Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005946.1 Hibiscus syriacus cultivar Beakdansim tig00013960_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: 2465359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2300096 original size:128 final size:128
Alignment explanation
Indices: 2299868--2300620 Score: 1285
Period size: 128 Copynumber: 5.9 Consensus size: 128
2299858 TTACCTGATT
2299868 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
2299933 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCAAT-GAGAAATAATAGG
2299996 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
**
2300061 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCAATGAGAAATAATAGG
*
2300124 TACTGATATATCAAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * * **
2300189 TGACGAAATAATGGAAGACGCCCCCCCCCCGGGAATGCGCCTTCATGTCCCCTGAGAAATAATAG
66 TGACGAAATAATGGAAG--G-CGCGCCCCCGGGAACGCGCCTTCATGTCCAATGAGAAATAATAG
2300254 G
128 G
2300255 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
2300320 TGACGAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCAAT-GAGAAATAATAGG
2300383 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
**
2300448 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCAATGAGAAATAATAGG
*
2300511 CACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
2300576 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGTCTTCATGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT
2300621 GAATAGTACT
Statistics
Matches: 594, Mismatches: 25, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
127 1 0.00
128 467 0.79
129 3 0.01
130 1 0.00
131 122 0.21
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCAATGAGAAATAATAGG
Found at i:2300582 original size:387 final size:387
Alignment explanation
Indices: 2299868--2300602 Score: 1416
Period size: 387 Copynumber: 1.9 Consensus size: 387
2299858 TTACCTGATT
2299868 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
2299933 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
66 TGACGAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
2299998 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
131 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
*
2300063 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTACT
196 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGCACT
2300128 GATATATCAAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
261 GATATATCAAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
2300193 GAAATAATGGAAGACGCCCCCCCCCCGGGAATGCGCCTTCATGTCCCCTGAGAAATAATAGG
326 GAAATAATGGAAGACGCCCCCCCCCCGGGAATGCGCCTTCATGTCCCCTGAGAAATAATAGG
2300255 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
2300320 TGACGAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
66 TGACGAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
2300385 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
131 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
2300450 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGCACT
196 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGCACT
*
2300515 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
261 GATATATCAAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
* *
2300580 GAAATAATGGAAGGCGCGCCCCC
326 GAAATAATGGAAGACGCCCCCCC
2300603 GGGAACGCGT
Statistics
Matches: 342, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
387 342 1.00
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (387 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGCACT
GATATATCAAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
GAAATAATGGAAGACGCCCCCCCCCCGGGAATGCGCCTTCATGTCCCCTGAGAAATAATAGG
Found at i:2300596 original size:256 final size:256
Alignment explanation
Indices: 2299868--2300627 Score: 1317
Period size: 259 Copynumber: 3.0 Consensus size: 256
2299858 TTACCTGATT
2299868 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** *
2299933 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGGT
2299997 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
130 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
*** *
2300062 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
195 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
*
2300124 TACTGATATATCAAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
2300189 TGACGAAATAATGGAAGACGCCCCCCCCCCGGGAATGCGCCTTCATGTCCCCTGAGAAATAATAG
66 TGACGAAATAATGGAAG--G-CGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAG
2300254 GTACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
128 GTACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
*
2300319 CTGACGAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
193 CTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
2300383 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
2300448 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGCA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTA
2300513 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
131 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
*
2300578 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGTCTTCATGTGAATAGT
196 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
2300628 ACTCCGATTA
Statistics
Matches: 478, Mismatches: 21, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
256 236 0.49
257 1 0.00
258 2 0.00
259 238 0.50
260 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (256 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTA
CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:2300711 original size:8 final size:8
Alignment explanation
Indices: 2300698--2300738 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2300688 TCACAATTTT
2300698 TCAAATTC
1 TCAAATTC
2300706 TCAAATTC
1 TCAAATTC
* *
2300714 CCAAACTC
1 TCAAATTC
2300722 T-AAATTC
1 TCAAATTC
2300729 TCAAATTC
1 TCAAATTC
2300737 TC
1 TC
2300739 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:2305600 original size:21 final size:20
Alignment explanation
Indices: 2305566--2305609 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2305556 AAACTATATT
* * *
2305566 ATAAAATTTTACATGATTCTA
1 ATAAAATATAACATCATTC-A
2305587 ATAAAATATAACATCATTCA
1 ATAAAATATAACATCATTCA
2305607 ATA
1 ATA
2305610 TACCAATCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (20 bp):
ATAAAATATAACATCATTCA
Found at i:2305876 original size:130 final size:130
Alignment explanation
Indices: 2305631--2305879 Score: 322
Period size: 130 Copynumber: 1.9 Consensus size: 130
2305621 TTTTTATTCT
* * *
2305631 AATAAAACTCGTCATATGAAATTGAACAAAATTTGTATACTACTCATCATTCCCTCTTGATAAGT
1 AATAAAACTCGTCATATGAAATTGAACAAAATTTGTATACAACTCATCATTCCATCGTGATAAGT
*** *
2305696 TATAATTTTTTAATATATTTTATGAAACCCGTCACCCTTTCATGACAAGTTTCAATATATTGAAA
66 TATAACAATTTAATATATTTTATGAAACCCGTCACCCTTTCACGACAAGTTTCAATATATTGAAA
* * * *
2305761 AATAGAACTCGTCATATGAAATTGAACAAAA-TTGTATAGAATTCATCATTCCATCGTGATGAGT
1 AATAAAACTCGTCATATGAAATTGAACAAAATTTGTATACAACTCATCATTCCATCGTGATAAGT
* * ** *
2305825 TCTATACAATTTAATATATTTTATGGAACTTGTCACACCTTT-ACGATAAGTTTCA
66 TATA-ACAATTTAATATATTTTATGAAACCCGTCAC-CCTTTCACGACAAGTTTCA
2305880 CGTGCAGAAT
Statistics
Matches: 101, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
129 30 0.30
130 66 0.65
131 5 0.05
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (130 bp):
AATAAAACTCGTCATATGAAATTGAACAAAATTTGTATACAACTCATCATTCCATCGTGATAAGT
TATAACAATTTAATATATTTTATGAAACCCGTCACCCTTTCACGACAAGTTTCAATATATTGAAA
Found at i:2317580 original size:15 final size:15
Alignment explanation
Indices: 2317560--2317594 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2317550 TTAAATATTA
*
2317560 ATTTTTTTTCAATTTT
1 ATTTTTTGTC-ATTTT
2317576 ATTTTTTGTCATTTT
1 ATTTTTTGTCATTTT
2317591 ATTT
1 ATTT
2317595 ATCTCTACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.74
Consensus pattern (15 bp):
ATTTTTTGTCATTTT
Found at i:2319368 original size:2 final size:2
Alignment explanation
Indices: 2319361--2319411 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
2319351 TTAAATTTAA
* * * *
2319361 AT AT AT AT AT AT AT AT AT A- AT AT TT AT AT AT TT A- AT TT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2319401 AT AT AT AT AT A
1 AT AT AT AT AT A
2319412 CCCGTTCCGA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2319373 original size:40 final size:40
Alignment explanation
Indices: 2319324--2319411 Score: 121
Period size: 40 Copynumber: 2.2 Consensus size: 40
2319314 AAATAATTAG
2319324 TATATATATA-ATAT-TAATAAATTTA-AT-TTAAATTTAAA
1 TATATATATATATATATAAT--ATTTATATATTAAATTTAAA
*
2319362 TATATATATATATATATAATATTTATATATTTAATTTAAA
1 TATATATATATATATATAATATTTATATATTAAATTTAAA
2319402 TATATATATA
1 TATATATATA
2319412 CCCGTTCCGA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
38 15 0.33
39 6 0.13
40 24 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (40 bp):
TATATATATATATATATAATATTTATATATTAAATTTAAA
Found at i:2319382 original size:46 final size:46
Alignment explanation
Indices: 2319324--2319411 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
2319314 AAATAATTAG
*
2319324 TATATATATAATATTAATAAATTTAATTTAAATTTAAATATATATA
1 TATATATATAATATTAATAAATTTAATTTAAATATAAATATATATA
* * *
2319370 TATATATATAATATTTATATATTTAATTTAAATATATATATA
1 TATATATATAATATTAATAAATTTAATTTAAATATAAATATA
2319412 CCCGTTCCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (46 bp):
TATATATATAATATTAATAAATTTAATTTAAATATAAATATATATA
Found at i:2320549 original size:13 final size:13
Alignment explanation
Indices: 2320531--2320556 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2320521 AAAGAATAAA
2320531 AACTTATTTTTAT
1 AACTTATTTTTAT
2320544 AACTTATTTTTAT
1 AACTTATTTTTAT
2320557 TTTTATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (13 bp):
AACTTATTTTTAT
Found at i:2322269 original size:11 final size:11
Alignment explanation
Indices: 2322255--2322314 Score: 68
Period size: 11 Copynumber: 5.5 Consensus size: 11
2322245 CTTGTTAGAG
2322255 TGTTATTAGTT
1 TGTTATTAGTT
* *
2322266 TGTTCTTATTT
1 TGTTATTAGTT
*
2322277 TGTTA-TGGTT
1 TGTTATTAGTT
*
2322287 TGTTATTTGTT
1 TGTTATTAGTT
2322298 TGTTATTAGTT
1 TGTTATTAGTT
*
2322309 TATTAT
1 TGTTAT
2322315 GGTTGTTGGT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
10 8 0.20
11 32 0.80
ACGTcount: A:0.15, C:0.02, G:0.17, T:0.67
Consensus pattern (11 bp):
TGTTATTAGTT
Found at i:2322292 original size:32 final size:32
Alignment explanation
Indices: 2322255--2322318 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
2322245 CTTGTTAGAG
* * *
2322255 TGTTATTAGTTTGTTCTTATTTTGTTATGGTT
1 TGTTATTAGTTTGTTATTAGTTTATTATGGTT
*
2322287 TGTTATTTGTTTGTTATTAGTTTATTATGGTT
1 TGTTATTAGTTTGTTATTAGTTTATTATGGTT
2322319 GTTGGTTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.14, C:0.02, G:0.19, T:0.66
Consensus pattern (32 bp):
TGTTATTAGTTTGTTATTAGTTTATTATGGTT
Found at i:2324038 original size:11 final size:11
Alignment explanation
Indices: 2324024--2324072 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
2324014 AATGTTAGAG
2324024 TGTTATTAGTT
1 TGTTATTAGTT
*
2324035 TGTTATTATTT
1 TGTTATTAGTT
*
2324046 TGTTA-TGGTT
1 TGTTATTAGTT
2324056 TGTTATTAGTT
1 TGTTATTAGTT
2324067 TGTTAT
1 TGTTAT
2324073 GGTTGTCGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 8 0.24
11 25 0.76
ACGTcount: A:0.16, C:0.00, G:0.18, T:0.65
Consensus pattern (11 bp):
TGTTATTAGTT
Found at i:2324058 original size:21 final size:21
Alignment explanation
Indices: 2324032--2324076 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
2324022 AGTGTTATTA
*
2324032 GTTTGTTATTATTTTGTTATG
1 GTTTGTTATTAGTTTGTTATG
2324053 GTTTGTTATTAGTTTGTTATG
1 GTTTGTTATTAGTTTGTTATG
2324074 GTT
1 GTT
2324077 GTCGGTTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.22, T:0.64
Consensus pattern (21 bp):
GTTTGTTATTAGTTTGTTATG
Found at i:2328600 original size:15 final size:15
Alignment explanation
Indices: 2328580--2328661 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
2328570 TTCCGGAAAA
*
2328580 TGAATTACTGGAGTT
1 TGAATTACTGGAATT
2328595 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
2328610 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
2328625 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
2328640 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
2328654 TGAATTAC
1 TGAATTAC
2328662 ATTTCTGGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
14 12 0.20
15 47 0.80
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:2328625 original size:45 final size:44
Alignment explanation
Indices: 2328574--2328661 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 44
2328564 TTGGTTTTCC
* **
2328574 GGAAAATGAATTACTGGAGTTTGAATTACTGGAATTTGAATTACT
1 GGAAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACT
2328619 GGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 GGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
2328662 ATTTCTGGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (44 bp):
GGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACT
Found at i:2328659 original size:29 final size:30
Alignment explanation
Indices: 2328580--2328661 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
2328570 TTCCGGAAAA
***
2328580 TGAATTACTGGAGTTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
2328610 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
2328640 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
2328662 ATTTCTGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:2328667 original size:20 final size:20
Alignment explanation
Indices: 2328644--2328693 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
2328634 GGAATTTGAA
2328644 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
2328664 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
2328684 TTCTGGAAAA
1 TTCTGGAAAA
2328694 CATCTGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:2328949 original size:30 final size:28
Alignment explanation
Indices: 2328893--2328994 Score: 93
Period size: 30 Copynumber: 3.5 Consensus size: 28
2328883 TTTACTAAAA
*
2328893 TATTATTGAAATATATAAATAA-TATTAT
1 TATTATT-AAATATATAAAAAATTATTAT
2328921 TCATTATTAAATATATAAAAAATTTATTAT
1 T-ATTATTAAATATATAAAAAA-TTATTAT
* *
2328951 ATATTATTAAA-ATAAAATAAAATATCTTA-
1 -TATTATTAAATATATAA-AAAAT-TATTAT
2328980 TATTATTATAATATA
1 TATTATTA-AATATA
2328995 ATTGATTATT
Statistics
Matches: 63, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
28 22 0.35
29 14 0.22
30 26 0.41
31 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (28 bp):
TATTATTAAATATATAAAAAATTATTAT
Found at i:2329008 original size:28 final size:28
Alignment explanation
Indices: 2328892--2329038 Score: 82
Period size: 28 Copynumber: 4.9 Consensus size: 28
2328882 CTTTACTAAA
* * * *
2328892 ATATTATTGAAAT-ATATAAATAATATT
1 ATATTATTAAAATAAAATAAATTATTTT
*
2328919 ATTCATTATTAAATATATAAA-AAATTTATTAT
1 A-T-ATTATTAAA-ATA-AAATAAA-TTATTTT
* *
2328951 ATATTATTAAAATAAAATAAAATATCTT
1 ATATTATTAAAATAAAATAAATTATTTT
* * **
2328979 ATATTATTATAATATAATTGATTATTTT
1 ATATTATTAAAATAAAATAAATTATTTT
2329007 ATATAATATTAAAAATATAATATAATATTATT
1 ATAT--TATT-AAAATA-AA-ATAA-ATTATT
2329039 ATAAATATTA
Statistics
Matches: 89, Mismatches: 18, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
27 1 0.01
28 34 0.38
29 14 0.16
30 15 0.17
31 9 0.10
32 8 0.09
33 2 0.02
34 6 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
ATATTATTAAAATAAAATAAATTATTTT
Found at i:2329017 original size:15 final size:16
Alignment explanation
Indices: 2328979--2329042 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 16
2328969 AAAATATCTT
2328979 ATATTATTATAATATA
1 ATATTATTATAATATA
*
2328995 ATTGATTATT-TTATATA
1 A-T-ATTATTATAATATA
*
2329012 ATATTAAAAATATAATATA
1 ATATT---ATTATAATATA
2329031 ATATTATTATAA
1 ATATTATTATAA
2329043 ATATTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
15 3 0.08
16 8 0.21
17 8 0.21
18 8 0.21
19 11 0.29
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
ATATTATTATAATATA
Found at i:2329042 original size:30 final size:30
Alignment explanation
Indices: 2328896--2329057 Score: 99
Period size: 31 Copynumber: 5.4 Consensus size: 30
2328886 ACTAAAATAT
*
2328896 TATTGAAATATATAA-ATAATATTATTCAT--
1 TATT-AAAAATATAATATAATATTATT-ATAA
* *
2328925 TATTAAATATATAA-AAAAT-TTATTAT-A
1 TATTAAAAATATAATATAATATTATTATAA
* * * *
2328952 TATTATTAAAATAAAATAAAATA-TCTTATAT
1 TATTA--AAAATATAATATAATATTATTATAA
* * *
2328983 TATT-ATAATATAAT-TGATTATTTTATATAA
1 TATTAAAAATATAATAT-AATATTAT-TATAA
2329013 TATTAAAAATATAATATAATATTATTATAAA
1 TATTAAAAATATAATATAATATTATTAT-AA
2329044 TATTAATAAATATA
1 TATTAA-AAATATA
2329058 TTTTAAATAT
Statistics
Matches: 106, Mismatches: 14, Indels: 23
0.74 0.10 0.16
Matches are distributed among these distances:
26 2 0.02
27 10 0.09
28 25 0.24
29 13 0.12
30 21 0.20
31 27 0.25
32 8 0.08
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (30 bp):
TATTAAAAATATAATATAATATTATTATAA
Found at i:2329052 original size:10 final size:10
Alignment explanation
Indices: 2329011--2329056 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
2329001 TATTTTATAT
2329011 AATATTAA-A
1 AATATTAATA
2329020 AATA-TAATA
1 AATATTAATA
2329029 TAATATTATTATA
1 -AATATTA--ATA
2329042 AATATTAATA
1 AATATTAATA
2329052 AATAT
1 AATAT
2329057 ATTTTAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
8 3 0.09
9 5 0.16
10 12 0.38
11 2 0.06
12 7 0.22
13 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AATATTAATA
Found at i:2329059 original size:21 final size:22
Alignment explanation
Indices: 2329012--2329068 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
2329002 ATTTTATATA
*
2329012 ATATTAAAAATA-TAATATAAT
1 ATATTATAAATATTAATATAAT
2329033 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
2329055 ATATTTTAAATATT
1 ATATTATAAATATT
2329069 TTAATAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 13 0.41
22 14 0.44
23 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:2329073 original size:23 final size:21
Alignment explanation
Indices: 2329019--2329068 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
2329009 ATAATATTAA
*
2329019 AAATA-TAATATAATATTATTAT
1 AAATATTAATA-AATA-TATTTT
2329041 AAATATTAATAAATATATTTT
1 AAATATTAATAAATATATTTT
2329062 AAATATT
1 AAATATT
2329069 TTAATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
22 9 0.35
23 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATATTAATAAATATATTTT
Found at i:2329316 original size:42 final size:42
Alignment explanation
Indices: 2329257--2329371 Score: 203
Period size: 42 Copynumber: 2.7 Consensus size: 42
2329247 ATGAATTACA
* *
2329257 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
2329299 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
*
2329341 TTCCAGAAAACGAATTACGTGAAACAAACAC
1 TTCCGGAAAACGAATTACGTGAAACAAACAC
2329372 TTAAATTCGG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
Found at i:2329923 original size:2 final size:2
Alignment explanation
Indices: 2329916--2329950 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2329906 TTAAGCGAAT
2329916 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2329951 TTTGTGATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2330904 original size:16 final size:17
Alignment explanation
Indices: 2330883--2330914 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2330873 CAATGTCATA
2330883 ATATTAT-TTTTATATT
1 ATATTATATTTTATATT
2330899 ATATTATATTTTATAT
1 ATATTATATTTTATAT
2330915 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:2332680 original size:10 final size:10
Alignment explanation
Indices: 2332647--2332758 Score: 56
Period size: 10 Copynumber: 11.1 Consensus size: 10
2332637 TCGTTTGTTG
2332647 TGTTCGTTTA
1 TGTTCGTTTA
*
2332657 TGTTCATTTATTA
1 TGTTC--GT-TTA
2332670 TGTTCGTTTA
1 TGTTCGTTTA
2332680 TGTTCG-TT-
1 TGTTCGTTTA
*
2332688 CGTT--TTTA
1 TGTTCGTTTA
*
2332696 --TTAGTTTA
1 TGTTCGTTTA
*
2332704 CGTTCGTTTA
1 TGTTCGTTTA
*
2332714 TGTTCGTTCGTTTT
1 ---T-GTTCGTTTA
*
2332728 TGTTAGTTTA
1 TGTTCGTTTA
*
2332738 CGTTCGTTTA
1 TGTTCGTTTA
2332748 TGTTCGTTTA
1 TGTTCGTTTA
2332758 T
1 T
2332759 CATTTAAATG
Statistics
Matches: 78, Mismatches: 11, Indels: 26
0.68 0.10 0.23
Matches are distributed among these distances:
6 2 0.03
7 2 0.03
8 7 0.09
9 2 0.03
10 46 0.59
11 2 0.03
12 1 0.01
13 8 0.10
14 8 0.10
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.60
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:2332690 original size:14 final size:14
Alignment explanation
Indices: 2332671--2332731 Score: 59
Period size: 14 Copynumber: 3.9 Consensus size: 14
2332661 CATTTATTAT
2332671 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
2332685 GTTCGTTTTTATTAGTTTAC
1 GTTCG--TTTA-T-G-TT-C
2332705 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
2332719 GTTCGTTTTTGTT
1 GTTCGTTTATGTT
2332732 AGTTTACGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
14 18 0.45
15 2 0.05
16 5 0.12
17 2 0.05
18 5 0.12
19 2 0.05
20 6 0.15
ACGTcount: A:0.08, C:0.11, G:0.20, T:0.61
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:2332709 original size:20 final size:20
Alignment explanation
Indices: 2332684--2332746 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
2332674 CGTTTATGTT
2332684 CGTTCGTTTTTATTAGTTTA
1 CGTTCGTTTTTATTAGTTTA
2332704 CGTTCG--TTTA-T-G-TT-
1 CGTTCGTTTTTATTAGTTTA
*
2332718 CGTTCGTTTTTGTTAGTTTA
1 CGTTCGTTTTTATTAGTTTA
2332738 CGTTCGTTT
1 CGTTCGTTT
2332747 ATGTTCGTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
14 6 0.17
15 2 0.06
16 4 0.11
17 2 0.06
18 5 0.14
19 2 0.06
20 15 0.42
ACGTcount: A:0.10, C:0.13, G:0.19, T:0.59
Consensus pattern (20 bp):
CGTTCGTTTTTATTAGTTTA
Found at i:2332713 original size:34 final size:34
Alignment explanation
Indices: 2332671--2332755 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
2332661 CATTTATTAT
2332671 GTTCGTTTATGTTCGTTCGTTTTTATTAGTTTAC
1 GTTCGTTTATGTTCGTTCGTTTTTATTAGTTTAC
*
2332705 GTTCGTTTATGTTCGTTCGTTTTTGTTAGTTTAC
1 GTTCGTTTATGTTCGTTCGTTTTTATTAGTTTAC
2332739 GTTCGTTTATGTTCGTT
1 GTTCGTTTATGTTCGTT
2332756 TATCATTTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.09, C:0.12, G:0.20, T:0.59
Consensus pattern (34 bp):
GTTCGTTTATGTTCGTTCGTTTTTATTAGTTTAC
Found at i:2332726 original size:24 final size:24
Alignment explanation
Indices: 2332699--2332745 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
2332689 GTTTTTATTA
* *
2332699 GTTTACGTTCGTTTATGTTCGTTC
1 GTTTACGTTAGTTTACGTTCGTTC
**
2332723 GTTTTTGTTAGTTTACGTTCGTT
1 GTTTACGTTAGTTTACGTTCGTT
2332746 TATGTTCGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.09, C:0.13, G:0.21, T:0.57
Consensus pattern (24 bp):
GTTTACGTTAGTTTACGTTCGTTC
Found at i:2332751 original size:20 final size:20
Alignment explanation
Indices: 2332684--2332757 Score: 70
Period size: 20 Copynumber: 4.0 Consensus size: 20
2332674 CGTTTATGTT
* *
2332684 CGTTCGTTTTTATTAGTTTA
1 CGTTCGTTTATGTTAGTTTA
2332704 CGTTCGTTTA---T-G-TT-
1 CGTTCGTTTATGTTAGTTTA
*
2332718 CGTTCGTTTTTGTTAGTTTA
1 CGTTCGTTTATGTTAGTTTA
*
2332738 CGTTCGTTTATGTTCGTTTA
1 CGTTCGTTTATGTTAGTTTA
2332758 TCATTTAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
14 9 0.20
15 2 0.05
16 1 0.02
17 2 0.05
18 1 0.02
19 2 0.05
20 27 0.61
ACGTcount: A:0.11, C:0.12, G:0.19, T:0.58
Consensus pattern (20 bp):
CGTTCGTTTATGTTAGTTTA
Found at i:2334841 original size:17 final size:18
Alignment explanation
Indices: 2334806--2334846 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
2334796 GTTGAAAGAA
2334806 GAAGAAGAAAGTAAAAAG
1 GAAGAAGAAAGTAAAAAG
2334824 GAAGAAGAAAGT-AAAAG
1 GAAGAAGAAAGTAAAAAG
2334841 GAAGAA
1 GAAGAA
2334847 AGGGGTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAGTAAAAAG
Found at i:2337667 original size:23 final size:23
Alignment explanation
Indices: 2337594--2337661 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
2337584 CAGCTCGTAT
*
2337594 AAATGCACCGAAGTGCCATGTAG
1 AAATGCACCGAAGTGCCATATAG
* * **
2337617 AATTGCACCGTAGTGCCGCATAG
1 AAATGCACCGAAGTGCCATATAG
2337640 AAATGCACCGAAGTGCCATATA
1 AAATGCACCGAAGTGCCATATA
2337662 ATAATGTCCA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.19
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCATATAG
Found at i:2339341 original size:16 final size:16
Alignment explanation
Indices: 2339302--2339344 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
2339292 ATCATCAGTT
*
2339302 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
2339318 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
2339335 CTTATCAATC
1 CTTATCAATC
2339345 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:2342006 original size:23 final size:23
Alignment explanation
Indices: 2341972--2342040 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
2341962 CACCACAGCT
* *
2341972 CGTATAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
2341995 CGTAGAATTGCACCGTAGTGTCG
1 CGTAGAAATGCACCGAAGTGCCA
2342018 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2342041 TATAATAATG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2342559 original size:23 final size:23
Alignment explanation
Indices: 2342525--2342593 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
2342515 CACCACAGCT
* *
2342525 CGTATAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
2342548 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
2342571 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2342594 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2342957 original size:553 final size:553
Alignment explanation
Indices: 2341911--2343012 Score: 2150
Period size: 553 Copynumber: 2.0 Consensus size: 553
2341901 CCATGAACAC
2341911 ATGTGAGAACTATAGATATGTGAGTCTATAGAGGTTGTGCACTAATGCTGTCACCACAGCTCGTA
1 ATGTGAGAACTATAGATATGTGAGTCTATAGAGGTTGTGCACTAATGCTGTCACCACAGCTCGTA
*
2341976 TAAATGCACCAAAGTGCCACGTAGAATTGCACCGTAGTGTCGCGTAGAAATGCACCGAAGTGCCA
66 TAAATGCACCAAAGTGCCACGTAGAATTGCACCGTAGTGCCGCGTAGAAATGCACCGAAGTGCCA
2342041 TATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAA
131 TATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAA
*
2342106 GTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAATATATATATGTCCCGAAGGACCGCGTA
196 GTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAATATATATATGTCCCGAAGGACCGCATA
2342171 GACCCTCGACTCTTGGCATGCCAACTATACCCCTAGCTCTCATGACACATAACATGGGCATTATC
261 GACCCTCGACTCTTGGCATGCCAACTATACCCCTAGCTCTCATGACACATAACATGGGCATTATC
2342236 ATTTATGTCATTTCACATGTTCACATATGCATATTACCTGGGCACGTAGTCTCATAGTTTTTGAA
326 ATTTATGTCATTTCACATGTTCACATATGCATATTACCTGGGCACGTAGTCTCATAGTTTTTGAA
2342301 CATAGCTCATTATCACATTTTCATATAATCACATAGTCACATAGTTCACTTACACGTAGATCATT
391 CATAGCTCATTATCACATTTTCATATAATCACATAGTCACATAGTTCACTTACACGTAGATCATT
*
2342366 TCTATATAATTCACATGTTACATATCTCAGGTTCTTGTATTCATATAACATATAATCACATTTAT
456 TCCATATAATTCACATGTTACATATCTCAGGTTCTTGTATTCATATAACATATAATCACATTTAT
*
2342431 TCATGTATAGTATTTCATCTAAACCGTATGCAT
521 TCATGTATAGCATTTCATCTAAACCGTATGCAT
2342464 ATGTGAGAACTATAGATATGTGAGTCTATAGAGGTTGTGCACTAATGCTGTCACCACAGCTCGTA
1 ATGTGAGAACTATAGATATGTGAGTCTATAGAGGTTGTGCACTAATGCTGTCACCACAGCTCGTA
2342529 TAAATGCACCAAAGTGCCACGTAGAATTGCACCGTAGTGCCGCGTAGAAATGCACCGAAGTGCCA
66 TAAATGCACCAAAGTGCCACGTAGAATTGCACCGTAGTGCCGCGTAGAAATGCACCGAAGTGCCA
2342594 TATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAA
131 TATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAA
*
2342659 GTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAATATATATATGTCCCGAAGGACTGCATA
196 GTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAATATATATATGTCCCGAAGGACCGCATA
2342724 GACCCTCGACTCTTGGCATGCCAACTATACCCCTAGCTCTCATGACACATAACATGGGCATTATC
261 GACCCTCGACTCTTGGCATGCCAACTATACCCCTAGCTCTCATGACACATAACATGGGCATTATC
2342789 ATTTATGTCATTTCACATGTTCACATATGCATATTACCTGGGCACGTAGTCTCATAGTTTTTGAA
326 ATTTATGTCATTTCACATGTTCACATATGCATATTACCTGGGCACGTAGTCTCATAGTTTTTGAA
*
2342854 CATAGCTCATTATCACATTTTCATATAATCACATAGTCACATAGTTCACTTACACGTAGATTATT
391 CATAGCTCATTATCACATTTTCATATAATCACATAGTCACATAGTTCACTTACACGTAGATCATT
2342919 TCCATATAATTCACATGTTACATATCTCAGGTTCTTGTATTCATATAACATATAATCACATTTAT
456 TCCATATAATTCACATGTTACATATCTCAGGTTCTTGTATTCATATAACATATAATCACATTTAT
2342984 TCATGTATAGCATTTCATCTAAACCGTAT
521 TCATGTATAGCATTTCATCTAAACCGTAT
2343013 AATAATGGCA
Statistics
Matches: 543, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
553 543 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (553 bp):
ATGTGAGAACTATAGATATGTGAGTCTATAGAGGTTGTGCACTAATGCTGTCACCACAGCTCGTA
TAAATGCACCAAAGTGCCACGTAGAATTGCACCGTAGTGCCGCGTAGAAATGCACCGAAGTGCCA
TATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAA
GTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAATATATATATGTCCCGAAGGACCGCATA
GACCCTCGACTCTTGGCATGCCAACTATACCCCTAGCTCTCATGACACATAACATGGGCATTATC
ATTTATGTCATTTCACATGTTCACATATGCATATTACCTGGGCACGTAGTCTCATAGTTTTTGAA
CATAGCTCATTATCACATTTTCATATAATCACATAGTCACATAGTTCACTTACACGTAGATCATT
TCCATATAATTCACATGTTACATATCTCAGGTTCTTGTATTCATATAACATATAATCACATTTAT
TCATGTATAGCATTTCATCTAAACCGTATGCAT
Found at i:2346656 original size:31 final size:31
Alignment explanation
Indices: 2346621--2346679 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2346611 TCTCAAACAG
2346621 TTATAAAAT-GATCATTAAATTTATCAAATTA
1 TTATAAAATAG-TCATTAAATTTATCAAATTA
*
2346652 TTATAAAATAGTCTTTAAATTTATCAAA
1 TTATAAAATAGTCATTAAATTTATCAAA
2346680 ATTAATCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (31 bp):
TTATAAAATAGTCATTAAATTTATCAAATTA
Found at i:2360397 original size:13 final size:13
Alignment explanation
Indices: 2360379--2360408 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2360369 TTTAATTACG
2360379 CGAGTCGGTTTCT
1 CGAGTCGGTTTCT
2360392 CGAGTCGGTTTCT
1 CGAGTCGGTTTCT
2360405 CGAG
1 CGAG
2360409 CCGAATCGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.10, C:0.23, G:0.33, T:0.33
Consensus pattern (13 bp):
CGAGTCGGTTTCT
Found at i:2363425 original size:15 final size:15
Alignment explanation
Indices: 2363393--2363426 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
2363383 AGTAAGCTTA
2363393 AATT-TTTTAAAAAT
1 AATTATTTTAAAAAT
2363407 -ATTATTTTAAAAAT
1 AATTATTTTAAAAAT
2363421 AATTAT
1 AATTAT
2363427 AAACTCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.17
14 10 0.56
15 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTATTTTAAAAAT
Found at i:2364392 original size:22 final size:22
Alignment explanation
Indices: 2364362--2364410 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2364352 TATAATTGAT
*
2364362 TATTTTATTATAATATTAAAAA
1 TATTATATTATAATATTAAAAA
* *
2364384 TATTATATTATATTATTATAAA
1 TATTATATTATAATATTAAAAA
2364406 TATTA
1 TATTA
2364411 ATAAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTATATTATAATATTAAAAA
Found at i:2364394 original size:30 final size:32
Alignment explanation
Indices: 2364360--2364418 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 32
2364350 AATATAATTG
*
2364360 ATTATTTTATTAT-AATATTAA-AAATATTAT
1 ATTATATTATTATAAATATTAATAAATATTAT
2364390 ATTATATTATTATAAATATTAATAAATAT
1 ATTATATTATTATAAATATTAATAAATAT
2364419 ATTATAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 12 0.46
31 8 0.31
32 6 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
ATTATATTATTATAAATATTAATAAATATTAT
Found at i:2364418 original size:22 final size:21
Alignment explanation
Indices: 2364374--2364480 Score: 73
Period size: 21 Copynumber: 5.1 Consensus size: 21
2364364 TTTTATTATA
* *
2364374 ATATTAAAAATATTATATTAT
1 ATATTATAAATATTATATAAT
2364395 ATTATTATAAATATTA-ATAAAT
1 A-TATTATAAATATTATAT-AAT
2364417 ATATTATAAATATT-T-TAAT
1 ATATTATAAATATTATATAAT
* *
2364436 A-ATTA-AAATTTTGATTAAAAT
1 ATATTATAAATATT-A-TATAAT
*
2364457 GATATTA-AAATATTTTATTAAT
1 -ATATTATAAATATTATA-TAAT
2364479 AT
1 AT
2364481 TAAATTCATA
Statistics
Matches: 69, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
17 6 0.09
18 4 0.06
19 4 0.06
20 2 0.03
21 23 0.33
22 20 0.29
23 10 0.14
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
ATATTATAAATATTATATAAT
Found at i:2364419 original size:24 final size:22
Alignment explanation
Indices: 2364370--2364440 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
2364360 ATTATTTTAT
* *
2364370 TATAATATTAAAAATATTATAT
1 TATATTATTAAAAATATTATAA
*
2364392 TATATTATTATAAATATTAATAA
1 TATATTATTAAAAATATT-ATAA
* *
2364415 -ATA-TATTATAAATATTTTAA
1 TATATTATTAAAAATATTATAA
2364435 TA-ATTA
1 TATATTA
2364441 AAATTTTGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
20 4 0.10
21 16 0.38
22 19 0.45
23 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATATTATTAAAAATATTATAA
Found at i:2364423 original size:21 final size:19
Alignment explanation
Indices: 2364367--2364430 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 19
2364357 TTGATTATTT
*
2364367 TATT-ATAATAT-TAAAAA
1 TATTAATAATATATATAAA
*
2364384 TATTATATTATATTATTATAAA
1 TATTA-ATAATA-TA-TATAAA
2364406 TATTAATAAATATATTATAAA
1 TATTAAT-AATATA-TATAAA
2364427 TATT
1 TATT
2364431 TTAATAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 4 0.11
19 5 0.13
20 1 0.03
21 15 0.39
22 13 0.34
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATTAATAATATATATAAA
Found at i:2371757 original size:42 final size:42
Alignment explanation
Indices: 2371705--2371786 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
2371695 TTTGAGAACA
* *
2371705 AAAAACGCCGCAATAGATCAAGATTTATAGCGGCGTTTTTCC
1 AAAAACGCCGCAAAAGATCAAGATCTATAGCGGCGTTTTTCC
* *
2371747 AAAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTT
1 AAAAACGCCGCAAAAGATCAAGATCTATAGCGGCGTTTTT
2371787 GGATACAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCAAAAGATCAAGATCTATAGCGGCGTTTTTCC
Found at i:2371805 original size:42 final size:43
Alignment explanation
Indices: 2371707--2371908 Score: 184
Period size: 43 Copynumber: 4.8 Consensus size: 43
2371697 TGAGAACAAA
* * * * **
2371707 AAACGCCGCAATAGATCAAGATTTATAGCGGCGTTTTTCCA-A-
1 AAACACCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATAC
*
2371749 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATAC
1 AAACACCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATAC
* * * * *
2371793 AAAC-GCG-TAAAGGTCAGAT-T-TAGTGGTGTTTTTGGATAT
1 AAACACCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
* * * *
2371832 AAACACCGCAAAAGGACAGATCTATTGTGGCATTTTTGGATAC
1 AAACACCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
2371875 AAACACCGCAAAAGAGT-AGATCTATAGCGGCGTT
1 AAACACCGCAAAAG-GTCAGATCTATAGCGGCGTT
2371909 ATTGAAAAAC
Statistics
Matches: 131, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
39 20 0.15
40 3 0.02
41 14 0.11
42 43 0.33
43 46 0.35
44 5 0.04
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (43 bp):
AAACACCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
Found at i:2375703 original size:41 final size:41
Alignment explanation
Indices: 2375634--2376132 Score: 493
Period size: 41 Copynumber: 12.1 Consensus size: 41
2375624 AGGGGCTCCA
* *
2375634 ACTAAAGCACGAGTCTATAACGGCGTTTGTATAAAAACGCC
1 ACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
* * * * **
2375675 ACTAAAGCATGAGTGTATAGCGGTGTTTGTA-AAAAAATCC
1 ACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
*
2375715 ACTAAAGTTA-GAGTCTATAGCGACGTTTGTATAAAAACGCC
1 ACTAAAG-TACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
* ** * *
2375756 ACTAAAGGATAAGTCTATAGCGGCGTTTGTATTAAAATGCC
1 ACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
* * * ** *
2375797 ACTAAAGTATGAGTCTTTAGCGACGTTTACATAAAAATGCC
1 ACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
*
2375838 ACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCC
1 ACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
* * *
2375879 ACTAAAATACGACTATATAGCGGCGTTTGTATTAAAAACGCC
1 ACTAAAGTACGAGTCTATAGCGGCGTTTGTA-TAAAAACGCC
* * * **
2375921 ACTAAAGAACGAGTCTTTAGCGTCGTTTGTATAAAAATACC
1 ACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
* *
2375962 ACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGTC
1 ACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
* * * * *
2376003 GCTAAAGTAC-AGTCTTTATCGGCGTTTGTCTTAAAAATGCC
1 ACTAAAGTACGAGTCTATAGCGGCGTTTGT-ATAAAAACGCC
* * * * * * *
2376044 ATTAAAGTATGAGTATTTAGCGGCGTTTGTTCTAAAAATGCT
1 ACTAAAGTACGAGTCTATAGCGGCGTTTG-TATAAAAACGCC
* * * *
2376086 GCTAAAGTAC-AGTCTTTAGCGGCTTTTGTTCTAAAAACGCC
1 ACTAAAGTACGAGTCTATAGCGGCGTTTG-TATAAAAACGCC
*
2376127 GCTAAA
1 ACTAAA
2376133 AATGCCGCTA
Statistics
Matches: 383, Mismatches: 68, Indels: 14
0.82 0.15 0.03
Matches are distributed among these distances:
40 50 0.13
41 265 0.69
42 67 0.17
43 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (41 bp):
ACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
Found at i:2376126 original size:206 final size:206
Alignment explanation
Indices: 2375634--2376073 Score: 555
Period size: 206 Copynumber: 2.1 Consensus size: 206
2375624 AGGGGCTCCA
* * * * ** * * * *
2375634 ACTAAAGCACGAGTCTATAACGGCGTTTGTATAAAAACGCCACTAAAGCATGAGTGTATAGCGGT
1 ACTAAAGTACGAGTATTTAGCGGCGTTTGTATAAAAACGCCACTAAAATACGACTATATAGCGGC
** * *
2375699 GTTTGTA--AAAAAATCCACTAAAGTTA-GAGTCTATAGCGACGTTTGTATAAAAACGCCACTAA
66 GTTTGTATTAAAAACGCCACTAAAG-AACGAGTCTATAGCGACGTTTGTATAAAAACACCACTAA
* * * *
2375761 AGGATAAGTCTATAGCGGCGTTTGTATTAAAATGCCACTAAAGTATGAGTCTTTAGCGACGTTTA
130 AGGACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTATCAGTCTTTAGCGACGTTTA
2375826 CATAAAAATGCC
195 CATAAAAATGCC
*
2375838 ACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAATACGACTATATAGCGGC
1 ACTAAAGTACGAGTATTTAGCGGCGTTTGTATAAAAACGCCACTAAAATACGACTATATAGCGGC
* * *
2375903 GTTTGTATTAAAAACGCCACTAAAGAACGAGTCTTTAGCGTCGTTTGTATAAAAATACCACTAAA
66 GTTTGTATTAAAAACGCCACTAAAGAACGAGTCTATAGCGACGTTTGTATAAAAACACCACTAAA
* * * * * *
2375968 GTACAAGTCTATAGCGGCGTTTGTATAAAAACGTCGCTAAAGTA-CAGTCTTTATCGGCGTTTGT
131 GGACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTATCAGTCTTTAGCGACGTTT-A
*
2376032 CTTAAAAATGCC
195 CATAAAAATGCC
* *
2376044 ATTAAAGTATGAGTATTTAGCGGCGTTTGT
1 ACTAAAGTACGAGTATTTAGCGGCGTTTGT
2376074 TCTAAAAATG
Statistics
Matches: 202, Mismatches: 30, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
204 63 0.31
205 16 0.08
206 123 0.61
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29
Consensus pattern (206 bp):
ACTAAAGTACGAGTATTTAGCGGCGTTTGTATAAAAACGCCACTAAAATACGACTATATAGCGGC
GTTTGTATTAAAAACGCCACTAAAGAACGAGTCTATAGCGACGTTTGTATAAAAACACCACTAAA
GGACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTATCAGTCTTTAGCGACGTTTAC
ATAAAAATGCC
Found at i:2377661 original size:31 final size:30
Alignment explanation
Indices: 2377626--2377703 Score: 97
Period size: 29 Copynumber: 2.6 Consensus size: 30
2377616 CGTCCCCAAC
*
2377626 AGGTCGCCATGCATTCCCCAAC-ACCCCTACA
1 AGGTCGCCATGCACTCCCCAACGA--CCTACA
* *
2377657 AGGTCGCCAAGCACT-CCCAGCGACCTACA
1 AGGTCGCCATGCACTCCCCAACGACCTACA
2377686 AGGTCGCCATGCACTCCC
1 AGGTCGCCATGCACTCCC
2377704 AGCGGCGACC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 20 0.49
30 7 0.17
31 14 0.34
ACGTcount: A:0.24, C:0.44, G:0.18, T:0.14
Consensus pattern (30 bp):
AGGTCGCCATGCACTCCCCAACGACCTACA
Found at i:2377688 original size:29 final size:29
Alignment explanation
Indices: 2377651--2377707 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
2377641 CCCCAACACC
2377651 CCTACAAGGTCGCCAAGCACTCCCAGCGA
1 CCTACAAGGTCGCCAAGCACTCCCAGCGA
*
2377680 CCTACAAGGTCGCCATGCACTCCCAGCG
1 CCTACAAGGTCGCCAAGCACTCCCAGCG
2377708 GCGACCAAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.42, G:0.21, T:0.12
Consensus pattern (29 bp):
CCTACAAGGTCGCCAAGCACTCCCAGCGA
Found at i:2377745 original size:18 final size:19
Alignment explanation
Indices: 2377722--2377760 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
2377712 CCAAGCTTCA
2377722 CGTGCTCCCCT-CTGCTCC
1 CGTGCTCCCCTCCTGCTCC
2377740 CGTGCTCCCCTCCTGCTCC
1 CGTGCTCCCCTCCTGCTCC
2377759 CG
1 CG
2377761 CTGCATGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.00, C:0.56, G:0.18, T:0.26
Consensus pattern (19 bp):
CGTGCTCCCCTCCTGCTCC
Found at i:2377917 original size:33 final size:32
Alignment explanation
Indices: 2377880--2377944 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 32
2377870 CAATTGTACA
2377880 ATTATTGGTGAAATAATTGAGGCAGCCGGTGAC
1 ATTATTGGTGAAATAATTGAGGCAGCC-GTGAC
2377913 ATTATTGGTGAAATAATTGAGGCAGCCGTGAC
1 ATTATTGGTGAAATAATTGAGGCAGCCGTGAC
2377945 CTAATTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 5 0.16
33 27 0.84
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.28
Consensus pattern (32 bp):
ATTATTGGTGAAATAATTGAGGCAGCCGTGAC
Found at i:2378047 original size:29 final size:27
Alignment explanation
Indices: 2377987--2378049 Score: 92
Period size: 26 Copynumber: 2.3 Consensus size: 27
2377977 AACATCAAAC
*
2377987 AAAGAAAGGGAGAAGAGATTGCAGCAG
1 AAAGAAAGGGAGAAGAAATTGCAGCAG
2378014 -AAGAAAGGGAGAAGAAATTGCAGCCGAG
1 AAAGAAAGGGAGAAGAAATTGCAG-C-AG
2378042 AAAGAAAG
1 AAAGAAAG
2378050 AAAGGGAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 22 0.69
27 1 0.03
28 2 0.06
29 7 0.22
ACGTcount: A:0.51, C:0.08, G:0.35, T:0.06
Consensus pattern (27 bp):
AAAGAAAGGGAGAAGAAATTGCAGCAG
Found at i:2378067 original size:13 final size:13
Alignment explanation
Indices: 2378044--2378090 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
2378034 CAGCCGAGAA
2378044 AGAAA-GAAAGGG
1 AGAAAGGAAAGGG
*
2378056 AGAAAGGAAAGGA
1 AGAAAGGAAAGGG
*
2378069 AGAAGAAGAAAGGG
1 AGAA-AGGAAAGGG
2378083 AGATAAGG
1 AGA-AAGG
2378091 CTCTTGTGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 5 0.18
13 10 0.36
14 12 0.43
15 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.02
Consensus pattern (13 bp):
AGAAAGGAAAGGG
Found at i:2378565 original size:15 final size:14
Alignment explanation
Indices: 2378545--2378575 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
2378535 TAGTATTAGT
2378545 TTATTATATTATAAG
1 TTATTATATTA-AAG
2378560 TTATTATATTAAAG
1 TTATTATATTAAAG
2378574 TT
1 TT
2378576 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:2380843 original size:21 final size:21
Alignment explanation
Indices: 2380817--2381000 Score: 81
Period size: 21 Copynumber: 8.3 Consensus size: 21
2380807 TTACTACATC
2380817 ATTAATATAAAATCATTAAAT
1 ATTAATATAAAATCATTAAAT
*
2380838 ATTAATAATAAATTATTATTACTAAT
1 ATTAAT-ATAAA--ATCATTA--AAT
* *
2380864 CATTACTATCAAATCATTAAAT
1 -ATTAATATAAAATCATTAAAT
*
2380886 ATTAATAATAAATTATTATTACTAAT
1 ATTAAT-ATAAA--ATCATTA--AAT
* * *
2380912 CATTACTATCAAATCATTAAAA
1 -ATTAATATAAAATCATTAAAT
* * *
2380934 ATTAATA-ATAAT--TTTATT
1 ATTAATATAAAATCATTAAAT
* * *
2380952 ATT-AT-TAATCATTACTAAAT
1 ATTAATATAA-AATCATTAAAT
*
2380972 CATTAATATCAAATCATTAAAT
1 -ATTAATATAAAATCATTAAAT
2380994 ATTAATA
1 ATTAATA
2381001 ATAATTTCAT
Statistics
Matches: 118, Mismatches: 26, Indels: 38
0.65 0.14 0.21
Matches are distributed among these distances:
17 3 0.03
18 8 0.07
20 6 0.05
21 27 0.23
22 24 0.20
23 2 0.02
24 24 0.20
26 14 0.12
27 10 0.08
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTAATATAAAATCATTAAAT
Found at i:2380868 original size:48 final size:48
Alignment explanation
Indices: 2380806--2380968 Score: 263
Period size: 48 Copynumber: 3.4 Consensus size: 48
2380796 CTATCAAATC
* *
2380806 ATTACTACATCATTAATATAAAATCATTAAATATTAATAATAAATTATT
1 ATTACTA-ATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
2380855 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
* *
2380903 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAA-ATTATT
*
2380952 ATTATTAATCATTACTA
1 ATTACTAATCATTACTA
2380969 AATCATTAAT
Statistics
Matches: 108, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
48 80 0.74
49 28 0.26
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (48 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
Found at i:2380982 original size:60 final size:60
Alignment explanation
Indices: 2380903--2381776 Score: 744
Period size: 60 Copynumber: 14.2 Consensus size: 60
2380893 ATAAATTATT
* * *
2380903 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTATTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
2380962 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
2381022 ATTTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
1 A-TTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* * *
2381083 ATTACTAAATCATTAATATCAAATTATTAAATATTAATAATAATTTCATTATTACTAATT
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* * *
2381143 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAAAAATTTTATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* *
2381202 ATTATTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
2381262 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* * * * * *
2381322 ATTACTATCAAATCATTAAATATTAATAACAATT---TCATTATTACTAA--TCATTACTA--AA
1 ATTAC--T-AAATCATT-ACTATCAA-ATC-ATTAAAT-ATTAATAATAATTTCATTATTACTAA
2381380 TC
59 TC
* * * * * * * *
2381382 ATTAATATCAAATCATTAAATAT-TAAT-AATAATTTCATTATTACTAA--TCATTACTA--AAT
1 ATT-A-CT-AAATCATT-ACTATCAAATCATTAA-AT-ATTAATAATAATTTCATTATTACTAAT
2381441 C
60 C
* * ** * ** * * *
2381442 ATTATTATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAA--ACATTGTTC
1 ATTACTA-AA--TCATTACTA-TCAAATCA-TTAAATA---TTAA-T-AA-TAATTTCATTATT-
* **
2381505 ATTGTTC
54 ACTAATC
* * * *
2381512 AAGT-CGTAAATTATTACTATCAAATCATTACTAAATCATTAAT-ATCAAATCATTAAATCTTAA
1 -ATTAC-TAAATCATTACTATCAAATCA-T--TAAAT-ATTAATAAT--AAT--TT-CA--TTAT
* *
2381575 TAATAAATT
53 TACT-AATC
* *
2381584 ATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTA--AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* * *
2381646 ATTACTAAATTATTAATATCAAATTATTAAATATTAATAATAA-TTCTATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTC-ATTATTACTAATC
*
2381706 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
2381766 ATTACTAAATC
1 ATTACTAAATC
2381777 TTATAAATAC
Statistics
Matches: 675, Mismatches: 87, Indels: 105
0.78 0.10 0.12
Matches are distributed among these distances:
56 2 0.00
57 1 0.00
58 4 0.01
59 66 0.10
60 388 0.57
61 64 0.09
62 20 0.03
63 17 0.03
64 18 0.03
65 6 0.01
66 7 0.01
67 15 0.02
68 12 0.02
69 10 0.01
70 12 0.02
71 10 0.01
72 5 0.01
73 18 0.03
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:2381036 original size:169 final size:169
Alignment explanation
Indices: 2380855--2381772 Score: 972
Period size: 169 Copynumber: 5.4 Consensus size: 169
2380845 ATAAATTATT
* *
2380855 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAAATT-ATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
*
2380918 TATCAAATCATTAAAAATTAATAATAATTTTATTATTATTAATCATTACTAAATCATTAATATCA
66 TATCAAATCATTAAAAATTAATAATAATTTCATTATTATTAATCATTACTAAATCATTAATATCA
2380983 AATCATTAAATATTAATAATAATTTCATTATTACTAATC
131 AATCATTAAATATTAATAATAATTTCATTATTACTAATC
* *
2381022 ATTTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTA
1 A-TTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTA
* *
2381087 CTAAATCATTAATATCAAATTATTAAATATTAATAATAATTTCATTATTACTAATTATTACT-AA
65 CT--ATC---AA-ATC--ATTA--AAA-ATTAATAATAATTTCATTATTATTAATCATTACTAAA
* * * *
2381151 TCATTACTATCAAATCATTAAAAATTAATAAAAATTTTATTATTACTAATC
119 TCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
2381202 ATTATTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
* * * * ** * *
2381267 --T-AAATCATTACTATCAAA-TCATTA-AATATTAATAACAATTTCATTATTACT-AATCATTA
66 TATCAAATCATTA--A--AAATTAATAATAAT-TTCATTATTA-TTAATCATTACTAAATCATTA
* *
2381326 CTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
125 ATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
2381371 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
* * * *
2381436 --T-AAATCATT----A-T--T-ATAATTTCATTACTAGTT-AT-GTAACGAAAAT-ATGGTTAA
66 TATCAAATCATTAAAAATTAATAATAATTTCATTATTA-TTAATCATTAC-TAAATCA---TTAA
* * * * ** * * *
2381487 TTGAACCAAA-CATTGTTCATTGTTCAAGTCGTAAATT-ATTACTATCAAATC
126 -T--ATCAAATCA---TTAAATATT-AA-TAATAATTTCATTATTA-CTAATC
* *
2381538 ATTACTAAATCATTAATATCAAATCATTAAATCTTAATAATAAATT-ATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
* *
2381602 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATTATTAATATCA
66 TATCAAATCATTAAAAATTAATAATAATTTCATTATTATTAATCATTACTAAATCATTAATATCA
*
2381667 AATTATTAAATATTAATAATAA-TTCTATTATTACTAATC
131 AATCATTAAATATTAATAATAATTTC-ATTATTACTAATC
* *
2381706 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
2381771 TA
66 TA
2381773 AATCTTATAA
Statistics
Matches: 637, Mismatches: 63, Indels: 100
0.80 0.08 0.12
Matches are distributed among these distances:
156 3 0.00
157 3 0.00
158 13 0.02
159 4 0.01
160 3 0.00
161 3 0.00
162 2 0.00
163 5 0.01
165 6 0.01
166 26 0.04
167 60 0.09
168 74 0.12
169 206 0.32
170 30 0.05
171 2 0.00
172 8 0.01
173 2 0.00
174 2 0.00
175 7 0.01
176 5 0.01
177 20 0.03
178 8 0.01
179 61 0.10
180 53 0.08
181 31 0.05
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (169 bp):
ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
TATCAAATCATTAAAAATTAATAATAATTTCATTATTATTAATCATTACTAAATCATTAATATCA
AATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:2381133 original size:22 final size:22
Alignment explanation
Indices: 2380985--2381073 Score: 57
Period size: 22 Copynumber: 4.3 Consensus size: 22
2380975 TAATATCAAA
2380985 TCATTAAATATTAATAATAATT
1 TCATTAAATATTAATAATAATT
* *
2381007 TCA-T---TATTACTAATCATT
1 TCATTAAATATTAATAATAATT
* * *
2381025 T-ACTAAATCATTACT-ATCAA-A
1 TCATTAAAT-ATTAATAAT-AATT
*
2381046 TCATTAAATATTAATAACAATT
1 TCATTAAATATTAATAATAATT
2381068 TCATTA
1 TCATTA
2381074 TTACTAATCA
Statistics
Matches: 50, Mismatches: 8, Indels: 18
0.66 0.11 0.24
Matches are distributed among these distances:
17 1 0.02
18 14 0.28
21 12 0.24
22 23 0.46
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (22 bp):
TCATTAAATATTAATAATAATT
Found at i:2381196 original size:109 final size:109
Alignment explanation
Indices: 2381083--2381769 Score: 518
Period size: 109 Copynumber: 6.1 Consensus size: 109
2381073 ATTACTAATC
* *
2381083 ATTACTAAATCATTAATATCAAATTATTAAATATTAATAATAATTTCATTATTACTAATTATTAC
1 ATTACT-AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
* *
2381148 T-AATCATTACTATCAAATCATTAAAAATTAATAAAAATTTTATT
65 TAAATCATTACTATCAAATCATTAAATATTAATAAAAATTTCATT
2381192 ATTACTAATCATTATTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTAC
1 A-T--T-A-C-----T-AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTAC
*
2381257 TAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATT
55 TAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAAAAATTTCATT
* *
2381312 ATTACTAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACT
1 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT
* *
2381377 AAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
66 AAATCATTACTATCAAATCATTAAATATTAATAAAAATTTCATT
* * * * * *
2381421 ATTACTAATCATT-A-CT-AAATCATT-ATTA-TAAT-TTCATTACTAGTTATGTAACGAAAAT-
1 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTC-A-TTAT-T-AC--TAATC
* * * * * * * *
2381479 ATGGTTAATTGAACCAAACATTGTTCATTGTTCAAGTC-GTAAATTATTACTATCAAA--TCATT
60 A---TT-ACT--A--AATCA---TT-ACT-ATCAAATCATTAAA-TATTAATA-AAAATTTCATT
* * *
2381541 ACTA--AATCATTAATATCAAATCATTAAATCTTAATAATAAATT-ATTATTACTAATCATTACT
1 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC-
* * * ** * *
2381603 ATCAAATCATTA--A--AAATTAAT-AATAATT--TCATTATTACTAATC
65 -T-AAATCATTACTATCAAATCATTAAAT-ATTAATAAAAATT--TCATT
* *
2381646 ATTACTAAATTATTAATATCAAATTATTAAATATTAATAATAA-TTCTATTATTACTAATCATTA
1 ATTACT-AATCATTAATATCAAATCATTAAATATTAATAATAATTTC-ATTATTACTAATCATTA
* *
2381710 CTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATC
64 CTAAATCATTACTATCAAATCATTAAATATTAATAAAAATTTCATT
2381756 ATTACTAATCATTA
1 ATTACTAATCATTA
2381770 CTAAATCTTA
Statistics
Matches: 461, Mismatches: 58, Indels: 118
0.72 0.09 0.19
Matches are distributed among these distances:
101 1 0.00
102 1 0.00
103 5 0.01
104 13 0.03
105 14 0.03
106 18 0.04
107 6 0.01
108 35 0.08
109 142 0.31
110 23 0.05
111 5 0.01
112 9 0.02
113 5 0.01
114 3 0.01
115 4 0.01
116 6 0.01
117 4 0.01
118 8 0.02
119 65 0.14
120 57 0.12
121 25 0.05
122 5 0.01
123 4 0.01
124 3 0.01
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.41
Consensus pattern (109 bp):
ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT
AAATCATTACTATCAAATCATTAAATATTAATAAAAATTTCATT
Found at i:2381297 original size:21 final size:21
Alignment explanation
Indices: 2381153--2381297 Score: 60
Period size: 21 Copynumber: 7.2 Consensus size: 21
2381143 ATTACTAATC
*
2381153 ATTACTATCAAATCATTAAAA
1 ATTACTATCAAATCATTAAAT
* * * *
2381174 ATTAATA-AAAAT--TTTATT
1 ATTACTATCAAATCATTAAAT
*
2381192 ATTACTAATC--ATTATTAAAT
1 ATTACT-ATCAAATCATTAAAT
*
2381212 CATTAATATCAAATCATTAAAT
1 -ATTACTATCAAATCATTAAAT
* * *
2381234 ATTA--AT--AATAATTTCATT
1 ATTACTATCAAATCA-TTAAAT
* *
2381252 ATTACTAATC--ATTACTAAAT
1 ATTACT-ATCAAATCATTAAAT
2381272 CATTACTATCAAATCATTAAAT
1 -ATTACTATCAAATCATTAAAT
2381294 ATTA
1 ATTA
2381298 ATAACAATTT
Statistics
Matches: 89, Mismatches: 20, Indels: 30
0.64 0.14 0.22
Matches are distributed among these distances:
17 4 0.04
18 18 0.20
19 3 0.03
20 17 0.19
21 30 0.34
22 17 0.19
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTACTATCAAATCATTAAAT
Found at i:2381310 original size:22 final size:22
Alignment explanation
Indices: 2381267--2381353 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 22
2381257 TAATCATTAC
* *
2381267 TAAATCATTACTATCAAATCAT
1 TAAATCATTAATAACAAATCAT
*
2381289 TAAAT-ATTAATAACAATTTCATTAT
1 TAAATCATTAATAACAA----ATCAT
* *
2381314 TACTAATCATTACTATCAAATCAT
1 TA--AATCATTAATAACAAATCAT
2381338 TAAAT-ATTAATAACAA
1 TAAATCATTAATAACAA
2381354 TTTCATTATT
Statistics
Matches: 50, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
21 18 0.36
22 8 0.16
24 6 0.12
25 6 0.12
27 3 0.06
28 9 0.18
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATCATTAATAACAAATCAT
Found at i:2381325 original size:49 final size:49
Alignment explanation
Indices: 2381262--2381377 Score: 223
Period size: 49 Copynumber: 2.3 Consensus size: 49
2381252 ATTACTAATC
2381262 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATT
1 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAACAATTTCATT
2381312 ATTACTAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATT
2381361 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
2381378 AATCATTAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
49 60 0.91
50 6 0.09
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATT
Found at i:2381346 original size:21 final size:20
Alignment explanation
Indices: 2381322--2381409 Score: 56
Period size: 21 Copynumber: 4.3 Consensus size: 20
2381312 ATTACTAATC
*
2381322 ATTACTATCAAATCATTAAAT
1 ATTAATATC-AATCATTAAAT
* * *
2381343 ATTAATAACAAT--TTCATT
1 ATTAATATCAATCATTAAAT
* * *
2381361 ATTACTAATC-ATTACTAAAT
1 ATTAAT-ATCAATCATTAAAT
2381381 CATTAATATCAAATCATTAAAT
1 -ATTAATATC-AATCATTAAAT
2381403 ATTAATA
1 ATTAATA
2381410 ATAATTTCAT
Statistics
Matches: 49, Mismatches: 12, Indels: 12
0.67 0.16 0.16
Matches are distributed among these distances:
18 11 0.22
19 2 0.04
20 9 0.18
21 19 0.39
22 8 0.16
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTAATATCAATCATTAAAT
Found at i:2381445 original size:21 final size:21
Alignment explanation
Indices: 2381361--2381445 Score: 54
Period size: 21 Copynumber: 4.2 Consensus size: 21
2381351 CAATTTCATT
*
2381361 ATTACTAATCATTACTAAATC
1 ATTAATAATCATTACTAAATC
* *
2381382 ATTAAT-ATCAAATCATTAAAT-
1 ATTAATAATC--ATTACTAAATC
* * *
2381403 ATTAATAATAATT--T-CATT
1 ATTAATAATCATTACTAAATC
*
2381421 ATTACTAATCATTACTAAATC
1 ATTAATAATCATTACTAAATC
2381442 ATTA
1 ATTA
2381446 TTATAATTTC
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
17 2 0.04
18 12 0.26
20 6 0.13
21 17 0.36
22 10 0.21
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAATAATCATTACTAAATC
Found at i:2381541 original size:14 final size:14
Alignment explanation
Indices: 2381519--2381566 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
2381509 TTCAAGTCGT
*
2381519 AAATTATTACTATC
1 AAATCATTACTATC
2381533 AAATCATTAC--T-
1 AAATCATTACTATC
*
2381544 AAATCATTAATATC
1 AAATCATTACTATC
2381558 AAATCATTA
1 AAATCATTA
2381567 AATCTTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 9 0.31
12 1 0.03
13 1 0.03
14 18 0.62
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:2381582 original size:21 final size:22
Alignment explanation
Indices: 2381518--2381624 Score: 74
Period size: 25 Copynumber: 4.6 Consensus size: 22
2381508 GTTCAAGTCG
* *
2381518 TAAATTATTACTATCAAATCATT
1 TAAATCATTAATATCAAATCA-T
2381541 ACTAAATCATTAATATCAAATCAT
1 --TAAATCATTAATATCAAATCAT
* *
2381565 TAAATC-TTAATAATAAATTATTAT
1 TAAATCATTAAT-ATCAA--ATCAT
*
2381589 TACTAATCATTACTATCAAATCAT
1 TA--AATCATTAATATCAAATCAT
*
2381613 TAAA-AATTAATA
1 TAAATCATTAATA
2381625 ATAATTTCAT
Statistics
Matches: 67, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
21 11 0.16
22 12 0.18
24 13 0.19
25 19 0.28
26 8 0.12
27 4 0.06
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATCATTAATATCAAATCAT
Found at i:2381600 original size:48 final size:49
Alignment explanation
Indices: 2381538--2381649 Score: 172
Period size: 48 Copynumber: 2.3 Consensus size: 49
2381528 CTATCAAATC
**
2381538 ATTACTAAATCATTAATATCAAATCATTAAATCTTAATAATAAATT-ATT
1 ATTACT-AATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATT
* *
2381587 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATT
2381636 ATTACTAATCATTA
1 ATTACTAATCATTA
2381650 CTAAATTATT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
48 35 0.60
49 23 0.40
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATT
Found at i:2381636 original size:36 final size:36
Alignment explanation
Indices: 2381595--2381663 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
2381585 TTATTACTAA
2381595 TCATTACTATCAAATCATTA-AAAATTAATAATAATT
1 TCATTACTA-CAAATCATTACAAAATTAATAATAATT
* * * *
2381631 TCATTATTACTAATCATTACTAAATTATTAATA
1 TCATTACTACAAATCATTACAAAATTAATAATA
2381664 TCAAATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 9 0.32
36 19 0.68
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (36 bp):
TCATTACTACAAATCATTACAAAATTAATAATAATT
Found at i:2381657 original size:21 final size:21
Alignment explanation
Indices: 2381633--2381723 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 21
2381623 TAATAATTTC
2381633 ATTATTACTAATCATTACTAA
1 ATTATTACTAATCATTACTAA
* *
2381654 ATTATTAAT-ATCAAATTATTAA
1 ATTATTACTAATC--ATTACTAA
* *
2381676 A-TATTAATAATAATT-CT--
1 ATTATTACTAATCATTACTAA
2381693 ATTATTACTAATCATTACTAA
1 ATTATTACTAATCATTACTAA
*
2381714 ATCATTACTA
1 ATTATTACTA
2381724 TCAAATCATT
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
17 1 0.02
18 12 0.21
19 3 0.05
20 6 0.11
21 24 0.43
22 10 0.18
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTATTACTAATCATTACTAA
Found at i:2383560 original size:5 final size:5
Alignment explanation
Indices: 2383529--2383558 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
2383519 TAAATCATTA
*
2383529 AATAT AATAT AATAT AATAT AATAT TATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT
2383559 TAATGATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
AATAT
Found at i:2384318 original size:28 final size:28
Alignment explanation
Indices: 2384278--2384337 Score: 104
Period size: 28 Copynumber: 2.1 Consensus size: 28
2384268 TTATATAATA
2384278 TAATATATAATAACTTAAACTAACAAAC
1 TAATATATAATAACTTAAACTAACAAAC
2384306 TAATATA-ATATAACTTAAACTAACAAAC
1 TAATATATA-ATAACTTAAACTAACAAAC
2384334 TAAT
1 TAAT
2384338 TAACTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 1 0.03
28 30 0.97
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
TAATATATAATAACTTAAACTAACAAAC
Found at i:2384790 original size:23 final size:23
Alignment explanation
Indices: 2384760--2384803 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2384750 GCTTGGCTAT
2384760 AATCTCCCAGCTATAGATGCAGG
1 AATCTCCCAGCTATAGATGCAGG
*
2384783 AATCTCCCAGCTATGGATGCA
1 AATCTCCCAGCTATAGATGCA
2384804 ACCCATGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (23 bp):
AATCTCCCAGCTATAGATGCAGG
Found at i:2384899 original size:29 final size:29
Alignment explanation
Indices: 2384867--2384949 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 29
2384857 GTCGAGGCTT
* *
2384867 GGTCGCTGGGATTGCTTGGCGACCTACAA
1 GGTCGCTGGGACTGCATGGCGACCTACAA
* ***
2384896 GGTCGCTGGGAGTGCATGGCGACCTTGTA
1 GGTCGCTGGGACTGCATGGCGACCTACAA
*
2384925 GGTCGCTGGGACTACATGGCGACCT
1 GGTCGCTGGGACTGCATGGCGACCT
2384950 GTATTGGGTG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.16, C:0.24, G:0.37, T:0.23
Consensus pattern (29 bp):
GGTCGCTGGGACTGCATGGCGACCTACAA
Found at i:2384980 original size:16 final size:16
Alignment explanation
Indices: 2384959--2384992 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2384949 TGTATTGGGT
2384959 GTTGGGTGCTGGGGAC
1 GTTGGGTGCTGGGGAC
2384975 GTTGGGTGCTGGGGAC
1 GTTGGGTGCTGGGGAC
2384991 GT
1 GT
2384993 GCATGGCGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.12, G:0.56, T:0.26
Consensus pattern (16 bp):
GTTGGGTGCTGGGGAC
Found at i:2386675 original size:11 final size:11
Alignment explanation
Indices: 2386656--2386690 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
2386646 TATATTTTTT
2386656 TAGTAAAATGA
1 TAGTAAAATGA
*
2386667 TAGTGAAATGA
1 TAGTAAAATGA
2386678 TAGTAAAATGA
1 TAGTAAAATGA
2386689 TA
1 TA
2386691 AACAAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (11 bp):
TAGTAAAATGA
Found at i:2387173 original size:2 final size:2
Alignment explanation
Indices: 2387166--2387210 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2387156 CCAAGTATAA
2387166 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2387208 CT C
1 CT C
2387211 AGTCATTTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2392937 original size:23 final size:23
Alignment explanation
Indices: 2392907--2392954 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2392897 AGGAGGCAAT
2392907 AGGATTCAGTTAGATGCCTGCTA
1 AGGATTCAGTTAGATGCCTGCTA
2392930 AGGATTCAGTTAGATGCCTGCTA
1 AGGATTCAGTTAGATGCCTGCTA
2392953 AG
1 AG
2392955 ACAGAAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (23 bp):
AGGATTCAGTTAGATGCCTGCTA
Found at i:2399195 original size:12 final size:13
Alignment explanation
Indices: 2399180--2399208 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2399170 CAAAAAAAAA
2399180 AAAACTAAAAC-T
1 AAAACTAAAACAT
2399192 AAAACTAAAACAT
1 AAAACTAAAACAT
2399205 AAAA
1 AAAA
2399209 AAACTAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.72, C:0.14, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAACTAAAACAT
Found at i:2400471 original size:31 final size:32
Alignment explanation
Indices: 2400400--2400481 Score: 118
Period size: 30 Copynumber: 2.7 Consensus size: 32
2400390 TGGGGTAAAC
*
2400400 TTGAA-TTTTTAAAATTTTA-GGGAAGGGAAT
1 TTGAACTTTATAAAATTTTAGGGGAAGGGAAT
*
2400430 TTGAAC-TTATAAAATTTTAGGGGAA-TGAAT
1 TTGAACTTTATAAAATTTTAGGGGAAGGGAAT
2400460 TTGAACTTTATAAAATTTTAGG
1 TTGAACTTTATAAAATTTTAGG
2400482 AGATAAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
30 27 0.57
31 20 0.43
ACGTcount: A:0.38, C:0.02, G:0.20, T:0.40
Consensus pattern (32 bp):
TTGAACTTTATAAAATTTTAGGGGAAGGGAAT
Found at i:2400518 original size:21 final size:19
Alignment explanation
Indices: 2400494--2400535 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
2400484 ATAAAAATTG
2400494 ATTTTTAATAGAAAATATATA
1 ATTTTT-ATA-AAAATATATA
*
2400515 ATTTTTTTAAAAATATATA
1 ATTTTTATAAAAATATATA
2400534 AT
1 AT
2400536 AATTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 2 0.10
21 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATTTTTATAAAAATATATA
Found at i:2400527 original size:19 final size:19
Alignment explanation
Indices: 2400505--2400545 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2400495 TTTTTAATAG
**
2400505 AAAATATATAATTTTTTTA
1 AAAATATATAATAATTTTA
2400524 AAAATATATAATAATTTTA
1 AAAATATATAATAATTTTA
2400543 AAA
1 AAA
2400546 TTTTAAGGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATATATAATAATTTTA
Found at i:2402191 original size:15 final size:14
Alignment explanation
Indices: 2402171--2402204 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2402161 AAATGTTATT
2402171 TTTATATTAAAAATA
1 TTTATA-TAAAAATA
*
2402186 TTTATATCAAAATA
1 TTTATATAAAAATA
2402200 TTTAT
1 TTTAT
2402205 TTTAGAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTATATAAAAATA
Found at i:2402731 original size:21 final size:20
Alignment explanation
Indices: 2402707--2402747 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2402697 TTCTTTAAAG
2402707 TATAATATTATGAATATATTT
1 TATAATATTAT-AATATATTT
* *
2402728 TATAATTTTATAATGTATTT
1 TATAATATTATAATATATTT
2402748 GGGATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TATAATATTATAATATATTT
Found at i:2407338 original size:2 final size:2
Alignment explanation
Indices: 2407331--2407359 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2407321 TCCGTCCCTG
2407331 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2407360 ATACTTTTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2410331 original size:20 final size:19
Alignment explanation
Indices: 2410277--2410323 Score: 78
Period size: 20 Copynumber: 2.5 Consensus size: 19
2410267 CTAAATTTGG
2410277 TATCGATACC-AAGGCCAA
1 TATCGATACCTAAGGCCAA
2410295 TATCGATACCCTAAGGCCAA
1 TATCGATA-CCTAAGGCCAA
2410315 TATCGATAC
1 TATCGATAC
2410324 TGACAGGCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.30
19 3 0.11
20 16 0.59
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (19 bp):
TATCGATACCTAAGGCCAA
Found at i:2411670 original size:22 final size:22
Alignment explanation
Indices: 2411644--2411704 Score: 122
Period size: 22 Copynumber: 2.8 Consensus size: 22
2411634 TAGTTGTATA
2411644 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
2411666 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
2411688 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
2411705 TAATTTATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATG
Found at i:2411764 original size:31 final size:31
Alignment explanation
Indices: 2411729--2411787 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2411719 AGTTGTATGT
* *
2411729 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
2411760 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
2411788 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:2412437 original size:32 final size:31
Alignment explanation
Indices: 2412377--2412438 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
2412367 AATGGCTAAC
* **
2412377 AATTTTATCAAATTATTATAAATTTATCATT
1 AATTTTATCAAACTATTATAAAACTATCATT
2412408 AATTTCTATCAAACTATTATAAAACTATCAT
1 AATTT-TATCAAACTATTATAAAACTATCAT
2412439 ATTTTTTTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.45
Consensus pattern (31 bp):
AATTTTATCAAACTATTATAAAACTATCATT
Found at i:2414934 original size:2 final size:2
Alignment explanation
Indices: 2414929--2414984 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
2414919 TTTCCAGTTT
2414929 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2414971 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
2414985 GTTTGATACT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2416553 original size:13 final size:13
Alignment explanation
Indices: 2416535--2416625 Score: 114
Period size: 13 Copynumber: 6.9 Consensus size: 13
2416525 CACAATACCA
2416535 CACATTCACATTT
1 CACATTCACATTT
2416548 CACATTCAC-TTCT
1 CACATTCACATT-T
2416561 CACATTCACATTT
1 CACATTCACATTT
*
2416574 CACATTTCACA-AT
1 CACA-TTCACATTT
2416587 CACATTTCACATTT
1 CACA-TTCACATTT
*
2416601 CACAATCACATTT
1 CACATTCACATTT
*
2416614 CACTTTCACATT
1 CACATTCACATT
2416626 CCCGATATAT
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
12 2 0.03
13 54 0.78
14 13 0.19
ACGTcount: A:0.31, C:0.32, G:0.00, T:0.37
Consensus pattern (13 bp):
CACATTCACATTT
Found at i:2416565 original size:20 final size:20
Alignment explanation
Indices: 2416547--2416623 Score: 115
Period size: 20 Copynumber: 4.0 Consensus size: 20
2416537 CATTCACATT
*
2416547 TCACA-TTCAC-TTCTCACAT
1 TCACATTTCACATT-TCACAA
2416566 TCACATTTCACATTTCACAA
1 TCACATTTCACATTTCACAA
2416586 TCACATTTCACATTTCACAA
1 TCACATTTCACATTTCACAA
2416606 TCACATTTCAC-TTTCACA
1 TCACATTTCACATTTCACA
2416624 TTCCCGATAT
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
19 12 0.22
20 41 0.75
21 2 0.04
ACGTcount: A:0.31, C:0.32, G:0.00, T:0.36
Consensus pattern (20 bp):
TCACATTTCACATTTCACAA
Found at i:2416577 original size:33 final size:33
Alignment explanation
Indices: 2416536--2416625 Score: 121
Period size: 33 Copynumber: 2.7 Consensus size: 33
2416526 ACAATACCAC
2416536 ACATTCACATTTCACATTCAC-TTCTCACA-TTC
1 ACATTCACATTTCACATTCACATT-TCACATTTC
*
2416568 ACATTTCACATTTCACAATCACATTTCACATTTC
1 ACA-TTCACATTTCACATTCACATTTCACATTTC
* *
2416602 ACAATCACATTTCACTTTCACATT
1 ACATTCACATTTCACATTCACATT
2416626 CCCGATATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
32 3 0.06
33 40 0.78
34 8 0.16
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (33 bp):
ACATTCACATTTCACATTCACATTTCACATTTC
Found at i:2418131 original size:19 final size:18
Alignment explanation
Indices: 2418107--2418147 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
2418097 ATAATTCATA
*
2418107 TAAAATATAAAAAAATATT
1 TAAAATACAAAAAAAT-TT
*
2418126 TAAAATACAAGAAAATTT
1 TAAAATACAAAAAAATTT
2418144 TAAA
1 TAAA
2418148 TTTTTAGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
TAAAATACAAAAAAATTT
Found at i:2421562 original size:2 final size:2
Alignment explanation
Indices: 2421551--2421581 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2421541 TATTTTAAAG
2421551 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2421582 CGAAAAGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2426370 original size:25 final size:25
Alignment explanation
Indices: 2426340--2426389 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2426330 TGAACAGTAA
2426340 TGAACAGTAACCTGTTACAGTACCG
1 TGAACAGTAACCTGTTACAGTACCG
*
2426365 TGAACAGTAACTTGTTACAGTACCG
1 TGAACAGTAACCTGTTACAGTACCG
2426390 ATTACACAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (25 bp):
TGAACAGTAACCTGTTACAGTACCG
Found at i:2427028 original size:24 final size:25
Alignment explanation
Indices: 2427001--2427063 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
2426991 AGCTTGTATA
2427001 AATTTGCACCGAAGTG-CCACGTAG
1 AATTTGCACCGAAGTGACCACGTAG
*
2427025 AATTTGTC-CCGAAG-GACCGCGTAG
1 AATTTG-CACCGAAGTGACCACGTAG
*
2427049 AA-ATGCACCGAAGTG
1 AATTTGCACCGAAGTG
2427064 TCACATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
22 1 0.03
23 9 0.27
24 22 0.67
25 1 0.03
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (25 bp):
AATTTGCACCGAAGTGACCACGTAG
Found at i:2428122 original size:25 final size:26
Alignment explanation
Indices: 2428094--2428144 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
2428084 AAAAACTCAT
*
2428094 CCATATC-GAAATTTCATCTA-AAAAC
1 CCATATCTCAAATTT-ATCTATAAAAC
*
2428119 CCATTTCTCAAATTTATCTATAAAAC
1 CCATATCTCAAATTTATCTATAAAAC
2428145 ATTTATCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.41, C:0.24, G:0.02, T:0.33
Consensus pattern (26 bp):
CCATATCTCAAATTTATCTATAAAAC
Found at i:2438862 original size:33 final size:32
Alignment explanation
Indices: 2438815--2438906 Score: 114
Period size: 32 Copynumber: 2.8 Consensus size: 32
2438805 ACAAAGTTTA
* *
2438815 CGAT-AATTGAAATACTTAAATACTTTCAAATT
1 CGATAAATTCAAATACTTAAA-ACTTCCAAATT
* *
2438847 CGATAAATTCAAATACTTAAAAATTCCAAGTT
1 CGATAAATTCAAATACTTAAAACTTCCAAATT
*
2438879 CGATAAATTTAAATACTTAAAAACTTCC
1 CGATAAATTCAAATACTT-AAAACTTCC
2438907 GAGTTTTTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
32 29 0.56
33 23 0.44
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (32 bp):
CGATAAATTCAAATACTTAAAACTTCCAAATT
Found at i:2439323 original size:27 final size:28
Alignment explanation
Indices: 2439261--2439317 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
2439251 AAATGCATAA
* *
2439261 AACTCATTTTTTGTAAAACACAATATCT
1 AACTCATTTTTCGTAAAACACAAAATCT
*
2439289 AATCTCATTTTTCGTAAAACAGAAAATCT
1 AA-CTCATTTTTCGTAAAACACAAAATCT
2439318 GATCATACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (28 bp):
AACTCATTTTTCGTAAAACACAAAATCT
Found at i:2439402 original size:27 final size:26
Alignment explanation
Indices: 2439359--2439418 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
2439349 ACTTTGAAGA
* * *
2439359 GTATTTTTCTAACAAATCTATTA-GGG
1 GTATTTTTCAAAAAAAT-AATTATGGG
2439385 GTATTTTTCAAGAAAAATAATTATGGG
1 GTATTTTTCAA-AAAAATAATTATGGG
2439412 GT-TTTTT
1 GTATTTTT
2439419 AATATAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.45
Consensus pattern (26 bp):
GTATTTTTCAAAAAAATAATTATGGG
Found at i:2446454 original size:23 final size:23
Alignment explanation
Indices: 2446428--2446474 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2446418 TTTATATATG
*
2446428 AGTTATAAATTTAATTAAATTTA
1 AGTTATAAATTCAATTAAATTTA
** *
2446451 AGTTATTTATTCATTTAAATTTA
1 AGTTATAAATTCAATTAAATTTA
2446474 A
1 A
2446475 TAACAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (23 bp):
AGTTATAAATTCAATTAAATTTA
Found at i:2448288 original size:25 final size:23
Alignment explanation
Indices: 2448254--2448307 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
2448244 GAATAAAATA
2448254 AATAATATTATTTATTAGAAAGATT
1 AATAATATTATTT-TTA-AAAGATT
* *
2448279 AATATTATTATTTTTAAAATATT
1 AATAATATTATTTTTAAAAGATT
2448302 AA-AATA
1 AATAATA
2448308 ATTTATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 3 0.12
23 8 0.31
24 3 0.12
25 12 0.46
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
AATAATATTATTTTTAAAAGATT
Found at i:2448465 original size:29 final size:30
Alignment explanation
Indices: 2448416--2448478 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
2448406 AATATTAAAA
* * * *
2448416 ATTATATTAATTATTTATTAAAATGAGATT
1 ATTAAATTAATTAATTATTAAAATAAGAAT
2448446 ATTAAATT-ATTAATTATTAAAATAAGAAT
1 ATTAAATTAATTAATTATTAAAATAAGAAT
2448475 ATTA
1 ATTA
2448479 TTATAATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (30 bp):
ATTAAATTAATTAATTATTAAAATAAGAAT
Found at i:2448511 original size:11 final size:10
Alignment explanation
Indices: 2448492--2448532 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
2448482 TAATATAATC
2448492 AAATTATATT
1 AAATTATATT
2448502 AAATTAATATT
1 AAATT-ATATT
2448513 AAA-TATA-T
1 AAATTATATT
2448521 AATATTATATT
1 AA-ATTATATT
2448532 A
1 A
2448533 TTAAAATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
8 3 0.11
9 4 0.15
10 10 0.37
11 10 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
AAATTATATT
Found at i:2456828 original size:10 final size:10
Alignment explanation
Indices: 2456815--2456848 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2456805 ATGTTTGTTT
*
2456815 GTTTATGTTC
1 GTTTATATTC
*
2456825 GTTTACATTC
1 GTTTATATTC
2456835 GTTTATATTC
1 GTTTATATTC
2456845 GTTT
1 GTTT
2456849 GTTTGTGTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.59
Consensus pattern (10 bp):
GTTTATATTC
Found at i:2456876 original size:23 final size:24
Alignment explanation
Indices: 2456832--2456887 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
2456822 TTCGTTTACA
**
2456832 TTCGTTTATATTCGTTTGTTTGTG
1 TTCGTTTATATTCGTTCATTTGTG
*
2456856 TTCGTTTA-GTTCGTTCATTTGTG
1 TTCGTTTATATTCGTTCATTTGTG
*
2456879 TTTGTTTAT
1 TTCGTTTAT
2456888 CATTTTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.09, C:0.09, G:0.20, T:0.62
Consensus pattern (24 bp):
TTCGTTTATATTCGTTCATTTGTG
Found at i:2458797 original size:2 final size:2
Alignment explanation
Indices: 2458790--2458818 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2458780 CCTTGTGTAT
2458790 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2458819 TTTTAACTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2460368 original size:19 final size:20
Alignment explanation
Indices: 2460325--2460368 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
2460315 TATATTCAGA
2460325 TCCTTTTCAGAACCCATTTT
1 TCCTTTTCAGAACCCATTTT
*
2460345 GCCTTTTCAG-ACCC-TTTCT
1 TCCTTTTCAGAACCCATTT-T
2460364 TCCTT
1 TCCTT
2460369 CCCAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 9 0.43
20 9 0.43
ACGTcount: A:0.14, C:0.34, G:0.07, T:0.45
Consensus pattern (20 bp):
TCCTTTTCAGAACCCATTTT
Found at i:2463609 original size:15 final size:15
Alignment explanation
Indices: 2463589--2463625 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
2463579 ATGTCACATT
2463589 CAGAGCCAATTCATA
1 CAGAGCCAATTCATA
2463604 CAGAGCCAATTCATA
1 CAGAGCCAATTCATA
2463619 CAGAGCC
1 CAGAGCC
2463626 TTTGAATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.30, G:0.16, T:0.16
Consensus pattern (15 bp):
CAGAGCCAATTCATA
Done.