indices: 2521463--2521513 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
2521453 TATCGATACA
2521463 ATGTATCGATACATAAGTG
1 ATGTATCGATACATAAGTG
*
2521482 ATGTATCGATACATAAGTT
1 ATGTATCGATACATAAGTG
*
2521501 TTGTATCGATACA
1 ATGTATCGATACA
2521514 ATTTAAGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (19 bp):
ATGTATCGATACATAAGTG
Found at i:2521487 original size:32 final size:33
Alignment explanation
Indices: 2521431--2521494 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2521421 TTCAACGATT
* *
2521431 TGTATCGATATATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGATGTATCGATACAA
2521464 TGTATCGATACAT-AAGTGATGTATCGATACA
1 TGTATCGATACATAAAGTGATGTATCGATACA
2521495 TAAGTTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGATGTATCGATACAA
Found at i:2521574 original size:13 final size:13
Alignment explanation
Indices: 2521556--2521580 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2521546 ATTACTCAAC
2521556 TGTATCGATACAT
1 TGTATCGATACAT
2521569 TGTATCGATACA
1 TGTATCGATACA
2521581 CTAATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2521633 original size:52 final size:52
Alignment explanation
Indices: 2521569--2521769 Score: 341
Period size: 52 Copynumber: 3.9 Consensus size: 52
2521559 ATCGATACAT
2521569 TGTATCGATACACTAATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
2521621 TGTATCGATACACTAATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
*
2521673 TGTATCGACACACTAATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
*** *
2521725 TGTATCGATACACT-ATAAAATGTATCGATACATGTAGGCAAATTT
1 TGTATCGATACACTAAT-CTTTGTATCGATACATGCAGGCAAATTT
2521770 TCATATTTCG
Statistics
Matches: 142, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
51 2 0.01
52 140 0.99
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (52 bp):
TGTATCGATACACTAATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:2527356 original size:52 final size:52
Alignment explanation
Indices: 2527272--2527395 Score: 187
Period size: 52 Copynumber: 2.4 Consensus size: 52
2527262 ATATGAAAAG
* * * *
2527272 TTGCTTGCATG-ATCGATACATTTAATAGTGTATCGATACATCTGGGCAGAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAT
*
2527323 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTAGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAT
*
2527375 TTGCCTACATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
2527396 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
51 10 0.15
52 56 0.85
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAT
Found at i:2527408 original size:52 final size:52
Alignment explanation
Indices: 2527279--2527415 Score: 163
Period size: 52 Copynumber: 2.7 Consensus size: 52
2527269 AAGTTGCTTG
* * * *
2527279 CATG-ATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAGATTTGCCTG
1 CATGTATCGATACA-TAAGATAGTGTATCGATACATCTAGGCAAATTTGCCTA
*** *
2527330 CATGTATCGATACATTTTATAATGTATCGATACATCTAGGCAAATTTGCCTA
1 CATGTATCGATACATAAGATAGTGTATCGATACATCTAGGCAAATTTGCCTA
2527382 CATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CATGTATCGATACATAAGAT-AGTGTATCGATACA
2527416 ATGTATCGAT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
51 8 0.11
52 66 0.89
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
CATGTATCGATACATAAGATAGTGTATCGATACATCTAGGCAAATTTGCCTA
Found at i:2527422 original size:13 final size:13
Alignment explanation
Indices: 2527404--2527428 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2527394 CAAAGATCAG
2527404 TGTATCGATACAA
1 TGTATCGATACAA
2527417 TGTATCGATACA
1 TGTATCGATACA
2527429 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2527515 original size:13 final size:13
Alignment explanation
Indices: 2527499--2527523 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2527489 CAAAAAAAAA
2527499 TGTATCGATACAT
1 TGTATCGATACAT
2527512 TGTATCGATACA
1 TGTATCGATACA
2527524 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2528496 original size:20 final size:20
Alignment explanation
Indices: 2528456--2528509 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
2528446 TTCTACAATT
* *
2528456 TGTATCGGTACAATTAGTGAA
1 TGTATCGATAC-ATCAGTGAA
2528477 TGTATCGATACATCAGTGAA
1 TGTATCGATACATCAGTGAA
2528497 TGTATCGATACAT
1 TGTATCGATACAT
2528510 GTCTCAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 21 0.68
21 10 0.32
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATCAGTGAA
Found at i:2533851 original size:2 final size:2
Alignment explanation
Indices: 2533846--2533887 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2533836 TATATATACA
2533846 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2533888 ACGTTAATTA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2533984 original size:2 final size:2
Alignment explanation
Indices: 2533977--2534001 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2533967 TAAATAGCAA
2533977 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 A
2534002 CATTTGAATT
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2535511 original size:2 final size:2
Alignment explanation
Indices: 2535506--2535533 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2535496 TATATATACA
2535506 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2535534 ACGTTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2535630 original size:2 final size:2
Alignment explanation
Indices: 2535623--2535653 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2535613 TAAATAGCAA
2535623 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 A
2535654 CACATTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2537555 original size:20 final size:21
Alignment explanation
Indices: 2537498--2537555 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
2537488 ACATAAGTAA
*
2537498 ATGTATCGATACATTCT-CTT
1 ATGTATCGATACATTTTGCTT
* * *
2537518 ATGTATCAATATAATTTGCTT
1 ATGTATCGATACATTTTGCTT
2537539 -TGTATCGATACATTTTG
1 ATGTATCGATACATTTTG
2537556 GGTTTTTGAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 27 0.90
21 3 0.10
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.47
Consensus pattern (21 bp):
ATGTATCGATACATTTTGCTT
Found at i:2539730 original size:2 final size:2
Alignment explanation
Indices: 2539725--2539755 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2539715 GTTTTTTAGA
2539725 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 A
2539756 ATGCCTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2542799 original size:2 final size:2
Alignment explanation
Indices: 2542794--2542821 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2542784 TATATATACA
2542794 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2542822 ACGTTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2544842 original size:20 final size:21
Alignment explanation
Indices: 2544785--2544842 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
2544775 ACATAAGTAA
*
2544785 ATGTATCGATACATTCT-CTT
1 ATGTATCGATACATTTTGCTT
* * *
2544805 ATGTATTGATATAATTTGCTT
1 ATGTATCGATACATTTTGCTT
2544826 -TGTATCGATACATTTTG
1 ATGTATCGATACATTTTG
2544843 GGTTTTTGAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 27 0.90
21 3 0.10
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (21 bp):
ATGTATCGATACATTTTGCTT
Found at i:2550073 original size:2 final size:2
Alignment explanation
Indices: 2550068--2550097 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2550058 TATATATACA
2550068 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2550098 ACGTTAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2553251 original size:15 final size:17
Alignment explanation
Indices: 2553231--2553262 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2553221 GACCAGGACC
2553231 GCATAA-TATT-ATTTT
1 GCATAATTATTAATTTT
2553246 GCATAATTATTAATTTT
1 GCATAATTATTAATTTT
2553263 ATATATGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (17 bp):
GCATAATTATTAATTTT
Found at i:2555901 original size:21 final size:19
Alignment explanation
Indices: 2555854--2555902 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
2555844 TACAATTTAA
*
2555854 TAGTGTATCAATACCTTGC
1 TAGTGTATCAATACATTGC
*
2555873 TTGTTGTATCAATACAATTGC
1 TAG-TGTATCAATAC-ATTGC
2555894 TAAGTGTAT
1 T-AGTGTAT
2555903 AAATCCAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.08
20 11 0.46
21 10 0.42
22 1 0.04
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (19 bp):
TAGTGTATCAATACATTGC
Found at i:2557502 original size:79 final size:79
Alignment explanation
Indices: 2557284--2557621 Score: 348
Period size: 79 Copynumber: 4.3 Consensus size: 79
2557274 TTGGGATAAC
* * * * *
2557284 AACGGGGCTGGAGTATCTCCGATTATGGAAAATAGGTGTTCT-GAAAATAAAATCGGGGTTGGAG
1 AACGGGGTTGGAGTATCCCCGATTATGGAAAATTGATGTT-TAGAAAATAAAATCGAGGTTGGAG
*
2557348 TATCCCCTCGGAAAT
65 TATCCCCTCGAAAAT
* * * * *
2557363 AACAGGGTT-GAGTATCCCTGATTATAGAAAA-TCAGTGTTTTGAAAATAAAATCGAGGTTGGAG
1 AACGGGGTTGGAGTATCCCCGATTATGGAAAATTGA-TGTTTAGAAAATAAAATCGAGGTTGGAG
2557426 TATCCCCTCGAAAAT
65 TATCCCCTCGAAAAT
* **
2557441 AACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGATGCTTTAG-AAATAAGGTCGAGGTTGGAG
1 AACGGGGTTGGAGTATCCCCGATTATGGAAAATTGATG-TTTAGAAAATAAAATCGAGGTTGGAG
*
2557505 TATCCCCACGAAAAT
65 TATCCCCTCGAAAAT
* * * * * ** * *
2557520 AAAGGGGTTGGAGTATCCCCGATTGTAAGAAATCAAT-AT-TTTAG-AAACAAAGCCGGGGTTGA
1 AACGGGGTTGGAGTATCCCCGATTAT-GGAAA--ATTGATGTTTAGAAAATAAAATCGAGGTTGG
2557582 AGTATCCCCTCGAAAAT
63 AGTATCCCCTCGAAAAT
*
2557599 AACGGGGTTGGAGTATCCTCGAT
1 AACGGGGTTGGAGTATCCCCGAT
2557622 GAAATAACGA
Statistics
Matches: 221, Mismatches: 30, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
77 1 0.00
78 66 0.30
79 140 0.63
80 10 0.05
81 2 0.01
82 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (79 bp):
AACGGGGTTGGAGTATCCCCGATTATGGAAAATTGATGTTTAGAAAATAAAATCGAGGTTGGAGT
ATCCCCTCGAAAAT
Found at i:2557613 original size:28 final size:29
Alignment explanation
Indices: 2557573--2557646 Score: 100
Period size: 28 Copynumber: 2.6 Consensus size: 29
2557563 GAAACAAAGC
*
2557573 CGGGGTTGAAGTATCCCCTCGA-AAATAA
1 CGGGGTTGGAGTATCCCCTCGAGAAATAA
2557601 CGGGGTTGGAGTAT--CCTCGATGAAATAA
1 CGGGGTTGGAGTATCCCCTCGA-GAAATAA
*
2557629 CGAGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
2557647 GATTGTGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
26 6 0.15
28 32 0.80
30 2 0.05
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (29 bp):
CGGGGTTGGAGTATCCCCTCGAGAAATAA
Found at i:2557614 original size:158 final size:157
Alignment explanation
Indices: 2557284--2557621 Score: 407
Period size: 158 Copynumber: 2.1 Consensus size: 157
2557274 TTGGGATAAC
* * * *
2557284 AACGGGGCTGGAGTATCTCCGATTATGGAAAATAGGTGTTCTGAAAATAAAATCGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGGAAAATAGATGTTCTGAAAATAAAATCGAGGTTGGAGT
* * * * * *
2557349 ATCCCCTCGGAAATAACAGGGTTGAGTATCCCTGATTATAGAAAATCAGTGTTTTGAAAATAAAA
66 ATCCCCACGAAAATAACAGGGTTGAGTATCCCCGATTATAGAAAATCAATATTTTGAAAACAAAA
* *
2557414 TCGAGGTTGGAGTATCCCCTCGAAAAT
131 CCGAGGTTGAAGTATCCCCTCGAAAAT
* * **
2557441 AACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGATGCTT-T-AGAAATAAGGTCGAGGTTGGA
1 AACGGGGTTGGAGTATCCCCGATTATGGAAAATAGATG-TTCTGA-AAATAAAATCGAGGTTGGA
*
2557504 GTATCCCCACGAAAATAA-AGGGGTTGGAGTATCCCCGATTGTA-AGAAATCAATATTTT-AGAA
64 GTATCCCCACGAAAATAACA-GGGTT-GAGTATCCCCGATTATAGA-AAATCAATATTTTGA-AA
* *
2557566 ACAAAGCCGGGGTTGAAGTATCCCCTCGAAAAT
125 ACAAAACCGAGGTTGAAGTATCCCCTCGAAAAT
*
2557599 AACGGGGTTGGAGTATCCTCGAT
1 AACGGGGTTGGAGTATCCCCGAT
2557622 GAAATAACGA
Statistics
Matches: 155, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
156 2 0.01
157 73 0.47
158 80 0.52
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (157 bp):
AACGGGGTTGGAGTATCCCCGATTATGGAAAATAGATGTTCTGAAAATAAAATCGAGGTTGGAGT
ATCCCCACGAAAATAACAGGGTTGAGTATCCCCGATTATAGAAAATCAATATTTTGAAAACAAAA
CCGAGGTTGAAGTATCCCCTCGAAAAT
Found at i:2560005 original size:20 final size:20
Alignment explanation
Indices: 2559980--2560054 Score: 132
Period size: 20 Copynumber: 3.8 Consensus size: 20
2559970 GTAAACCTAG
2559980 AATGTATCGATACAATGAAT
1 AATGTATCGATACAATGAAT
2560000 AATGTATCGATACAATGAAT
1 AATGTATCGATACAATGAAT
*
2560020 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAT
*
2560040 AATGTATTGATACAA
1 AATGTATCGATACAA
2560055 ATTGTGAACA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATGAAT
Found at i:2560766 original size:41 final size:41
Alignment explanation
Indices: 2560709--2560816 Score: 137
Period size: 41 Copynumber: 2.6 Consensus size: 41
2560699 GACTAAGGAA
*
2560709 AAAAAGGAAATAAAATGCATCCTGCCCTTTGAAGACAAAGG
1 AAAAAGGAAATTAAATGCATCCTGCCCTTTGAAGACAAAGG
** ** *
2560750 AAAAAGGAAATTAAATGTGTCCTGCTTTTTGAGGACAAAGG
1 AAAAAGGAAATTAAATGCATCCTGCCCTTTGAAGACAAAGG
2560791 AAAAAGGAGAA-TAAAGTGCATCCTGC
1 AAAAAGGA-AATTAAA-TGCATCCTGC
2560817 TATTTGAGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 47 0.82
42 10 0.18
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (41 bp):
AAAAAGGAAATTAAATGCATCCTGCCCTTTGAAGACAAAGG
Found at i:2560766 original size:84 final size:83
Alignment explanation
Indices: 2560644--2560816 Score: 183
Period size: 84 Copynumber: 2.1 Consensus size: 83
2560634 GAAGGGGGCG
* * ** *
2560644 TCCTGCTCTTTGAGGATTAAGGAAAAGGAGAATGAAATGGGTCATG-TTCCTTAG-GGACTAAGG
1 TCCTGCCCTTTGAAGACAAAGGAAAAGGAGAATGAAATGGGTCATGCTT--TTAGAGGACAAAGG
2560707 AAAAAAAGGA-AATAAAATGCA
64 --AAAAAGGAGAATAAAATGCA
* * * *
2560728 TCCTGCCCTTTGAAGACAAAGGAAAAAGGA-AATTAAATGTGTCCTGCTTTTTGAGGACAAAGGA
1 TCCTGCCCTTTGAAGACAAAGG-AAAAGGAGAATGAAATGGGTCATGCTTTTAGAGGACAAAGGA
*
2560792 AAAAGGAGAATAAAGTGCA
65 AAAAGGAGAATAAAATGCA
2560811 TCCTGC
1 TCCTGC
2560817 TATTTGAGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
82 8 0.11
83 19 0.25
84 39 0.52
85 9 0.12
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (83 bp):
TCCTGCCCTTTGAAGACAAAGGAAAAGGAGAATGAAATGGGTCATGCTTTTAGAGGACAAAGGAA
AAAGGAGAATAAAATGCA
Found at i:2560944 original size:80 final size:84
Alignment explanation
Indices: 2560720--2560996 Score: 284
Period size: 80 Copynumber: 3.4 Consensus size: 84
2560710 AAAAGGAAAT
* * * * * *
2560720 AAAATGCATCCTGCCCTTTGAAGAC--AAA-GG-AAA-AAGGAAATTAAATGTGTCCTGCTTTTT
1 AAAAGGCATCCTGCTCTTTGAGGACTAAAAGGGAAAAGAAGGAAATGAAATGCGTCCTGCTCTTT
* *
2560780 GAGGACAAAGGAAAAAGGAGA
66 GAGGACAAAGG--AGAGAAGA
* * * * **
2560801 ATAAAGTGCATCCTGCTATTTGAGAACTAGAAGGGAAAAGAAGGAAATGAAGTGCGTTTTGCTCT
1 A-AAAG-GCATCCTGCTCTTTGAGGACTAAAAGGGAAAAGAAGGAAATGAAATGCGTCCTGCTCT
2560866 TTGAGGACAAAGG-GA-AA-A
64 TTGAGGACAAAGGAGAGAAGA
*
2560884 AAAAGGCATCCTGCTCTTTGAGGA-TAAAAGGGAAAAGAAGGAAATGAAATGTGTCCTGCTCTTT
1 AAAAGGCATCCTGCTCTTTGAGGACTAAAAGGGAAAAGAAGGAAATGAAATGCGTCCTGCTCTTT
*
2560948 GAGGACAAAGGAGAGAAGG
66 GAGGACAAAGGAGAGAAGA
** *
2560967 AAAAGGTGTCCTCCTCTTTGAGGACTAAAA
1 AAAAGGCATCCTGCTCTTTGAGGACTAAAA
2560997 AGTGCCATCA
Statistics
Matches: 160, Mismatches: 25, Indels: 19
0.78 0.12 0.09
Matches are distributed among these distances:
80 46 0.29
81 20 0.12
82 9 0.06
83 39 0.24
84 6 0.04
85 3 0.02
86 2 0.01
87 3 0.02
88 32 0.20
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (84 bp):
AAAAGGCATCCTGCTCTTTGAGGACTAAAAGGGAAAAGAAGGAAATGAAATGCGTCCTGCTCTTT
GAGGACAAAGGAGAGAAGA
Found at i:2561229 original size:62 final size:62
Alignment explanation
Indices: 2560963--2561732 Score: 948
Period size: 61 Copynumber: 12.6 Consensus size: 62
2560953 CAAAGGAGAG
* * * * *
2560963 AAGGAAAAGGTGTCCTCCTCTTTGAGGACTA-AAAAGTGCCATCAACTCGTGTGAGCTTTGAA
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT-AA
* * * *
2561025 AA-GAAAAGGTGTCCTGCTCTTTGAGGACT-GGAAGGTGCCACCAACTTGTGTGGGCTTTGCA
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT-AA
* * * **
2561086 AA-GAGAAA-GCATCCTGCTCTTTGAGGACT-GGAAGGTGCCACCAACTTGTGTGATCTTTAA
1 AAGGA-AAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
* * * *
2561146 AAGGAGAAA-GCATCCTGCTCTTTGAGGACTGGAAAAGTTCCACCAACTTGTATGGGCTTTAA
1 AAGGA-AAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
* * * *
2561208 AAGGAAAAGGTGTCCTACTCTTTAAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAA
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
* * * *
2561269 AAGGAAAAGACGTCATGCTCTTTAAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAA
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
* * * * * *
2561330 AAAGAAAAGGCGTTCTACTCTTTGAAGACTAAAAAAAAGTGCCACCAACTTGTATGGGCTTTAA
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACT--AGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
*
2561394 AAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAATGCCACCAACTTGTGTGGGCTTT--
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
* * * *
2561453 ---G-AAAGGCGTCATGCTCTTTGAGGACTAG-AAGGTGCCACCAATTTGTGTGGGCTCTAA
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
* *
2561510 AAGGAAAAGGCATCCTGCTCCTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAA
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
* * *
2561571 AAGGAAAAGGCGTCTTGCTTTTTGAGGACTAGAAAAGTGCTACCAACTTGTGTGGGCTTTAA
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
* * *
2561633 AAGGAAAAGGCGTCCTGCTTTTTGAGGACTAGAAAAATGCCACCAACTTGTGCGGGCTTTAA
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
2561695 AAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTG
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTG
2561733 AAAGGAGAAA
Statistics
Matches: 622, Mismatches: 69, Indels: 35
0.86 0.10 0.05
Matches are distributed among these distances:
55 47 0.08
56 2 0.00
60 5 0.01
61 344 0.55
62 170 0.27
63 1 0.00
64 53 0.09
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (62 bp):
AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
Found at i:2567027 original size:19 final size:19
Alignment explanation
Indices: 2567003--2567052 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
2566993 AAACAGTAAA
2567003 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
*
2567022 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
2567041 TGTATCGATACA
1 TGTATCGATACA
2567053 ATGTATCGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:2567111 original size:20 final size:20
Alignment explanation
Indices: 2567086--2567136 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
2567076 CAAGGAAATA
2567086 TATCGATACATT-ACTCAATG
1 TATCGATACATTGA-TCAATG
**
2567106 TATCGATACATTGATCTTTG
1 TATCGATACATTGATCAATG
2567126 TATCGATACAT
1 TATCGATACAT
2567137 CTGGGAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (20 bp):
TATCGATACATTGATCAATG
Found at i:2581082 original size:6 final size:6
Alignment explanation
Indices: 2581067--2581182 Score: 103
Period size: 6 Copynumber: 18.7 Consensus size: 6
2581057 CGTCCTCTAC
*
2581067 AAAA-A AAAACA AAAACA AAACAAA ACAAACA AAAA-A AAAACAA AAAACAAA
1 AAAACA AAAACA AAAACA AAA-ACA A-AAACA AAAACA AAAAC-A AAAAC--A
* *
2581118 AAAACA AAAA-A AAAAAA AAAACAAA AAAACA AAAAAA AAAACA AAAACA
1 AAAACA AAAACA AAAACA AAAAC--A AAAACA AAAACA AAAACA AAAACA
* *
2581167 ACAACA ACAACA AAAA
1 AAAACA AAAACA AAAA
2581183 GGGTCCAGAT
Statistics
Matches: 95, Mismatches: 7, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
5 14 0.15
6 54 0.57
7 12 0.13
8 15 0.16
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:2581106 original size:25 final size:26
Alignment explanation
Indices: 2581065--2581182 Score: 145
Period size: 26 Copynumber: 4.5 Consensus size: 26
2581055 TGCGTCCTCT
*
2581065 ACAAAAAAAAACAAAAAC-AAAACAAA
1 ACAAACAAAAA-AAAAACAAAAACAAA
2581091 ACAAACAAAAAAAAAACAAAAAACAAA
1 ACAAACAAAAAAAAAAC-AAAAACAAA
*
2581118 A-AAACAAAAAAAAAAAAAAAACAAA
1 ACAAACAAAAAAAAAACAAAAACAAA
2581143 A-AAACAAAAAAAAAAACAAAAACAACA
1 ACAAAC-AAAAAAAAAACAAAAACAA-A
*
2581170 AC-AACAACAAAAA
1 ACAAACAAAAAAAA
2581183 GGGTCCAGAT
Statistics
Matches: 83, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
25 20 0.24
26 49 0.59
27 14 0.17
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (26 bp):
ACAAACAAAAAAAAAACAAAAACAAA
Found at i:2581113 original size:32 final size:29
Alignment explanation
Indices: 2581067--2581182 Score: 133
Period size: 32 Copynumber: 3.7 Consensus size: 29
2581057 CGTCCTCTAC
2581067 AAAAAAAAACAAAAACAAAACAAAACAAACA
1 AAAAAAAAACAAAAACAAAA-AAAA-AAACA
*
2581098 AAAAAAAAACAAAAAACAAAAAAACAAAAAAA
1 AAAAAAAAAC-AAAAAC-AAAAAA-AAAAACA
2581130 AAAAAAAAACAAAAAAACAAAAAAAAAAACA
1 AAAAAAAAAC--AAAAACAAAAAAAAAAACA
* *
2581161 AAAACAACAACAACAACAAAAA
1 AAAA-AAAAACAAAAACAAAAA
2581183 GGGTCCAGAT
Statistics
Matches: 76, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
30 10 0.13
31 20 0.26
32 33 0.43
33 13 0.17
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (29 bp):
AAAAAAAAACAAAAACAAAAAAAAAAACA
Found at i:2581182 original size:1 final size:1
Alignment explanation
Indices: 2581067--2581164 Score: 97
Period size: 1 Copynumber: 98.0 Consensus size: 1
2581057 CGTCCTCTAC
* * * * * * * *
2581067 AAAAAAAAACAAAAACAAAACAAAACAAACAAAAAAAAAACAAAAAACAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
2581132 AAAAAAACAAAAAAACAAAAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2581165 CAACAACAAC
Statistics
Matches: 75, Mismatches: 22, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 75 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2582656 original size:28 final size:28
Alignment explanation
Indices: 2582616--2582828 Score: 293
Period size: 28 Copynumber: 7.6 Consensus size: 28
2582606 CATTCCTCAC
2582616 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
1 CTTTT-CAAAGCCCACAAGTCAGTGGCAT
* * *
2582645 TTTTTCCAAGCCCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
2582673 CTTTTCAAAACCCACAAGTCGGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
2582701 CTTTTCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* * * *
2582729 CTTTTCCAAGCCCATAAGTCAATGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
2582757 CTTTTCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
2582785 CTTTTCAAAGCCTACAAGTCAGTGGCAA
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
2582813 C-CTTCAAAACCCACAA
1 CTTTTCAAAGCCCACAA
2582829 AATAGTGGCA
Statistics
Matches: 161, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
27 12 0.07
28 145 0.90
29 4 0.02
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.24
Consensus pattern (28 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCAT
Found at i:2582700 original size:56 final size:56
Alignment explanation
Indices: 2582613--2582858 Score: 291
Period size: 56 Copynumber: 4.4 Consensus size: 56
2582603 AGACATTCCT
* *
2582613 CACCTTTTCCAAAGCCCACAAGTCAGTGGCATTTTTTCCAAGCCCACAAGTCAGTGG
1 CACCTTTT-CAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGG
* *
2582670 CACCTTTTCAAAACCCACAAGTCGGTGGCATCTTTTCAAAGCCCACAAGTCAGTGG
1 CACCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGG
* * * * *
2582726 CATCTTTTCCAAGCCCATAAGTCAATGGCACCTTTTCAAAGCCCACAAGTCAGTGG
1 CACCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGG
* * * * * *
2582782 CATCTTTTCAAAGCCTACAAGTCAGTGGCAAC-CTTCAAAACCCACAAAAT-AGTGG
1 CACCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCAC-AAGTCAGTGG
* *
2582837 CAACC-TTTAAAAGCACACAAGT
1 C-ACCTTTTCAAAGCCCACAAGT
2582859 TGGTGCAACC
Statistics
Matches: 164, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
55 31 0.19
56 125 0.76
57 8 0.05
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (56 bp):
CACCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGG
Found at i:2582724 original size:84 final size:84
Alignment explanation
Indices: 2582616--2582811 Score: 329
Period size: 84 Copynumber: 2.3 Consensus size: 84
2582606 CATTCCTCAC
* *
2582616 CTTTTCCAAAGCCCACAAGTCAGTGGCATTTTTTCCAAGCCCACAAGTCAGTGGCACCTTTTCAA
1 CTTTT-CAAAGCCCACAAGTCAGTGGCATCTTTTCCAAGCCCACAAGTCAATGGCACCTTTTCAA
*
2582681 AACCCACAAGTCGGTGGCAT
65 AACCCACAAGTCAGTGGCAT
*
2582701 CTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAGCCCATAAGTCAATGGCACCTTTTCAAA
1 CTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAGCCCACAAGTCAATGGCACCTTTTCAAA
*
2582766 GCCCACAAGTCAGTGGCAT
66 ACCCACAAGTCAGTGGCAT
*
2582785 CTTTTCAAAGCCTACAAGTCAGTGGCA
1 CTTTTCAAAGCCCACAAGTCAGTGGCA
2582812 ACCTTCAAAA
Statistics
Matches: 105, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
84 100 0.95
85 5 0.05
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (84 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAGCCCACAAGTCAATGGCACCTTTTCAAA
ACCCACAAGTCAGTGGCAT
Found at i:2582850 original size:55 final size:57
Alignment explanation
Indices: 2582759--2582884 Score: 127
Period size: 55 Copynumber: 2.2 Consensus size: 57
2582749 AATGGCACCT
* * * * *
2582759 TTTCAAAGCCCAC-AAGTCAGTGGCATCTTTTCAAAGC-CTACAAGTCAGTGGCAA-CC
1 TTTCAAAACCCACAAAATCAGTGGCAACCTTTAAAAGCAC-ACAAGTCAGT-GCAACCC
**
2582815 -TTCAAAACCCACAAAAT-AGTGGCAACCTTTAAAAGCACACAAGTTGGTGCAACCC
1 TTTCAAAACCCACAAAATCAGTGGCAACCTTTAAAAGCACACAAGTCAGTGCAACCC
2582870 TTTCAAAATCCCACA
1 TTTCAAAA-CCCACA
2582885 CAAGTTGGTG
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
54 4 0.07
55 37 0.64
56 11 0.19
57 6 0.10
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (57 bp):
TTTCAAAACCCACAAAATCAGTGGCAACCTTTAAAAGCACACAAGTCAGTGCAACCC
Found at i:2582884 original size:29 final size:29
Alignment explanation
Indices: 2582836--2582894 Score: 68
Period size: 31 Copynumber: 2.0 Consensus size: 29
2582826 CAAAATAGTG
2582836 GCAACCTTTAAAAG-C-ACACAAGTTGGT
1 GCAACCTTTAAAAGCCAACACAAGTTGGT
* *
2582863 GCAACCCTTTCAAAATCCCACACAAGTTGGT
1 GCAA-CCTTT-AAAAGCCAACACAAGTTGGT
2582894 G
1 G
2582895 GCATCTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 4 0.15
28 5 0.19
29 4 0.15
30 1 0.04
31 13 0.48
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (29 bp):
GCAACCTTTAAAAGCCAACACAAGTTGGT
Found at i:2582963 original size:49 final size:49
Alignment explanation
Indices: 2582906--2583244 Score: 327
Period size: 49 Copynumber: 6.8 Consensus size: 49
2582896 CATCTTCTTC
*
2582906 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
* * *
2582955 TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCACCCT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
* * *
2583004 TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
* * * * * * *
2583053 TAAGTCCCATATCGCTGGCCTTGAATCATCATATTAGCGCCTTCGTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--C-TCACCTT
** * * * * *
2583105 TAAAACCAATGTCGATGGCCTTGAATCAGCATATTGCCACTCTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
* * * * * ** * *
2583154 TAAGTCCGATATCGTTGGCCTCGAATCAGCATATTGGCATCTTTAACATT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCCTCACCTT
* **
2583204 CCTAAGCCCAATGTCGCTGGCCTTGTCTCAGCACATTGGCA
1 --TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
2583245 TTCTTCATCA
Statistics
Matches: 241, Mismatches: 43, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
49 165 0.68
50 7 0.03
52 69 0.29
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (49 bp):
TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
Found at i:2583075 original size:98 final size:98
Alignment explanation
Indices: 2582906--2583289 Score: 373
Period size: 101 Copynumber: 3.9 Consensus size: 98
2582896 CATCTTCTTC
* * * * *
2582906 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTTTAAGTCCAATGTTGCT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCT
* *
2582971 GGCCTTGAATCAGCACATTGGCACCTTCACCCT
66 GGCCTTGAATCAGCATATTGGCACCTTCATCCT
* *
2583004 TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCCATATCGCT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCT
* * * *
2583069 GGCCTTGAATCATCATATTAGCGCCTTCGTCATCTT
66 GGCCTTGAATCAGCATATTGGCACC-T--TCATCCT
** * * * * *
2583105 TAAAACCAATGTCGATGGCCTTGAATCAGCATATTGCCA-CTCTCATCTTTAAGTCCGATATCGT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT-TCATCTTTAAGTCCAATATCGC
* *
2583169 TGGCCTCGAATCAGCATATTGGCATCTTTAACATTCC-
65 TGGCCTTGAATCAGCATATTGGCA-CCTT--CA-TCCT
* ** * * *
2583206 TAAGCCCAATGTCGCTGGCCTTGTCTCAGCACATTGGCATTCTTCATC---AAGTCTAAATGTCG
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTTCATCTTTAAGTC-CAATATCG
**
2583268 CTGGCCAGGAATCAGCATATTG
64 CTGGCCTTGAATCAGCATATTG
2583290 TCATTCTTCG
Statistics
Matches: 235, Mismatches: 40, Indels: 20
0.80 0.14 0.07
Matches are distributed among these distances:
98 79 0.34
99 7 0.03
100 26 0.11
101 113 0.48
102 8 0.03
103 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (98 bp):
TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCT
GGCCTTGAATCAGCATATTGGCACCTTCATCCT
Found at i:2584062 original size:19 final size:19
Alignment explanation
Indices: 2584034--2584083 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
2584024 AAACAGTAAA
*
2584034 TGTATTGATACATAAGTGT-
1 TGTATCGATACATAAGT-TC
2584053 TGTATCGATACATAAGTTC
1 TGTATCGATACATAAGTTC
2584072 TGTATCGATACA
1 TGTATCGATACA
2584084 ATGTATCGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 1 0.03
19 28 0.97
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATAAGTTC
Found at i:2584754 original size:53 final size:50
Alignment explanation
Indices: 2584641--2585258 Score: 488
Period size: 43 Copynumber: 12.7 Consensus size: 50
2584631 GATGTTAATG
* * * * * * * * *
2584641 TGCTAATTCACGGTCAGCGACATTAGACTTGAAGATGAGAAGAATGGCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGA-AAG-GTGCCAATA
* * ** *
2584693 TGCTGATTCAAGGCCAACAACATTGGGTTTTAAAAATGATGAAGGCGCCAATA
1 TGCTGATTCAAGGCCAGCGACATT-GGACTTAAAAATGA--AAGGTGCCAATA
* * * *
2584746 TGCTGATTCAAGGCCAGCGATACTGGACTTAAAAAT-AAAGGTGACAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGAAAGGTGCCAATA
*
2584795 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGATGACAAAGGTACCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAA-ATG--AAAGGTGCCAATA
* *
2584848 TGCTGATTCAAGGCCAGCGATATTGGAC-T-----T-AAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGAAAGGTGCCAATA
* * *
2584891 TGCTGATTCAAGGCCAGTGACATTGGGCTTAAAAGATGACAAAGGCGCCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAA-ATG--AAAGGTGCCAATA
* * *
2584944 TGCTGATTCAATGCCAGCGATATTGGAC-T-----T-AAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGAAAGGTGCCAATA
* * *
2584987 TGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATAACAAAGGCGCCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAA-AT--GAAAGGTGCCAATA
* *
2585040 TGCTGATTCAAGGCCAGCGATATTGGAC-T-----T-AAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGAAAGGTGCCAATA
* *
2585083 TGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGAT-AAGGGTGCCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAA-ATGAAAGGTGCCAATA
* * *
2585133 TGCTGATTCAAGGCCAGCGATATTGGAC-T-----TG-GAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGAAAGGTGCCAATA
* * * * *
2585176 TGCTAATTCAAGGCCAGCTACATTGGACTTAAAGATG-ATGATGCCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGAAAGGTGCCAATA
* *
2585225 TGCTGATTCAAGGCCAGCGATATTGGGCTTAAAA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAA
2585259 GAAGATGCCA
Statistics
Matches: 454, Mismatches: 72, Indels: 83
0.75 0.12 0.14
Matches are distributed among these distances:
43 144 0.32
44 4 0.01
46 3 0.01
49 81 0.18
50 42 0.09
51 1 0.00
52 32 0.07
53 143 0.31
54 4 0.01
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.24
Consensus pattern (50 bp):
TGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGAAAGGTGCCAATA
Found at i:2584922 original size:96 final size:96
Alignment explanation
Indices: 2584688--2585257 Score: 805
Period size: 96 Copynumber: 5.9 Consensus size: 96
2584678 AGAAGAATGG
* * * **
2584688 CAATGTGCTGATTCAAGGCCAACAACATTGGGTTTTAAAA-ATGATGAAGGCGCCAATATGCTGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGG-CTTAAAAGATGACAAAGGCGCCAATATGCTGA
* *
2584752 TTCAAGGCCAGCGATACTGGACTTAAAAATAAAGGTGA
65 TTCAAGGCCAGCGATATTGGAC-T-----TAAAGGTGC
* **
2584790 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGATGACAAAGGTACCAATATGCTGAT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATGACAAAGGCGCCAATATGCTGAT
2584855 TCAAGGCCAGCGATATTGGACTTAAAGGTGC
66 TCAAGGCCAGCGATATTGGACTTAAAGGTGC
*
2584886 CAATGTGCTGATTCAAGGCCAGTGACATTGGGCTTAAAAGATGACAAAGGCGCCAATATGCTGAT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATGACAAAGGCGCCAATATGCTGAT
*
2584951 TCAATGCCAGCGATATTGGACTTAAAGGTGC
66 TCAAGGCCAGCGATATTGGACTTAAAGGTGC
*
2584982 CAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATAACAAAGGCGCCAATATGCTGAT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATGACAAAGGCGCCAATATGCTGAT
2585047 TCAAGGCCAGCGATATTGGACTTAAAGGTGC
66 TCAAGGCCAGCGATATTGGACTTAAAGGTGC
* *
2585078 CAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGAT---AAGGGTGCCAATATGCTGAT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATGACAAAGGCGCCAATATGCTGAT
**
2585140 TCAAGGCCAGCGATATTGGACTTGGAGGTGC
66 TCAAGGCCAGCGATATTGGACTTAAAGGTGC
* * * * **
2585171 CAATGTGCTAATTCAAGGCCAGCTACATTGGACTT-AAAGATG---ATGATGCCAATATGCTGAT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATGACAAAGGCGCCAATATGCTGAT
*
2585232 TCAAGGCCAGCGATATTGGGCTTAAA
66 TCAAGGCCAGCGATATTGGACTTAAA
2585258 AGAAGATGCC
Statistics
Matches: 436, Mismatches: 30, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
92 46 0.11
93 79 0.18
96 234 0.54
101 7 0.02
102 70 0.16
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (96 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATGACAAAGGCGCCAATATGCTGAT
TCAAGGCCAGCGATATTGGACTTAAAGGTGC
Found at i:2585303 original size:33 final size:32
Alignment explanation
Indices: 2585264--2585456 Score: 230
Period size: 32 Copynumber: 6.0 Consensus size: 32
2585254 TAAAAGAAGA
*
2585264 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGT
1 TGCCACCGACTTGTGTGGGC-TTTGAAGAAGGT
* *
2585297 TGCCACCGACTTGTGTGGGCTTT-AGAGGAGAT
1 TGCCACCGACTTGTGTGGGCTTTGA-AGAAGGT
* * * *
2585329 TGCTACCAACTTGTGTGGGCTTTAGAAAAAGTT
1 TGCCACCGACTTGTGTGGGCTTT-GAAGAAGGT
*
2585362 TACCACCGACTTGTGTGGGCTTTGAA-AAGGAT
1 TGCCACCGACTTGTGTGGGCTTTGAAGAAGG-T
*
2585394 TGCCACTGACTTGTGTGGGCTTTGAA-AAGGAT
1 TGCCACCGACTTGTGTGGGCTTTGAAGAAGG-T
*
2585426 TGCCATCGACTTGTGTGGGCTTTGAAGAAGG
1 TGCCACCGACTTGTGTGGGCTTTGAAGAAGG
2585457 GAAAGGTGCC
Statistics
Matches: 139, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
31 4 0.03
32 87 0.63
33 47 0.34
34 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (32 bp):
TGCCACCGACTTGTGTGGGCTTTGAAGAAGGT
Found at i:2585351 original size:65 final size:64
Alignment explanation
Indices: 2585264--2585456 Score: 246
Period size: 65 Copynumber: 3.0 Consensus size: 64
2585254 TAAAAGAAGA
* *
2585264 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTT-AGAGGAGA
1 TGCCACCAACTTGTGTGGGCTTTTGAA-AAGGTTGCCACCGACTTGTGTGGGCTTTGAAAAG-GA
2585328 T
64 T
* * * *
2585329 TGCTACCAACTTGTGTGGGCTTTAGAAAAAGTTTACCACCGACTTGTGTGGGCTTTGAAAAGGAT
1 TGCCACCAACTTGTGTGGGCTTTTG-AAAAGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGAT
** *
2585394 TGCCACTGACTTGTGTGGGC-TTTGAAAAGGATTGCCATCGACTTGTGTGGGCTTTGAAGAAGG
1 TGCCACCAACTTGTGTGGGCTTTTGAAAAGG-TTGCCACCGACTTGTGTGGGCTTTGAA-AAGG
2585457 GAAAGGTGCC
Statistics
Matches: 111, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
63 5 0.05
64 28 0.25
65 73 0.66
66 5 0.05
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (64 bp):
TGCCACCAACTTGTGTGGGCTTTTGAAAAGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGAT
Found at i:2585438 original size:97 final size:98
Alignment explanation
Indices: 2585266--2585448 Score: 264
Period size: 97 Copynumber: 1.9 Consensus size: 98
2585256 AAAGAAGATG
* *
2585266 CCACCAACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAGGAGATTG
1 CCACCAACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAAAAGAGATTG
*
2585331 CTACCAACTTGTGTGGGCTTTAGAAAAAGTTTA
66 CCACCAACTTGTGTGGGCTTTAGAAAAAGTTTA
* *
2585364 CCACCGACTTGTGTGGGC-TTTGAA-AAGGATTGCCACTGACTTGTGTGGGCTTTGAAAAG-GAT
1 CCACCAACTTGTGTGGGCTTTTGAAGAAGG-TTGCCACCGACTTGTGTGGGCTTT-AAAAGAGAT
* *
2585426 TGCCATCGACTTGTGTGGGCTTT
64 TGCCACCAACTTGTGTGGGCTTT
2585449 GAAGAAGGGA
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
96 4 0.05
97 52 0.68
98 20 0.26
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (98 bp):
CCACCAACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAAAAGAGATTG
CCACCAACTTGTGTGGGCTTTAGAAAAAGTTTA
Found at i:2585505 original size:34 final size:33
Alignment explanation
Indices: 2585458--2585760 Score: 245
Period size: 34 Copynumber: 9.3 Consensus size: 33
2585448 TGAAGAAGGG
2585458 AAAGGTGCCACAGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACAGAGTTGTGGGC-TTAAAAAGAA
* * * *
2585492 AAATGTGCCACAGAGTTGTGGACTTAGAAGGAA
1 AAAGGTGCCACAGAGTTGTGGGCTTAAAAAGAA
*
2585525 AAAGAGTGTCACAGAGTTGTGGGCTT-AAAAG--
1 AAAG-GTGCCACAGAGTTGTGGGCTTAAAAAGAA
* * * *
2585556 ---GGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGGTGCCACAGAGTTGTGGGCTTAAAAAGAA
* *
2585586 AAAGAATGCCACGGAGTTGTGGGCTT-AAAAG--
1 AAAG-GTGCCACAGAGTTGTGGGCTTAAAAAGAA
* * * * *
2585617 ---GGTGCCACGGAGTTATGGACTTAGAAGGAA
1 AAAGGTGCCACAGAGTTGTGGGCTTAAAAAGAA
*
2585647 AAAGAATGCCACAGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACAGAGTTGTGGGC-TTAAAAAGAA
* * * *
2585682 AAAGGTGCCATAGAGTTGTGGACTTAGAAGGAA
1 AAAGGTGCCACAGAGTTGTGGGCTTAAAAAGAA
*
2585715 AAAGAGTGCCA-TGAAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACAG-AGTTGTGGGC-TTAAAAAGAA
2585750 AAAGGTGCCAC
1 AAAGGTGCCAC
2585761 TAAGTCGTGG
Statistics
Matches: 211, Mismatches: 38, Indels: 39
0.73 0.13 0.14
Matches are distributed among these distances:
27 36 0.17
28 8 0.04
33 32 0.15
34 111 0.53
35 24 0.11
ACGTcount: A:0.36, C:0.12, G:0.32, T:0.20
Consensus pattern (33 bp):
AAAGGTGCCACAGAGTTGTGGGCTTAAAAAGAA
Found at i:2585548 original size:68 final size:68
Alignment explanation
Indices: 2585458--2585814 Score: 403
Period size: 61 Copynumber: 5.5 Consensus size: 68
2585448 TGAAGAAGGG
*
2585458 AAAG-GTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAATGTGCCACAGAGTTGTGGACTTAGAAG
1 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAGAAG
2585522 GAA
66 GAA
* *
2585525 AAAGAGTGTCACAGAGTTGTGGGC-TT-AAAAG-----GGTGCCACGGAGTTGTGGACTTAGAAG
1 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAGAAG
2585583 GAA
66 GAA
* * * *
2585586 AAAGAATGCCACGGAGTTGTGGGC-TT-AAAAG-----GGTGCCACGGAGTTATGGACTTAGAAG
1 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAGAAG
2585644 GAA
66 GAA
* *
2585647 AAAGAATGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCATAGAGTTGTGGACTTAGAAG
1 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAGAAG
2585712 GAA
66 GAA
* * *
2585715 AAAGAGTGCCA-TGAAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACTA-AGTCGTGGACTTTG-
1 AAAGAGTGCCACAG-AGTTGTGGGCTTTAAAAAGAAAAAGGTGCCAC-AGAGTTGTGGACTTAGA
2585777 A-GACA
64 AGGA-A
* * * *
2585782 AAA-AATGCCACTGAGTCGTGGACTTTAAAAAGA
1 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGA
2585815 GATTGCCACT
Statistics
Matches: 259, Mismatches: 19, Indels: 25
0.85 0.06 0.08
Matches are distributed among these distances:
61 108 0.42
62 2 0.01
63 5 0.02
66 31 0.12
67 14 0.05
68 98 0.38
69 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.21
Consensus pattern (68 bp):
AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAGAAG
GAA
Found at i:2585568 original size:27 final size:27
Alignment explanation
Indices: 2585524--2585644 Score: 107
Period size: 27 Copynumber: 4.2 Consensus size: 27
2585514 CTTAGAAGGA
* * * *
2585524 AAAAGAGTGTCACAGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
2585551 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
2585578 AGAAGGAAAAAGAATGCCACGGAGTTGTGGGCTT
1 AAAAGG-----G--TGCCACGGAGTTGTGGACTT
*
2585612 AAAAGGGTGCCACGGAGTTATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
2585639 AGAAGG
1 AAAAGG
2585645 AAAAAGAATG
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
27 51 0.66
29 1 0.01
32 1 0.01
34 24 0.31
ACGTcount: A:0.31, C:0.12, G:0.36, T:0.21
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGACTT
Found at i:2585786 original size:34 final size:32
Alignment explanation
Indices: 2585665--2585838 Score: 104
Period size: 34 Copynumber: 5.3 Consensus size: 32
2585655 CCACAGAGTT
* * *
2585665 GTGGGCTTTAAAAAGAAAAAGGTGCCATAGAGTT
1 GTGGACTTTGAAAA-AAAAAGGTGCCATA-AGTC
* ** *
2585699 GTGGACTTAGAAGGAAAAAGAGTGCCATGAAGTT
1 GTGGACTTTGAAAAAAAAAG-GTGCCAT-AAGTC
* *
2585733 GTGGGCTTTAAAAAGAAAAAGGTGCCACTAAGTC
1 GTGGACTTTGAAAA-AAAAAGGTGCCA-TAAGTC
* *
2585767 GTGGACTTTGAGACAAAAAA--TGCCACTGAGTC
1 GTGGACTTTGA-AAAAAAAAGGTGCCA-TAAGTC
* * * *
2585799 GTGGACTTT-AAAAAGAGA-TTGCCACTGAGTC
1 GTGGACTTTGAAAAAAAAAGGTGCCA-TAAGTC
2585830 GTGGACTTT
1 GTGGACTTT
2585839 AAGAAGGTAT
Statistics
Matches: 116, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
30 5 0.04
31 22 0.19
32 20 0.17
33 6 0.05
34 53 0.46
35 10 0.09
ACGTcount: A:0.35, C:0.13, G:0.28, T:0.24
Consensus pattern (32 bp):
GTGGACTTTGAAAAAAAAAGGTGCCATAAGTC
Found at i:2585793 original size:32 final size:31
Alignment explanation
Indices: 2585713--2585840 Score: 113
Period size: 31 Copynumber: 4.1 Consensus size: 31
2585703 ACTTAGAAGG
* *
2585713 AAAAAGAG--TGCCA-TGAAGTTGTGGGCTTT
1 AAAAAGAGAATGCCACTG-AGTCGTGGACTTT
* *
2585742 AAAAAGAAAAAGGTGCCACTAAGTCGTGGACTTT
1 AAAAAG-AGAA--TGCCACTGAGTCGTGGACTTT
2585776 GAGACAAA-A-AATGCCACTGAGTCGTGGACTTT
1 -A-A-AAAGAGAATGCCACTGAGTCGTGGACTTT
*
2585808 AAAAAGAGATTGCCACTGAGTCGTGGACTTT
1 AAAAAGAGAATGCCACTGAGTCGTGGACTTT
2585839 AA
1 AA
2585841 GAAGGTATTT
Statistics
Matches: 82, Mismatches: 6, Indels: 20
0.76 0.06 0.19
Matches are distributed among these distances:
29 9 0.11
30 3 0.04
31 25 0.30
32 20 0.24
34 18 0.22
35 3 0.04
36 1 0.01
37 3 0.04
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (31 bp):
AAAAAGAGAATGCCACTGAGTCGTGGACTTT
Found at i:2594139 original size:52 final size:52
Alignment explanation
Indices: 2594058--2594186 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
2594048 CGAAATATGA
*
2594058 AAATTTGCCTGCATGTATCGATACATTTCATGGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
2594110 AAATTTGCCTGTATGTATCGATACGTTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
2594162 AAATTTACCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
2594187 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:2594197 original size:52 final size:50
Alignment explanation
Indices: 2594058--2594206 Score: 174
Period size: 52 Copynumber: 2.9 Consensus size: 50
2594048 CGAAATATGA
**
2594058 AAATTTGCCTGCATGTATCGATACATTTCATGGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACACATCA--GTGTATCGATACATCTGGGC
* *
2594110 AAATTTGCCTGTATGTATCGATACGTTTCAT-AGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATAC---ACATCAGTGTATCGATACATCTGGGC
* *
2594162 AAATTTACCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATAC--ACATCAGTGTATCGATACA
2594207 ATATATCGAT
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
51 2 0.02
52 79 0.95
54 1 0.01
55 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (50 bp):
AAATTTGCCTGCATGTATCGATACACATCAGTGTATCGATACATCTGGGC
Found at i:2594296 original size:19 final size:18
Alignment explanation
Indices: 2594272--2594333 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
2594262 AGTGATACAT
2594272 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
2594291 TGTATCGAT----AC--A
1 TGTATCGATACAAACTTA
2594303 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
2594322 TGTATCGATACA
1 TGTATCGATACA
2594334 TTGTATCAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
12 10 0.28
14 2 0.06
17 2 0.06
19 22 0.61
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:2594307 original size:12 final size:12
Alignment explanation
Indices: 2594290--2594314 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2594280 TACAAAACTT
2594290 ATGTATCGATAC
1 ATGTATCGATAC
2594302 ATGTATCGATAC
1 ATGTATCGATAC
2594314 A
1 A
2594315 ACACTTATGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:2594309 original size:31 final size:32
Alignment explanation
Indices: 2594265--2594348 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 32
2594255 GCTTCGTAGT
2594265 GATACATTGTATCGATACAAAACTTATGTATC
1 GATACATTGTATCGATACAAAACTTATGTATC
*
2594297 GATACA-TGTATCGATACAACACTTATGTATC
1 GATACATTGTATCGATACAAAACTTATGTATC
*
2594328 GATACATTGTATCAATACAAA
1 GATACATTGTATCGATACAAA
2594349 CCGTTGAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
31 30 0.62
32 18 0.38
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (32 bp):
GATACATTGTATCGATACAAAACTTATGTATC
Found at i:2598723 original size:4 final size:4
Alignment explanation
Indices: 2598714--2598738 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2598704 AAAATAAAAC
2598714 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
2598739 CCTCAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2600557 original size:28 final size:28
Alignment explanation
Indices: 2600517--2600593 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 28
2600507 GAAACAAAGC
* *
2600517 CGGGGTTGAAGTATCCCC-TTGGAAATAA
1 CGGGGTTGGAGTATCCCCGAT-GAAATAA
2600545 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
2600573 CGAGGTTGGAATATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2600594 TGTGAAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 43 0.98
29 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2604914 original size:17 final size:18
Alignment explanation
Indices: 2604886--2604975 Score: 60
Period size: 17 Copynumber: 4.9 Consensus size: 18
2604876 TTATTATCCC
* *
2604886 TTTATTTTTTTAATTTTA
1 TTTATATTTTTAATATTA
2604904 TTTA-ATTTTTAA-ATTA
1 TTTATATTTTTAATATTA
* *
2604920 TTTATATCTTTAATAATA
1 TTTATATTTTTAATATTA
**
2604938 TGAATATCATTTTAATATATA
1 TTTATAT--TTTTAATAT-TA
*
2604959 TTT-TATTATTTATTATT
1 TTTATATT-TTTAATATT
2604976 TGTATAAATA
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
16 7 0.13
17 14 0.25
18 14 0.25
19 7 0.13
20 10 0.18
21 3 0.05
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (18 bp):
TTTATATTTTTAATATTA
Found at i:2605004 original size:10 final size:11
Alignment explanation
Indices: 2604961--2605014 Score: 51
Period size: 10 Copynumber: 5.0 Consensus size: 11
2604951 AATATATATT
2604961 TTATTATTT-A
1 TTATTATTTAA
2604971 TTATT-TGTATAA
1 TTATTAT-T-TAA
* *
2604983 ATATAATTTAA
1 TTATTATTTAA
2604994 TTATT-TTTAA
1 TTATTATTTAA
2605004 TTATTATTTAA
1 TTATTATTTAA
2605015 AAAAATATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
9 1 0.03
10 16 0.46
11 12 0.34
12 5 0.14
13 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (11 bp):
TTATTATTTAA
Found at i:2606752 original size:79 final size:78
Alignment explanation
Indices: 2606529--2606756 Score: 237
Period size: 79 Copynumber: 2.9 Consensus size: 78
2606519 TGGAGATAAC
* * *
2606529 AACGGGGCTGGAGTATCCCCGATTATGGAAAATCGGTG-TTCTGGAAATAAATCGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATCGGTGATT-TAGAAATAAATCGGGGTTGGAGT
*
2606593 ATCCCCTCAGAAAT
65 ATCCCCTCAAAAAT
** * * ** *
2606607 AACAAGGTTGGAGTATCCCTGATTAT-AGAAAATCGGT-ATTTTGAAAATAAAATCAAGGCTGGA
1 AACGGGGTTGGAGTATCCCCGATTATGA-AAAATCGGTGATTTAG-AAAT-AAATCGGGGTTGGA
2606670 GTATCCCCTCAAAAAT
63 GTATCCCCTCAAAAAT
* * * ** *
2606686 AACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGATGATTTAGAAATAAGGCCGGGGTTGAAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATCGGTGATTTAGAAATAA-ATCGGGGTTGGAGT
2606751 ATCCCC
65 ATCCCC
2606757 GATTGTGAGA
Statistics
Matches: 120, Mismatches: 23, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
77 2 0.02
78 39 0.32
79 73 0.61
80 6 0.05
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (78 bp):
AACGGGGTTGGAGTATCCCCGATTATGAAAAATCGGTGATTTAGAAATAAATCGGGGTTGGAGTA
TCCCCTCAAAAAT
Found at i:2606795 original size:51 final size:51
Alignment explanation
Indices: 2606688--2606797 Score: 132
Period size: 51 Copynumber: 2.2 Consensus size: 51
2606678 TCAAAAATAA
* * *
2606688 CGGGGTTGGAGTATCCCCAATTGTGAAAAATCGATGATTTAGAAATAAGGC
1 CGGGGTTGAAGTATCCCCAATTGTGAAAAATCAATGATTTAGAAATAAAGC
* * * *
2606739 CGGGGTTGAAGTATCCCCGATTGTGAGAAATCAAT-ATTTTGAAAATAAAGT
1 CGGGGTTGAAGTATCCCCAATTGTGAAAAATCAATGATTTAG-AAATAAAGC
*
2606790 TGGGGTTG
1 CGGGGTTG
2606798 GAGCATCCTC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
50 5 0.10
51 45 0.90
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (51 bp):
CGGGGTTGAAGTATCCCCAATTGTGAAAAATCAATGATTTAGAAATAAAGC
Found at i:2606828 original size:28 final size:27
Alignment explanation
Indices: 2606795--2606849 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
2606785 AAAGTTGGGG
2606795 TTGGAGCATCCTCTCG-GAAATAACGGGA
1 TTGGAGCATCC-C-CGAGAAATAACGGGA
*
2606823 TTGGAGTATCCCCGATGAAATAACGGG
1 TTGGAGCATCCCCGA-GAAATAACGGG
2606850 GTTGAGTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 2 0.08
27 1 0.04
28 21 0.88
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (27 bp):
TTGGAGCATCCCCGAGAAATAACGGGA
Found at i:2606864 original size:27 final size:28
Alignment explanation
Indices: 2606811--2606865 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
2606801 CATCCTCTCG
*
2606811 GAAATAACGGGATTGGAGTATCCCCGAT
1 GAAATAACGGGATTGGAGTACCCCCGAT
*
2606839 GAAATAACGGGGTT-GAGTACCCCCGAT
1 GAAATAACGGGATTGGAGTACCCCCGAT
2606866 TGTGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.20
Consensus pattern (28 bp):
GAAATAACGGGATTGGAGTACCCCCGAT
Found at i:2606879 original size:107 final size:108
Alignment explanation
Indices: 2606739--2607082 Score: 464
Period size: 109 Copynumber: 3.2 Consensus size: 108
2606729 GAAATAAGGC
* * * * ** *
2606739 CGGGGTTGAAGTATCCCCGATTGTG-AGAAATCAATATTTT-GAAAATAAAGTTGGGGTTGGAGC
1 CGGGGTTGGAGTACCCCCGATTGTGAAAAAATCAATATTTTAG-ATATAAAGCCGGGGTTGGAGT
2606802 ATCCTCTCGGAAATAACGG-GATTGGAGTATCCCCGATGAAATAA
65 ATCCTCTCGGAAATAACGGAG-TTGGAGTATCCCCGATGAAATAA
* *
2606846 CGGGGTT-GAGTACCCCCGATTGTGAAAAAATCAATATTTTAGATATAAAGCCGAGGTTAGAGTA
1 CGGGGTTGGAGTACCCCCGATTGTGAAAAAATCAATATTTTAGATATAAAGCCGGGGTTGGAGTA
* ** *
2606910 TCCCCTCAAAAATAACGGAGTTGAAGTATCCCCGATGAAATAA
66 TCCTCTCGGAAATAACGGAGTTGGAGTATCCCCGATGAAATAA
* *
2606953 CAGGGGTTGGAGTACCCCCAATTGTGAAAAAATCAATATTTTAGATATAAAGCCGGGATTGGAGT
1 C-GGGGTTGGAGTACCCCCGATTGTGAAAAAATCAATATTTTAGATATAAAGCCGGGGTTGGAGT
*
2607018 AT-CTCCTCGGAAATAACGGAGTTAGAGTATCCCCGATGAAATAA
65 ATCCT-CTCGGAAATAACGGAGTTGGAGTATCCCCGATGAAATAA
*
2607062 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTACCCCCGAT
2607083 GAAATAATGA
Statistics
Matches: 207, Mismatches: 24, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
106 15 0.07
107 75 0.36
108 27 0.13
109 90 0.43
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (108 bp):
CGGGGTTGGAGTACCCCCGATTGTGAAAAAATCAATATTTTAGATATAAAGCCGGGGTTGGAGTA
TCCTCTCGGAAATAACGGAGTTGGAGTATCCCCGATGAAATAA
Found at i:2607058 original size:28 final size:28
Alignment explanation
Indices: 2607011--2607107 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
2607001 AAAGCCGGGA
2607011 TTGGAGTATCTCCTCG--GAAATAACGGAG
1 TTGGAGTATC-CC-CGATGAAATAACGGAG
* *
2607039 TTAGAGTATCCCCGATGAAATAACGGGG
1 TTGGAGTATCCCCGATGAAATAACGGAG
*
2607067 TTGGAGTATCCCCGATGAAATAA-TGAG
1 TTGGAGTATCCCCGATGAAATAACGGAG
2607094 ATTGGAGTATCCCC
1 -TTGGAGTATCCCC
2607108 AATTGTGATA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
26 2 0.03
27 4 0.07
28 55 0.90
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.25
Consensus pattern (28 bp):
TTGGAGTATCCCCGATGAAATAACGGAG
Found at i:2607155 original size:51 final size:51
Alignment explanation
Indices: 2607095--2607263 Score: 189
Period size: 51 Copynumber: 3.3 Consensus size: 51
2607085 AATAATGAGA
* **
2607095 TTGGAGTATCCCCAATTGTGATAATTTTG-TGTTTTGGAAATAAAATCGGAG
1 TTGGAGTATCCCCAATTGAGA-AAAATTGATGTTTTGGAAATAAAATCGGAG
** * * * *
2607146 TTGGAGTATCCCTGATTGCGAAAAATCGATGCTTTAGAAATAAAATCGGAG
1 TTGGAGTATCCCCAATTGAGAAAAATTGATGTTTTGGAAATAAAATCGGAG
* * *
2607197 TTGGAGTATCCCCATTTAAGAAAAATTGATGTTTTGGAAATGAAAACCGG-G
1 TTGGAGTATCCCCAATTGAGAAAAATTGATGTTTTGGAAAT-AAAATCGGAG
2607248 ATTGGAGTATCCCCAA
1 -TTGGAGTATCCCCAA
2607264 GATGAAAAAT
Statistics
Matches: 97, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
50 4 0.04
51 72 0.74
52 21 0.22
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (51 bp):
TTGGAGTATCCCCAATTGAGAAAAATTGATGTTTTGGAAATAAAATCGGAG
Found at i:2610279 original size:18 final size:18
Alignment explanation
Indices: 2610238--2610273 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2610228 TTGTAAGAAA
2610238 AATA-AATAAAAATTATC
1 AATATAATAAAAATTATC
*
2610255 AATATAATAAATATTATC
1 AATATAATAAAAATTATC
2610273 A
1 A
2610274 TGATAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (18 bp):
AATATAATAAAAATTATC
Found at i:2610656 original size:6 final size:7
Alignment explanation
Indices: 2610639--2610670 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
2610629 AATCAAACTT
2610639 GGAAAAA
1 GGAAAAA
2610646 GGAAAAA
1 GGAAAAA
*
2610653 GAAAAAA
1 GGAAAAA
2610660 GGAAAAA
1 GGAAAAA
2610667 GGAA
1 GGAA
2610671 GTTGACGGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (7 bp):
GGAAAAA
Found at i:2610991 original size:17 final size:17
Alignment explanation
Indices: 2610929--2610992 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 17
2610919 TTAAAAATTT
2610929 AAAAT-AAT-TTTAATA
1 AAAATAAATATTTAATA
*
2610944 TTAAATAAATA-TTAAT-
1 -AAAATAAATATTTAATA
* *
2610960 ATAATAAATAATTAATA
1 AAAATAAATATTTAATA
*
2610977 AAAATATATATTTAAT
1 AAAATAAATATTTAAT
2610993 TTAATTTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
15 8 0.21
16 9 0.24
17 21 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATAAATATTTAATA
Found at i:2613652 original size:2 final size:2
Alignment explanation
Indices: 2613645--2613680 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2613635 TACTTACATC
2613645 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
2613681 GTGCTTGATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2619011 original size:21 final size:21
Alignment explanation
Indices: 2618968--2619011 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2618958 GATGTATTGG
**
2618968 TTGGATAAAAAAATGCATTTT
1 TTGGATAAAAAAATGCAACTT
* *
2618989 TTGGATGAAAAAATGTAACTT
1 TTGGATAAAAAAATGCAACTT
2619010 TT
1 TT
2619012 AATAACCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.39
Consensus pattern (21 bp):
TTGGATAAAAAAATGCAACTT
Found at i:2620899 original size:39 final size:40
Alignment explanation
Indices: 2620841--2620929 Score: 112
Period size: 39 Copynumber: 2.3 Consensus size: 40
2620831 TAAATTTTAA
*
2620841 AATATAA-ATAATTTAATTTATTTTTTA-ATATTAAAATAT
1 AATATAATATAATATAATTTATTTTTTATATATTAAAA-AT
*
2620880 AATATAATATAATAT-ATTTATTTTTTATATTTTAAAAAT
1 AATATAATATAATATAATTTATTTTTTATATATTAAAAAT
* *
2620919 GATTTAATATA
1 AATATAATATA
2620930 TAAAATATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
39 30 0.68
40 14 0.32
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (40 bp):
AATATAATATAATATAATTTATTTTTTATATATTAAAAAT
Found at i:2620965 original size:20 final size:20
Alignment explanation
Indices: 2620920--2620965 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2620910 TTTAAAAATG
2620920 ATTTAATATATAAAATATAA
1 ATTTAATATATAAAATATAA
* **
2620940 AATTAATATATATTATATAA
1 ATTTAATATATAAAATATAA
*
2620960 TTTTAA
1 ATTTAA
2620966 AATAGTGAGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTTAATATATAAAATATAA
Found at i:2623956 original size:29 final size:29
Alignment explanation
Indices: 2623918--2623985 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
2623908 ATCAAACTAT
2623918 TATTAATTTTAAAATAAATTAGTAAAATAA
1 TATT-ATTTTAAAATAAATTAGTAAAATAA
* * * *
2623948 TATTATTTTAAAATTATTTATTGAAATAA
1 TATTATTTTAAAATAAATTAGTAAAATAA
*
2623977 TATTGTTTT
1 TATTATTTT
2623986 GCTCATTTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 29 0.88
30 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (29 bp):
TATTATTTTAAAATAAATTAGTAAAATAA
Found at i:2624148 original size:9 final size:9
Alignment explanation
Indices: 2624134--2624197 Score: 53
Period size: 10 Copynumber: 6.9 Consensus size: 9
2624124 TATTTTATTA
2624134 TTAAAATAT
1 TTAAAATAT
2624143 TTAAAATTAT
1 TTAAAA-TAT
2624153 TTGATAAATAT
1 TT-A-AAATAT
2624164 TTAAAA-AT
1 TTAAAATAT
2624172 ATT-AAA-AT
1 -TTAAAATAT
2624180 TTAAAATAAT
1 TTAAAAT-AT
*
2624190 GTAAAATA
1 TTAAAATA
2624198 ATTTTTTATG
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
7 2 0.04
8 10 0.21
9 12 0.26
10 14 0.30
11 6 0.13
12 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (9 bp):
TTAAAATAT
Found at i:2624152 original size:21 final size:22
Alignment explanation
Indices: 2624128--2624175 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
2624118 TAAGTATATT
*
2624128 TTATTATTA-AAATATTTAAAA
1 TTATTATGATAAATATTTAAAA
2624149 TTATT-TGATAAATATTTAAAA
1 TTATTATGATAAATATTTAAAA
*
2624170 ATATTA
1 TTATTA
2624176 AAATTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TTATTATGATAAATATTTAAAA
Found at i:2624334 original size:21 final size:19
Alignment explanation
Indices: 2624310--2624364 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
2624300 TTTATTATAA
2624310 AAATATCTAAAATTATTTGAT
1 AAATATCTAAAATTATTT--T
* **
2624331 AAATATTTAAAAAAATTTT
1 AAATATCTAAAATTATTTT
2624350 AAA-ATCTAAAATTAT
1 AAATATCTAAAATTAT
2624365 GTTACATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 9 0.32
19 4 0.14
21 15 0.54
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (19 bp):
AAATATCTAAAATTATTTT
Found at i:2624594 original size:172 final size:168
Alignment explanation
Indices: 2624125--2624671 Score: 549
Period size: 173 Copynumber: 3.2 Consensus size: 168
2624115 TAATAAGTAT
* * *
2624125 ATTTTATTATTAAAATATTTAAAATTATTTGATAAATATTT-AAAAATATTAAAATTTAAAATAA
1 ATTTTATTATTAAAATATCTAAAATTATTTGATAAATATTTAAAAAAT-TTAAAATCTAAAATTA
* * * *
2624189 TGTAAAAT-AATTTTTTATGCTTAAAAAATTATCGTATTTTACTATGAAAGTATCAATATATATA
65 TGTAAAATAAATTTTTGA--CTTAAGAAATTATCGTATTTTAATATAAAAGTATCAAT-T-TATA
* * * * *** *
2624253 TATTTTTAATATTTACTATTTTATAATTTTTTAACCCATAAATGC
126 T-TTTTTAAGACTTAATATTTTA-AAATTTTTAATTGACAAATGC
*
2624298 ATTTTATTATAAAAATATCTAAAATTATTTGATAAATATTTAAAAAAATTTTAAAATCTAAAATT
1 ATTTTATTATTAAAATATCTAAAATTATTTGATAAATATTT-AAAAAA-TTTAAAATCTAAAATT
* * * * * *
2624363 ATGTTACATAAATTTTTTAGTTTAAGAAACTATCGTATTTTAATATTAAAGTATCAATTTATATT
64 ATGTAAAATAAATTTTTGA-CTTAAGAAATTATCGTATTTTAATATAAAAGTATCAATTTATATT
* *
2624428 TTTTCAAGACTTATTATTTTAAAATTTTTAATATGAGAAATGC
128 TTTT-AAGACTTAATATTTTAAAATTTTTAAT-TGACAAATGC
* ** * *
2624471 ATTTTATTATTATAATATCTAAAATTATCGGGTACATATTTAAAAAATTTAAAAATCTAAAATTA
1 ATTTTATTATTAAAATATCTAAAATTATTTGATAAATATTTAAAAAATTT-AAAATCTAAAATTA
* * * * * * *
2624536 TATAAAACAAACTTTTTGACTTGAGAAATTGTCGTATTTTAATACAAAAGTGTCAATTTATGTTT
65 TGTAAAATAAA-TTTTTGACTTAAGAAATTATCGTATTTTAATATAAAAGTATCAATTTA--TAT
* * * *
2624601 TTCTTTGAGACTTAATATTTCATAATTTTTAGCTTGACAAATGC
127 TT-TTTAAGACTTAATATTTTAAAATTTTTA-ATTGACAAATGC
*
2624645 AATTTATTATTAAAATATCTAAAATTA
1 ATTTTATTATTAAAATATCTAAAATTA
2624672 CCTAATAACT
Statistics
Matches: 316, Mismatches: 46, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
171 3 0.01
172 75 0.24
173 105 0.33
174 60 0.19
175 63 0.20
176 10 0.03
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (168 bp):
ATTTTATTATTAAAATATCTAAAATTATTTGATAAATATTTAAAAAATTTAAAATCTAAAATTAT
GTAAAATAAATTTTTGACTTAAGAAATTATCGTATTTTAATATAAAAGTATCAATTTATATTTTT
TAAGACTTAATATTTTAAAATTTTTAATTGACAAATGC
Found at i:2625125 original size:173 final size:164
Alignment explanation
Indices: 2624946--2625393 Score: 451
Period size: 174 Copynumber: 2.6 Consensus size: 164
2624936 AAAGAATATG
*
2624946 TTTTACATAATTTTAGATTTTAATTTTTTAAATATTTACTAGATCAATTTAGATATTTTAATCAT
1 TTTTACATAATTTTAGATTTTAATTTTTTAAATATTTACTAGAT-AATTTAGATATTTTAATAAT
* *
2625011 AAAATATATTTA-CTGGGTAAAAAATTATGAAATAATAAGT-CTTAAAGAAAAACATAAATGGGT
65 AAAATATATTTATC-AGGTAAAAAATTATGAAATAATAAGTAC-CAAAG--AAA-AT---T--GT
* * * ** *
2625074 GTTTTAG-TATTAAAGTA-AGATAATTTCTCAAGTCA-AATCATTTT
120 ATATTAGCTATTAAAATACA-ATAATTTCTCAAGT-ATAAAAATTCT
* * * *
2625118 ATTTTACATAATTTTAGATTTAAAATTTTTTAAAAATTTA-TCGGATAATTTTATATATTTTAAT
1 -TTTTACATAATTTTAGATTT-TAATTTTTTAAATATTTACT-AGATAA-TTTAGATATTTTAAT
* *
2625182 AATAAAATATATTTATCAGTTAAAACATTAT-AAATAATAAGTACCAAAGAAAATTGTATATTAG
62 AATAAAATATATTTATCAGGTAAAAAATTATGAAATAATAAGTACCAAAGAAAATTGTATATTAG
* *
2625246 CACTATTAAAATACAATAGTTTCTTAAGTATAAAAATTCT
127 --CTATTAAAATACAATAATTTCTCAAGTATAAAAATTCT
* *
2625286 TTTCACATAATTTTAGATTTTAATAATTTTTAAATATTTACTAGATAATTTTGAATATTTTTAAT
1 TTTTACATAATTTTAGATTTTAAT--TTTTTAAATATTTACTAGATAATTTAG-ATA-TTTTAAT
* *
2625351 AATAAAATGTATTTATCAAGTAAAAAATTATGAAATAATAAGT
62 AATAAAATATATTTATCAGGTAAAAAATTATGAAATAATAAGT
2625394 TGAAAAAAAA
Statistics
Matches: 232, Mismatches: 27, Indels: 35
0.79 0.09 0.12
Matches are distributed among these distances:
165 7 0.03
166 3 0.01
167 24 0.10
168 48 0.21
169 36 0.16
170 13 0.06
171 3 0.01
173 38 0.16
174 59 0.25
175 1 0.00
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.43
Consensus pattern (164 bp):
TTTTACATAATTTTAGATTTTAATTTTTTAAATATTTACTAGATAATTTAGATATTTTAATAATA
AAATATATTTATCAGGTAAAAAATTATGAAATAATAAGTACCAAAGAAAATTGTATATTAGCTAT
TAAAATACAATAATTTCTCAAGTATAAAAATTCT
Found at i:2625355 original size:22 final size:21
Alignment explanation
Indices: 2625306--2625355 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
2625296 TTTTAGATTT
* *
2625306 TAATAATTTTTAAATATTTAC
1 TAATAATTTTGAAATATTTAA
*
2625327 TAGATAATTTTGAATATTTTTAA
1 TA-ATAATTTTGAA-ATATTTAA
2625350 TAATAA
1 TAATAA
2625356 AATGTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 14 0.58
23 8 0.33
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (21 bp):
TAATAATTTTGAAATATTTAA
Found at i:2626195 original size:32 final size:33
Alignment explanation
Indices: 2626135--2626199 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
2626125 CATAGCGAGA
*
2626135 TGTATCGATACATTATACTTTGTATCGATACAT
1 TGTATCGATACATTATACATTGTATCGATACAT
* *
2626168 TGTATTGATACA-TATTCATTGTATCGATACAT
1 TGTATCGATACATTATACATTGTATCGATACAT
2626200 GCACAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATTATACATTGTATCGATACAT
Found at i:2626287 original size:33 final size:33
Alignment explanation
Indices: 2626250--2626314 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2626240 TACCACTATT
* *
2626250 TGTATCGATACATGGC-ACATTGTATCGATACAA
1 TGTATCGATACATGACGA-ATTATATCGATACAA
2626283 TGTATCGATACATGACGAATTATATCGATACA
1 TGTATCGATACATGACGAATTATATCGATACA
2626315 TTGTCCCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (33 bp):
TGTATCGATACATGACGAATTATATCGATACAA
Found at i:2626288 original size:13 final size:13
Alignment explanation
Indices: 2626270--2626294 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2626260 CATGGCACAT
2626270 TGTATCGATACAA
1 TGTATCGATACAA
2626283 TGTATCGATACA
1 TGTATCGATACA
2626295 TGACGAATTA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2627387 original size:27 final size:27
Alignment explanation
Indices: 2627354--2627428 Score: 78
Period size: 34 Copynumber: 2.5 Consensus size: 27
2627344 AAAGGACCAC
*
2627354 AAGGAGGAAGATGATGTTGTCATTCCA
1 AAGGAGGAAGATGACGTTGTCATTCCA
2627381 AAGGAGGAAGAGAGAAGGTGACGTTGTCATTCCA
1 AAGGA-G--GA-AG-A--TGACGTTGTCATTCCA
2627415 AAGGAGGAAGATGA
1 AAGGAGGAAGATGA
2627429 GTGGGATGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
27 8 0.20
28 1 0.03
29 1 0.03
30 4 0.10
31 4 0.10
32 1 0.03
33 1 0.03
34 20 0.50
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (27 bp):
AAGGAGGAAGATGACGTTGTCATTCCA
Found at i:2627409 original size:34 final size:34
Alignment explanation
Indices: 2627360--2627425 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
2627350 CCACAAGGAG
*
2627360 GAAGATGATGTTGTCATTCCAAAGGAGGAAGAGA
1 GAAGATGACGTTGTCATTCCAAAGGAGGAAGAGA
*
2627394 GAAGGTGACGTTGTCATTCCAAAGGAGGAAGA
1 GAAGATGACGTTGTCATTCCAAAGGAGGAAGA
2627426 TGAGTGGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.33, T:0.20
Consensus pattern (34 bp):
GAAGATGACGTTGTCATTCCAAAGGAGGAAGAGA
Found at i:2632539 original size:13 final size:13
Alignment explanation
Indices: 2632521--2632547 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2632511 ACAATGTTTT
2632521 TTGTATCGATACA
1 TTGTATCGATACA
2632534 TTGTATCGATACA
1 TTGTATCGATACA
2632547 T
1 T
2632548 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2635070 original size:20 final size:19
Alignment explanation
Indices: 2635021--2635081 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
2635011 GCTTTGTATC
*
2635021 GATACATTGTATCGATTCAT
1 GATA-ATTGTATCGATACAT
* *
2635041 GTTCATTGTATCGATACAT
1 GATAATTGTATCGATACAT
*
2635060 GCATAATTGTATTGATACAT
1 G-ATAATTGTATCGATACAT
2635080 GA
1 GA
2635082 AAATGGCAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.39
Consensus pattern (19 bp):
GATAATTGTATCGATACAT
Found at i:2635134 original size:20 final size:20
Alignment explanation
Indices: 2635109--2635195 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
2635099 CTACCACTGT
* *
2635109 TTGTATCGATACATGGCACA
1 TTGTATCGATACATGACAAA
2635129 TTGTATCGATACATGACAAA
1 TTGTATCGATACATGACAAA
*
2635149 TTGTAT---T-GAT-AC-AA
1 TTGTATCGATACATGACAAA
*
2635163 -TGTATCAATACATGACAAA
1 TTGTATCGATACATGACAAA
2635182 TTGTATCGATACAT
1 TTGTATCGATACAT
2635196 TGTCCCAAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
13 5 0.09
14 2 0.04
15 2 0.04
16 3 0.05
17 3 0.05
18 2 0.04
19 2 0.04
20 36 0.65
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATGACAAA
Found at i:2635174 original size:33 final size:33
Alignment explanation
Indices: 2635130--2635194 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
2635120 CATGGCACAT
* *
2635130 TGTATCGATACATGACAAATTGTATTGATACAA
1 TGTATCAATACATGACAAATTGTATCGATACAA
2635163 TGTATCAATACATGACAAATTGTATCGATACA
1 TGTATCAATACATGACAAATTGTATCGATACA
2635195 TTGTCCCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (33 bp):
TGTATCAATACATGACAAATTGTATCGATACAA
Found at i:2636290 original size:53 final size:54
Alignment explanation
Indices: 2636210--2636320 Score: 215
Period size: 53 Copynumber: 2.1 Consensus size: 54
2636200 GAGCTTACAA
2636210 ATATTTTTCTTTAACAAGTTTAGGAATAAGTGATATTAAAGGGTATATATTTT-
1 ATATTTTTCTTTAACAAGTTTAGGAATAAGTGATATTAAAGGGTATATATTTTC
2636263 ATATTTTTCTTTAACAAGTTTAGGAATAAGTGATATTAAAGGGTATATATTTTC
1 ATATTTTTCTTTAACAAGTTTAGGAATAAGTGATATTAAAGGGTATATATTTTC
2636317 ATAT
1 ATAT
2636321 CCTAATGAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 53 0.93
54 4 0.07
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (54 bp):
ATATTTTTCTTTAACAAGTTTAGGAATAAGTGATATTAAAGGGTATATATTTTC
Found at i:2639828 original size:20 final size:20
Alignment explanation
Indices: 2639786--2639839 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
2639776 TTCAACAATT
2639786 TGTATTGATACAATAAGGCAA
1 TGTATTGATAC-ATAAGGCAA
*
2639807 TGTATCGATACATAAGTG-AA
1 TGTATTGATACATAAG-GCAA
2639827 TGTATTGATACAT
1 TGTATTGATACAT
2639840 GCCTGAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (20 bp):
TGTATTGATACATAAGGCAA
Found at i:2640888 original size:20 final size:21
Alignment explanation
Indices: 2640863--2640901 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2640853 TCTAAACAAC
*
2640863 CCATGTT-CATTCATTTTAGG
1 CCATGTTCCATGCATTTTAGG
2640883 CCATGTTCCATGCATTTTA
1 CCATGTTCCATGCATTTTA
2640902 ACATATCCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.44
Consensus pattern (21 bp):
CCATGTTCCATGCATTTTAGG
Found at i:2653618 original size:142 final size:139
Alignment explanation
Indices: 2653420--2653819 Score: 502
Period size: 142 Copynumber: 2.8 Consensus size: 139
2653410 AATGATATAA
*
2653420 TATTTAATTTTTTAATTTTT--AAAAATCTCATTTCGTATTTTAATGGAGAACCAAAAAGATACG
1 TATTTAA-TTTTT-ATTTTTCAAAAAAT-TCATTTCGTATCTTAATGGAGAACCAAAAAGATACG
* * *
2653483 AAAAGTTTTGAAGATTTCTATACCCTTACAAAAAATCATGCGAATATTAGAAATCTTGAAAAATT
63 AAAATTTTTAAAGATTTCTATACCCTTACGAAAAA-CATG-GAATATTAGAAATCTTGAAAAATT
2653548 AAGATAATAATTTTT
126 AAGATAATAA-TTTT
* *
2653563 TATTTAATTTTTATTTTTCAAAAAATTTATTTCGTATCTTAATGGAGAACTAAAAAGATACGAAA
1 TATTTAATTTTTATTTTTCAAAAAATTCATTTCGTATCTTAATGGAGAACCAAAAAGATACGAAA
* * * * * *
2653628 TTTTTTTAAGATTTCTATACCCTTACGGAAAACCATAAGAATATTAAAAATTTTGAAAAATTAAG
66 ATTTTTAAAGATTTCTATACCCTTAC-GAAAAACAT-GGAATATTAGAAATCTTGAAAAATTAAG
2653693 ATAATAATTTT
129 ATAATAATTTT
* * * * **
2653704 TATTTAATTTTTAATTTTCAAAAAATTCA--TCATACCTTAATGGAGAACCGAAAAGATATAAAA
1 TATTTAATTTTTATTTTTCAAAAAATTCATTTCGTATCTTAATGGAGAACCAAAAAGATACGAAA
* *
2653767 ATTTTTAAAGATTTTTATACCCCTACGAAAAACTATAGGAATATTAGAAATCT
66 ATTTTTAAAGATTTCTATACCCTTACGAAAAAC-AT-GGAATATTAGAAATCT
2653820 AAAAAAAAAT
Statistics
Matches: 225, Mismatches: 27, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
138 6 0.03
139 66 0.29
141 37 0.16
142 99 0.44
143 17 0.08
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (139 bp):
TATTTAATTTTTATTTTTCAAAAAATTCATTTCGTATCTTAATGGAGAACCAAAAAGATACGAAA
ATTTTTAAAGATTTCTATACCCTTACGAAAAACATGGAATATTAGAAATCTTGAAAAATTAAGAT
AATAATTTT
Found at i:2654565 original size:14 final size:14
Alignment explanation
Indices: 2654546--2654604 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
2654536 GTTTAGCTTT
2654546 TTTTTTTCTCTCTC
1 TTTTTTTCTCTCTC
*
2654560 TTTTTTTCTTTCTTTTTC
1 TTTTTTTC--TC--TCTC
*
2654578 TTTCTTTTTTCTCTC
1 TTT-TTTTCTCTCTC
2654593 TTTTTTTCTCTC
1 TTTTTTTCTCTC
2654605 CATTTTCTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 16 0.44
15 6 0.17
16 2 0.06
17 2 0.06
18 6 0.17
19 4 0.11
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTTTCTCTCTC
Found at i:2654577 original size:10 final size:10
Alignment explanation
Indices: 2654562--2654597 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
2654552 TCTCTCTCTT
2654562 TTTTTCTTTC
1 TTTTTCTTTC
2654572 TTTTTCTTTC
1 TTTTTCTTTC
*
2654582 TTTTTTCTCTC
1 -TTTTTCTTTC
2654593 TTTTT
1 TTTTT
2654598 TTCTCTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:2654602 original size:10 final size:10
Alignment explanation
Indices: 2654556--2654603 Score: 53
Period size: 10 Copynumber: 4.5 Consensus size: 10
2654546 TTTTTTTCTC
2654556 TCTCTTTTTT
1 TCTCTTTTTT
2654566 TCT-TTCTTTT
1 TCTCTT-TTTT
2654576 TCTTTCTTTTTT
1 TC--TCTTTTTT
2654588 CTCTCTTTTTT
1 -TCTCTTTTTT
2654599 TCTCT
1 TCTCT
2654604 CCATTTTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
9 2 0.06
10 14 0.42
11 8 0.24
12 5 0.15
13 4 0.12
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (10 bp):
TCTCTTTTTT
Found at i:2654610 original size:14 final size:12
Alignment explanation
Indices: 2654546--2654604 Score: 70
Period size: 12 Copynumber: 5.0 Consensus size: 12
2654536 GTTTAGCTTT
2654546 TTTTTTTCTCTC
1 TTTTTTTCTCTC
2654558 TCTTTTTT-TCT-
1 T-TTTTTTCTCTC
*
2654569 TTCTTTTTCTTTC
1 TT-TTTTTCTCTC
2654582 -TTTTTTCTCTC
1 TTTTTTTCTCTC
2654593 TTTTTTTCTCTC
1 TTTTTTTCTCTC
2654605 CATTTTCTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
10 1 0.03
11 15 0.38
12 18 0.45
13 6 0.15
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTTCTCTC
Found at i:2656014 original size:152 final size:153
Alignment explanation
Indices: 2655037--2655981 Score: 1022
Period size: 153 Copynumber: 6.2 Consensus size: 153
2655027 ACTCAAAAAA
* * * * ** **
2655037 AAAATAAATTGAA-TTTTCTAAACTAATTTACTATGAATTTAATGAA-AATATTTGATTAATTTT
1 AAAATAAATTGAATTTTTCAAAACTGATTTAATATCAA-TTAAACAATAATATTTGAAGAATTTT
* * ** * * * * *
2655100 AAAAATTTTGAACCGAAAAAAATCCAACTAAAAAAAATTTACAGAGTAAAAGA-TTTCGTATTTT
65 AAAAATTATAAACTTAGAAAAATCCTACT--AAAAAATTTACAGAGTAAAAAACTCTCATATTTT
*
2655164 GGA-AATAGAAAAAATCTAAAACTCAT
128 -GATAATAGAAAAATTCTAAAACTCAT
*
2655190 AAAATAAATTAAATTTTTCAAAACTGATTTAATATCAATTAAACAATAATATTTGAAGAATTTTA
1 AAAATAAATTGAATTTTTCAAAACTGATTTAATATCAATTAAACAATAATATTTGAAGAATTTTA
* * * * * *
2655255 AAAATTATAAACTAAGAAAAATCGTACTGAAAAATTTA-TGATGTAGAAAACTCT-ATATTTCGA
66 AAAATTATAAACTTAGAAAAATCCTACTAAAAAATTTACAGA-GTAAAAAACTCTCATATTTTGA
*
2655318 TAATAGGAAAAATTTTAAAACTCAT
130 TAATA-GAAAAATTCTAAAACTCAT
* * *
2655343 AAAATAAATTGAATTTCTCAAAACTAATTTAATATCAATTAAACAATAATATTTAAAGAATTTTA
1 AAAATAAATTGAATTTTTCAAAACTGATTTAATATCAATTAAACAATAATATTTGAAGAATTTTA
* ** * * *
2655408 AAAATTATAAACTTAGAAAAATCTTACCGAAAAATTTACATAGTAAAAAA-TTTCATATTTCGAT
66 AAAATTATAAACTTAGAAAAATCCTACTAAAAAATTTACAGAGTAAAAAACTCTCATATTTTGAT
* *
2655472 AACAAGAAAAATTCTAAAACTTAT
131 AA-TAGAAAAATTCTAAAACTCAT
* * * * *
2655496 ATAATAAATTGAATTTTTAAAAACTGATTTAATCTCAATTAAACAATAATATTTGAAGAAATTTG
1 AAAATAAATTGAATTTTTCAAAACTGATTTAATATCAATTAAACAATAATATTTGAAGAATTTTA
* * * * *
2655561 AAAATTATAAACTTAGAAAAAT-CTCACCATACAATTTACGGAGTAGAAAACT-TCATATTTTGA
66 AAAATTATAAACTTAGAAAAATCCT-ACTAAAAAATTTACAGAGTAAAAAACTCTCATATTTTGA
*
2655624 TAATAGAAGAAATTTTAAAACTCAT
130 TAATAGAA-AAATTCTAAAACTCAT
* * * **
2655649 AAAATAAATTAAATTTCTT-AAAACTAATTTAGTGCCAATTAAACAATAATATTTGAAGAATTTT
1 AAAATAAATTGAATTT-TTCAAAACTGATTTAATATCAATTAAACAATAATATTTGAAGAATTTT
* * * *
2655713 GAAAA-TATAAACTTAAAAAAATCCTA-TCAAAAAATTTACTA-AGTAAAAAAC-ATCGTATTTT
65 AAAAATTATAAACTTAGAAAAATCCTACT-AAAAAATTTAC-AGAGTAAAAAACTCTCATATTTT
* * * *
2655774 AATAAAAAGAAAAATTATAAAATTCAT
128 GAT-AATAGAAAAATTCTAAAACTCAT
* ** *
2655801 AAAATAAATTGAATTTTTCAAAAATGATTTTGTATCAATTAAAAAATAATATTTGAAGAATTTTA
1 AAAATAAATTGAATTTTTCAAAACTGATTTAATATCAATTAAACAATAATATTTGAAGAATTTTA
* *
2655866 AAAATTATAAACTTAGAAAAATCCTA-TAAAAAATTTACGGAGTAAAAAACTCT-GTATTTTGAT
66 AAAATTATAAACTTAGAAAAATCCTACTAAAAAATTTACAGAGTAAAAAACTCTCATATTTTGAT
2655929 AATAGGAAAAATTCTAAAACTCAT
131 AATA-GAAAAATTCTAAAACTCAT
* * *
2655953 AAACTAAATTGAATTTTTCCAAATTGATT
1 AAAATAAATTGAATTTTTCAAAACTGATT
2655982 CTATGATGAT
Statistics
Matches: 675, Mismatches: 94, Indels: 47
0.83 0.12 0.06
Matches are distributed among these distances:
151 9 0.01
152 221 0.33
153 383 0.57
154 62 0.09
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (153 bp):
AAAATAAATTGAATTTTTCAAAACTGATTTAATATCAATTAAACAATAATATTTGAAGAATTTTA
AAAATTATAAACTTAGAAAAATCCTACTAAAAAATTTACAGAGTAAAAAACTCTCATATTTTGAT
AATAGAAAAATTCTAAAACTCAT
Found at i:2656066 original size:152 final size:151
Alignment explanation
Indices: 2655170--2656076 Score: 656
Period size: 153 Copynumber: 5.9 Consensus size: 151
2655160 TTTTGGAAAT
* * * * ** *
2655170 AGAAAAAATCTAAAACTCATAAAATAAATTAAATTTTTCAAAACTGATTTAATATCAATTAAACA
1 AGAAAAATTATAAAACTCATAAAATAAATTGAATTTTTCAAAAATGATTTTGTATCAATTAAAAA
* * * * * * * * *
2655235 ATAATATTTGAAGAATTTTAAAAATTATAAACTAAGAAAAATCGTA-CTGAAAAATTTATGATGT
66 AGAATATTTAAAGAATTCTAAAAATTATAAAATTAGAAAAATCCTATC-AAAAAATTTACGA-AT
* * *
2655299 AGAAAACTC-TATATTTCGATAATA
129 AAAAAACTCGTAT-TTT-AATAAAA
* * * * * ** *
2655323 GGAAAAATTTTAAAACTCATAAAATAAATTGAATTTCTCAAAACTAATTTAATATCAATTAAACA
1 AGAAAAATTATAAAACTCATAAAATAAATTGAATTTTTCAAAAATGATTTTGTATCAATTAAAAA
* * * * * *
2655388 ATAATATTTAAAGAATTTTAAAAATTATAAACTTAGAAAAATCTTACCGAAAAATTTAC-ATAGT
66 AGAATATTTAAAGAATTCTAAAAATTATAAAATTAGAAAAATCCTATCAAAAAATTTACGA-A-T
* * ** *
2655452 AAAAAATTTCATATTTCGATAACA
129 AAAAAA-CTCGTATTTTAATAAAA
* * * ** * *
2655476 AGAAAAATTCTAAAACTTATATAATAAATTGAATTTTT-AAAAACTGATTTAATCTCAATTAAAC
1 AGAAAAATTATAAAACTCATAAAATAAATTGAATTTTTCAAAAA-TGATTTTGTATCAATTAAAA
* * * * * * *
2655540 AATAATATTTGAAGAAATT-TGAAAATTATAAACTTAGAAAAAT-CTCACCATACAATTTACGGA
65 AAGAATATTTAAAG-AATTCTAAAAATTATAAAATTAGAAAAATCCT-ATCAAAAAATTTAC-GA
* * * * *
2655603 GTAGAAAACTTCATATTTTGAT-AAT
127 ATAAAAAAC-TCGTATTTTAATAAAA
* * * * * **
2655628 AGAAGAAATTTTAAAACTCATAAAATAAATTAAATTTCTT-AAAACTAATTTAGTGCCAATTAAA
1 AGAA-AAATTATAAAACTCATAAAATAAATTGAATTT-TTCAAAAATGATTTTGTATCAATTAAA
* * * * * * * *
2655692 CAATAATATTTGAAGAATTTTGAAAA-TATAAACTTAAAAAAATCCTATCAAAAAATTTACTAAG
64 AAAGAATATTTAAAGAATTCTAAAAATTATAAAATTAGAAAAATCCTATCAAAAAATTTACGAA-
2655756 TAAAAAACATCGTATTTTAATAAAA
128 TAAAAAAC-TCGTATTTTAATAAAA
*
2655781 AGAAAAATTATAAAATTCATAAAATAAATTGAATTTTTCAAAAATGATTTTGTATCAATTAAAAA
1 AGAAAAATTATAAAACTCATAAAATAAATTGAATTTTTCAAAAATGATTTTGTATCAATTAAAAA
* * * * *
2655846 ATAATATTTGAAGAATTTTAAAAATTATAAACTTAGAAAAATCCTAT-AAAAAATTTACGGAGTA
66 AGAATATTTAAAGAATTCTAAAAATTATAAAATTAGAAAAATCCTATCAAAAAATTTAC-GAATA
* *
2655910 AAAAACTCTGTATTTTGATAATA
130 AAAAACTC-GTATTTTAATAAAA
* * * * * * *
2655933 GGAAAAATTCTAAAACTCATAAACTAAATTGAATTTTTCCAAATTGATTCTATG-AT-GATTTAA
1 AGAAAAATTATAAAACTCATAAAATAAATTGAATTTTTCAAAAATGATT-T-TGTATCAATTAAA
** * * * *
2655996 GGAGAATATTTAAAGAATTCT-AAAGTT-TAAAATTCA-AGGAAATTCTATCAAAAATTTTACGA
64 AAAGAATATTTAAAGAATTCTAAAAATTATAAAATT-AGA-AAAATCCTATCAAAAAATTTACGA
2656058 ATAAAAAAAGCTCGTATTT
127 AT-AAAAAA-CTCGTATTT
2656077 CACTTTTGGG
Statistics
Matches: 638, Mismatches: 89, Indels: 55
0.82 0.11 0.07
Matches are distributed among these distances:
150 7 0.01
151 22 0.03
152 249 0.39
153 339 0.53
154 17 0.03
155 4 0.01
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (151 bp):
AGAAAAATTATAAAACTCATAAAATAAATTGAATTTTTCAAAAATGATTTTGTATCAATTAAAAA
AGAATATTTAAAGAATTCTAAAAATTATAAAATTAGAAAAATCCTATCAAAAAATTTACGAATAA
AAAACTCGTATTTTAATAAAA
Found at i:2656720 original size:16 final size:17
Alignment explanation
Indices: 2656690--2656722 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2656680 ACCCAAACAA
2656690 AATTAAATATCTATATT
1 AATTAAATATCTATATT
*
2656707 AATT-AATATTTATATT
1 AATTAAATATCTATATT
2656723 TTTTTGTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTAAATATCTATATT
Found at i:2662734 original size:16 final size:16
Alignment explanation
Indices: 2662714--2662761 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 16
2662704 TCAAATTTTG
*
2662714 AAAAAATTCAAATCAAT
1 AAAAAATTCAAA-AAAT
*
2662731 AAAAAAATCAAAAAAT
1 AAAAAATTCAAAAAAT
2662747 -AAAAATT-AAAAAAT
1 AAAAAATTCAAAAAAT
2662761 A
1 A
2662762 TAACTAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 7 0.26
15 6 0.22
16 3 0.11
17 11 0.41
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAAAATTCAAAAAAT
Found at i:2662863 original size:19 final size:18
Alignment explanation
Indices: 2662832--2662880 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 18
2662822 TCATACTTCT
2662832 ATTTCATGCATTGCACTC
1 ATTTCATGCATTGCACTC
**
2662850 ATTTCATCGCATTGCTTTC
1 ATTTCAT-GCATTGCACTC
2662869 ATTTCATGCATT
1 ATTTCATGCATT
2662881 CATGTGCAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.20, C:0.24, G:0.10, T:0.45
Consensus pattern (18 bp):
ATTTCATGCATTGCACTC
Found at i:2664909 original size:64 final size:64
Alignment explanation
Indices: 2664807--2664932 Score: 209
Period size: 64 Copynumber: 2.0 Consensus size: 64
2664797 GGGGATACTG
2664807 CAACCCCGTTTTTAAACTCATCAAAATTTAAATATTATTT-TGTCTAAATTATCATTGTCGGGAT
1 CAACCCCGTTTTTAAACTCATCAAAATTTAAATATTATTTGT-TCTAAATTATCATTGTCGGGAT
* * *
2664871 CAACCCTGTTTTTAAACTCATCGAAATTTAAATCTTATTTGTTCTAAATTATCATTGTCGGG
1 CAACCCCGTTTTTAAACTCATCAAAATTTAAATATTATTTGTTCTAAATTATCATTGTCGGG
2664933 GATACTCCAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
64 57 0.98
65 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.41
Consensus pattern (64 bp):
CAACCCCGTTTTTAAACTCATCAAAATTTAAATATTATTTGTTCTAAATTATCATTGTCGGGAT
Found at i:2666013 original size:19 final size:19
Alignment explanation
Indices: 2665991--2666038 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
2665981 GTAAAACAAA
2665991 AAAACAAAAAAA-AAAGAAG
1 AAAACAAAAAAATAAA-AAG
*
2666010 AAAACAAAAAAATAAAATG
1 AAAACAAAAAAATAAAAAG
2666029 AAAA-AAAAAA
1 AAAACAAAAAA
2666039 GTGCAAAAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 6 0.22
19 18 0.67
20 3 0.11
ACGTcount: A:0.85, C:0.04, G:0.06, T:0.04
Consensus pattern (19 bp):
AAAACAAAAAAATAAAAAG
Found at i:2666032 original size:28 final size:29
Alignment explanation
Indices: 2665966--2666033 Score: 86
Period size: 27 Copynumber: 2.4 Consensus size: 29
2665956 GAGCTCCCTT
**
2665966 CAAAATGATGAAGAAGTAAAACAAAAAAA
1 CAAAATGAAAAAGAAGTAAAACAAAAAAA
*
2665995 CAAAA-AAAAAAGAAG-AAAACAAAAAAA
1 CAAAATGAAAAAGAAGTAAAACAAAAAAA
*
2666022 TAAAATGAAAAA
1 CAAAATGAAAAA
2666034 AAAAAGTGCA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 16 0.48
28 12 0.36
29 5 0.15
ACGTcount: A:0.76, C:0.06, G:0.10, T:0.07
Consensus pattern (29 bp):
CAAAATGAAAAAGAAGTAAAACAAAAAAA
Found at i:2667364 original size:31 final size:31
Alignment explanation
Indices: 2667284--2667385 Score: 125
Period size: 32 Copynumber: 3.3 Consensus size: 31
2667274 AATCCTTCAA
* *
2667284 ATCTTTTTCCAAAAGTCCACAACTTAGTGGC
1 ATCTTTTTCCCAAAGTCCACGACTTAGTGGC
*
2667315 ATCTCTTTTCCCAAAGTCCACGACTTAATGGC
1 ATCT-TTTTCCCAAAGTCCACGACTTAGTGGC
* * *
2667347 ATC-TTTTCTTCAAAGTCCATGACTCAGTGGC
1 ATCTTTTTC-CCAAAGTCCACGACTTAGTGGC
2667378 ATCTTTTT
1 ATCTTTTT
2667386 TCTTTTTTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
30 5 0.08
31 25 0.41
32 31 0.51
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.36
Consensus pattern (31 bp):
ATCTTTTTCCCAAAGTCCACGACTTAGTGGC
Found at i:2667463 original size:61 final size:60
Alignment explanation
Indices: 2667389--2667612 Score: 208
Period size: 61 Copynumber: 3.7 Consensus size: 60
2667379 TCTTTTTTCT
*
2667389 TTTTTAAGTCCACAACTTCATGGCACTCTTTTTCCTTTTAAGTTCACAACTCCATGGCACC
1 TTTTTAAGTCCACAACTTCATGGCAC-CTTTTTCCTTTTAAGTCCACAACTCCATGGCACC
* * * * *
2667450 TTTTTAAGTCCACAA-TTCCATGGTATC-TTTT-C-TCTAAGTCCACAACTCCGTGTCACC
1 TTTTTAAGTCCACAACTT-CATGGCACCTTTTTCCTTTTAAGTCCACAACTCCATGGCACC
* * * *
2667507 TTTTTTTTTAAGTCCACAAC-TCTGTGGCACATTTTTCTCTTTCAGAGCCCACAACTCCATGGCA
1 ----TTTTTAAGTCCACAACTTC-ATGGCACCTTTTTC-CTTTTA-AGTCCACAACTCCATGGCA
2667571 -C
59 CC
* *
2667572 TCTTTTAAATCCACAACTTCATGGCACCTTTTTCTTTTTAA
1 T-TTTTAAGTCCACAACTTCATGGCACCTTTTTCCTTTTAA
2667613 AGCTCATAAC
Statistics
Matches: 129, Mismatches: 20, Indels: 29
0.72 0.11 0.16
Matches are distributed among these distances:
57 21 0.16
58 1 0.01
59 4 0.03
60 5 0.04
61 46 0.36
62 30 0.23
63 2 0.02
64 1 0.01
65 3 0.02
66 16 0.12
ACGTcount: A:0.23, C:0.29, G:0.10, T:0.39
Consensus pattern (60 bp):
TTTTTAAGTCCACAACTTCATGGCACCTTTTTCCTTTTAAGTCCACAACTCCATGGCACC
Found at i:2667613 original size:33 final size:32
Alignment explanation
Indices: 2667383--2667873 Score: 199
Period size: 27 Copynumber: 15.6 Consensus size: 32
2667373 GTGGCATCTT
2667383 TTTTCTTTTTTAAGTCCACAACTTCATGGCACTC
1 TTTTC-TTTTTAAGTCCACAACTTCATGGCAC-C
* * *
2667417 TTTTTCCTTTTAAGTTCACAACTCCATGGCA-C
1 -TTTTCTTTTTAAGTCCACAACTTCATGGCACC
* *
2667449 ----CTTTTTAAGTCCACAA-TTCCATGGTATC
1 TTTTCTTTTTAAGTCCACAACTT-CATGGCACC
* * * *
2667477 TTTTC--TCTAAGTCCACAACTCCGTGTCACC
1 TTTTCTTTTTAAGTCCACAACTTCATGGCACC
* *
2667507 TTTT-TTTTTAAGTCCACAAC-TCTGTGGCACAT
1 TTTTCTTTTTAAGTCCACAACTTC-ATGGCAC-C
* * *
2667539 TTTTCTCTTTCAGAGCCCACAACTCCATGGCA-C
1 TTTTCT-TTTTA-AGTCCACAACTTCATGGCACC
*
2667572 ---TC-TTTTAAATCCACAACTTCATGGCACC
1 TTTTCTTTTTAAGTCCACAACTTCATGGCACC
* ** *
2667600 TTTTTCTTTTTAAAG-CTCATAACTTTGTGGCATC
1 -TTTTCTTTTT-AAGTC-CACAACTTCATGGCACC
* * * * *
2667634 TTTTCCTTTTCAGTCTACAACTCCATGACACC
1 TTTTCTTTTTAAGTCCACAACTTCATGGCACC
** *
2667666 ----C-TTTTAAGTCCACAACCCCATGACACC
1 TTTTCTTTTTAAGTCCACAACTTCATGGCACC
* * **
2667693 TTTTTCTTTTCAAAGCCCACAACTTTGTGGCACC
1 -TTTTCTTTT-TAAGTCCACAACTTCATGGCACC
* * * *
2667727 TTTTCTTTTCAAAGTTCACAAC-TCTGTGGCATC
1 TTTTCTTTT-TAAGTCCACAACTTC-ATGGCACC
* * *
2667760 TTGTTCCTTTTAAGCCCACAACTTCGTGGCACC
1 TT-TTCTTTTTAAGTCCACAACTTCATGGCACC
* * *
2667793 ----C-TTTTAAGTCCACAACTCCGTGGCGCC
1 TTTTCTTTTTAAGTCCACAACTTCATGGCACC
** * * * * *
2667820 TTTTTCTTTACAAAGCCCATAACTTCGTGGTATC
1 -TTTTCTTT-TTAAGTCCACAACTTCATGGCACC
2667854 TTTTCTTTTTAAGTCCACAA
1 TTTTCTTTTTAAGTCCACAA
2667874 TTTCGTGACA
Statistics
Matches: 341, Mismatches: 74, Indels: 85
0.68 0.15 0.17
Matches are distributed among these distances:
26 1 0.00
27 82 0.24
28 8 0.02
30 24 0.07
31 20 0.06
32 31 0.09
33 74 0.22
34 81 0.24
35 19 0.06
36 1 0.00
ACGTcount: A:0.22, C:0.29, G:0.11, T:0.38
Consensus pattern (32 bp):
TTTTCTTTTTAAGTCCACAACTTCATGGCACC
Found at i:2667656 original size:93 final size:92
Alignment explanation
Indices: 2667488--2667737 Score: 272
Period size: 93 Copynumber: 2.7 Consensus size: 92
2667478 TTTCTCTAAG
* * * * * *
2667488 TCCACAACTCCGTGTCACCTTTTT-TTTT--AAGTCCACAACTCTGTGGCACATTTTTCTCTTTC
1 TCCACAACCCCATGACACCTTTTTCTTTTCAAAGCCCACAACTTTGTGGCAC-CTTTTCT-TTTC
* * * *
2667550 AGAGCCCACAACTCCATGGCACTCTTTTAAA
64 --AGTCTACAACTCCATGACACCCTTTTAAA
** * * * * *
2667581 TCCACAACTTCATGGCACCTTTTTCTTTTTAAAGCTCATAACTTTGTGGCATCTTTTCCTTTTCA
1 TCCACAACCCCATGACACCTTTTTCTTTTCAAAGCCCACAACTTTGTGGCACCTTTT-CTTTTCA
*
2667646 GTCTACAACTCCATGACACCCTTTTAAG
65 GTCTACAACTCCATGACACCCTTTTAAA
2667674 TCCACAACCCCATGACACCTTTTTCTTTTCAAAGCCCACAACTTTGTGGCACCTTTTCTTTTCA
1 TCCACAACCCCATGACACCTTTTTCTTTTCAAAGCCCACAACTTTGTGGCACCTTTTCTTTTCA
2667738 AAGTTCACAA
Statistics
Matches: 132, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
92 7 0.05
93 95 0.72
94 4 0.03
95 8 0.06
96 18 0.14
ACGTcount: A:0.22, C:0.31, G:0.10, T:0.37
Consensus pattern (92 bp):
TCCACAACCCCATGACACCTTTTTCTTTTCAAAGCCCACAACTTTGTGGCACCTTTTCTTTTCAG
TCTACAACTCCATGACACCCTTTTAAA
Done.