Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000186.1 Hibiscus syriacus cultivar Beakdansim tig00000329_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3152351
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 15 of 17
Found at i:2694161 original size:23 final size:23
Alignment explanation
Indices: 2694123--2694177 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
2694113 TTTCTAGGGG
*
2694123 CACATAGAATTTGTCCCGAAGGAC
1 CACATAGAA-ATGTCCCGAAGGAC
* *
2694147 CACGTAGAAATGTCCCGAATGAC
1 CACATAGAAATGTCCCGAAGGAC
2694170 CACATAGA
1 CACATAGA
2694178 TGTCTCGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (23 bp):
CACATAGAAATGTCCCGAAGGAC
Found at i:2694232 original size:21 final size:21
Alignment explanation
Indices: 2694199--2694293 Score: 73
Period size: 21 Copynumber: 4.4 Consensus size: 21
2694189 AACACTCCTT
*
2694199 AAGGATCACATATATATTCCA
1 AAGGACCACATATATATTCCA
* * * * *
2694220 AAGGACCAAATATGTGTCCCG
1 AAGGACCACATATATATTCCA
* *
2694241 AAGAACCGCATATATATTCCA
1 AAGGACCACATATATATTCCA
** *
2694262 AAGGATTACATATATATATCCCG
1 AAGGACCACATATATAT-T-CCA
2694285 AAGGACCAC
1 AAGGACCAC
2694294 GTAGAACCCT
Statistics
Matches: 52, Mismatches: 20, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
21 42 0.81
22 1 0.02
23 9 0.17
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (21 bp):
AAGGACCACATATATATTCCA
Found at i:2698240 original size:12 final size:14
Alignment explanation
Indices: 2698223--2698259 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2698213 ATAAATTTAT
2698223 AAAATT-TAAA-AA
1 AAAATTATAAATAA
2698235 AAAATTATAAATAA
1 AAAATTATAAATAA
*
2698249 AAAACTATAAA
1 AAAATTATAAA
2698260 GATAACTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 6 0.27
13 4 0.18
14 12 0.55
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAATTATAAATAA
Found at i:2702754 original size:28 final size:28
Alignment explanation
Indices: 2702714--2702771 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
2702704 AACATATAGC
2702714 AAATGCAATAATTATAATAATTTTAATA
1 AAATGCAATAATTATAATAATTTTAATA
*
2702742 AAATGCAATAATTATAATAATTTTAGTA
1 AAATGCAATAATTATAATAATTTTAATA
2702770 AA
1 AA
2702772 TGATATATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.38
Consensus pattern (28 bp):
AAATGCAATAATTATAATAATTTTAATA
Found at i:2702972 original size:14 final size:14
Alignment explanation
Indices: 2702936--2702973 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
2702926 TAGAATAAAA
2702936 TAAAAATAATATTT
1 TAAAAATAATATTT
2702950 TATAAAATAAT-TATT
1 TA-AAAATAATAT-TT
2702965 TAAAAATAA
1 TAAAAATAA
2702974 CTGTAGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAAAATAATATTT
Found at i:2724534 original size:20 final size:21
Alignment explanation
Indices: 2724509--2724642 Score: 139
Period size: 21 Copynumber: 6.5 Consensus size: 21
2724499 TTTTCCCAAT
*
2724509 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2724529 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
2724550 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2724570 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
2724591 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2724611 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2724632 TCGCAATGCGA
1 TCGCAATGCGA
2724643 TACTGACTAT
Statistics
Matches: 90, Mismatches: 21, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
20 43 0.48
21 47 0.52
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2724656 original size:20 final size:19
Alignment explanation
Indices: 2724631--2724745 Score: 86
Period size: 20 Copynumber: 5.7 Consensus size: 19
2724621 AATTGGGAAA
*
2724631 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* * *
2724651 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATACTAC--T
*
2724672 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATAC-TACT
*
2724692 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* *
2724712 TTCGCAACGCGATAATACAT
1 ATCGCAACGCGATACTAC-T
*
2724732 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
2724746 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.06
20 47 0.60
21 23 0.29
22 3 0.04
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (19 bp):
ATCGCAACGCGATACTACT
Found at i:2724657 original size:41 final size:41
Alignment explanation
Indices: 2724509--2724642 Score: 268
Period size: 41 Copynumber: 3.3 Consensus size: 41
2724499 TTTTCCCAAT
2724509 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
2724550 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
2724591 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
2724632 TCGCAATGCGA
1 TCGCAATGCGA
2724643 TACTGACTAT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:2724673 original size:41 final size:41
Alignment explanation
Indices: 2724628--2724705 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
2724618 GCGAATTGGG
* * *
2724628 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
* *
2724669 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
2724706 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
Found at i:2724941 original size:22 final size:22
Alignment explanation
Indices: 2724913--2724956 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2724903 CACTCTCTCA
2724913 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
2724935 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2724957 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2725245 original size:20 final size:20
Alignment explanation
Indices: 2725220--2725257 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2725210 TGATTCTCTC
2725220 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
2725240 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
2725258 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:2727139 original size:19 final size:20
Alignment explanation
Indices: 2727085--2727151 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
2727075 TAGTTTACTT
* *
2727085 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
2727105 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
2727125 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
2727144 TCGCAACG
1 TCGCAACG
2727152 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2727159 original size:14 final size:14
Alignment explanation
Indices: 2727140--2727229 Score: 90
Period size: 14 Copynumber: 5.9 Consensus size: 14
2727130 ATGCGAAATG
2727140 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2727154 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
2727170 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
2727186 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
2727202 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2727218 AAAATCGCAACG
1 AAAATCGCAACG
2727230 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
14 30 0.47
16 16 0.25
18 18 0.28
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2727182 original size:32 final size:33
Alignment explanation
Indices: 2727124--2727246 Score: 223
Period size: 32 Copynumber: 3.8 Consensus size: 33
2727114 GGAAATGGCT
2727124 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2727157 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2727189 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2727221 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
2727247 TGCGATTTGT
Statistics
Matches: 88, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
32 63 0.72
33 25 0.28
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2727300 original size:18 final size:16
Alignment explanation
Indices: 2727258--2727306 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 16
2727248 GCGATTTGTG
2727258 TTTCGCGTTGCGATTT
1 TTTCGCGTTGCGATTT
*
2727274 TGT--CGTTGCGATTT
1 TTTCGCGTTGCGATTT
2727288 CATTTCGCGTTGCGATTT
1 --TTTCGCGTTGCGATTT
2727306 T
1 T
2727307 AAGTTTCGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 11 0.41
16 5 0.19
18 11 0.41
ACGTcount: A:0.08, C:0.18, G:0.24, T:0.49
Consensus pattern (16 bp):
TTTCGCGTTGCGATTT
Found at i:2727319 original size:20 final size:18
Alignment explanation
Indices: 2727258--2727320 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 18
2727248 GCGATTTGTG
2727258 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTAA
* *
2727274 TGT--CGTTGCGATTTCA
1 TTTCGCGTTGCGATTTAA
2727290 TTTCGCGTTGCGATTTTAA
1 TTTCGCGTTGCGA-TTTAA
*
2727309 GTTTCGTGTTGC
1 -TTTCGCGTTGC
2727321 CAAAGTAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 11 0.30
16 4 0.11
18 8 0.22
19 4 0.11
20 10 0.27
ACGTcount: A:0.10, C:0.17, G:0.25, T:0.48
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTAA
Found at i:2729194 original size:14 final size:14
Alignment explanation
Indices: 2729175--2729210 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2729165 ATTGTTTAAT
2729175 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2729189 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2729203 TGATTTGT
1 TGATTTGT
2729211 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2729336 original size:14 final size:14
Alignment explanation
Indices: 2729317--2729367 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 14
2729307 CGAAATGGCT
2729317 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
2729331 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
2729350 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
2729364 ATCG
1 ATCG
2729368 TAATGCGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 15 0.47
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.34
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.12
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:2729363 original size:19 final size:19
Alignment explanation
Indices: 2729327--2729363 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2729317 ATCGCAACGA
* *
2729327 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAAAT
2729346 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
2729364 ATCGTAATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:2730514 original size:24 final size:24
Alignment explanation
Indices: 2730487--2730540 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2730477 GTATTCGAAA
* *
2730487 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
2730511 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
2730535 TTTGAT
1 TTTGAT
2730541 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:2733042 original size:19 final size:19
Alignment explanation
Indices: 2733020--2733078 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
2733010 GGAAATTACT
2733020 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2733039 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2733053 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2733072 ATTGCAA
1 ATCGCAA
2733079 CGCTAATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.50
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2733224 original size:14 final size:14
Alignment explanation
Indices: 2733205--2733241 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2733195 CATCAATTAA
2733205 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2733219 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2733233 ACAAATCAA
1 ACAAATCAA
2733242 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2734683 original size:42 final size:42
Alignment explanation
Indices: 2734637--2734720 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
2734627 CGATGACAGT
* * *
2734637 GGCCTCTTGAACGGTGGGAGGGGACTCCCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCCCGAGGAATGATAGG
* ** *
2734679 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCCCGAGGAATGATAGG
2734721 CGAGTCAGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.23, C:0.18, G:0.39, T:0.20
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCCCGAGGAATGATAGG
Found at i:2736765 original size:33 final size:33
Alignment explanation
Indices: 2736708--2736806 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
2736698 ACGAGATAAT
*
2736708 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
2736742 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
2736775 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
2736807 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:2736800 original size:19 final size:19
Alignment explanation
Indices: 2736683--2736867 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
2736673 TCTTTTGGTT
*
2736683 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
2736702 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
2736722 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
2736740 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
2736756 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
2736774 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2736789 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
2736809 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2736828 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2736847 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2736866 GA
1 GA
2736868 TTTTGGTTTC
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 62 0.45
20 45 0.33
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2736821 original size:39 final size:38
Alignment explanation
Indices: 2736778--2736867 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
2736768 GCGACCAGAC
2736778 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
2736817 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
2736855 AATCGCAATGCGA
1 AATCGCAACGCGA
2736868 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:2736896 original size:19 final size:19
Alignment explanation
Indices: 2736863--2736929 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
2736853 AAAATCGCAA
**
2736863 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
2736882 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
2736901 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
2736921 TGCGATTTT
1 TGCGATTTT
2736930 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:2737471 original size:20 final size:20
Alignment explanation
Indices: 2737446--2737498 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2737436 GCGCTATGTA
2737446 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
2737466 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
2737486 TATCTCGTTGCGA
1 AATCGCGTTGCGA
2737499 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:2737532 original size:20 final size:20
Alignment explanation
Indices: 2737507--2737560 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2737497 GATTTTGTAT
2737507 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
2737527 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
2737547 TATCGCATTGCGAT
1 TATCGCATTGCGAT
2737561 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:2737545 original size:61 final size:61
Alignment explanation
Indices: 2737447--2737563 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
2737437 CGCTATGTAA
* * * * *
2737447 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
2737508 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
2737564 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:2737579 original size:61 final size:61
Alignment explanation
Indices: 2737447--2737581 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
2737437 CGCTATGTAA
* * * * * ** *
2737447 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
2737508 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
2737570 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
2737582 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:2737671 original size:21 final size:21
Alignment explanation
Indices: 2737631--2737671 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2737621 ATTGTATACC
**
2737631 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
2737652 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
2737672 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:2742391 original size:25 final size:25
Alignment explanation
Indices: 2742363--2742416 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
2742353 CCTCCCTAAA
2742363 ACCTAGATTGGAGGAAAAAAAGTAT
1 ACCTAGATTGGAGGAAAAAAAGTAT
*
2742388 ACCTAGATTGGAGGAAAAAGAGTAT
1 ACCTAGATTGGAGGAAAAAAAGTAT
2742413 ACCT
1 ACCT
2742417 TGAAGTGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.20
Consensus pattern (25 bp):
ACCTAGATTGGAGGAAAAAAAGTAT
Found at i:2753875 original size:17 final size:17
Alignment explanation
Indices: 2753853--2753887 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2753843 TAATATTCTT
2753853 TTATAAATTTAAATTTA
1 TTATAAATTTAAATTTA
2753870 TTATAAATTTAAATTTA
1 TTATAAATTTAAATTTA
2753887 T
1 T
2753888 ATATTTGTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATAAATTTAAATTTA
Found at i:2754118 original size:2 final size:2
Alignment explanation
Indices: 2754113--2754145 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2754103 TTTTTAAATA
2754113 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2754146 TTTTGGGTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2759225 original size:15 final size:15
Alignment explanation
Indices: 2759190--2759227 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2759180 AACAAAAGTG
2759190 AAAATAA-ATAAATA
1 AAAATAATATAAATA
* *
2759204 AATATAATATATATA
1 AAAATAATATAAATA
2759219 AAAATAATA
1 AAAATAATA
2759228 ATAATATGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATAATATAAATA
Found at i:2760572 original size:7 final size:6
Alignment explanation
Indices: 2760562--2760630 Score: 58
Period size: 7 Copynumber: 11.5 Consensus size: 6
2760552 AAGAAAAAAA
2760562 AATAAGT AATAAAT AA-AAT AA-AAT AAATAAT AATAAAT AATAAT AATAATT
1 AATAA-T AAT-AAT AATAAT AATAAT -AATAAT AAT-AAT AATAAT AATAA-T
2760613 AAT-AT AATAA- AA-AAT AAT
1 AATAAT AATAAT AATAAT AAT
2760631 TTAAAATTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 17
0.76 0.00 0.24
Matches are distributed among these distances:
4 2 0.04
5 16 0.30
6 15 0.28
7 19 0.35
8 2 0.04
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (6 bp):
AATAAT
Found at i:2760595 original size:3 final size:3
Alignment explanation
Indices: 2760562--2760630 Score: 58
Period size: 3 Copynumber: 23.0 Consensus size: 3
2760552 AAGAAAAAAA
2760562 AAT AAGT AAT AAAT AA- AAT AA- AAT AAAT AAT AAT AAAT AAT AAT AAT
1 AAT AA-T AAT -AAT AAT AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT
2760609 AATT AAT -AT AAT AA- AA- AAT AAT
1 AA-T AAT AAT AAT AAT AAT AAT AAT
2760631 TTAAAATTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 18
0.76 0.00 0.24
Matches are distributed among these distances:
2 10 0.18
3 32 0.56
4 15 0.26
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2760601 original size:28 final size:29
Alignment explanation
Indices: 2760569--2760629 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
2760559 AAAAATAAGT
*
2760569 AATAAATAA-AATAAAATAA-ATAATAATA
1 AATAAATAATAAT-AAATAATATAATAAAA
*
2760597 AAT-AATAATAATAATTAATATAATAAAA
1 AATAAATAATAATAAATAATATAATAAAA
2760625 AATAA
1 AATAA
2760630 TTTAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
27 10 0.36
28 17 0.61
29 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (29 bp):
AATAAATAATAATAAATAATATAATAAAA
Found at i:2760630 original size:25 final size:24
Alignment explanation
Indices: 2760568--2760646 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 24
2760558 AAAAAATAAG
*
2760568 TAATAAATAA-AATAAAATAAATAA
1 TAATAAATAATAATAAAATTAAT-A
2760592 TAATAAATAATAATAATAATTAATA
1 TAATAAATAATAATAA-AATTAATA
*
2760617 TAATAAAAAATAATTTAAAATT-ATA
1 TAATAAATAATAA--TAAAATTAATA
2760642 TAATA
1 TAATA
2760647 TATATGTTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
24 10 0.20
25 26 0.53
26 10 0.20
27 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
TAATAAATAATAATAAAATTAATA
Found at i:2760680 original size:36 final size:35
Alignment explanation
Indices: 2760620--2760724 Score: 131
Period size: 36 Copynumber: 2.9 Consensus size: 35
2760610 ATTAATATAA
2760620 TAAAAAATAA-TTTAAAATTATATAATATATATGT
1 TAAAAAATAATTTTAAAATTATATAATATATATGT
*
2760654 TAAAAAATAATTTTCAAAATTATATAATATATATTT
1 TAAAAAATAATTTT-AAAATTATATAATATATATGT
* ** *
2760690 TCAAAAATTGTTTTAAAAACTTATATATTATATAT
1 TAAAAAATAATTTT-AAAA-TTATATAATATATAT
2760725 ATTTTTCAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
34 10 0.16
35 3 0.05
36 35 0.56
37 14 0.23
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (35 bp):
TAAAAAATAATTTTAAAATTATATAATATATATGT
Found at i:2760715 original size:66 final size:65
Alignment explanation
Indices: 2760645--2760783 Score: 151
Period size: 64 Copynumber: 2.1 Consensus size: 65
2760635 AATTATATAA
*
2760645 TATATATGTTAAAAAATAATTTTC-AAAATTATATAATATAT-A-TTTTCAAAAATTGTTTTAAA
1 TATATAT-TT-AAAAATAATTTTCAAAAACTATATAATATATAAGTTTTCAAAAA-TGTTTTAAA
2760707 AACT
63 AA-T
* * * *
2760711 TATATA-TTATATATATTTTTCAAAAACTATATAATATATACATGTTTTCGAAAATGTTTTAAAA
1 TATATATTTAAAAATAATTTTCAAAAACTATATAATATATA-A-GTTTTCAAAAATGTTTTAAAA
2760775 AT
64 AT
2760777 TATATAT
1 TATATAT
2760784 CATATATATT
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
63 10 0.16
64 18 0.29
66 14 0.23
67 11 0.18
68 9 0.15
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (65 bp):
TATATATTTAAAAATAATTTTCAAAAACTATATAATATATAAGTTTTCAAAAATGTTTTAAAAAT
Found at i:2760735 original size:27 final size:28
Alignment explanation
Indices: 2760698--2760764 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
2760688 TTTCAAAAAT
* *
2760698 TGTTTT-AAAAACTTATATATTATATATA
1 TGTTTTCAAAAAC-TATATAATATATACA
2760726 T-TTTTCAAAAACTATATAATATATACA
1 TGTTTTCAAAAACTATATAATATATACA
*
2760753 TGTTTTCGAAAA
1 TGTTTTCAAAAA
2760765 TGTTTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 18 0.53
28 16 0.47
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (28 bp):
TGTTTTCAAAAACTATATAATATATACA
Found at i:2760758 original size:29 final size:27
Alignment explanation
Indices: 2760700--2760758 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
2760690 TCAAAAATTG
*
2760700 TTTTAAAAACTTATATATTATATATAT
1 TTTTAAAAACTTATATATTATACATAT
*
2760727 TTTTCAAAAAC-TATATAATATATACATGT
1 TTTT-AAAAACTTATAT-AT-TATACATAT
2760756 TTT
1 TTT
2760759 CGAAAATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 9 0.33
28 8 0.30
29 10 0.37
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (27 bp):
TTTTAAAAACTTATATATTATACATAT
Found at i:2760793 original size:66 final size:63
Alignment explanation
Indices: 2760663--2760800 Score: 183
Period size: 64 Copynumber: 2.2 Consensus size: 63
2760653 TTAAAAAATA
* *
2760663 ATTTTC-AAAATTATATAATATATATTTTCAAAAATTGTTTTAAAAACTTATATATTATATAT
1 ATTTTCAAAAACTATATAATATATATTTTCAAAAATTGTTTTAAAAACTTATATATCATATAT
*
2760725 ATTTTTCAAAAACTATATAATATATACATGTTTTCGAAAA-TGTTTTAAAAA-TTATATATCATA
1 A-TTTTCAAAAACTATATAATATAT--A--TTTTCAAAAATTGTTTTAAAAACTTATATATCATA
2760788 TAT
61 TAT
2760791 ATTTTCAAAA
1 ATTTTCAAAA
2760801 TATTTTATAA
Statistics
Matches: 67, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
62 1 0.01
63 5 0.07
64 16 0.24
65 9 0.13
66 16 0.24
67 11 0.16
68 9 0.13
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.46
Consensus pattern (63 bp):
ATTTTCAAAAACTATATAATATATATTTTCAAAAATTGTTTTAAAAACTTATATATCATATAT
Found at i:2760821 original size:38 final size:36
Alignment explanation
Indices: 2760723--2761169 Score: 165
Period size: 37 Copynumber: 11.8 Consensus size: 36
2760713 TATATTATAT
*
2760723 ATATTTTTCAAAAACTATATAATATATACATGTTTTCGAAA
1 ATATTTTT-AAAAACTATAT-ATATAT--ATATTTTC-AAA
* *
2760764 AT-GTTTTAAAAATTATATATCATATATATTTTCAAA
1 ATATTTTTAAAAACTATATAT-ATATATATTTTCAAA
*
2760800 ATATTTTATAAAAACCATATAT-TATATAATTTTCAAA
1 ATATTTT-TAAAAACTATATATATATAT-ATTTTCAAA
* *
2760837 ATGA--TTT-CAAACTATATAATATATATATTTTAAAA
1 AT-ATTTTTAAAAACTATAT-ATATATATATTTTCAAA
* * * *
2760872 ACTAATTTTCAAAACTATATA-ACATATATTTTAAAAAA
1 A-TATTTTTAAAAACTATATATATATATATTTT--CAAA
* * * * *
2760910 ATAATTTTCAAAACTA-AT-TTTCA-AAACTATAT-AATA
1 ATATTTTTAAAAACTATATATAT-ATATA-T-TTTCAA-A
2760946 TATATATTTTAAAAACTAATTTTCAAAACTATATAATATATATTT-AGAA
1 -ATAT-TTTTAAAAACT-A---T----A-TATAT-ATATAT-TTTCA-AA
* * * *
2760995 ACTAATTTTCAAAATTATATAATATATATGTTTTTCAAAA
1 A-TATTTTTAAAAACTATAT-ATATATAT-ATTTTC-AAA
* * **
2761035 ATGTTTTTAAAAGCTATATATTATATATATTTAGAAA
1 ATATTTTTAAAAACTATATA-TATATATATTTTCAAA
* *
2761072 A-A-ATTCAAAAACTATATAT-TATATATTTTCAAA
1 ATATTTTTAAAAACTATATATATATATATTTTCAAA
*
2761105 ATATTTTATAAAAACCATATAT-TATATAATTTTCAAA
1 ATATTTT-TAAAAACTATATATATATAT-ATTTTCAAA
*
2761142 ATGA--TTT-CAAACTATATAATATATATAT
1 AT-ATTTTTAAAAACTATAT-ATATATATAT
2761170 AAAAAAATGG
Statistics
Matches: 316, Mismatches: 44, Indels: 98
0.69 0.10 0.21
Matches are distributed among these distances:
33 13 0.04
34 18 0.06
35 35 0.11
36 57 0.18
37 60 0.19
38 46 0.15
39 43 0.14
40 13 0.04
41 3 0.01
44 1 0.00
47 2 0.01
48 11 0.03
49 11 0.03
50 3 0.01
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.43
Consensus pattern (36 bp):
ATATTTTTAAAAACTATATATATATATATTTTCAAA
Found at i:2760885 original size:13 final size:13
Alignment explanation
Indices: 2760863--2760976 Score: 64
Period size: 13 Copynumber: 9.0 Consensus size: 13
2760853 TAATATATAT
*
2760863 ATTTTAAAAACTA
1 ATTTTCAAAACTA
2760876 ATTTTCAAAACT-
1 ATTTTCAAAACTA
* *
2760888 A-TAT-AACA-TA
1 ATTTTCAAAACTA
* *
2760898 TATTTTAAAAAAATA
1 -ATTTT-CAAAACTA
2760913 ATTTTCAAAACTA
1 ATTTTCAAAACTA
2760926 ATTTTCAAAACT-
1 ATTTTCAAAACTA
*
2760938 A-TAT-AATATA-TA
1 ATTTTCAA-A-ACTA
*
2760950 TATTTTAAAAACTA
1 -ATTTTCAAAACTA
2760964 ATTTTCAAAACTA
1 ATTTTCAAAACTA
2760977 TATAATATAT
Statistics
Matches: 78, Mismatches: 10, Indels: 26
0.68 0.09 0.23
Matches are distributed among these distances:
9 1 0.01
10 5 0.06
11 7 0.09
12 5 0.06
13 43 0.55
14 13 0.17
15 4 0.05
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (13 bp):
ATTTTCAAAACTA
Found at i:2760925 original size:50 final size:51
Alignment explanation
Indices: 2760863--2760976 Score: 185
Period size: 50 Copynumber: 2.3 Consensus size: 51
2760853 TAATATATAT
*
2760863 ATTTTAAAAACTAATTTTCAAAACTATATAACATATAT-TTTAAAAAAATA
1 ATTTTCAAAACTAATTTTCAAAACTATATAACATATATATTTAAAAAAATA
* * *
2760913 ATTTTCAAAACTAATTTTCAAAACTATATAATATATATATTTTAAAAACTA
1 ATTTTCAAAACTAATTTTCAAAACTATATAACATATATATTTAAAAAAATA
2760964 ATTTTCAAAACTA
1 ATTTTCAAAACTA
2760977 TATAATATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 36 0.61
51 23 0.39
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (51 bp):
ATTTTCAAAACTAATTTTCAAAACTATATAACATATATATTTAAAAAAATA
Found at i:2760955 original size:88 final size:83
Alignment explanation
Indices: 2760825--2761009 Score: 289
Period size: 88 Copynumber: 2.2 Consensus size: 83
2760815 CATATATTAT
*
2760825 ATAATTTTCAAAATGATTTCAAACTATATAATATATATATTTTAAAAACTAATTTTCAAAACTAT
1 ATAATTTTCAAAATAATTTCAAACTATATAATATATATATTTTAAAAACTAATTTTCAAAACTAT
2760890 ATAACATATATTTTAAAAAA
66 ATAACATATA-TTT-AAAAA
2760910 ATAATTTTCAAAACTAATTTTCAAAACTATATAATATATATATTTTAAAAACTAATTTTCAAAAC
1 ATAATTTTCAAAA-TAA-TTTC-AAACTATATAATATATATATTTTAAAAACTAATTTTCAAAAC
* *
2760975 TATATAATATATATTTAGAAA
63 TATATAACATATATTTAAAAA
*
2760996 CTAATTTTCAAAAT
1 ATAATTTTCAAAAT
2761010 TATATAATAT
Statistics
Matches: 93, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
85 14 0.15
86 18 0.19
87 7 0.08
88 54 0.58
ACGTcount: A:0.50, C:0.09, G:0.01, T:0.41
Consensus pattern (83 bp):
ATAATTTTCAAAATAATTTCAAACTATATAATATATATATTTTAAAAACTAATTTTCAAAACTAT
ATAACATATATTTAAAAA
Found at i:2761004 original size:35 final size:35
Alignment explanation
Indices: 2760919--2761174 Score: 172
Period size: 35 Copynumber: 7.1 Consensus size: 35
2760909 AATAATTTTC
2760919 AAAACTAATTTTCAAAACTATATAATATATATATTTTA
1 AAAACTAATTTTCAAAACTATAT-A-ATATATA-TTTA
2760957 AAAACTAATTTTCAAAACTATATAATATATATTTA
1 AAAACTAATTTTCAAAACTATATAATATATATTTA
* *
2760992 GAAACTAATTTTCAAAATTATATAATATATATGTTTTTCA
1 AAAACTAATTTTCAAAACTATATAATATATA----TTT-A
* *
2761032 AAAA-T-GTTTTTAAAAGCTATATATTATATATATTTA
1 AAAACTAATTTTCAAAA-CTATATA--ATATATATTTA
* *
2761068 GAAAA--AA--TTCAAAAACTATATATTATATATTTTC
1 -AAAACTAATTTTC-AAAACTATATAATATATA-TTTA
* * * * *
2761102 AAAA-TATTTTATAAAAACCATATATTATATAATTTTC
1 AAAACTAATTT-TCAAAACTATATAATATAT-A-TTTA
* *
2761139 AAAA-TGA-TTTC-AAACTATATAATATATATATA
1 AAAACTAATTTTCAAAACTATATAATATATATTTA
2761171 AAAA
1 AAAA
2761175 AATGGACGAA
Statistics
Matches: 181, Mismatches: 20, Indels: 40
0.75 0.08 0.17
Matches are distributed among these distances:
32 6 0.03
33 11 0.06
34 18 0.10
35 43 0.24
36 31 0.17
37 20 0.11
38 31 0.17
39 10 0.06
40 4 0.02
41 7 0.04
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (35 bp):
AAAACTAATTTTCAAAACTATATAATATATATTTA
Found at i:2761004 original size:73 final size:71
Alignment explanation
Indices: 2760920--2761169 Score: 240
Period size: 73 Copynumber: 3.5 Consensus size: 71
2760910 ATAATTTTCA
*
2760920 AAACTAATTTTCAAAACTATATAATATATATATTTTAAAAACTAATTTTCAAAACTATATAATAT
1 AAACTAA-TTTCAAAACTATATAATATATATATTTTAAAAA-TAATTTTAAAAACTATATAATAT
2760985 ATATTTAG
64 ATATTTAG
* * ** *
2760993 AAACTAATTTTCAAAATTATATAATATATATGTTTTTCAAAAATGTTTTTAAAAGCTATATATTA
1 AAACTAA-TTTCAAAACTATATAATATATAT-ATTTT-AAAAATAATTTTAAAAACTATATA--A
2761058 TATATATTTAG
61 TATATATTTAG
* * * * *
2761069 AAA--AAATTCAAAAACTATAT-AT-TATATATTTTCAAAATATTTTATAAAAACCATATATTAT
1 AAACTAATTTC-AAAACTATATAATATATATATTTTAAAAATAATTT-TAAAAACTATATAATAT
**
2761130 ATAATTTTC
64 AT-ATTTAG
* *
2761139 AAAATGATTTC-AAACTATATAATATATATAT
1 AAACTAATTTCAAAACTATATAATATATATAT
2761170 AAAAAAATGG
Statistics
Matches: 148, Mismatches: 18, Indels: 23
0.78 0.10 0.12
Matches are distributed among these distances:
69 5 0.03
70 25 0.17
71 17 0.11
72 16 0.11
73 35 0.24
74 30 0.20
75 5 0.03
76 15 0.10
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.42
Consensus pattern (71 bp):
AAACTAATTTCAAAACTATATAATATATATATTTTAAAAATAATTTTAAAAACTATATAATATAT
ATTTAG
Found at i:2761986 original size:85 final size:84
Alignment explanation
Indices: 2761766--2762827 Score: 1169
Period size: 85 Copynumber: 12.8 Consensus size: 84
2761756 GCTATGTTGT
* * * * ** *
2761766 AAATGATATGACCTCGAAGTTGAGTGTAATCGAACTCGGGGGTC--T-TTGGCAGATAGCCCTTC
1 AAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTC
* *
2761828 TCGACTTAAGCTATGCTGT
66 TCGACTTAAGTTATGCTGC
* * *
2761847 AAATGATGTG-CCTTGGAGCTGAGTGTAATCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTT
1 AAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTT
* *
2761911 CTAGACTTAAGTTGTGCTGC
65 CTCGACTTAAGTTATGCTGC
*
2761931 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
1 AAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTT
2761996 CTCGACTTAAGTTATGCTGC
65 CTCGACTTAAGTTATGCTGC
* ** * *
2762016 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T-TTGGCAGATAGCCTTTC
1 AAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTC
*
2762078 TCGACTTAAGCTATGCTGC
66 TCGACTTAAGTTATGCTGC
* * * *
2762097 AAATGATGTGCCGTTG-AGCTGA-TCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGATAACCCT
1 AAATGATGTGCCCTTGAAGCTGAGT-GTAATCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCT
2762160 TCTCGACTTAAGTTATGCTGC
64 TCTCGACTTAAGTTATGCTGC
* ** *
2762181 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTTGTTGGCAGACAACCCTT
1 AAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTT
* * *
2762246 GTAGACTTAAGTTGTGCTGC
65 CTCGACTTAAGTTATGCTGC
* * * *
2762266 AAATGATGTGCCGTTG-AGCTGA-TCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGATAACCCT
1 AAATGATGTGCCCTTGAAGCTGAGT-GTAATCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCT
2762329 TCTCGACTTAAGTTATGCTGC
64 TCTCGACTTAAGTTATGCTGC
* ** *
2762350 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTTGTTGGCAGACAACCCTT
1 AAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTT
* * * *
2762415 GTAGACTTAAGTTGTGTTGC
65 CTCGACTTAAGTTATGCTGC
* * * *
2762435 AAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
1 AAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTT
2762499 CTCGACTTAAGTTATGCTGC
65 CTCGACTTAAGTTATGCTGC
* * ** *
2762519 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGGGGGTC--T-TTGGCAGATAGCCCTTC
1 AAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTC
* * *
2762581 TTGACTTAAGCTATTCTGC
66 TCGACTTAAGTTATGCTGC
* * * * * **
2762600 AAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTC
1 AAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTC
* * * *
2762664 TAGCCTTGAGTTATGCTGT
66 TCGACTTAAGTTATGCTGC
* * * *
2762683 AAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACT-TAAGGGTC--T-TTGGCAGATAGCCCTT
1 AAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGAA-GGTCTTTGTTGGCAGATAACCCTT
* *
2762744 CTCGACTTAAGCTATTCTGC
65 CTCGACTTAAGTTATGCTGC
* * * * * *
2762764 AAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTGGTGGCAGGTAGCCCTTC
1 AAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTC
2762827 T
66 T
2762828 GGCCTTGAGC
Statistics
Matches: 818, Mismatches: 134, Indels: 57
0.81 0.13 0.06
Matches are distributed among these distances:
79 1 0.00
80 98 0.12
81 135 0.17
82 19 0.02
83 46 0.06
84 251 0.31
85 260 0.32
86 8 0.01
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (84 bp):
AAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTC
TCGACTTAAGTTATGCTGC
Found at i:2762042 original size:250 final size:250
Alignment explanation
Indices: 2761766--2762827 Score: 1347
Period size: 250 Copynumber: 4.3 Consensus size: 250
2761756 GCTATGTTGT
* * *
2761766 AAATGATATGACCTCGAAGTTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
*
2761831 ACTTAAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCAAAGGTCTTTTGT
66 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCAAAGGTCTTTTGT
* *
2761896 TGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAAT
131 TGGCAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAAT
2761961 CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
196 CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
*
2762016 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCTTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
* * *
2762081 ACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGA-TCGTAGTCAAACTCAAAGGTCTTTG
66 ACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGT-GTAATCGAACTCAAAGGTCTTTT
* * *
2762144 GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTA
129 GTTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTA
** * * * * *
2762209 ATCGAACTCGGGGGTCTTTTGTTGGCAGACAACCCTTGTAGACTTAAGTTGTGCTGC
194 ATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
* * * * *** *
2762266 AAATGATGTGCCGTTG-AGCTGA-TCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGATAACCCT
1 AAATGATGTGCCCTCGAAGCTGAGT-GTAATCGAACTCGGGGGTC--T--TTGGCAGATAGCCCT
* * * ***
2762329 TCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
61 TCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGTGTAATCGAACTCAAAGGTC
* * * * *
2762394 TTTTGTTGGCAGACAACCCTTGTAGACTTAAGTTGTGTTGCAAATGATATG-CCTTGGAGCTGAG
125 TTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAG
* *
2762458 CGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
190 TGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
* *
2762519 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTTG
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
* * * *
2762584 ACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGC
66 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCAAAGGTCTTTTGT
** * * * * * *
2762648 TAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAAT
131 TGGCAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAAT
* * * *
2762713 CGAACT-TAAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGC
196 CGAACTCGAA-GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
* * * * ** *
2762764 AAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTGGCAGGTAGCCCTTCT
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT--TGGCAGATAGCCCTTCT
2762828 GGCCTTGAGC
Statistics
Matches: 698, Mismatches: 98, Indels: 36
0.84 0.12 0.04
Matches are distributed among these distances:
244 28 0.04
245 43 0.06
246 16 0.02
247 1 0.00
248 42 0.06
249 73 0.10
250 283 0.41
251 3 0.00
252 1 0.00
253 121 0.17
254 85 0.12
255 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (250 bp):
AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCAAAGGTCTTTTGT
TGGCAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAAT
CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
Found at i:2762337 original size:169 final size:165
Alignment explanation
Indices: 2761811--2762827 Score: 1344
Period size: 169 Copynumber: 6.1 Consensus size: 165
2761801 TCGGGGGTCT
* * * * *
2761811 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTG-CCTTGGAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
*** * *
2761875 TCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATGT
66 TCGAACTCGGGGGTC---T-TTGGCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
* * * * *
2761940 GCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGG
127 G-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
2761980 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
* * * *
2762045 TCGAACTCGGGGGTCTTTGGCAGATAGCCTTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCG
66 TCGAACTCGGGGGTCTTTGGCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCC-
* *
2762110 TT-GAGCTGATCGTAGTCAAACTCAAAGGTCTTTGG
130 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
2762145 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
* * *
2762210 TCGAACTCGGGGGTCTTTTGTTGGCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGATGT
66 TCGAACTCGGGGGTC---T-TTGGCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
* *
2762275 GCCGTT-GAGCTGATCGTAGTCAAACTCAAAGGTCTTTGG
127 GCC-TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
2762314 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
* * * * *
2762379 TCGAACTCGGGGGTCTTTTGTTGGCAGACAACCCTTGTAGACTTAAGTTGTGTTGCAAATGATAT
66 TCGAACTCGGGGGTC---T-TTGGCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
*
2762444 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
127 GCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
2762483 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
* * * * *
2762548 TCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCT
66 TCGAACTCGGGGGTCTTTGGCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCT
2762613 TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT-G
131 TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
* ** * * * * * * *
2762647 CTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
*** * * * *
2762712 TCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCT
66 TCGAACTCGGGGGTCTTTGGCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCT
*
2762777 TGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTGG
131 TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
* *
2762811 -TGGCAGGTAGCCCTTCT
1 TTGGCAGATAACCCTTCT
2762828 GGCCTTGAGC
Statistics
Matches: 778, Mismatches: 62, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
163 15 0.02
164 148 0.19
165 181 0.23
166 42 0.05
167 1 0.00
168 3 0.00
169 360 0.46
170 28 0.04
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (165 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
TCGAACTCGGGGGTCTTTGGCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCT
TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
Found at i:2762518 original size:503 final size:497
Alignment explanation
Indices: 2761811--2762827 Score: 1520
Period size: 503 Copynumber: 2.0 Consensus size: 497
2761801 TCGGGGGTCT
* * *
2761811 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGTGTAAT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCGAAGCTGAGTGTAAT
*
2761876 CGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATGTG
66 CGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATG
*
2761941 CCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAA
131 CCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAA
2762006 GTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATA
196 GTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATA
* *
2762071 GCCTTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGATCGTAGTCAAACTCAA
261 GCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCAAACTCAA
* ** * *
2762135 AGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAG
325 AGGTCTTT-GCTAACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAG
** * * *
2762200 CTGAGTGTAATCGAACTCGGGGGTCTTTTGTTGGCAGACAACCCTTGTAGACTTAAGTTGTGCTG
389 CTGAGTGTAATCGAACTCAAGGGTC---T-TTGGCAGACAACCCTTCTAGACTTAAGCTATGCTG
*
2762265 CAAATGATGTGCCGTT-GAGCTGATCGTAGTCAAACTCAAAGGTCTTTGG
450 CAAATGATGTGCC-TTGGAGCTGAGCGTAGTCAAACTCAAAGGTC-TTGG
* *
2762314 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTCGAAGCTGAGTGTAA
*** * *
2762379 TCGAACTCGGGGGTCTTTTGTTGGCAGACAACCCTTGTAGACTTAAGTTGTGTTGCAAATGATAT
65 TCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
* * *
2762444 G-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
130 GCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
*
2762508 AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGGGGGTCTTTGGCAGAT
195 AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGAT
* * *
2762573 AGCCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
260 AGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAA
* * * * *
2762638 AGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGC
325 AGGTCTTTGCTAACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGC
* * * * *
2762703 TGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAAT
390 TGAGTGTAATCGAACTCAAGGGTCTTTGGCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAAT
* *
2762768 GATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGG
455 GATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTGG
*
2762811 -TGGCAGGTAGCCCTTCT
1 TTGGCAGATAGCCCTTCT
2762828 GGCCTTGAGC
Statistics
Matches: 465, Mismatches: 46, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
496 15 0.03
497 6 0.01
498 66 0.14
499 1 0.00
502 70 0.15
503 231 0.50
504 76 0.16
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (497 bp):
TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCGAAGCTGAGTGTAAT
CGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATG
CCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAA
GTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATA
GCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAA
GGTCTTTGCTAACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCT
GAGTGTAATCGAACTCAAGGGTCTTTGGCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATG
ATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTGG
Found at i:2766241 original size:19 final size:19
Alignment explanation
Indices: 2766217--2766262 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
2766207 AGTTAATGTG
2766217 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
2766236 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
2766255 AATGCAAA
1 AATGCAAA
2766263 ATGTCTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:2769478 original size:13 final size:13
Alignment explanation
Indices: 2769452--2769529 Score: 76
Period size: 13 Copynumber: 6.2 Consensus size: 13
2769442 CAAAATGAGA
* *
2769452 AAATAAAAAAAAT
1 AAATAATAATAAT
2769465 AAA-AATAAGTAAT
1 AAATAATAA-TAAT
2769478 AAATAA-AAT-A-
1 AAATAATAATAAT
2769488 AAATAAATAATAAT
1 AAAT-AATAATAAT
2769502 AAATAATAATAAT
1 AAATAATAATAAT
*
2769515 AATTAAT-ATAAT
1 AAATAATAATAAT
2769527 AAA
1 AAA
2769530 AAAAAATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
10 4 0.07
11 3 0.05
12 15 0.27
13 27 0.49
14 6 0.11
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.26
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:2769481 original size:17 final size:16
Alignment explanation
Indices: 2769451--2769531 Score: 66
Period size: 14 Copynumber: 5.2 Consensus size: 16
2769441 ACAAAATGAG
*
2769451 AAAATAA-AAAAAATA
1 AAAATAATAATAAATA
2769466 AAAATAAGTAATAAAT-
1 AAAATAA-TAATAAATA
2769482 AAAATAA-AATAAATA
1 AAAATAATAATAAATA
*
2769497 ATAAT-A-AAT-AATA
1 AAAATAATAATAAATA
*
2769510 ATAATAATTAATATAATA
1 AAAATAA-TAATA-AATA
2769528 AAAA
1 AAAA
2769532 AAAATTTTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
13 9 0.16
14 12 0.22
15 11 0.20
16 10 0.18
17 6 0.11
18 7 0.13
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (16 bp):
AAAATAATAATAAATA
Found at i:2769489 original size:31 final size:31
Alignment explanation
Indices: 2769451--2769536 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 31
2769441 ACAAAATGAG
*
2769451 AAAATAAAAAAAATAAAAATAAGTAATAAAT
1 AAAATAAAAAAAATAAAAATAAATAATAAAT
* *
2769482 AAAATAAAATAAATAATAATAAATAAT-AAT
1 AAAATAAAAAAAATAAAAATAAATAATAAAT
* * * *
2769512 AATAATTAATATAATAAAAAAAAAT
1 AA-AATAAAAAAAATAAAAATAAAT
2769537 TTTTTTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 5 0.11
31 40 0.89
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.24
Consensus pattern (31 bp):
AAAATAAAAAAAATAAAAATAAATAATAAAT
Found at i:2769493 original size:10 final size:10
Alignment explanation
Indices: 2769451--2769536 Score: 56
Period size: 10 Copynumber: 8.5 Consensus size: 10
2769441 ACAAAATGAG
2769451 AAAATAAAA-
1 AAAATAAAAT
2769460 AAAATAAAAAT
1 AAAAT-AAAAT
2769471 AAGTAAT-AAAT
1 AA--AATAAAAT
2769482 AAAATAAAAT
1 AAAATAAAAT
2769492 -AAATAATAAT
1 AAAATAA-AAT
2769502 -AAATAATAAT
1 AAAATAA-AAT
*
2769512 AATAAT-TAAT
1 AA-AATAAAAT
* *
2769522 ATAATAAAAA
1 AAAATAAAAT
2769532 AAAAT
1 AAAAT
2769537 TTTTTTAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
9 17 0.27
10 31 0.49
11 9 0.14
12 3 0.05
13 3 0.05
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.24
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:2769501 original size:3 final size:3
Alignment explanation
Indices: 2769462--2769528 Score: 59
Period size: 3 Copynumber: 21.7 Consensus size: 3
2769452 AAATAAAAAA
*
2769462 AAT AAA AAT AAGT AAT AAAT AA- AAT AA- AAT AAAT AAT AAT AAAT AAT
1 AAT AAT AAT AA-T AAT -AAT AAT AAT AAT AAT -AAT AAT AAT -AAT AAT
2769509 AAT AAT AATT AAT -AT AAT AA
1 AAT AAT AA-T AAT AAT AAT AA
2769529 AAAAAAATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
2 6 0.11
3 33 0.61
4 15 0.28
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:2769525 original size:28 final size:24
Alignment explanation
Indices: 2769452--2769534 Score: 89
Period size: 25 Copynumber: 3.3 Consensus size: 24
2769442 CAAAATGAGA
2769452 AAATAAAA-AAAATAAAAATAAGTAAT
1 AAATAAAATAAAAT--AAATAA-TAAT
2769478 AAATAAAATAAAATAAATAATAAT
1 AAATAAAATAAAATAAATAATAAT
*
2769502 AAATAATAATAATAATTAAT-ATAAT
1 AAATAA-AATAA-AATAAATAATAAT
*
2769527 AAAAAAAA
1 AAATAAAA
2769535 ATTTTTTTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
24 12 0.23
25 21 0.40
26 14 0.27
27 5 0.10
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (24 bp):
AAATAAAATAAAATAAATAATAAT
Found at i:2769595 original size:34 final size:35
Alignment explanation
Indices: 2769530--2769634 Score: 120
Period size: 36 Copynumber: 2.9 Consensus size: 35
2769520 ATATAATAAA
* *
2769530 AAAAAATTTTTTTAAAATTATATAATATATATGTT
1 AAAAAATATTTTCAAAATTATATAATATATATGTT
*
2769565 AAAAAATAATTTTCAAAATTATATAATATATATTTT
1 AAAAAAT-ATTTTCAAAATTATATAATATATATGTT
* * * *
2769601 CAAAAATTGTTTTAAAAACTTATATATTATATAT
1 -AAAAAATATTTTCAAAA-TTATATAATATATAT
2769635 ATTTTTCAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
35 7 0.12
36 33 0.55
37 20 0.33
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.46
Consensus pattern (35 bp):
AAAAAATATTTTCAAAATTATATAATATATATGTT
Found at i:2769625 original size:66 final size:65
Alignment explanation
Indices: 2769555--2769693 Score: 151
Period size: 64 Copynumber: 2.1 Consensus size: 65
2769545 AATTATATAA
*
2769555 TATATATGTTAAAAAATAATTTTC-AAAATTATATAATATAT-A-TTTTCAAAAATTGTTTTAAA
1 TATATAT-TT-AAAAATAATTTTCAAAAACTATATAATATATAAGTTTTCAAAAA-TGTTTTAAA
2769617 AAC
63 AAC
* * * *
2769620 T-TATATATTATATATATTTTTCAAAAACTATATAATATATACATGTTTTCGAAAATGTTTTAAA
1 TATATAT-TTAAAAATAATTTTCAAAAACTATATAATATATA-A-GTTTTCAAAAATGTTTTAAA
2769684 AAC
63 AAC
2769687 TATATAT
1 TATATAT
2769694 CATATATATT
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
63 10 0.16
64 23 0.37
65 1 0.02
66 1 0.02
67 13 0.21
68 14 0.23
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (65 bp):
TATATATTTAAAAATAATTTTCAAAAACTATATAATATATAAGTTTTCAAAAATGTTTTAAAAAC
Found at i:2769645 original size:27 final size:28
Alignment explanation
Indices: 2769608--2769674 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
2769598 TTTCAAAAAT
* *
2769608 TGTTTT-AAAAACTTATATATTATATATA
1 TGTTTTCAAAAAC-TATATAATATATACA
2769636 T-TTTTCAAAAACTATATAATATATACA
1 TGTTTTCAAAAACTATATAATATATACA
*
2769663 TGTTTTCGAAAA
1 TGTTTTCAAAAA
2769675 TGTTTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 18 0.53
28 16 0.47
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (28 bp):
TGTTTTCAAAAACTATATAATATATACA
Found at i:2769668 original size:29 final size:27
Alignment explanation
Indices: 2769610--2769668 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
2769600 TCAAAAATTG
*
2769610 TTTTAAAAACTTATATATTATATATAT
1 TTTTAAAAACTTATATATTATACATAT
*
2769637 TTTTCAAAAAC-TATATAATATATACATGT
1 TTTT-AAAAACTTATAT-AT-TATACATAT
2769666 TTT
1 TTT
2769669 CGAAAATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 9 0.33
28 8 0.30
29 10 0.37
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (27 bp):
TTTTAAAAACTTATATATTATACATAT
Found at i:2769704 original size:66 final size:63
Alignment explanation
Indices: 2769573--2769710 Score: 183
Period size: 64 Copynumber: 2.2 Consensus size: 63
2769563 TTAAAAAATA
* *
2769573 ATTTTC-AAAATTATATAATATATATTTTCAAAAATTGTTTTAAAAACTTATATATTATATAT
1 ATTTTCAAAAACTATATAATATATATTTTCAAAAATTGTTTTAAAAACTTATATATCATATAT
*
2769635 ATTTTTCAAAAACTATATAATATATACATGTTTTCGAAAA-TGTTTTAAAAAC-TATATATCATA
1 A-TTTTCAAAAACTATATAATATAT--A--TTTTCAAAAATTGTTTTAAAAACTTATATATCATA
2769698 TAT
61 TAT
2769701 ATTTTCAAAA
1 ATTTTCAAAA
2769711 TATTTTATAA
Statistics
Matches: 67, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
62 1 0.01
63 5 0.07
64 16 0.24
65 9 0.13
66 15 0.22
67 12 0.18
68 9 0.13
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (63 bp):
ATTTTCAAAAACTATATAATATATATTTTCAAAAATTGTTTTAAAAACTTATATATCATATAT
Found at i:2769731 original size:38 final size:38
Alignment explanation
Indices: 2769665--2769753 Score: 114
Period size: 38 Copynumber: 2.4 Consensus size: 38
2769655 TATATACATG
*
2769665 TTTTCGAAAATG--TTT-TAAAAACTATATATCATATATA
1 TTTTC-AAAATGATTTTATAAAAACCATATATCATATA-A
*
2769702 TTTTCAAAAT-ATTTTATAAAAACCATATATTATATAA
1 TTTTCAAAATGATTTTATAAAAACCATATATCATATAA
2769739 TTTTCAAAATGATTT
1 TTTTCAAAATGATTT
2769754 CAAACTATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
36 5 0.11
37 19 0.41
38 22 0.48
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (38 bp):
TTTTCAAAATGATTTTATAAAAACCATATATCATATAA
Found at i:2769772 original size:36 final size:36
Alignment explanation
Indices: 2769644--2770043 Score: 171
Period size: 37 Copynumber: 10.5 Consensus size: 36
2769634 TATTTTTCAA
* *
2769644 AAACTATATA-ATATATACATGTTTTCGAAAAT-GTTTTAA
1 AAACTATATATATATATA-A--TTTTC-AAAATAATTTT-C
* *
2769683 AAACTATATATCATATAT-ATTTTCAAAATATTTTATAA
1 AAACTATATAT-ATATATAATTTTCAAAATAATTT-T-C
* *
2769721 AAACCATATAT-TATATAATTTTCAAAATGA-TTTC
1 AAACTATATATATATATAATTTTCAAAATAATTTTC
*
2769755 AAACTATATA-ATATATATATTTTAAAAACTAATTTTC
1 AAACTATATATATATATA-ATTTTCAAAA-TAATTTTC
* *
2769792 AAAACTATATA-ACATAT-ATTTTAAAAAAATAATTTTC
1 -AAACTATATATATATATAATTTT--CAAAATAATTTTC
*
2769829 AAAACTAATTTTCAAAACTATATAATATATATATATTAAAAACTAATTTTC
1 -AAACT-A---T----A-TATAT-ATATA-AT-T-TTCAAAA-TAATTTTC
** *
2769880 AAAACTATATA-ATATAT-ATTTAGAAACTAATTTTC
1 -AAACTATATATATATATAATTTTCAAAATAATTTTC
* ** ** *
2769915 AAAATTATATAATATATATGTTTTTCAAAAATGTTTTTA
1 -AAACTATAT-ATATATATAATTTTC-AAAATAATTTTC
* *
2769954 AAAGCTATATAT-TATAT-ATTTTCAAAATATTTTATAA
1 AAA-CTATATATATATATAATTTTCAAAATAATTT-T-C
* *
2769991 AAACCATATAT-TATATAATTTTCAAAATGA-TTTC
1 AAACTATATATATATATAATTTTCAAAATAATTTTC
2770025 AAACTATATAATATATATA
1 AAACTATAT-ATATATATA
2770044 TATATAAAAT
Statistics
Matches: 294, Mismatches: 29, Indels: 79
0.73 0.07 0.20
Matches are distributed among these distances:
34 23 0.08
35 39 0.13
36 50 0.17
37 64 0.22
38 44 0.15
39 24 0.08
40 4 0.01
41 9 0.03
42 2 0.01
43 1 0.00
45 1 0.00
46 2 0.01
47 2 0.01
48 4 0.01
50 8 0.03
51 15 0.05
52 2 0.01
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (36 bp):
AAACTATATATATATATAATTTTCAAAATAATTTTC
Found at i:2769795 original size:13 final size:13
Alignment explanation
Indices: 2769773--2769848 Score: 61
Period size: 13 Copynumber: 6.0 Consensus size: 13
2769763 TAATATATAT
*
2769773 ATTTTAAAAACTA
1 ATTTTCAAAACTA
2769786 ATTTTCAAAACT-
1 ATTTTCAAAACTA
* *
2769798 A-TAT-AACA-TA
1 ATTTTCAAAACTA
* *
2769808 TATTTTAAAAAAATA
1 -ATTTT-CAAAACTA
2769823 ATTTTCAAAACTA
1 ATTTTCAAAACTA
2769836 ATTTTCAAAACTA
1 ATTTTCAAAACTA
2769849 TATAATATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
9 1 0.02
10 3 0.06
11 3 0.06
12 3 0.06
13 30 0.60
14 8 0.16
15 2 0.04
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTTTCAAAACTA
Found at i:2769835 original size:50 final size:51
Alignment explanation
Indices: 2769773--2769886 Score: 178
Period size: 50 Copynumber: 2.3 Consensus size: 51
2769763 TAATATATAT
*
2769773 ATTTTAAAAACTAATTTTCAAAACTATATAACATATAT-T-TTAAAAAAATA
1 ATTTTCAAAACTAATTTTCAAAACTATATAACATATATATATT-AAAAAATA
* *
2769823 ATTTTCAAAACTAATTTTCAAAACTATATAATATATATATATTAAAAACTA
1 ATTTTCAAAACTAATTTTCAAAACTATATAACATATATATATTAAAAAATA
2769874 ATTTTCAAAACTA
1 ATTTTCAAAACTA
2769887 TATAATATAT
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
50 36 0.61
51 21 0.36
52 2 0.03
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (51 bp):
ATTTTCAAAACTAATTTTCAAAACTATATAACATATATATATTAAAAAATA
Found at i:2769868 original size:88 final size:83
Alignment explanation
Indices: 2769735--2769919 Score: 280
Period size: 88 Copynumber: 2.2 Consensus size: 83
2769725 CATATATTAT
* *
2769735 ATAATTTTCAAAATGATTTCAAACTATATAATATATATATTTTAAAAACTAATTTTCAAAACTAT
1 ATAATTTTCAAAATAATTTCAAACTATATAATATATATATATTAAAAACTAATTTTCAAAACTAT
2769800 ATAACATATATTTTAAAAAA
66 ATAACATATA-TTT-AAAAA
2769820 ATAATTTTCAAAACTAATTTTCAAAACTATATAATATATATATATTAAAAACTAATTTTCAAAAC
1 ATAATTTTCAAAA-TAA-TTTC-AAACTATATAATATATATATATTAAAAACTAATTTTCAAAAC
* *
2769885 TATATAATATATATTTAGAAA
63 TATATAACATATATTTAAAAA
*
2769906 CTAATTTTCAAAAT
1 ATAATTTTCAAAAT
2769920 TATATAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
85 14 0.15
86 18 0.20
87 7 0.08
88 53 0.58
ACGTcount: A:0.50, C:0.09, G:0.01, T:0.40
Consensus pattern (83 bp):
ATAATTTTCAAAATAATTTCAAACTATATAATATATATATATTAAAAACTAATTTTCAAAACTAT
ATAACATATATTTAAAAA
Found at i:2769913 original size:73 final size:71
Alignment explanation
Indices: 2769830--2770042 Score: 216
Period size: 73 Copynumber: 2.9 Consensus size: 71
2769820 ATAATTTTCA
*
2769830 AAACTAATTTTCAAAACTATATAATATATATATATTAAAAACTAATTTTCAAAACTATATAATAT
1 AAACTAATTTTCAAAACTATATAATATATATATTTTAAAAA-T-ATTTTCAAAACTATATAATAT
*
2769895 ATATTTAG
64 ATATTTAC
* * * * *
2769903 AAACTAATTTTCAAAATTATATAATATATATGTTTTTCAAAAATGTTTTTAAAAGCTATATATTA
1 AAACTAATTTTCAAAACTATATAATATATAT-ATTTT-AAAAATATTTTCAAAA-CTATATAATA
*
2769968 TATATTTTC
63 TATATTTAC
* * * * * *
2769977 AAAATATTTTATAAAAACCATATATTATATA-ATTTTCAAAATGA-TTTC-AAACTATATAATAT
1 AAACTAATTT-TCAAAACTATATAATATATATATTTTAAAAAT-ATTTTCAAAACTATATAATAT
2770039 ATAT
64 ATAT
2770043 ATATATAAAA
Statistics
Matches: 116, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
70 14 0.12
71 3 0.03
72 8 0.07
73 42 0.36
74 28 0.24
75 21 0.18
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (71 bp):
AAACTAATTTTCAAAACTATATAATATATATATTTTAAAAATATTTTCAAAACTATATAATATAT
ATTTAC
Found at i:2769914 original size:35 final size:36
Alignment explanation
Indices: 2769829--2770044 Score: 167
Period size: 35 Copynumber: 5.9 Consensus size: 36
2769819 AATAATTTTC
2769829 AAAACTAATTTTCAAAACTATATAATATATATATATTA
1 AAAACTAATTTTCAAAACTATAT-A-ATATATATATTA
2769867 AAAACTAATTTTCAAAACTATATAATATATAT-TTA
1 AAAACTAATTTTCAAAACTATATAATATATATATTA
* * *
2769902 GAAACTAATTTTCAAAATTATATAATATATATGTTTTTCA
1 AAAACTAATTTTCAAAACTATATAATATATA---TATT-A
* * * * *
2769942 AAAA-T-GTTTTTAAAAGCTATATATTATATATTTTC
1 AAAACTAATTTTCAAAA-CTATATAATATATATATTA
* * * * * *
2769977 AAAA-TATTTTATAAAAACCATATATTATATAATTTTC
1 AAAACTAATTT-TCAAAACTATATAATATAT-ATATTA
*
2770014 AAAA-TGA-TTTC-AAACTATATAATATATATAT
1 AAAACTAATTTTCAAAACTATATAATATATATAT
2770045 ATATAAAATG
Statistics
Matches: 152, Mismatches: 17, Indels: 23
0.79 0.09 0.12
Matches are distributed among these distances:
33 3 0.02
34 14 0.09
35 38 0.25
36 29 0.19
37 17 0.11
38 32 0.21
39 15 0.10
40 4 0.03
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (36 bp):
AAAACTAATTTTCAAAACTATATAATATATATATTA
Found at i:2771816 original size:14 final size:14
Alignment explanation
Indices: 2771797--2771842 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
2771787 TAATTTATAT
*
2771797 TCATTTATGTTTGC
1 TCATTTATGTTCGC
2771811 TCATTTATGTTCGC
1 TCATTTATGTTCGC
* *
2771825 TCGTTTATGTTCGT
1 TCATTTATGTTCGC
2771839 TCAT
1 TCAT
2771843 GTTTTCCAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.13, C:0.17, G:0.15, T:0.54
Consensus pattern (14 bp):
TCATTTATGTTCGC
Found at i:2774072 original size:19 final size:20
Alignment explanation
Indices: 2774045--2774085 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2774035 CAAGGGTTAG
2774045 GCCAAACA-G-ATTGTGATTT
1 GCCAAACAGGAATTG-GATTT
*
2774064 GCCATACAGGAATTGGATTT
1 GCCAAACAGGAATTGGATTT
2774084 GC
1 GC
2774086 AGACAAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 7 0.37
20 8 0.42
21 4 0.21
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (20 bp):
GCCAAACAGGAATTGGATTT
Found at i:2777851 original size:14 final size:14
Alignment explanation
Indices: 2777832--2777867 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
2777822 GTAAAAATAT
*
2777832 AATAAAAGTGATTA
1 AATAAAAGTAATTA
2777846 AATAAAAGTAATTA
1 AATAAAAGTAATTA
2777860 AAGTAAAA
1 AA-TAAAA
2777868 ATAAGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (14 bp):
AATAAAAGTAATTA
Found at i:2779613 original size:25 final size:28
Alignment explanation
Indices: 2779552--2779613 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 28
2779542 TTTTTCTTGC
2779552 GTTTTTTCTTTTTCTTTTTCGAACAGCTT
1 GTTTTTT-TTTTTCTTTTTCGAACAGCTT
* * *
2779581 CTTCTTTTTTTT-TTTTT-GAACTG-TT
1 GTTTTTTTTTTTCTTTTTCGAACAGCTT
2779606 GTTTTTTT
1 GTTTTTTT
2779614 AACATTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
25 8 0.29
26 5 0.18
27 5 0.18
28 5 0.18
29 5 0.18
ACGTcount: A:0.08, C:0.13, G:0.10, T:0.69
Consensus pattern (28 bp):
GTTTTTTTTTTTCTTTTTCGAACAGCTT
Found at i:2782552 original size:11 final size:11
Alignment explanation
Indices: 2782536--2782590 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
2782526 TGCTTGAATG
2782536 AATAAAAATAA
1 AATAAAAATAA
*
2782547 AAT-AAAATGA
1 AATAAAAATAA
*
2782557 AACAAAAAGTAA
1 AATAAAAA-TAA
2782569 AGATAAAAATAA
1 A-ATAAAAATAA
2782581 AGA-AAAAATA
1 A-ATAAAAATA
2782591 TAATGGAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
10 8 0.22
11 14 0.38
12 9 0.24
13 6 0.16
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:2783542 original size:11 final size:11
Alignment explanation
Indices: 2783526--2783580 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
2783516 TGCTTGAATG
2783526 AATAAAAATAA
1 AATAAAAATAA
*
2783537 AAT-AAAATGA
1 AATAAAAATAA
*
2783547 AACAAAAAGTAA
1 AATAAAAA-TAA
2783559 AGATAAAAATAA
1 A-ATAAAAATAA
2783571 AGA-AAAAATA
1 A-ATAAAAATA
2783581 TAATGGAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
10 8 0.22
11 14 0.38
12 9 0.24
13 6 0.16
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:2784221 original size:990 final size:992
Alignment explanation
Indices: 2782300--2784282 Score: 3691
Period size: 990 Copynumber: 2.0 Consensus size: 992
2782290 GGAAAAGGGA
*
2782300 AAAATTGGGGTTGGCTAACGTGCGCCGACCTCCTCCATGGGTTCTGCTATCGTGTGCCATTTAGT
1 AAAATTGGGGTTGGCTAACGTGCGCCGACCTCCTCCATGGGTCCTGCTATCGTGTGCCATTTAGT
* *
2782365 GAAACGGGGCTCACGGCTAGGGTATTTTTTTTTGCTTTGTGCGATTTTTAACTGCTCTGTAGGTT
66 GAAACGGGGCGCACGGCTAGGGTATTTTTTTTTGCTTTGTGCGATTTTTAACTGCTATGTAGGTT
*
2782430 CCGAAAGTTGCACTCTTCGAATGGAATTTCCGCAATTTTAAGTTTGAATAAAAATATTCGGTTCC
131 CCGAAAGTTGCACTCTTCGAATGAAATTTCCGCAATTTTAAGTTTGAATAAAAATATTCGGTTCC
2782495 TGCAAAATAAAAATAAAAATTAAATTAAACATGCTTGAATGAATAAAAATAAAATAAAATGAAAC
196 TGCAAAATAAAAATAAAAATTAAATTAAACATGCTTGAATGAATAAAAATAAAATAAAATGAAAC
2782560 AAAAAGTAAAGATAAAAATAAAGAAAAAATATAATGGAATTGAAAACAATGGGTTGCCTCCCATG
261 AAAAAGTAAAGATAAAAATAAAGAAAAAATATAATGGAATTGAAAACAATGGGTTGCCTCCCATG
2782625 AAGCGCTTTTGTTTAACGTCGTTAGCTCGACGACCTGATTCAGACTACCGGTTCTTCCAAGTTGA
326 AAGCGCTTTTGTTTAACGTCGTTAGCTCGACGACCTGATTCAGACTACCGGTTCTTCCAAGTTGA
* * *
2782690 GATCTTCAAGTAGGCAAACTTCGTTATTCACATAATATGGTTTAATCTTGTGTCCATTTACTTTA
391 GATCTTCAAGTAGACAAACTTCGCTATTCACATAATATGGTTTAATCCTGTGTCCATTTACTTTA
*
2782755 AACCAAGTGCCCGAATTGTCTTCAATTTCGACAACGCCATGAGGAAATATTCCAGTTACTGTATA
456 AACCAAGTGCCCAAATTGTCTTCAATTTCGACAACGCCATGAGGAAATATTCCAGTTACTGTATA
* *
2782820 AGGTCCATTTCATTTTGATCGAAGTTTACCTGCAAAAAGTTTTAATTTTGAGTTAAAAAGAAGAA
521 AGGTCCATTACATTTTGATCGAAGTTTACCTGCAAAAAGTTTTAATTTTGAGTTAAAAAAAAGAA
* *
2782885 CTTTTTTTCCGATAGAAAAAGATTTAGAAACAATTTTTCGATCATGGAATTCTTTTGTTTTGTCC
586 CTTTTTGTCCAATAGAAAAAGATTTAGAAACAATTTTTCGATCATGGAATTCTTTTGTTTTGTCC
2782950 TTATATATTTTGGCGTTGTCGTAAGCATCTCTCCGGATTTCCTCAAGCTCTTGTATATGTAACTT
651 TTATATATTTTGGCGTTGTCGTAAGCATCTCTCCGGATTTCCTCAAGCTCTTGTATATGTAACTT
*
2783015 TCGTGTTTCGCCAATCGCTTCTAGCTCCATATTGTACTGTTTTACGGCCCAATATGCCTTGTGTT
716 TCGTGTTTCGCCAATCGCTTCTAGCTCCATATTGCACTGTTTTACGGCCCAATATGCCTTGTGTT
2783080 CTAGCTCGACAGGTAAATGGCACGGCTTACCGAACACAAGGCGGTATGGTGACATGCCAATAGGT
781 CTAGCTCGACAGGTAAATGGCACGGCTTACCGAACACAAGGCGGTATGGTGACATGCCAATAGGT
* *
2783145 CCTTTGTATGCAGTCCGATAAGCTCACAGAGCGTCAATTAATTTCAAGCTCCAATCCTTGCGATT
846 CCTTTGTATGCAGTCCGATAAGCCCACAAAGCGTCAATTAATTTCAAGCTCCAATCCTTGCGATT
2783210 TGGCTTAACTATTTTCTCAAGAATCATCTTTATTTCTCGGTTTGAAATTTCTGCTTGTCCGTTTG
911 TGGCTTAACTATTTTCTCAAGAATCATCTTTATTTCTCGGTTTGAAATTTCTGCTTGTCCGTTTG
2783275 TTTGTGGATGATAAGTT
976 TTTGTGGATGATAAGTT
*
2783292 AAAATTGGGGTTGGCTAACGTGCGCTGACCTCCTCCATGGGTCCTGCTATCGTGTGCCATTTAGT
1 AAAATTGGGGTTGGCTAACGTGCGCCGACCTCCTCCATGGGTCCTGCTATCGTGTGCCATTTAGT
*
2783357 GAAACGGTGCGCACGGCTAGGGTATTTTTTTTTGCTTTGTGCGATTTTTAACTGCTATGTAGGTT
66 GAAACGGGGCGCACGGCTAGGGTATTTTTTTTTGCTTTGTGCGATTTTTAACTGCTATGTAGGTT
* * *
2783422 CCGAAAGTTGTACTCTTTGAATGAAATTTCTGCAATTTTAAGTTTGAATAAAAATATTCGGTTCC
131 CCGAAAGTTGCACTCTTCGAATGAAATTTCCGCAATTTTAAGTTTGAATAAAAATATTCGGTTCC
2783487 TGCAAAAT-AAAA-AAAAATTAAATTAAACATGCTTGAATGAATAAAAATAAAATAAAATGAAAC
196 TGCAAAATAAAAATAAAAATTAAATTAAACATGCTTGAATGAATAAAAATAAAATAAAATGAAAC
2783550 AAAAAGTAAAGATAAAAATAAAGAAAAAATATAATGGAATTGAAAACAATGGGTTGCCTCCCATG
261 AAAAAGTAAAGATAAAAATAAAGAAAAAATATAATGGAATTGAAAACAATGGGTTGCCTCCCATG
2783615 AAGCGCTTTTGTTTAACGTCGTTAGCTCGACGACCTGATTCAGACTACCGGTTCTTCCAAGTTGA
326 AAGCGCTTTTGTTTAACGTCGTTAGCTCGACGACCTGATTCAGACTACCGGTTCTTCCAAGTTGA
*
2783680 GATCTTCAAGTAGACAAACTTCGCTATTCGCATAATATGGTTTAATCCTGTGTCCATTTACTTTA
391 GATCTTCAAGTAGACAAACTTCGCTATTCACATAATATGGTTTAATCCTGTGTCCATTTACTTTA
* **
2783745 AACCGAGTGCCCAAATTGTCTTCAATTTCGACTGCGCCATGAGGAAATATTCCAGTTACTGTATA
456 AACCAAGTGCCCAAATTGTCTTCAATTTCGACAACGCCATGAGGAAATATTCCAGTTACTGTATA
*
2783810 AGGTCCATTACATTTTGATCGAAGTTTACCTGCTAAAAGTTTTAATTTTGAGTTAAAAAAAAGAA
521 AGGTCCATTACATTTTGATCGAAGTTTACCTGCAAAAAGTTTTAATTTTGAGTTAAAAAAAAGAA
2783875 CTTTTTGTCCAATAGAAAAAGATTTAGAAACAATTTTTCGATCATGGAATTCTTTTGTTTTGTCC
586 CTTTTTGTCCAATAGAAAAAGATTTAGAAACAATTTTTCGATCATGGAATTCTTTTGTTTTGTCC
2783940 TTATATATTTTGGCGTTGTCGTAAGCATCTCTCCGGATTTCCTCAAGCTCTTGTATATGTAACTT
651 TTATATATTTTGGCGTTGTCGTAAGCATCTCTCCGGATTTCCTCAAGCTCTTGTATATGTAACTT
*
2784005 TCGTGTTTCGCCAATCGCTTCTAGCTCCATATTGCATTGTTTTACGGCCCAATATGCCTTGTGTT
716 TCGTGTTTCGCCAATCGCTTCTAGCTCCATATTGCACTGTTTTACGGCCCAATATGCCTTGTGTT
2784070 CTAGCTCGACAGGTAAATGGCACGGCTTACCGAACACAAGGCGGTATGGTGACATGCCAATAGGT
781 CTAGCTCGACAGGTAAATGGCACGGCTTACCGAACACAAGGCGGTATGGTGACATGCCAATAGGT
*
2784135 CCTTTGTATGCAGTCTGATAAGCCCACAAAGCGTCAATTAATTTCAAGCTCCAATCCTTGCGATT
846 CCTTTGTATGCAGTCCGATAAGCCCACAAAGCGTCAATTAATTTCAAGCTCCAATCCTTGCGATT
* *
2784200 TGGCTTAACTATTTTCTCAAGAATCATCTTTATTTCTCGGTTTGAAATTTCTTCTTGTCTGTTTG
911 TGGCTTAACTATTTTCTCAAGAATCATCTTTATTTCTCGGTTTGAAATTTCTGCTTGTCCGTTTG
2784265 TTTGTGGATGATAAGTT
976 TTTGTGGATGATAAGTT
2784282 A
1 A
2784283 TGGCAATTCT
Statistics
Matches: 962, Mismatches: 29, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
990 764 0.79
991 4 0.00
992 194 0.20
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (992 bp):
AAAATTGGGGTTGGCTAACGTGCGCCGACCTCCTCCATGGGTCCTGCTATCGTGTGCCATTTAGT
GAAACGGGGCGCACGGCTAGGGTATTTTTTTTTGCTTTGTGCGATTTTTAACTGCTATGTAGGTT
CCGAAAGTTGCACTCTTCGAATGAAATTTCCGCAATTTTAAGTTTGAATAAAAATATTCGGTTCC
TGCAAAATAAAAATAAAAATTAAATTAAACATGCTTGAATGAATAAAAATAAAATAAAATGAAAC
AAAAAGTAAAGATAAAAATAAAGAAAAAATATAATGGAATTGAAAACAATGGGTTGCCTCCCATG
AAGCGCTTTTGTTTAACGTCGTTAGCTCGACGACCTGATTCAGACTACCGGTTCTTCCAAGTTGA
GATCTTCAAGTAGACAAACTTCGCTATTCACATAATATGGTTTAATCCTGTGTCCATTTACTTTA
AACCAAGTGCCCAAATTGTCTTCAATTTCGACAACGCCATGAGGAAATATTCCAGTTACTGTATA
AGGTCCATTACATTTTGATCGAAGTTTACCTGCAAAAAGTTTTAATTTTGAGTTAAAAAAAAGAA
CTTTTTGTCCAATAGAAAAAGATTTAGAAACAATTTTTCGATCATGGAATTCTTTTGTTTTGTCC
TTATATATTTTGGCGTTGTCGTAAGCATCTCTCCGGATTTCCTCAAGCTCTTGTATATGTAACTT
TCGTGTTTCGCCAATCGCTTCTAGCTCCATATTGCACTGTTTTACGGCCCAATATGCCTTGTGTT
CTAGCTCGACAGGTAAATGGCACGGCTTACCGAACACAAGGCGGTATGGTGACATGCCAATAGGT
CCTTTGTATGCAGTCCGATAAGCCCACAAAGCGTCAATTAATTTCAAGCTCCAATCCTTGCGATT
TGGCTTAACTATTTTCTCAAGAATCATCTTTATTTCTCGGTTTGAAATTTCTGCTTGTCCGTTTG
TTTGTGGATGATAAGTT
Found at i:2789133 original size:14 final size:14
Alignment explanation
Indices: 2789114--2789149 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
2789104 GTAAAAAGAT
*
2789114 AATAAAAGTGATTA
1 AATAAAAGTAATTA
2789128 AATAAAAGTAATTA
1 AATAAAAGTAATTA
2789142 AAGTAAAA
1 AA-TAAAA
2789150 ATAAGAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (14 bp):
AATAAAAGTAATTA
Found at i:2791322 original size:7 final size:7
Alignment explanation
Indices: 2791310--2791335 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2791300 TATTTATTTT
2791310 AATCTAA
1 AATCTAA
2791317 AATCTAA
1 AATCTAA
2791324 AATCTAA
1 AATCTAA
2791331 AATCT
1 AATCT
2791336 CTAATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (7 bp):
AATCTAA
Found at i:2798351 original size:23 final size:23
Alignment explanation
Indices: 2798325--2798372 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2798315 ATAAAGTACA
*
2798325 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
2798348 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
2798371 AT
1 AT
2798373 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:2799123 original size:18 final size:18
Alignment explanation
Indices: 2799100--2799135 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2799090 CGAAATATAT
2799100 TTGAAATTCAAACTCAAA
1 TTGAAATTCAAACTCAAA
* *
2799118 TTGAAATTTAAATTCAAA
1 TTGAAATTCAAACTCAAA
2799136 CTCCAATTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (18 bp):
TTGAAATTCAAACTCAAA
Found at i:2799365 original size:23 final size:23
Alignment explanation
Indices: 2799339--2799403 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
2799329 ATGCGAGATA
2799339 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
**
2799362 GATACCTATTACATTATATAAGG
1 GATACCTATTACATTATATAAAC
* *
2799385 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
2799404 GTTTACCTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:2802242 original size:184 final size:184
Alignment explanation
Indices: 2801933--2803156 Score: 2313
Period size: 184 Copynumber: 6.7 Consensus size: 184
2801923 TTTTAAATGG
* *
2801933 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
2801998 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
2802063 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
2802117 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
2802182 TAAGATCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
2802247 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
2802301 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
2802366 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
2802431 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
* *
2802485 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTGGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
2802550 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
2802615 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
2802669 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
2802734 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
* *
2802799 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCTAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
* *
2802853 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTGGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
2802918 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
2802983 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
2803037 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
**
2803102 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
2803157 ATGTTGAAAG
Statistics
Matches: 1015, Mismatches: 25, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
184 1015 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:2804635 original size:3 final size:3
Alignment explanation
Indices: 2804627--2804719 Score: 87
Period size: 3 Copynumber: 31.0 Consensus size: 3
2804617 ACTTGTTTGG
* * * * **
2804627 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC AGC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
2804675 AGC TTC ATC GTC ATC ATC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
2804720 GTCAGCTTCA
Statistics
Matches: 69, Mismatches: 21, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.25, C:0.34, G:0.06, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:2804644 original size:12 final size:12
Alignment explanation
Indices: 2804627--2804723 Score: 97
Period size: 12 Copynumber: 8.1 Consensus size: 12
2804617 ACTTGTTTGG
*
2804627 ATCATCATCTTC
1 ATCATCATCGTC
*
2804639 ATCATCATCATC
1 ATCATCATCGTC
*
2804651 ATCATCGTCAG-C
1 ATCATCATC-GTC
* *
2804663 ATCTTCATCGCC
1 ATCATCATCGTC
* *
2804675 AGCTTCATCGTC
1 ATCATCATCGTC
*
2804687 ATCATCATCATC
1 ATCATCATCGTC
2804699 ATCATCATCGTC
1 ATCATCATCGTC
*
2804711 ATCTTCATCGTC
1 ATCATCATCGTC
2804723 A
1 A
2804724 GCTTCATCTT
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
11 1 0.01
12 70 0.99
ACGTcount: A:0.25, C:0.34, G:0.07, T:0.34
Consensus pattern (12 bp):
ATCATCATCGTC
Found at i:2804702 original size:48 final size:48
Alignment explanation
Indices: 2804631--2804731 Score: 159
Period size: 48 Copynumber: 2.1 Consensus size: 48
2804621 GTTTGGATCA
* *
2804631 TCATCTTCATCATCATCATCATCATCGTCAG-CATCTTCATCGCCAGCT
1 TCATCGTCATCATCATCATCATCATCATC-GTCATCTTCATCGCCAGCT
*
2804679 TCATCGTCATCATCATCATCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCGTCATCATCATCATCATCATCATCGTCATCTTCATCGCCAGCT
2804727 TCATC
1 TCATC
2804732 TTCTGCGACC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
47 1 0.02
48 48 0.98
ACGTcount: A:0.23, C:0.35, G:0.08, T:0.35
Consensus pattern (48 bp):
TCATCGTCATCATCATCATCATCATCATCGTCATCTTCATCGCCAGCT
Found at i:2806536 original size:199 final size:199
Alignment explanation
Indices: 2806196--2806826 Score: 1163
Period size: 199 Copynumber: 3.1 Consensus size: 199
2806186 TTTAAATTAG
*
2806196 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
2806261 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
2806326 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
2806391 AAAA
196 AAAA
2806395 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
2806460 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
2806525 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
2806590 AAAA
196 AAAA
*
2806594 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
2806659 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
2806724 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCGTGCACCTTGTTTTTAATTCATTCTG
131 CGACAC-TTTTTATATATGGATCGACACTTTAT--G-G-GTGCACCTTGTTTTTAATTCATTCTG
*
2806789 GAAAAAAAA
191 GGAAAAAAA
* *
2806798 TTTCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
2806827 TGACCCTTAA
Statistics
Matches: 421, Mismatches: 6, Indels: 5
0.97 0.01 0.01
Matches are distributed among these distances:
199 332 0.79
200 26 0.06
202 1 0.00
203 1 0.00
204 61 0.14
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
AAAA
Found at i:2806935 original size:19 final size:19
Alignment explanation
Indices: 2806908--2806952 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2806898 ATTCACATAA
*
2806908 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
2806927 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
2806946 AAAATTA
1 AAAATTA
2806953 ACTCGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:2808780 original size:33 final size:33
Alignment explanation
Indices: 2808743--2808808 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2808733 CATCTTAATA
*
2808743 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
2808776 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
2808809 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:2810966 original size:24 final size:24
Alignment explanation
Indices: 2810929--2810981 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
2810919 CCGTTCTATC
2810929 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
2810953 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
2810977 TATTT
1 TATTT
2810982 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:2811172 original size:20 final size:19
Alignment explanation
Indices: 2811126--2811172 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2811116 TCCGGTATCA
*
2811126 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
2811145 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
2811166 TTTTACC
1 TTTTACC
2811173 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:2811322 original size:20 final size:20
Alignment explanation
Indices: 2811297--2811338 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2811287 TTTAAATTTG
2811297 CCGGTTTTATCAT-TTTGTTA
1 CCGGTTTTATCATATTT-TTA
2811317 CCGGTTTTATCATATTTTTA
1 CCGGTTTTATCATATTTTTA
2811337 CC
1 CC
2811339 TGGTATATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.17, C:0.19, G:0.12, T:0.52
Consensus pattern (20 bp):
CCGGTTTTATCATATTTTTA
Found at i:2813047 original size:20 final size:19
Alignment explanation
Indices: 2813024--2813070 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
2813014 CGATATACCA
2813024 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
2813044 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
2813064 GGTAAAA
1 GGTAAAA
2813071 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2813147 original size:181 final size:181
Alignment explanation
Indices: 2812812--2813283 Score: 712
Period size: 181 Copynumber: 2.6 Consensus size: 181
2812802 GATCCAAATT
* * * * *
2812812 AAAAATGTGTCGATCTAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATAGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-ACAAATGATA
* * * * *
2812877 AAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
65 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
2812942 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTAGATACTTTTA
130 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTAGATACTTTAA
*
2812994 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAAC-AAATGATA
* *
2813059 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
65 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** * *
2813123 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAA
130 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTAGATACTTTAA
* *
2813175 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAATGATAA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAATGATAA
* *
2813240 AACCGGTAAAATGATACCAGATATATTGAAAGTGTCGATACTTT
66 AACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
2813284 TGTAGTACTT
Statistics
Matches: 265, Mismatches: 24, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
180 50 0.19
181 118 0.45
182 97 0.37
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (181 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAATGATAA
AACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCG
TGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTAGATACTTTAA
Found at i:2813253 original size:17 final size:18
Alignment explanation
Indices: 2813214--2813255 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
2813204 AGGTAAAAAT
2813214 ATGATAAAACCGGTATCAA
1 ATGATAAAACCGGTA-CAA
2813233 ATGATAAAACCGGTA-AA
1 ATGATAAAACCGGTACAA
2813250 ATGATA
1 ATGATA
2813256 CCAGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.35
19 15 0.65
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.21
Consensus pattern (18 bp):
ATGATAAAACCGGTACAA
Found at i:2815496 original size:21 final size:21
Alignment explanation
Indices: 2815470--2815534 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
2815460 AAGACAATCA
*
2815470 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
2815491 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
2815512 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
2815533 AG
1 AG
2815535 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:2815610 original size:33 final size:33
Alignment explanation
Indices: 2815568--2815633 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2815558 AAATAGATGG
*
2815568 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
2815601 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
2815634 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:2817449 original size:19 final size:19
Alignment explanation
Indices: 2817425--2817473 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
2817415 AATGTAGGGT
2817425 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
2817444 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
2817463 TATTTTTGTAT
1 TAATTTTGTAT
2817474 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:2817978 original size:200 final size:200
Alignment explanation
Indices: 2817632--2818350 Score: 1384
Period size: 200 Copynumber: 3.6 Consensus size: 200
2817622 ATATAAAGTG
2817632 TCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
1 TCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
*
2817697 TATAAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATAGTTTTTGTCCA
66 TATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATAGTTTTTGTCCA
2817762 GAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATATAAAGTGTCGATCCCAA
131 GAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATATAAAGTGTCGATCCCAA
2817827 AAACA
196 AAACA
* *
2817832 TCAAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTT
1 TCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
*
2817897 TATGAGAGAATATATCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATAGTTTTTGTCCA
66 TATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATAGTTTTTGTCCA
*
2817962 GAATGAATGGCCAACAGGGTGCAACAATAAAGTGTCGATCCATATATATAAAGTGTCGATCCCAA
131 GAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATATAAAGTGTCGATCCCAA
2818027 AAACA
196 AAACA
*
2818032 TCGAAACCCAAAAGTATAATGTAATATGTAATTTTTTAATCTAACCGGTACAAGTATACCGGTTT
1 TCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
2818097 TATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATAGTTTTTGTCCA
66 TATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATAGTTTTTGTCCA
2818162 GAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATATAAAGTGTCGATCCCAA
131 GAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATATAAAGTGTCGATCCCAA
2818227 AAACA
196 AAACA
2818232 TCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
1 TCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
2818297 TATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA
66 TATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA
2818351 TTAATTTAAA
Statistics
Matches: 508, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
200 508 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (200 bp):
TCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
TATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATAGTTTTTGTCCA
GAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATATAAAGTGTCGATCCCAA
AAACA
Found at i:2819821 original size:6 final size:6
Alignment explanation
Indices: 2819810--2819873 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
2819800 TAAGCGGTCA
* * * * *
2819810 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGATG ATGACG ATGAAG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* *
2819858 CTGACG ATGAAG ATGA
1 ATGAAG ATGAAG ATGA
2819874 TGACGATGAT
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.39, C:0.09, G:0.33, T:0.19
Consensus pattern (6 bp):
ATGAAG
Found at i:2819832 original size:12 final size:12
Alignment explanation
Indices: 2819810--2819873 Score: 92
Period size: 12 Copynumber: 5.3 Consensus size: 12
2819800 TAAGCGGTCA
*
2819810 ATGAAGATGAAG
1 ATGACGATGAAG
*
2819822 CTGACGATGAAG
1 ATGACGATGAAG
*
2819834 ATGACGATGATG
1 ATGACGATGAAG
2819846 ATGACGATGAAG
1 ATGACGATGAAG
*
2819858 CTGACGATGAAG
1 ATGACGATGAAG
2819870 ATGA
1 ATGA
2819874 TGACGATGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 45 1.00
ACGTcount: A:0.39, C:0.09, G:0.33, T:0.19
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:2819847 original size:3 final size:3
Alignment explanation
Indices: 2819827--2819907 Score: 81
Period size: 3 Copynumber: 27.0 Consensus size: 3
2819817 TGAAGCTGAC
* * * * * * *
2819827 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GAC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
2819875 GAC GAT GAT AAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
2819908 CCAAACAAGT
Statistics
Matches: 60, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.37, C:0.06, G:0.32, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:2819862 original size:36 final size:36
Alignment explanation
Indices: 2819810--2819891 Score: 121
Period size: 36 Copynumber: 2.3 Consensus size: 36
2819800 TAAGCGGTCA
*
2819810 ATGAAGATGAAGCTGACGATGAAGATGACGATGATG
1 ATGAAGATGAAGCTGACGATGAAGATGACGACGATG
* *
2819846 ATGACGATGAAGCTGACGATGAAGATGATGACGATG
1 ATGAAGATGAAGCTGACGATGAAGATGACGACGATG
2819882 AT-AATGATGA
1 ATGAA-GATGA
2819892 TGATGATGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 1 0.02
36 40 0.98
ACGTcount: A:0.39, C:0.09, G:0.32, T:0.21
Consensus pattern (36 bp):
ATGAAGATGAAGCTGACGATGAAGATGACGACGATG
Found at i:2822152 original size:183 final size:183
Alignment explanation
Indices: 2821877--2822369 Score: 898
Period size: 183 Copynumber: 2.7 Consensus size: 183
2821867 GCAATGCTAT
*
2821877 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
* *
2821942 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTGTCAAAACGTGTCGAC
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATT-TAAAAAAGTGTCGAC
*
2822006 AGTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
130 AGTTACACATCGAAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
2822060 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
1 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
2822125 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACA
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACA
* *
2822190 TTTACACATCGAAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAAC
131 GTTACACATCGAAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
*
2822243 CGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
1 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
*
2822308 GTGTCGGTACTTTATGTCCAGTTTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
2822370 GTAATTTTAA
Statistics
Matches: 301, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
183 297 0.99
184 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (183 bp):
CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACA
GTTACACATCGAAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
Found at i:2825248 original size:23 final size:23
Alignment explanation
Indices: 2825217--2825289 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
2825207 ATAGGTAAAA
* *
2825217 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGTGCTT
* *
2825240 ATATAATGTAATAGGTATTGTTT
1 ATATAATGTAATAGGTAGTGCTT
*
2825263 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
2825286 ATAT
1 ATAT
2825290 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.03, G:0.22, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:2825678 original size:23 final size:23
Alignment explanation
Indices: 2825647--2825719 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
2825637 ATAGGTAAAA
*
2825647 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
2825670 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
2825693 ATATAATGAAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
2825716 ATAT
1 ATAT
2825720 TGTAAAGTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:2825814 original size:430 final size:431
Alignment explanation
Indices: 2825013--2826062 Score: 2014
Period size: 430 Copynumber: 2.4 Consensus size: 431
2825003 GTTAATGTTT
2825013 TTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAA
1 TTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAA
2825078 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATC
66 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATC
2825143 AATTACATAACTTTAAACAAAGTATCGATCCTTTTTATAAAAAAGTATAGACACTTTCAATATAA
131 AATTACATAACTTTAAACAAAGTATCGATCCTTTTTATAAAAAAGTATAGACACTTTCAATATAA
* *
2825208 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATTGTTTATATAATGTA
196 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGAA
2825273 ATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTG
261 ATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTG
2825338 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAATAATTATAGG
326 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAATAATTATAGG
2825403 CGTCTAATGATTTATTTTTTACGTTAAAATATATATTATTG
391 CGTCTAATGATTTATTTTTTACGTTAAAATATATATTATTG
2825444 TTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAA
1 TTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAA
2825509 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACATC
66 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATC
2825573 AATTACATAACTTTAAACAAAGTATCGATCCTTTTTATAAAAAAGTATAGACACTTTCAATATAA
131 AATTACATAACTTTAAACAAAGTATCGATCCTTTTTATAAAAAAGTATAGACACTTTCAATATAA
2825638 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGAA
196 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGAA
2825703 ATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTG
261 ATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTG
*
2825768 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
326 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAATAATTATAGG
**
2825833 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTG
391 CGTCTAATGATTTATTTTTTACGTTAAAATATATATTATTG
2825874 TTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAA
1 TTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAA
* *
2825939 TGAAATTATTAAATTCATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATA
66 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATC
*
2826004 AATTACATAACTTTAAACAAAGTATCGATCCTTTTTAT-AAAAAGTATGGACACTTTCAA
131 AATTACATAACTTTAAACAAAGTATCGATCCTTTTTATAAAAAAGTATAGACACTTTCAA
2826063 CATATTATAA
Statistics
Matches: 610, Mismatches: 8, Indels: 3
0.98 0.01 0.00
Matches are distributed among these distances:
430 444 0.73
431 166 0.27
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (431 bp):
TTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAA
TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATC
AATTACATAACTTTAAACAAAGTATCGATCCTTTTTATAAAAAAGTATAGACACTTTCAATATAA
TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGAA
ATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTG
TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAATAATTATAGG
CGTCTAATGATTTATTTTTTACGTTAAAATATATATTATTG
Found at i:2838124 original size:3 final size:3
Alignment explanation
Indices: 2838099--2838150 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
2838089 AAAAGGTATG
* * * * *
2838099 AAT ATT AAT AA- AAT AAT ATT AAT AAT AAT GAT AAT AAC ACT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2838146 AAT AA
1 AAT AA
2838151 AATGTCGGAC
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2844946 original size:119 final size:114
Alignment explanation
Indices: 2844797--2845027 Score: 313
Period size: 119 Copynumber: 2.0 Consensus size: 114
2844787 AGTTCCTACA
*
2844797 AAATCAAAGAAAAATGTAATCTACTCTGGGTAAATAAAGAAACACGTTGAAGTTGTTTTTAAACT
1 AAATCAAAGAAAAATGTAATCTACTCTGGGTAAATAAAGAAACACGTTGAAGTTGTGTTT--ACT
* * *
2844862 ATGATATTGGGCGT-AAAAGGTGAGAGTTAAAATGTGAGGTTAAAGACATAGC
64 ATGATATTGGGAGTAAAAAAGT--GAGTTAAAATGCGAGGTTAAAGACATAGC
* *
2844914 AAATCAAAGAAAAAAATGTAATTTAC-CGTGGGTGAATAAAGAAACACGTTGAAGTTGTGTTTAC
1 AAATCAAAG--AAAAATGTAATCTACTC-TGGGTAAATAAAGAAACACGTTGAAGTTGTGTTTAC
* *
2844978 TCTGATATTGGGAGTAAAAAAGTGAGTTAAAATGCGAGGTTAAAGGCATA
63 TATGATATTGGGAGTAAAAAAGTGAGTTAAAATGCGAGGTTAAAGACATA
2845028 ATAATCCAAC
Statistics
Matches: 102, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
116 25 0.25
117 24 0.24
118 7 0.07
119 46 0.45
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (114 bp):
AAATCAAAGAAAAATGTAATCTACTCTGGGTAAATAAAGAAACACGTTGAAGTTGTGTTTACTAT
GATATTGGGAGTAAAAAAGTGAGTTAAAATGCGAGGTTAAAGACATAGC
Found at i:2847024 original size:2 final size:2
Alignment explanation
Indices: 2847019--2847048 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2847009 ATCATTTTTA
2847019 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
2847049 TCACTATTCA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2847143 original size:21 final size:22
Alignment explanation
Indices: 2847102--2847149 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
2847092 ATAATTTTAT
*
2847102 AATTA-ATATTTTAATTCATAA
1 AATTATATATTTTAAATCATAA
*
2847123 AATTATATTTTTTAAAT-ATAA
1 AATTATATATTTTAAATCATAA
*
2847144 ATTTAT
1 AATTAT
2847150 TAATTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
AATTATATATTTTAAATCATAA
Found at i:2848544 original size:35 final size:37
Alignment explanation
Indices: 2848491--2848566 Score: 97
Period size: 36 Copynumber: 2.1 Consensus size: 37
2848481 AATAATTATA
*
2848491 TAAATATTATTTTAAT-AAAA-AATATAACATCATTTT
1 TAAATATTATTTTAATAAAAAGAATATAACAAC-TTTT
2848527 TAAATAATTA-TTT-ATAAAAAGAATATAACAACTTTT
1 TAAAT-ATTATTTTAATAAAAAGAATATAACAACTTTT
2848563 TAAA
1 TAAA
2848567 GAAAATATAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
35 2 0.06
36 20 0.56
37 14 0.39
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (37 bp):
TAAATATTATTTTAATAAAAAGAATATAACAACTTTT
Found at i:2848563 original size:36 final size:36
Alignment explanation
Indices: 2848491--2848566 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
2848481 AATAATTATA
*
2848491 TAAATATTATTTTAATAAAAAATATAACATCATTTT
1 TAAATATTATTTTAATAAAAAATATAACAACATTTT
*
2848527 TAAATAATTATTTATAA-AAAGAATATAACAAC-TTTT
1 TAAAT-ATTATTT-TAATAAAAAATATAACAACATTTT
2848563 TAAA
1 TAAA
2848567 GAAAATATAC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 13 0.36
37 20 0.56
38 3 0.08
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (36 bp):
TAAATATTATTTTAATAAAAAATATAACAACATTTT
Found at i:2849577 original size:72 final size:72
Alignment explanation
Indices: 2849454--2849591 Score: 206
Period size: 72 Copynumber: 1.9 Consensus size: 72
2849444 TTTTAAGTTT
* * * *
2849454 AATAATTAAAAAATATTTTTAAACATATTTTTTATTTAAAATACTTTAAAATATGATAATTTAGT
1 AATAATTAAAAAATATTTTTAAACATATTTATTATTTAAAATAATTGAAAATATGATAATTCAGT
2849519 GGGTTCC
66 GGGTTCC
* *
2849526 AATAATTAAAAAATATTTTTAAATATATTTATTATTTAAAA-AATTCGAAAATATTATAATTCAG
1 AATAATTAAAAAATATTTTTAAACATATTTATTATTTAAAATAATT-GAAAATATGATAATTCAG
2849590 TG
65 TG
2849592 AGCCCTATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
71 3 0.05
72 56 0.95
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (72 bp):
AATAATTAAAAAATATTTTTAAACATATTTATTATTTAAAATAATTGAAAATATGATAATTCAGT
GGGTTCC
Found at i:2853654 original size:13 final size:13
Alignment explanation
Indices: 2853636--2853662 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2853626 GCACTACAAC
2853636 TTGCTCAGGAACA
1 TTGCTCAGGAACA
2853649 TTGCTCAGGAACA
1 TTGCTCAGGAACA
2853662 T
1 T
2853663 GAGGGCGGCT
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:0.22, G:0.22, T:0.26
Consensus pattern (13 bp):
TTGCTCAGGAACA
Found at i:2858005 original size:23 final size:23
Alignment explanation
Indices: 2857979--2858047 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
2857969 TCTCGATCCA
2857979 TCTCTGTTGAACCCGACTCCACT
1 TCTCTGTTGAACCCGACTCCACT
** *
2858002 TCTCTAATG--CTCGA-TCCA--
1 TCTCTGTTGAACCCGACTCCACT
2858020 TCTCTGTTGAACCCGACTCCACT
1 TCTCTGTTGAACCCGACTCCACT
2858043 TCTCT
1 TCTCT
2858048 AATGCGTTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
18 7 0.20
20 8 0.23
21 8 0.23
23 12 0.34
ACGTcount: A:0.17, C:0.38, G:0.12, T:0.33
Consensus pattern (23 bp):
TCTCTGTTGAACCCGACTCCACT
Done.