Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 7 of 126
Found at i:2306803 original size:23 final size:23
Alignment explanation
Indices: 2306776--2306833 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
2306766 AAGGTTTATA
2306776 TGTTAAAAAAATCTTTGAAAAAT
1 TGTTAAAAAAATCTTTGAAAAAT
2306799 TGTTAAAAAAATCTTTGAAAAAT
1 TGTTAAAAAAATCTTTGAAAAAT
*
2306822 TGTAAAAAAAAT
1 TGTTAAAAAAAT
2306834 TAATTAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (23 bp):
TGTTAAAAAAATCTTTGAAAAAT
Found at i:2306955 original size:10 final size:11
Alignment explanation
Indices: 2306922--2306956 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
2306912 TAAAATAATT
2306922 AAAAATCATAA
1 AAAAATCATAA
*
2306933 AGAAATCATAA
1 AAAAATCATAA
2306944 AAAAAT-ATAA
1 AAAAATCATAA
2306954 AAA
1 AAA
2306957 TATATCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 7 0.32
11 15 0.68
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.17
Consensus pattern (11 bp):
AAAAATCATAA
Found at i:2306985 original size:19 final size:19
Alignment explanation
Indices: 2306944--2307007 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
2306934 GAAATCATAA
*
2306944 AAAAATATAAAAATA-TATC
1 AAAAAT-TAAAAATATTATT
2306963 AAAAATTAAAAATATTATT
1 AAAAATTAAAAATATTATT
* *
2306982 AAAACTTATACAA-ATTA-T
1 AAAAATTA-AAAATATTATT
2307000 AAAAATTA
1 AAAAATTA
2307008 TTAAAACTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
18 16 0.41
19 20 0.51
20 3 0.08
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATTAAAAATATTATT
Found at i:2306996 original size:28 final size:28
Alignment explanation
Indices: 2306965--2307072 Score: 107
Period size: 28 Copynumber: 3.8 Consensus size: 28
2306955 AATATATCAA
2306965 AAATTA-AAAATATTATTAAAACTTATAC
1 AAATTATAAAA-ATTATTAAAACTTATAC
2306993 AAATTATAAAAATTATTAAAACTTATA-
1 AAATTATAAAAATTATTAAAACTTATAC
*
2307020 AATATTATAATAAATT-TTAATAAATTATA-
1 AA-ATTATAA-AAATTATTAA-AACTTATAC
* *
2307049 AAATTTTTATAAAATTAATAAAAC
1 AAA-TTATA-AAAATTATTAAAAC
2307073 ATATTTAAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
27 2 0.03
28 34 0.49
29 29 0.42
30 4 0.06
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (28 bp):
AAATTATAAAAATTATTAAAACTTATAC
Found at i:2307005 original size:9 final size:9
Alignment explanation
Indices: 2306943--2307071 Score: 98
Period size: 9 Copynumber: 13.4 Consensus size: 9
2306933 AGAAATCATA
*
2306943 AAAAAATAT
1 AAAAATTAT
2306952 AAAAATATAT
1 AAAAAT-TAT
2306962 CAAAAATTA-
1 -AAAAATTAT
2306971 AAAATATTATT
1 AAAA-ATTA-T
*
2306982 AAAACTTAT
1 AAAAATTAT
*
2306991 ACAAATTAT
1 AAAAATTAT
2307000 AAAAATTATT
1 AAAAATTA-T
*
2307010 AAAACTTAT
1 AAAAATTAT
*
2307019 AAATATTAT
1 AAAAATTAT
*
2307028 AATAAATTTT
1 AA-AAATTAT
2307038 AATAAATTAT
1 AA-AAATTAT
* *
2307048 AAAATTTTT
1 AAAAATTAT
2307057 ATAAAATTAAT
1 A-AAAATT-AT
2307068 AAAA
1 AAAA
2307072 CATATTTAAA
Statistics
Matches: 96, Mismatches: 15, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
8 4 0.04
9 40 0.42
10 40 0.42
11 12 0.12
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAAATTAT
Found at i:2307060 original size:31 final size:28
Alignment explanation
Indices: 2306949--2307051 Score: 59
Period size: 28 Copynumber: 3.6 Consensus size: 28
2306939 CATAAAAAAA
* *
2306949 TATAAAAATATATCAAAAATTAAAAATAT
1 TATAAAAAT-TATTAAAAATTATAAATAT
* * *
2306978 TATTAAAACTTA-TACAAATTATAAAAAT
1 TA-TAAAAATTATTAAAAATTATAAATAT
* * *
2307006 TATTAAAACTTA-TAAATATTATAATAAAT
1 TA-TAAAAATTATTAAAAATTATAA-ATAT
*
2307035 TTTAATAAATTA-TAAAA
1 TATAA-AAATTATTAAAA
2307052 TTTTTATAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
28 37 0.61
29 18 0.30
30 6 0.10
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (28 bp):
TATAAAAATTATTAAAAATTATAAATAT
Found at i:2313186 original size:21 final size:21
Alignment explanation
Indices: 2313160--2313199 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2313150 TGTTTTTAAG
2313160 TATATAATAT-TATATTATATT
1 TATATAATATATA-ATTATATT
*
2313181 TATATATTATATAATTATA
1 TATATAATATATAATTATA
2313200 GCACATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATATAATATATAATTATATT
Found at i:2314586 original size:2 final size:2
Alignment explanation
Indices: 2314579--2314633 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
2314569 TCGGAGGGTA
2314579 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2314621 AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT
2314634 TTAAATAATA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2315697 original size:29 final size:30
Alignment explanation
Indices: 2315642--2315710 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
2315632 AAAGTTAAAT
* **
2315642 TATGAATTTT-TATTTTTAGAGGAATCAAA
1 TATGAATTTTAAATTTCAAGAGGAATCAAA
2315671 TATGAATTTTAAATTTCAAGAGG-ATCAAA
1 TATGAATTTTAAATTTCAAGAGGAATCAAA
*
2315700 -ATGAAATTTAA
1 TATGAATTTTAA
2315711 CCATTAGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 10 0.29
29 16 0.46
30 9 0.26
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.39
Consensus pattern (30 bp):
TATGAATTTTAAATTTCAAGAGGAATCAAA
Found at i:2316276 original size:20 final size:21
Alignment explanation
Indices: 2316253--2316294 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2316243 ACATAAACTA
2316253 TTAAA-ATAATAAAAATATAT
1 TTAAATATAATAAAAATATAT
*
2316273 TTAAATTATTATAAAAATATAT
1 TTAAA-TATAATAAAAATATAT
2316295 AATTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
22 14 0.74
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAAATATAATAAAAATATAT
Found at i:2316860 original size:16 final size:16
Alignment explanation
Indices: 2316814--2316860 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
2316804 ATAACTTAAA
*
2316814 CTCAACACTTAATTTT
1 CTCAGCACTTAATTTT
* *
2316830 -TCGGTACTT-ATTTT
1 CTCAGCACTTAATTTT
2316844 CTCAGCACTTAATTTT
1 CTCAGCACTTAATTTT
2316860 C
1 C
2316861 CAATTTATCA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
14 5 0.21
15 13 0.54
16 6 0.25
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.47
Consensus pattern (16 bp):
CTCAGCACTTAATTTT
Found at i:2331818 original size:25 final size:22
Alignment explanation
Indices: 2331781--2331831 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
2331771 AATTGGATTT
2331781 TTTTTCTAGTTAAATTTTGTTATA
1 TTTTTCTAGTTAAATTTT-TT-TA
* *
2331805 TTTTTCTAATTTAACTTTTTTTA
1 TTTTTCT-AGTTAAATTTTTTTA
2331828 TTTT
1 TTTT
2331832 AAGAATGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.25
24 9 0.38
25 9 0.38
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTTTCTAGTTAAATTTTTTTA
Found at i:2332625 original size:43 final size:43
Alignment explanation
Indices: 2332564--2332652 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
2332554 TTTAAATTAA
*
2332564 TTAATTTTTGTCTATCGAGTCTTAACTCGATTAGTATTGGTAT
1 TTAATTTTTGTCTATCGAGTCTTAACTCGATTAGTATTAGTAT
* *
2332607 TTAATTTTTGTCTATCGAGTGTTAATTCGATTAGTATTAGTAT
1 TTAATTTTTGTCTATCGAGTCTTAACTCGATTAGTATTAGTAT
2332650 TTA
1 TTA
2332653 GGAGGACGTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.51
Consensus pattern (43 bp):
TTAATTTTTGTCTATCGAGTCTTAACTCGATTAGTATTAGTAT
Found at i:2337225 original size:17 final size:16
Alignment explanation
Indices: 2337199--2337231 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
2337189 TCATGTATAA
2337199 TTTTAATACATATTTT
1 TTTTAATACATATTTT
2337215 TTTTGAATACATATTTT
1 TTTT-AATACATATTTT
2337232 AATACATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTTAATACATATTTT
Found at i:2338047 original size:12 final size:13
Alignment explanation
Indices: 2338018--2338078 Score: 59
Period size: 13 Copynumber: 4.4 Consensus size: 13
2338008 TTGGGTCAAA
2338018 AAAAATATTTTTC
1 AAAAATATTTTTC
* *
2338031 TAAAATATTTTTA
1 AAAAATATTTTTC
2338044 AAAATATATTTGGTGTC
1 AAAA-ATATTT--T-TC
*
2338061 AAAAATATTTTTG
1 AAAAATATTTTTC
2338074 AAAAA
1 AAAAA
2338079 CTCAAAAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
13 20 0.51
14 7 0.18
16 7 0.18
17 5 0.13
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.43
Consensus pattern (13 bp):
AAAAATATTTTTC
Found at i:2348605 original size:20 final size:20
Alignment explanation
Indices: 2348580--2348621 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2348570 GAAATCATTG
2348580 TAAGAGATGCCAACCAATTC
1 TAAGAGATGCCAACCAATTC
2348600 TAAGAGATGCCAACCAATTC
1 TAAGAGATGCCAACCAATTC
2348620 TA
1 TA
2348622 TCTTTTCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.21
Consensus pattern (20 bp):
TAAGAGATGCCAACCAATTC
Found at i:2353186 original size:29 final size:29
Alignment explanation
Indices: 2353127--2353185 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2353117 TTTAACTTAA
*
2353127 TGTGAAATTTTATACATGTACTTTGATTT
1 TGTGAAATTTTATACATGAACTTTGATTT
* *
2353156 TGTGTAATTTTATACATGAAATTTTGATTT
1 TGTGAAATTTTATACATG-AACTTTGATTT
2353186 GATCCGATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.53
Consensus pattern (29 bp):
TGTGAAATTTTATACATGAACTTTGATTT
Found at i:2364941 original size:21 final size:21
Alignment explanation
Indices: 2364896--2364937 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2364886 TTTTAAAAAA
* *
2364896 TAAACCATTTTTAAATTATAT
1 TAAACCATTATTAAATCATAT
2364917 TAAACCA-TATTAAATCATAT
1 TAAACCATTATTAAATCATAT
2364937 T
1 T
2364938 TAAATAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAACCATTATTAAATCATAT
Found at i:2365603 original size:20 final size:20
Alignment explanation
Indices: 2365587--2365626 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2365577 AAATTTAAGG
2365587 ATTTTT-TAATTTTTTTAAA
1 ATTTTTATAATTTTTTTAAA
*
2365606 ATTTTTATAATTTTATTAAA
1 ATTTTTATAATTTTTTTAAA
2365626 A
1 A
2365627 ATATAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTTATAATTTTTTTAAA
Found at i:2367159 original size:19 final size:19
Alignment explanation
Indices: 2367137--2367178 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2367127 TTAAATTACG
* *
2367137 TTATTCTCCTTAATATTT-A
1 TTATTATCCCTAA-ATTTAA
2367156 TTATTATCCCTAAATTTAA
1 TTATTATCCCTAAATTTAA
2367175 TTAT
1 TTAT
2367179 CAAGTTGAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATTATCCCTAAATTTAA
Found at i:2373348 original size:4 final size:4
Alignment explanation
Indices: 2373341--2373375 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
2373331 TCTAATAAAT
*
2373341 ATAC ATAC ATAC ATAC ATAC ATAT ATATC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA-C ATAC AT
2373376 TTTGAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.89
5 3 0.11
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (4 bp):
ATAC
Found at i:2375188 original size:15 final size:15
Alignment explanation
Indices: 2375168--2375197 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2375158 ATCATCAGTC
2375168 TAATTTTAAATATTT
1 TAATTTTAAATATTT
*
2375183 TAATTTTAACTATTT
1 TAATTTTAAATATTT
2375198 AAAATGATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
TAATTTTAAATATTT
Found at i:2379188 original size:21 final size:21
Alignment explanation
Indices: 2379150--2379189 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2379140 TTTAGTTATT
*
2379150 TTTTTATTTTATGAAATTTAA
1 TTTTTATTTTATCAAATTTAA
* *
2379171 TTTTTATTTTTTCTAATTT
1 TTTTTATTTTATCAAATTT
2379190 CAAAATTCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTTTATTTTATCAAATTTAA
Found at i:2381118 original size:22 final size:20
Alignment explanation
Indices: 2381082--2381122 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 20
2381072 AGATGGTGTA
2381082 ATATATATACACATGTATAC
1 ATATATATACACATGTATAC
2381102 ATATATATACATGCATGTATA
1 ATATATATACA--CATGTATA
2381123 GTTTTACTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (20 bp):
ATATATATACACATGTATAC
Found at i:2385623 original size:12 final size:12
Alignment explanation
Indices: 2385606--2385630 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2385596 GACATGTGCT
2385606 TTTTTTTAAATA
1 TTTTTTTAAATA
2385618 TTTTTTTAAATA
1 TTTTTTTAAATA
2385630 T
1 T
2385631 ATTATTATTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTTTAAATA
Found at i:2408611 original size:3 final size:3
Alignment explanation
Indices: 2408603--2408629 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2408593 TTAGATTAAA
2408603 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
2408630 TTCCACCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2410987 original size:29 final size:29
Alignment explanation
Indices: 2410937--2411000 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
2410927 TCATAAATTT
*
2410937 AGAATTTAATCTTTATACTTTTAT-TTTTA
1 AGAA-TTAATCCTTATACTTTTATATTTTA
* *
2410966 AGAATTAATCCTTCTACATTTTTTATTTTA
1 AGAATTAATCCTTATAC-TTTTATATTTTA
2410996 A-AATT
1 AGAATT
2411001 TAAGTCCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 11 0.37
29 13 0.43
30 6 0.20
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (29 bp):
AGAATTAATCCTTATACTTTTATATTTTA
Found at i:2411524 original size:13 final size:15
Alignment explanation
Indices: 2411508--2411545 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2411498 TGAATATTAA
2411508 TTTTATTATA-A-GT
1 TTTTATTATATATGT
2411521 TTTTATTATATATGT
1 TTTTATTATATATGT
*
2411536 TTTTTTTATA
1 TTTTATTATA
2411546 CAATGGTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 1 0.05
15 11 0.50
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (15 bp):
TTTTATTATATATGT
Found at i:2419745 original size:8 final size:8
Alignment explanation
Indices: 2419732--2419774 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
2419722 ACATCATAAT
2419732 TATATTAA
1 TATATTAA
2419740 TATATTAAA
1 TATATT-AA
*
2419749 TGTAATTCAA
1 TAT-ATT-AA
2419759 TATATTAA
1 TATATTAA
2419767 TATATTAA
1 TATATTAA
2419775 ATGTAATTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 16 0.53
9 7 0.23
10 7 0.23
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (8 bp):
TATATTAA
Found at i:2419762 original size:27 final size:27
Alignment explanation
Indices: 2419732--2419794 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
2419722 ACATCATAAT
2419732 TATATTAATATATTAAATGTAATTCAA
1 TATATTAATATATTAAATGTAATTCAA
2419759 TATATTAATATATTAAATGTAATTCAA
1 TATATTAATATATTAAATGTAATTCAA
*
2419786 TATAATAAT
1 TATATTAAT
2419795 TGATTGTGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (27 bp):
TATATTAATATATTAAATGTAATTCAA
Found at i:2420267 original size:29 final size:28
Alignment explanation
Indices: 2420213--2420268 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
2420203 TGATAGAAAT
*
2420213 AAAATTATAAAACCTAAATTCACCAAAAA
1 AAAATTATAAAACCTAAAAT-ACCAAAAA
2420242 AAAATTTATAAAACCTAAAGAT-CCAAA
1 AAAA-TTATAAAACCTAAA-ATACCAAA
2420269 GTTAAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 9 0.38
30 14 0.58
31 1 0.04
ACGTcount: A:0.61, C:0.16, G:0.02, T:0.21
Consensus pattern (28 bp):
AAAATTATAAAACCTAAAATACCAAAAA
Found at i:2422420 original size:3 final size:3
Alignment explanation
Indices: 2422412--2422443 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2422402 TTTATTTGGG
2422412 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2422444 AGGTAATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2424348 original size:6 final size:6
Alignment explanation
Indices: 2424333--2424363 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2424323 GCCAAGACCA
*
2424333 GGGTCT GGGTCC GGGTCC GGGTCC GGGTCC G
1 GGGTCC GGGTCC GGGTCC GGGTCC GGGTCC G
2424364 ATCAAATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.29, G:0.52, T:0.19
Consensus pattern (6 bp):
GGGTCC
Found at i:2425557 original size:19 final size:20
Alignment explanation
Indices: 2425522--2425569 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2425512 ATAAATATTT
*
2425522 TAATATTTTCGAAT-AAAAA
1 TAATATTTTCAAATAAAAAA
2425541 TAAATATTTT-AAATAAAAAA
1 T-AATATTTTCAAATAAAAAA
2425561 TAATATTTT
1 TAATATTTT
2425570 TTGAGATTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
TAATATTTTCAAATAAAAAA
Found at i:2425948 original size:62 final size:62
Alignment explanation
Indices: 2425850--2425967 Score: 218
Period size: 62 Copynumber: 1.9 Consensus size: 62
2425840 TTAATTACAC
*
2425850 CAATTTTTACTGATTAATTTTAATTCAATTAGTATGAATATTATTATCAATACAGATTATAT
1 CAATTTTTACTGATTAATTTTAATTCAATTAATATGAATATTATTATCAATACAGATTATAT
*
2425912 CAATTTTTACTGATTAATTTTAATTCAATTAATATGAGTATTATTATCAATACAGA
1 CAATTTTTACTGATTAATTTTAATTCAATTAATATGAATATTATTATCAATACAGA
2425968 AAAACGTGGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (62 bp):
CAATTTTTACTGATTAATTTTAATTCAATTAATATGAATATTATTATCAATACAGATTATAT
Found at i:2429348 original size:22 final size:23
Alignment explanation
Indices: 2429323--2429377 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
2429313 AAAATACTTC
* *
2429323 TTATATTTATTATCATA-ATTTA
1 TTATTTTTATTATCATATATTAA
2429345 TTATTTTTCA-TATCATATATTAA
1 TTATTTTT-ATTATCATATATTAA
2429368 TTATTTTTAT
1 TTATTTTTAT
2429378 GTAGCATGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTTTTATTATCATATATTAA
Found at i:2429373 original size:23 final size:22
Alignment explanation
Indices: 2429333--2429375 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
2429323 TTATATTTAT
*
2429333 TATCATAATTTATTATTTTTCA
1 TATCATAATTAATTATTTTTCA
2429355 TATCATATATTAATTATTTTT
1 TATCATA-ATTAATTATTTTT
2429376 ATGTAGCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (22 bp):
TATCATAATTAATTATTTTTCA
Found at i:2440810 original size:61 final size:61
Alignment explanation
Indices: 2440713--2440831 Score: 195
Period size: 61 Copynumber: 2.0 Consensus size: 61
2440703 CTTTTCACAT
* *
2440713 TCTTCGATATCTGATAGGTATATTGGATACTGATTAAATTTAGAGTCTAACTGAATTAGAC
1 TCTTCGATATCAGATAGGTATATTGGATACTAATTAAATTTAGAGTCTAACTGAATTAGAC
*
2440774 TCTTCGATATCAGATAGGTATATTGGACT-CTAATTAAATTTAGAGTCTAGCTGAATTA
1 TCTTCGATATCAGATAGGTATATTGGA-TACTAATTAAATTTAGAGTCTAACTGAATTA
2440832 AACTTGAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 53 0.98
62 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.38
Consensus pattern (61 bp):
TCTTCGATATCAGATAGGTATATTGGATACTAATTAAATTTAGAGTCTAACTGAATTAGAC
Found at i:2450891 original size:46 final size:45
Alignment explanation
Indices: 2450824--2450914 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 45
2450814 TCAAGTTTAG
2450824 TCAACATCCAATTTTCTCATTCTTCTAGAGCCCTTGCCCAAATCT
1 TCAACATCCAATTTTCTCATTCTTCTAGAGCCCTTGCCCAAATCT
*
2450869 TCAACATCCAAGTTTTCTCATTCTTCTAGAGCCCTTGGCCAAATCT
1 TCAACATCCAA-TTTTCTCATTCTTCTAGAGCCCTTGCCCAAATCT
2450915 ATAATATTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 11 0.25
46 33 0.75
ACGTcount: A:0.24, C:0.32, G:0.09, T:0.35
Consensus pattern (45 bp):
TCAACATCCAATTTTCTCATTCTTCTAGAGCCCTTGCCCAAATCT
Found at i:2462065 original size:30 final size:30
Alignment explanation
Indices: 2462016--2462091 Score: 111
Period size: 30 Copynumber: 2.6 Consensus size: 30
2462006 ATGTACCAAA
* *
2462016 TTGA-TACCAACTTAGAAAAAGTGTCAAGT
1 TTGAGTACCAAATTAAAAAAAGTGTCAAGT
2462045 TT-ATGTACCAAATTAAAAAAAGTGTCAAGT
1 TTGA-GTACCAAATTAAAAAAAGTGTCAAGT
2462075 TTGAGTACCAAATTAAA
1 TTGAGTACCAAATTAAA
2462092 TCAATAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 1 0.02
29 2 0.05
30 38 0.90
31 1 0.02
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (30 bp):
TTGAGTACCAAATTAAAAAAAGTGTCAAGT
Found at i:2462444 original size:16 final size:15
Alignment explanation
Indices: 2462426--2462466 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
2462416 TTTGTTTTTT
2462426 TTTTAATTTTTAAAA
1 TTTTAATTTTTAAAA
**
2462441 TTTTCGTGTTTTAAAA
1 TTTTAAT-TTTTAAAA
2462457 TTTTAATTTT
1 TTTTAATTTT
2462467 AACTTAAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.63
Consensus pattern (15 bp):
TTTTAATTTTTAAAA
Found at i:2467797 original size:8 final size:7
Alignment explanation
Indices: 2467779--2467847 Score: 56
Period size: 7 Copynumber: 10.3 Consensus size: 7
2467769 AAATTTATTG
2467779 TTTTTAA
1 TTTTTAA
2467786 TTTTTAA
1 TTTTTAA
2467793 TTTTT-A
1 TTTTTAA
2467799 TTATTT-A
1 TT-TTTAA
**
2467806 TTCCTAA
1 TTTTTAA
2467813 TTTTTAA
1 TTTTTAA
*
2467820 TTATT-A
1 TTTTTAA
*
2467826 TTATT-A
1 TTTTTAA
*
2467832 TTTATAA
1 TTTTTAA
2467839 TTTTTAA
1 TTTTTAA
2467846 TT
1 TT
2467848 AATTAGAGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
6 14 0.27
7 37 0.73
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (7 bp):
TTTTTAA
Found at i:2467816 original size:26 final size:26
Alignment explanation
Indices: 2467783--2467848 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
2467773 TTATTGTTTT
* *
2467783 TAATTTTTAATTTTTATTATTTATTCC
1 TAATTTTTAATTATTATTA-TTATTCA
*
2467810 TAATTTTTAATTATTATTATTATTTA
1 TAATTTTTAATTATTATTATTATTCA
2467836 TAATTTTTAATTA
1 TAATTTTTAATTA
2467849 ATTAGAGTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
26 18 0.50
27 18 0.50
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (26 bp):
TAATTTTTAATTATTATTATTATTCA
Found at i:2467852 original size:27 final size:26
Alignment explanation
Indices: 2467773--2467848 Score: 98
Period size: 27 Copynumber: 2.9 Consensus size: 26
2467763 TGGACTAAAT
* * *
2467773 TTATTGTTTTTAATTTTTAATTTTTA
1 TTATTATTTATAATTTTTAATTATTA
**
2467799 TTATTTATTCCTAATTTTTAATTATTA
1 TTA-TTATTTATAATTTTTAATTATTA
2467826 TTATTATTTATAATTTTTAATTA
1 TTATTATTTATAATTTTTAATTA
2467849 ATTAGAGTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 21 0.49
27 22 0.51
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (26 bp):
TTATTATTTATAATTTTTAATTATTA
Found at i:2471792 original size:27 final size:26
Alignment explanation
Indices: 2471762--2471852 Score: 67
Period size: 27 Copynumber: 3.3 Consensus size: 26
2471752 GAATTTGATA
2471762 TTTTTTTTTTAATTTGGTACTTAAACT
1 TTTTTTTTTTAATTTGGTACTT-AACT
** * *
2471789 TTTTTCATTAAATTTGGTATTTGAACTT
1 TTTTTTTTTTAATTTGGTACTT-AAC-T
*
2471817 GCCATTTTTTTTTTAATTTGGTACCTAA-T
1 ----TTTTTTTTTTAATTTGGTACTTAACT
2471846 TTTTTTT
1 TTTTTTT
2471853 ATCCAATTTG
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
25 7 0.14
27 21 0.43
28 1 0.02
29 1 0.02
31 2 0.04
32 17 0.35
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.62
Consensus pattern (26 bp):
TTTTTTTTTTAATTTGGTACTTAACT
Found at i:2471885 original size:60 final size:58
Alignment explanation
Indices: 2471761--2471914 Score: 173
Period size: 59 Copynumber: 2.6 Consensus size: 58
2471751 TGAATTTGAT
* * * * ** * *
2471761 ATTTTTTTTTTAATTTGGTACTTAAACTTTTTTCATTAAATTTGGTATTTGAACTTGCC
1 ATTTTTTTTTTAATTTGGTACCT-AACTTTTTTTATCAAATTTGATACCTAAACTTGCA
* *
2471820 ATTTTTTTTTTAATTTGGTACCTAATTTTTTTTATCCAATTTGATACCTAAACTTAGCA
1 ATTTTTTTTTTAATTTGGTACCTAACTTTTTTTATCAAATTTGATACCTAAACTT-GCA
*
2471879 ATTTTTTTTCTTAATTTAGTACCTAAGCTTTTTTTA
1 ATTTTTTTT-TTAATTTGGTACCTAA-CTTTTTTTA
2471915 GATTCAACTT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
58 24 0.30
59 33 0.41
60 15 0.19
61 8 0.10
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.56
Consensus pattern (58 bp):
ATTTTTTTTTTAATTTGGTACCTAACTTTTTTTATCAAATTTGATACCTAAACTTGCA
Found at i:2472191 original size:30 final size:30
Alignment explanation
Indices: 2472141--2472212 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
2472131 AAAATGTTAA
* *
2472141 AGTACCAACTTAAAAAAAAGTGTCAAGTTT-
1 AGTACCAAATT-AGAAAAAGTGTCAAGTTTG
*
2472171 ATGTACCAAATTAGAAAAAGTGTTAAGTTTG
1 A-GTACCAAATTAGAAAAAGTGTCAAGTTTG
2472202 AGTACCAAATT
1 AGTACCAAATT
2472213 GGACCAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 27 0.73
31 10 0.27
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.29
Consensus pattern (30 bp):
AGTACCAAATTAGAAAAAGTGTCAAGTTTG
Found at i:2472196 original size:89 final size:89
Alignment explanation
Indices: 2472083--2472258 Score: 241
Period size: 89 Copynumber: 2.0 Consensus size: 89
2472073 AAAAAATTAG
**
2472083 GTACCAAATTAGGAAAAAGAGTTAAG-TTCATGTACCAAATTGGACC-TCAAAATGTTAAAGTAC
1 GTACCAAATTAGGAAAAAGAGTTAAGTTTCA-GTACCAAATTGGACCAT-AAAAAATT-AAGTAC
*
2472146 CAACTTAAAAAAAAGTGTCAAGTTTAT
63 CAAATTAAAAAAAAGTGTCAAGTTTAT
* *
2472173 GTACCAAATTA-GAAAAAGTGTTAAGTTTGAGTACCAAATTGGACCAATAAAAAATTAAGTACCA
1 GTACCAAATTAGGAAAAAGAGTTAAGTTTCAGTACCAAATTGGACC-ATAAAAAATTAAGTACCA
*
2472237 AATTAAAAAGAAGTGTCAAGTT
65 AATTAAAAAAAAGTGTCAAGTT
2472259 GAAGTATGAA
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
89 56 0.73
90 20 0.26
91 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (89 bp):
GTACCAAATTAGGAAAAAGAGTTAAGTTTCAGTACCAAATTGGACCATAAAAAATTAAGTACCAA
ATTAAAAAAAAGTGTCAAGTTTAT
Found at i:2482901 original size:14 final size:15
Alignment explanation
Indices: 2482864--2482901 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2482854 ATTTTAAAGT
*
2482864 TTATAATATTTTTTA
1 TTATATTATTTTTTA
*
2482879 TTATGTTATTTTTTA
1 TTATATTATTTTTTA
2482894 -TATATTAT
1 TTATATTAT
2482902 GTAATTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TTATATTATTTTTTA
Found at i:2491717 original size:38 final size:38
Alignment explanation
Indices: 2491666--2491741 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
2491656 TAAGTATTGA
2491666 AATTTAACCCATATATATGTAGTTGGATTTATTAGTTT
1 AATTTAACCCATATATATGTAGTTGGATTTATTAGTTT
2491704 AATTTAACCCATATATATGTAGTTGGATTTATTAGTTT
1 AATTTAACCCATATATATGTAGTTGGATTTATTAGTTT
2491742 TTAGAAATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.47
Consensus pattern (38 bp):
AATTTAACCCATATATATGTAGTTGGATTTATTAGTTT
Found at i:2499684 original size:3 final size:3
Alignment explanation
Indices: 2499669--2499707 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
2499659 CAAAATCCAA
*
2499669 AAT AAT CAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2499708 GAATATTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2500799 original size:27 final size:27
Alignment explanation
Indices: 2500763--2500828 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
2500753 TCAAAAAAAA
* * *
2500763 GTCAACGGTCAAAGTCAACGGTCAACG
1 GTCAATGGTCAAAATCAACGATCAACG
* *
2500790 GTCGATGGTCAAAATCAACGATCAATG
1 GTCAATGGTCAAAATCAACGATCAACG
2500817 GTCAATGGTCAA
1 GTCAATGGTCAA
2500829 TAGTAAAAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (27 bp):
GTCAATGGTCAAAATCAACGATCAACG
Found at i:2500807 original size:20 final size:20
Alignment explanation
Indices: 2500784--2500821 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2500774 AAGTCAACGG
* *
2500784 TCAACGGTCGATGGTCAAAA
1 TCAACGATCAATGGTCAAAA
2500804 TCAACGATCAATGGTCAA
1 TCAACGATCAATGGTCAA
2500822 TGGTCAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCAACGATCAATGGTCAAAA
Found at i:2500842 original size:34 final size:34
Alignment explanation
Indices: 2500777--2500857 Score: 80
Period size: 34 Copynumber: 2.5 Consensus size: 34
2500767 ACGGTCAAAG
* *
2500777 TCAACGGTCAACGGTCGATGGTCAAAATCAACGA
1 TCAACGGTCAACGGTCAATAGTCAAAATCAACGA
* *
2500811 TCAATGGTCAATGGTCAATAGT-AAAAGTCAAC-A
1 TCAACGGTCAACGGTCAATAGTCAAAA-TCAACGA
*
2500844 GC--CGGTCAACGGTC
1 TCAACGGTCAACGGTC
2500858 TATCAACGGC
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
31 10 0.26
33 6 0.15
34 23 0.59
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (34 bp):
TCAACGGTCAACGGTCAATAGTCAAAATCAACGA
Found at i:2500874 original size:11 final size:11
Alignment explanation
Indices: 2500846--2500897 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
2500836 AGTCAACAGC
2500846 CGGTCAACGGT
1 CGGTCAACGGT
** *
2500857 CTATCAACGGC
1 CGGTCAACGGT
2500868 CGGTCAACGGT
1 CGGTCAACGGT
* *
2500879 TGGTCAATGGT
1 CGGTCAACGGT
2500890 CGGTCAAC
1 CGGTCAAC
2500898 CGTTTGACTT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.21, C:0.27, G:0.31, T:0.21
Consensus pattern (11 bp):
CGGTCAACGGT
Found at i:2500885 original size:22 final size:22
Alignment explanation
Indices: 2500837--2500897 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
2500827 AATAGTAAAA
*
2500837 GTCAACAGCCGGTCAACGGTCT
1 GTCAACGGCCGGTCAACGGTCT
*
2500859 ATCAACGGCCGGTCAACGGT-T
1 GTCAACGGCCGGTCAACGGTCT
* *
2500880 GGTCAATGGTCGGTCAAC
1 -GTCAACGGCCGGTCAAC
2500898 CGTTTGACTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 1 0.03
22 32 0.97
ACGTcount: A:0.23, C:0.28, G:0.30, T:0.20
Consensus pattern (22 bp):
GTCAACGGCCGGTCAACGGTCT
Found at i:2501320 original size:11 final size:11
Alignment explanation
Indices: 2501304--2501378 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
2501294 AAGTGTGATT
*
2501304 AAAAGAGGAAG
1 AAAAGAGAAAG
2501315 AAAAGAGAAAAG
1 AAAAGAG-AAAG
2501327 AAAAGAGAAAG
1 AAAAGAGAAAG
2501338 AAATA-AGAAATG
1 AAA-AGAGAAA-G
* * *
2501350 AATGAGAAAAAT
1 AA-AAGAGAAAG
2501362 AAAAGAGAAAG
1 AAAAGAGAAAG
*
2501373 GAAAGA
1 AAAAGA
2501379 TGAGAGGCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 30 0.59
12 17 0.33
13 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.05
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:2501327 original size:12 final size:12
Alignment explanation
Indices: 2501312--2501376 Score: 55
Period size: 12 Copynumber: 5.5 Consensus size: 12
2501302 TTAAAAGAGG
2501312 AAGAAAAGAGAA
1 AAGAAAAGAGAA
2501324 AAGAAAAGAG-A
1 AAGAAAAGAGAA
2501335 AAGAAATA-AGAA
1 AAGAAA-AGAGAA
* *
2501347 ATG-AATGAGAAA
1 AAGAAAAGAG-AA
*
2501359 AATAAAAGAGAA
1 AAGAAAAGAGAA
*
2501371 AGGAAA
1 AAGAAA
2501377 GATGAGAGGC
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
11 13 0.32
12 23 0.56
13 5 0.12
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (12 bp):
AAGAAAAGAGAA
Found at i:2501346 original size:23 final size:23
Alignment explanation
Indices: 2501304--2501376 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
2501294 AAGTGTGATT
*
2501304 AAAAGAGGAAGAAAAGAGAAAAG
1 AAAAGAGAAAGAAAAGAGAAAAG
*
2501327 AAAAGAGAAAGAAATA-AGAAATG
1 AAAAGAGAAAGAAA-AGAGAAAAG
* * * *
2501350 AATGAGAAAAATAAAAGAGAAAGG
1 AA-AAGAGAAAGAAAAGAGAAAAG
2501374 AAA
1 AAA
2501377 GATGAGAGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
23 22 0.55
24 18 0.45
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (23 bp):
AAAAGAGAAAGAAAAGAGAAAAG
Found at i:2506819 original size:3 final size:3
Alignment explanation
Indices: 2506811--2506838 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2506801 CAAAATCCAA
2506811 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2506839 TAGAATATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2507933 original size:13 final size:13
Alignment explanation
Indices: 2507917--2507946 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2507907 AGGTCAATGG
2507917 TCAAAGTCAACGA
1 TCAAAGTCAACGA
*
2507930 TCAAAGTCACCGA
1 TCAAAGTCAACGA
2507943 TCAA
1 TCAA
2507947 CGGTCAATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.27, G:0.13, T:0.17
Consensus pattern (13 bp):
TCAAAGTCAACGA
Found at i:2507958 original size:7 final size:7
Alignment explanation
Indices: 2507908--2508009 Score: 64
Period size: 7 Copynumber: 14.9 Consensus size: 7
2507898 TTCAAAAAAA
*
2507908 GGTCAAT
1 GGTCAAC
2507915 GGTCAA-
1 GGTCAAC
*
2507921 AGTCAAC
1 GGTCAAC
*
2507928 GATCAA-
1 GGTCAAC
* *
2507934 AGTCACC
1 GGTCAAC
*
2507941 GATCAAC
1 GGTCAAC
*
2507948 GGTCAAT
1 GGTCAAC
*
2507955 GGTCAAT
1 GGTCAAC
* *
2507962 AGTCAAA
1 GGTCAAC
2507969 GGTCAAC
1 GGTCAAC
*
2507976 GGTCAAT
1 GGTCAAC
*
2507983 GGTTAAC
1 GGTCAAC
*
2507990 GGTCAAT
1 GGTCAAC
*
2507997 GGTTAAC
1 GGTCAAC
2508004 GGTCAA
1 GGTCAA
2508010 AGTCAACAGC
Statistics
Matches: 70, Mismatches: 23, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
6 8 0.11
7 62 0.89
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.22
Consensus pattern (7 bp):
GGTCAAC
Found at i:2507960 original size:14 final size:14
Alignment explanation
Indices: 2507943--2508009 Score: 89
Period size: 14 Copynumber: 4.8 Consensus size: 14
2507933 AAGTCACCGA
2507943 TCAACGGTCAATGG
1 TCAACGGTCAATGG
** *
2507957 TCAATAGTCAAAGG
1 TCAACGGTCAATGG
2507971 TCAACGGTCAATGG
1 TCAACGGTCAATGG
*
2507985 TTAACGGTCAATGG
1 TCAACGGTCAATGG
*
2507999 TTAACGGTCAA
1 TCAACGGTCAA
2508010 AGTCAACAGC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 46 1.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (14 bp):
TCAACGGTCAATGG
Found at i:2507967 original size:21 final size:21
Alignment explanation
Indices: 2507908--2507999 Score: 82
Period size: 21 Copynumber: 4.5 Consensus size: 21
2507898 TTCAAAAAAA
2507908 GGTCAATGGTCAA-AGTCAAC
1 GGTCAATGGTCAATAGTCAAC
* * **
2507928 GATCAA-AGTC-ACCGATCAAC
1 GGTCAATGGTCAATAG-TCAAC
*
2507948 GGTCAATGGTCAATAGTCAAA
1 GGTCAATGGTCAATAGTCAAC
* * *
2507969 GGTCAACGGTCAATGGTTAAC
1 GGTCAATGGTCAATAGTCAAC
2507990 GGTCAATGGT
1 GGTCAATGGT
2508000 TAACGGTCAA
Statistics
Matches: 55, Mismatches: 13, Indels: 7
0.73 0.17 0.09
Matches are distributed among these distances:
18 1 0.02
19 4 0.07
20 15 0.27
21 33 0.60
22 2 0.04
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.22
Consensus pattern (21 bp):
GGTCAATGGTCAATAGTCAAC
Found at i:2507974 original size:28 final size:28
Alignment explanation
Indices: 2507943--2508018 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
2507933 AAGTCACCGA
*
2507943 TCAACGGTCAATGGTCAATAGTCAAAGG
1 TCAACGGTCAATGGTCAACAGTCAAAGG
* * *
2507971 TCAACGGTCAATGGTTAACGGTCAATGG
1 TCAACGGTCAATGGTCAACAGTCAAAGG
* *
2507999 TTAACGGTCAA-AGTCAACAG
1 TCAACGGTCAATGGTCAACAG
2508019 CCGGTCAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 6 0.15
28 34 0.85
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.22
Consensus pattern (28 bp):
TCAACGGTCAATGGTCAACAGTCAAAGG
Found at i:2508474 original size:23 final size:24
Alignment explanation
Indices: 2508448--2508512 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
2508438 TGTGATTAAA
*
2508448 AGAGGAAGAAAATAGAAAAGAAT-
1 AGAGAAAGAAAATAGAAAAGAATG
*
2508471 AGAGAAAG-AAATAAGAAAGGAATG
1 AGAGAAAGAAAAT-AGAAAAGAATG
* *
2508495 AGAAAAAGAAAAGAGAAA
1 AGAGAAAGAAAATAGAAA
2508513 GGAAATATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 4 0.11
23 16 0.46
24 12 0.34
25 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.26, T:0.06
Consensus pattern (24 bp):
AGAGAAAGAAAATAGAAAAGAATG
Found at i:2508478 original size:11 final size:11
Alignment explanation
Indices: 2508458--2508513 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
2508448 AGAGGAAGAA
2508458 AATAGA-AAAG
1 AATAGAGAAAG
2508468 AATAGAGAAAG
1 AATAGAGAAAG
2508479 AAATA-AGAAAGG
1 -AATAGAGAAA-G
*
2508491 AATGAGAAAAAG
1 AAT-AGAGAAAG
*
2508503 AAAAGAGAAAG
1 AATAGAGAAAG
2508514 GAAATATGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 6 0.16
11 19 0.50
12 9 0.24
13 4 0.11
ACGTcount: A:0.68, C:0.00, G:0.25, T:0.07
Consensus pattern (11 bp):
AATAGAGAAAG
Found at i:2523970 original size:3 final size:3
Alignment explanation
Indices: 2523964--2523997 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2523954 TTGTTGTTGT
*
2523964 TGC TGC TGC TGC TGC TGC TGC TGC TGT TGC TGC T
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC T
2523998 CAGGGTACGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.29, G:0.32, T:0.38
Consensus pattern (3 bp):
TGC
Found at i:2527532 original size:16 final size:17
Alignment explanation
Indices: 2527503--2527535 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2527493 TTATTTTTTA
2527503 AATCGAAAAAAGAAAGG
1 AATCGAAAAAAGAAAGG
*
2527520 AATC-AAAAGAGAAAGG
1 AATCGAAAAAAGAAAGG
2527536 GCAAAAAATT
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:0.64, C:0.06, G:0.24, T:0.06
Consensus pattern (17 bp):
AATCGAAAAAAGAAAGG
Found at i:2530734 original size:12 final size:12
Alignment explanation
Indices: 2530717--2530743 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2530707 GTGATGATGA
2530717 TGGCGGTGGAGG
1 TGGCGGTGGAGG
2530729 TGGCGGTGGAGG
1 TGGCGGTGGAGG
2530741 TGG
1 TGG
2530744 TGGGGGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.67, T:0.19
Consensus pattern (12 bp):
TGGCGGTGGAGG
Found at i:2532926 original size:29 final size:30
Alignment explanation
Indices: 2532873--2532931 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
2532863 GAATTGGATC
* * *
2532873 AAATCAAAATTTTATGTATATAATTGCACA
1 AAATCAAAATTTCATATATACAATTGCACA
2532903 AAATCAAAA-TTCATATATACAATTGCACA
1 AAATCAAAATTTCATATATACAATTGCACA
2532932 TTAAACTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATATATACAATTGCACA
Found at i:2533672 original size:28 final size:28
Alignment explanation
Indices: 2533632--2533686 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
2533622 TAAATCTTTG
2533632 TCATTTCTTTCA-TTCCTAATTCTTTATA
1 TCATTTCTTTCATTTCCTAATT-TTTATA
*
2533660 TCATCTTC-TTCATTTTCTAATTTTTAT
1 TCAT-TTCTTTCATTTCCTAATTTTTAT
2533687 TAGGCATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (28 bp):
TCATTTCTTTCATTTCCTAATTTTTATA
Found at i:2544182 original size:24 final size:24
Alignment explanation
Indices: 2544154--2544209 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
2544144 CTCCCTTCAA
2544154 TCGTAGACGTAGCCCTTCTCCAAT
1 TCGTAGACGTAGCCCTTCTCCAAT
* *
2544178 TCGTAGGCGTAGCCGTTCTCCAAT
1 TCGTAGACGTAGCCCTTCTCCAAT
*
2544202 TCGCAGAC
1 TCGTAGAC
2544210 CTCTTCGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.32, G:0.21, T:0.27
Consensus pattern (24 bp):
TCGTAGACGTAGCCCTTCTCCAAT
Found at i:2546643 original size:13 final size:13
Alignment explanation
Indices: 2546607--2546636 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2546597 GTTTCTTAAG
2546607 GTTTTTGTTATTT
1 GTTTTTGTTATTT
2546620 GTTTTTGTTATTT
1 GTTTTTGTTATTT
2546633 -TTTT
1 GTTTT
2546637 ATTTTATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.07, C:0.00, G:0.13, T:0.80
Consensus pattern (13 bp):
GTTTTTGTTATTT
Found at i:2547105 original size:6 final size:6
Alignment explanation
Indices: 2547094--2547122 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2547084 CTTTAGAAAA
2547094 AAAATC AAAATC AAAATC AAAATC AAAAT
1 AAAATC AAAATC AAAATC AAAATC AAAAT
2547123 TTTTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATC
Found at i:2551706 original size:19 final size:18
Alignment explanation
Indices: 2551665--2551706 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
2551655 TTATTTTCAT
*
2551665 TATTTATTAAAAAATTAA
1 TATTTATTAAAAAAATAA
2551683 TATTTAATTAAAATAAATAA
1 TATTT-ATTAAAA-AAATAA
2551703 -ATTT
1 TATTT
2551707 GATTTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 11 0.52
20 5 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATTTATTAAAAAAATAA
Found at i:2557900 original size:1 final size:1
Alignment explanation
Indices: 2557896--2557925 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
2557886 TTTTTTTTTT
2557896 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
2557926 TTAGCAGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:2559541 original size:37 final size:38
Alignment explanation
Indices: 2559474--2559562 Score: 171
Period size: 37 Copynumber: 2.4 Consensus size: 38
2559464 CAATACCCAC
2559474 AACTTTAATAAGTTTATTTTTTCTTTTTTGAATTTAAT
1 AACTTTAATAAGTTTATTTTTTCTTTTTTGAATTTAAT
2559512 AACTTTAATAAGTTTA-TTTTTCTTTTTTGAATTTAAT
1 AACTTTAATAAGTTTATTTTTTCTTTTTTGAATTTAAT
2559549 AACTTTAATAAGTT
1 AACTTTAATAAGTT
2559563 GAATGTGAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 35 0.69
38 16 0.31
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (38 bp):
AACTTTAATAAGTTTATTTTTTCTTTTTTGAATTTAAT
Found at i:2563376 original size:28 final size:29
Alignment explanation
Indices: 2563333--2563387 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
2563323 AGTTCAAGCA
* *
2563333 CCAATGTGTAAACAATTGTCTAGTTCAGT
1 CCAATGTGAAAACAATTGTCAAGTTCAGT
2563362 CCAATGT-AAAACAATTGTCAAGTTCA
1 CCAATGTGAAAACAATTGTCAAGTTCA
2563388 AGACTTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (29 bp):
CCAATGTGAAAACAATTGTCAAGTTCAGT
Found at i:2565431 original size:23 final size:24
Alignment explanation
Indices: 2565404--2565448 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
2565394 TTTAGATCTC
2565404 ATAAATATGTGGTTT-TTTTTTGG
1 ATAAATATGTGGTTTATTTTTTGG
2565427 ATAAATATGTGGTTTATTTTTT
1 ATAAATATGTGGTTTATTTTTT
2565449 AATCACTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (24 bp):
ATAAATATGTGGTTTATTTTTTGG
Found at i:2565651 original size:15 final size:17
Alignment explanation
Indices: 2565619--2565653 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
2565609 CACCAAAAGG
2565619 AAATATTATTATCTTTT
1 AAATATTATTATCTTTT
2565636 AAATATT-TTA-CTTTT
1 AAATATTATTATCTTTT
2565651 AAA
1 AAA
2565654 AGTTTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 3 0.17
17 7 0.39
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (17 bp):
AAATATTATTATCTTTT
Found at i:2569481 original size:13 final size:14
Alignment explanation
Indices: 2569455--2569483 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2569445 CCCCAAAATT
2569455 ATACCCACAAAAAA
1 ATACCCACAAAAAA
2569469 ATACCCA-AAAAAA
1 ATACCCACAAAAAA
2569482 AT
1 AT
2569484 TTCAAGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.66, C:0.24, G:0.00, T:0.10
Consensus pattern (14 bp):
ATACCCACAAAAAA
Found at i:2569872 original size:2 final size:2
Alignment explanation
Indices: 2569865--2569915 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
2569855 GGATTTAAAA
2569865 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2569907 AT AT TT AT A
1 AT AT AT AT A
2569916 AATTTTCAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2594579 original size:22 final size:22
Alignment explanation
Indices: 2594524--2594580 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
2594514 AAAATTTCTA
*
2594524 TTATTATTTTGCTGTCATTTTG
1 TTATTATTTTACTGTCATTTTG
* * *
2594546 ATGTTGTTTTACTGTCATTTTG
1 TTATTATTTTACTGTCATTTTG
*
2594568 TTATTATATTACT
1 TTATTATTTTACT
2594581 ACTATTTTGT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.18, C:0.09, G:0.12, T:0.61
Consensus pattern (22 bp):
TTATTATTTTACTGTCATTTTG
Found at i:2595298 original size:126 final size:125
Alignment explanation
Indices: 2595073--2595299 Score: 294
Period size: 128 Copynumber: 1.8 Consensus size: 125
2595063 GCTTGTGCCG
* * * * *
2595073 TAATAATTTGATTTTACTTGTTCGGATATATTTCTACTCAGTTGTGCTATAATAGTTCAATTCTA
1 TAATAATTTGATTCTACTTATTCGGATATATTTCTACTCAGTTATACTATAATAATTCAATTCTA
* * *
2595138 CTAATTTGGGATTTGTATTTATGTTTGTAGTTTATACTCTCTCTCTTTTTCGTTTATGTTA
66 CTAATTTGGCATCTGTA-TTATGTTTGCAGTTTATACTCTCTCTCTTTTTCGTTTATGTTA
* **
2595199 TAATAATTTGATTCTACTTATTCGGATACATATTTTTACTTGGTTATACTATAATAATTCAATTC
1 TAATAATTTGATTCTACTTATTCGGAT--ATATTTCTACTCAGTTATACTATAATAATTCAATTC
* * *
2595264 TATTAGTTTGGCATCTGTA-TATGTTTGCGGTTTATA
64 TACTAATTTGGCATCTGTATTATGTTTGCAGTTTATA
2595300 TATTTTTTAT
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
126 40 0.47
128 45 0.53
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (125 bp):
TAATAATTTGATTCTACTTATTCGGATATATTTCTACTCAGTTATACTATAATAATTCAATTCTA
CTAATTTGGCATCTGTATTATGTTTGCAGTTTATACTCTCTCTCTTTTTCGTTTATGTTA
Found at i:2595944 original size:2 final size:2
Alignment explanation
Indices: 2595932--2595963 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2595922 AATTCTCAAA
*
2595932 AT AT AT CT 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
2595964 CACGAGTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2596839 original size:22 final size:22
Alignment explanation
Indices: 2596814--2596875 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
2596804 TCTAACTATC
2596814 ATACCATTAGTAAACTTTAATT
1 ATACCATTAGTAAACTTTAATT
* * *
2596836 ATA-CTTTAATTATACTTTAATT
1 ATACCATT-AGTAAACTTTAATT
2596858 ATACCATTAGTAAACTTT
1 ATACCATTAGTAAACTTT
2596876 CAAAACTACA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 3 0.09
22 26 0.81
23 3 0.09
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.45
Consensus pattern (22 bp):
ATACCATTAGTAAACTTTAATT
Found at i:2596843 original size:11 final size:11
Alignment explanation
Indices: 2596827--2596861 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
2596817 CCATTAGTAA
2596827 ACTTTAATTAT
1 ACTTTAATTAT
2596838 ACTTTAATTAT
1 ACTTTAATTAT
2596849 ACTTTAATTAT
1 ACTTTAATTAT
2596860 AC
1 AC
2596862 CATTAGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.51
Consensus pattern (11 bp):
ACTTTAATTAT
Found at i:2597514 original size:26 final size:24
Alignment explanation
Indices: 2597477--2597545 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 24
2597467 TATTAGACTA
*
2597477 AAATTTTAAAATATAAAAAAAATT
1 AAATTTGAAAATATAAAAAAAATT
*
2597501 AAACGTTTGAAAATAAAAATAAAAAATT
1 AAA--TTTGAAAAT-ATAA-AAAAAATT
2597529 AAATTTGAAAATATAAA
1 AAATTTGAAAATATAAA
2597546 CTTAGAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 4 0.11
25 3 0.08
26 17 0.45
27 3 0.08
28 11 0.29
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (24 bp):
AAATTTGAAAATATAAAAAAAATT
Found at i:2598498 original size:24 final size:25
Alignment explanation
Indices: 2598465--2598519 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
2598455 TTAGCTTCAC
*
2598465 TTTTTTCAATTTT-TAATTATTT-TA
1 TTTTTGCAATTTTAT-ATTATTTATA
2598489 TTTTTGCAATTTTATATTATTTAATA
1 TTTTTGCAATTTTATATTATTT-ATA
2598515 TTTTT
1 TTTTT
2598520 ATAAATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 19 0.70
25 1 0.04
26 7 0.26
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTTTGCAATTTTATATTATTTATA
Found at i:2598621 original size:27 final size:25
Alignment explanation
Indices: 2598546--2598615 Score: 79
Period size: 27 Copynumber: 2.7 Consensus size: 25
2598536 CTTTAATAGT
* * *
2598546 ATTTTTATAATTTTTGAAAATTCT-
1 ATTTTTTTTATTTTTAAAAATTCTA
2598570 ATTTTTTAAATTATTTTTAAAAATTCTA
1 ATTTTTT---TTATTTTTAAAAATTCTA
2598598 ATTTTTTTTATTTTTAAA
1 ATTTTTTTTATTTTTAAA
2598616 TAAATTTACA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 6 0.15
25 11 0.28
27 15 0.38
28 7 0.18
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (25 bp):
ATTTTTTTTATTTTTAAAAATTCTA
Found at i:2598632 original size:27 final size:25
Alignment explanation
Indices: 2598580--2598634 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 25
2598570 ATTTTTTAAA
*
2598580 TTATTTTTAAAAATTCTAATTTTTT
1 TTATTTTTAAAAATTCTAATTATTT
2598605 TTATTTTTAAATAAATT-TACATTATTT
1 TTATTTTT-AA-AAATTCTA-ATTATTT
2598632 TTA
1 TTA
2598635 ATATTTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 8 0.31
26 4 0.15
27 14 0.54
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (25 bp):
TTATTTTTAAAAATTCTAATTATTT
Found at i:2599131 original size:2 final size:2
Alignment explanation
Indices: 2599126--2599161 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2599116 AAGAGGTGTG
2599126 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2599162 ATCAAGTGGA
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):
TA
Found at i:2612031 original size:16 final size:16
Alignment explanation
Indices: 2612006--2612037 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2611996 AATTACGTTT
2612006 ATTTTCTTTAAATTAA
1 ATTTTCTTTAAATTAA
*
2612022 ATTTTTTTTAAATTAA
1 ATTTTCTTTAAATTAA
2612038 TGTATTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTCTTTAAATTAA
Found at i:2631863 original size:41 final size:41
Alignment explanation
Indices: 2631802--2631897 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
2631792 TTATTCGTAG
*
2631802 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTAGGTGACT
1 AGAATTCTTGTTAAGCTGGAGATTGTTAGAATTAGGTGACT
*
2631843 AGAATTCTTGTTAAGCTGGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGCTGGAGATTGTTAGAATTAGGTGACT
2631884 AGAATTCTTGTTAA
1 AGAATTCTTGTTAA
2631898 AATAAAATTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.38
Consensus pattern (41 bp):
AGAATTCTTGTTAAGCTGGAGATTGTTAGAATTAGGTGACT
Found at i:2634119 original size:17 final size:17
Alignment explanation
Indices: 2634073--2634126 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 17
2634063 ATTGCCTTCC
*
2634073 TTTTATTTGTTTTGATATT
1 TTTTATTTATTTTG-T-TT
2634092 ATTTTATTTA-TTTGTTT
1 -TTTTATTTATTTTGTTT
2634109 TTTTAATTTATTTTGTTT
1 TTTT-ATTTATTTTGTTT
2634127 CAGTTTGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
16 4 0.13
17 7 0.23
18 8 0.26
19 4 0.13
20 8 0.26
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (17 bp):
TTTTATTTATTTTGTTT
Found at i:2634241 original size:2 final size:2
Alignment explanation
Indices: 2634234--2634259 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2634224 TTTTCAAAAG
2634234 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
2634260 TAGGATCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2639577 original size:15 final size:15
Alignment explanation
Indices: 2639522--2639577 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 15
2639512 TCAAACTATA
2639522 ATTATTTATAA-TA-
1 ATTATTTATAATTAT
2639535 ATTAATTT-TAATTAT
1 ATT-ATTTATAATTAT
*
2639550 AATTATTCA-AATTAT
1 -ATTATTTATAATTAT
2639565 ATTATTTATAATT
1 ATTATTTATAATT
2639578 CAATTGTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
13 6 0.17
14 13 0.37
15 13 0.37
16 3 0.09
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATTTATAATTAT
Found at i:2641012 original size:30 final size:30
Alignment explanation
Indices: 2640783--2641023 Score: 356
Period size: 30 Copynumber: 8.0 Consensus size: 30
2640773 CAATTTTTTG
*
2640783 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
2640813 AAAGTTTTGGGGTCAAAATATAATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
* * *
2640843 AAAGTTTCGGGGTTAAAATATGATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
* *
2640873 AAAGTTCTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
* *
2640903 AAAGTTTCGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
* * *
2640933 AAAGTTTCGAGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
* *
2640963 AAAGTTTTGGGGTTAAAATATGATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
2640993 AAAGTTTTGGGGTCAAAATATAATTTCTGGA
1 AAAGTTTTGGGGTCAAAATATAATTT-TGGA
2641024 CAATTTAGGG
Statistics
Matches: 191, Mismatches: 19, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
30 187 0.98
31 4 0.02
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (30 bp):
AAAGTTTTGGGGTCAAAATATAATTTTGGA
Found at i:2642880 original size:6 final size:6
Alignment explanation
Indices: 2642861--2642952 Score: 95
Period size: 6 Copynumber: 15.5 Consensus size: 6
2642851 AAGTTAAAAA
**
2642861 AAATTT ATAATTT AAATTT AAATTT AAATTT -AAGGT AAATTT AAATAATT
1 AAATTT A-AATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAAT--TT
2642911 AAATTT AAATTT AAGA--T AAATTT AAATTT AAA--T AAATTT AAA
1 AAATTT AAATTT AA-ATTT AAATTT AAATTT AAATTT AAATTT AAA
2642953 ATCAATTTAA
Statistics
Matches: 73, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
4 5 0.07
5 6 0.08
6 49 0.67
7 7 0.10
8 6 0.08
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (6 bp):
AAATTT
Found at i:2642901 original size:11 final size:11
Alignment explanation
Indices: 2642885--2642935 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
2642875 AATTTAAATT
*
2642885 TAAATTTAAGG
1 TAAATTTAAGA
2642896 TAAATTTAA-A
1 TAAATTTAAGA
* **
2642906 T-AATTAAATT
1 TAAATTTAAGA
2642916 TAAATTTAAGA
1 TAAATTTAAGA
2642927 TAAATTTAA
1 TAAATTTAA
2642936 ATTTAAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 24 0.75
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (11 bp):
TAAATTTAAGA
Found at i:2642937 original size:37 final size:38
Alignment explanation
Indices: 2642874--2642952 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 38
2642864 TTTATAATTT
*
2642874 AAATTTAAATTTAAATTTAAGGTAAATTTAAATAA-TT
1 AAATTTAAATTTAAATTAAAGGTAAATTTAAATAATTT
**
2642911 AAATTTAAATTTAAGA-TAAATTTAAATTTAAATAAATTT
1 AAATTTAAATTTAA-ATTAAAGGTAAATTTAAAT-AATTT
2642950 AAA
1 AAA
2642953 ATCAATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 28 0.78
38 3 0.08
39 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (38 bp):
AAATTTAAATTTAAATTAAAGGTAAATTTAAATAATTT
Found at i:2642954 original size:17 final size:16
Alignment explanation
Indices: 2642861--2642952 Score: 107
Period size: 17 Copynumber: 5.6 Consensus size: 16
2642851 AAGTTAAAAA
2642861 AAATTTATAATTTAAATTT
1 AAATTTA-AATTTAAA--T
*
2642880 AAATTTAAATTTAAGGT
1 AAATTTAAATTTAA-AT
*
2642897 AAATTTAAA--TAATT
1 AAATTTAAATTTAAAT
2642911 AAATTTAAATTTAAGAT
1 AAATTTAAATTTAA-AT
2642928 AAATTTAAATTTAAAT
1 AAATTTAAATTTAAAT
2642944 AAATTTAAA
1 AAATTTAAA
2642953 ATCAATTTAA
Statistics
Matches: 66, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
14 10 0.15
15 3 0.05
16 14 0.21
17 25 0.38
18 7 0.11
19 7 0.11
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
AAATTTAAATTTAAAT
Found at i:2651529 original size:7 final size:7
Alignment explanation
Indices: 2651517--2651546 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
2651507 GATAGCACTA
2651517 GTGACAT
1 GTGACAT
2651524 GTGACAT
1 GTGACAT
2651531 GTGACAT
1 GTGACAT
2651538 GTGACAT
1 GTGACAT
2651545 GT
1 GT
2651547 ATAAGAGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (7 bp):
GTGACAT
Found at i:2652574 original size:23 final size:24
Alignment explanation
Indices: 2652530--2652582 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
2652520 GCTTATATTT
*
2652530 TCAAATTAAATATTTTACAAGGTA
1 TCAAATTAAATATTTTACAAGGAA
**
2652554 TCAAATTAAAT-TTTTTTAAGGAA
1 TCAAATTAAATATTTTACAAGGAA
2652577 TCAAAT
1 TCAAAT
2652583 ATCAACATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (24 bp):
TCAAATTAAATATTTTACAAGGAA
Found at i:2655150 original size:12 final size:12
Alignment explanation
Indices: 2655133--2655157 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2655123 CTCCTCCATC
2655133 GTGTTCATATGG
1 GTGTTCATATGG
2655145 GTGTTCATATGG
1 GTGTTCATATGG
2655157 G
1 G
2655158 GAAGAGACGT
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:0.16, C:0.08, G:0.36, T:0.40
Consensus pattern (12 bp):
GTGTTCATATGG
Found at i:2668434 original size:23 final size:23
Alignment explanation
Indices: 2668386--2668434 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2668376 TAAAATTTTC
* * **
2668386 AGATTAGGCATTAGAACAAATTT
1 AGATTAAGCAATAGAACAAAACT
2668409 AGATTAAGCAATAGAACAAAACT
1 AGATTAAGCAATAGAACAAAACT
2668432 AGA
1 AGA
2668435 GGGAGTTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.51, C:0.10, G:0.16, T:0.22
Consensus pattern (23 bp):
AGATTAAGCAATAGAACAAAACT
Found at i:2670792 original size:160 final size:162
Alignment explanation
Indices: 2670611--2670955 Score: 444
Period size: 162 Copynumber: 2.1 Consensus size: 162
2670601 ATTTTAACTA
* * * * *
2670611 ATTTTTAATTTAATCCTTTGACTGTTTGACTGTACCAGAGATTGCCACGTGTCT-TTTTTTGCTT
1 ATTTATAAATTAATCCTTTGACTGTTTGACTGCACCAGAGACTGCCACGTGTCTCTTTTTGGCTT
* *
2670675 ATTTACGCATTTAGTCCCTGC-ATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATT
66 ATTTACGCATTTAGTCCCTGCTATTTTTAACTTATTTTAATTTAATCCCTAAATCAACTTTTATT
2670739 TAATTACAAAACTGGCCC-AATAATTTTTCAAG
131 TAATTACAAAACTGGCCCAAAT-ATTTTTCAAG
* * * *
2670771 GTTTATAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCTACGTGTCTCTTTTTGGCTT
1 ATTTATAAATTAATCCTTTGACTGTTTGACTGCACCAGAGACTGCCACGTGTCTCTTTTTGGCTT
** * * * * * *
2670836 ATTTGTGCATTTAGTCCTTTCTATTTTTAACTTATTTTAATTTAGTCCTTGAATTAACTTTTATT
66 ATTTACGCATTTAGTCCCTGCTATTTTTAACTTATTTTAATTTAATCCCTAAATCAACTTTTATT
* * *
2670901 TAATTACAAAATTGGTCCAAATTTTTTTCAAG
131 TAATTACAAAACTGGCCCAAATATTTTTCAAG
* *
2670933 ATTTTTAAATTAATCCCTTGACT
1 ATTTATAAATTAATCCTTTGACT
2670956 TCTAGATGCC
Statistics
Matches: 156, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
160 46 0.29
161 26 0.17
162 81 0.52
163 3 0.02
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.47
Consensus pattern (162 bp):
ATTTATAAATTAATCCTTTGACTGTTTGACTGCACCAGAGACTGCCACGTGTCTCTTTTTGGCTT
ATTTACGCATTTAGTCCCTGCTATTTTTAACTTATTTTAATTTAATCCCTAAATCAACTTTTATT
TAATTACAAAACTGGCCCAAATATTTTTCAAG
Found at i:2671063 original size:30 final size:30
Alignment explanation
Indices: 2671027--2671231 Score: 202
Period size: 30 Copynumber: 6.9 Consensus size: 30
2671017 AAATTATCCA
*
2671027 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
2671057 AAAATTACTTTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
**
2671087 AAAATTACATTTTGACCCCAAAACTTTTTG
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * **
2671117 AAAATTATATTTTGGCCCTTAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
2671147 AAAATCATATTTTGACCCCAAAA-TTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * * *
2671176 AAAAAATTGCATTTTTACCTCGAAAC-TTT-C
1 --AAAATTACATTTTGACCCCAAAACTTTTCC
* *
2671206 AAAATTACCA-TTTCACCCCCAAACTT
1 AAAATTA-CATTTTGACCCCAAAACTT
2671232 CCCTAAATCC
Statistics
Matches: 143, Mismatches: 27, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
28 17 0.12
29 9 0.06
30 97 0.68
31 20 0.14
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:2671270 original size:58 final size:58
Alignment explanation
Indices: 2671205--2671335 Score: 190
Period size: 58 Copynumber: 2.2 Consensus size: 58
2671195 TCGAAACTTT
* * *
2671205 CAAAATTACCATTTCACCCCCAAACTTCCCTAAATCCCGTTTTAAACATCGATTTTAC
1 CAAAATTACCATTTCACCCCCAAACTTCCCTAAATCCCATTTTAAACACCGATTTCAC
* * * *
2671263 TAAAATTACCATTTCACCCTCAAACTTCCCTAAATCCCATTTTTAACCCCGATTTCAC
1 CAAAATTACCATTTCACCCCCAAACTTCCCTAAATCCCATTTTAAACACCGATTTCAC
2671321 CAAAATCTACCATTT
1 CAAAAT-TACCATTT
2671336 TGTCCCCGGG
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
58 56 0.88
59 8 0.12
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.32
Consensus pattern (58 bp):
CAAAATTACCATTTCACCCCCAAACTTCCCTAAATCCCATTTTAAACACCGATTTCAC
Found at i:2680493 original size:18 final size:19
Alignment explanation
Indices: 2680470--2680508 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2680460 CTGACTTTTA
2680470 GAATTTTT-AGTTGGATTT
1 GAATTTTTCAGTTGGATTT
*
2680488 GAATTTTTCTGTTGGATTT
1 GAATTTTTCAGTTGGATTT
2680507 GA
1 GA
2680509 TTTCCAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.21, C:0.03, G:0.23, T:0.54
Consensus pattern (19 bp):
GAATTTTTCAGTTGGATTT
Found at i:2683063 original size:12 final size:13
Alignment explanation
Indices: 2683039--2683067 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2683029 CGGTCCGATC
2683039 ATATTATTTTTTT
1 ATATTATTTTTTT
2683052 ATATTA-TTTTTT
1 ATATTATTTTTTT
2683064 ATAT
1 ATAT
2683068 AAAAACAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATATTATTTTTTT
Found at i:2686458 original size:27 final size:27
Alignment explanation
Indices: 2686408--2686486 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 27
2686398 TTGGGGTCTT
* * **
2686408 CCTCATCTTCCTCCTCAGTTGAAGAC-
1 CCTCTTCTTCTTCCTCAGAAGAAGACG
*
2686434 CCTTCTTCTTCTTCCTCAGAAGAAGTCG
1 CC-TCTTCTTCTTCCTCAGAAGAAGACG
* * *
2686462 CCTCTTCATCTTCTTCAGAGGAAGA
1 CCTCTTCTTCTTCCTCAGAAGAAGA
2686487 AGCGGCTGGT
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
26 2 0.05
27 38 0.90
28 2 0.05
ACGTcount: A:0.20, C:0.33, G:0.14, T:0.33
Consensus pattern (27 bp):
CCTCTTCTTCTTCCTCAGAAGAAGACG
Found at i:2686557 original size:4 final size:4
Alignment explanation
Indices: 2686550--2686578 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2686540 GAGAGAGAGA
2686550 GAGG GAGG GAGG GAGG GAGG GAGG GAGG G
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG G
2686579 GAGAGGCTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:2688490 original size:27 final size:27
Alignment explanation
Indices: 2688452--2688505 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2688442 AATAACATAC
2688452 ATTTTTTTGGATACGGTGAATGTGTAA
1 ATTTTTTTGGATACGGTGAATGTGTAA
2688479 ATTTTTTTGGATACGGTGAATGTGTAA
1 ATTTTTTTGGATACGGTGAATGTGTAA
2688506 GAAATTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.04, G:0.26, T:0.44
Consensus pattern (27 bp):
ATTTTTTTGGATACGGTGAATGTGTAA
Found at i:2697041 original size:4 final size:4
Alignment explanation
Indices: 2697034--2697102 Score: 77
Period size: 4 Copynumber: 17.2 Consensus size: 4
2697024 AAATAAACGG
* * * *
2697034 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GGAA GGAA GAAT GAGAG GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA
*
2697083 GAAA G-AA GAAT GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA G
2697103 GTAATGTGTA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
3 3 0.05
4 50 0.89
5 3 0.05
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (4 bp):
GAAA
Found at i:2700141 original size:28 final size:27
Alignment explanation
Indices: 2700110--2700165 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
2700100 TTAGGGCTTG
* *
2700110 AAGTTTAGGGTTTAAAGTTTATAGTTTT
1 AAGTGTAGAGTTTAAAGTTTAT-GTTTT
* *
2700138 AAGTGTCGAGTTTAAGGTTTATGTTTT
1 AAGTGTAGAGTTTAAAGTTTATGTTTT
2700165 A
1 A
2700166 GGGTTAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.27, C:0.02, G:0.23, T:0.48
Consensus pattern (27 bp):
AAGTGTAGAGTTTAAAGTTTATGTTTT
Found at i:2700288 original size:184 final size:184
Alignment explanation
Indices: 2699979--2700354 Score: 581
Period size: 184 Copynumber: 2.0 Consensus size: 184
2699969 GGTTTTGGAA
* **
2699979 TTAGGGTTAAGGATTTCTAATTTAAGGTTTTGGAACGTAATTTTTAAAAGTATCACAACCTCGAA
1 TTAGGGTTAAAGATTTCTAATTTAAGGTTTTAAAACGTAATTTTTAAAAGTATCACAACCTCGAA
2700044 ACTTTTCATTTATTGTCTCTATTTGTGGTTTTTTAAAAAAGTTTCATGTATAGAATTTAGGGCTT
66 ACTTTTCATTTATTGTCTCTATTTGTGGTTTTTTAAAAAAGTTTCATGTATAGAATTTAGGGCTT
* * *
2700109 GAAGTTTAGGGTTTAAAGTTTATAGTTTTAAGTGTCGAGTTTAAGGTTTATGTT
131 GAAGTTTAGGATTTAAAGCTTATAGTTTTAAGTGTCGAGTTTAAGGTTTAGGTT
* * *
2700163 TTAGGGTTAAAGATTTCTAATTTAGGGTTTTAAAATGTAATTTTTGAAAGTATCACAACCTCGAA
1 TTAGGGTTAAAGATTTCTAATTTAAGGTTTTAAAACGTAATTTTTAAAAGTATCACAACCTCGAA
* * * * *
2700228 ACTTTTCATTTATTGTCTTTATTTGTGGTTTTTTAAAAATGTTTCATTTATAGGATTTAGGGTTT
66 ACTTTTCATTTATTGTCTCTATTTGTGGTTTTTTAAAAAAGTTTCATGTATAGAATTTAGGGCTT
** * *
2700293 GAAGTTTAGGATTTATGGCTTATGGTTTTAAGTGTCGAGTTTAGGGTTTAGGTT
131 GAAGTTTAGGATTTAAAGCTTATAGTTTTAAGTGTCGAGTTTAAGGTTTAGGTT
*
2700347 TTAAGGTT
1 TTAGGGTT
2700355 TAATGTTATG
Statistics
Matches: 173, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
184 173 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.46
Consensus pattern (184 bp):
TTAGGGTTAAAGATTTCTAATTTAAGGTTTTAAAACGTAATTTTTAAAAGTATCACAACCTCGAA
ACTTTTCATTTATTGTCTCTATTTGTGGTTTTTTAAAAAAGTTTCATGTATAGAATTTAGGGCTT
GAAGTTTAGGATTTAAAGCTTATAGTTTTAAGTGTCGAGTTTAAGGTTTAGGTT
Found at i:2700601 original size:21 final size:20
Alignment explanation
Indices: 2700569--2700615 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
2700559 TTAGGGTCCA
*
2700569 ATTGCCTCGAAGGAGTAGAGT
1 ATTG-CTCGAAGGAGTAAAGT
2700590 ATTGCTCGGAAGGAGTAAAGT
1 ATTGCTC-GAAGGAGTAAAGT
2700611 ATTGC
1 ATTGC
2700616 GATGGCTCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.30, C:0.13, G:0.32, T:0.26
Consensus pattern (20 bp):
ATTGCTCGAAGGAGTAAAGT
Found at i:2702463 original size:30 final size:30
Alignment explanation
Indices: 2702369--2702463 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 30
2702359 CCAAAATGAG
* *
2702369 TTATTTACTAAAATGGTACAAAATATATAT
1 TTATTTACTAAAATGGTACAAAATAAAAAT
* * * * * * **
2702399 TTATATACCAAATTGGTATCCACA-CACCA-
1 TTATTTACTAAAATGGTA-CAAAATAAAAAT
2702428 TTATTTACTAAAATGGTACAAAATAAAAAT
1 TTATTTACTAAAATGGTACAAAATAAAAAT
2702458 TTATTT
1 TTATTT
2702464 TGTACCATTT
Statistics
Matches: 45, Mismatches: 17, Indels: 6
0.66 0.25 0.09
Matches are distributed among these distances:
28 3 0.07
29 17 0.38
30 22 0.49
31 3 0.07
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (30 bp):
TTATTTACTAAAATGGTACAAAATAAAAAT
Done.