Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 80 of 103
Found at i:29961225 original size:94 final size:92
Alignment explanation
Indices: 29961126--29961296 Score: 227
Period size: 92 Copynumber: 1.8 Consensus size: 92
29961116 TTACATTAAT
* * * * *
29961126 AAAATATTTCATGAAATATTCTAATTCCATAATA-TTTTTGTTCAAAATCATCAAAATTGAAAGT
1 AAAATATTTCATGAAATATTCCAATTCCAT--TACTTTAT-ATCAAAATCAACAAAATTGAAAAT
*
29961190 ATAGTTACAAAATTTGTCATTTGTATTACC
63 ATAGTGACAAAATTTGTCATTTGTATTACC
* *
29961220 AAAATATTTCGTGAAATATTCCAATTCCATTACTTTATATCAATATCAACAAAATTGAAAATATA
1 AAAATATTTCATGAAATATTCCAATTCCATTACTTTATATCAAAATCAACAAAATTGAAAATATA
*
29961285 GTGATAAAATTT
66 GTGACAAAATTT
29961297 AATAAAATTA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
92 35 0.52
93 4 0.06
94 28 0.42
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.39
Consensus pattern (92 bp):
AAAATATTTCATGAAATATTCCAATTCCATTACTTTATATCAAAATCAACAAAATTGAAAATATA
GTGACAAAATTTGTCATTTGTATTACC
Found at i:29962460 original size:35 final size:35
Alignment explanation
Indices: 29962359--29962547 Score: 195
Period size: 35 Copynumber: 5.4 Consensus size: 35
29962349 ATTAAACAAT
* *
29962359 TTAATTAAAAAATTTTAATCAATTAGGCCCAATAAC
1 TTAATTAAATAA-TTTAATTAATTAGGCCCAATAAC
* * * *
29962395 TTAATTAAACAAACTTAATCAATTAAGCCCAATAAC
1 TTAATTAAA-TAATTTAATTAATTAGGCCCAATAAC
*** *
29962431 TTAATTGTTTAATTTAATTAATTAGGCCCAATGAC
1 TTAATTAAATAATTTAATTAATTAGGCCCAATAAC
* * * *
29962466 TTAATTAAACAATTTAATTAATTAGGCCTAATGAT
1 TTAATTAAATAATTTAATTAATTAGGCCCAATAAC
*
29962501 TTAATTAAATAATTTAATTAATTAGG--C-ACAAC
1 TTAATTAAATAATTTAATTAATTAGGCCCAATAAC
*
29962533 TTAATTAAACAATTT
1 TTAATTAAATAATTT
29962548 TAATCAAGTG
Statistics
Matches: 130, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
32 16 0.12
35 75 0.58
36 36 0.28
37 3 0.02
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.37
Consensus pattern (35 bp):
TTAATTAAATAATTTAATTAATTAGGCCCAATAAC
Found at i:29962520 original size:70 final size:69
Alignment explanation
Indices: 29962356--29962554 Score: 231
Period size: 70 Copynumber: 2.8 Consensus size: 69
29962346 TTAATTAAAC
* * *
29962356 AATTTAATTAAAAAATTTTAATCAATTAGGCCCAATAACTTAATTAAACAAACTTAATCAATTAA
1 AATTTAATTAAATAA-TTTAATTAATTAGGCCCAAT-ACTTAATTAAAC-AATTTAATCAATTAA
29962421 GCCCAAT
63 GCCCAAT
* *** * *
29962428 AACTTAATTGTTTAATTTAATTAATTAGGCCCAATGACTTAATTAAACAATTTAATTAATTAGGC
1 AATTTAATTAAATAATTTAATTAATTAGGCCCAAT-ACTTAATTAAACAATTTAATCAATTAAGC
*
29962493 CTAAT
65 CCAAT
* *
29962498 GATTTAATTAAATAATTTAATTAATTAGGCAC-A-ACTTAATTAAACAATTTTAATCAA
1 AATTTAATTAAATAATTTAATTAATTAGGCCCAATACTTAATTAAACAA-TTTAATCAA
29962555 GTGCTTGAGA
Statistics
Matches: 108, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
67 14 0.13
68 8 0.07
69 1 0.01
70 44 0.41
71 31 0.29
72 10 0.09
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (69 bp):
AATTTAATTAAATAATTTAATTAATTAGGCCCAATACTTAATTAAACAATTTAATCAATTAAGCC
CAAT
Found at i:29965071 original size:17 final size:17
Alignment explanation
Indices: 29965049--29965105 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
29965039 AAACTTTATG
29965049 TTATATAAAAATACTTT
1 TTATATAAAAATACTTT
**
29965066 TTATATTTTCAAA-A-TTT
1 TTATA--TAAAAATACTTT
*
29965083 TNATATAAAAATACTTT
1 TTATATAAAAATACTTT
29965100 TTATAT
1 TTATAT
29965106 TTTCAAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
15 4 0.13
16 1 0.03
17 20 0.67
18 1 0.03
19 4 0.13
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
TTATATAAAAATACTTT
Found at i:29975474 original size:24 final size:24
Alignment explanation
Indices: 29975401--29975495 Score: 75
Period size: 24 Copynumber: 3.7 Consensus size: 24
29975391 TTATTATTAA
*
29975401 TTTTATATAATATAACTTTTAATATAT
1 TTTTAT-TAATATAA-TTTT-ATTTAT
* *
29975428 TTTTAATGTCATATATTTATTATTT-T
1 TTTT-AT-TAATATAATT-TTATTTAT
*
29975454 TATTTATTATTATAATTTTATTTAT
1 T-TTTATTAATATAATTTTATTTAT
*
29975479 TTTTTTTAATATAATTT
1 TTTTATTAATATAATTT
29975496 CTTATATTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
24 20 0.36
25 9 0.16
26 4 0.07
27 12 0.22
28 10 0.18
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (24 bp):
TTTTATTAATATAATTTTATTTAT
Found at i:29975505 original size:27 final size:28
Alignment explanation
Indices: 29975445--29975515 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 28
29975435 GTCATATATT
29975445 TATTATTTTTATTTATTATTATAATTTTA
1 TATTATTTTTATTTA-TATTATAATTTTA
29975474 T-TTATTTTT-TTTA-A-TATAATTTCTTA
1 TATTATTTTTATTTATATTATAA-TT-TTA
29975500 TATTATATATTTATTT
1 TATTAT-T-TTTATTT
29975516 TAATTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
24 5 0.14
25 3 0.08
26 4 0.11
27 8 0.22
28 9 0.25
29 4 0.11
30 3 0.08
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (28 bp):
TATTATTTTTATTTATATTATAATTTTA
Found at i:29980191 original size:12 final size:12
Alignment explanation
Indices: 29980174--29980199 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29980164 ATATATGGCC
29980174 ATCTTATTAATT
1 ATCTTATTAATT
29980186 ATCTTATTAATT
1 ATCTTATTAATT
29980198 AT
1 AT
29980200 AATAGCTGTT
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:0.08, G:0.00, T:0.58
Consensus pattern (12 bp):
ATCTTATTAATT
Found at i:29983817 original size:33 final size:34
Alignment explanation
Indices: 29983775--29983839 Score: 114
Period size: 35 Copynumber: 1.9 Consensus size: 34
29983765 ATTAGCATGG
29983775 GGCTACCCTA-GCTCCCATTGGCATAGCTATGTC
1 GGCTACCCTACGCTCCCATTGGCATAGCTATGTC
29983808 GGCTACCCTAGCGCTCCCATTGGCATAGCTAT
1 GGCTACCCTA-CGCTCCCATTGGCATAGCTAT
29983840 ATGTAGCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 10 0.33
35 20 0.67
ACGTcount: A:0.18, C:0.34, G:0.22, T:0.26
Consensus pattern (34 bp):
GGCTACCCTACGCTCCCATTGGCATAGCTATGTC
Found at i:29983925 original size:23 final size:24
Alignment explanation
Indices: 29983895--29983945 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
29983885 ACTGACTGAG
29983895 AAAG-GAAGG-AAAAAAAAAGAAA
1 AAAGAGAAGGAAAAAAAAAAGAAA
*
29983917 AAAGAGAAGGAAAAAAAAAATAAA
1 AAAGAGAAGGAAAAAAAAAAGAAA
29983941 AAAGA
1 AAAGA
29983946 AAGAGGAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 4 0.15
23 5 0.19
24 17 0.65
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (24 bp):
AAAGAGAAGGAAAAAAAAAAGAAA
Found at i:29983952 original size:25 final size:24
Alignment explanation
Indices: 29983900--29983953 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
29983890 CTGAGAAAGG
*
29983900 AAGG-AAAAAAAAAGAAAAAAGAG
1 AAGGAAAAAAAAAAGAAAAAAGAA
*
29983923 AAGGAAAAAAAAAATAAAAAAGAA
1 AAGGAAAAAAAAAAGAAAAAAGAA
29983947 AGAGGAA
1 A-AGGAA
29983954 GGACAACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 4 0.15
24 18 0.67
25 5 0.19
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (24 bp):
AAGGAAAAAAAAAAGAAAAAAGAA
Found at i:29984070 original size:24 final size:26
Alignment explanation
Indices: 29984038--29984107 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 26
29984028 GATAAAAAGG
29984038 AAAAAAAAAAAAGAAGAA-AAGGAAA
1 AAAAAAAAAAAAGAAGAAGAAGGAAA
*
29984063 AAAAAAAAACAACA-AAGAAGATGGAAA
1 AAAAAAAAA-AA-AGAAGAAGAAGGAAA
29984090 AAGAAAAAAAAAAGAAGA
1 AA-AAAAAAAAAAGAAGA
29984108 GAAAATGGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
25 9 0.23
26 8 0.21
27 15 0.38
28 7 0.18
ACGTcount: A:0.80, C:0.03, G:0.16, T:0.01
Consensus pattern (26 bp):
AAAAAAAAAAAAGAAGAAGAAGGAAA
Found at i:29984079 original size:21 final size:22
Alignment explanation
Indices: 29984032--29984074 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
29984022 TTAAATGATA
*
29984032 AAAAGGAAAAAAAAAAAAGAAG
1 AAAAGGAAAAAAAAAAAACAAG
29984054 AAAAGGAAAAAAAAAAAACAA
1 AAAAGGAAAAAAAAAAAACAA
29984075 CAAAGAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAAGGAAAAAAAAAAAACAAG
Found at i:29984110 original size:29 final size:27
Alignment explanation
Indices: 29984038--29984117 Score: 94
Period size: 25 Copynumber: 3.0 Consensus size: 27
29984028 GATAAAAAGG
29984038 AAAAAAAAAAAAGAAGA-AAA-GGAAA
1 AAAAAAAAAAAAGAAGAGAAATGGAAA
* *
29984063 AAAAAAAAACAACAA-AGAAGATGGAAA
1 AAAAAAAAAAAAGAAGAGAA-ATGGAAA
29984090 AAGAAAAAAAAAAGAAGAGAAAATGGAA
1 AA-AAAAAAAAAAGAAGAG-AAATGGAA
29984118 TGACAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
24 1 0.02
25 15 0.33
26 1 0.02
27 7 0.16
28 11 0.24
29 8 0.18
30 2 0.04
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.03
Consensus pattern (27 bp):
AAAAAAAAAAAAGAAGAGAAATGGAAA
Found at i:29996982 original size:6 final size:6
Alignment explanation
Indices: 29996968--29997013 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
29996958 AAGTATATTA
* *
29996968 TTTTGC TTTTAC TTTTTC TTTT-C TTTT-- TTTTAC TTTTAC TTTTAC
1 TTTTAC TTTTAC TTTTAC TTTTAC TTTTAC TTTTAC TTTTAC TTTTAC
29997013 T
1 T
29997014 GAAAAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
4 4 0.11
5 5 0.14
6 27 0.75
ACGTcount: A:0.09, C:0.15, G:0.02, T:0.74
Consensus pattern (6 bp):
TTTTAC
Found at i:29997450 original size:32 final size:32
Alignment explanation
Indices: 29997414--29997482 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
29997404 TTTTGTGTGG
29997414 CATTTTCTGGGTTTTGATTCTTTTTTTCTTTT
1 CATTTTCTGGGTTTTGATTCTTTTTTTCTTTT
* * *
29997446 CATTTTGTGGGTTTTTATTGTTTTTTTCTTTT
1 CATTTTCTGGGTTTTGATTCTTTTTTTCTTTT
*
29997478 TATTT
1 CATTT
29997483 ATGATTCAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.07, C:0.09, G:0.13, T:0.71
Consensus pattern (32 bp):
CATTTTCTGGGTTTTGATTCTTTTTTTCTTTT
Found at i:30006513 original size:266 final size:266
Alignment explanation
Indices: 30006039--30006837 Score: 1562
Period size: 266 Copynumber: 3.0 Consensus size: 266
30006029 GGAAACTCTG
30006039 GGTCAGGTAATTTGCTTCTCTCTCTTTCTAAAATGAATCACACACATGCACATATAACAAAATAT
1 GGTCAGGTAATTTGCTTCTCTCTCTTTCTAAAATGAATCACACACATGCACATATAACAAAATAT
*
30006104 AGTAAGAATTTAGGGGTTTCATGAAACTCGTTGATCGTAATTTCATTTAGTTGGTATACTGAAGC
66 AGTAAGAATTTAGGGGTTTCATGAAACTCGTTGATCGTAATTTCATTTAGTTGGTATACTGAAAC
30006169 TCTAGTTATTCACGATTAGATGCTTGATGGCCATGAGAATACCTTGGAAGTTTCAACCAGCCAAC
131 TCTAGTTATTCACGATTAGATGCTTGATGGCCATGAGAATACCTTGGAAGTTTCAACCAGCCAAC
30006234 AACAAAGAAGTCCATTGAAGCAGAAAACTCTGGATTCTTTCACGAAGCGCTGTAACAGCATCGAT
196 AACAAAGAAGTCCATTGAAGCAGAAAACTCTGGATTCTTTCACGAAGCGCTGTAACAGCATCGAT
30006299 GATGCT
261 GATGCT
30006305 GGTCAGGTAATTTGCTTCTCTCTCTTTCTAAAATGAATCACACACATGCACATATAACAAAATAT
1 GGTCAGGTAATTTGCTTCTCTCTCTTTCTAAAATGAATCACACACATGCACATATAACAAAATAT
30006370 AGTAAGAATTTAGGGGTTTCATGAAACTCGTTGATCGTAATTTCATTTAGTTGGTATACTGAAAC
66 AGTAAGAATTTAGGGGTTTCATGAAACTCGTTGATCGTAATTTCATTTAGTTGGTATACTGAAAC
*
30006435 TCTAGTTATTCATGATTAGATGCTTGATGGCCATGAGAATACCTTGGAAGTTTCAACCAGCCAAC
131 TCTAGTTATTCACGATTAGATGCTTGATGGCCATGAGAATACCTTGGAAGTTTCAACCAGCCAAC
30006500 AACAAAGAAGTCCATTGAAGCAGAAAACTCTGGATTCTTTCACGAAGCGCTGTAACAGCATCGAT
196 AACAAAGAAGTCCATTGAAGCAGAAAACTCTGGATTCTTTCACGAAGCGCTGTAACAGCATCGAT
30006565 GATGCT
261 GATGCT
30006571 GGTCAGGTAATTTGCTTCTCTCTCTTTCTAAAATGAATCACACACATGCACATATAACAAAATAT
1 GGTCAGGTAATTTGCTTCTCTCTCTTTCTAAAATGAATCACACACATGCACATATAACAAAATAT
30006636 AGTAAGAATTTAGGGGTTTCATGAAACTCGTTGATCGTAATTTCATTTAGTTGGTATACTGAAAC
66 AGTAAGAATTTAGGGGTTTCATGAAACTCGTTGATCGTAATTTCATTTAGTTGGTATACTGAAAC
30006701 TCTAGTTATTCACGATTAGATGCTTGATGGCCATGAGAATACCTTGGAAGTTTCAACCAGCCAAC
131 TCTAGTTATTCACGATTAGATGCTTGATGGCCATGAGAATACCTTGGAAGTTTCAACCAGCCAAC
* *
30006766 AACAAAGAAGTCCACTGAAGCAGAAAACTCTGGATTCTTTCATGAAGCGCTGTAACAGCATCGAT
196 AACAAAGAAGTCCATTGAAGCAGAAAACTCTGGATTCTTTCACGAAGCGCTGTAACAGCATCGAT
30006831 GATGCT
261 GATGCT
30006837 G
1 G
30006838 AACATCAATC
Statistics
Matches: 528, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
266 528 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (266 bp):
GGTCAGGTAATTTGCTTCTCTCTCTTTCTAAAATGAATCACACACATGCACATATAACAAAATAT
AGTAAGAATTTAGGGGTTTCATGAAACTCGTTGATCGTAATTTCATTTAGTTGGTATACTGAAAC
TCTAGTTATTCACGATTAGATGCTTGATGGCCATGAGAATACCTTGGAAGTTTCAACCAGCCAAC
AACAAAGAAGTCCATTGAAGCAGAAAACTCTGGATTCTTTCACGAAGCGCTGTAACAGCATCGAT
GATGCT
Found at i:30011778 original size:27 final size:28
Alignment explanation
Indices: 30011748--30011804 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
30011738 ATGGTTGGGG
* *
30011748 AATAGCTTTTA-AAAT-TGATAAGATTAA
1 AATAGCATTTATAAATGTGA-AAAATTAA
*
30011775 AATATCATTTATAAATGTGAAAAATTAA
1 AATAGCATTTATAAATGTGAAAAATTAA
30011803 AA
1 AA
30011805 CTCTAAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 9 0.36
28 13 0.52
29 3 0.12
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.35
Consensus pattern (28 bp):
AATAGCATTTATAAATGTGAAAAATTAA
Found at i:30012159 original size:8 final size:8
Alignment explanation
Indices: 30012146--30012173 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
30012136 TCGACAAGGA
30012146 AAAAAAAG
1 AAAAAAAG
30012154 AAAAAAAG
1 AAAAAAAG
30012162 AAAAAAAG
1 AAAAAAAG
30012170 AAAA
1 AAAA
30012174 TTGATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:30012259 original size:37 final size:37
Alignment explanation
Indices: 30012180--30012270 Score: 91
Period size: 37 Copynumber: 2.5 Consensus size: 37
30012170 AAAATTGATT
* *
30012180 TAAAATTAAAAGTTTAA-AAATTAATTTTTAAATGATA
1 TAAAATTAAAATTTTAATAAATTAATGTTTAAAT-ATA
*
30012217 AAAAATTAAAATTTTAATTATAA-TAATGTTTAAAT-TA
1 TAAAATTAAAATTTTAA-TA-AATTAATGTTTAAATATA
*
30012254 TAAAA-TAAAATATTAAT
1 TAAAATTAAAATTTTAAT
30012271 GTTTAACTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
35 1 0.02
36 10 0.22
37 21 0.46
39 12 0.26
40 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (37 bp):
TAAAATTAAAATTTTAATAAATTAATGTTTAAATATA
Found at i:30012322 original size:19 final size:19
Alignment explanation
Indices: 30012279--30012324 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
30012269 ATGTTTAACT
*
30012279 TATTAAA-TTTTATTAATA
1 TATTAAATTTTTATTAAAA
30012297 TATTAAATTTTTATTAAAA
1 TATTAAATTTTTATTAAAA
30012316 -ATATAAATT
1 TAT-TAAATT
30012325 AAAAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TATTAAATTTTTATTAAAA
Found at i:30015290 original size:18 final size:18
Alignment explanation
Indices: 30015240--30015324 Score: 59
Period size: 18 Copynumber: 4.7 Consensus size: 18
30015230 AGGGATCAGT
* *
30015240 GAGGAAGAAGGAGAGCAA
1 GAGGAAGGAGGAGAGGAA
* *
30015258 GAGGAAGGTA-CAGAGGGA
1 GAGGAAGG-AGGAGAGGAA
*
30015276 GAGGAAGGAGGAGAGGAT
1 GAGGAAGGAGGAGAGGAA
* *
30015294 GAGGATTGCA-GAGATGGAA
1 GAGGA-AGGAGGAGA-GGAA
30015313 -AGGAAGGAGGAG
1 GAGGAAGGAGGAG
30015325 TTGAAGCATC
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
17 3 0.06
18 41 0.82
19 6 0.12
ACGTcount: A:0.41, C:0.04, G:0.49, T:0.06
Consensus pattern (18 bp):
GAGGAAGGAGGAGAGGAA
Found at i:30020172 original size:25 final size:25
Alignment explanation
Indices: 30020144--30020192 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
30020134 TTAATAATTG
30020144 ATAATTAAATATTAATATTTTATTT
1 ATAATTAAATATTAATATTTTATTT
*
30020169 ATAATTTAATATTAATATTTTATT
1 ATAATTAAATATTAATATTTTATT
30020193 AAAAGTTGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
ATAATTAAATATTAATATTTTATTT
Found at i:30020183 original size:32 final size:31
Alignment explanation
Indices: 30020127--30020187 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
30020117 ATTTATAATT
*
30020127 TATTTTATTAATAATTGATAATTAAATATTAA
1 TATTTTATTAATAATTAATAATT-AATATTAA
*
30020159 TATTTTATTTATAATTTAAT-ATTAATATT
1 TATTTTATTAATAA-TTAATAATTAATATT
30020188 TTATTAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 6 0.23
32 16 0.62
33 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (31 bp):
TATTTTATTAATAATTAATAATTAATATTAA
Found at i:30021104 original size:54 final size:54
Alignment explanation
Indices: 30021040--30021201 Score: 306
Period size: 54 Copynumber: 3.0 Consensus size: 54
30021030 CAAACTTCGG
*
30021040 ACTCTTCTCCAAGGTAACAAAAATACTCTAAATTCCCTCTCTTTCATATTTTAA
1 ACTCTTCTCCAAGGTAACAAAAATACTCTAAATTCCCTCTCTTTCTTATTTTAA
30021094 ACTCTTCTCCAAGGTAACAAAAATACTCTAAATTCCCTCTCTTTCTTATTTTAA
1 ACTCTTCTCCAAGGTAACAAAAATACTCTAAATTCCCTCTCTTTCTTATTTTAA
*
30021148 ACTCTTCTCCAAGGTAACAATAATACTCTAAATTCCCTCTCTTTCTTATTTTAA
1 ACTCTTCTCCAAGGTAACAAAAATACTCTAAATTCCCTCTCTTTCTTATTTTAA
30021202 TAATTTTTCA
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 106 1.00
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (54 bp):
ACTCTTCTCCAAGGTAACAAAAATACTCTAAATTCCCTCTCTTTCTTATTTTAA
Found at i:30025035 original size:119 final size:121
Alignment explanation
Indices: 30024888--30025115 Score: 343
Period size: 119 Copynumber: 1.9 Consensus size: 121
30024878 TTATTATTAC
* * *
30024888 TATTTAAATAATGTTTTTAGAAATAAACATGAGGTGGAATGATATAGGCTGGAGACAAA-AG-GA
1 TATTTAAATAATATTTTTAGAAATAAACATGAGGTGGAATGATACAGGCTGCAGACAAAGAGAGA
* *
30024951 CACCAGGAATGGTTATAAATTACAGTTCCTTTGTGCAATTATAGGTTTTTTTTTAT
66 CACCAGGAATGGTTATAAATTACAGTTCCTATGTGAAATTATAGGTTTTTTTTTAT
* * *
30025007 TATTTAAATAATATTTTTGGTAATAAACATGAGGTGGAATGATACAGGGTGCAGACAAAGAGAGA
1 TATTTAAATAATATTTTTAGAAATAAACATGAGGTGGAATGATACAGGCTGCAGACAAAGAGAGA
* * *
30025072 CACCAGGGATGGTTATATATTTCAGTTCCTATGTGAAATTATAG
66 CACCAGGAATGGTTATAAATTACAGTTCCTATGTGAAATTATAG
30025116 TTATTATTAG
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
119 53 0.55
120 2 0.02
121 41 0.43
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (121 bp):
TATTTAAATAATATTTTTAGAAATAAACATGAGGTGGAATGATACAGGCTGCAGACAAAGAGAGA
CACCAGGAATGGTTATAAATTACAGTTCCTATGTGAAATTATAGGTTTTTTTTTAT
Found at i:30030751 original size:2 final size:2
Alignment explanation
Indices: 30030744--30030769 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30030734 NNNNTACTAC
30030744 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
30030770 AAATTCAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30032094 original size:7 final size:7
Alignment explanation
Indices: 30032082--30032106 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30032072 CCACCATATC
30032082 TTGGTGG
1 TTGGTGG
30032089 TTGGTGG
1 TTGGTGG
30032096 TTGGTGG
1 TTGGTGG
30032103 TTGG
1 TTGG
30032107 AGCTCTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.56, T:0.44
Consensus pattern (7 bp):
TTGGTGG
Found at i:30034490 original size:33 final size:33
Alignment explanation
Indices: 30034408--30034497 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 33
30034398 TACAAAATAT
* * *
30034408 GAAGACCAGCTAAGAGAGGAGATGAAGACGGGG
1 GAAGACCAACTAAGAGAGGAGAGGAAGACGGGC
* * *
30034441 GAAGGCCGACTAAGAGAGGAGAGGAAGACGGTC
1 GAAGACCAACTAAGAGAGGAGAGGAAGACGGGC
* *
30034474 GAAGATCAACTGAGAGAGGAGAGG
1 GAAGACCAACTAAGAGAGGAGAGG
30034498 CTTTTCGGGG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.39, C:0.12, G:0.42, T:0.07
Consensus pattern (33 bp):
GAAGACCAACTAAGAGAGGAGAGGAAGACGGGC
Found at i:30042845 original size:26 final size:27
Alignment explanation
Indices: 30042800--30042851 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
30042790 GGAAATTAGA
* *
30042800 AAATAAAAAAAGAGTTATGTATGTTGG
1 AAATAAAAAAAGAATCATGTATGTTGG
*
30042827 AAATAAAAAAA-AATCATGTTTGTTG
1 AAATAAAAAAAGAATCATGTATGTTG
30042852 AAAAAGATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.31
Consensus pattern (27 bp):
AAATAAAAAAAGAATCATGTATGTTGG
Found at i:30043506 original size:17 final size:17
Alignment explanation
Indices: 30043463--30043508 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
30043453 AGGAAAAAAA
30043463 ATTAAAAT-AAAA-TAT
1 ATTAAAATAAAAATTAT
*
30043478 A-TAATATAAAAAATTAT
1 ATTAAAAT-AAAAATTAT
30043495 ATTAAAATAAAAAT
1 ATTAAAATAAAAAT
30043509 AAAATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 5 0.20
15 1 0.04
16 4 0.16
17 10 0.40
18 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTAAAATAAAAATTAT
Found at i:30043506 original size:18 final size:17
Alignment explanation
Indices: 30043463--30043507 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
30043453 AGGAAAAAAA
30043463 ATTAAAAT--AAAATAT
1 ATTAAAATAAAAAATAT
*
30043478 A-TAATATAAAAAATTAT
1 ATTAAAATAAAAAA-TAT
30043495 ATTAAAATAAAAA
1 ATTAAAATAAAAA
30043508 TAAAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 5 0.21
15 1 0.04
16 4 0.17
17 4 0.17
18 10 0.42
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATTAAAATAAAAAATAT
Found at i:30043525 original size:31 final size:31
Alignment explanation
Indices: 30043463--30043555 Score: 123
Period size: 31 Copynumber: 3.0 Consensus size: 31
30043453 AGGAAAAAAA
* *
30043463 ATTAAAATAAAATATATAATATAAAAAATTAT
1 ATTAAAATAAAA-ATAAAATATATAAAATTAT
*
30043495 ATTAAAATAAAAATAAAATATATAAGATTAT
1 ATTAAAATAAAAATAAAATATATAAAATTAT
* * *
30043526 AATAAAATAAAAATAAAACATATAACATTA
1 ATTAAAATAAAAATAAAATATATAAAATTA
30043556 AAAATATATT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
31 43 0.78
32 12 0.22
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (31 bp):
ATTAAAATAAAAATAAAATATATAAAATTAT
Found at i:30043600 original size:68 final size:69
Alignment explanation
Indices: 30043460--30043600 Score: 153
Period size: 69 Copynumber: 2.1 Consensus size: 69
30043450 TAAAGGAAAA
* * * *
30043460 AAAATTAAAATAAAATATATAATATAAAAAATTATATTAAAATAAAAATAAAATATATAAGATTA
1 AAAATAAAAATAAAACATATAACATAAAAAATTATATTAAAATAAAAATAAAATATATAAAATTA
*
30043525 TAAT
66 CAAT
* * * **
30043529 AAAATAAAAATAAAACATATAACATTAAAAA-TATATTTAAGA-AATAATATTATATA-AAAATT
1 AAAATAAAAATAAAACATATAACATAAAAAATTATA-TTAAAATAAAAATAAAATATATAAAATT
30043591 AACAAT
65 -ACAAT
30043597 AAAA
1 AAAA
30043601 AATACAAATA
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
67 5 0.08
68 23 0.38
69 32 0.53
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (69 bp):
AAAATAAAAATAAAACATATAACATAAAAAATTATATTAAAATAAAAATAAAATATATAAAATTA
CAAT
Found at i:30043778 original size:15 final size:15
Alignment explanation
Indices: 30043758--30043801 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
30043748 CGTTATATTT
30043758 CTTACAATCACATTG
1 CTTACAATCACATTG
*
30043773 CTTACAATGACATTG
1 CTTACAATCACATTG
*
30043788 TTTACAATCACATT
1 CTTACAATCACATT
30043802 ATTTGTAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.36
Consensus pattern (15 bp):
CTTACAATCACATTG
Found at i:30051640 original size:38 final size:38
Alignment explanation
Indices: 30051589--30051664 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
30051579 TGTATACATA
30051589 GCAAAACTTAACAATTAAGCTTTGAACGGTAGCTAGGC
1 GCAAAACTTAACAATTAAGCTTTGAACGGTAGCTAGGC
30051627 GCAAAACTTAACAATTAAGCTTTGAACGGTAGCTAGGC
1 GCAAAACTTAACAATTAAGCTTTGAACGGTAGCTAGGC
30051665 ACAAGAATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (38 bp):
GCAAAACTTAACAATTAAGCTTTGAACGGTAGCTAGGC
Found at i:30055010 original size:11 final size:11
Alignment explanation
Indices: 30054994--30055035 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
30054984 AGAGGGCATC
30054994 GTGGGGGTGGT
1 GTGGGGGTGGT
30055005 GTGGGGGTGG-
1 GTGGGGGTGGT
*
30055015 G-GGGGTTGGT
1 GTGGGGGTGGT
30055025 GTGGGGTGTGG
1 GTGGGG-GTGG
30055036 CTTGGGGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 7 0.27
10 2 0.08
11 14 0.54
12 3 0.12
ACGTcount: A:0.00, C:0.00, G:0.74, T:0.26
Consensus pattern (11 bp):
GTGGGGGTGGT
Found at i:30055020 original size:19 final size:21
Alignment explanation
Indices: 30054996--30055035 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
30054986 AGGGCATCGT
30054996 GGGGG-TGGTGTGGGG-GTGG
1 GGGGGTTGGTGTGGGGTGTGG
30055015 GGGGGTTGGTGTGGGGTGTGG
1 GGGGGTTGGTGTGGGGTGTGG
30055036 CTTGGGGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 10 0.53
21 4 0.21
ACGTcount: A:0.00, C:0.00, G:0.75, T:0.25
Consensus pattern (21 bp):
GGGGGTTGGTGTGGGGTGTGG
Found at i:30062365 original size:24 final size:24
Alignment explanation
Indices: 30062338--30062384 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
30062328 AGACATAAAA
30062338 ATTTTTATATCTTAAATGTATCGT
1 ATTTTTATATCTTAAATGTATCGT
30062362 ATTTTTATATCTTAAATGTATCG
1 ATTTTTATATCTTAAATGTATCG
30062385 AATACGATTA
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:0.30, C:0.09, G:0.09, T:0.53
Consensus pattern (24 bp):
ATTTTTATATCTTAAATGTATCGT
Found at i:30065803 original size:11 final size:11
Alignment explanation
Indices: 30065787--30065816 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
30065777 ATGAAAAAGC
*
30065787 TGGAGGAAACT
1 TGGAGGAAAAT
30065798 TGGAGGAAAAT
1 TGGAGGAAAAT
30065809 TGGAGGAA
1 TGGAGGAA
30065817 GACCATAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.03, G:0.40, T:0.17
Consensus pattern (11 bp):
TGGAGGAAAAT
Found at i:30067180 original size:5 final size:5
Alignment explanation
Indices: 30067170--30067208 Score: 51
Period size: 5 Copynumber: 7.2 Consensus size: 5
30067160 TTATGTGAAA
30067170 ATTTT ATTTT ATATTT ATTTAT ATTTT AATTTT ATTTT A
1 ATTTT ATTTT AT-TTT ATTT-T ATTTT -ATTTT ATTTT A
30067209 AAAATAATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 16 0.52
6 15 0.48
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (5 bp):
ATTTT
Found at i:30067191 original size:53 final size:53
Alignment explanation
Indices: 30067096--30067196 Score: 132
Period size: 53 Copynumber: 1.9 Consensus size: 53
30067086 TAGAGCACAA
* *
30067096 CTTACAATATTTAATGTAAAAATTTAATATTAAATTTTTTTATGTTTTTATCT
1 CTTACAATATTTAATGTAAAAATTTAATATTAAATTTATTTATATTTTTATCT
* * * *
30067149 CTTACAATATCTT-ATGTGAAAATTTTATTTTATATTTATTTATATTTT
1 CTTACAATAT-TTAATGTAAAAATTTAATATTAAATTTATTTATATTTT
30067197 AATTTTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 39 0.95
54 2 0.05
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (53 bp):
CTTACAATATTTAATGTAAAAATTTAATATTAAATTTATTTATATTTTTATCT
Found at i:30067196 original size:17 final size:16
Alignment explanation
Indices: 30067170--30067208 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
30067160 TTATGTGAAA
30067170 ATTTTATTTT-ATATTT
1 ATTTTATTTTAAT-TTT
30067186 ATTTATATTTTAATTTT
1 ATTT-TATTTTAATTTT
30067203 ATTTTA
1 ATTTTA
30067209 AAAATAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.29
17 13 0.62
18 2 0.10
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTATTTTAATTTT
Found at i:30067209 original size:11 final size:10
Alignment explanation
Indices: 30067170--30067208 Score: 51
Period size: 11 Copynumber: 3.6 Consensus size: 10
30067160 TTATGTGAAA
30067170 ATTTTATTTT
1 ATTTTATTTT
30067180 ATATTTATTTAT
1 AT-TTTATTT-T
30067192 ATTTTAATTTT
1 ATTTT-ATTTT
30067203 ATTTTA
1 ATTTTA
30067209 AAAATAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 3 0.12
11 16 0.62
12 7 0.27
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
ATTTTATTTT
Found at i:30074045 original size:2 final size:2
Alignment explanation
Indices: 30074032--30074082 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
30074022 ATCATAATCA
*
30074032 AT AT AN 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
30074074 AT AT AT AT A
1 AT AT AT AT A
30074083 AAACATGTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:30075554 original size:15 final size:15
Alignment explanation
Indices: 30075536--30075591 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
30075526 ATCTTCATTT
30075536 TCATCTCCTTCCATG
1 TCATCTCCTTCCATG
* *
30075551 TCATCTTCTT-CATCT
1 TCATCTCCTTCCAT-G
* *
30075566 TCATCTCTTTGCATG
1 TCATCTCCTTCCATG
*
30075581 TCATCTTCTTC
1 TCATCTCCTTC
30075592 ATCCTTAATC
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
14 3 0.10
15 25 0.81
16 3 0.10
ACGTcount: A:0.12, C:0.34, G:0.05, T:0.48
Consensus pattern (15 bp):
TCATCTCCTTCCATG
Found at i:30075563 original size:30 final size:30
Alignment explanation
Indices: 30075527--30075594 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
30075517 TTCATCTTTA
*
30075527 TCTTCATTTTCATCTCCTTCCATGTCATCT
1 TCTTCATCTTCATCTCCTTCCATGTCATCT
* *
30075557 TCTTCATCTTCATCTCTTTGCATGTCATCT
1 TCTTCATCTTCATCTCCTTCCATGTCATCT
30075587 TCTTCATC
1 TCTTCATC
30075595 CTTAATCAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.13, C:0.32, G:0.04, T:0.50
Consensus pattern (30 bp):
TCTTCATCTTCATCTCCTTCCATGTCATCT
Found at i:30078881 original size:65 final size:65
Alignment explanation
Indices: 30078802--30078934 Score: 230
Period size: 65 Copynumber: 2.0 Consensus size: 65
30078792 GTTGACTCAT
*
30078802 TTTCATAACTATAATTGAAAGTAACTTCCAGACCCATAACATCTTTAACCATTCTATTATATGGA
1 TTTCATAACTATAATTGAAAGTAACTTCCAGACCCATAACATCTCTAACCATTCTATTATATGGA
** *
30078867 TTTCATAACTATAATTGAAAGTAACTTCCAGACCTGTAGCATCTCTAACCATTCTATTATATGGA
1 TTTCATAACTATAATTGAAAGTAACTTCCAGACCCATAACATCTCTAACCATTCTATTATATGGA
30078932 TTT
1 TTT
30078935 TCTATTTTCT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.37
Consensus pattern (65 bp):
TTTCATAACTATAATTGAAAGTAACTTCCAGACCCATAACATCTCTAACCATTCTATTATATGGA
Found at i:30081869 original size:92 final size:91
Alignment explanation
Indices: 30081707--30082004 Score: 434
Period size: 92 Copynumber: 3.2 Consensus size: 91
30081697 AGTGAGCCAA
* *
30081707 CAAATGCGTTTCACTCTCTGCTCTAGGGAAAGTGACGAGTCAGCCAGCAAATCGGTTTCAGCTAA
1 CAAATG-GTTTCACCCTCTGCTCTAGGGAAAGTGACGAGTCAGCCAGCAAATCGGTTTCAGCCAA
* *
30081772 GGGTCTCGGCACAAGAAGTGGATCAAC
65 GGGTCTCGGCACAAGAAGGGGATCCAC
* * * * *
30081799 CAAATGGATTTCACCCTTTGCTCTTGGGAAAGTGACGAATCAGGCAGCAAATCGATTTCAGCCAA
1 CAAATGG-TTTCACCCTCTGCTCTAGGGAAAGTGACGAGTCAGCCAGCAAATCGGTTTCAGCCAA
*
30081864 AGGTCTCGGCACAAGAAGGGGATCCAC
65 GGGTCTCGGCACAAGAAGGGGATCCAC
* *
30081891 CAAATGGGTTTCACCCTCTGCTCTCGGAAAAGTGACGAGTCAGCCAGCAAATCGGTTTCAGCCAA
1 CAAAT-GGTTTCACCCTCTGCTCTAGGGAAAGTGACGAGTCAGCCAGCAAATCGGTTTCAGCCAA
30081956 GGGTCTCGGCACAAGAAGGGGATCCAC
65 GGGTCTCGGCACAAGAAGGGGATCCAC
* *
30081983 CAAATGGGGTTCAGCCTCTGCT
1 CAAAT-GGTTTCACCCTCTGCT
30082005 GTCGGCACAA
Statistics
Matches: 185, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
91 1 0.01
92 182 0.98
93 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (91 bp):
CAAATGGTTTCACCCTCTGCTCTAGGGAAAGTGACGAGTCAGCCAGCAAATCGGTTTCAGCCAAG
GGTCTCGGCACAAGAAGGGGATCCAC
Found at i:30081903 original size:45 final size:45
Alignment explanation
Indices: 30081854--30082022 Score: 142
Period size: 45 Copynumber: 3.7 Consensus size: 45
30081844 AGCAAATCGA
* *
30081854 TTTCAGCCAAAGGTCTCGGCACAAGAAGGGGATCCACCAAATGGG
1 TTTCAGCCAATGCTCTCGGCACAAGAAGGGGATCCACCAAATGGG
* ** * * ** * * *
30081899 TTTCACCCTCTGCTCTCGG-AAAAGTGACGAGTCAGCCAGCAAATCGG
1 TTTCAGCCAATGCTCTCGGCACAA--GAAG-GGGATCCACCAAATGGG
* *
30081946 TTTCAGCCAAGGGTCTCGGCACAAGAAGGGGATCCACCAAATGGG
1 TTTCAGCCAATGCTCTCGGCACAAGAAGGGGATCCACCAAATGGG
* ** *
30081991 GTTCAGCCTCTGCTGTCGGCACAAGAAGGGGA
1 TTTCAGCCAATGCTCTCGGCACAAGAAGGGGA
30082023 AGCAAAGTTA
Statistics
Matches: 90, Mismatches: 30, Indels: 8
0.70 0.23 0.06
Matches are distributed among these distances:
44 3 0.03
45 52 0.58
46 6 0.07
47 26 0.29
48 3 0.03
ACGTcount: A:0.27, C:0.26, G:0.29, T:0.18
Consensus pattern (45 bp):
TTTCAGCCAATGCTCTCGGCACAAGAAGGGGATCCACCAAATGGG
Found at i:30081963 original size:47 final size:48
Alignment explanation
Indices: 30081735--30081966 Score: 119
Period size: 47 Copynumber: 5.0 Consensus size: 48
30081725 TGCTCTAGGG
*
30081735 AAAGTGACGAGTCAGCCAGCAAATCGGTTTCAGCTAAGGGTCTCGGCACA
1 AAAGTGACGAGTCAGCCAGCAAATCGGTTTCAGCCAAGGGTCTCGG--CA
* * *** * * *
30081785 AGAAGTG--GA-TCA---ACCAAAT-GGATTTCACCCTTTGCTCTTGG-G
1 A-AAGTGACGAGTCAGCCAGCAAATCGG-TTTCAGCCAAGGGTCTCGGCA
* * * *
30081827 AAAGTGACGAATCAGGCAGCAAATCGATTTCAGCCAAAGGTCTCGGCA
1 AAAGTGACGAGTCAGCCAGCAAATCGGTTTCAGCCAAGGGTCTCGGCA
* * ** * * * * *** *
30081875 CAA--GAAG-GGGATCCACCAAATGGGTTTCACCCTCTGCTCTCGG-A
1 AAAGTGACGAGTCAGCCAGCAAATCGGTTTCAGCCAAGGGTCTCGGCA
30081919 AAAGTGACGAGTCAGCCAGCAAATCGGTTTCAGCCAAGGGTCTCGGCA
1 AAAGTGACGAGTCAGCCAGCAAATCGGTTTCAGCCAAGGGTCTCGGCA
30081967 CAAGAAGGGG
Statistics
Matches: 123, Mismatches: 45, Indels: 30
0.62 0.23 0.15
Matches are distributed among these distances:
41 5 0.04
42 1 0.01
43 2 0.02
44 8 0.07
45 41 0.33
46 6 0.05
47 45 0.37
48 7 0.06
49 2 0.02
50 1 0.01
51 5 0.04
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.20
Consensus pattern (48 bp):
AAAGTGACGAGTCAGCCAGCAAATCGGTTTCAGCCAAGGGTCTCGGCA
Found at i:30082607 original size:2 final size:2
Alignment explanation
Indices: 30082602--30082636 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
30082592 ATCATANATA
30082602 AT AT AT AT AT AT A- 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
30082637 TCTATAGCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30083014 original size:174 final size:172
Alignment explanation
Indices: 30082755--30083103 Score: 574
Period size: 174 Copynumber: 2.0 Consensus size: 172
30082745 TATTAACTAA
30082755 TTACAATTAAAACGTACATAAAGTAATTATTATTTTTTTAATTGATTATTATATCTTATAATGTA
1 TTACAATTAAAACGTACATAAAGTAATTATTATTTTTTTAATTGATTATTATATCTTATAATGTA
* *
30082820 TTTTTATAAAATTAACAAATTTATTTTGTTCTTTTTATAAATTCTTTAATGTTATAAAATTAATG
66 TTTTAATAAAATTAACAAATTTATCTTGTTCTTTTTATAAATTCTTTAATGTTATAAAATTAATG
* * *
30082885 AATTTTGAATTATTAATTTATAATGTATGATTTAATAAATTT
131 AATTTAGAATTATTAATTTATAATATATGATTTAATAAAGTT
* * * *
30082927 TTACAATTATAACGTTCATAAAGT-ATTATTATTTTTTGTTTATTTGATTATTATATCTTATCAT
1 TTACAATTAAAACGTACATAAAGTAATTATTA--TTTT-TTTAATTGATTATTATATCTTATAAT
*
30082991 GTATTTTAATAAAATTTACAAATTTATCTTGTTCTTTTTATAAATTCTTTAATGTTATAAAATTA
63 GTATTTTAATAAAATTAACAAATTTATCTTGTTCTTTTTATAAATTCTTTAATGTTATAAAATTA
30083056 ATGAATTTAGAATTATTAATTTATAATATATGATTTAATAAAGTT
128 ATGAATTTAGAATTATTAATTTATAATATATGATTTAATAAAGTT
30083101 TTA
1 TTA
30083104 AAAAATGTGC
Statistics
Matches: 164, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
171 7 0.04
172 22 0.13
173 4 0.02
174 131 0.80
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.52
Consensus pattern (172 bp):
TTACAATTAAAACGTACATAAAGTAATTATTATTTTTTTAATTGATTATTATATCTTATAATGTA
TTTTAATAAAATTAACAAATTTATCTTGTTCTTTTTATAAATTCTTTAATGTTATAAAATTAATG
AATTTAGAATTATTAATTTATAATATATGATTTAATAAAGTT
Found at i:30084212 original size:108 final size:108
Alignment explanation
Indices: 30084100--30084318 Score: 314
Period size: 108 Copynumber: 2.0 Consensus size: 108
30084090 CACATCTCAA
* * * *
30084100 TTCTCATTACTTTCTTCTTCTCTGCTTAAC-CTTGATGGGTTCTTCTTTAATTTTTTGTTGTTCC
1 TTCTCACTACTTTCCTCTTCTCTGCTTAACTCTTGATGGGTTCTTCTTTAATTTCTTATTGTTCC
* * * *
30084164 TGTATCCTTGATTATTGGTGCAAACTAATTAAGAAGAGTTTTCT
66 -ATATCCCTGATTATTGGTGCAAACTAATTAAAAAGAGTTTGCT
* * *
30084208 TTCTCACTACTTTCCTCTTCTTTGCTTAACTTTTGATGGGTTCTTCTTTAATTTCTTATTGTTTC
1 TTCTCACTACTTTCCTCTTCTCTGCTTAACTCTTGATGGGTTCTTCTTTAATTTCTTATTGTTCC
*
30084273 ATATCCCTGATTATTTGTGCAAACTAATTAAAAAGAGTTTGCT
66 ATATCCCTGATTATTGGTGCAAACTAATTAAAAAGAGTTTGCT
30084316 TTC
1 TTC
30084319 CTTTTCTCTG
Statistics
Matches: 98, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
108 68 0.69
109 30 0.31
ACGTcount: A:0.20, C:0.18, G:0.12, T:0.50
Consensus pattern (108 bp):
TTCTCACTACTTTCCTCTTCTCTGCTTAACTCTTGATGGGTTCTTCTTTAATTTCTTATTGTTCC
ATATCCCTGATTATTGGTGCAAACTAATTAAAAAGAGTTTGCT
Found at i:30084468 original size:15 final size:15
Alignment explanation
Indices: 30084431--30084481 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
30084421 TCAGTTTTTG
*
30084431 CTACTTTCCTCTTCT
1 CTACTTTCTTCTTCT
** *
30084446 CTGTTTTCTTGTTCT
1 CTACTTTCTTCTTCT
30084461 CTACTTTCTTCTTCT
1 CTACTTTCTTCTTCT
*
30084476 TTACTT
1 CTACTT
30084482 AACCTTGCTG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.06, C:0.29, G:0.04, T:0.61
Consensus pattern (15 bp):
CTACTTTCTTCTTCT
Found at i:30084631 original size:30 final size:31
Alignment explanation
Indices: 30084597--30084662 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
30084587 TAACCTTAGG
* *
30084597 TTCTCACTGCTTCCTCTT-TTTTATTTCTTC
1 TTCTCACTGCTTCCTCTTATCTGATTTCTTC
* * *
30084627 TTCTCATTGTTTCCTCTTATCTGCTTTCTTC
1 TTCTCACTGCTTCCTCTTATCTGATTTCTTC
30084658 TTCTC
1 TTCTC
30084663 TACTTTTCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.06, C:0.30, G:0.05, T:0.59
Consensus pattern (31 bp):
TTCTCACTGCTTCCTCTTATCTGATTTCTTC
Found at i:30084681 original size:43 final size:42
Alignment explanation
Indices: 30084628--30084710 Score: 121
Period size: 43 Copynumber: 2.0 Consensus size: 42
30084618 TATTTCTTCT
*
30084628 TCTCATTGTTTCCTCTTATCTGCTTTCTTCTTCTCTACTTTTC
1 TCTCATTGTTTCCTATTATCTGCTTTCTT-TTCTCTACTTTTC
* * *
30084671 TCTCGTTGTTTCCTATTTTTTGCTTTCTTTTCTCTACTTT
1 TCTCATTGTTTCCTATTATCTGCTTTCTTTTCTCTACTTT
30084711 CCTTTTCTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 11 0.31
43 25 0.69
ACGTcount: A:0.06, C:0.27, G:0.06, T:0.61
Consensus pattern (42 bp):
TCTCATTGTTTCCTATTATCTGCTTTCTTTTCTCTACTTTTC
Found at i:30084715 original size:15 final size:14
Alignment explanation
Indices: 30084693--30084724 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
30084683 CTATTTTTTG
30084693 CTTTCTTTTCTCTA
1 CTTTCTTTTCTCTA
30084707 CTTTCCTTTTCTCTA
1 CTTT-CTTTTCTCTA
30084722 CTT
1 CTT
30084725 AACCTTGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.06, C:0.31, G:0.00, T:0.62
Consensus pattern (14 bp):
CTTTCTTTTCTCTA
Found at i:30085036 original size:14 final size:14
Alignment explanation
Indices: 30084972--30085037 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
30084962 TGGGTTCTCA
* *
30084972 CTACTTCCTCTTCT
1 CTACTTTCTCTTAT
* * *
30084986 CTGCTTTCTTTTTCT
1 CTACTTTC-TCTTAT
30085001 CTACTTTCCTCTTA-
1 CTACTTT-CTCTTAT
*
30085015 CTATTTTCTCTTAT
1 CTACTTTCTCTTAT
30085029 CTACTTTCT
1 CTACTTTCT
30085038 TTTTCTCTGT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
13 6 0.15
14 20 0.49
15 14 0.34
16 1 0.02
ACGTcount: A:0.09, C:0.32, G:0.02, T:0.58
Consensus pattern (14 bp):
CTACTTTCTCTTAT
Found at i:30085221 original size:31 final size:29
Alignment explanation
Indices: 30085163--30085242 Score: 74
Period size: 31 Copynumber: 2.7 Consensus size: 29
30085153 TAGCCCTGGG
* * *
30085163 TTTTCATTGTTTCTTCTTCTTCGCTTTTTTC
1 TTTTCACTGTTTCCTCTTCTTCAC--TTTTC
30085194 TTTTCACTGTTTCCTCTTC-TCTACTTTTC
1 TTTTCACTGTTTCCTCTTCTTC-ACTTTTC
* *
30085223 -TTTCACTATTTCCTTTTCTT
1 TTTTCACTGTTTCCTCTTCTT
30085243 TGCTTTCGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
28 16 0.38
29 6 0.14
30 2 0.05
31 18 0.43
ACGTcount: A:0.06, C:0.26, G:0.04, T:0.64
Consensus pattern (29 bp):
TTTTCACTGTTTCCTCTTCTTCACTTTTC
Found at i:30085831 original size:22 final size:22
Alignment explanation
Indices: 30085801--30085843 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
30085791 GTGAACATAT
30085801 GAAAAGAACAAGCAAATGATAA
1 GAAAAGAACAAGCAAATGATAA
*
30085823 GAAAGGAACAAGCAAATGATA
1 GAAAAGAACAAGCAAATGATA
30085844 CGAAGAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.60, C:0.09, G:0.21, T:0.09
Consensus pattern (22 bp):
GAAAAGAACAAGCAAATGATAA
Found at i:30086403 original size:38 final size:37
Alignment explanation
Indices: 30086350--30086449 Score: 114
Period size: 37 Copynumber: 2.7 Consensus size: 37
30086340 CACCCAGCTA
* *
30086350 ATGTGCAACCCCCACATCACGCACATAGCTGAA-GTCATT
1 ATGTGCAACCCCCACATCACGCACA-A-C-AAATGCCATT
* * *
30086389 GTGTGC-ACCCCCACATCGCTCACAACAAATGCCATT
1 ATGTGCAACCCCCACATCACGCACAACAAATGCCATT
30086425 ATGTGCAACCCCCACATCACGCACA
1 ATGTGCAACCCCCACATCACGCACA
30086450 GGCCATATCA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
35 2 0.04
36 11 0.22
37 17 0.33
38 16 0.31
39 5 0.10
ACGTcount: A:0.30, C:0.38, G:0.14, T:0.18
Consensus pattern (37 bp):
ATGTGCAACCCCCACATCACGCACAACAAATGCCATT
Found at i:30092791 original size:19 final size:19
Alignment explanation
Indices: 30092769--30092805 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
30092759 AATTAATAAA
30092769 TTAACATAATTATA-ATATG
1 TTAACAT-ATTATATATATG
30092788 TTAACATATTATATATAT
1 TTAACATATTATATATAT
30092806 ACATATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (19 bp):
TTAACATATTATATATATG
Found at i:30095781 original size:16 final size:16
Alignment explanation
Indices: 30095762--30095801 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
30095752 TTAATGAATT
*
30095762 TATTAATTATATAAAA
1 TATTAATTAAATAAAA
*
30095778 TATTAATTAAATAAGA
1 TATTAATTAAATAAAA
30095794 TAATTAAT
1 T-ATTAAT
30095802 AAAAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TATTAATTAAATAAAA
Found at i:30100805 original size:2 final size:2
Alignment explanation
Indices: 30100798--30100832 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
30100788 TCAATATAGT
30100798 TA TA TA TA TA TA TA TA TA GTA 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
30100833 ATAACATGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:30100822 original size:17 final size:17
Alignment explanation
Indices: 30100800--30100832 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
30100790 AATATAGTTA
30100800 TATATATATATATATAG
1 TATATATATATATATAG
30100817 TATATATATATATATA
1 TATATATATATATATA
30100833 ATAACATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TATATATATATATATAG
Found at i:30100863 original size:2 final size:2
Alignment explanation
Indices: 30100856--30100893 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
30100846 NNCATAATCA
30100856 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT 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
30100894 AATAACATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30100887 original size:65 final size:58
Alignment explanation
Indices: 30100783--30100904 Score: 158
Period size: 65 Copynumber: 2.0 Consensus size: 58
30100773 TATACTTAAT
30100783 CATAATCAATATAGTTATATATATATATATATAGTATATATATATATATAATAACATGTA
1 CATAATCAATATAGTTATATATATATATAT-TAGTATATATATATATA-AATAACATGTA
30100843 NNNNNCATAATCAATATA-TATATATATATATATATTA-TATATATATATATAAATAACATGTA
1 -----CATAATCAATATAGT-TATATATATATATATTAGTATATATATATATAAATAACATGTA
30100905 AGGAAAAACC
Statistics
Matches: 56, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
62 11 0.20
63 14 0.25
64 3 0.05
65 28 0.50
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.40
Consensus pattern (58 bp):
CATAATCAATATAGTTATATATATATATATTAGTATATATATATATAAATAACATGTA
Found at i:30102402 original size:16 final size:16
Alignment explanation
Indices: 30102383--30102436 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
30102373 TTAATAAATT
*
30102383 TATTAATTATATAAAA
1 TATTAATTAAATAAAA
*
30102399 TATTAATTAAATAAGA
1 TATTAATTAAATAAAA
*
30102415 TAATTAA-TAAAAAAAA
1 T-ATTAATTAAATAAAA
30102431 T-TTAAT
1 TATTAAT
30102437 AGTTCCATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
14 4 0.12
16 23 0.72
17 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
TATTAATTAAATAAAA
Found at i:30103815 original size:2 final size:2
Alignment explanation
Indices: 30103810--30103857 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
30103800 GTGTGTGTGC
30103810 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
30103852 AT AT AT
1 AT AT AT
30103858 GTGTGTGTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30103862 original size:2 final size:2
Alignment explanation
Indices: 30103857--30103892 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
30103847 TATATATATA
30103857 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
30103893 AATTTTAAAA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:30107349 original size:2 final size:2
Alignment explanation
Indices: 30107342--30107371 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
30107332 GATGCAAATC
*
30107342 TA TA TA TA GA 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
30107372 GTTACAAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:30107725 original size:29 final size:28
Alignment explanation
Indices: 30107688--30107759 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
30107678 ATCAAAAAAG
* *
30107688 TTAATTAAATTTTTATTTTT-TTATTATGT
1 TTAAATAAATTTTTATTTTTATT-TTAT-A
*
30107717 TTAAATAAATTATTAATTTTTATTTTATA
1 TTAAATAAATT-TTTATTTTTATTTTATA
*
30107746 TTAAATAAGTTTTT
1 TTAAATAAATTTTT
30107760 CTTGCTAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.06
29 20 0.56
30 12 0.33
31 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (28 bp):
TTAAATAAATTTTTATTTTTATTTTATA
Found at i:30116554 original size:2 final size:2
Alignment explanation
Indices: 30116541--30116576 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
30116531 AGCTATTGAG
* *
30116541 AT AT AC AT AT AT AT AT AC 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
30116577 TTTAGTGATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:30116558 original size:12 final size:12
Alignment explanation
Indices: 30116541--30116576 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
30116531 AGCTATTGAG
30116541 ATATACATATAT
1 ATATACATATAT
30116553 ATATACATATAT
1 ATATACATATAT
*
30116565 ATATATATATAT
1 ATATACATATAT
30116577 TTTAGTGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (12 bp):
ATATACATATAT
Found at i:30127068 original size:37 final size:41
Alignment explanation
Indices: 30127024--30127099 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
30127014 GTGATTTTTT
30127024 AATATTATATTT-T-TA-AA-ATATTAATAATATCTATACC
1 AATATTATATTTATATATAACATATTAATAATATCTATACC
* *
30127061 AATATTATATTTATATATAACATATTCATAATATTTATA
1 AATATTATATTTATATATAACATATTAATAATATCTATA
30127100 TAATATAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 12 0.36
38 1 0.03
39 2 0.06
40 2 0.06
41 16 0.48
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (41 bp):
AATATTATATTTATATATAACATATTAATAATATCTATACC
Found at i:30131379 original size:20 final size:20
Alignment explanation
Indices: 30131333--30131381 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
30131323 ATTTTTATTG
*
30131333 TAAAAGAGAGAAAAAAATTT
1 TAAAAAAGAGAAAAAAATTT
** *
30131353 TGTAAAAGAGAAAATAATTT
1 TAAAAAAGAGAAAAAAATTT
30131373 TAAAAAAGA
1 TAAAAAAGA
30131382 AAGACAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.22
Consensus pattern (20 bp):
TAAAAAAGAGAAAAAAATTT
Found at i:30131382 original size:18 final size:20
Alignment explanation
Indices: 30131330--30131383 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 20
30131320 AGCATTTTTA
30131330 TTGTAAAAGAGAGAAAAAAATT
1 TTGTAAAA-A-AGAAAAAAATT
* *
30131352 TTGTAAAAGAGAAAATAA-T
1 TTGTAAAAAAGAAAAAAATT
30131371 TT-TAAAAAAGAAA
1 TTGTAAAAAAGAAA
30131384 GACAGTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 10 0.34
19 3 0.10
20 8 0.28
22 8 0.28
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (20 bp):
TTGTAAAAAAGAAAAAAATT
Found at i:30132318 original size:40 final size:40
Alignment explanation
Indices: 30132265--30132343 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
30132255 TTTATAGAGA
* *
30132265 AAAGGGACCCTTACACTAGTTCGTTGCATTTTACCCATAG
1 AAAGGGACCCTTACACTAGTTCATTGCACTTTACCCATAG
* *
30132305 AAAGGGACTCTTACACTAGTTCATTGCACTTTGCCCATA
1 AAAGGGACCCTTACACTAGTTCATTGCACTTTACCCATA
30132344 AAAAAAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (40 bp):
AAAGGGACCCTTACACTAGTTCATTGCACTTTACCCATAG
Found at i:30138338 original size:12 final size:13
Alignment explanation
Indices: 30138321--30138351 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
30138311 TAATTATTTT
30138321 TATTTTATTAT-A
1 TATTTTATTATCA
30138333 TATTTTATTATCA
1 TATTTTATTATCA
30138346 TATTTT
1 TATTTT
30138352 CTATTCTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTTATTATCA
Found at i:30138490 original size:14 final size:14
Alignment explanation
Indices: 30138471--30138531 Score: 60
Period size: 16 Copynumber: 4.5 Consensus size: 14
30138461 GTGAACAAAA
30138471 ATTATATATTTTTT
1 ATTATATATTTTTT
30138485 ATTATACTACTTTTATT
1 ATTATA-TA-TTTT-TT
30138502 -TTATATA-TTTTT
1 ATTATATATTTTTT
30138514 A-TAT-T-TTTTTT
1 ATTATATATTTTTT
30138525 ATTATAT
1 ATTATAT
30138532 TTTCCATAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
11 7 0.17
12 8 0.20
13 4 0.10
14 6 0.15
15 4 0.10
16 9 0.22
17 2 0.05
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTATATATTTTTT
Found at i:30138532 original size:14 final size:14
Alignment explanation
Indices: 30138471--30138534 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 14
30138461 GTGAACAAAA
*
30138471 ATTATATATTTTTT
1 ATTATATTTTTTTT
* **
30138485 ATTATACTACTTTT
1 ATTATATTTTTTTT
* * *
30138499 ATTTTA-TATATTT
1 ATTATATTTTTTTT
30138512 -TTATATTTTTTTT
1 ATTATATTTTTTTT
30138525 ATTATATTTT
1 ATTATATTTT
30138535 CCATAAGCAA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
12 4 0.11
13 10 0.26
14 24 0.63
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTATATTTTTTTT
Found at i:30138781 original size:27 final size:28
Alignment explanation
Indices: 30138744--30138796 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
30138734 GTTTAAATTG
* *
30138744 TTATTATTTTATCTCTTTTTTTTATCAT
1 TTATTATTTTATCTATTATTTTTATCAT
*
30138772 TTATTA-TTTATTTATTATTTTTATC
1 TTATTATTTTATCTATTATTTTTATC
30138797 GAGTAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (28 bp):
TTATTATTTTATCTATTATTTTTATCAT
Found at i:30139891 original size:25 final size:25
Alignment explanation
Indices: 30139817--30139891 Score: 123
Period size: 25 Copynumber: 3.0 Consensus size: 25
30139807 CCGTTTCTTT
* * *
30139817 TTTTGCTTTCTCACCCAAAATCTCT
1 TTTTGCTCTCTCACCCAAGATCTCC
30139842 TTTTGCTCTCTCACCCAAGATCTCC
1 TTTTGCTCTCTCACCCAAGATCTCC
30139867 TTTTGCTCTCTCACCCAAGATCTCC
1 TTTTGCTCTCTCACCCAAGATCTCC
30139892 CCCTTCCTCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.17, C:0.37, G:0.07, T:0.39
Consensus pattern (25 bp):
TTTTGCTCTCTCACCCAAGATCTCC
Found at i:30140231 original size:24 final size:24
Alignment explanation
Indices: 30140202--30140249 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
30140192 CTCTCTCCCT
*
30140202 TTTTTTTCATTTCTTCTTTATTTTAA
1 TTTTTATCATTT-TT-TTTATTTTAA
30140228 TTTTTATCATTTTTTTTATTTT
1 TTTTTATCATTTTTTTTATTTT
30140250 TCGTTTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 2 0.10
26 11 0.52
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTTATCATTTTTTTTATTTTAA
Found at i:30141078 original size:8 final size:8
Alignment explanation
Indices: 30141054--30141112 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
30141044 AAAAATATTC
30141054 ATAATTTTA
1 ATAA-TTTA
30141063 ATTAATTTA
1 A-TAATTTA
*
30141072 ATAATTTT
1 ATAATTTA
30141080 ATATATTTA
1 ATA-ATTTA
* *
30141089 ATTATATA
1 ATAATTTA
30141097 A-AA-TTA
1 ATAATTTA
30141103 ATAATTTA
1 ATAATTTA
30141111 AT
1 AT
30141113 TTTCAATAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
6 3 0.08
7 3 0.08
8 19 0.47
9 12 0.30
10 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
ATAATTTA
Found at i:30142555 original size:16 final size:16
Alignment explanation
Indices: 30142530--30142591 Score: 61
Period size: 16 Copynumber: 3.5 Consensus size: 16
30142520 AACTAAGCAT
*
30142530 AATCATAGCAAACCCA
1 AATCACAGCAAACCCA
30142546 AATCACAGCAAACCCAAA
1 AATCACAGCAAACCC--A
30142564 ATATTTTCACAGCAAACCCA
1 A-A---TCACAGCAAACCCA
30142584 AATCACAG
1 AATCACAG
30142592 TCAGCATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
16 20 0.51
18 2 0.05
19 2 0.05
20 2 0.05
22 13 0.33
ACGTcount: A:0.48, C:0.31, G:0.06, T:0.15
Consensus pattern (16 bp):
AATCACAGCAAACCCA
Found at i:30142757 original size:23 final size:24
Alignment explanation
Indices: 30142729--30142791 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
30142719 ATGGAAGAGT
*
30142729 GACTGAGAGAAAGAGGGGAA-GAC
1 GACTGAGAGAAAGAGGGGAATAAC
30142752 GACTGAGAG-AAGAGGGGAATAAC
1 GACTGAGAGAAAGAGGGGAATAAC
* *
30142775 GACTTAGTGAAAGAGGG
1 GACTGAGAGAAAGAGGG
30142792 AAAGGAGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.29
23 18 0.51
24 7 0.20
ACGTcount: A:0.41, C:0.08, G:0.41, T:0.10
Consensus pattern (24 bp):
GACTGAGAGAAAGAGGGGAATAAC
Found at i:30144046 original size:15 final size:15
Alignment explanation
Indices: 30144026--30144059 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
30144016 TAACATTACA
30144026 AAAATTA-TAACTTAT
1 AAAATTATTAA-TTAT
30144041 AAAATTATTAATTAT
1 AAAATTATTAATTAT
30144056 AAAA
1 AAAA
30144060 AAATATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.83
16 3 0.17
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATTATTAATTAT
Found at i:30145935 original size:19 final size:21
Alignment explanation
Indices: 30145898--30145936 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
30145888 AATTTTTTTT
*
30145898 AAAAAATTTTTGTTCTTTAAA
1 AAAAAAGTTTTGTTCTTTAAA
30145919 AAAAAAGTTTT-TT-TTTAA
1 AAAAAAGTTTTGTTCTTTAA
30145937 GAGTTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (21 bp):
AAAAAAGTTTTGTTCTTTAAA
Found at i:30146859 original size:24 final size:25
Alignment explanation
Indices: 30146815--30146863 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
30146805 AATTATTTTC
*
30146815 ATTTTATATATTTTTAATATAATTA
1 ATTTTATATATTATTAATATAATTA
*
30146840 ATTTTAT-TATTATTATTATAATTA
1 ATTTTATATATTATTAATATAATTA
30146864 TAAAATTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTTTATATATTATTAATATAATTA
Found at i:30147239 original size:17 final size:17
Alignment explanation
Indices: 30147217--30147250 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
30147207 ATGCATCAAT
30147217 ATATATACTTAAA-AATA
1 ATATATA-TTAAATAATA
30147234 ATATATATTAAATAATA
1 ATATATATTAAATAATA
30147251 TGAATATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATATATTAAATAATA
Found at i:30147672 original size:15 final size:15
Alignment explanation
Indices: 30147654--30147686 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
30147644 TATCATTACA
*
30147654 AAAATTATTACTTAT
1 AAAATTATTAATTAT
30147669 AAAATTATTAATTAT
1 AAAATTATTAATTAT
30147684 AAA
1 AAA
30147687 TACATATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAATTATTAATTAT
Found at i:30148432 original size:27 final size:27
Alignment explanation
Indices: 30148398--30148451 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
30148388 TATGTTAATA
30148398 TTTTTGAAAACAATTTTACAAATTATT
1 TTTTTGAAAACAATTTTACAAATTATT
** *
30148425 TTTTTGAAAGGATTTTTACAAATTATT
1 TTTTTGAAAACAATTTTACAAATTATT
30148452 ATATTAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.50
Consensus pattern (27 bp):
TTTTTGAAAACAATTTTACAAATTATT
Found at i:30149519 original size:18 final size:18
Alignment explanation
Indices: 30149496--30149562 Score: 52
Period size: 18 Copynumber: 3.8 Consensus size: 18
30149486 AATGGTAGAT
30149496 ATTTTATTAATTATCTTA
1 ATTTTATTAATTATCTTA
30149514 ATTTTA-TATATT-T-TTA
1 ATTTTATTA-ATTATCTTA
***
30149530 ATACAATTAATTATCTT-
1 ATTTTATTAATTATCTTA
30149547 ATTATTATTAAATTAT
1 ATT-TTATT-AATTAT
30149563 GAGATCTCCC
Statistics
Matches: 37, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
16 9 0.24
17 8 0.22
18 14 0.38
19 6 0.16
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTATTAATTATCTTA
Found at i:30153337 original size:2 final size:2
Alignment explanation
Indices: 30153332--30153381 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
30153322 TGGATATATA
30153332 AG AG AG AG AG AG AG AG AG A- AG AG AG A- AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
30153372 AG AG AG AG AG
1 AG AG AG AG AG
30153382 TTTTATTTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30159363 original size:116 final size:116
Alignment explanation
Indices: 30159159--30159389 Score: 347
Period size: 116 Copynumber: 2.0 Consensus size: 116
30159149 TTCATTGACA
* * *
30159159 ACACCATCAAAAGAACCCATTAAACTACAATCTTGCCTTGGAAAGAGAAAGAAGAGGGACTAGGG
1 ACACCAGCAAAAGAACCCATTAAACTACAATCTTACCTAGGAAAGAGAAAGAAGAGGGACTAGGG
* *
30159224 GTGTGGGTGGAGGGAGTGGCTAGAGAGAGGAAGACAA-TGATAGGGAAATGG
66 GGGTGGGTGGAGGGAGCGGCTAGAGAGAGGAAGA-AACTGATAGGGAAATGG
* * *
30159275 ACACCAGCAAAAGAACCCATTAAACTATAATCTTACCTAGGAAGGAGAGAGAAGAGGGACTAGGG
1 ACACCAGCAAAAGAACCCATTAAACTACAATCTTACCTAGGAAAGAGAAAGAAGAGGGACTAGGG
* *
30159340 GGGTGGGTGGAGGGAGCGGCTAGAGTGAGGGAGAAATCTGATAGGGAAAT
66 GGGTGGGTGGAGGGAGCGGCTAGAGAGAGGAAGAAA-CTGATAGGGAAAT
30159390 AGAAAACTTG
Statistics
Matches: 103, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
115 2 0.02
116 89 0.86
117 12 0.12
ACGTcount: A:0.37, C:0.13, G:0.35, T:0.15
Consensus pattern (116 bp):
ACACCAGCAAAAGAACCCATTAAACTACAATCTTACCTAGGAAAGAGAAAGAAGAGGGACTAGGG
GGGTGGGTGGAGGGAGCGGCTAGAGAGAGGAAGAAACTGATAGGGAAATGG
Found at i:30171633 original size:10 final size:10
Alignment explanation
Indices: 30171605--30171656 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
30171595 ACATCATAGG
30171605 TTAATTAATA
1 TTAATTAATA
*
30171615 TAAAATTAATA
1 T-TAATTAATA
30171626 TTAATTAAT-
1 TTAATTAATA
*
30171635 TTCAACTAATA
1 TT-AATTAATA
*
30171646 TAAATTAATA
1 TTAATTAATA
30171656 T
1 T
30171657 GACAAGTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
9 2 0.06
10 22 0.65
11 10 0.29
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (10 bp):
TTAATTAATA
Found at i:30173442 original size:26 final size:26
Alignment explanation
Indices: 30173406--30173600 Score: 106
Period size: 26 Copynumber: 7.4 Consensus size: 26
30173396 CAGAAGTGCT
* * *
30173406 CAAGGTTGTTCCATGCGCGGAAGCAC
1 CAAGGGTGTTCCAAGCGTGGAAGCAC
* *
30173432 CAAGGGTGTTCCAAGCATGGAAACAC
1 CAAGGGTGTTCCAAGCGTGGAAGCAC
* * ***
30173458 CCAGGGAGTTCCAAGCGTGGAAGTGT
1 CAAGGGTGTTCCAAGCGTGGAAGCAC
** ** *
30173484 CGGGGGTGTTCCAAGCG-CAAAGACGC
1 CAAGGGTGTTCCAAGCGTGGAAG-CAC
* ** *
30173510 TCAAGGGTGTTCTAAGTATGGAAGCGCC
1 -CAAGGGTGTTCCAAGCGTGGAAGC-AC
* * * **
30173538 CAGGGGCGTTTCAAGCGCAGAAGCATC
1 CAAGGGTGTTCCAAGCGTGGAAGCA-C
*
30173565 C-AGGGTGTTCCAAGCGTGGAAGCTC
1 CAAGGGTGTTCCAAGCGTGGAAGCAC
*
30173590 CAAGGATGTTC
1 CAAGGGTGTTC
30173601 TAAGAGTAGA
Statistics
Matches: 120, Mismatches: 43, Indels: 12
0.69 0.25 0.07
Matches are distributed among these distances:
25 5 0.04
26 80 0.67
27 31 0.26
28 4 0.03
ACGTcount: A:0.25, C:0.23, G:0.33, T:0.18
Consensus pattern (26 bp):
CAAGGGTGTTCCAAGCGTGGAAGCAC
Found at i:30173585 original size:53 final size:53
Alignment explanation
Indices: 30173458--30173587 Score: 129
Period size: 53 Copynumber: 2.5 Consensus size: 53
30173448 ATGGAAACAC
* * * * * *
30173458 CCAGGGAGTTCCAAGCGTGGAAGTGTCGGGGGTGTTCCAAGCGCAAAGACGCT
1 CCAGGGTGTTCCAAGCGTGGAAGCGCCAGGGGCGTTCCAAGCGCAAAGACGAT
* * ** *
30173511 CAAGGGTGTTCTAAGTATGGAAGCGCCCAGGGGCGTTTCAAGCGCAGAAG-C-AT
1 CCAGGGTGTTCCAAGCGTGGAAGCG-CCAGGGGCGTTCCAAGCGCA-AAGACGAT
30173564 CCAGGGTGTTCCAAGCGTGGAAGC
1 CCAGGGTGTTCCAAGCGTGGAAGC
30173588 TCCAAGGATG
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
53 40 0.67
54 17 0.28
55 3 0.05
ACGTcount: A:0.24, C:0.22, G:0.36, T:0.18
Consensus pattern (53 bp):
CCAGGGTGTTCCAAGCGTGGAAGCGCCAGGGGCGTTCCAAGCGCAAAGACGAT
Found at i:30173705 original size:26 final size:26
Alignment explanation
Indices: 30173670--30173737 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 26
30173660 ATGGAAATGC
30173670 CCAA-CGTGGAAGCGCCCAAAGAGTT
1 CCAAGCGTGGAAGCGCCCAAAGAGTT
**
30173695 CCAAGCGTGGAAGCGCCCAGGGAGTT
1 CCAAGCGTGGAAGCGCCCAAAGAGTT
* *
30173721 CCAAGTGTGGATGCGCC
1 CCAAGCGTGGAAGCGCC
30173738 TAAGGGTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
25 4 0.11
26 34 0.89
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.13
Consensus pattern (26 bp):
CCAAGCGTGGAAGCGCCCAAAGAGTT
Found at i:30173752 original size:27 final size:26
Alignment explanation
Indices: 30173670--30173779 Score: 89
Period size: 27 Copynumber: 4.2 Consensus size: 26
30173660 ATGGAAATGC
*
30173670 CCAA-CGTGGAAGCGCCCAA-AGAGTT
1 CCAAGCGTGGAAGCG-CCAAGGGAGTT
*
30173695 CCAAGCGTGGAAGCGCCCAGGGAGTT
1 CCAAGCGTGGAAGCGCCAAGGGAGTT
* * *
30173721 CCAAGTGTGGATGCGCCTAAGGGTGTT
1 CCAAGCGTGGAAGCGCC-AAGGGAGTT
* * * * *
30173748 TCAAGCGTGTAAGCACCTAGGGGCGTT
1 CCAAGCGTGGAAGCGCC-AAGGGAGTT
30173775 CCAAG
1 CCAAG
30173780 TGCAAAAACG
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
25 7 0.10
26 30 0.44
27 31 0.46
ACGTcount: A:0.25, C:0.25, G:0.34, T:0.17
Consensus pattern (26 bp):
CCAAGCGTGGAAGCGCCAAGGGAGTT
Found at i:30173830 original size:27 final size:26
Alignment explanation
Indices: 30173800--30173869 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
30173790 TCAAAAAGTG
* *
30173800 TTCCAAGCATAGAAGTGCT-CAGGAGCA
1 TTCCAAGCACAGAAGCG-TACAGG-GCA
*
30173827 TTCCAAGCACAAAAGCGTACAGGGCA
1 TTCCAAGCACAGAAGCGTACAGGGCA
30173853 TTCCAAGCACAGAAGCG
1 TTCCAAGCACAGAAGCG
30173870 CCCAAAGAGC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 20 0.53
27 18 0.47
ACGTcount: A:0.36, C:0.26, G:0.24, T:0.14
Consensus pattern (26 bp):
TTCCAAGCACAGAAGCGTACAGGGCA
Found at i:30173860 original size:26 final size:27
Alignment explanation
Indices: 30173819--30173896 Score: 86
Period size: 26 Copynumber: 2.9 Consensus size: 27
30173809 TAGAAGTGCT
30173819 CAGGAGCATTCCAAGCACAAAAGCGTA
1 CAGGAGCATTCCAAGCACAAAAGCGTA
* **
30173846 CAGG-GCATTCCAAGCACAGAAGCGCC
1 CAGGAGCATTCCAAGCACAAAAGCGTA
* * *
30173872 CAAAGAGCACTACAAGCACAAAAGC
1 C-AGGAGCATTCCAAGCACAAAAGC
30173897 ACACAAGAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 20 0.48
27 6 0.14
28 16 0.38
ACGTcount: A:0.41, C:0.29, G:0.22, T:0.08
Consensus pattern (27 bp):
CAGGAGCATTCCAAGCACAAAAGCGTA
Found at i:30173908 original size:16 final size:18
Alignment explanation
Indices: 30173872--30173908 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
30173862 CAGAAGCGCC
*
30173872 CAAAGAGCACTACAAGCA
1 CAAAGAGCACTACAAGAA
30173890 CAAA-AGCAC-ACAAGAA
1 CAAAGAGCACTACAAGAA
30173906 CAA
1 CAA
30173909 GCATAGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 5 0.28
18 4 0.22
ACGTcount: A:0.57, C:0.27, G:0.14, T:0.03
Consensus pattern (18 bp):
CAAAGAGCACTACAAGAA
Found at i:30182129 original size:13 final size:14
Alignment explanation
Indices: 30182092--30182126 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
30182082 ATTTTAATTT
30182092 TATTAAATTAA-AA
1 TATTAAATTAATAA
*
30182105 TTTTAAATTAATAA
1 TATTAAATTAATAA
30182119 TATTAAAT
1 TATTAAAT
30182127 AATTTGTCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TATTAAATTAATAA
Found at i:30183166 original size:19 final size:18
Alignment explanation
Indices: 30183142--30183190 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
30183132 TAATATAAAG
30183142 AAATTAAAAATATTTACAA
1 AAATTAAAAA-ATTTACAA
*
30183161 AAATTATATAAATTTATC-A
1 AAATTA-AAAAATTTA-CAA
30183180 AAATTAAAAAA
1 AAATTAAAAAA
30183191 AATTACAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 4 0.15
19 18 0.69
20 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATTAAAAAATTTACAA
Found at i:30186029 original size:22 final size:23
Alignment explanation
Indices: 30185987--30186033 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
30185977 TAAATATTAC
* *
30185987 TAAATAAAGTTAACTTAATTGTT
1 TAAAAAAAATTAACTTAATTGTT
30186010 TAAAAAAAATTAA-TTAATTGTT
1 TAAAAAAAATTAACTTAATTGTT
30186032 TA
1 TA
30186034 TTTGATAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (23 bp):
TAAAAAAAATTAACTTAATTGTT
Found at i:30186115 original size:9 final size:9
Alignment explanation
Indices: 30186097--30186129 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
30186087 ATATGGATCT
30186097 AAAT-AAAA
1 AAATAAAAA
30186105 AAATAAAAA
1 AAATAAAAA
30186114 AAATAAATAA
1 AAATAAA-AA
30186124 AAATAA
1 AAATAA
30186130 TTCATGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 4 0.17
9 11 0.48
10 8 0.35
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (9 bp):
AAATAAAAA
Found at i:30193985 original size:34 final size:34
Alignment explanation
Indices: 30193942--30194011 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
30193932 TATATATATA
30193942 CTCCTCTTTTGTGAATTATCAATAGGACCCTTTG
1 CTCCTCTTTTGTGAATTATCAATAGGACCCTTTG
*
30193976 CTCCTCTTTTGTGAATTCTCAATAGGACCCTTTG
1 CTCCTCTTTTGTGAATTATCAATAGGACCCTTTG
30194010 CT
1 CT
30194012 TCCATAGGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.19, C:0.26, G:0.14, T:0.41
Consensus pattern (34 bp):
CTCCTCTTTTGTGAATTATCAATAGGACCCTTTG
Found at i:30202853 original size:2 final size:2
Alignment explanation
Indices: 30202846--30202881 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
30202836 CTAACATATA
30202846 AG AG AG 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 AG AG AG
30202882 TAAATTTTCT
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):
AG
Found at i:30206719 original size:2 final size:2
Alignment explanation
Indices: 30206612--30206705 Score: 75
Period size: 2 Copynumber: 46.0 Consensus size: 2
30206602 ATAGAGTGAT
* ** *
30206612 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA GC TA NGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * *
30206655 -A AA GGA TA GA GTGA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA -T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30206696 TA TA TA TA TA
1 TA TA TA TA TA
30206706 CACACACATA
Statistics
Matches: 77, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
1 2 0.03
2 71 0.92
3 3 0.04
4 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.09, T:0.41
Consensus pattern (2 bp):
TA
Found at i:30209095 original size:78 final size:80
Alignment explanation
Indices: 30208942--30209098 Score: 185
Period size: 78 Copynumber: 1.9 Consensus size: 80
30208932 TAAAAAATTT
* *
30208942 TAAAAATAGATAATTAGTTTTATATATAAGAAATAAAATAGTTGCTAGAAATCATTAAATATATC
1 TAAAAATAGATAATTAGTTTTATATAT----AATAAAATAGTTGCTAGAAATCATTAAATACATA
30209007 TTACCATTAGTTGATTGGA
62 TTACCATTAGTTGATTGGA
* * * *
30209026 TAAAAATAGTTAATTAGTTTTATATAT-A-AAAATAGTTG-TTGAAGATTATTAAATACGTATTA
1 TAAAAATAGATAATTAGTTTTATATATAATAAAATAGTTGCTAGAA-ATCATTAAATACATATTA
*
30209088 CCTTTAGTTGA
65 CCATTAGTTGA
30209099 AATTGGTNTT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
77 4 0.06
78 34 0.52
79 1 0.02
84 26 0.40
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.39
Consensus pattern (80 bp):
TAAAAATAGATAATTAGTTTTATATATAATAAAATAGTTGCTAGAAATCATTAAATACATATTAC
CATTAGTTGATTGGA
Found at i:30209371 original size:13 final size:13
Alignment explanation
Indices: 30209344--30209379 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
30209334 TATATTTTTA
30209344 ATATAATTA-ATT
1 ATATAATTATATT
30209356 ATATAATTATATT
1 ATATAATTATATT
*
30209369 ATAAAATTATA
1 ATATAATTATA
30209380 GAGCTTCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATAATTATATT
Found at i:30209371 original size:23 final size:23
Alignment explanation
Indices: 30209312--30209379 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
30209302 AATTAGGTAT
*
30209312 TTAT-TAATTAT-TT-TAATT-T
1 TTATATAATTATATTATAATTAA
* * *
30209331 TTATATATTTTTAATATAATTAA
1 TTATATAATTATATTATAATTAA
30209354 TTATATAATTATATTATAA--AA
1 TTATATAATTATATTATAATTAA
30209375 TTATA
1 TTATA
30209380 GAGCTTCCTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
19 4 0.11
20 5 0.13
21 8 0.21
22 5 0.13
23 16 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTATATAATTATATTATAATTAA
Found at i:30210926 original size:2 final size:2
Alignment explanation
Indices: 30210919--30210946 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30210909 AAGAATTAAA
30210919 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
30210947 TCGTTATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30211712 original size:7 final size:7
Alignment explanation
Indices: 30211700--30211724 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30211690 GATTTTGACA
30211700 AAAAAAC
1 AAAAAAC
30211707 AAAAAAC
1 AAAAAAC
30211714 AAAAAAC
1 AAAAAAC
30211721 AAAA
1 AAAA
30211725 GAAAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:30212771 original size:2 final size:2
Alignment explanation
Indices: 30212764--30212811 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
30212754 ATTTAATTTT
30212764 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
30212806 TA TA TA
1 TA TA TA
30212812 GATGCATTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30215029 original size:16 final size:17
Alignment explanation
Indices: 30214997--30215029 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
30214987 AATAACTATT
30214997 ATTTTATATTTAATAAA
1 ATTTTATATTTAATAAA
*
30215014 ATTTTA-ATTTATTAAA
1 ATTTTATATTTAATAAA
30215030 CATATATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTATATTTAATAAA
Found at i:30230861 original size:67 final size:67
Alignment explanation
Indices: 30230753--30230889 Score: 274
Period size: 67 Copynumber: 2.0 Consensus size: 67
30230743 TTTCTTTCTC
30230753 CTTTGGGAGGAATCGATATTTGTTTGCTTCCAATCATCCTTTCATGAGAATGCCTAACCATTAAA
1 CTTTGGGAGGAATCGATATTTGTTTGCTTCCAATCATCCTTTCATGAGAATGCCTAACCATTAAA
30230818 GG
66 GG
30230820 CTTTGGGAGGAATCGATATTTGTTTGCTTCCAATCATCCTTTCATGAGAATGCCTAACCATTAAA
1 CTTTGGGAGGAATCGATATTTGTTTGCTTCCAATCATCCTTTCATGAGAATGCCTAACCATTAAA
30230885 GG
66 GG
30230887 CTT
1 CTT
30230890 CAAAACCCGA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (67 bp):
CTTTGGGAGGAATCGATATTTGTTTGCTTCCAATCATCCTTTCATGAGAATGCCTAACCATTAAA
GG
Found at i:30235897 original size:21 final size:20
Alignment explanation
Indices: 30235859--30235903 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
30235849 ATAAAAATTT
*
30235859 ATTT-AAAATTTTTTAAATA
1 ATTTAAAAATTTTTCAAATA
30235878 ATTTAAAAACTTTTTCAAATA
1 ATTTAAAAA-TTTTTCAAATA
*
30235899 TTTTA
1 ATTTA
30235904 TATTTTTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 4 0.18
21 14 0.64
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTAAAAATTTTTCAAATA
Done.