Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 91 of 91
Found at i:35889176 original size:2 final size:2
Alignment explanation
Indices: 35889169--35889200 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35889159 TTGGCACAAG
35889169 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35889201 TTTATGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35893437 original size:16 final size:17
Alignment explanation
Indices: 35893416--35893449 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
35893406 ATTTTTTTAT
35893416 TTTTTAAA-AAATAAAA
1 TTTTTAAATAAATAAAA
*
35893432 TTTTTAAATTAATAAAA
1 TTTTTAAATAAATAAAA
35893449 T
1 T
35893450 AAAATATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTTTAAATAAATAAAA
Found at i:35896288 original size:6 final size:6
Alignment explanation
Indices: 35896277--35896302 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
35896267 GTTAATTCGA
35896277 TTAATT TTAATT TTAATT TTAATT TT
1 TTAATT TTAATT TTAATT TTAATT TT
35896303 TTAATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTAATT
Found at i:35898016 original size:19 final size:18
Alignment explanation
Indices: 35897980--35898014 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35897970 ATTTATTAAT
*
35897980 TTTTAAATAAATATTTTA
1 TTTTAAAAAAATATTTTA
35897998 TTTTAAAAAAATATTTT
1 TTTTAAAAAAATATTTT
35898015 TAGTAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTAAAAAAATATTTTA
Found at i:35899253 original size:3 final size:3
Alignment explanation
Indices: 35899247--35899271 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35899237 TAAGATAAAT
35899247 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
35899272 GGGTTACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:35900403 original size:23 final size:23
Alignment explanation
Indices: 35900367--35900467 Score: 79
Period size: 20 Copynumber: 4.5 Consensus size: 23
35900357 TTATTTGATT
*
35900367 TTTAAAATGTTAATAA-TT-TAA
1 TTTAAAATATTAATAATTTATAA
35900388 -TTAAAATATTAATAATTTATAA
1 TTTAAAATATTAATAATTTATAA
* *
35900410 TTTATAATATTAATATTTTAATATAA
1 TTTAAAATATTAATA-ATT--TATAA
* **
35900436 TTT-AATTATTAATTTTTTATAA
1 TTTAAAATATTAATAATTTATAA
35900458 -TT-AAATATTA
1 TTTAAAATATTA
35900468 TTATGATTAA
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
20 14 0.21
21 11 0.16
22 8 0.12
23 13 0.19
24 5 0.07
25 8 0.12
26 8 0.12
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
TTTAAAATATTAATAATTTATAA
Found at i:35900453 original size:25 final size:26
Alignment explanation
Indices: 35900405--35900467 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 26
35900395 ATTAATAATT
35900405 TATAATTTATAATATTAATATTTTAA
1 TATAATTTATAATATTAATATTTTAA
*
35900431 TATAATTTA-ATTATTAAT-TTTT--
1 TATAATTTATAATATTAATATTTTAA
35900453 TATAA-TTA-AATATTA
1 TATAATTTATAATATTA
35900468 TTATGATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 9 0.26
22 5 0.14
24 4 0.11
25 8 0.23
26 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TATAATTTATAATATTAATATTTTAA
Found at i:35900476 original size:16 final size:17
Alignment explanation
Indices: 35900452--35900484 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35900442 TATTAATTTT
35900452 TTATAATT-AAATATTA
1 TTATAATTAAAATATTA
*
35900468 TTATGATTAAAATATTA
1 TTATAATTAAAATATTA
35900485 ATAATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTATAATTAAAATATTA
Found at i:35901105 original size:63 final size:63
Alignment explanation
Indices: 35901038--35901161 Score: 212
Period size: 63 Copynumber: 2.0 Consensus size: 63
35901028 GATAATTAAC
* *
35901038 TATTCTCTTTACCAAACGTGCACTAAAGGAGATAAAAAAGGAAAAGACAATGAAAAATAGGGT
1 TATTCTCTGTACCAAACGCGCACTAAAGGAGATAAAAAAGGAAAAGACAATGAAAAATAGGGT
* *
35901101 TATTCTCTGTATCAAACGCGCACTAACGGAGATAAAAAAGGAAAAGACAATGAAAAATAGG
1 TATTCTCTGTACCAAACGCGCACTAAAGGAGATAAAAAAGGAAAAGACAATGAAAAATAGG
35901162 AATCTGATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.48, C:0.14, G:0.19, T:0.19
Consensus pattern (63 bp):
TATTCTCTGTACCAAACGCGCACTAAAGGAGATAAAAAAGGAAAAGACAATGAAAAATAGGGT
Found at i:35905046 original size:36 final size:36
Alignment explanation
Indices: 35904996--35905075 Score: 151
Period size: 36 Copynumber: 2.2 Consensus size: 36
35904986 GAACGACAAT
*
35904996 GAGACCAACAAACAGGAGGAAGATGTTAGCCAGCAG
1 GAGAACAACAAACAGGAGGAAGATGTTAGCCAGCAG
35905032 GAGAACAACAAACAGGAGGAAGATGTTAGCCAGCAG
1 GAGAACAACAAACAGGAGGAAGATGTTAGCCAGCAG
35905068 GAGAACAA
1 GAGAACAA
35905076 TGATGAGAGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.45, C:0.17, G:0.30, T:0.07
Consensus pattern (36 bp):
GAGAACAACAAACAGGAGGAAGATGTTAGCCAGCAG
Found at i:35905120 original size:48 final size:48
Alignment explanation
Indices: 35905032--35905189 Score: 205
Period size: 48 Copynumber: 3.4 Consensus size: 48
35905022 TAGCCAGCAG
* *
35905032 GAGAACAACAAACAGGAGGAAGATGTTAGCCAGCAGGAGAACAATGAT
1 GAGAGCAACAAAAAGGAGGAAGATGTTAGCCAGCAGGAGAACAATGAT
* *
35905080 GAGAGCAAGAAAAAGGGGGAAGATGTTAGCCAGCAGGAGAACAATGAT
1 GAGAGCAACAAAAAGGAGGAAGATGTTAGCCAGCAGGAGAACAATGAT
* * * * * *
35905128 GAGAGCAACAAAATGGACGAAGATGCTAG-CA--AGAAGAAGAGTGAT
1 GAGAGCAACAAAAAGGAGGAAGATGTTAGCCAGCAGGAGAACAATGAT
35905173 GAGAGCAACAAAAAGGA
1 GAGAGCAACAAAAAGGA
35905190 CAAAGATGCT
Statistics
Matches: 97, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
45 27 0.28
47 2 0.02
48 68 0.70
ACGTcount: A:0.47, C:0.12, G:0.32, T:0.09
Consensus pattern (48 bp):
GAGAGCAACAAAAAGGAGGAAGATGTTAGCCAGCAGGAGAACAATGAT
Found at i:35905179 original size:21 final size:21
Alignment explanation
Indices: 35905155--35905225 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
35905145 CGAAGATGCT
35905155 AGCAAGAAGAAGAGTGATGAG
1 AGCAAGAAGAAGAGTGATGAG
* * ** **
35905176 AGCAACAAAAAGGACAAAGATGCT
1 AGCAAGAAGAA-G--AGTGATGAG
*
35905200 AGAAAGAAGAAGAGTGATGAG
1 AGCAAGAAGAAGAGTGATGAG
35905221 AGCAA
1 AGCAA
35905226 CAAAAGGAAG
Statistics
Matches: 33, Mismatches: 14, Indels: 6
0.62 0.26 0.11
Matches are distributed among these distances:
21 18 0.55
22 1 0.03
23 1 0.03
24 13 0.39
ACGTcount: A:0.52, C:0.08, G:0.31, T:0.08
Consensus pattern (21 bp):
AGCAAGAAGAAGAGTGATGAG
Found at i:35905183 original size:45 final size:45
Alignment explanation
Indices: 35905124--35905230 Score: 187
Period size: 45 Copynumber: 2.4 Consensus size: 45
35905114 AGGAGAACAA
* * *
35905124 TGATGAGAGCAACAAAATGGACGAAGATGCTAGCAAGAAGAAGAG
1 TGATGAGAGCAACAAAAAGGACAAAGATGCTAGAAAGAAGAAGAG
35905169 TGATGAGAGCAACAAAAAGGACAAAGATGCTAGAAAGAAGAAGAG
1 TGATGAGAGCAACAAAAAGGACAAAGATGCTAGAAAGAAGAAGAG
35905214 TGATGAGAGCAACAAAA
1 TGATGAGAGCAACAAAA
35905231 GGAAGGCAGT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.50, C:0.10, G:0.29, T:0.10
Consensus pattern (45 bp):
TGATGAGAGCAACAAAAAGGACAAAGATGCTAGAAAGAAGAAGAG
Found at i:35905235 original size:24 final size:24
Alignment explanation
Indices: 35905163--35905235 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 24
35905153 CTAGCAAGAA
35905163 GAAGAGTGATGAGAGCAACAAAAAG
1 GAAGAGTGATGAGAGCAAC-AAAAG
* ** *
35905188 GACA-A-AGATGCTAG-AA-AGAA-
1 GA-AGAGTGATGAGAGCAACAAAAG
35905208 GAAGAGTGATGAGAGCAACAAAAG
1 GAAGAGTGATGAGAGCAACAAAAG
35905232 GAAG
1 GAAG
35905236 GCAGTGCTCC
Statistics
Matches: 34, Mismatches: 8, Indels: 13
0.62 0.15 0.24
Matches are distributed among these distances:
19 1 0.03
20 3 0.09
21 9 0.26
22 2 0.06
23 5 0.15
24 10 0.29
25 3 0.09
26 1 0.03
ACGTcount: A:0.52, C:0.08, G:0.32, T:0.08
Consensus pattern (24 bp):
GAAGAGTGATGAGAGCAACAAAAG
Found at i:35906055 original size:30 final size:30
Alignment explanation
Indices: 35906019--35906149 Score: 181
Period size: 30 Copynumber: 4.4 Consensus size: 30
35906009 TCTTACAGGC
* **
35906019 ACGGTAACGGAAACTGCGCAAAACGAAGGT
1 ACGGTAACGGAAACTGAGCAAAAAAAAGGT
35906049 ACGGTAACGGAAACTGAGCAAAAAAAAGGT
1 ACGGTAACGGAAACTGAGCAAAAAAAAGGT
* * **
35906079 ACGGCAACGGAAACTGCGCAAAACGAAGGT
1 ACGGTAACGGAAACTGAGCAAAAAAAAGGT
35906109 ACGGTAACGGAAACTGAGCAAAAAAAAGGT
1 ACGGTAACGGAAACTGAGCAAAAAAAAGGT
* *
35906139 ACAGCAACGGA
1 ACGGTAACGGA
35906150 CAGGTTATCC
Statistics
Matches: 88, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 88 1.00
ACGTcount: A:0.45, C:0.18, G:0.28, T:0.08
Consensus pattern (30 bp):
ACGGTAACGGAAACTGAGCAAAAAAAAGGT
Found at i:35906117 original size:60 final size:60
Alignment explanation
Indices: 35906019--35906149 Score: 244
Period size: 60 Copynumber: 2.2 Consensus size: 60
35906009 TCTTACAGGC
*
35906019 ACGGTAACGGAAACTGCGCAAAACGAAGGTACGGTAACGGAAACTGAGCAAAAAAAAGGT
1 ACGGCAACGGAAACTGCGCAAAACGAAGGTACGGTAACGGAAACTGAGCAAAAAAAAGGT
35906079 ACGGCAACGGAAACTGCGCAAAACGAAGGTACGGTAACGGAAACTGAGCAAAAAAAAGGT
1 ACGGCAACGGAAACTGCGCAAAACGAAGGTACGGTAACGGAAACTGAGCAAAAAAAAGGT
*
35906139 ACAGCAACGGA
1 ACGGCAACGGA
35906150 CAGGTTATCC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.45, C:0.18, G:0.28, T:0.08
Consensus pattern (60 bp):
ACGGCAACGGAAACTGCGCAAAACGAAGGTACGGTAACGGAAACTGAGCAAAAAAAAGGT
Found at i:35908124 original size:21 final size:21
Alignment explanation
Indices: 35908081--35908129 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
35908071 TTTTAAGAAA
* *
35908081 TTTTATATTAAAATTTTAAAT
1 TTTTATAATAAAATTGTAAAT
35908102 TTTTATAATAAAA-TGTAATAT
1 TTTTATAATAAAATTGTAA-AT
*
35908123 TTGTATA
1 TTTTATA
35908130 CAAAATGCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTATAATAAAATTGTAAAT
Found at i:35926356 original size:7 final size:7
Alignment explanation
Indices: 35926345--35926375 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
35926335 CCGAGATATT
*
35926345 GTTGTCT
1 GTTGTCC
35926352 GTTGTCC
1 GTTGTCC
35926359 GTTGTCC
1 GTTGTCC
35926366 GTTGTCC
1 GTTGTCC
35926373 GTT
1 GTT
35926376 TTCTGTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.23, G:0.29, T:0.48
Consensus pattern (7 bp):
GTTGTCC
Found at i:35926364 original size:14 final size:14
Alignment explanation
Indices: 35926345--35926382 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
35926335 CCGAGATATT
35926345 GTTGTCTGTTGTCC
1 GTTGTCTGTTGTCC
*
35926359 GTTGTCCGTTGTCC
1 GTTGTCTGTTGTCC
*
35926373 GTTTTCTGTT
1 GTTGTCTGTT
35926383 TCACCCAGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.00, C:0.21, G:0.26, T:0.53
Consensus pattern (14 bp):
GTTGTCTGTTGTCC
Found at i:35927921 original size:19 final size:20
Alignment explanation
Indices: 35927897--35927941 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
35927887 ATAAGACAGT
35927897 AGCAAAAAG-GAAAAACAAA
1 AGCAAAAAGAGAAAAACAAA
* *
35927916 AGCAAAGAGAGAACAACAAA
1 AGCAAAAAGAGAAAAACAAA
35927936 AG-AAAA
1 AGCAAAA
35927942 TGTTTACGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.71, C:0.11, G:0.18, T:0.00
Consensus pattern (20 bp):
AGCAAAAAGAGAAAAACAAA
Found at i:35936108 original size:36 final size:37
Alignment explanation
Indices: 35936038--35936113 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 37
35936028 TTACAGAACA
* *
35936038 TTTCTTTGAATAGATGTAAACAAACATCAACATGAAT
1 TTTCTTTAAATAGATGTAAACAAAAATCAACATGAAT
* *
35936075 TTTCTTTAAATAGATGT-AACAAAAATGACCATGAAT
1 TTTCTTTAAATAGATGTAAACAAAAATCAACATGAAT
35936111 TTT
1 TTT
35936114 ATAGACAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
36 19 0.54
37 16 0.46
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.36
Consensus pattern (37 bp):
TTTCTTTAAATAGATGTAAACAAAAATCAACATGAAT
Found at i:35940749 original size:24 final size:25
Alignment explanation
Indices: 35940722--35940782 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
35940712 GTTTGATATA
*
35940722 TTATATATTAATTTTTAAA-A-AAAT
1 TTATA-ATTAATTGTTAAAGATAAAT
*
35940746 TTATAATATAAATGTTAAAGATAAAT
1 TTATAAT-TAATTGTTAAAGATAAAT
35940772 TTATAATTAAT
1 TTATAATTAAT
35940783 AATAAAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 2 0.06
24 14 0.45
25 4 0.13
26 11 0.35
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (25 bp):
TTATAATTAATTGTTAAAGATAAAT
Found at i:35943394 original size:50 final size:50
Alignment explanation
Indices: 35943319--35943419 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 50
35943309 TTTCTTTGTT
* *
35943319 GATAATATTAATGTAATTTGTTAATTATGGTCCATTTTTAGACTTCAAAG
1 GATAATATTAAAGTAATTTGCTAATTATGGTCCATTTTTAGACTTCAAAG
*
35943369 GATAATATTAAAGTAATTTGCTAATTATGGTCCATTTTTAGACTTGAAAG
1 GATAATATTAAAGTAATTTGCTAATTATGGTCCATTTTTAGACTTCAAAG
35943419 G
1 G
35943420 CTGAATTCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.42
Consensus pattern (50 bp):
GATAATATTAAAGTAATTTGCTAATTATGGTCCATTTTTAGACTTCAAAG
Found at i:35951847 original size:2 final size:2
Alignment explanation
Indices: 35951840--35951899 Score: 81
Period size: 2 Copynumber: 31.0 Consensus size: 2
35951830 TTCTTCACTC
*
35951840 CT CT CT CT CT CT CT CT CT CT CT CT -T CT TT CT -T NC- CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -CT CT CT CT
35951880 CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT
35951900 TTTTCCTTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
1 3 0.06
2 49 0.94
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:35963770 original size:117 final size:117
Alignment explanation
Indices: 35963564--35963799 Score: 454
Period size: 117 Copynumber: 2.0 Consensus size: 117
35963554 AAACCTGTAC
*
35963564 TCTGAGCACCATACGGTCCACTTAAAGGTGAAGATCCAGGAAAACCAGCAGAAGGCTCTGCTTTA
1 TCTGAGCACCATACGGCCCACTTAAAGGTGAAGATCCAGGAAAACCAGCAGAAGGCTCTGCTTTA
*
35963629 GGATAAACAGGTGGTGAATTAGCAGCCGGATATCTTACTGGCTCAGCTTGAT
66 GGACAAACAGGTGGTGAATTAGCAGCCGGATATCTTACTGGCTCAGCTTGAT
35963681 TCTGAGCACCATACGGCCCACTTAAAGGTGAAGATCCAGGAAAACCAGCAGAAGGCTCTGCTTTA
1 TCTGAGCACCATACGGCCCACTTAAAGGTGAAGATCCAGGAAAACCAGCAGAAGGCTCTGCTTTA
35963746 GGACAAACAGGTGGTGAATTAGCAGCCGGATATCTTACTGGCTCAGCTTGAT
66 GGACAAACAGGTGGTGAATTAGCAGCCGGATATCTTACTGGCTCAGCTTGAT
35963798 TC
1 TC
35963800 GGAAAAGAAC
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 117 1.00
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.22
Consensus pattern (117 bp):
TCTGAGCACCATACGGCCCACTTAAAGGTGAAGATCCAGGAAAACCAGCAGAAGGCTCTGCTTTA
GGACAAACAGGTGGTGAATTAGCAGCCGGATATCTTACTGGCTCAGCTTGAT
Found at i:35965518 original size:30 final size:30
Alignment explanation
Indices: 35965484--35965554 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
35965474 ATTTCCTCTT
*
35965484 AAAATAAAAATGTGAAAAGTCATTATTCTA
1 AAAATTAAAATGTGAAAAGTCATTATTCTA
35965514 AAAATTAAAATGTGAAAAGTCATTATTCTA
1 AAAATTAAAATGTGAAAAGTCATTATTCTA
35965544 AAAATTAAAAT
1 AAAATTAAAAT
35965555 ATAAAAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.55, C:0.06, G:0.08, T:0.31
Consensus pattern (30 bp):
AAAATTAAAATGTGAAAAGTCATTATTCTA
Found at i:35965561 original size:14 final size:14
Alignment explanation
Indices: 35965542--35965604 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
35965532 GTCATTATTC
35965542 TAAAAATTAAAATA
1 TAAAAATTAAAATA
*
35965556 TAAAAATT--TATCA
1 TAAAAATTAAAAT-A
*
35965569 AAAAAATTAAAATA
1 TAAAAATTAAAATA
*
35965583 TAAAAAGCTTAATATA
1 TAAAAA--TTAAAATA
35965599 TAAAAA
1 TAAAAA
35965605 ATTCTTGAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
12 2 0.05
13 8 0.21
14 14 0.36
15 2 0.05
16 13 0.33
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.29
Consensus pattern (14 bp):
TAAAAATTAAAATA
Found at i:35985594 original size:2 final size:2
Alignment explanation
Indices: 35985587--35985619 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35985577 TGAACTTTCT
35985587 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
35985620 GTCCCTGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:35999367 original size:89 final size:88
Alignment explanation
Indices: 35999241--35999435 Score: 238
Period size: 89 Copynumber: 2.2 Consensus size: 88
35999231 ATTTTTTATT
**
35999241 ATTA-TTTATTTTTATTAGATTTTTTAAATATTAATAATCTAGATTTTAATTAAAATATTAATA-
1 ATTATTTTA-TTTTATTTTATTTTTTAAATATTAATAA--TAGA---TAATTAAAATATTAATAT
*
35999304 ATTA-ATAATTTAAATATTATTATGATTA
60 ATTATATAATTTAAATATTATTATGATAA
* * * *
35999332 A-T-TTTTATTTTATTTTATTTTTTAAATATTAATAATAGATCATTTAAATATTAATATTTTATT
1 ATTATTTTATTTTATTTTATTTTTTAAATATTAATAATAGATAATTAAAATATTAATATATTATA
35999395 TAATTTAAATATTATTATGATAA
66 TAATTTAAATATTATTATGATAA
35999418 ATTATTTTATTTTATTTT
1 ATTATTTTATTTTATTTT
35999436 NNNNNNNNNN
Statistics
Matches: 92, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
84 15 0.16
85 3 0.03
86 23 0.25
87 5 0.05
88 14 0.15
89 26 0.28
90 5 0.05
91 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (88 bp):
ATTATTTTATTTTATTTTATTTTTTAAATATTAATAATAGATAATTAAAATATTAATATATTATA
TAATTTAAATATTATTATGATAA
Found at i:35999541 original size:33 final size:32
Alignment explanation
Indices: 35999497--35999558 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
35999487 TAATTTAAAT
35999497 ATTAATATTTTATTTAATTTATATATTATTATG
1 ATTAATATTTTATTTAATTT-TATATTATTATG
* * *
35999530 ATTAATTTTTTATTTTATTTTATTTTATT
1 ATTAATATTTTATTTAATTTTATATTATT
35999559 TTTTTAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 8 0.31
33 18 0.69
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (32 bp):
ATTAATATTTTATTTAATTTTATATTATTATG
Found at i:35999748 original size:25 final size:25
Alignment explanation
Indices: 35999708--35999759 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
35999698 AATAATTGAT
*
35999708 AATTTAAATATTAATATTTTATTTAA
1 AATTTAAATATAAATATTTTA-TTAA
35999734 AATTT-AATATAAATATTTTATTAA
1 AATTTAAATATAAATATTTTATTAA
35999758 AA
1 AA
35999760 GTTAGAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 6 0.24
25 14 0.56
26 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AATTTAAATATAAATATTTTATTAA
Found at i:35999750 original size:31 final size:32
Alignment explanation
Indices: 35999689--35999750 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 32
35999679 ATTTATAATT
*
35999689 TATTTTATTAATAATTGATAATTTAAATATTAA
1 TATTTTATTAATAATT-ATAATATAAATATTAA
35999722 TATTTTATTTAA-AATT-TAATATAAATATT
1 TATTTTA-TTAATAATTATAATATAAATATT
35999751 TTATTAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 12 0.44
33 11 0.41
34 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (32 bp):
TATTTTATTAATAATTATAATATAAATATTAA
Found at i:36023896 original size:15 final size:15
Alignment explanation
Indices: 36023878--36023925 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
36023868 AAGAAATAAA
36023878 TATTTTTAAAATTAT
1 TATTTTTAAAATTAT
*
36023893 TATTTTCAAAAATTAAT
1 TATTTT-TAAAATT-AT
* *
36023910 GATTTTTAAATTTAT
1 TATTTTTAAAATTAT
36023925 T
1 T
36023926 TAGTAATCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
15 8 0.31
16 11 0.42
17 7 0.27
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (15 bp):
TATTTTTAAAATTAT
Found at i:36026113 original size:2 final size:2
Alignment explanation
Indices: 36026106--36026144 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
36026096 ACAAAGGCTA
** *
36026106 AT AT AT AT AT AT AT AT AT AT AT AT GC AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36026145 CTGCAATTCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36040216 original size:3 final size:3
Alignment explanation
Indices: 36040203--36040245 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
36040193 GAGAAGGTCA
* *
36040203 AAG AGG AAG AAG AA- AACC AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG AAG A
36040246 GGCAGAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.89
4 2 0.06
ACGTcount: A:0.65, C:0.05, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:36056607 original size:30 final size:29
Alignment explanation
Indices: 36056573--36056650 Score: 97
Period size: 27 Copynumber: 2.7 Consensus size: 29
36056563 ACCTCAAGGC
* *
36056573 TACCCACCAGCTGGATATCCTCCTGGTGGA
1 TACCCTCCATCTGG-TATCCTCCTGGTGGA
*
36056603 TACCCTCCATCTGG--TCATCCTGGTGGA
1 TACCCTCCATCTGGTATCCTCCTGGTGGA
36056630 TACCCTCCATCTGGTTATCCT
1 TACCCTCCATCTGG-TATCCT
36056651 GGTGCATCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 26 0.63
30 15 0.37
ACGTcount: A:0.17, C:0.35, G:0.19, T:0.29
Consensus pattern (29 bp):
TACCCTCCATCTGGTATCCTCCTGGTGGA
Found at i:36056629 original size:27 final size:27
Alignment explanation
Indices: 36056593--36056654 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
36056583 CTGGATATCC
36056593 TCCTGGTGGATACCCTCCATCTGGTCA
1 TCCTGGTGGATACCCTCCATCTGGTCA
*
36056620 TCCTGGTGGATACCCTCCATCTGGTTA
1 TCCTGGTGGATACCCTCCATCTGGTCA
36056647 TCCTGGTG
1 TCCTGGTG
36056655 CATCTCATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.13, C:0.31, G:0.24, T:0.32
Consensus pattern (27 bp):
TCCTGGTGGATACCCTCCATCTGGTCA
Found at i:36056991 original size:24 final size:24
Alignment explanation
Indices: 36056910--36056984 Score: 132
Period size: 24 Copynumber: 3.1 Consensus size: 24
36056900 AGCATCATGG
*
36056910 TGGCAAATTCAAGCATGGGAAGCA
1 TGGCAAATTTAAGCATGGGAAGCA
36056934 TGGCAAATTTAAGCATGGGAAGCA
1 TGGCAAATTTAAGCATGGGAAGCA
*
36056958 TGGCAAATTTAAGCATGGAAAGCA
1 TGGCAAATTTAAGCATGGGAAGCA
36056982 TGG
1 TGG
36056985 ATTATTTGGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.20
Consensus pattern (24 bp):
TGGCAAATTTAAGCATGGGAAGCA
Found at i:36074634 original size:2 final size:2
Alignment explanation
Indices: 36074627--36074669 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
36074617 TAATTTAATG
36074627 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36074669 A
1 A
36074670 AACTTACAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36082301 original size:328 final size:330
Alignment explanation
Indices: 36081806--36082413 Score: 794
Period size: 328 Copynumber: 1.8 Consensus size: 330
36081796 TTTTCTATTT
*
36081806 AATTAATTTTTTTTACACCTTATGTCAAAAATAAATTGTTTTGACATTTGAAGTTTTTTTTTGTT
1 AATTAATTTTTTTTACACCTTATGTCAAAAATAAATTGTTTTGACATTTGAAG-------TGGTT
* * *
36081871 TTTTATTTTTATTTATTTTAATAAAAAATACTTAAAAACAATAATTTCTAACTTTTAATGTTTAG
59 TCTTACTTTTATTTATTTTAATAAAAAATACTTAAAAACAATAATTTCTAACTTTTAATGCTTAG
* * * *
36081936 AAGATAGATTTATTTAATATTTATTAATTATAATTTAATATTATTTTT-ATCTATATTT-TTTTA
124 AAGATAGATTCATTTAATATTTATCAATTACAATTTAATATTATTTTTCATCTAT-TTTCTCTTA
* * * * *
36081999 TTCTGTATGAACCTAAATCTATAATATATAGATATCTCTTTTATACATTAATGTTTAAATT-TCA
188 TTCTGCATCAACCTAAATCTATAATATATAGACATCTCTTTTATACATGAATATTTAAATTCT-A
* *
36082063 ATAAATATCCATCAAATTCATTATATAAAAGTAGGATAATTGATTGAGTTAATTAATTGACATTT
252 ATAAACATCAATCAAATTCATTATATAAAAGTAGGATAATTGATTGAGTTAATTAATTGACATTT
36082128 GTCATTCTTAATTA
317 GTCATTCTTAATTA
* *
36082142 AATT-ATTTTTTTTACACCTTATGTCAAAAATAAATTATTTTTGACATTTGAAG-GGTTTCTTCC
1 AATTAATTTTTTTTACACCTTATGTCAAAAATAAATT-GTTTTGACATTTGAAGTGGTTTCTTAC
* * * * *
36082205 TTTTATTTTTTTTAGTAAAAAATACTTGAAAACAATAATTTTTAACTTTTAATGCTTATAAGATA
65 TTTTATTTATTTTAATAAAAAATACTTAAAAACAATAATTTCTAACTTTTAATGCTTAGAAGATA
* * *
36082270 TATTCATTTAGTATTTATCAATTACAATTTAATATTATTTTTCGTCTATTTTCTCTTATTCTGCA
130 GATTCATTTAATATTTATCAATTACAATTTAATATTATTTTTCATCTATTTTCTCTTATTCTGCA
** ** * * *
36082335 TCAATGTGGATCTATAGTATATAGACATCTTTTTTGTACATGAATATTTAAATTCTAATAAACAT
195 TCAACCTAAATCTATAATATATAGACATCTCTTTTATACATGAATATTTAAATTCTAATAAACAT
*
36082400 CAATCCAATTCATT
260 CAATCAAATTCATT
36082414 GAACAAAAAA
Statistics
Matches: 235, Mismatches: 33, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
328 105 0.45
329 78 0.33
330 1 0.00
335 32 0.14
336 19 0.08
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (330 bp):
AATTAATTTTTTTTACACCTTATGTCAAAAATAAATTGTTTTGACATTTGAAGTGGTTTCTTACT
TTTATTTATTTTAATAAAAAATACTTAAAAACAATAATTTCTAACTTTTAATGCTTAGAAGATAG
ATTCATTTAATATTTATCAATTACAATTTAATATTATTTTTCATCTATTTTCTCTTATTCTGCAT
CAACCTAAATCTATAATATATAGACATCTCTTTTATACATGAATATTTAAATTCTAATAAACATC
AATCAAATTCATTATATAAAAGTAGGATAATTGATTGAGTTAATTAATTGACATTTGTCATTCTT
AATTA
Found at i:36083135 original size:17 final size:19
Alignment explanation
Indices: 36083113--36083156 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
36083103 TAGTAACTAT
36083113 TTTATATTGACA-GGTT-C
1 TTTATATTGACACGGTTGC
*
36083130 TTTATATT-ATACGGTTGC
1 TTTATATTGACACGGTTGC
36083148 TTTATATTG
1 TTTATATTG
36083157 TATAACTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 2 0.09
17 12 0.52
18 9 0.39
ACGTcount: A:0.23, C:0.09, G:0.16, T:0.52
Consensus pattern (19 bp):
TTTATATTGACACGGTTGC
Found at i:36098587 original size:21 final size:22
Alignment explanation
Indices: 36098563--36098614 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
36098553 CTTTATTTAT
36098563 ATAATTA-TATAATAATTATAA
1 ATAATTATTATAATAATTATAA
36098584 ATAA-TATTATAATAATTATAA
1 ATAATTATTATAATAATTATAA
36098605 ATAA-TATTAT
1 ATAATTATTAT
36098615 TTTGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAATTATTATAATAATTATAA
Found at i:36107150 original size:30 final size:30
Alignment explanation
Indices: 36107115--36107184 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
36107105 TAATTGTAAA
*
36107115 ATTTATTTAACTTAAAACAAAAGTAAAAAG
1 ATTTATTTAACTTAAAACAAAAGCAAAAAG
* *
36107145 ATTTATTTAACTTAAAACAAGAGCATAAAG
1 ATTTATTTAACTTAAAACAAAAGCAAAAAG
*
36107175 AATTATTTAA
1 ATTTATTTAA
36107185 ATTTTTGTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (30 bp):
ATTTATTTAACTTAAAACAAAAGCAAAAAG
Found at i:36123936 original size:2 final size:2
Alignment explanation
Indices: 36123929--36123973 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
36123919 CTCTAATTAC
36123929 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36123971 TA T
1 TA T
36123974 GTGTATGTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36129634 original size:42 final size:44
Alignment explanation
Indices: 36129565--36129652 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 44
36129555 TGAAGAAATG
* *
36129565 GTAGGAAGAGAAACAAGAGAGAGAGCTTCTATAACTAAGCTTCA
1 GTAGGAAGAAAAACAAGAGAGAGAGCTTCTATAAATAAGCTTCA
36129609 GTAGGAAGAAAAAC-AG-GA-ATGAGCTTCTATAAATAAGCTTCA
1 GTAGGAAGAAAAACAAGAGAGA-GAGCTTCTATAAATAAGCTTCA
36129651 GT
1 GT
36129653 TATCAGGAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
41 1 0.02
42 25 0.61
43 2 0.05
44 13 0.32
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.20
Consensus pattern (44 bp):
GTAGGAAGAAAAACAAGAGAGAGAGCTTCTATAAATAAGCTTCA
Found at i:36133031 original size:41 final size:41
Alignment explanation
Indices: 36132986--36133069 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
36132976 AATTAATTAT
* *
36132986 TAAGTTATTAGATTAAACTATTGATATATAATATGTTATGA
1 TAAGTTATTAGATTAAACTATTAAGATATAATATGTTATGA
* ** * *
36133027 TAAGTTATTAGGTTTGACTGTTAAGATATAATATGTTGTGA
1 TAAGTTATTAGATTAAACTATTAAGATATAATATGTTATGA
36133068 TA
1 TA
36133070 GACTAAAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (41 bp):
TAAGTTATTAGATTAAACTATTAAGATATAATATGTTATGA
Found at i:36133681 original size:18 final size:19
Alignment explanation
Indices: 36133648--36133683 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
36133638 AATATATGAG
*
36133648 TAAATAGAATATAAATAAA
1 TAAATAGAATAAAAATAAA
36133667 TAAATA-AATAAAAATAA
1 TAAATAGAATAAAAATAA
36133684 TAATTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (19 bp):
TAAATAGAATAAAAATAAA
Found at i:36133694 original size:21 final size:22
Alignment explanation
Indices: 36133661--36133702 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
36133651 ATAGAATATA
36133661 AATAAATAAATAAA-TAAAAAT
1 AATAAATAAATAAATTAAAAAT
* *
36133682 AATAATTATATAAATTAAAAA
1 AATAAATAAATAAATTAAAAA
36133703 AAACTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AATAAATAAATAAATTAAAAAT
Found at i:36143185 original size:16 final size:17
Alignment explanation
Indices: 36143161--36143194 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
36143151 TAGGATTGTA
36143161 TTTTATTTAA-TTTAGT
1 TTTTATTTAATTTTAGT
*
36143177 TTTTTTTTAATTTTAGT
1 TTTTATTTAATTTTAGT
36143194 T
1 T
36143195 GATTTTAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTTATTTAATTTTAGT
Found at i:36143917 original size:26 final size:26
Alignment explanation
Indices: 36143888--36143937 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
36143878 TGTTAGCTAG
36143888 TTTTTGATAAGGCATTGCATGACTAA
1 TTTTTGATAAGGCATTGCATGACTAA
*
36143914 TTTTTTATAAGGCATTGCATGACT
1 TTTTTGATAAGGCATTGCATGACT
36143938 TGTTAGTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (26 bp):
TTTTTGATAAGGCATTGCATGACTAA
Found at i:36143976 original size:23 final size:24
Alignment explanation
Indices: 36143921--36143986 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 24
36143911 TAATTTTTTA
*
36143921 TAAGGCATTGCATGACTT-GTTAG
1 TAAGGCATTGCGTGACTTAGTTAG
*
36143944 TAATGCATTGCGTGA-TTAGTTAG
1 TAAGGCATTGCGTGACTTAGTTAG
* *
36143967 TAAGGTATTGTGTGACTTAG
1 TAAGGCATTGCGTGACTTAG
36143987 ACATTACTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 2 0.06
23 30 0.83
24 4 0.11
ACGTcount: A:0.26, C:0.09, G:0.27, T:0.38
Consensus pattern (24 bp):
TAAGGCATTGCGTGACTTAGTTAG
Found at i:36152543 original size:18 final size:18
Alignment explanation
Indices: 36152522--36152558 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
36152512 CGAAAAGATA
36152522 CATGCTCGAAGAAAGCAG
1 CATGCTCGAAGAAAGCAG
*
36152540 CATGCTCGGAGAAAGCAG
1 CATGCTCGAAGAAAGCAG
36152558 C
1 C
36152559 TTCAGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.24, G:0.30, T:0.11
Consensus pattern (18 bp):
CATGCTCGAAGAAAGCAG
Found at i:36156919 original size:2 final size:2
Alignment explanation
Indices: 36156912--36156941 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
36156902 ATAGCCTGAT
36156912 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
36156942 CTGAGGTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:36161463 original size:4 final size:4
Alignment explanation
Indices: 36161454--36161483 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
36161444 CGTTTTACTA
36161454 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
36161484 CATAACTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:36182293 original size:33 final size:33
Alignment explanation
Indices: 36182236--36182313 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
36182226 CAAAAAGTTT
* *
36182236 GAAAAGTGGA-TTTTTTTTTTATAATTCAGGTC
1 GAAAAGTGAATTTTTTTTTTTATAATTCAAGTC
*
36182268 GAAAAGT-AATTTTTTCTTTTTATAATTGAAGTC
1 GAAAAGTGAATTTTTT-TTTTTATAATTCAAGTC
36182301 GAAAAGTGAATTT
1 GAAAAGTGAATTT
36182314 CAATCCTTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
31 1 0.03
32 12 0.30
33 22 0.55
34 5 0.12
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (33 bp):
GAAAAGTGAATTTTTTTTTTTATAATTCAAGTC
Found at i:36184356 original size:6 final size:6
Alignment explanation
Indices: 36184345--36184369 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
36184335 TCAATGATGC
36184345 GGATAG GGATAG GGATAG GGATAG G
1 GGATAG GGATAG GGATAG GGATAG G
36184370 CGTGTTGGAG
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:0.32, C:0.00, G:0.52, T:0.16
Consensus pattern (6 bp):
GGATAG
Found at i:36192148 original size:7 final size:7
Alignment explanation
Indices: 36192136--36192161 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
36192126 CCCAGAAGAG
36192136 GAAATCT
1 GAAATCT
36192143 GAAATCT
1 GAAATCT
36192150 GAAATCT
1 GAAATCT
36192157 GAAAT
1 GAAAT
36192162 GATGAGTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (7 bp):
GAAATCT
Found at i:36203141 original size:12 final size:12
Alignment explanation
Indices: 36203124--36203164 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
36203114 TATCAAATAT
36203124 AAATTTTAAAAA
1 AAATTTTAAAAA
*
36203136 AAATTTAAAAAA
1 AAATTTTAAAAA
36203148 AAATAATTTAAAAA
1 AAAT--TTTAAAAA
36203162 AAA
1 AAA
36203165 AAATTTAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 15 0.60
14 10 0.40
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAATTTTAAAAA
Found at i:36203155 original size:15 final size:14
Alignment explanation
Indices: 36203131--36203178 Score: 78
Period size: 15 Copynumber: 3.3 Consensus size: 14
36203121 TATAAATTTT
36203131 AAAAAAAATTTAAA
1 AAAAAAAATTTAAA
36203145 AAAAAATAATTTAAA
1 AAAAAA-AATTTAAA
36203160 AAAAAAAATTTAAGA
1 AAAAAAAATTTAA-A
36203175 AAAA
1 AAAA
36203179 GCTCCTGTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 13 0.41
15 19 0.59
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (14 bp):
AAAAAAAATTTAAA
Found at i:36220251 original size:17 final size:16
Alignment explanation
Indices: 36220220--36220259 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
36220210 TATCTCATTC
36220220 AATTT-TAATTTTTTT
1 AATTTATAATTTTTTT
36220235 AATTTATAATATTTTTT
1 AATTTATAAT-TTTTTT
*
36220252 TATTTATA
1 AATTTATA
36220260 TTTATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.23
16 4 0.18
17 13 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
AATTTATAATTTTTTT
Found at i:36220262 original size:14 final size:14
Alignment explanation
Indices: 36220243--36220277 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
36220233 TTAATTTATA
36220243 ATATTTTTTTATTT
1 ATATTTTTTTATTT
*
36220257 ATATTTATTTATTT
1 ATATTTTTTTATTT
*
36220271 TTATTTT
1 ATATTTT
36220278 ATTTGTTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
ATATTTTTTTATTT
Found at i:36228189 original size:14 final size:13
Alignment explanation
Indices: 36228156--36228183 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
36228146 CAAAAATTAT
36228156 AACTTATAAAAAA
1 AACTTATAAAAAA
36228169 AACTTATAAAAAA
1 AACTTATAAAAAA
36228182 AA
1 AA
36228184 ATTTATCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (13 bp):
AACTTATAAAAAA
Found at i:36241057 original size:2 final size:2
Alignment explanation
Indices: 36241050--36241110 Score: 106
Period size: 2 Copynumber: 30.5 Consensus size: 2
36241040 ACTAGACATC
36241050 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36241092 AT AT AT CAT AT AT A- AT AT A
1 AT AT AT -AT AT AT AT AT AT A
36241111 AAGAAAGAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.02
2 54 0.95
3 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36249003 original size:2 final size:2
Alignment explanation
Indices: 36248996--36249038 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
36248986 AGTAGTTTCT
*
36248996 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36249038 T
1 T
36249039 TCTCAGCCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:36250001 original size:33 final size:33
Alignment explanation
Indices: 36249938--36250001 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
36249928 TTAAGACTTA
**
36249938 TTTTTGAGATAACTGATGTACTCAACTTATTTG
1 TTTTTGAGATAACTGACATACTCAACTTATTTG
* * *
36249971 TTTTTGAGATATCTGACATAGTCAATTTATT
1 TTTTTGAGATAACTGACATACTCAACTTATT
36250002 CTTGAGTAGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (33 bp):
TTTTTGAGATAACTGACATACTCAACTTATTTG
Found at i:36269145 original size:46 final size:46
Alignment explanation
Indices: 36269092--36269197 Score: 167
Period size: 46 Copynumber: 2.3 Consensus size: 46
36269082 CAACAGCAAC
*
36269092 GTCTGTCTATATTCTTATCGTTAATTTAACTTTAATACTGCCTTCT
1 GTCTGTCTATATTCTTATCGTTAATTTAACTTTAATACTCCCTTCT
* **
36269138 GTCTGTCTATATTCTTATCTTTAATTTAACTTTGTTACTCCCTTCT
1 GTCTGTCTATATTCTTATCGTTAATTTAACTTTAATACTCCCTTCT
*
36269184 GTCCGTCTATATTC
1 GTCTGTCTATATTC
36269198 ATTCTATAGG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.19, C:0.22, G:0.08, T:0.51
Consensus pattern (46 bp):
GTCTGTCTATATTCTTATCGTTAATTTAACTTTAATACTCCCTTCT
Found at i:36275234 original size:90 final size:90
Alignment explanation
Indices: 36275081--36275261 Score: 362
Period size: 90 Copynumber: 2.0 Consensus size: 90
36275071 AAACCCAGAA
36275081 ACGCAGGAAAGAGAATAAGAAAGAGACTTCCAAAACTTGACCAGGATTGAGCGCAGAATTACATG
1 ACGCAGGAAAGAGAATAAGAAAGAGACTTCCAAAACTTGACCAGGATTGAGCGCAGAATTACATG
36275146 ATATTTATGTAATTTGTAAAGCGGT
66 ATATTTATGTAATTTGTAAAGCGGT
36275171 ACGCAGGAAAGAGAATAAGAAAGAGACTTCCAAAACTTGACCAGGATTGAGCGCAGAATTACATG
1 ACGCAGGAAAGAGAATAAGAAAGAGACTTCCAAAACTTGACCAGGATTGAGCGCAGAATTACATG
36275236 ATATTTATGTAATTTGTAAAGCGGT
66 ATATTTATGTAATTTGTAAAGCGGT
36275261 A
1 A
36275262 GAATTGCACA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.23
Consensus pattern (90 bp):
ACGCAGGAAAGAGAATAAGAAAGAGACTTCCAAAACTTGACCAGGATTGAGCGCAGAATTACATG
ATATTTATGTAATTTGTAAAGCGGT
Found at i:36278329 original size:21 final size:20
Alignment explanation
Indices: 36278305--36278344 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
36278295 GAATAGACCT
36278305 TTGGAATCTTGAAGTTAAAAG
1 TTGG-ATCTTGAAGTTAAAAG
* *
36278326 TTGGTTCTTGAATTTAAAA
1 TTGGATCTTGAAGTTAAAA
36278345 TCTGTTCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGGATCTTGAAGTTAAAAG
Found at i:36288870 original size:16 final size:16
Alignment explanation
Indices: 36288851--36288905 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
36288841 ATTATATTTT
*
36288851 TAATAATTTTTTAAAA
1 TAATAATTTATTAAAA
**
36288867 TAATTGTTTATT-AAA
1 TAATAATTTATTAAAA
36288882 TAATTAATTTAATTAAAA
1 TAA-TAATTT-ATTAAAA
36288900 -AATAAT
1 TAATAAT
36288906 AAAATAATCT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 6 0.19
16 17 0.55
17 5 0.16
18 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
TAATAATTTATTAAAA
Found at i:36289214 original size:14 final size:14
Alignment explanation
Indices: 36289195--36289221 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36289185 CTGTTATATA
36289195 GATTTTAATTTAAT
1 GATTTTAATTTAAT
36289209 GATTTTAATTTAA
1 GATTTTAATTTAA
36289222 AAATTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (14 bp):
GATTTTAATTTAAT
Found at i:36297425 original size:77 final size:77
Alignment explanation
Indices: 36297298--36297448 Score: 243
Period size: 77 Copynumber: 2.0 Consensus size: 77
36297288 AATACACGAA
36297298 AACAACCACATTCTATCACCAAAATATACCCCTAACTCCATCCACCCACCA-CTATATGGTACAG
1 AACAACCACATTCTATCACCAAAATATACCCCTAACTCCATCCACCCACCATC-ATATGGTACAG
*
36297362 CTTCACCATTGAC
65 CTACACCATTGAC
* *
36297375 AACAACCACATTCTATCACCCAAAA-ATACCCCTAACTCCGTCCACCCACCATCATATTGTACAG
1 AACAACCACATTCTATCA-CCAAAATATACCCCTAACTCCATCCACCCACCATCATATGGTACAG
36297439 CTACACCATT
65 CTACACCATT
36297449 AACACCTCCA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
77 62 0.90
78 7 0.10
ACGTcount: A:0.35, C:0.38, G:0.05, T:0.22
Consensus pattern (77 bp):
AACAACCACATTCTATCACCAAAATATACCCCTAACTCCATCCACCCACCATCATATGGTACAGC
TACACCATTGAC
Found at i:36298567 original size:24 final size:24
Alignment explanation
Indices: 36298535--36298581 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
36298525 TATCTATATA
36298535 AACAGAATCTCCAAAGACTGAAAG
1 AACAGAATCTCCAAAGACTGAAAG
36298559 AACAGAATCTCCAAAGACTGAAA
1 AACAGAATCTCCAAAGACTGAAA
36298582 AGGTAATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.51, C:0.21, G:0.15, T:0.13
Consensus pattern (24 bp):
AACAGAATCTCCAAAGACTGAAAG
Found at i:36314983 original size:109 final size:105
Alignment explanation
Indices: 36314791--36314987 Score: 236
Period size: 109 Copynumber: 1.8 Consensus size: 105
36314781 ATTCTAAAAT
* * * * * * *
36314791 GAACTCTATTAATTAATAAAATATAGAAATTAGTATAGAAATTTTTTTTATAACATTAGAATGAC
1 GAACCCTATTAATTAACAAAATATAAAAATTAGTATACAAATTTCTTTAATAACATTAAAATGAC
*
36314856 ATAATCAATATTTTAATATAAAAATTAATATATTTATCAG
66 ATAATCAATATTTAAATATAAAAATTAATATATTTATCAG
*
36314896 GAACCCTATTAATTAACAAATATGTAAAAAATTAGTATACAAATTTACTTTAATAACATTAAAAA
1 GAACCCTATTAATTAACAAA-ATAT-AAAAATTAGTATACAAATTT-CTTTAATAACATT-AAAA
*
36314961 TTG-CATAA-CTGATATTTAAATATAAAA
62 -TGACATAATC-AATATTTAAATATAAAA
36314988 GTAAATGGGC
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
105 18 0.24
106 3 0.04
107 18 0.24
108 12 0.16
109 23 0.30
110 2 0.03
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (105 bp):
GAACCCTATTAATTAACAAAATATAAAAATTAGTATACAAATTTCTTTAATAACATTAAAATGAC
ATAATCAATATTTAAATATAAAAATTAATATATTTATCAG
Found at i:36316999 original size:26 final size:27
Alignment explanation
Indices: 36316955--36317006 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
36316945 AACTAATGAA
* *
36316955 CAAAGATACATGCATGAAAATGAAGAG
1 CAAAGATACATGCAGGAAAAAGAAGAG
*
36316982 CAAAGA-AGATGCAGGAAAAAGAAGA
1 CAAAGATACATGCAGGAAAAAGAAGA
36317007 CTGACATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.56, C:0.10, G:0.25, T:0.10
Consensus pattern (27 bp):
CAAAGATACATGCAGGAAAAAGAAGAG
Found at i:36318216 original size:19 final size:19
Alignment explanation
Indices: 36318192--36318237 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
36318182 ATCACATGTC
36318192 TAACATTTTTTTAATACAT
1 TAACATTTTTTTAATACAT
36318211 TAACATTTTTTTAATACAT
1 TAACATTTTTTTAATACAT
36318230 TAACATTT
1 TAACATTT
36318238 CATCCGTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (19 bp):
TAACATTTTTTTAATACAT
Found at i:36318834 original size:15 final size:15
Alignment explanation
Indices: 36318797--36318845 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
36318787 ATAAATTTTG
36318797 AAAAATTTAAAA-AA
1 AAAAATTTAAAAGAA
36318811 AAAGTAATTTAAAAGAA
1 AAA--AATTTAAAAGAA
**
36318828 AAAAATTTTCAAGAA
1 AAAAATTTAAAAGAA
36318843 AAA
1 AAA
36318846 TTCTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 3 0.10
15 13 0.43
16 9 0.30
17 5 0.17
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.22
Consensus pattern (15 bp):
AAAAATTTAAAAGAA
Found at i:36319052 original size:49 final size:48
Alignment explanation
Indices: 36318981--36319074 Score: 118
Period size: 49 Copynumber: 1.9 Consensus size: 48
36318971 TAATTTTAAC
*
36318981 TAAAATTATAATTTGTAAAAAAAATTATTAAATAA-TTTTAATTTAATTT
1 TAAAATTATAATTTGTAAAAAAAATTA-T-AATAACTTTTAAATTAATTT
* * * *
36319030 TAAAATTATTATTTTTATAAAAATTTATAATAACTTTTAAATTAA
1 TAAAATTATAATTTGTAAAAAAAATTATAATAACTTTTAAATTAA
36319075 AAAGAAGCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
47 5 0.13
48 11 0.28
49 23 0.59
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (48 bp):
TAAAATTATAATTTGTAAAAAAAATTATAATAACTTTTAAATTAATTT
Found at i:36321850 original size:9 final size:9
Alignment explanation
Indices: 36321836--36321861 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
36321826 TAAAAGAGGT
36321836 CCTCCACCA
1 CCTCCACCA
36321845 CCTCCACCA
1 CCTCCACCA
36321854 CCTCCACC
1 CCTCCACC
36321862 TCATAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.69, G:0.00, T:0.12
Consensus pattern (9 bp):
CCTCCACCA
Found at i:36324241 original size:55 final size:55
Alignment explanation
Indices: 36324156--36324267 Score: 163
Period size: 55 Copynumber: 2.0 Consensus size: 55
36324146 AGCCTGCTTT
* * *
36324156 ATGTCATAAGTATGTCAAATTTAATCTTTTTCTTGGA-TTTTCATTTTAGATTTTG
1 ATGTCAGAAGTATGTCAAATTTAATATTTTTCTTGAATTTTTC-TTTTAGATTTTG
* *
36324211 ATGTCAGAAGTATGTTAATTTTAATATTTTTCTTGAATTTTTCTTTTAGATTTTG
1 ATGTCAGAAGTATGTCAAATTTAATATTTTTCTTGAATTTTTCTTTTAGATTTTG
36324266 AT
1 AT
36324268 TGAAAGTGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 46 0.90
56 5 0.10
ACGTcount: A:0.26, C:0.07, G:0.12, T:0.54
Consensus pattern (55 bp):
ATGTCAGAAGTATGTCAAATTTAATATTTTTCTTGAATTTTTCTTTTAGATTTTG
Found at i:36332916 original size:21 final size:23
Alignment explanation
Indices: 36332891--36332935 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 23
36332881 AATATAAATA
*
36332891 ATTTTTAAAT-TTATTT-ATTTT
1 ATTTTTAAATGATATTTAATTTT
36332912 A-TTTTAAATGATATTTAATTTT
1 ATTTTTAAATGATATTTAATTTT
36332934 AT
1 AT
36332936 CTATATTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
20 8 0.40
21 6 0.30
22 6 0.30
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
ATTTTTAAATGATATTTAATTTT
Found at i:36332920 original size:31 final size:33
Alignment explanation
Indices: 36332885--36332949 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 33
36332875 GTTAACAATA
* *
36332885 TAAATAATTTTTAAATTTAT-T-TATTTTATTT
1 TAAATAATATTTAAATTTATCTATATTCTATTT
* *
36332916 TAAATGATATTTAATTTTATCTATATTCTATTT
1 TAAATAATATTTAAATTTATCTATATTCTATTT
36332949 T
1 T
36332950 TTTAAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 17 0.61
32 1 0.04
33 10 0.36
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.62
Consensus pattern (33 bp):
TAAATAATATTTAAATTTATCTATATTCTATTT
Found at i:36340951 original size:23 final size:21
Alignment explanation
Indices: 36340908--36340951 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
36340898 ATCCTAACCG
*
36340908 AACTAACCGAAAAACCGAACT
1 AACTAACCGAAAAACCAAACT
36340929 AACTGAACCGAAAAAACCAAACT
1 AACT-AACCG-AAAAACCAAACT
36340952 CATTTCGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 5 0.25
23 11 0.55
ACGTcount: A:0.55, C:0.27, G:0.09, T:0.09
Consensus pattern (21 bp):
AACTAACCGAAAAACCAAACT
Found at i:36342910 original size:25 final size:25
Alignment explanation
Indices: 36342882--36342931 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
36342872 TTTTTATTTT
36342882 GATGTTGATGCTATG-TTGGACTTTA
1 GATGTTGATGCTA-GATTGGACTTTA
*
36342907 GATGTTGGTGCTAGATTGGACTTTA
1 GATGTTGATGCTAGATTGGACTTTA
36342932 AAAGTAAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.20, C:0.08, G:0.30, T:0.42
Consensus pattern (25 bp):
GATGTTGATGCTAGATTGGACTTTA
Found at i:36346881 original size:15 final size:14
Alignment explanation
Indices: 36346854--36346888 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
36346844 AATTATAACA
36346854 ATATTATAATTATC
1 ATATTATAATTATC
*
36346868 ATATTATAAATTATT
1 ATATTAT-AATTATC
36346883 ATATTA
1 ATATTA
36346889 ATTATAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATTATAATTATC
Found at i:36347618 original size:80 final size:80
Alignment explanation
Indices: 36347485--36347635 Score: 257
Period size: 80 Copynumber: 1.9 Consensus size: 80
36347475 GTAGTTCTGG
* * *
36347485 TCAAGCTGGAATTGGAGGTGTGCTTCAAGACTATCATGGTGTTATAAAAAGCCAAATTCTGTAAA
1 TCAAGCTGGAATTGGAGGTGTGCTTCAAGACAACCATGGTGTTATAAAAAGCCAAATTCTCTAAA
36347550 GCCATGGGATTCTCA
66 GCCATGGGATTCTCA
*
36347565 TCAAGCTGGAATTGGAGGTGTGCTTCGAGACAACCATGGTGTTATAAAAAGCCAAATTCTCTAAA
1 TCAAGCTGGAATTGGAGGTGTGCTTCAAGACAACCATGGTGTTATAAAAAGCCAAATTCTCTAAA
*
36347630 GTCATG
66 GCCATG
36347636 TGAATTGTGG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (80 bp):
TCAAGCTGGAATTGGAGGTGTGCTTCAAGACAACCATGGTGTTATAAAAAGCCAAATTCTCTAAA
GCCATGGGATTCTCA
Found at i:36348442 original size:33 final size:33
Alignment explanation
Indices: 36348400--36348469 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 33
36348390 ATTAAAATAA
36348400 AAAACATTAAAATAAAATATATAATATAA-AAATC
1 AAAACATTAAAATAAAATA-A-AATATAAGAAATC
*
36348434 AAAA-ATTAAAATAAAATAAAATATAAGAAATT
1 AAAACATTAAAATAAAATAAAATATAAGAAATC
36348466 AAAA
1 AAAA
36348470 TTTATATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
31 7 0.21
32 9 0.26
33 14 0.41
34 4 0.12
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.24
Consensus pattern (33 bp):
AAAACATTAAAATAAAATAAAATATAAGAAATC
Found at i:36348470 original size:25 final size:24
Alignment explanation
Indices: 36348392--36348470 Score: 63
Period size: 25 Copynumber: 3.0 Consensus size: 24
36348382 ACGTTATAAT
*
36348392 TAAAATAAAAAACATTAAAA-TAAAA
1 TAAAATAAAAATCA--AAAATTAAAA
36348417 TATATAATATAAAAATCAAAAATTAAAA
1 TA-A-AATA-AAAA-TCAAAAATTAAAA
36348445 TAAAATAAAATAT-AAGAAATTAAAA
1 TAAAATAAAA-ATCAA-AAATTAAAA
36348470 T
1 T
36348471 TTATATAATA
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
24 2 0.04
25 16 0.35
26 6 0.13
27 9 0.20
28 11 0.24
29 2 0.04
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.25
Consensus pattern (24 bp):
TAAAATAAAAATCAAAAATTAAAA
Found at i:36348533 original size:13 final size:13
Alignment explanation
Indices: 36348488--36348535 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
36348478 ATATAGGTAA
*
36348488 AAAAAATTAAAAT
1 AAAAAATTATAAT
*
36348501 AAAATA-TATAAT
1 AAAAAATTATAAT
*
36348513 ATAAAAATTATATT
1 A-AAAAATTATAAT
36348527 AAAAAATTA
1 AAAAAATTA
36348536 AAAAATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 6 0.21
13 17 0.59
14 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAAATTATAAT
Found at i:36348622 original size:67 final size:67
Alignment explanation
Indices: 36348491--36348622 Score: 144
Period size: 67 Copynumber: 2.0 Consensus size: 67
36348481 TAGGTAAAAA
* * * *
36348491 AAATTAAAATAAAATATATAATATAAAAATTATATTAAAAAATTAAAAAATATAAGATTATAATA
1 AAATAAAAATAAAATATATAATATAAAAATTATATTAAAAAATGAAAAAATATAAAAATATAATA
36348556 GG
66 GG
* * **
36348558 AAATAAAAATAAAATATATGACAT-TAAAAA-TATATTTAAAAGATGATATTATATAAAAAT-TA
1 AAATAAAAATAAAATATAT-A-ATATAAAAATTATA-TTAAAAAATGAAAAAATATAAAAATATA
36348620 ATA
63 ATA
36348623 ATAAAAAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
67 27 0.50
68 25 0.46
69 2 0.04
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.32
Consensus pattern (67 bp):
AAATAAAAATAAAATATATAATATAAAAATTATATTAAAAAATGAAAAAATATAAAAATATAATA
GG
Found at i:36348813 original size:15 final size:15
Alignment explanation
Indices: 36348793--36348850 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
36348783 TACTTTCCCC
*
36348793 GCAATCACATTGCTT
1 GCAATCACATTACTT
36348808 GCAATCACATTACTT
1 GCAATCACATTACTT
*
36348823 GCAATCACATTACCT
1 GCAATCACATTACTT
*
36348838 GTAATCACATTAC
1 GCAATCACATTAC
36348851 ATTGTAAAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.33, C:0.28, G:0.09, T:0.31
Consensus pattern (15 bp):
GCAATCACATTACTT
Found at i:36349997 original size:7 final size:7
Alignment explanation
Indices: 36349985--36350139 Score: 109
Period size: 7 Copynumber: 21.9 Consensus size: 7
36349975 TTAATATTAC
36349985 AGGGTTT
1 AGGGTTT
36349992 AGGGTTT
1 AGGGTTT
*
36349999 -GGGATT
1 AGGGTTT
*
36350005 AGGGGTT
1 AGGGTTT
36350012 AGGGTTT
1 AGGGTTT
*
36350019 GGGGTTT
1 AGGGTTT
* *
36350026 GGGGGTT
1 AGGGTTT
*
36350033 GGGGTTT
1 AGGGTTT
36350040 -GAGGTTT
1 AG-GGTTT
36350047 AGGGTTT
1 AGGGTTT
*
36350054 AGGGGTT
1 AGGGTTT
*
36350061 GGGGTTT
1 AGGGTTT
*
36350068 -GGGGTT
1 AGGGTTT
*
36350074 AGGGGTT
1 AGGGTTT
*
36350081 GGGGTTT
1 AGGGTTT
*
36350088 GGGGGTTT
1 -AGGGTTT
36350096 AGGGTTT
1 AGGGTTT
36350103 AGAAGGTTT
1 AG--GGTTT
36350112 AGGGTTTT
1 AGGG-TTT
*
36350120 AGGGGTT
1 AGGGTTT
* *
36350127 AAGGTTG
1 AGGGTTT
36350134 AGGGTT
1 AGGGTT
36350140 GAAGGTTTTT
Statistics
Matches: 122, Mismatches: 18, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
6 11 0.09
7 89 0.73
8 15 0.12
9 7 0.06
ACGTcount: A:0.12, C:0.00, G:0.51, T:0.37
Consensus pattern (7 bp):
AGGGTTT
Found at i:36350010 original size:21 final size:21
Alignment explanation
Indices: 36349986--36350102 Score: 114
Period size: 20 Copynumber: 5.6 Consensus size: 21
36349976 TAATATTACA
*
36349986 GGGTTTAGGGTTTGGGATTAG
1 GGGTTTAGGGTTTGGGGTTAG
*
36350007 GGG-TTAGGGTTTGGGGTTTG
1 GGGTTTAGGGTTTGGGGTTAG
* * *
36350027 GGGGTTGGGGTTTGAGGTTTA-
1 GGGTTTAGGGTTTG-GGGTTAG
* *
36350048 GGGTTTAGGGGTTGGGGTTTG
1 GGGTTTAGGGTTTGGGGTTAG
* *
36350069 GGG-TTAGGGGTTGGGGTTTGG
1 GGGTTTAGGGTTTGGGG-TTAG
36350090 GGGTTTAGGGTTT
1 GGGTTTAGGGTTT
36350103 AGAAGGTTTA
Statistics
Matches: 79, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
20 35 0.44
21 32 0.41
22 12 0.15
ACGTcount: A:0.08, C:0.00, G:0.54, T:0.38
Consensus pattern (21 bp):
GGGTTTAGGGTTTGGGGTTAG
Found at i:36350900 original size:7 final size:7
Alignment explanation
Indices: 36350873--36350923 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
36350863 CTTGCTGTTG
*
36350873 AGGGTTG
1 AGGGTTT
*
36350880 AGGGTTG
1 AGGGTTT
*
36350887 AAGGTTT
1 AGGGTTT
36350894 AGGGTTT
1 AGGGTTT
36350901 A-GGTTT
1 AGGGTTT
*
36350907 A-AGTTT
1 AGGGTTT
36350913 AGGGTTT
1 AGGGTTT
36350920 AGGG
1 AGGG
36350924 CTTTTTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
6 11 0.29
7 27 0.71
ACGTcount: A:0.20, C:0.00, G:0.43, T:0.37
Consensus pattern (7 bp):
AGGGTTT
Found at i:36357253 original size:6 final size:7
Alignment explanation
Indices: 36357207--36357413 Score: 112
Period size: 7 Copynumber: 30.3 Consensus size: 7
36357197 TTCAAGTGTT
36357207 GGTTTAG
1 GGTTTAG
*
36357214 GGTTTGG
1 GGTTTAG
*
36357221 GGTTTAA
1 GGTTTAG
36357228 GGTTTAAG
1 GGTTT-AG
36357236 GGTTTAG
1 GGTTTAG
36357243 GGTTT-G
1 GGTTTAG
36357249 GGTTT--
1 GGTTTAG
36357254 GGTGTTAG
1 GGT-TTAG
36357262 GG-TTAG
1 GGTTTAG
36357268 GGTTTAG
1 GGTTTAG
*
36357275 GGGTTAG
1 GGTTTAG
*
36357282 GGTATA-
1 GGTTTAG
* *
36357288 AGATTA-
1 GGTTTAG
*
36357294 AGTTTA-
1 GGTTTAG
36357300 GGTTTAG
1 GGTTTAG
36357307 GGTTTAGG
1 GGTTTA-G
***
36357315 GGTCGGG
1 GGTTTAG
*
36357322 GGTTTGG
1 GGTTTAG
36357329 GGTTGT-G
1 GGTT-TAG
*
36357336 GGTTTGG
1 GGTTTAG
*
36357343 GGGTTAG
1 GGTTTAG
36357350 GAG-TTA-
1 G-GTTTAG
*
36357356 GGTTGAG
1 GGTTTAG
36357363 GGTTTAG
1 GGTTTAG
36357370 GGTTTAG
1 GGTTTAG
*
36357377 GGGTT-G
1 GGTTTAG
*
36357383 AGTTTAG
1 GGTTTAG
*
36357390 GGTTTGGG
1 GGTTT-AG
*
36357398 GGTTTGG
1 GGTTTAG
*
36357405 GGGTTAG
1 GGTTTAG
36357412 GG
1 GG
36357414 GTTTTGGGNA
Statistics
Matches: 158, Mismatches: 28, Indels: 28
0.74 0.13 0.13
Matches are distributed among these distances:
5 4 0.03
6 35 0.22
7 99 0.63
8 20 0.13
ACGTcount: A:0.14, C:0.00, G:0.48, T:0.38
Consensus pattern (7 bp):
GGTTTAG
Found at i:36357399 original size:20 final size:20
Alignment explanation
Indices: 36357364--36357401 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
36357354 TAGGTTGAGG
36357364 GTTTAGGGTTTAGGGGTTGA
1 GTTTAGGGTTTAGGGGTTGA
*
36357384 GTTTAGGGTTTGGGGGTT
1 GTTTAGGGTTTAGGGGTT
36357402 TGGGGGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.47, T:0.42
Consensus pattern (20 bp):
GTTTAGGGTTTAGGGGTTGA
Found at i:36357406 original size:27 final size:26
Alignment explanation
Indices: 36357308--36357411 Score: 83
Period size: 27 Copynumber: 4.0 Consensus size: 26
36357298 TAGGTTTAGG
* *
36357308 GTTTAGGGGTCGGGGGTTTGGGGTT-
1 GTTTAGGGTTTGGGGGTTTGGGGTTA
* *
36357333 G--T-GGGTTTGGGGGTTAGGAGTTA
1 GTTTAGGGTTTGGGGGTTTGGGGTTA
* *
36357356 GGTTGAGGGTTT-AGGGTTTAGGGGTTGA
1 -GTTTAGGGTTTGGGGGTTT-GGGGTT-A
36357384 GTTTAGGGTTTGGGGGTTTGGGGGTTA
1 GTTTAGGGTTTGGGGGTTT-GGGGTTA
36357411 G
1 G
36357412 GGGTTTTGGG
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
22 16 0.27
23 1 0.02
24 1 0.02
25 1 0.02
26 5 0.08
27 23 0.38
28 13 0.22
ACGTcount: A:0.10, C:0.01, G:0.53, T:0.37
Consensus pattern (26 bp):
GTTTAGGGTTTGGGGGTTTGGGGTTA
Found at i:36364223 original size:32 final size:34
Alignment explanation
Indices: 36364177--36364294 Score: 165
Period size: 32 Copynumber: 3.6 Consensus size: 34
36364167 TTTAGTTTAG
36364177 TTTAGTTTAGTTTAGTTTATTTATTTATTTTAT-
1 TTTAGTTTAGTTTAGTTTATTTATTTATTTTATA
*
36364210 TTTA-TTTAGTTTAGTTTATTTATTTATTTATTTA
1 TTTAGTTTAGTTTAGTTTATTTATTTATTT-TATA
*
36364244 TTTA-TTTAGTTTTAGTTTAGTT-TTTATTTT-TA
1 TTTAGTTTAG-TTTAGTTTATTTATTTATTTTATA
36364276 TTTAGTTTAGTTTAGTTTA
1 TTTAGTTTAGTTTAGTTTA
Statistics
Matches: 79, Mismatches: 2, Indels: 9
0.88 0.02 0.10
Matches are distributed among these distances:
32 40 0.51
33 12 0.15
34 16 0.20
35 11 0.14
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.69
Consensus pattern (34 bp):
TTTAGTTTAGTTTAGTTTATTTATTTATTTTATA
Found at i:36364259 original size:6 final size:5
Alignment explanation
Indices: 36364166--36364294 Score: 125
Period size: 5 Copynumber: 27.0 Consensus size: 5
36364156 TTTTGTTTTG
* *
36364166 GTTTA GTTTA GTTTA GTTTA GTTTA GTTTA -TTTA -TTTA TTTTA TTTTA
1 GTTTA GTTTA GTTTA GTTTA GTTTA GTTTA GTTTA GTTTA GTTTA GTTTA
36364214 -TTTA GTTTA GTTTA -TTTA -TTTA -TTTA -TTTA -TTTA -TTTA GTTTTA
1 GTTTA GTTTA GTTTA GTTTA GTTTA GTTTA GTTTA GTTTA GTTTA G-TTTA
*
36364258 GTTTA GTTTTTA TTTTTA -TTTA GTTTA GTTTA GTTTA
1 GTTTA G--TTTA -GTTTA GTTTA GTTTA GTTTA GTTTA
Statistics
Matches: 115, Mismatches: 1, Indels: 16
0.87 0.01 0.12
Matches are distributed among these distances:
4 40 0.35
5 62 0.54
6 9 0.08
7 4 0.03
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (5 bp):
GTTTA
Done.