Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 123 of 198
Found at i:39544805 original size:28 final size:28
Alignment explanation
Indices: 39544749--39544806 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
39544739 TAAATTCTCA
* **
39544749 TAAACTAGATATTCGATTATATTTATTT
1 TAAAATAGATATTCGATTATATCGATTT
* *
39544777 TAAAATAGATATTCGATTATCTCGGTTT
1 TAAAATAGATATTCGATTATATCGATTT
39544805 TA
1 TA
39544807 GAATGAAGCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (28 bp):
TAAAATAGATATTCGATTATATCGATTT
Found at i:39545179 original size:68 final size:68
Alignment explanation
Indices: 39545095--39545494 Score: 426
Period size: 68 Copynumber: 5.8 Consensus size: 68
39545085 AAAAGGAAGT
* * * * *
39545095 ATAAGTAATATCAAATTAAAATATTTAAAAAGTAAAAGAATAATAAATGAATAAATAGATAATAA
1 ATAAATAATATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAATAAATAAATAGATAATAA
39545160 AAA
66 AAA
* * *
39545163 ATACATAATATTAAATTTAAGTATTTAAGAAGTAAAAGAATAATAAATAAATAAATTGATAA-AA
1 ATAAATAATATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAATAAATAAATAGATAATAA
*
39545227 CAA
66 AAA
*
39545230 ATACAATAATGTTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAACAAATAAATAAATAGAT
1 ATA-AATAATATTAAATTTAAGTATTTAAAAAGTAAAAGAATAAT----AAATAAATAAATAGAT
39545295 -ATAATAAA
61 AATAA-AAA
39545303 TATAAATAATATTAAATTTAAGTATTTAAAAAGCT-AAAG---AA-AAATAAATAAATA-A-AA-
1 -ATAAATAATATTAAATTTAAGTATTTAAAAAG-TAAAAGAATAATAAATAAATAAATAGATAAT
* *
39545360 CAAAT
64 AAAAA
* * *
39545365 ATAAATAATATTAAATTTAGGTATTTGAAAAGTAAAAGAATAATAAACAAATAAGTAAATAGAT-
1 ATAAATAATATTAAATTTAAGTATTTAAAAAGTAAAAGAATAAT----AAATAAATAAATAGATA
39545429 ATAACAAA
62 ATAA-AAA
* * * *
39545437 TATAAATAATATTAATTTTAGGTACTTAAAAAGTAACAGAATAATAAATAAATAAATA
1 -ATAAATAATATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAATAAATAAATA
39545495 AAACAAATAT
Statistics
Matches: 281, Mismatches: 27, Indels: 47
0.79 0.08 0.13
Matches are distributed among these distances:
60 1 0.00
61 34 0.12
62 2 0.01
63 1 0.00
64 4 0.01
65 13 0.05
67 7 0.02
68 92 0.33
69 24 0.09
70 4 0.01
71 2 0.01
72 19 0.07
73 74 0.26
74 4 0.01
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (68 bp):
ATAAATAATATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAATAAATAAATAGATAATAA
AAA
Found at i:39545370 original size:61 final size:62
Alignment explanation
Indices: 39545274--39545507 Score: 220
Period size: 61 Copynumber: 3.6 Consensus size: 62
39545264 AAAAGAATAA
* * * * * *
39545274 TAAACAAATAAATAAATAGATATAATAAATATAAATAATATTAAATTTAAGTATTTAAAAAG
1 TAAAGAAACAAATAAATAAATAAAACAAATATAAATAATATTAAATTTAGGTATTTAAAAAG
*
39545336 CTAAAG-AA-AAATAAATAAATAAAACAAATATAAATAATATTAAATTTAGGTATTTGAAAAG
1 -TAAAGAAACAAATAAATAAATAAAACAAATATAAATAATATTAAATTTAGGTATTTAAAAAG
* * *
39545397 TAAAAGAATAATAAACAAATAAGTAAATAGATATAACAAATATAAATAATATTAATTTTAGGTAC
1 T-AAAG------AAACAAATAAATAAAT--A-A-AACAAATATAAATAATATTAAATTTAGGTAT
39545462 TTAAAAAG
55 TTAAAAAG
*
39545470 TAACAGAATAATAAATAAATAAATAAAACAAATATAAA
1 TAA-AG-A-AACAAATAAATAAATAAAACAAATATAAA
39545508 AAGATGAAAT
Statistics
Matches: 143, Mismatches: 13, Indels: 28
0.78 0.07 0.15
Matches are distributed among these distances:
60 1 0.01
61 52 0.36
62 2 0.01
63 4 0.03
65 12 0.08
66 1 0.01
67 1 0.01
68 3 0.02
69 24 0.17
71 1 0.01
72 3 0.02
73 39 0.27
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.28
Consensus pattern (62 bp):
TAAAGAAACAAATAAATAAATAAAACAAATATAAATAATATTAAATTTAGGTATTTAAAAAG
Found at i:39545414 original size:134 final size:134
Alignment explanation
Indices: 39545094--39545507 Score: 511
Period size: 134 Copynumber: 3.0 Consensus size: 134
39545084 GAAAAGGAAG
* * * * *
39545094 TATAAGTAATATCAAATTAAAATATTTAAAAAGTAAAAGAATAAT----AAATGAATAAATAGAT
1 TATAAATAATATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAACAAATAAATAAATAGAT
* *
39545155 AATAAAAA-ATACATAATATTAAATTTAAGTATTTAAGAAGTAAAAGAATAATAAATAAATAAAT
66 -ATAAAAATATAAATAATATTAAATTTAAGTATTTAAAAAGT-AAAG-A-AATAAATAAAT-AA-
39545219 TGATAAAACAAA
125 --ATAAAACAAA
* *
39545231 TA-CAATAATGTTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAACAAATAAATAAATAGAT
1 TATAAATAATATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAACAAATAAATAAATAGAT
39545295 ATAATAAATATAAATAATATTAAATTTAAGTATTTAAAAAGCTAAAG-AA-AAATAAATAAATAA
66 ATAA-AAATATAAATAATATTAAATTTAAGTATTTAAAAAG-TAAAGAAATAAATAAATAAATAA
39545358 AACAAA
129 AACAAA
* * *
39545364 TATAAATAATATTAAATTTAGGTATTTGAAAAGTAAAAGAATAATAAACAAATAAGTAAATAGAT
1 TATAAATAATATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAACAAATAAATAAATAGAT
* * *
39545429 ATAACAAATATAAATAATATTAATTTTAGGTACTTAAAAAGTAACAGAATAATAAATAAATAAAT
66 ATAA-AAATATAAATAATATTAAATTTAAGTATTTAAAAAGTAA-AG-A-AATAAATAAATAAAT
39545494 AAAACAAA
127 AAAACAAA
39545502 TATAAA
1 TATAAA
39545508 AAGATGAAAT
Statistics
Matches: 246, Mismatches: 18, Indels: 25
0.85 0.06 0.09
Matches are distributed among these distances:
133 15 0.06
134 96 0.39
136 38 0.15
137 12 0.05
138 28 0.11
139 4 0.02
140 18 0.07
141 34 0.14
142 1 0.00
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (134 bp):
TATAAATAATATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAACAAATAAATAAATAGAT
ATAAAAATATAAATAATATTAAATTTAAGTATTTAAAAAGTAAAGAAATAAATAAATAAATAAAA
CAAA
Found at i:39545436 original size:73 final size:73
Alignment explanation
Indices: 39545344--39545496 Score: 234
Period size: 73 Copynumber: 2.1 Consensus size: 73
39545334 AGCTAAAGAA
* *
39545344 AAATAAATAAATAAAACAAATATAAATAATATTAAATTTAGGTATTTGAAAAGTAAAAGAATAAT
1 AAATAAATAAATAAAACAAATATAAATAATATTAAATTTAGGTACTTAAAAAGTAAAAGAATAAT
39545409 AAACAAAT
66 AAACAAAT
* * * * *
39545417 AAGTAAATAGATATAACAAATATAAATAATATTAATTTTAGGTACTTAAAAAGTAACAGAATAAT
1 AAATAAATAAATAAAACAAATATAAATAATATTAAATTTAGGTACTTAAAAAGTAAAAGAATAAT
*
39545482 AAATAAAT
66 AAACAAAT
39545490 AAATAAA
1 AAATAAA
39545497 ACAAATATAA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.28
Consensus pattern (73 bp):
AAATAAATAAATAAAACAAATATAAATAATATTAAATTTAGGTACTTAAAAAGTAAAAGAATAAT
AAACAAAT
Found at i:39551874 original size:15 final size:16
Alignment explanation
Indices: 39551854--39551884 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39551844 AAGAATATCA
39551854 TTTAAAA-TTATTATT
1 TTTAAAATTTATTATT
39551869 TTTAAAATTTATTATT
1 TTTAAAATTTATTATT
39551885 AAAATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAAAATTTATTATT
Found at i:39551945 original size:16 final size:16
Alignment explanation
Indices: 39551899--39551948 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
39551889 TAAAATTAAA
39551899 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
**
39551916 A-A--AATAATACATT
1 ATATTAATAATTTATT
39551929 ATATTAATAATTTATT
1 ATATTAATAATTTATT
39551945 ATAT
1 ATAT
39551949 GACTAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 10 0.38
14 1 0.04
16 14 0.54
17 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:39556050 original size:2 final size:2
Alignment explanation
Indices: 39556045--39556071 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39556035 GAATGGTATA
39556045 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
39556072 AGTTGTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:39557155 original size:11 final size:11
Alignment explanation
Indices: 39557141--39557171 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
39557131 TCTTTATTCT
39557141 CTTTCATTCCA
1 CTTTCATTCCA
39557152 CTTTCATTCCA
1 CTTTCATTCCA
39557163 CTTTCATTC
1 CTTTCATTC
39557172 ATATTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.35, G:0.00, T:0.48
Consensus pattern (11 bp):
CTTTCATTCCA
Found at i:39560433 original size:32 final size:32
Alignment explanation
Indices: 39560391--39560454 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
39560381 AGCGCTGCAC
* *
39560391 CTTGCTTCAGACCTTTGGTCTCCTGGCCGTCG
1 CTTGCTTCAGACCCTTGGTCTCCGGGCCGTCG
*
39560423 CTTGTTTCAGACCCTTGGTCTCCGGGCCGTCG
1 CTTGCTTCAGACCCTTGGTCTCCGGGCCGTCG
39560455 TGCGTCTGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.06, C:0.34, G:0.27, T:0.33
Consensus pattern (32 bp):
CTTGCTTCAGACCCTTGGTCTCCGGGCCGTCG
Found at i:39561686 original size:15 final size:15
Alignment explanation
Indices: 39561668--39561709 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
39561658 TTTATGCATT
*
39561668 TCATTATTATTGTCA
1 TCATTATTATTATCA
39561683 TCATTATTATTATCA
1 TCATTATTATTATCA
*
39561698 TCATTTTTATTA
1 TCATTATTATTA
39561710 GTGCTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.57
Consensus pattern (15 bp):
TCATTATTATTATCA
Found at i:39562521 original size:22 final size:22
Alignment explanation
Indices: 39562478--39562522 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39562468 TCGTGGACCA
* *
39562478 AAATCGTTGTTTTAATAAAATC
1 AAATCGTTGTATTAAAAAAATC
39562500 AAATCGTT-TATTAAAAACAATC
1 AAATCGTTGTATTAAAAA-AATC
39562522 A
1 A
39562523 CTTTTCGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.36
Consensus pattern (22 bp):
AAATCGTTGTATTAAAAAAATC
Found at i:39563647 original size:13 final size:13
Alignment explanation
Indices: 39563611--39563650 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
39563601 AGTTTGGCAA
39563611 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
39563624 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
39563637 TGTTTTTGAAAAG
1 TGCTTTTGAAAAG
39563650 T
1 T
39563651 TTGGTTTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.28, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:39573951 original size:13 final size:13
Alignment explanation
Indices: 39573933--39573957 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39573923 CAATTGTGGA
39573933 TATTAAAAACTAT
1 TATTAAAAACTAT
39573946 TATTAAAAACTA
1 TATTAAAAACTA
39573958 GGAGATCAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
TATTAAAAACTAT
Found at i:39588085 original size:31 final size:31
Alignment explanation
Indices: 39588006--39588086 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
39587996 TTAGTTCATG
* *
39588006 AACTTGGTAATTGTTCTCATATTGAAGCTTA
1 AACTTGGTAATTGTTCCCATATTGAAGCCTA
* *
39588037 AA-TTAGGCACTTGTTCCCATATTGAAGCCTA
1 AACTT-GGTAATTGTTCCCATATTGAAGCCTA
* *
39588068 AACTTGGTAAATATTCCCA
1 AACTTGGTAATTGTTCCCA
39588087 AGTTATGGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
30 2 0.05
31 36 0.90
32 2 0.05
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (31 bp):
AACTTGGTAATTGTTCCCATATTGAAGCCTA
Found at i:39589255 original size:6 final size:6
Alignment explanation
Indices: 39589220--39589244 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
39589210 GAATTTTTTT
39589220 TATAAA TATAAA TATAAA TATAAA T
1 TATAAA TATAAA TATAAA TATAAA T
39589245 TTAATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TATAAA
Found at i:39591176 original size:2 final size:2
Alignment explanation
Indices: 39591169--39591199 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39591159 AGTCTTTACA
39591169 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39591200 ATTAGGTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39594522 original size:2 final size:2
Alignment explanation
Indices: 39594517--39594552 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
39594507 GTGCGTATGT
39594517 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
39594553 CAAAGTNNNN
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:39596508 original size:71 final size:71
Alignment explanation
Indices: 39596424--39596567 Score: 234
Period size: 71 Copynumber: 2.0 Consensus size: 71
39596414 ATAGATATCG
* *
39596424 CGATACTCAGGGTAAGATATTGCAACGTTGTTGACAATTTTAAAATAGGGTGCTCCTTGGCAAGT
1 CGATACTCAGGGTAAGATATTGCAACATTGTTGACAATCTTAAAATAGGGTGCTCCTTGGCAAGT
39596489 GGGTAT
66 GGGTAT
* * * *
39596495 CGATACTCAGGGTAGGATATTGCGACATTGTTGATAATCTTAAAATAGGGTGCTCCTTGGCAGGT
1 CGATACTCAGGGTAAGATATTGCAACATTGTTGACAATCTTAAAATAGGGTGCTCCTTGGCAAGT
39596560 GGGTAT
66 GGGTAT
39596566 CG
1 CG
39596568 CAATACCCAA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (71 bp):
CGATACTCAGGGTAAGATATTGCAACATTGTTGACAATCTTAAAATAGGGTGCTCCTTGGCAAGT
GGGTAT
Found at i:39598277 original size:17 final size:18
Alignment explanation
Indices: 39598252--39598296 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
39598242 GGTGTTGGTG
**
39598252 ATATTTTATTATTATTTA
1 ATATTTTATTATTAAATA
39598270 AT-TTTTATT-TTAAATA
1 ATATTTTATTATTAAATA
39598286 ATATTTTATTA
1 ATATTTTATTA
39598297 AGATATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 7 0.30
17 14 0.61
18 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATATTTTATTATTAAATA
Found at i:39606196 original size:49 final size:49
Alignment explanation
Indices: 39606137--39606234 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
39606127 ATACGAAGTA
*
39606137 TGAAATGAAATGTATGAATGAATTTAGCAAAAACAGAAACTTCAACAAT
1 TGAAATGAAATGTATGAATGAATTTAGCAAAAACAAAAACTTCAACAAT
39606186 TGAAATGAAATGTATGAATGAATTTAGCAAAAACAAAAACTTCAACAAT
1 TGAAATGAAATGTATGAATGAATTTAGCAAAAACAAAAACTTCAACAAT
39606235 CAATAACATG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.24
Consensus pattern (49 bp):
TGAAATGAAATGTATGAATGAATTTAGCAAAAACAAAAACTTCAACAAT
Found at i:39607568 original size:11 final size:11
Alignment explanation
Indices: 39607552--39607601 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
39607542 GAATTTCGTT
39607552 AATATTATTTA
1 AATATTATTTA
39607563 AATATTATTTA
1 AATATTATTTA
*
39607574 AATATTTATTTT
1 AATA-TTATTTA
*
39607586 AATATTATTTT
1 AATATTATTTA
39607597 AATAT
1 AATAT
39607602 CTACAGTAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
11 27 0.73
12 10 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
AATATTATTTA
Found at i:39607584 original size:23 final size:23
Alignment explanation
Indices: 39607552--39607601 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
39607542 GAATTTCGTT
39607552 AATA-TTATTTAAATATTATTTA
1 AATATTTATTTAAATATTATTTA
* *
39607574 AATATTTATTTTAATATTATTTT
1 AATATTTATTTAAATATTATTTA
39607597 AATAT
1 AATAT
39607602 CTACAGTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
AATATTTATTTAAATATTATTTA
Found at i:39608236 original size:6 final size:6
Alignment explanation
Indices: 39608225--39608257 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
39608215 TTTATTGTTG
39608225 TTTATT TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTT
39608258 TGAAAAACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:39608817 original size:3 final size:3
Alignment explanation
Indices: 39608804--39608839 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
39608794 CTACCATCTT
*
39608804 TTA TTA TTTA TTA TTA CTA TTA TTA TTA TTA TTA TT
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
39608840 TTACAATTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39609016 original size:23 final size:22
Alignment explanation
Indices: 39608973--39609018 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
39608963 ATATCTATGT
* **
39608973 TCTTATAATGTACATGTTTATA
1 TCTTATAATGTAAATACTTATA
39608995 TCTTATATATGTAAATACTTATA
1 TCTTATA-ATGTAAATACTTATA
39609018 T
1 T
39609019 TTTCATGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.50
Consensus pattern (22 bp):
TCTTATAATGTAAATACTTATA
Found at i:39611199 original size:19 final size:19
Alignment explanation
Indices: 39611175--39611221 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
39611165 AACGTCTCTT
*
39611175 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
39611194 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
39611213 TATGCATTA
1 TTTGCATTA
39611222 GATTTTCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:39612465 original size:17 final size:18
Alignment explanation
Indices: 39612443--39612479 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
39612433 TTATTCTTTT
39612443 ATTCTTTCATCCA-AATC
1 ATTCTTTCATCCATAATC
*
39612460 ATTCTTTCATTCATAATC
1 ATTCTTTCATCCATAATC
39612478 AT
1 AT
39612480 ACTGTGCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTCTTTCATCCATAATC
Found at i:39613241 original size:8 final size:8
Alignment explanation
Indices: 39613230--39613283 Score: 56
Period size: 8 Copynumber: 6.5 Consensus size: 8
39613220 AATCAAAGTC
*
39613230 AAAATAGA
1 AAAAAAGA
*
39613238 AAAAAAAA
1 AAAAAAGA
39613246 AGAAAAAGA
1 A-AAAAAGA
39613255 AAAAAAGA
1 AAAAAAGA
39613263 AAAGAAA-A
1 AAA-AAAGA
39613271 ATAAAAAGA
1 A-AAAAAGA
39613280 AAAA
1 AAAA
39613284 GAAAAAGGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
8 25 0.64
9 14 0.36
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.04
Consensus pattern (8 bp):
AAAAAAGA
Found at i:39613258 original size:25 final size:25
Alignment explanation
Indices: 39613230--39613283 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
39613220 AATCAAAGTC
*
39613230 AAAATAGAAAAAAAAAAGAAAAAGA
1 AAAAAAGAAAAAAAAAAGAAAAAGA
* *
39613255 AAAAAAGAAAAGAAAAATAAAAAGA
1 AAAAAAGAAAAAAAAAAGAAAAAGA
39613280 AAAA
1 AAAA
39613284 GAAAAAGGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.04
Consensus pattern (25 bp):
AAAAAAGAAAAAAAAAAGAAAAAGA
Found at i:39613290 original size:6 final size:6
Alignment explanation
Indices: 39613230--39613290 Score: 79
Period size: 6 Copynumber: 10.0 Consensus size: 6
39613220 AATCAAAGTC
* *
39613230 AAAATAG AAAAA- AAAAAG AAAAAG AAAAAA AGAAAAG AAAAAT AAAAAG
1 AAAA-AG AAAAAG AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG
39613279 AAAAAG AAAAAG
1 AAAAAG AAAAAG
39613291 GAGAGGTCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
5 5 0.10
6 34 0.71
7 9 0.19
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:39615886 original size:96 final size:96
Alignment explanation
Indices: 39615722--39616759 Score: 1137
Period size: 100 Copynumber: 10.8 Consensus size: 96
39615712 GTAACCATAG
*
39615722 ATTGCAATTTAAAAGATCGAAGCCACAACG-GCGAATCTTACTTTCAGGCGATGCAGCGGAACAA
1 ATTGCAA-TTAAAAGATCGAAGCCACAACGAGCGAATCTTACTTTCAGGCGATGCAGCGGAACAG
39615786 ATTGAAGCTACAACGGCGAGTCTCACTTCCCC
65 ATTGAAGCTACAACGGCGAGTCTCACTTCCCC
* *
39615818 ATTGCAATTTAAAAGATCGAAGCCACAACGAG-GAATCTTACTTTCAGGCGATACAGCGGAATAG
1 ATTGCAA-TTAAAAGATCGAAGCCACAACGAGCGAATCTTACTTTCAGGCGATGCAGCGGAACAG
39615882 ATTGAAGCTACAACGGCGAGTCTCACTTCCCC
65 ATTGAAGCTACAACGGCGAGTCTCACTTCCCC
** *
39615914 ATTGCAATTTAAAAGATTAAAGCCACAACG-GCGAATCTTACTTTCAGGCGATGCAGCAGAACAG
1 ATTGCAA-TTAAAAGATCGAAGCCACAACGAGCGAATCTTACTTTCAGGCGATGCAGCGGAACAG
*
39615978 ATTGAAGCTACAACGGCGAGTCTCCCTTCCCC
65 ATTGAAGCTACAACGGCGAGTCTCACTTCCCC
* *
39616010 ATTGCAA-T---AGATCGAAGCCACAACG-GCGAATCTTACTTCCAGGCGATGCAGCGGAACAAA
1 ATTGCAATTAAAAGATCGAAGCCACAACGAGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
*
39616070 TTGAAGCTACAAAGGCGAGTCTCACTTCCCC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
* *
39616101 ATTGCAA-T---AGATCGAAGCCACAA-TAGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
1 ATTGCAATTAAAAGATCGAAGCCACAACGAGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
*
39616161 TTGAAGCTACAACGGTGAGTCTCACTTCCCC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
*
39616192 ATTGCAATTTAAAAGATCGAAGCCACAACGA-CGAATCTTACTTTCAGGCGATGCAGCGAAACAG
1 ATTGCAA-TTAAAAGATCGAAGCCACAACGAGCGAATCTTACTTTCAGGCGATGCAGCGGAACAG
39616256 ATTGAAGCTACAACGGCGAGTCTCACTTCCCC
65 ATTGAAGCTACAACGGCGAGTCTCACTTCCCC
* * * *
39616288 ATTG----TAATAGATCGAAGCCACAACG-GTGAATCTTACTTCCAGGCGATGCAGCGGAATAGA
1 ATTGCAATTAAAAGATCGAAGCCACAACGAGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
*
39616348 TTGAAGCTACAACAGCGAGTCTCACTTCCCTGAC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCC---C
* * * * * *
39616382 ATTGCAATTAAGAAGATTGAAGCTACAAC-AGCGGATCTTATTTTCCTA-GCGTTGCAGTGGAAC
1 ATTGCAATTAA-AAGATCGAAGCCACAACGAGCGAATCTTACTTT-C-AGGCGATGCAGCGGAAC
* *
39616445 AGATTGAAGCTACAACAGCG-GATCTTACTTCCCTGAC
63 AGATTGAAGCTACAACGGCGAG-TCTCACTTCCC---C
** * * * * *
39616482 ATTGCAATTAAGAAGATTAAAGCTACAAC-AGCGGATCTTACTTTCCTA-ACGTTGCAGTGGAAC
1 ATTGCAATTAA-AAGATCGAAGCCACAACGAGCGAATCTTACTTT-C-AGGCGATGCAGCGGAAC
** *
39616545 AGATTGAAGCTACAACAACG-GATCTTACTTCCCTGAC
63 AGATTGAAGCTACAACGGCGAG-TCTCACTTCCC---C
* * * * * *
39616582 ATTGCAATTAAGAAGATTGAAGCTACAAC-AGTGGATCTTACTTTCCTA-GCGTTGCAGTGGAAC
1 ATTGCAATTAA-AAGATCGAAGCCACAACGAGCGAATCTTACTTT-C-AGGCGATGCAGCGGAAC
* *
39616645 AGATTGAAGCTACAACAGCG-GATCTTACTTCCCTGAC
63 AGATTGAAGCTACAACGGCGAG-TCTCACTTCCC---C
* * * * *
39616682 ATTGCAATTAAGAAGATTGAAGCTACAAC-AGCGGATCTTACTTTCCTA-GCGTTGCAGTGGAAC
1 ATTGCAATTAA-AAGATCGAAGCCACAACGAGCGAATCTTACTTT-C-AGGCGATGCAGCGGAAC
39616745 AGATTGAAGCTACAA
63 AGATTGAAGCTACAA
39616760 TAGCGGATCT
Statistics
Matches: 870, Mismatches: 50, Indels: 40
0.91 0.05 0.04
Matches are distributed among these distances:
91 248 0.29
93 1 0.00
94 6 0.01
95 1 0.00
96 267 0.31
97 2 0.00
98 3 0.00
99 25 0.03
100 316 0.36
101 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (96 bp):
ATTGCAATTAAAAGATCGAAGCCACAACGAGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
TTGAAGCTACAACGGCGAGTCTCACTTCCCC
Found at i:39616097 original size:49 final size:49
Alignment explanation
Indices: 39616018--39616376 Score: 230
Period size: 49 Copynumber: 7.7 Consensus size: 49
39616008 CCATTGCAAT
* *
39616018 AGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAAC
1 AGATTGAAGCCACAACGGCGAATCTCACTTCCAGGCGATGCAGCGGAAC
* * * * * * *
39616067 AAATTGAAGCTACAAAGGCGAGTCTCACTTCC---CCAT--TGC--AAT
1 AGATTGAAGCCACAACGGCGAATCTCACTTCCAGGCGATGCAGCGGAAC
* ** *
39616109 AGATCGAAGCCACAATAGCGAATCTTACTTCCAGGCGATGCAGCGGAAC
1 AGATTGAAGCCACAACGGCGAATCTCACTTCCAGGCGATGCAGCGGAAC
* * * * **** *
39616158 AGATTGAAGCTACAACGGTGAGTCTCACTTCC---CCATTGCAATTTAAA
1 AGATTGAAGCCACAACGGCGAATCTCACTTCCAGGCGA-TGCAGCGGAAC
* * * * *
39616205 AGATCGAAGCCACAACGACGAATCTTACTTTCAGGCGATGCAGCGAAAC
1 AGATTGAAGCCACAACGGCGAATCTCACTTCCAGGCGATGCAGCGGAAC
* * ** * *
39616254 AGATTGAAGCTACAACGGCGAGTCTCACTTCC---C----CATTGTAAT
1 AGATTGAAGCCACAACGGCGAATCTCACTTCCAGGCGATGCAGCGGAAC
* * * *
39616296 AGATCGAAGCCACAACGGTGAATCTTACTTCCAGGCGATGCAGCGGAAT
1 AGATTGAAGCCACAACGGCGAATCTCACTTCCAGGCGATGCAGCGGAAC
* * *
39616345 AGATTGAAGCTACAACAGCGAGTCTCACTTCC
1 AGATTGAAGCCACAACGGCGAATCTCACTTCC
39616377 CTGACATTGC
Statistics
Matches: 223, Mismatches: 69, Indels: 36
0.68 0.21 0.11
Matches are distributed among these distances:
42 59 0.26
44 2 0.01
45 4 0.02
46 6 0.03
47 33 0.15
49 117 0.52
50 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (49 bp):
AGATTGAAGCCACAACGGCGAATCTCACTTCCAGGCGATGCAGCGGAAC
Found at i:39616405 original size:50 final size:48
Alignment explanation
Indices: 39616345--39617226 Score: 947
Period size: 50 Copynumber: 17.7 Consensus size: 48
39616335 GCAGCGGAAT
* *
39616345 AGATTGAAGCTACAACAGC-GAGTCTCACTTCCCTGACATTGCAATTAAGA
1 AGATTGAAGCTACAACAGCGGA-TCTTACTTCCCT-ACATTGCAATGAA-A
* * * * *
39616395 AGATTGAAGCTACAACAGCGGATCTTATTTTCCTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAAT-GAAA
*
39616445 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAGA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCT-ACATTGCAATGAA-A
* * * * *
39616495 AGATTAAAGCTACAACAGCGGATCTTACTTTCCTAACGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCT-ACATTGCAAT-GAAA
* *
39616545 AGATTGAAGCTACAACAACGGATCTTACTTCCCTGACATTGCAATTAAGA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCT-ACATTGCAATGAA-A
* * * * *
39616595 AGATTGAAGCTACAACAGTGGATCTTACTTTCCTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAAT-GAAA
*
39616645 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAGA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCT-ACATTGCAATGAA-A
* * * *
39616695 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAAT-GAAA
* * * *
39616745 AGATTGAAGCTACAATAGCGGATCTTACTTTCCTAGCATTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAAT-GAAA
* *
39616795 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGGCATTGCAATTAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCT-ACATTGCAATGAAA
* * *
39616844 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAATGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAAT-GAAA
* *
39616894 AGATTGAAGCTACAACAGCGGATCTCACTTCCCTGACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCT-ACATTGCAA-TGAAA
* * * * * *
39616944 AGATTGAAGCCACAACAGCGGACCTTACTTTCCTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAAT-GAAA
* *
39616994 AGATTGAAGCTACAACAGCGGATCTCACTTCCCTGACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCT-ACATTGCAA-TGAAA
* * * * **
39617044 AGATTGAAGCTACAACAGCAGATCTTACTTTCCTAGCGTTGCAGTGGAGT
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAAT-GAAA
* * * **
39617094 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAGT
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAAT-GAAA
*
39617144 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCT-ACATTGCAA-TGAAA
39617194 AGATTGAAGCTACAACAGCGGATCTTACTTCCC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCC
39617227 AGGCGATGCA
Statistics
Matches: 711, Mismatches: 95, Indels: 52
0.83 0.11 0.06
Matches are distributed among these distances:
49 56 0.08
50 637 0.90
51 18 0.03
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (48 bp):
AGATTGAAGCTACAACAGCGGATCTTACTTCCCTACATTGCAATGAAA
Found at i:39616475 original size:100 final size:100
Alignment explanation
Indices: 39616317--39617403 Score: 1166
Period size: 100 Copynumber: 10.9 Consensus size: 100
39616307 ACAACGGTGA
* * * *
39616317 ATCTTAC-TTCC-AGGCGATGCAGCGGAATAGATTGAAGCTACAACAGC-GAGTCTCACTTCCCT
1 ATCTTACTTTCCTA-GCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGA-TCTTACTTCCCT
39616379 GACATTGCAATTAAGAAGATTGAAGCTACAACAGCGG
64 GACATTGCAATTAAGAAGATTGAAGCTACAACAGCGG
*
39616416 ATCTTATTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA
1 ATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA
*
39616481 CATTGCAATTAAGAAGATTAAAGCTACAACAGCGG
66 CATTGCAATTAAGAAGATTGAAGCTACAACAGCGG
* *
39616516 ATCTTACTTTCCTAACGTTGCAGTGGAACAGATTGAAGCTACAACAACGGATCTTACTTCCCTGA
1 ATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA
*
39616581 CATTGCAATTAAGAAGATTGAAGCTACAACAGTGG
66 CATTGCAATTAAGAAGATTGAAGCTACAACAGCGG
39616616 ATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA
1 ATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA
39616681 CATTGCAATTAAGAAGATTGAAGCTACAACAGCGG
66 CATTGCAATTAAGAAGATTGAAGCTACAACAGCGG
* *
39616716 ATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAATAGCGGATCTTACTTTCCT-A
1 ATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA
* * *
39616780 GCATTGCAGTGGAA-CAGATTGAAGCTACAACAGCGG
66 -CATTGCAAT-TAAGAAGATTGAAGCTACAACAGCGG
* * * * * * *
39616816 ATCTTACTTCCCTGGCATTGCAAT-TAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCT-A
1 ATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA
* * *
39616879 GCGTTGCAATGGAA-CAGATTGAAGCTACAACAGCGG
66 -CATTGCAAT-TAAGAAGATTGAAGCTACAACAGCGG
* * * * ** * * * *
39616915 ATCTCACTTCCCT-GACATTGCAATTAAAAAGATTGAAGCCACAACAGCGGACCTTACTTTCCT-
1 ATCTTACTTTCCTAG-CGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTG
* * * *
39616978 AGCGTTGCAGTGGAA-CAGATTGAAGCTACAACAGCGG
65 A-CATTGCAAT-TAAGAAGATTGAAGCTACAACAGCGG
* * * * ** * * *
39617015 ATCTCACTTCCCT-GACATTGCAATTAAAAAGATTGAAGCTACAACAGCAGATCTTACTTTCCT-
1 ATCTTACTTTCCTAG-CGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTG
* * ** *
39617078 AGCGTTGCAGTGGAGTAGATTGAAGCTACAACAGCGG
65 A-CATTGCAATTAAGAAGATTGAAGCTACAACAGCGG
**
39617115 ATCTTACTTTCCTAGCGTTGCAGTGGAGTAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA
1 ATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA
*
39617180 CATTGCAATTAAAAAGATTGAAGCTACAACAGCGG
66 CATTGCAATTAAGAAGATTGAAGCTACAACAGCGG
* * ** * * * **
39617215 ATCTTAC-TTCCCAGGCGATGCAGTGGAACAGATTGAAGCTATGACGGTGAATCTCGCTT-CCTC
1 ATCTTACTTTCCTA-GCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCT-
* * * ** *
39617278 GACATCGCAACTCAA-AAGATTGAAGCCACAATGGCGA
64 GACATTGCAA-TTAAGAAGATTGAAGCTACAACAGCGG
* ** * * * * * * **
39617315 ATCTTAC-TTCCCAGGCAATGCAGCGGAACAGATTGAAGCTACGACAGTGAATCTCATTTCCCCA
1 ATCTTACTTTCCTA-GCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTG
*
39617379 ACATTGCAAGTAA-ATAGATTGAAGC
65 ACATTGCAATTAAGA-AGATTGAAGC
39617404 CACGACGGTG
Statistics
Matches: 891, Mismatches: 82, Indels: 29
0.89 0.08 0.03
Matches are distributed among these distances:
98 1 0.00
99 111 0.12
100 767 0.86
101 12 0.01
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (100 bp):
ATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA
CATTGCAATTAAGAAGATTGAAGCTACAACAGCGG
Found at i:39617368 original size:50 final size:50
Alignment explanation
Indices: 39616317--39617361 Score: 915
Period size: 50 Copynumber: 20.9 Consensus size: 50
39616307 ACAACGGTGA
* *
39616317 ATCTTACTT-CCAGGCGA-TGCAGCGGAATAGATTGAAGCTACAACAGC-G
1 ATCTTACTTCCCAGGC-ATTGCAGTGGAAAAGATTGAAGCTACAACAGCGG
* * * * *
39616365 AGTCTCACTTCCCTGACATTGCAAT-TAAGAAGATTGAAGCTACAACAGCGG
1 A-TCTTACTTCCCAGGCATTGCAGTGGAA-AAGATTGAAGCTACAACAGCGG
* * * *
39616416 ATCTTATTTTCCTA-GCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGG
1 ATCTTA-CTTCCCAGGCATTGCAGTGGAAAAGATTGAAGCTACAACAGCGG
* * * * *
39616466 ATCTTACTTCCCTGACATTGCAAT-TAAGAAGATTAAAGCTACAACAGCGG
1 ATCTTACTTCCCAGGCATTGCAGTGGAA-AAGATTGAAGCTACAACAGCGG
* * * * *
39616516 ATCTTACTTTCCTA-ACGTTGCAGTGGAACAGATTGAAGCTACAACAACGG
1 ATCTTAC-TTCCCAGGCATTGCAGTGGAAAAGATTGAAGCTACAACAGCGG
* * * * *
39616566 ATCTTACTTCCCTGACATTGCAAT-TAAGAAGATTGAAGCTACAACAGTGG
1 ATCTTACTTCCCAGGCATTGCAGTGGAA-AAGATTGAAGCTACAACAGCGG
* * *
39616616 ATCTTACTTTCCTA-GCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGG
1 ATCTTAC-TTCCCAGGCATTGCAGTGGAAAAGATTGAAGCTACAACAGCGG
* * * *
39616666 ATCTTACTTCCCTGACATTGCAAT-TAAGAAGATTGAAGCTACAACAGCGG
1 ATCTTACTTCCCAGGCATTGCAGTGGAA-AAGATTGAAGCTACAACAGCGG
* * * *
39616716 ATCTTACTTTCCTA-GCGTTGCAGTGGAACAGATTGAAGCTACAATAGCGG
1 ATCTTAC-TTCCCAGGCATTGCAGTGGAAAAGATTGAAGCTACAACAGCGG
* *
39616766 ATCTTACTTTCCTA-GCATTGCAGTGGAACAGATTGAAGCTACAACAGCGG
1 ATCTTAC-TTCCCAGGCATTGCAGTGGAAAAGATTGAAGCTACAACAGCGG
* * *
39616816 ATCTTACTTCCCTGGCATTGCAAT-TAAAAGATTGAAGCTACAACAGCGG
1 ATCTTACTTCCCAGGCATTGCAGTGGAAAAGATTGAAGCTACAACAGCGG
* * * *
39616865 ATCTTACTTTCCTA-GCGTTGCAATGGAACAGATTGAAGCTACAACAGCGG
1 ATCTTAC-TTCCCAGGCATTGCAGTGGAAAAGATTGAAGCTACAACAGCGG
* * * * ** *
39616915 ATCTCACTTCCCTGACATTGCAATTAAAAAGATTGAAGCCACAACAGCGG
1 ATCTTACTTCCCAGGCATTGCAGTGGAAAAGATTGAAGCTACAACAGCGG
* * * *
39616965 ACCTTACTTTCCTA-GCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGG
1 ATCTTAC-TTCCCAGGCATTGCAGTGGAAAAGATTGAAGCTACAACAGCGG
* * * * ** *
39617015 ATCTCACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCAG
1 ATCTTACTTCCCAGGCATTGCAGTGGAAAAGATTGAAGCTACAACAGCGG
* * **
39617065 ATCTTACTTTCCTA-GCGTTGCAGTGGAGTAGATTGAAGCTACAACAGCGG
1 ATCTTAC-TTCCCAGGCATTGCAGTGGAAAAGATTGAAGCTACAACAGCGG
* * **
39617115 ATCTTACTTTCCTA-GCGTTGCAGTGGAGTAGATTGAAGCTACAACAGCGG
1 ATCTTAC-TTCCCAGGCATTGCAGTGGAAAAGATTGAAGCTACAACAGCGG
* * * **
39617165 ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGG
1 ATCTTACTTCCCAGGCATTGCAGTGGAAAAGATTGAAGCTACAACAGCGG
* ** * * *
39617215 ATCTTACTTCCCAGGCGA-TGCAGTGGAACAGATTGAAGCTATGACGGTGA
1 ATCTTACTTCCCAGGC-ATTGCAGTGGAAAAGATTGAAGCTACAACAGCGG
** * * * * * ** *
39617265 ATCTCGCTTCCTC-GACATCGCAACT-CAAAAGATTGAAGCCACAATGGCGA
1 ATCTTACTTCC-CAGGCATTGC-AGTGGAAAAGATTGAAGCTACAACAGCGG
* * * *
39617315 ATCTTACTTCCCAGGCAATGCAGCGGAACAGATTGAAGCTACGACAG
1 ATCTTACTTCCCAGGCATTGCAGTGGAAAAGATTGAAGCTACAACAG
39617362 TGAATCTCAT
Statistics
Matches: 801, Mismatches: 163, Indels: 64
0.78 0.16 0.06
Matches are distributed among these distances:
48 1 0.00
49 86 0.11
50 676 0.84
51 38 0.05
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (50 bp):
ATCTTACTTCCCAGGCATTGCAGTGGAAAAGATTGAAGCTACAACAGCGG
Found at i:39617404 original size:100 final size:99
Alignment explanation
Indices: 39615722--39617425 Score: 825
Period size: 100 Copynumber: 17.4 Consensus size: 99
39615712 GTAACCATAG
* * * * *
39615722 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTT-TCAGGCGATGCAGCGGAACAA
1 ATTGCAA-CTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCAATGCAGCGGAACAG
* * * *
39615786 ATTGAAGCTACAACGGCGAGTCTCACTT-CCC--C
65 ATTGAAGCTACGACAGTGAATCTCACTTCCCCGAC
* * * * * *
39615818 ATTGCAATTTAAAAGATCGAAGCCACAACGAG-GAATCTTACTT-TCAGGCGATACAGCGGAATA
1 ATTGCAA-CTAAAAGATTGAAGCCACAACG-GCGAATCTTACTTCCCAGGCAATGCAGCGGAACA
* * * *
39615881 GATTGAAGCTACAACGGCGAGTCTCACTT-CCC--C
64 GATTGAAGCTACGACAGTGAATCTCACTTCCCCGAC
* * * * *
39615914 ATTGCAATTTAAAAGATTAAAGCCACAACGGCGAATCTTACTT-TCAGGCGATGCAGCAGAACAG
1 ATTGCAA-CTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCAATGCAGCGGAACAG
* * * * *
39615978 ATTGAAGCTACAACGGCGAGTCTCCCTT-CCC--C
65 ATTGAAGCTACGACAGTGAATCTCACTTCCCCGAC
* * *
39616010 ATTGCAA-T---AGATCGAAGCCACAACGGCGAATCTTACTT-CCAGGCGATGCAGCGGAACAAA
1 ATTGCAACTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCAATGCAGCGGAACAGA
* * *
39616070 TTGAAGCTAC-AAAGGCGAGTCTCACTT-CCC--C
66 TTGAAGCTACGACA-GTGAATCTCACTTCCCCGAC
* ** *
39616101 ATTGCAA-T---AGATCGAAGCCACAATAGCGAATCTTACTT-CCAGGCGATGCAGCGGAACAGA
1 ATTGCAACTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCAATGCAGCGGAACAGA
* * *
39616161 TTGAAGCTACAACGGTGAGTCTCACTT-CCC--C
66 TTGAAGCTACGACAGTGAATCTCACTTCCCCGAC
* * * * * *
39616192 ATTGCAATTTAAAAGATCGAAGCCACAACGACGAATCTTACTT-TCAGGCGATGCAGCGAAACAG
1 ATTGCAA-CTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCAATGCAGCGGAACAG
* * * *
39616256 ATTGAAGCTACAACGGCGAGTCTCACTT-CCC--C
65 ATTGAAGCTACGACAGTGAATCTCACTTCCCCGAC
* * * * *
39616288 ATTG----TAATAGATCGAAGCCACAACGGTGAATCTTACTT-CCAGGCGATGCAGCGGAATAGA
1 ATTGCAACTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCAATGCAGCGGAACAGA
* * * *
39616348 TTGAAGCTACAACAGCGAGTCTCACTTCCCTGAC
66 TTGAAGCTACGACAGTGAATCTCACTTCCCCGAC
* * * * * * ** *
39616382 ATTGCAATTAAGAAGATTGAAGCTACAACAGCGGATCTTATTTTCCTA-GCGTTGCAGTGGAACA
1 ATTGCAACTAA-AAGATTGAAGCCACAACGGCGAATCTTA-CTTCCCAGGCAATGCAGCGGAACA
* * * * *
39616446 GATTGAAGCTACAACAGCGGATCTTACTTCCCTGAC
64 GATTGAAGCTACGACAGTGAATCTCACTTCCCCGAC
* * * * * * * ** *
39616482 ATTGCAATTAAGAAGATTAAAGCTACAACAGCGGATCTTACTTTCCTA-ACGTTGCAGTGGAACA
1 ATTGCAACTAA-AAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCAGGCAATGCAGCGGAACA
* ** * * *
39616546 GATTGAAGCTACAACAACGGATCTTACTTCCCTGAC
64 GATTGAAGCTACGACAGTGAATCTCACTTCCCCGAC
* * * * * * ** *
39616582 ATTGCAATTAAGAAGATTGAAGCTACAACAGTGGATCTTACTTTCCTA-GCGTTGCAGTGGAACA
1 ATTGCAACTAA-AAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCAGGCAATGCAGCGGAACA
* * * * *
39616646 GATTGAAGCTACAACAGCGGATCTTACTTCCCTGAC
64 GATTGAAGCTACGACAGTGAATCTCACTTCCCCGAC
* * * * * ** *
39616682 ATTGCAATTAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GCGTTGCAGTGGAACA
1 ATTGCAACTAA-AAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCAGGCAATGCAGCGGAACA
* * * * * * *
39616746 GATTGAAGCTACAATAGCGGATCTTACTT-TCCTAGC
64 GATTGAAGCTACGACAGTGAATCTCACTTCCCCGA-C
* * * * * * * *** *
39616782 ATTGC-AGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGGCATTGCA-ATTAAAA
1 ATTGCAACT--AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCAATGCAGCGGAACA
* * * * * *
39616845 GATTGAAGCTACAACAGCGGATCTTACTT-TCCTAGC
64 GATTGAAGCTACGACAGTGAATCTCACTTCCCCGA-C
* * * * * * * * * **** *
39616881 GTTGCAA-TGGAACAGATTGAAGCTACAACAGCGGATCTCACTTCCCTGACATTGCAATTAAAAA
1 ATTGCAACT--AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCAATGCAGCGGAACA
* * * * * * * *
39616945 GATTGAAGCCACAACAGCGGACCTTACTT-TCCTAGC
64 GATTGAAGCTACGACAGTGAATCTCACTTCCCCGA-C
* * * * * * * * * * **** *
39616981 GTTGC-AGTGGAACAGATTGAAGCTACAACAGCGGATCTCACTTCCCTGACATTGCAATTAAAAA
1 ATTGCAACT--AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCAATGCAGCGGAACA
* * * * *
39617045 GATTGAAGCTACAACAG-CAGATCTTACTT-TCCTAGC
64 GATTGAAGCTACGACAGTGA-ATCTCACTTCCCCGA-C
* * ** * * * * ** * **
39617081 GTTGC-AGTGGAGTAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GCGTTGCAGTGGAGT
1 ATTGCAACT--AAAAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCAGGCAATGCAGCGGAAC
* * * * *
39617144 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGAC
63 AGATTGAAGCTACGACAGTGAATCTCACTTCCCCGAC
* * * * * *
39617181 ATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCAGGCGATGCAGTGGAACAG
1 ATTGCAACT-AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCAATGCAGCGGAACAG
* * * *
39617246 ATTGAAGCTATGACGGTGAATCTCGCTTCCTCGAC
65 ATTGAAGCTACGACAGTGAATCTCACTTCCCCGAC
* *
39617281 ATCGCAACTCAAAAGATTGAAGCCACAATGGCGAATCTTACTTCCCAGGCAATGCAGCGGAACAG
1 ATTGCAACT-AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCAATGCAGCGGAACAG
* *
39617346 ATTGAAGCTACGACAGTGAATCTCATTTCCCCAAC
65 ATTGAAGCTACGACAGTGAATCTCACTTCCCCGAC
* * *
39617381 ATTGCAAGTAAATAGATTGAAGCCACGACGGTGAATCTTACTTCC
1 ATTGCAACTAAA-AGATTGAAGCCACAACGGCGAATCTTACTTCC
39617426 TGAAATTGCA
Statistics
Matches: 1434, Mismatches: 140, Indels: 64
0.88 0.09 0.04
Matches are distributed among these distances:
90 1 0.00
91 239 0.17
92 3 0.00
93 1 0.00
94 6 0.00
95 1 0.00
96 267 0.19
97 1 0.00
98 3 0.00
99 128 0.09
100 772 0.54
101 12 0.01
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (99 bp):
ATTGCAACTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCAATGCAGCGGAACAGA
TTGAAGCTACGACAGTGAATCTCACTTCCCCGAC
Found at i:39617764 original size:44 final size:44
Alignment explanation
Indices: 39617650--39617765 Score: 153
Period size: 44 Copynumber: 2.6 Consensus size: 44
39617640 ACGAAGAGTT
* * *
39617650 ACAAATCCTATCTCCCTGAAGTTGCAATGGAGCGGATTAAAATT
1 ACAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATG
*
39617694 ACAAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAATG
1 ACAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATG
** *
39617738 ATGAATCCTATACT-TCTGAAGTTGCAGT
1 ACAAATCCTAT-CTCCCTGAAGTTGCAGT
39617766 AGGTCGGATT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 61 0.97
45 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (44 bp):
ACAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATG
Found at i:39618642 original size:16 final size:16
Alignment explanation
Indices: 39618621--39618655 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
39618611 TTTTATCTCT
*
39618621 TTTTTATTGTTGTTTA
1 TTTTTATTGTTATTTA
*
39618637 TTTTTATTTTTATTTA
1 TTTTTATTGTTATTTA
39618653 TTT
1 TTT
39618656 ATTTATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (16 bp):
TTTTTATTGTTATTTA
Found at i:39619344 original size:3 final size:3
Alignment explanation
Indices: 39619331--39619396 Score: 114
Period size: 3 Copynumber: 21.7 Consensus size: 3
39619321 TTACCATCTT
*
39619331 TTA TTA TTTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39619377 TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
39619397 TTACAATTTC
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39619473 original size:2 final size:2
Alignment explanation
Indices: 39619463--39619497 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
39619453 TTTTTATCCG
* *
39619463 TA TA AA TA TA TA TA TA TA TT TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39619498 GCACATTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39619591 original size:22 final size:22
Alignment explanation
Indices: 39619549--39619593 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39619539 ATATCTACGT
**
39619549 TCTTATAATGTACATGTTTATA
1 TCTTATAATGTACATACTTATA
39619571 TCTTATATATGTA-ATACTTATA
1 TCTTATA-ATGTACATACTTATA
39619593 T
1 T
39619594 TTTCATGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (22 bp):
TCTTATAATGTACATACTTATA
Found at i:39621603 original size:26 final size:26
Alignment explanation
Indices: 39621574--39621642 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
39621564 GCAAGTACTC
39621574 CACAGCTCGTGTGAGCA-GTCCTATTT
1 CACAGCTCGTGTGAGCATG-CCTATTT
*
39621600 CACAACTCGTGTGAGCATGCCTATTT
1 CACAGCTCGTGTGAGCATGCCTATTT
*
39621626 CACAGCTCATGTGAGCA
1 CACAGCTCGTGTGAGCA
39621643 ACTATGTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
26 38 0.97
27 1 0.03
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCATGCCTATTT
Found at i:39628464 original size:21 final size:20
Alignment explanation
Indices: 39628435--39628478 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
39628425 GACTAATTTG
*
39628435 AAAAGAAATTAAATTAAATAT
1 AAAAGAAATTAAAATAAA-AT
*
39628456 AAAATAAATTAAAATAAAAT
1 AAAAGAAATTAAAATAAAAT
39628476 AAA
1 AAA
39628479 GTTTTGGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAAGAAATTAAAATAAAAT
Found at i:39628468 original size:10 final size:10
Alignment explanation
Indices: 39628435--39628478 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
39628425 GACTAATTTG
*
39628435 AAAAGAAATT
1 AAAATAAATT
*
39628445 AAATTAAATAT
1 AAAATAAAT-T
39628456 AAAATAAATT
1 AAAATAAATT
*
39628466 AAAATAAAAT
1 AAAATAAATT
39628476 AAA
1 AAA
39628479 GTTTTGGTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (10 bp):
AAAATAAATT
Found at i:39632021 original size:18 final size:19
Alignment explanation
Indices: 39632000--39632037 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
39631990 TTTTAAAAAA
39632000 TATAAAT-TTTAAATTTTT
1 TATAAATATTTAAATTTTT
*
39632018 TATAAATATTTGAATTTTT
1 TATAAATATTTAAATTTTT
39632037 T
1 T
39632038 TTTTGTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TATAAATATTTAAATTTTT
Found at i:39632036 original size:27 final size:28
Alignment explanation
Indices: 39631975--39632036 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
39631965 ATTTTTTTTA
39631975 GAATTTTTAGAATTTTTTTAAAAAATAT
1 GAATTTTTAGAATTTTTTTAAAAAATAT
* * *
39632003 -AAATTTTA-AA-TTTTTTATAAATATTT
1 GAATTTTTAGAATTTTTTTA-AAAAATAT
39632029 GAATTTTT
1 GAATTTTT
39632037 TTTTTGTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
25 7 0.25
26 8 0.29
27 13 0.46
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (28 bp):
GAATTTTTAGAATTTTTTTAAAAAATAT
Found at i:39637995 original size:69 final size:69
Alignment explanation
Indices: 39637754--39637997 Score: 253
Period size: 69 Copynumber: 3.6 Consensus size: 69
39637744 ACTCGCAACT
* *
39637754 CAACACAGCTCGCAAACCTACGTTCCCAACTAATATTA-AAAGGATCG-TCAGTTTATGATCGCA
1 CAACACAGCTCGCGAACCTACGTTCCCAACTAATATTATAAAGGCTCGCT-AGTTTATGATCGCA
*
39637817 ACCTC
65 GCCTC
* * * * * * * **
39637822 AAACACAGCTCGTGAACCTAC-ATCCCAGCTGATATTATAAAGGCCCACCGGTTTATGATCGCAG
1 CAACACAGCTCGCGAACCTACGTTCCCAACTAATATTATAAAGGCTCGCTAGTTTATGATCGCAG
*
39637886 GCTC
66 CCTC
* * * * * *
39637890 CAACACAGCTCGCGGACCTACATTCCCAGA-TGATATTATAAAAGCTTGCTAGTTTATGATTGCA
1 CAACACAGCTCGCGAACCTACGTTCCCA-ACTAATATTATAAAGGCTCGCTAGTTTATGATCGCA
39637954 GCCTC
65 GCCTC
* *
39637959 CAACACAGCTTGCGGACCTACGTTCCCAACTAATATTAT
1 CAACACAGCTCGCGAACCTACGTTCCCAACTAATATTAT
39637998 GTAACAGCCC
Statistics
Matches: 142, Mismatches: 29, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
67 13 0.09
68 59 0.42
69 70 0.49
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.25
Consensus pattern (69 bp):
CAACACAGCTCGCGAACCTACGTTCCCAACTAATATTATAAAGGCTCGCTAGTTTATGATCGCAG
CCTC
Found at i:39639395 original size:41 final size:41
Alignment explanation
Indices: 39639309--39639387 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
39639299 CCTGTAAATT
* * *
39639309 ATATCAGGCTTTATACCTAGTAGGCTTCGTGCTGGTGTACC
1 ATATCAGGCTATATACCTAGCAGGCTTCGTGCCGGTGTACC
*
39639350 ATATCAGGCTATATGCCTAGCAGGCTTCGTGCCGGTGT
1 ATATCAGGCTATATACCTAGCAGGCTTCGTGCCGGTGT
39639388 GTCATATCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.32
Consensus pattern (41 bp):
ATATCAGGCTATATACCTAGCAGGCTTCGTGCCGGTGTACC
Found at i:39639408 original size:41 final size:41
Alignment explanation
Indices: 39639309--39639417 Score: 119
Period size: 41 Copynumber: 2.7 Consensus size: 41
39639299 CCTGTAAATT
* * * *
39639309 ATATCAGGCTTTATACCTAGTAGGCTTCGTGCTGGTGTACC
1 ATATCAGGCTATATGCCTAGAAGGCTTCGTGCCGGTGTACC
* **
39639350 ATATCAGGCTATATGCCTAGCAGGCTTCGTGCCGGTGTGTC
1 ATATCAGGCTATATGCCTAGAAGGCTTCGTGCCGGTGTACC
* * * *
39639391 ATATCTGGTTTTGTGCCTAGAAGGCTT
1 ATATCAGGCTATATGCCTAGAAGGCTT
39639418 TATGTCGATG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.34
Consensus pattern (41 bp):
ATATCAGGCTATATGCCTAGAAGGCTTCGTGCCGGTGTACC
Found at i:39639703 original size:2 final size:2
Alignment explanation
Indices: 39639696--39639726 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39639686 AATTATATGT
39639696 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39639727 TTGCTTAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39640791 original size:27 final size:27
Alignment explanation
Indices: 39640741--39640793 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
39640731 TGCTAGTGTA
*
39640741 GAATTAATAATTAATATGTAAATATTT
1 GAATTAATAATTAATATGGAAATATTT
*
39640768 GAATTAATAATTAATATGGGAATATT
1 GAATTAATAATTAATATGGAAATATT
39640794 CGGCAATAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (27 bp):
GAATTAATAATTAATATGGAAATATTT
Found at i:39641355 original size:103 final size:103
Alignment explanation
Indices: 39641170--39641441 Score: 330
Period size: 103 Copynumber: 2.7 Consensus size: 103
39641160 TGATCGCAAC
* * *
39641170 CTCCGAAACAACTAGCGGACCTACGGTCCCAACTGATACTTAAAGGTTAGTTGAGTTAAGCTCGC
1 CTCCCAAACAGCTAGCGGACCTACGGTCCCAACTGATACTTAAAGGTTAGCTGAGTTAAGCTCGC
* * *
39641235 TATCTGAATTATTTGAGTTAGTAGAGTTAAGCTCACAA
66 AATCTGAATTATCTGAGTTAGAAGAGTTAAGCTCACAA
* * * *
39641273 CTCCCAAACAGCTAGCGGACCTACGTTCCGAGCTGATACTTAAAGGTTAGCTGAGTTAAGCTTGC
1 CTCCCAAACAGCTAGCGGACCTACGGTCCCAACTGATACTTAAAGGTTAGCTGAGTTAAGCTCGC
* *
39641338 AATTTGAATTATCTGAGTTGGAAGAGTTAAGCTCACAA
66 AATCTGAATTATCTGAGTTAGAAGAGTTAAGCTCACAA
* ** * * * * * * * *
39641376 CTCCCAAATAGCTAGCTAACCTATGTTCCCAACTAATGC-TCAAGGTTAGCTAATTTAAGATCGC
1 CTCCCAAACAGCTAGCGGACCTACGGTCCCAACTGATACTTAAAGGTTAGCTGAGTTAAGCTCGC
39641440 AA
66 AA
39641442 CCTAATTTCC
Statistics
Matches: 144, Mismatches: 25, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
102 22 0.15
103 122 0.85
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (103 bp):
CTCCCAAACAGCTAGCGGACCTACGGTCCCAACTGATACTTAAAGGTTAGCTGAGTTAAGCTCGC
AATCTGAATTATCTGAGTTAGAAGAGTTAAGCTCACAA
Found at i:39648474 original size:7 final size:8
Alignment explanation
Indices: 39648452--39648481 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
39648442 AAGCTATAGA
39648452 TTTTCTTTC
1 TTTT-TTTC
39648461 TTTTTTTC
1 TTTTTTTC
39648469 TTTTTTTC
1 TTTTTTTC
39648477 TTTTT
1 TTTTT
39648482 GCAATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTC
Found at i:39649832 original size:2 final size:2
Alignment explanation
Indices: 39649821--39649849 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
39649811 AACTGGAGCT
39649821 TA TA -A 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
39649850 ATGATTTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:39654267 original size:17 final size:17
Alignment explanation
Indices: 39654245--39654278 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39654235 AATACTAATA
39654245 ATTTTATCAAATTATAT
1 ATTTTATCAAATTATAT
*
39654262 ATTTTATTAAATTATAT
1 ATTTTATCAAATTATAT
39654279 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTATCAAATTATAT
Found at i:39654362 original size:17 final size:17
Alignment explanation
Indices: 39654245--39654378 Score: 84
Period size: 18 Copynumber: 8.0 Consensus size: 17
39654235 AATACTAATA
*
39654245 ATTTTATCAAATTATAT
1 ATTTTATTAAATTATAT
39654262 ATTTTATTAAA-T-TAT
1 ATTTTATTAAATTATAT
* *
39654277 A-TTTAAT-AATAAT-T
1 ATTTTATTAAATTATAT
** *
39654291 ATTTTAAATTATTTTTTAT
1 ATTTT--ATTAAATTATAT
* * *
39654310 AGTATTA-TATATTAT-G
1 A-TTTTATTAAATTATAT
*
39654326 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATT-ATAT
39654344 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
39654361 ATTTTTATTAAATTATAT
1 A-TTTTATTAAATTATAT
39654379 TTAATAATAA
Statistics
Matches: 89, Mismatches: 16, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
13 2 0.02
14 7 0.08
15 12 0.13
16 7 0.08
17 25 0.28
18 31 0.35
19 2 0.02
20 3 0.03
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:39654570 original size:39 final size:41
Alignment explanation
Indices: 39654525--39654630 Score: 126
Period size: 44 Copynumber: 2.5 Consensus size: 41
39654515 TTTCCTTATG
* * *
39654525 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAT
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
39654565 C-ATTACGCCTCTATTCCATTCCATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTC---T--ATTCCATTCAACCAAACAAAAGAATTAC
39654610 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
39654631 ACACCTTTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
39 9 0.16
40 1 0.02
41 8 0.14
42 1 0.02
43 1 0.02
44 23 0.41
45 3 0.05
46 10 0.18
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.30
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:39654605 original size:44 final size:46
Alignment explanation
Indices: 39654538--39654630 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
39654528 TTACACCTCT
* *
39654538 ATTCCATTCAACCAAACACAAGAA-TATC-ATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
39654582 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
39654628 ATT
1 ATT
39654631 ACACCTTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 23 0.51
45 3 0.07
46 19 0.42
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.29
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
Found at i:39654641 original size:16 final size:16
Alignment explanation
Indices: 39654612--39654649 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
39654602 AGAATTACCT
*
39654612 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
39654628 ATTACACCTTTATTCC
1 ATTACACCTCTATTCC
39654644 ATTACA
1 ATTACA
39654650 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.26, C:0.32, G:0.03, T:0.39
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:39654840 original size:16 final size:16
Alignment explanation
Indices: 39654816--39654885 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
39654806 TTTGGTTCAC
*
39654816 CGTATTGGAATAGAGG
1 CGTAATGGAATAGAGG
* *
39654832 CGTAATGGATTAAAGG
1 CGTAATGGAATAGAGG
*
39654848 CGTAATGGATTAGAGG
1 CGTAATGGAATAGAGG
*
39654864 TGTAATGGAATAGAGG
1 CGTAATGGAATAGAGG
39654880 CGTAAT
1 CGTAAT
39654886 AGCAAATCAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.34, C:0.06, G:0.34, T:0.26
Consensus pattern (16 bp):
CGTAATGGAATAGAGG
Found at i:39654925 original size:45 final size:44
Alignment explanation
Indices: 39654864--39654954 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 44
39654854 GGATTAGAGG
*
39654864 TGTAATGGAATAGAGGCGTAATAGCAAATCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGCATAATAG-AAATC-ATGTGTTTGGTTGAA
* *
39654909 TGTAATGGAATAGAGGCATAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCATAATAGAAATCATGTGTTTGGTTGAA
39654953 TG
1 TG
39654955 GAATAGAGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 18 0.43
45 23 0.55
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCATAATAGAAATCATGTGTTTGGTTGAA
Found at i:39655136 original size:16 final size:16
Alignment explanation
Indices: 39655099--39655166 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 16
39655089 TTAATCATAT
*
39655099 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
39655115 TT-AAATATATTATAA
1 TTAAAATATATTATAA
*
39655130 TTAAAATATATAATTTAA
1 TTAAAATATAT--TATAA
39655148 -TAAAAT-TATTAATAA
1 TTAAAATATATT-ATAA
39655163 TTAA
1 TTAA
39655167 CATTCTTATA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 4 0.09
15 13 0.30
16 16 0.37
17 6 0.14
18 4 0.09
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:39655140 original size:18 final size:18
Alignment explanation
Indices: 39655119--39655166 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
39655109 TTATTATTAA
39655119 ATATATTATAATTAAAAT
1 ATATATTATAATTAAAAT
39655137 ATATAATT-TAA-TAAAAT
1 ATAT-ATTATAATTAAAAT
*
39655154 -TAT-TAATAATTAA
1 ATATATTATAATTAA
39655167 CATTCTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 3 0.12
16 6 0.23
17 6 0.23
18 7 0.27
19 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATTATAATTAAAAT
Found at i:39655147 original size:14 final size:15
Alignment explanation
Indices: 39655108--39655149 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
39655098 TTTAAACATA
*
39655108 ATTATTATTAAATAT
1 ATTATAATTAAATAT
39655123 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
39655137 A-TATAATTTAATA
1 ATTATAATTAAATA
39655150 AAATTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:39655237 original size:120 final size:120
Alignment explanation
Indices: 39655097--39655448 Score: 582
Period size: 120 Copynumber: 2.9 Consensus size: 120
39655087 ATTTAATCAT
*
39655097 ATTTAAACATAATTATTATTAAATAT-ATTATAATTAAAATATATAATTTAATAAAATTATTAAT
1 ATTT-AACATAATTATTATTAAATATAATT-TAATTAAAATATATAATTTAATAAAATTCTTAAT
* * *
39655161 AATT-AACATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
64 -ATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAGATA
39655218 ATTTAACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
1 ATTTAACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
* *
39655283 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATAATATAAAATATA
66 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAGATA
* * *
39655338 ATTTAAAATGATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAT
1 ATTTAACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
39655403 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
66 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
39655449 AAATCATAAT
Statistics
Matches: 219, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
119 3 0.01
120 209 0.95
121 7 0.03
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAGATA
Found at i:39655260 original size:18 final size:17
Alignment explanation
Indices: 39655239--39655273 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
39655229 TTATTATTAA
39655239 ATATAATTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
39655257 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
39655274 TCTTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:39655467 original size:23 final size:21
Alignment explanation
Indices: 39655423--39655463 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
39655413 TATATGAATT
39655423 TACTAAAATCATAATATATAA
1 TACTAAAATCATAATATATAA
39655444 TACTAAAATCATAATATATA
1 TACTAAAATCATAATATATA
39655464 TAATTTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (21 bp):
TACTAAAATCATAATATATAA
Found at i:39661331 original size:22 final size:22
Alignment explanation
Indices: 39661306--39661350 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
39661296 TGAGATGAAA
39661306 CCATATAGGCAAATACCCCATT
1 CCATATAGGCAAATACCCCATT
39661328 CCATATAGGCAAATACCCCATT
1 CCATATAGGCAAATACCCCATT
39661350 C
1 C
39661351 TTGAATTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.33, G:0.09, T:0.22
Consensus pattern (22 bp):
CCATATAGGCAAATACCCCATT
Found at i:39664065 original size:21 final size:21
Alignment explanation
Indices: 39664040--39664079 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
39664030 AACAGGACTG
39664040 CTGATGTGG-CAAGTTAACTAA
1 CTGATGTGGTC-AGTTAACTAA
39664061 CTGATGTGGTCAGTTAACT
1 CTGATGTGGTCAGTTAACT
39664080 TATCACGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.33
Consensus pattern (21 bp):
CTGATGTGGTCAGTTAACTAA
Found at i:39667512 original size:21 final size:21
Alignment explanation
Indices: 39667455--39667528 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
39667445 ACTAAGTAGT
** *
39667455 TGCCCCAACTCAGCAACAGTC
1 TGCCCCAACTCAGCAGGAGGC
*
39667476 TACCCCAACTCAGCAGGAGGC
1 TGCCCCAACTCAGCAGGAGGC
*
39667497 TGCCCCAACTCAGCAGGAGGT
1 TGCCCCAACTCAGCAGGAGGC
*
39667518 TGTCCCAACTC
1 TGCCCCAACTC
39667529 CTTGCCAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.26, C:0.39, G:0.20, T:0.15
Consensus pattern (21 bp):
TGCCCCAACTCAGCAGGAGGC
Found at i:39668744 original size:3 final size:3
Alignment explanation
Indices: 39668738--39668820 Score: 157
Period size: 3 Copynumber: 27.7 Consensus size: 3
39668728 TAATGTTACC
39668738 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
39668786 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
39668821 ATTTCCATTT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:39668882 original size:12 final size:12
Alignment explanation
Indices: 39668865--39668890 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39668855 TATATGTGCC
39668865 ATGTTATATTAT
1 ATGTTATATTAT
39668877 ATGTTATATTAT
1 ATGTTATATTAT
39668889 AT
1 AT
39668891 TATTATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (12 bp):
ATGTTATATTAT
Found at i:39668944 original size:16 final size:17
Alignment explanation
Indices: 39668909--39668953 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
39668899 TATAAGTGCT
*
39668909 TATATATATATATTTCA
1 TATATATATATATTTAA
*
39668926 TATATA-ATTTATTTAA
1 TATATATATATATTTAA
39668942 TATATATATATA
1 TATATATATATA
39668954 AATACTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATTTAA
Found at i:39668944 original size:27 final size:25
Alignment explanation
Indices: 39668914--39668973 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
39668904 GTGCTTATAT
* *
39668914 ATATATATTTCATATATAATTTATTTA
1 ATATATATAT-ATAAATAATTT-TTTA
* *
39668941 ATATATATATATAAATACTTTTTTT
1 ATATATATATATAAATAATTTTTTA
39668966 ATATATAT
1 ATATATAT
39668974 GCATATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 11 0.38
26 9 0.31
27 9 0.31
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (25 bp):
ATATATATATATAAATAATTTTTTA
Found at i:39669164 original size:22 final size:22
Alignment explanation
Indices: 39669136--39669288 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
39669126 TTTATTGTTC
*
39669136 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
39669158 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
39669180 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
39669202 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
39669224 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
39669246 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
39669268 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
39669289 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:39672270 original size:23 final size:23
Alignment explanation
Indices: 39672244--39672287 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
39672234 TTCTTACTGC
*
39672244 AGTAATTTTCAGGGTATTACAGT
1 AGTAATTTTCAGGATATTACAGT
39672267 AGTAATTTTCAGGATATTACA
1 AGTAATTTTCAGGATATTACA
39672288 CGTAAATTTG
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:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (23 bp):
AGTAATTTTCAGGATATTACAGT
Found at i:39682074 original size:22 final size:21
Alignment explanation
Indices: 39682028--39682074 Score: 51
Period size: 22 Copynumber: 2.1 Consensus size: 21
39682018 ATAATATAGA
*
39682028 TTTAATAAATGCAGAAAAATCT
1 TTTAATAAATGAAGAAAAA-CT
39682050 TTTAATAAATGGAAAGAAAAA-T
1 TTTAATAAAT-G-AAGAAAAACT
39682072 TTT
1 TTT
39682075 GAACTGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 14 0.64
23 1 0.05
24 7 0.32
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.34
Consensus pattern (21 bp):
TTTAATAAATGAAGAAAAACT
Found at i:39692167 original size:16 final size:16
Alignment explanation
Indices: 39692143--39692173 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39692133 CTACTCATGA
*
39692143 AAAATAATAAATAAAC
1 AAAAGAATAAATAAAC
39692159 AAAAGAATAAATAAA
1 AAAAGAATAAATAAA
39692174 ATTTAAAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.16
Consensus pattern (16 bp):
AAAAGAATAAATAAAC
Found at i:39708286 original size:27 final size:27
Alignment explanation
Indices: 39708247--39708344 Score: 115
Period size: 27 Copynumber: 3.6 Consensus size: 27
39708237 AAAGGTTGTT
* * *
39708247 AAATGACCGAAATACCCTCGACGGGTA
1 AAATTACCAAAATACCCTCGAAGGGTA
*
39708274 AAATTACCAAAATACCCTCGAATGGTA
1 AAATTACCAAAATACCCTCGAAGGGTA
** * *
39708301 AAATTACTGAAATACTCTTGAAGGGTA
1 AAATTACCAAAATACCCTCGAAGGGTA
*
39708328 AAATTACTAAAATACCC
1 AAATTACCAAAATACCC
39708345 CTGTAAGGTA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.22
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGAAGGGTA
Found at i:39708354 original size:27 final size:27
Alignment explanation
Indices: 39708256--39708358 Score: 104
Period size: 27 Copynumber: 3.8 Consensus size: 27
39708246 TAAATGACCG
* *
39708256 AAATA-CCCTCGACGGGTAAAATTACCA
1 AAATACCCCT-GAAGGGTAAAATTACTA
* *
39708283 AAATA-CCCTCGAATGGTAAAATTACTG
1 AAATACCCCT-GAAGGGTAAAATTACTA
* *
39708310 AAATACTCTTGAAGGGTAAAATTACTA
1 AAATACCCCTGAAGGGTAAAATTACTA
39708337 AAATACCCCTGTAA-GGTAAAAT
1 AAATACCCCTG-AAGGGTAAAAT
39708359 GACCGTAATG
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
27 60 0.94
28 4 0.06
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (27 bp):
AAATACCCCTGAAGGGTAAAATTACTA
Found at i:39708380 original size:54 final size:53
Alignment explanation
Indices: 39708247--39708383 Score: 134
Period size: 54 Copynumber: 2.5 Consensus size: 53
39708237 AAAGGTTGTT
* *
39708247 AAATGACCGAAATACCCTCGACGGGTAAAATTACCAAAATACCCTCGAATGGTA
1 AAATGACCGAAATCCCCTGGA-GGGTAAAATTACCAAAATACCCTCGAATGGTA
* * * * * *
39708301 AAATTACTGAAATACTCTTGAAGGGTAAAATTACTAAAATACCC-CTGTAA-GGTA
1 AAATGACCGAAAT-CCCCTGGAGGGTAAAATTACCAAAATACCCTC-G-AATGGTA
*
39708355 AAATGACCGTAATGCCCCTGGAGGGTAAA
1 AAATGACCGAAAT-CCCCTGGAGGGTAAA
39708384 TGAATGATTT
Statistics
Matches: 65, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
53 1 0.02
54 59 0.91
55 5 0.08
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (53 bp):
AAATGACCGAAATCCCCTGGAGGGTAAAATTACCAAAATACCCTCGAATGGTA
Found at i:39710005 original size:29 final size:28
Alignment explanation
Indices: 39709915--39710043 Score: 134
Period size: 28 Copynumber: 4.6 Consensus size: 28
39709905 TTCAAAAATG
*
39709915 TAAAATTTGAAAAAT-AGTGGCAAAACTG
1 TAAAATTTGAAAAATAAG-GGCAAAACTA
* * * * *
39709943 TAAAATATGAAAAACAAGGGAAAAATTG
1 TAAAATTTGAAAAATAAGGGCAAAACTA
* *
39709971 TAAAATTTGAAAAATAAGGGCCAAATTA
1 TAAAATTTGAAAAATAAGGGCAAAACTA
*
39709999 TAAAAATTTGAAAAATAAAGGCAAAACTA
1 T-AAAATTTGAAAAATAAGGGCAAAACTA
* *
39710028 TAAAATATAAAAAATA
1 TAAAATTTGAAAAATA
39710044 GGGGACACAC
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
28 58 0.68
29 27 0.32
ACGTcount: A:0.59, C:0.05, G:0.13, T:0.22
Consensus pattern (28 bp):
TAAAATTTGAAAAATAAGGGCAAAACTA
Found at i:39720036 original size:69 final size:69
Alignment explanation
Indices: 39719934--39720091 Score: 237
Period size: 69 Copynumber: 2.3 Consensus size: 69
39719924 TATACACTGC
* *
39719934 CATGGTCCAACCATGGTCTTACATCTGAAAAACTACCATAGCCTCACTATGGTCTTACATAAACA
1 CATGTTCCAACCATGGTCTTACATCTGAAAAACTACCATAGCCTCACTACGGTCTTACATAAACA
39719999 TTGT
66 TTGT
* * * * *
39720003 CATGTTCCAACCATGGTTTTACGTCTGAAAAACTACCATAGTCTCGCTACGGTCTTACGTAAACA
1 CATGTTCCAACCATGGTCTTACATCTGAAAAACTACCATAGCCTCACTACGGTCTTACATAAACA
39720068 TTGT
66 TTGT
39720072 CAT-TGTCCAACCATGGTCTT
1 CATGT-TCCAACCATGGTCTT
39720092 GTATATCTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
68 1 0.01
69 79 0.99
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (69 bp):
CATGTTCCAACCATGGTCTTACATCTGAAAAACTACCATAGCCTCACTACGGTCTTACATAAACA
TTGT
Found at i:39722360 original size:16 final size:18
Alignment explanation
Indices: 39722334--39722367 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
39722324 TAGAACCGGG
39722334 TTGATAAATTT-ATTTAA
1 TTGATAAATTTGATTTAA
39722351 TTGA-AAATTTGATTTAA
1 TTGATAAATTTGATTTAA
39722368 ATTAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (18 bp):
TTGATAAATTTGATTTAA
Found at i:39728240 original size:39 final size:39
Alignment explanation
Indices: 39728141--39728242 Score: 141
Period size: 39 Copynumber: 2.6 Consensus size: 39
39728131 CATATTCACT
* * * *
39728141 TTTAATCATATATCACATTACACATATAATCTCATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
39728180 TTTAAGTATATACCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
39728219 TTTAGGCATATATCACAATACTCA
1 TTTAAGCATATATCACAATACTCA
39728243 AAAACATGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.43, C:0.21, G:0.03, T:0.33
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:39730042 original size:14 final size:13
Alignment explanation
Indices: 39730025--39730072 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 13
39730015 ATTCTAGTAG
39730025 GTTAATTTAAGTTA
1 GTTAATTTAA-TTA
39730039 GTTAATTTAATTA
1 GTTAATTTAATTA
39730052 GTTTAA-TTAATATA
1 G-TTAATTTAAT-TA
39730066 -TTAATTT
1 GTTAATTT
39730073 GGATCAATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 4 0.13
13 11 0.35
14 16 0.52
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
GTTAATTTAATTA
Found at i:39732224 original size:17 final size:17
Alignment explanation
Indices: 39732199--39732231 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
39732189 CAAAGTTTAC
39732199 AATTCAAAACATTCAAA
1 AATTCAAAACATTCAAA
*
39732216 AATTTAAAACATTCAA
1 AATTCAAAACATTCAA
39732232 TTTACAACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (17 bp):
AATTCAAAACATTCAAA
Found at i:39734217 original size:30 final size:29
Alignment explanation
Indices: 39734187--39734283 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 29
39734177 AACCGTCCTT
* *
39734187 TTTTA-TATTCGATGGTCGAGACCATCCC
1 TTTTATTAATCGATGGTCGACACCATCCC
*
39734215 TTTTCATTAATCGATGGTCGTCACCATCCC
1 TTTT-ATTAATCGATGGTCGACACCATCCC
* * * *
39734245 TTTTCA-TAGTTGATGGTGGTCACCATCCC
1 TTTT-ATTAATCGATGGTCGACACCATCCC
39734274 TTTTCATTAA
1 TTTT-ATTAA
39734284 CCAGTACCGA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
28 4 0.07
29 27 0.46
30 28 0.47
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (29 bp):
TTTTATTAATCGATGGTCGACACCATCCC
Found at i:39734218 original size:29 final size:29
Alignment explanation
Indices: 39734186--39734373 Score: 147
Period size: 29 Copynumber: 6.5 Consensus size: 29
39734176 TAACCGTCCT
* **
39734186 TTTTTATATTCGATGGTCGAGACCATCCC
1 TTTTCATATTCGATGGTCGTCACCATCCC
*
39734215 TTTTCATTAATCGATGGTCGTCACCATCCC
1 TTTTCA-TATTCGATGGTCGTCACCATCCC
*
39734245 TTTTCATAGTT-GATGGTGGTCACCATCCC
1 TTTTCATA-TTCGATGGTCGTCACCATCCC
* * *
39734274 TTTTCAT-TAACCA--GTACCG-AAGCCATCCC
1 TTTTCATAT-TCGATGGT--CGTCA-CCATCCC
* * * *
39734303 -TTTCAAATTTGATAGTTGTCACCATCCC
1 TTTTCATATTCGATGGTCGTCACCATCCC
39734331 TTTTCATAATT-GATGGTCGTCACCATCCC
1 TTTTCAT-ATTCGATGGTCGTCACCATCCC
*
39734360 TTTTCATAATCGAT
1 TTTTCATATTCGAT
39734374 AGCCGAAGCT
Statistics
Matches: 125, Mismatches: 20, Indels: 28
0.72 0.12 0.16
Matches are distributed among these distances:
27 3 0.02
28 17 0.14
29 73 0.58
30 32 0.26
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (29 bp):
TTTTCATATTCGATGGTCGTCACCATCCC
Found at i:39734357 original size:57 final size:58
Alignment explanation
Indices: 39734207--39734362 Score: 178
Period size: 57 Copynumber: 2.7 Consensus size: 58
39734197 GATGGTCGAG
* *
39734207 ACCATCCCTTTTCATTAATCGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTGGTC
1 ACCATCCCTTTTCATTAATCGATGGTCGTCACCATCCC-TTTCAAAGTTGATAGTGGTC
* * * *
39734266 ACCATCCCTTTTCATTAA-CCA--GTACCG-AAGCCATCCCTTTCAAATTTGATAGTTGTC
1 ACCATCCCTTTTCATTAATCGATGGT--CGTCA-CCATCCCTTTCAAAGTTGATAGTGGTC
*
39734323 ACCATCCCTTTTCA-TAATTGATGGTCGTCACCATCCCTTT
1 ACCATCCCTTTTCATTAATCGATGGTCGTCACCATCCCTTT
39734363 TCATAATCGA
Statistics
Matches: 81, Mismatches: 9, Indels: 16
0.76 0.08 0.15
Matches are distributed among these distances:
56 5 0.06
57 44 0.54
58 12 0.15
59 20 0.25
ACGTcount: A:0.22, C:0.29, G:0.13, T:0.36
Consensus pattern (58 bp):
ACCATCCCTTTTCATTAATCGATGGTCGTCACCATCCCTTTCAAAGTTGATAGTGGTC
Found at i:39735602 original size:27 final size:26
Alignment explanation
Indices: 39735582--39735903 Score: 237
Period size: 27 Copynumber: 12.3 Consensus size: 26
39735572 GGGTATAATA
39735582 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
*
39735609 GTCATTTTACTCTAT--GGG-----G
1 GTCATTTTACCCTATGGGGGTATTTG
*
39735628 GTCATTTTACCCTATGGGGATATTTTG
1 GTCATTTTACCCTATGGGGGTA-TTTG
* * **
39735655 GTCATTTTACCCTCTGGAGGTAGTTCA
1 GTCATTTTACCCTATGGGGGTA-TTTG
* *
39735682 GCCATTTTACCCTATGGGAGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
** *
39735709 AACATTTTAGCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* *
39735736 ATCATTTTACCCTATTGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* * * *
39735763 ATCATTTTACCCTTTAGGGATATTTTG
1 GTCATTTTACCCTATGGGGGTA-TTTG
*
39735790 GTCAATTTACCCTAT-GGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* * *
39735816 GTCATTTTACCCTATAGAGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTT-G
**
39735843 GTCATTTTACCCTATAAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTA-TTTG
* ** * *
39735870 GTCATTTCAATCTTTGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
39735897 GTCATTT
1 GTCATTT
39735904 ATTGACCTCT
Statistics
Matches: 241, Mismatches: 40, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
19 15 0.06
21 2 0.01
25 6 0.02
26 25 0.10
27 187 0.78
28 6 0.02
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (26 bp):
GTCATTTTACCCTATGGGGGTATTTG
Found at i:39735632 original size:19 final size:19
Alignment explanation
Indices: 39735608--39735646 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
39735598 GGGGTATTTC
*
39735608 GGTCATTTTACTCTATGGG
1 GGTCATTTTACCCTATGGG
39735627 GGTCATTTTACCCTATGGG
1 GGTCATTTTACCCTATGGG
39735646 G
1 G
39735647 ATATTTTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.18, G:0.28, T:0.38
Consensus pattern (19 bp):
GGTCATTTTACCCTATGGG
Found at i:39735652 original size:18 final size:19
Alignment explanation
Indices: 39735610--39735653 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
39735600 GGTATTTCGG
* *
39735610 TCATTTTACTCTATGGGGG
1 TCATTTTACCCTATGGGGA
39735629 TCATTTTACCCTATGGGGA
1 TCATTTTACCCTATGGGGA
39735648 T-ATTTT
1 TCATTTT
39735654 GGTCATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.18, C:0.16, G:0.20, T:0.45
Consensus pattern (19 bp):
TCATTTTACCCTATGGGGA
Found at i:39735769 original size:81 final size:81
Alignment explanation
Indices: 39735630--39735903 Score: 279
Period size: 81 Copynumber: 3.4 Consensus size: 81
39735620 CTATGGGGGT
* * * * *
39735630 CATTTTACCCTATGGGGATATTTTGGTCATTTTACCCT-CTGGAGGTAGTTCAGCCATTTTACCC
1 CATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATTGG-GGTATTTCAGTCATTTTACCC
39735694 TAT-GGGAGTATTTCGAA
65 TATAGGGA-TATTTCGAA
* *
39735711 CATTTTAGCCTATGGGGGTATTTCGATCATTTTACCCTATTGGGGTATTTC-GATCATTTTACCC
1 CATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATTGGGGTATTTCAG-TCATTTTACCC
* * **
39735775 TTTAGGGATATTTTGGT
65 TATAGGGATATTTCGAA
* * *
39735792 CAATTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATAGAGGTATTTCAGTCATTTTACCCT
1 CATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATTGGGGTATTTCAGTCATTTTACCCT
* **
39735856 ATAAGGG-TATTTTGGT
66 AT-AGGGATATTTCGAA
* ** * *
39735872 CATTTCAATCTTTGAGGGTATTTCGGTCATTT
1 CATTTTACCCTATGGGGGTATTTCGGTCATTT
39735904 ATTGACCTCT
Statistics
Matches: 164, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
80 65 0.40
81 92 0.56
82 7 0.04
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (81 bp):
CATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATTGGGGTATTTCAGTCATTTTACCCT
ATAGGGATATTTCGAA
Found at i:39735892 original size:54 final size:53
Alignment explanation
Indices: 39735628--39735903 Score: 272
Period size: 54 Copynumber: 5.1 Consensus size: 53
39735618 CTCTATGGGG
* * *
39735628 GTCATTTTACCCTATGGGGATATTTTGGTCATTTTACCCTCTG-GAGGTAGTTCA
1 GTCATTTTACCCTATGGGG-TATTTCGGTCATTTTACCCTATGAG-GGTATTTCA
* ** * *
39735682 GCCATTTTACCCTATGGGAGTATTTCGAACATTTTAGCCTATGGGGGTATTTC-
1 GTCATTTTACCCTATGGG-GTATTTCGGTCATTTTACCCTATGAGGGTATTTCA
* * **
39735735 GATCATTTTACCCTATTGGGGTATTTCGATCATTTTACCCT-TTAGGGATATTTTG
1 G-TCATTTTACCCTA-TGGGGTATTTCGGTCATTTTACCCTATGAGGG-TATTTCA
*
39735790 GTCAATTTACCCTATGGGGTATTTCGGTCATTTTACCCTAT-AGAGGTATTTCA
1 GTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATGAG-GGTATTTCA
* * * ** * *
39735843 GTCATTTTACCCTATAAGGGTATTTTGGTCATTTCAATCTTTGAGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCA
39735897 GTCATTT
1 GTCATTT
39735904 ATTGACCTCT
Statistics
Matches: 187, Mismatches: 25, Indels: 20
0.81 0.11 0.09
Matches are distributed among these distances:
53 50 0.27
54 128 0.68
55 9 0.05
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.42
Consensus pattern (53 bp):
GTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCA
Found at i:39735894 original size:107 final size:107
Alignment explanation
Indices: 39735687--39735904 Score: 271
Period size: 107 Copynumber: 2.0 Consensus size: 107
39735677 GTTCAGCCAT
* * * *
39735687 TTTACCCTATGGGAGTATTTCGAACATTTTAGCCTATGGGGGTATTTCGATCATTTTACCCTATT
1 TTTACCCTATGGGAGTATTTCGAACATTTTACCCTATAGAGGTATTTCGATCATTTTACCCTATA
* * * *
39735752 GGGGTATTTCGATCATTTTACCCTTTAGGGATATTTTGGTCAA
66 AGGGTATTTCGATCATTTCAACCTTTAGGGATATTTCGGTC-A
**
39735795 TTTACCCTATGGG-GTATTTCGGTCATTTTACCCTATAGAGGTATTTC-AGTCATTTTACCCTAT
1 TTTACCCTATGGGAGTATTTCGAACATTTTACCCTATAGAGGTATTTCGA-TCATTTTACCCTAT
* * *
39735858 AAGGGTATTTTGGTCATTTCAATCTTTGAGGG-TATTTCGGTCA
65 AAGGGTATTTCGATCATTTCAACCTTT-AGGGATATTTCGGTCA
39735901 TTTA
1 TTTA
39735905 TTGACCTCTT
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
106 6 0.06
107 72 0.76
108 17 0.18
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.43
Consensus pattern (107 bp):
TTTACCCTATGGGAGTATTTCGAACATTTTACCCTATAGAGGTATTTCGATCATTTTACCCTATA
AGGGTATTTCGATCATTTCAACCTTTAGGGATATTTCGGTCA
Found at i:39737341 original size:16 final size:17
Alignment explanation
Indices: 39737310--39737342 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
39737300 TCAATGTCTC
*
39737310 CCTATAGTTTTCAGTTT
1 CCTATAGTTCTCAGTTT
39737327 CCTATAG-TCTCAGTTT
1 CCTATAGTTCTCAGTTT
39737343 ACTCTAACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.48
Consensus pattern (17 bp):
CCTATAGTTCTCAGTTT
Found at i:39745757 original size:50 final size:50
Alignment explanation
Indices: 39745633--39745867 Score: 210
Period size: 49 Copynumber: 4.7 Consensus size: 50
39745623 GATAATAACA
* * * * *
39745633 TGCCAAAGCCATATCACAGACATGGTCTTACATGGGACGTT-TCTTGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATCT-CGG
* * * * *
39745682 TGCCAATGCCATATCCCATATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATCTCGG
* * * ** *
39745732 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGACCTCTAATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATCTCGG
* * * *
39745781 TGCCAACGCCATGTCACAGACATGATTTTAGATGGGA-TGTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAGT-TCTCATCTCGG
* *
39745831 TGCCAACGCCATGTCCAAGACATGATCTTACATGGGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
39745868 CCTCATCCTC
Statistics
Matches: 153, Mismatches: 28, Indels: 9
0.81 0.15 0.05
Matches are distributed among these distances:
48 4 0.03
49 75 0.49
50 74 0.48
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATCTCGG
Found at i:39751580 original size:17 final size:17
Alignment explanation
Indices: 39751550--39751599 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
39751540 TTCCTTATTG
* *
39751550 GTTTAATTGGTTTAGTT
1 GTTTATTTGTTTTAGTT
39751567 GTTTATTTGTTTTA-TT
1 GTTTATTTGTTTTAGTT
*
39751583 -TCTTATTTATTTTAGTT
1 GT-TTATTTGTTTTAGTT
39751600 ATTTGTTTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 1 0.04
16 13 0.46
17 14 0.50
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.68
Consensus pattern (17 bp):
GTTTATTTGTTTTAGTT
Found at i:39761037 original size:74 final size:74
Alignment explanation
Indices: 39760959--39761099 Score: 255
Period size: 74 Copynumber: 1.9 Consensus size: 74
39760949 CTCGATTTAC
* *
39760959 AATATTTTTAAAATTTAAATTTCCAAATGGTAATTTAATAATATTTAACTTATAAAATTTGAATA
1 AATATTTTTAAAATTTAAATTCCCAAATGGTAATTTAATAATATTTAACATATAAAATTTGAATA
39761024 TTCTTCTAT
66 TTCTTCTAT
*
39761033 AATATTTTTAAAATTTAAATTCCCAAATGGTAATTTAATGATATTTAACATATAAAATTTGAATA
1 AATATTTTTAAAATTTAAATTCCCAAATGGTAATTTAATAATATTTAACATATAAAATTTGAATA
39761098 TT
66 TT
39761100 TTCATTTGTT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 64 1.00
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.45
Consensus pattern (74 bp):
AATATTTTTAAAATTTAAATTCCCAAATGGTAATTTAATAATATTTAACATATAAAATTTGAATA
TTCTTCTAT
Found at i:39774995 original size:22 final size:22
Alignment explanation
Indices: 39774946--39774999 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
39774936 AAATCGGATC
* *
39774946 CAACTCCACCTCCACCGATTCA
1 CAACTCCACGTCCACCGATCCA
39774968 CAACTCCACGTCCA-CGACTCCA
1 CAACTCCACGTCCACCGA-TCCA
*
39774990 CGACTCCACG
1 CAACTCCACG
39775000 GTGCTTCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.26, C:0.50, G:0.09, T:0.15
Consensus pattern (22 bp):
CAACTCCACGTCCACCGATCCA
Found at i:39775411 original size:3 final size:3
Alignment explanation
Indices: 39775403--39775461 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
39775393 AATTTTGATT
39775403 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39775451 TTA TTA TTA TT
1 TTA TTA TTA TT
39775462 TGGCTTTGGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39776771 original size:7 final size:8
Alignment explanation
Indices: 39776745--39776769 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
39776735 TAAAATATTT
39776745 AAGTTAAA
1 AAGTTAAA
39776753 AAGTTAAA
1 AAGTTAAA
39776761 AAGTTAAA
1 AAGTTAAA
39776769 A
1 A
39776770 GTAATTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (8 bp):
AAGTTAAA
Found at i:39776946 original size:16 final size:16
Alignment explanation
Indices: 39776925--39776958 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
39776915 ATATAAATTC
39776925 AATAACAATTAATTTT
1 AATAACAATTAATTTT
*
39776941 AATAACAATTAGTTTT
1 AATAACAATTAATTTT
39776957 AA
1 AA
39776959 CTTTTAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (16 bp):
AATAACAATTAATTTT
Found at i:39777372 original size:3 final size:3
Alignment explanation
Indices: 39777364--39777422 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
39777354 ATTTCATTCA
39777364 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39777412 ATT ATT ATT AT
1 ATT ATT ATT AT
39777423 GGGTTAATAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:39780756 original size:21 final size:22
Alignment explanation
Indices: 39780727--39780773 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
39780717 CAGAAGGAGT
*
39780727 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
*
39780749 GAGT-GTACTCCGTAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
39780770 GAGT
1 GAGT
39780774 TTGAGCAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.23
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:39791119 original size:42 final size:43
Alignment explanation
Indices: 39791055--39791141 Score: 113
Period size: 42 Copynumber: 2.0 Consensus size: 43
39791045 TTAACATAAG
* * * *
39791055 TCAAGCTTAAGCCACAGGAAAGCTGA-GTCTATCAATTTTTTC
1 TCAAACTTAAGCCACAGAAAAGCTGACCTCTATCAATTTTGTC
* *
39791097 TCAAACTTAAGCCATAGAAAAGCTGACCTTTATCAATTTTGTC
1 TCAAACTTAAGCCACAGAAAAGCTGACCTCTATCAATTTTGTC
39791140 TC
1 TC
39791142 GCTGCTTGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
42 23 0.61
43 15 0.39
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (43 bp):
TCAAACTTAAGCCACAGAAAAGCTGACCTCTATCAATTTTGTC
Found at i:39792327 original size:23 final size:23
Alignment explanation
Indices: 39792297--39792342 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
39792287 TATGGTTTAA
* *
39792297 GGTTTAGGGGTTAGGAGTTAGGG
1 GGTTTAGGGGTTAAGAGCTAGGG
39792320 GGTTTAGGGGTTAAGAGCTAGGG
1 GGTTTAGGGGTTAAGAGCTAGGG
39792343 ATTTAAGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.02, G:0.50, T:0.28
Consensus pattern (23 bp):
GGTTTAGGGGTTAAGAGCTAGGG
Found at i:39792714 original size:19 final size:18
Alignment explanation
Indices: 39792690--39792728 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
39792680 AATTATAAGA
39792690 AAAAATAAAATACAAAAAT
1 AAAAATAAAATA-AAAAAT
**
39792709 AAAAATGGAATAAAAAAT
1 AAAAATAAAATAAAAAAT
39792727 AA
1 AA
39792729 TTCTTTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAAATAAAATAAAAAAT
Found at i:39803183 original size:66 final size:65
Alignment explanation
Indices: 39803076--39803246 Score: 209
Period size: 66 Copynumber: 2.6 Consensus size: 65
39803066 GAGCAAATTA
* * * *
39803076 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
39803140 G
65 G
* *
39803141 CTACAACTGAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCTA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
39803206 G
65 G
* * ** *
39803207 CAGCAGCTTAAAGCAGATGCGGCAGTAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
39803247 CGGCAGCTAG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.02
66 84 0.92
67 5 0.05
ACGTcount: A:0.41, C:0.18, G:0.27, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:39803241 original size:21 final size:21
Alignment explanation
Indices: 39803217--39803316 Score: 67
Period size: 21 Copynumber: 4.8 Consensus size: 21
39803207 CAGCAGCTTA
*
39803217 AAGCAGATGCGGCAG-TAAGAG
1 AAGCAGAGGCGGCAGCT-AGAG
39803238 AAGCAGAGGCGGCAGCTAGAG
1 AAGCAGAGGCGGCAGCTAGAG
* * * * * *
39803259 AAGTACAGGCTGCAACGAGGG
1 AAGCAGAGGCGGCAGCTAGAG
*** * *
39803280 AAGCAGAGGCTAAAGCGAGGG
1 AAGCAGAGGCGGCAGCTAGAG
*
39803301 AAGCAGAGGCTGCAGC
1 AAGCAGAGGCGGCAGC
39803317 GAGGGAAGAA
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
21 63 0.98
22 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.40, T:0.07
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCTAGAG
Found at i:39803317 original size:21 final size:21
Alignment explanation
Indices: 39803237--39803329 Score: 105
Period size: 21 Copynumber: 4.4 Consensus size: 21
39803227 GGCAGTAAGA
* * *
39803237 GAAGCAGAGGCGGCAGCTAGA
1 GAAGCAGAGGCTGCAGCGAGG
* * *
39803258 GAAGTACAGGCTGCAACGAGG
1 GAAGCAGAGGCTGCAGCGAGG
**
39803279 GAAGCAGAGGCTAAAGCGAGG
1 GAAGCAGAGGCTGCAGCGAGG
39803300 GAAGCAGAGGCTGCAGCGAGG
1 GAAGCAGAGGCTGCAGCGAGG
*
39803321 GAAGAAGAG
1 GAAGCAGAG
39803330 CAGCGTCAAA
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.35, C:0.16, G:0.43, T:0.05
Consensus pattern (21 bp):
GAAGCAGAGGCTGCAGCGAGG
Found at i:39803786 original size:87 final size:86
Alignment explanation
Indices: 39803681--39803859 Score: 322
Period size: 87 Copynumber: 2.1 Consensus size: 86
39803671 GGCCTTTAGT
* *
39803681 GCGTTTTTGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCGAAGCGCCG
1 GCGTTTTAGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCG-TTTGTGGTCAAAGCGCCG
*
39803746 CTATAGATCAGGGTCTATTGCG
65 CTATAGATCAGGGTCTATTCCG
39803768 GCGTTTTAGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGC
1 GCGTTTTAGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGC
39803833 TATAGATCAGGGTCTATTCCG
66 TATAGATCAGGGTCTATTCCG
39803854 GCGTTT
1 GCGTTT
39803860 GAGAAAAAAA
Statistics
Matches: 89, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
86 44 0.49
87 45 0.51
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.31
Consensus pattern (86 bp):
GCGTTTTAGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGC
TATAGATCAGGGTCTATTCCG
Found at i:39803814 original size:43 final size:42
Alignment explanation
Indices: 39803674--39803839 Score: 185
Period size: 43 Copynumber: 3.9 Consensus size: 42
39803664 AGGTGTTGGC
39803674 CTTTAGT-GCGTTTTTGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CTTTAGTGGCG-TTTTGGGGAAAGCGCCGCTAAAGATTAGGTT
* * *
39803716 CTTTAGTGGCGTTTTGTGGTCG-AAGCGCCGCTATAGATCAGGGT
1 CTTTAGTGGCGTTTTG-GG--GAAAGCGCCGCTAAAGATTAGGTT
*
39803760 CTATT-GCGGCGTTTTAGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CT-TTAGTGGCGTTTT-GGGGAAAGCGCCGCTAAAGATTAGGTT
** *
39803803 CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGAT
1 CTTTAGTGGCGTTT-TGGGGAAAGCGCCGCTAAAGAT
39803840 CAGGGTCTAT
Statistics
Matches: 104, Mismatches: 11, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
42 15 0.14
43 52 0.50
44 33 0.32
45 4 0.04
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.31
Consensus pattern (42 bp):
CTTTAGTGGCGTTTTGGGGAAAGCGCCGCTAAAGATTAGGTT
Found at i:39803857 original size:43 final size:43
Alignment explanation
Indices: 39803693--39803860 Score: 171
Period size: 43 Copynumber: 3.9 Consensus size: 43
39803683 GTTTTTGGGG
* * * *
39803693 AAAGCGCCGCTAAAGATTAGGTTCT-TTAGTGGCGTTTTGTGGTC
1 AAAGCGCCGCTATAGATCAGGGTCTATT-GCGGCG-TTTGTGGTC
* **
39803737 GAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTT-TAGGGG
1 AAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGT-GGTC
* * * *
39803780 AAAGCGCCGCTAAAGATTAGGTTCT-TTAGTGGCGTTTGTGGTC
1 AAAGCGCCGCTATAGATCAGGGTCTATT-GCGGCGTTTGTGGTC
*
39803823 AAAGCGCCGCTATAGATCAGGGTCTATTCCGGCGTTTG
1 AAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTG
39803861 AGAAAAAAAC
Statistics
Matches: 100, Mismatches: 19, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
42 3 0.03
43 66 0.66
44 29 0.29
45 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.30
Consensus pattern (43 bp):
AAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGTGGTC
Found at i:39803879 original size:86 final size:87
Alignment explanation
Indices: 39803697--39803881 Score: 291
Period size: 86 Copynumber: 2.1 Consensus size: 87
39803687 TTGGGGAAAG
*
39803697 CGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCGAAGCGCCGCTATAGATCAGGGTCT
1 CGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCT
* * *** *
39803762 ATTGCGGCGTTTTAGGGGAAAG
66 ATTCCGGCGTTTGAGAAAAAAA
39803784 CGCCGCTAAAGATTAGGTTCTTTAGTGGCG-TTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCT
1 CGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCT
39803848 ATTCCGGCGTTTGAGAAAAAAA
66 ATTCCGGCGTTTGAGAAAAAAA
*
39803870 CGCCACTAAAGA
1 CGCCGCTAAAGA
39803882 CCCTGATCTA
Statistics
Matches: 90, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
86 60 0.67
87 30 0.33
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.28
Consensus pattern (87 bp):
CGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCT
ATTCCGGCGTTTGAGAAAAAAA
Found at i:39805335 original size:34 final size:35
Alignment explanation
Indices: 39805287--39805359 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
39805277 TCGTGTGACC
** *
39805287 CAAATTCTAAGAGATTGTTTGTAAGTCAAGTTAAA
1 CAAATTCTAAGAGATTACTTGCAAGTCAAGTTAAA
* *
39805322 CAAA-TCTAAGAGATTACTTGCAAGTTAAGTTAGA
1 CAAATTCTAAGAGATTACTTGCAAGTCAAGTTAAA
39805356 CAAA
1 CAAA
39805360 ATATAATTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 29 0.88
35 4 0.12
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (35 bp):
CAAATTCTAAGAGATTACTTGCAAGTCAAGTTAAA
Found at i:39805683 original size:42 final size:43
Alignment explanation
Indices: 39805619--39805705 Score: 113
Period size: 42 Copynumber: 2.0 Consensus size: 43
39805609 TTAACATAAG
* * * *
39805619 TCAAGCTTAAGCCACAGGAAAGCTGA-GTCTATCAATTTTTTC
1 TCAAACTTAAGCCACAGAAAAGCTGACCTCTATCAATTTTGTC
* *
39805661 TCAAACTTAAGCCATAGAAAAGCTGACCTTTATCAATTTTGTC
1 TCAAACTTAAGCCACAGAAAAGCTGACCTCTATCAATTTTGTC
39805704 TC
1 TC
39805706 GCTGCTTGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
42 23 0.61
43 15 0.39
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (43 bp):
TCAAACTTAAGCCACAGAAAAGCTGACCTCTATCAATTTTGTC
Found at i:39807410 original size:12 final size:12
Alignment explanation
Indices: 39807393--39807417 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39807383 TTAAATCTAC
39807393 AATAACAAAAAA
1 AATAACAAAAAA
39807405 AATAACAAAAAA
1 AATAACAAAAAA
39807417 A
1 A
39807418 TACAAAACGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AATAACAAAAAA
Done.