Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 119 of 120
Found at i:34805440 original size:11 final size:11
Alignment explanation
Indices: 34805424--34805451 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
34805414 TTCAGATTCA
34805424 AAAAAAAAAAC
1 AAAAAAAAAAC
34805435 AAAAAAAAAAC
1 AAAAAAAAAAC
34805446 AAAAAA
1 AAAAAA
34805452 TGAAAGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:34807694 original size:98 final size:98
Alignment explanation
Indices: 34807571--34807765 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
34807561 AAAAATCATG
*
34807571 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
34807636 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
* *
34807669 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGGATCGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
*
34807734 AAATCTTGGATGAGTGGATGTTCTTTTAAAGT
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGT
34807766 TTTATTGTAT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
Found at i:34808781 original size:45 final size:45
Alignment explanation
Indices: 34808661--34808774 Score: 147
Period size: 45 Copynumber: 2.5 Consensus size: 45
34808651 AGCCTATTTG
* *
34808661 CACCGATTAATGGTTTATCCACACTGTATTAGCAGTTTTTATCTG
1 CACCGATTAATGGTTTATCCACACTGTATTAGCAGCTTTTATCTA
* * * *
34808706 CACCAATTATTGATTTATCCACACTGTATTAGTAGCTTTTATCTA
1 CACCGATTAATGGTTTATCCACACTGTATTAGCAGCTTTTATCTA
* * *
34808751 TACCGATTAGTGGTTTACCCACAC
1 CACCGATTAATGGTTTATCCACAC
34808775 CATATTAACA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (45 bp):
CACCGATTAATGGTTTATCCACACTGTATTAGCAGCTTTTATCTA
Found at i:34816103 original size:2 final size:2
Alignment explanation
Indices: 34816098--34816123 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34816088 TTATTATCAC
34816098 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
34816124 GTGTGTGTGT
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):
AT
Found at i:34817239 original size:51 final size:50
Alignment explanation
Indices: 34817163--34817598 Score: 360
Period size: 51 Copynumber: 8.6 Consensus size: 50
34817153 CCGGTTCACA
* * *
34817163 TAGTAGCATGCACATAGTACTACACAGGTGACCATCA-CTATCCGATACACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCA--AGCTATCCGATACACG
* * * * *
34817214 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCCGGTACGCA
1 TAGTAGCCTTCACATAGTACTACACACGTGA-CCAAGCTATCCGATACACG
* * * * * *
34817265 TAGTAGCCTGCACATAGTACTACACATGCGACCTATC-ATTCTGATACACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTA-TCCGATACACG
* * * * * * *
34817315 TAGTAGCCTACACATAGTACTACACACGTGATCAAGTTTTTCGGTTCACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTATCCGATACACG
* * * * * *
34817365 AAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTTTTCGGTACACA
1 TAGTAGCCTTCACATAGTACTACACACGTGA-CCAAGCTATCCGATACACG
* * **
34817416 TAGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTAT-CGATACACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCA--AGCTATCCGATACACG
* * * *
34817467 TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCT-TCTCGGTACACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACC-AAGCTATC-CGATACACG
* * * ** *
34817518 TTGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTAT-CGATACATG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCA--AGCTATCCGATACACG
*
34817569 TAGTAGCCTTCACACAGTACTACACACGTG
1 TAGTAGCCTTCACATAGTACTACACACGTG
34817599 TTCATCGATA
Statistics
Matches: 309, Mismatches: 63, Indels: 26
0.78 0.16 0.07
Matches are distributed among these distances:
49 2 0.01
50 82 0.27
51 216 0.70
52 8 0.03
53 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.27
Consensus pattern (50 bp):
TAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTATCCGATACACG
Found at i:34817339 original size:101 final size:103
Alignment explanation
Indices: 34817153--34817390 Score: 321
Period size: 101 Copynumber: 2.4 Consensus size: 103
34817143 ATCAATTATA
* *
34817153 CCGGTTCA--CATAGTAGCATGCACATAGTACTACACAGGTGACCATCACTATCCGATACACGTA
1 CCGGTTCACGCATAGTAGCCTGCACATAGTACTACACAGGCGACCATCACTATCCGATACACGTA
*
34817216 GTAGCCTGCACATAGTACTACACACGTGATCGAAGCTAT
66 GTAGCCTACACATAGTACTACACACGTGATC-AAGCTAT
* *
34817255 CCGG-T-ACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGATACACGT
1 CCGGTTCACGCATAGTAGCCTGCACATAGTACTACACAGGCGACC-ATCACTATCCGATACACGT
* *
34817316 AGTAGCCTACACATAGTACTACACACGTGATCAAGTTTT
65 AGTAGCCTACACATAGTACTACACACGTGATCAAGCTAT
* *
34817355 TCGGTTCACG-A-AGTAGCCTTCACATAGTACTACACA
1 CCGGTTCACGCATAGTAGCCTGCACATAGTACTACACA
34817391 CGTGATCAAA
Statistics
Matches: 122, Mismatches: 9, Indels: 12
0.85 0.06 0.08
Matches are distributed among these distances:
100 33 0.27
101 45 0.37
102 40 0.33
103 4 0.03
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (103 bp):
CCGGTTCACGCATAGTAGCCTGCACATAGTACTACACAGGCGACCATCACTATCCGATACACGTA
GTAGCCTACACATAGTACTACACACGTGATCAAGCTAT
Found at i:34817438 original size:151 final size:153
Alignment explanation
Indices: 34817163--34817548 Score: 451
Period size: 151 Copynumber: 2.5 Consensus size: 153
34817153 CCGGTTCACA
* * * * * * * *
34817163 TAGTAGCATGCACATAGTACTACACAGGTGACCATCA-CTATC-CGATACACGTAGTAGCCTGCA
1 TAGTAGCCTACACACAGTACTACACAAGTGACCA-AAGCT-TCTCGGTACACGAAGTAGCCTTCA
* *
34817226 CATAGTACTACACACGTGATCGAAGCTATCCGGTACGCATAGTAGCCTGCACATAGTACTACACA
64 CATAGTACTACACACGTGATCAAAGCTATCCGGTACACATAGTAGCCTGCACATAGTACTACACA
*
34817291 TGCGACCTATCA-TTCT-GATACACG
129 TGCGACC-ATCATTTATCGATACACG
* * * * * *
34817315 TAGTAGCCTACACATAGTACTACACACGTGATC-AAGTTTTTCGGTTCACGAAGTAGCCTTCACA
1 TAGTAGCCTACACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACGAAGTAGCCTTCACA
* * * *
34817379 TAGTACTACACACGTGATCAAAGCTTTTCGGTACACATAGTAGCCTTCACTTAGTACTACACATG
66 TAGTACTACACACGTGATCAAAGCTATCCGGTACACATAGTAGCCTGCACATAGTACTACACATG
* *
34817444 TGACCATTATTTATCGATACACG
131 CGACCATCATTTATCGATACACG
* *
34817467 TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACAC-ATTGTAGCCTTCAC
1 TAGTAGCCTACACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACGA-AGTAGCCTTCAC
* *
34817531 TTAGTACTACACATGTGA
65 ATAGTACTACACACGTGA
34817549 CCATTATTTA
Statistics
Matches: 198, Mismatches: 30, Indels: 11
0.83 0.13 0.05
Matches are distributed among these distances:
150 5 0.03
151 86 0.43
152 67 0.34
153 40 0.20
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (153 bp):
TAGTAGCCTACACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACGAAGTAGCCTTCACA
TAGTACTACACACGTGATCAAAGCTATCCGGTACACATAGTAGCCTGCACATAGTACTACACATG
CGACCATCATTTATCGATACACG
Found at i:34817503 original size:102 final size:102
Alignment explanation
Indices: 34817265--34817594 Score: 416
Period size: 102 Copynumber: 3.3 Consensus size: 102
34817255 CCGGTACGCA
* * * * * * * * *
34817265 TAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCT-GATACACGTAGTAGCCTACAC
1 TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGC-TTCTCGGTACACATAGTAGCCTTCAC
* * * * * *
34817328 ATAGTACTACACACGTGATCA--AGTTTTTCGGTTCACG
65 TTAGTACTACACATGTGACCATTA-TTTATCGATACACG
* * * * *
34817365 AAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTTTTCGGTACACATAGTAGCCTTCACT
1 TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATAGTAGCCTTCACT
34817430 TAGTACTACACATGTGACCATTATTTATCGATACACG
66 TAGTACTACACATGTGACCATTATTTATCGATACACG
*
34817467 TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATTGTAGCCTTCACT
1 TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATAGTAGCCTTCACT
*
34817532 TAGTACTACACATGTGACCATTATTTATCGATACATG
66 TAGTACTACACATGTGACCATTATTTATCGATACACG
34817569 TAGTAGCCTTCACACAGTACTACACA
1 TAGTAGCCTTCACACAGTACTACACA
34817595 CGTGTTCATC
Statistics
Matches: 202, Mismatches: 24, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
100 31 0.15
101 38 0.19
102 132 0.65
103 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (102 bp):
TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATAGTAGCCTTCACT
TAGTACTACACATGTGACCATTATTTATCGATACACG
Found at i:34817573 original size:153 final size:150
Alignment explanation
Indices: 34817163--34817594 Score: 424
Period size: 151 Copynumber: 2.8 Consensus size: 150
34817153 CCGGTTCACA
* * * * * * *
34817163 TAGTAGCATGCACATAGTACTACACAGGTGACCATCA-CTATC-CGATACACGTAGTAGCCTGCA
1 TAGTAGCCTACACACAGTACTACACAAGTGACCA--AGCT-TCTCGGTACACGAAGTAGCCTTCA
* * * * * * *
34817226 CATAGTACTACACACGTGATCGAAGCTATCCGGTACGCATAGTAGCCTGCACATAGTACTACACA
63 CATAGTACTACACACGTGA-CCAAACTTTTCGATACACATAGTAGCCTTCACATAGTACTACACA
*
34817291 TGCGACCTATCATTCTGATACACG
127 TGCGACCTATCATTATGATACACG
* * * * * *
34817315 TAGTAGCCTACACATAGTACTACACACGTGATCAAGTTTTTCGGTTCACGAAGTAGCCTTCACAT
1 TAGTAGCCTACACACAGTACTACACAAGTGACCAAGCTTCTCGGTACACGAAGTAGCCTTCACAT
* * * *
34817380 AGTACTACACACGTGATCAAAGCTTTTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGT
66 AGTACTACACACGTGACCAAA-CTTTTCGATACACATAGTAGCCTTCACATAGTACTACACATGC
*
34817445 GACC-ATTATTTATCGATACACG
130 GACCTATCA-TTAT-GATACACG
* *
34817467 TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACAC-ATTGTAGCCTTCAC
1 TAGTAGCCTACACACAGTACTACACAAGTGACC-AAGCTTCTCGGTACACGA-AGTAGCCTTCAC
* * * ** *
34817531 TTAGTACTACACATGTGACCATTA-TTTATCGATACATGTAGTAGCCTTCACACAGTACTACACA
64 ATAGTACTACACACGTGACCA-AACTTT-TCGATACACATAGTAGCCTTCACATAGTACTACACA
34817595 CGTGTTCATC
Statistics
Matches: 233, Mismatches: 38, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
150 7 0.03
151 81 0.35
152 71 0.30
153 73 0.31
154 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (150 bp):
TAGTAGCCTACACACAGTACTACACAAGTGACCAAGCTTCTCGGTACACGAAGTAGCCTTCACAT
AGTACTACACACGTGACCAAACTTTTCGATACACATAGTAGCCTTCACATAGTACTACACATGCG
ACCTATCATTATGATACACG
Found at i:34825089 original size:19 final size:16
Alignment explanation
Indices: 34825055--34825087 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
34825045 TGGATGCTTT
34825055 GTTGTACAAGGAAGCA
1 GTTGTACAAGGAAGCA
34825071 GTTGTACAAGGAAGCA
1 GTTGTACAAGGAAGCA
34825087 G
1 G
34825088 CAAAAAGCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.33, T:0.18
Consensus pattern (16 bp):
GTTGTACAAGGAAGCA
Found at i:34828844 original size:2 final size:2
Alignment explanation
Indices: 34828837--34828881 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
34828827 TATAAGTTGG
34828837 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
34828879 AT A
1 AT A
34828882 CTNNNNNNNN
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34829597 original size:18 final size:17
Alignment explanation
Indices: 34829574--34829634 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
34829564 CAAAGCACCA
34829574 GGTCCGATGGCAGACCCG
1 GGTCCGATGGCAG-CCCG
* *
34829592 GGTCCGATGGCCGCCCCT
1 GGTCCGATGGCAG-CCCG
*
34829610 GGTCCGATGGCTGCGCCG
1 GGTCCGATGGCAGC-CCG
34829628 GGTCCGA
1 GGTCCGA
34829635 AAGTTGCGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 1 0.03
18 36 0.97
ACGTcount: A:0.10, C:0.36, G:0.39, T:0.15
Consensus pattern (17 bp):
GGTCCGATGGCAGCCCG
Found at i:34833208 original size:21 final size:21
Alignment explanation
Indices: 34833165--34833208 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
34833155 CTCAACTTCC
* **
34833165 TCCCCGTACTATATGTATTAT
1 TCCCCGTACAATATGTACCAT
*
34833186 TCCCCGTAGAATATGTACCAT
1 TCCCCGTACAATATGTACCAT
34833207 TC
1 TC
34833209 TATCGATCTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.36
Consensus pattern (21 bp):
TCCCCGTACAATATGTACCAT
Found at i:34849392 original size:43 final size:42
Alignment explanation
Indices: 34849343--34849455 Score: 154
Period size: 43 Copynumber: 2.6 Consensus size: 42
34849333 TATGATTTCG
* * *
34849343 TGTAAGACCATGTCTGGGACATTGGCATCGGTATGAGATTACC
1 TGTAAGACCATATCTGGGACA-TGGCATCGGTATGAGATAACA
* *
34849386 TGTAAGACCCTATCTGGGACAGTGGCATCGGTATGTGATAACA
1 TGTAAGACCATATCTGGGACA-TGGCATCGGTATGAGATAACA
*
34849429 TGTAAGACCATATCTGGGATATGGCAT
1 TGTAAGACCATATCTGGGACATGGCAT
34849456 TGTATGTGAT
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
42 6 0.10
43 56 0.90
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGACATGGCATCGGTATGAGATAACA
Found at i:34850053 original size:23 final size:23
Alignment explanation
Indices: 34850022--34850149 Score: 57
Period size: 23 Copynumber: 5.4 Consensus size: 23
34850012 AATGATAAGG
*
34850022 TGCTATCCAAATTGGTGCTTAAA
1 TGCTGTCCAAATTGGTGCTTAAA
* **
34850045 TGCTGTCC-ATTTTTTAGCAAATT-AA
1 TGCTGTCCAAATTGGT-GC---TTAAA
* *
34850070 TGTTGTCCAAATTGGTGCTTAAT
1 TGCTGTCCAAATTGGTGCTTAAA
** *
34850093 TGCTGTCC--ATTCTTTAGCATATTAA
1 TGCTGTCCAAATT-GGT-GC-T-TAAA
* *
34850118 TGCTATCCAAATTAGTGCTTAAA
1 TGCTGTCCAAATTGGTGCTTAAA
34850141 TGCTGTCCA
1 TGCTGTCCA
34850150 TTTTTGTACA
Statistics
Matches: 74, Mismatches: 19, Indels: 24
0.63 0.16 0.21
Matches are distributed among these distances:
21 3 0.04
22 7 0.09
23 30 0.41
24 2 0.03
25 22 0.30
26 7 0.09
27 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.40
Consensus pattern (23 bp):
TGCTGTCCAAATTGGTGCTTAAA
Found at i:34850098 original size:48 final size:48
Alignment explanation
Indices: 34850022--34850173 Score: 216
Period size: 48 Copynumber: 3.2 Consensus size: 48
34850012 AATGATAAGG
*
34850022 TGCTATCCAAATTGGTGCTTAAATGCTGTCCATTTTTTAGCAAATTAA
1 TGCTGTCCAAATTGGTGCTTAAATGCTGTCCATTTTTTAGCAAATTAA
* * * *
34850070 TGTTGTCCAAATTGGTGCTTAATTGCTGTCCATTCTTTAGCATATTAA
1 TGCTGTCCAAATTGGTGCTTAAATGCTGTCCATTTTTTAGCAAATTAA
* * *
34850118 TGCTATCCAAATTAGTGCTTAAATGCTGTCCATTTTTGTA-CAAATCAA
1 TGCTGTCCAAATTGGTGCTTAAATGCTGTCCATTTTT-TAGCAAATTAA
34850166 TGCTGTCC
1 TGCTGTCC
34850174 GAATGTTGTT
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
48 88 0.98
49 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.40
Consensus pattern (48 bp):
TGCTGTCCAAATTGGTGCTTAAATGCTGTCCATTTTTTAGCAAATTAA
Found at i:34850962 original size:2 final size:2
Alignment explanation
Indices: 34850901--34850947 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
34850891 TTTGGTTATG
34850901 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
34850943 TA TA T
1 TA TA T
34850948 GAATTTAACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34851664 original size:28 final size:28
Alignment explanation
Indices: 34851632--34851700 Score: 138
Period size: 28 Copynumber: 2.5 Consensus size: 28
34851622 TTTTCCTTTA
34851632 TACTTTATTTTGAATTTTCTGAAATAAT
1 TACTTTATTTTGAATTTTCTGAAATAAT
34851660 TACTTTATTTTGAATTTTCTGAAATAAT
1 TACTTTATTTTGAATTTTCTGAAATAAT
34851688 TACTTTATTTTGA
1 TACTTTATTTTGA
34851701 TTGATATTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (28 bp):
TACTTTATTTTGAATTTTCTGAAATAAT
Found at i:34853582 original size:21 final size:21
Alignment explanation
Indices: 34853544--34853583 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
34853534 TTATTAATTA
* **
34853544 TTATTTAATAAATTATAGAAT
1 TTATCTAATAAAAAATAGAAT
34853565 TTATCTAATAAAAAATAGA
1 TTATCTAATAAAAAATAGA
34853584 GAATTTATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (21 bp):
TTATCTAATAAAAAATAGAAT
Found at i:34856052 original size:27 final size:27
Alignment explanation
Indices: 34856013--34856065 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
34856003 TTGCGGACTG
34856013 AAAAAGGGCCAGAGCAAAGCACTCCTA
1 AAAAAGGGCCAGAGCAAAGCACTCCTA
* **
34856040 AAAAAGGGTCAGAGCAGGGCACTCCT
1 AAAAAGGGCCAGAGCAAAGCACTCCT
34856066 TTTCTAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.25, G:0.26, T:0.09
Consensus pattern (27 bp):
AAAAAGGGCCAGAGCAAAGCACTCCTA
Found at i:34860457 original size:9 final size:10
Alignment explanation
Indices: 34860435--34860469 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
34860425 TTTAAAATAT
*
34860435 TAAAAATTAC
1 TAAAAATTAG
34860445 TAAAAATT-G
1 TAAAAATTAG
34860454 TAAAAATTAG
1 TAAAAATTAG
34860464 TAAAAA
1 TAAAAA
34860470 CATTAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (10 bp):
TAAAAATTAG
Found at i:34860476 original size:19 final size:20
Alignment explanation
Indices: 34860428--34860498 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 20
34860418 AATTTATTTT
*
34860428 AAAATAT-TAAAAATTACTA
1 AAAATATATAAAAATTAGTA
*
34860447 AAAAT-TGTAAAAATTAGTA
1 AAAATATATAAAAATTAGTA
* * *
34860466 AAAACAT-TAAAATTTTGTA
1 AAAATATATAAAAATTAGTA
34860485 AAAATATATAAAAA
1 AAAATATATAAAAA
34860499 AAATTTAGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
18 1 0.02
19 36 0.84
20 6 0.14
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (20 bp):
AAAATATATAAAAATTAGTA
Found at i:34860483 original size:29 final size:29
Alignment explanation
Indices: 34860451--34860541 Score: 91
Period size: 29 Copynumber: 3.1 Consensus size: 29
34860441 TTACTAAAAA
34860451 TTGTAAAAATTAGTAAAAACA-TTAAAATT
1 TTGTAAAAATTA-TAAAAACATTTAAAATT
*
34860480 TTGTAAAAATATATAAAAAAAATTTAGAAA--
1 TTGTAAAAAT-TAT-AAAAACATTTA-AAATT
34860510 -TGTAAAAATTATTAAAAACATTGTAAAATT
1 TTGTAAAAATTA-TAAAAACATT-TAAAATT
34860540 TT
1 TT
34860542 CAACATCTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
28 13 0.25
29 23 0.45
30 8 0.16
31 4 0.08
32 3 0.06
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (29 bp):
TTGTAAAAATTATAAAAACATTTAAAATT
Found at i:34866453 original size:55 final size:53
Alignment explanation
Indices: 34866384--34866499 Score: 162
Period size: 56 Copynumber: 2.1 Consensus size: 53
34866374 TTCATTCATG
34866384 AATTTCTAAACAAATATATGAAA-AAAAAACAAGAGAAAACCCTTTTTGTAAAAAT
1 AATTTC-AAACAAATATATGAAAGAAAAAACAAGAGAAAACCCTTTTT-T-AAAAT
* * *
34866439 AATTTCAAAGCAAATATGTGAAAGAAAATACAAGAGAAAACGCTTTTTTAAAAT
1 AATTTCAAA-CAAATATATGAAAGAAAAAACAAGAGAAAACCCTTTTTTAAAAT
34866493 AATTTCA
1 AATTTCA
34866500 TTCATGAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
54 15 0.27
55 19 0.34
56 22 0.39
ACGTcount: A:0.53, C:0.10, G:0.09, T:0.27
Consensus pattern (53 bp):
AATTTCAAACAAATATATGAAAGAAAAAACAAGAGAAAACCCTTTTTTAAAAT
Found at i:34866690 original size:63 final size:63
Alignment explanation
Indices: 34866439--34866936 Score: 392
Period size: 63 Copynumber: 7.7 Consensus size: 63
34866429 TTGTAAAAAT
* * *
34866439 AATTTCAAAGCAAATATGTGAAAGAAAATACAAGAGAAAACGCTTTTTTAAAATA-ATTTCATTC
1 AATTTCAAAACAAATATATG--A-AAAA-ACAAGAGAAAAC-CTTTTTTAAAAAATATTTCATTC
34866503 ATG
61 ATG
* * **
34866506 AATTTCAAAGCAAATATATGGAAAAACAAGAGAAAACCCTCTTTTT-AGTAAT-TTT-ATTCATG
1 AATTTCAAAACAAATATATGAAAAAACAAGAGAAAA-CCT-TTTTTAAAAAATATTTCATTCATG
* * ***
34866568 AATTTCAGAACAAAGATATGAACAAAAACAAGAGAAAACCTTCTTTT-TTTAATAATTTCATTCA
1 AATTTCAAAACAAATATATG-A-AAAAACAAGAGAAAACCTT-TTTTAAAAAAT-ATTTCATTCA
34866632 TG
62 TG
34866634 AATTTCAAAACAAA-ATATGAAAAAACAAGAGAAAACCTTTTTTAAAAAATAGTTTCATTCATG
1 AATTTCAAAACAAATATATGAAAAAACAAGAGAAAACCTTTTTTAAAAAATA-TTTCATTCATG
* * * *
34866697 AATCTCAAAGCAAATATATGGAGAAAAGAAGAAGAGAGAAAACC-CTTTTAAAAAA-A--TCATT
1 AATTTCAAAACAAATATAT---GAAAA-AA-CA-AGAGAAAACCTTTTTTAAAAAATATTTCATT
34866758 CATG
60 CATG
* * * * *
34866762 AAATTCAAAACAAATATATGATAAAACAAGAGAAATCCCTTTTTTGAAAAAAAAAAATTCATTCA
1 AATTTCAAAACAAATATATGAAAAAACAAGAGAAA-ACCTTTTTT---AAAAAATATTTCATTCA
34866827 TG
62 TG
* * * * *
34866829 AATCTCAAAGCAAATATATGAAGAAAAAAAAAGAGAAAACC-CTTTTAAAAAA-A-ATCATTCAT
1 AATTTCAAAACAAATATAT---GAAAAAACAAGAGAAAACCTTTTTTAAAAAATATTTCATTCAT
34866891 G
63 G
* * * * *
34866892 AAATTCAGAACAAATATATGATAGAACAAGAGAAATCCCTTTTTT
1 AATTTCAAAACAAATATATGAAAAAACAAGAGAAA-ACCTTTTTT
34866937 TTTTTAAATC
Statistics
Matches: 357, Mismatches: 43, Indels: 67
0.76 0.09 0.14
Matches are distributed among these distances:
59 7 0.02
60 16 0.04
61 8 0.02
62 38 0.11
63 98 0.27
64 37 0.10
65 40 0.11
66 20 0.06
67 49 0.14
68 7 0.02
69 13 0.04
70 24 0.07
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.27
Consensus pattern (63 bp):
AATTTCAAAACAAATATATGAAAAAACAAGAGAAAACCTTTTTTAAAAAATATTTCATTCATG
Found at i:34866746 original size:128 final size:126
Alignment explanation
Indices: 34866443--34866936 Score: 484
Period size: 130 Copynumber: 3.8 Consensus size: 126
34866433 AAAAATAATT
* * * * * *
34866443 TCAAAGCAAATATGTGAAAGAAAATACAAGAGAAAACGCTTTTTTAAAATAATTTCATTCATGAA
1 TCAAAGCAAATATATG-GAGAAAAAAAAAGAGAAAAC-C-CTTTTAAAA-AA-ATCATTCATGAA
* * * **
34866508 TTTCAAAGCAAATATATGGAAAAACAAGAGAAA-ACCCTCTTTTT-AGTAAT-TTT-ATTCATGA
61 ATTCAAAACAAATATATGAAAAAACAAGAGAAATA-CCT-TTTTTAAAAAATATTTCATTCATGA
*
34866569 ATT
124 ATC
* * * **
34866572 TCAGAA-CAAAGATAT-GA-ACAAAAACAAGAGAAAACCTTCTTTTTTTAATAATTTCATTCATG
1 TCA-AAGCAAATATATGGAGA-AAAAAAAAGAGAAAACC--C---TTTTAAAAAAATCATTCATG
*
34866634 AATTTCAAAACAAA-ATATGAAAAAACAAGAGAAA-ACCTTTTTTAAAAAATAGTTTCATTCATG
59 AAATTCAAAACAAATATATGAAAAAACAAGAGAAATACCTTTTTTAAAAAATA-TTTCATTCATG
34866697 AATC
123 AATC
34866701 TCAAAGCAAATATATGGAGAAAAGAAGAAGAGAGAAAACCCTTTTAAAAAAATCATTCATGAAAT
1 TCAAAGCAAATATATGGAGAAAA-AA-AA-AGAGAAAACCCTTTTAAAAAAATCATTCATGAAAT
* * * *
34866766 TCAAAACAAATATATGATAAAACAAGAGAAATCCCTTTTTTGAAAAAAAAAAATTCATTCATGAA
63 TCAAAACAAATATATGAAAAAACAAGAGAAATACCTTTTTT---AAAAAATATTTCATTCATGAA
34866831 TC
125 TC
*
34866833 TCAAAGCAAATATATGAAGAAAAAAAAAGAGAAAACCCTTTTAAAAAAAATCATTCATGAAATTC
1 TCAAAGCAAATATATGGAGAAAAAAAAAGAGAAAACCCTTTT-AAAAAAATCATTCATGAAATTC
* * * *
34866898 AGAACAAATATATGATAGAACAAGAGAAATCCCTTTTTT
65 AAAACAAATATATGAAAAAACAAGAGAAATACCTTTTTT
34866937 TTTTTAAATC
Statistics
Matches: 318, Mismatches: 25, Indels: 43
0.82 0.06 0.11
Matches are distributed among these distances:
125 5 0.02
126 9 0.03
127 37 0.12
128 58 0.18
129 66 0.21
130 83 0.26
131 6 0.02
132 37 0.12
133 17 0.05
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.27
Consensus pattern (126 bp):
TCAAAGCAAATATATGGAGAAAAAAAAAGAGAAAACCCTTTTAAAAAAATCATTCATGAAATTCA
AAACAAATATATGAAAAAACAAGAGAAATACCTTTTTTAAAAAATATTTCATTCATGAATC
Found at i:34867334 original size:4 final size:4
Alignment explanation
Indices: 34867317--34867365 Score: 89
Period size: 4 Copynumber: 12.2 Consensus size: 4
34867307 AATATGCATG
*
34867317 TGTA TGTG TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
34867365 T
1 T
34867366 ATACCTTGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:34872955 original size:16 final size:18
Alignment explanation
Indices: 34872923--34872958 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
34872913 AATATATTGT
34872923 AATATTTGTATTATTTAA
1 AATATTTGTATTATTTAA
34872941 AATATTT-TA-TATTTAA
1 AATATTTGTATTATTTAA
34872957 AA
1 AA
34872959 GACATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 2 0.11
18 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
AATATTTGTATTATTTAA
Found at i:34874670 original size:17 final size:17
Alignment explanation
Indices: 34874648--34874681 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34874638 TATTGGGTTC
34874648 ACCAAAAAGTCTCTTTA
1 ACCAAAAAGTCTCTTTA
* *
34874665 ACCAAATAGTTTCTTTA
1 ACCAAAAAGTCTCTTTA
34874682 CAAGCCTCAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (17 bp):
ACCAAAAAGTCTCTTTA
Found at i:34881643 original size:24 final size:24
Alignment explanation
Indices: 34881615--34881662 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
34881605 ATTTGGTGAG
* *
34881615 TTTAAA-TATAATTTACTCTAATTT
1 TTTAAATTA-AATTGACACTAATTT
34881639 TTTAAATTAAATTGACACTAATTT
1 TTTAAATTAAATTGACACTAATTT
34881663 AAAATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTAAATTAAATTGACACTAATTT
Found at i:34883881 original size:30 final size:28
Alignment explanation
Indices: 34883841--34883896 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 28
34883831 ATATATTTGA
34883841 ACCACAATCAAAGTTTCATGCGTATAATTCC
1 ACCACAATCAAAG-TTCAT--GTATAATTCC
34883872 ACCA-AATCAAAGTTCATGTATAATT
1 ACCACAATCAAAGTTCATGTATAATT
34883897 TTGAGATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 8 0.32
29 5 0.20
30 8 0.32
31 4 0.16
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (28 bp):
ACCACAATCAAAGTTCATGTATAATTCC
Found at i:34884650 original size:3 final size:3
Alignment explanation
Indices: 34884642--34884668 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
34884632 GCCTACTTTT
34884642 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
34884669 TTTCATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:34885322 original size:23 final size:23
Alignment explanation
Indices: 34885293--34885342 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
34885283 TATTCACCAC
34885293 ATAAATAATAATTA-TTATACAAT
1 ATAAATAAT-ATTATTTATACAAT
* *
34885316 ATAAATAATTTTATTTATATAAT
1 ATAAATAATATTATTTATACAAT
34885339 ATAA
1 ATAA
34885343 GTTACGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATAAATAATATTATTTATACAAT
Found at i:34885502 original size:2 final size:2
Alignment explanation
Indices: 34885497--34885526 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34885487 TTTATTTATG
34885497 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
34885527 CCATGCTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34890560 original size:2 final size:2
Alignment explanation
Indices: 34890555--34890593 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
34890545 TGTGTATATA
34890555 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T- TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
34890594 GGTTTCAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:34891250 original size:83 final size:83
Alignment explanation
Indices: 34891153--34891317 Score: 267
Period size: 83 Copynumber: 2.0 Consensus size: 83
34891143 GTAAAGTATG
* *
34891153 ATTCTTCAATTTTTTTTAAATAATATTTATATCGAACATAATATGTATTCGATATTCACTCAAAT
1 ATTCTTCAAATTTTTTTAAATAATATTTATATCAAACATAATATGTATTCGATATTCACTCAAAT
*
34891218 TCAAGTAACAAATTGGGT
66 CCAAGTAACAAATTGGGT
* *
34891236 ATTCTTCAAATTTTTTTAAATAATATTTATATCAAACATAATATGTATTCGATATTCGCTCACAT
1 ATTCTTCAAATTTTTTTAAATAATATTTATATCAAACATAATATGTATTCGATATTCACTCAAAT
* *
34891301 CCGAGTAACAGATTGGG
66 CCAAGTAACAAATTGGG
34891318 GATATGGTCT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 75 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (83 bp):
ATTCTTCAAATTTTTTTAAATAATATTTATATCAAACATAATATGTATTCGATATTCACTCAAAT
CCAAGTAACAAATTGGGT
Found at i:34892466 original size:18 final size:19
Alignment explanation
Indices: 34892443--34892478 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
34892433 ATAATTTTGG
*
34892443 AATTTTTATAAA-TATTTA
1 AATTTTTACAAATTATTTA
34892461 AATTTTTACAAATTATTT
1 AATTTTTACAAATTATTT
34892479 TGAATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
AATTTTTACAAATTATTTA
Found at i:34892968 original size:21 final size:21
Alignment explanation
Indices: 34892944--34892986 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
34892934 ATGGGTAAAA
*
34892944 TTTTTACACAAATTCATATTT
1 TTTTTACACAAATTAATATTT
* *
34892965 TTTTTATACAAGTTAATATTT
1 TTTTTACACAAATTAATATTT
34892986 T
1 T
34892987 AACAATACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTTACACAAATTAATATTT
Found at i:34898588 original size:25 final size:26
Alignment explanation
Indices: 34898541--34898592 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
34898531 GCCCATTTTT
* * *
34898541 AATAAACATTAAAAAATTGTTTTAAA
1 AATAAAAAATAAAAAATTATTTTAAA
34898567 AATAAAAAATAAAAAA-TATTTTAAA
1 AATAAAAAATAAAAAATTATTTTAAA
34898592 A
1 A
34898593 GTATTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (26 bp):
AATAAAAAATAAAAAATTATTTTAAA
Found at i:34905482 original size:68 final size:69
Alignment explanation
Indices: 34905400--34905527 Score: 197
Period size: 69 Copynumber: 1.9 Consensus size: 69
34905390 TTACCCTATA
* * *
34905400 TTCTACCCTTAATATTATATC-AAAAAAAAGAGAGTAGAGATTATATTCATGAATCATATTACCT
1 TTCTACCCTTAATATTATATCGAAAAAAAAGAGAGTAAAGATCATATTCATAAATCATATTACCT
34905464 CATC
66 CATC
*
34905468 TTCTATCCC-TAATATTGTATCGAAAAAAAAGAGAGTAAAGATCATATTCATAAATCATAT
1 TTCTA-CCCTTAATATTATATCGAAAAAAAAGAGAGTAAAGATCATATTCATAAATCATAT
34905528 ATTCGGAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
68 16 0.30
69 38 0.70
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (69 bp):
TTCTACCCTTAATATTATATCGAAAAAAAAGAGAGTAAAGATCATATTCATAAATCATATTACCT
CATC
Found at i:34911679 original size:23 final size:23
Alignment explanation
Indices: 34911653--34911699 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
34911643 AAATTAGTCC
34911653 TTCAATAATTAAATGGGTAAATT
1 TTCAATAATTAAATGGGTAAATT
34911676 TTCAATAATTAAATGGGTAAATT
1 TTCAATAATTAAATGGGTAAATT
34911699 T
1 T
34911700 CAGTCTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.40
Consensus pattern (23 bp):
TTCAATAATTAAATGGGTAAATT
Found at i:34914791 original size:2 final size:2
Alignment explanation
Indices: 34914784--34914816 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
34914774 CAAACTCTCC
*
34914784 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34914817 GAGTTTTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:34915865 original size:21 final size:21
Alignment explanation
Indices: 34915824--34915867 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
34915814 TTTTAAGAGG
* *
34915824 TTTGAAATTGAATTATAAATT
1 TTTGAAATTAAAATATAAATT
34915845 TTTGAAAGTTAAAATAT-AATT
1 TTTGAAA-TTAAAATATAAATT
34915866 TT
1 TT
34915868 ATCATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (21 bp):
TTTGAAATTAAAATATAAATT
Found at i:34918189 original size:5 final size:6
Alignment explanation
Indices: 34918162--34918187 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
34918152 TTTATTGTTG
34918162 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
34918188 TATGTGAATC
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:34918273 original size:2 final size:2
Alignment explanation
Indices: 34918266--34918296 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
34918256 TAAATAAATA
34918266 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34918297 GAATTAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34918441 original size:2 final size:2
Alignment explanation
Indices: 34918434--34918461 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
34918424 AATAATAATA
34918434 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
34918462 GAATTGAATA
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:34919095 original size:45 final size:46
Alignment explanation
Indices: 34918990--34919124 Score: 193
Period size: 45 Copynumber: 3.0 Consensus size: 46
34918980 ATTTACCGGC
* * * *
34918990 TTACTGATTAAGCAC-TTATGTGCCGACTACTGTTACTGTTACTGA
1 TTACTGATTCAGCACTTTGTGTGTCGAATACTGTTACTGTTACTGA
*
34919035 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTG-
1 TTACTGATTCAGCACTTTGTGTGTCGAATACTGTTACTGTTACTGA
* *
34919080 TTACAGATTCAGCACTTTGTGTGTTGAATACTGTTACTGTTACTG
1 TTACTGATTCAGCACTTTGTGTGTCGAATACTGTTACTGTTACTG
34919125 CTACTGTTAC
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 55 0.68
46 26 0.32
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (46 bp):
TTACTGATTCAGCACTTTGTGTGTCGAATACTGTTACTGTTACTGA
Found at i:34919119 original size:6 final size:6
Alignment explanation
Indices: 34919108--34919150 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
34919098 GTGTGTTGAA
*
34919108 TACTGT TACTGT TACTGC TACTGT TACTGAT TACTGT ATACTG
1 TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT -TACTG
34919151 GTGTGTTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
6 22 0.67
7 11 0.33
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (6 bp):
TACTGT
Found at i:34919131 original size:18 final size:19
Alignment explanation
Indices: 34919108--34919143 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
34919098 GTGTGTTGAA
34919108 TACTGTTACTG-TTACTGC
1 TACTGTTACTGATTACTGC
34919126 TACTGTTACTGATTACTG
1 TACTGTTACTGATTACTG
34919144 TATACTGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.44
Consensus pattern (19 bp):
TACTGTTACTGATTACTGC
Found at i:34919655 original size:13 final size:15
Alignment explanation
Indices: 34919637--34919668 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
34919627 TATATGAAAT
34919637 AATGATT-TT-ATGA
1 AATGATTATTGATGA
34919650 AATGATTATTGATGA
1 AATGATTATTGATGA
34919665 AATG
1 AATG
34919669 CATGAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (15 bp):
AATGATTATTGATGA
Found at i:34940226 original size:16 final size:16
Alignment explanation
Indices: 34940198--34940248 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
34940188 CTAATAATAC
*
34940198 TATTATTTTTATATAT
1 TATTATCTTTATATAT
34940214 TATGTA-CTTTATAT-T
1 TAT-TATCTTTATATAT
*
34940229 ATATTATTTTTATATAT
1 -TATTATCTTTATATAT
34940246 TAT
1 TAT
34940249 ATATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 3 0.10
16 23 0.79
17 3 0.10
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TATTATCTTTATATAT
Found at i:34940255 original size:16 final size:16
Alignment explanation
Indices: 34940204--34940255 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 16
34940194 ATACTATTAT
*
34940204 TTTTATATATTATGTA
1 TTTTATATATTATATA
*
34940220 -CTT-TATATTATATTA
1 TTTTATATATTATA-TA
34940235 TTTTTATATATTATATA
1 -TTTTATATATTATATA
34940252 TTTT
1 TTTT
34940256 TTTATAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
14 8 0.28
15 4 0.14
16 4 0.14
17 4 0.14
18 9 0.31
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTTATATATTATATA
Found at i:34940339 original size:16 final size:16
Alignment explanation
Indices: 34940308--34940337 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34940298 ATGATTATAG
34940308 AAAAAATTTAATAAAT
1 AAAAAATTTAATAAAT
34940324 AAAAAATTT-ATAAA
1 AAAAAATTTAATAAA
34940338 ATTATTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAAATTTAATAAAT
Found at i:34942219 original size:23 final size:22
Alignment explanation
Indices: 34942187--34942248 Score: 88
Period size: 22 Copynumber: 2.7 Consensus size: 22
34942177 TCCGGCTCAT
*
34942187 TTTTTAATTAAAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAACTA-A
34942211 TTTTTATTAAAATTAAAACTAA
1 TTTTTATTAAAATTAAAACTAA
*
34942233 TTGTTATTAAAATTAA
1 TTTTTATTAAAATTAA
34942249 TTGTTATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 15 0.42
24 5 0.14
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAACTAA
Found at i:34942243 original size:16 final size:16
Alignment explanation
Indices: 34942222--34942278 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
34942212 TTTTATTAAA
*
34942222 ATTAAAACTAATTGTT
1 ATTAAAATTAATTGTT
34942238 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
* *
34942254 ATCAAAATTAATTATT
1 ATTAAAATTAATTGTT
34942270 ATTAAAATT
1 ATTAAAATT
34942279 GTATCAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:34942372 original size:28 final size:27
Alignment explanation
Indices: 34942332--34942388 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 27
34942322 ATCTAACATT
* * *
34942332 TTGTTAGTAAAATTATTAATTGTATTAA
1 TTGTTACTAAAATTATCAAAT-TATTAA
34942360 TTGTTACTAAAATTATCAAATTATTAA
1 TTGTTACTAAAATTATCAAATTATTAA
34942387 TT
1 TT
34942389 ATTAATTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (27 bp):
TTGTTACTAAAATTATCAAATTATTAA
Found at i:34942404 original size:76 final size:82
Alignment explanation
Indices: 34942324--34942485 Score: 237
Period size: 83 Copynumber: 2.0 Consensus size: 82
34942314 TTTGTAAAAT
34942324 CTAACATTTTGTTAGT-AAA-ATT-A-TTAATTGTATTAATTGTTACTAAAATTATCAAATTAT-
1 CTAACATTTTGTTAGTAAAATATTAATTTAATTGTATTAATTGTTACTAAAATTATCAAATTATA
34942384 T-AATTATTAATTGTTA
66 TAAATTATTAATTGTTA
*
34942400 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATT
1 CTAACATTTTGTTAGTAAAA-TATTAA-T-TTAATTGTATTAATTGTTACTAAAATTATCAAATT
34942465 ATATCAAATTATTAATTGTTA
63 ATAT-AAATTATTAATTGTTA
34942486 ATTGTATTAA
Statistics
Matches: 75, Mismatches: 1, Indels: 10
0.87 0.01 0.12
Matches are distributed among these distances:
76 16 0.21
77 3 0.04
79 3 0.04
80 1 0.01
83 36 0.48
84 1 0.01
86 15 0.20
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (82 bp):
CTAACATTTTGTTAGTAAAATATTAATTTAATTGTATTAATTGTTACTAAAATTATCAAATTATA
TAAATTATTAATTGTTA
Found at i:34942434 original size:40 final size:40
Alignment explanation
Indices: 34942324--34942437 Score: 141
Period size: 40 Copynumber: 3.0 Consensus size: 40
34942314 TTTGTAAAAT
34942324 CTAACATTTTGTTAGTAAAATTATTAATTGTATTAATTGTTA
1 CTAACATTTTGTTAGTAAAATTATTAATTG--TTAATTGTTA
* * *
34942366 CTAA-A----ATTA-TCAAATTATTAATTATTAATTGTTA
1 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTTA
34942400 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGT
1 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGT
34942438 ATTAATTGTT
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
34 14 0.23
35 1 0.02
36 13 0.22
37 3 0.05
39 3 0.05
40 21 0.35
41 1 0.02
42 4 0.07
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (40 bp):
CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTTA
Found at i:34948284 original size:378 final size:377
Alignment explanation
Indices: 34947584--34948306 Score: 983
Period size: 378 Copynumber: 1.9 Consensus size: 377
34947574 CATCATCTTC
* * *
34947584 ACAAAGCTTCTCCAAATGATGACTCGTTTCAATTTGTCCGTTAAAGTGTTGACTTTTTTCTCGAA
1 ACAAAGCTTCTCCAAATGAAGACTCGTTTCAATTTGTCCATTAAAGTGTTGACTTTCTTCTCGAA
34947649 CCTCATTAATCGATTCCCTTCTGCCTTCCATTTGTTCTTCAAACCCTTCCGTTCTTCCATCACAA
66 CCTCATTAATCGATTCCCTTCTGCCTTCCATTTGTTCTTCAAACCCTTCCGTTCTTCCATCACAA
34947714 GCTCTATCCTGGCCTTTCACTTCAACACTTTGTCTTTCAACTTCACACCGAGTTTCAGATTCTGC
131 GCTCTATCCTGGCCTTTCACTTCAACACTTTGTCTTTCAACTTCACACCGAGTTTCAGATTC-GC
* ** * * * *
34947779 AGCTTGACCACTGTTTACCCCATTACAGACATCAAAAGCCTCGACTTCACTCCACTTCCCTTGGA
195 AGCTCGACCACCATTTACCCCACTACAGACATCAAAAGCCTCAACTTCACTCCACTTCCCTCGAA
* * * * * * * *
34947844 CTAAAGTTTGATCTTCCTTCTCAACGCTATTTGAAACGTTCAACCTATGACTCATTTCCTCCTCA
260 CCAAAGCTCGATCTTCCTTCTCAACACAATTTGAAACGTTCAACCCAAGACTCATCTCCTCCTCA
34947909 TT-CTGCAAATCACCATCATCTTCTTTATTAACGCATACGATCTCTCCATTCCT
325 TTCCTG-AAATCACCATCATCTTCTTTATTAACGCATACGATCTCTCCATTCCT
*
34947962 ACAAAGCTTCTCCAAATGAAGACTCAG-TTCAATTTGTTCATTAAAGTGTTGACTTTCTTCTCGA
1 ACAAAGCTTCTCCAAATGAAGACTC-GTTTCAATTTGTCCATTAAAGTGTTGACTTTCTTCTCGA
* *
34948026 ACCTCATTAATGGATTCCCTTCTGCCTTCCATTTGTTCTTCAAACCCTTCCGTTCTTTCATCACA
65 ACCTCATTAATCGATTCCCTTCTGCCTTCCATTTGTTCTTCAAACCCTTCCGTTCTTCCATCACA
* *
34948091 AGCTCTATTCC-GGCCATTT-ACTTCAACACTTTGTCTTTCAACTTCACATCG-TTTCTCAGATT
130 AGCTCTA-TCCTGGCC-TTTCACTTCAACACTTTGTCTTTCAACTTCACACCGAGTT-TCAGATT
* * * ** * *
34948153 C-CAGAACTCGATCACCATTTACTCCACTCCATCCATTGAAAA-CCTCAACTTCACTCCCCTTCC
192 CGCAG--CTCGACCACCATTTACCCCACTACAGACA-TCAAAAGCCTCAACTTCACTCCACTTCC
* * * *
34948216 CTCGAACCAAGGCTCGATCTTCCTTCTCATCACAATTTGAAACTTTCAACCCAAGACTCGTCTCC
254 CTCGAACCAAAGCTCGATCTTCCTTCTCAACACAATTTGAAACGTTCAACCCAAGACTCATCTCC
** *
34948281 TCCTTGTTCCTGAAATCTCCATCATC
319 TCCTCATTCCTGAAATCACCATCATC
34948307 CATACAAACC
Statistics
Matches: 300, Mismatches: 37, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
376 3 0.01
377 2 0.01
378 280 0.93
379 15 0.05
ACGTcount: A:0.24, C:0.32, G:0.10, T:0.35
Consensus pattern (377 bp):
ACAAAGCTTCTCCAAATGAAGACTCGTTTCAATTTGTCCATTAAAGTGTTGACTTTCTTCTCGAA
CCTCATTAATCGATTCCCTTCTGCCTTCCATTTGTTCTTCAAACCCTTCCGTTCTTCCATCACAA
GCTCTATCCTGGCCTTTCACTTCAACACTTTGTCTTTCAACTTCACACCGAGTTTCAGATTCGCA
GCTCGACCACCATTTACCCCACTACAGACATCAAAAGCCTCAACTTCACTCCACTTCCCTCGAAC
CAAAGCTCGATCTTCCTTCTCAACACAATTTGAAACGTTCAACCCAAGACTCATCTCCTCCTCAT
TCCTGAAATCACCATCATCTTCTTTATTAACGCATACGATCTCTCCATTCCT
Found at i:34949222 original size:17 final size:20
Alignment explanation
Indices: 34949200--34949240 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
34949190 ATATTTTTAA
*
34949200 ATTTTTTTCC-ATTT-TTTT
1 ATTTTTTCCCAATTTATTTT
34949218 ATTTTTTCCCAATTTATTTT
1 ATTTTTTCCCAATTTATTTT
34949238 ATT
1 ATT
34949241 ATAATATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 4 0.20
20 7 0.35
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTTTTCCCAATTTATTTT
Found at i:34949700 original size:19 final size:20
Alignment explanation
Indices: 34949676--34949714 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
34949666 TTTTGTTACG
34949676 ATAAATCTAAAAT-TTTAAC
1 ATAAATCTAAAATATTTAAC
*
34949695 ATAAATCTCAAATATTTAAC
1 ATAAATCTAAAATATTTAAC
34949715 CTATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAATCTAAAATATTTAAC
Found at i:34958466 original size:36 final size:36
Alignment explanation
Indices: 34958426--34958515 Score: 108
Period size: 36 Copynumber: 2.5 Consensus size: 36
34958416 TGAAAACTTT
* **
34958426 GGACAGTTTGTTCCAGTCAGCGGTGCTGAGAGCTTC
1 GGACAGTTTGTTCCAGTCAGCAGTGCCAAGAGCTTC
* * *
34958462 GGACAGTTTGTCCCAGTCGGCAGTGCCAATAGCTTC
1 GGACAGTTTGTTCCAGTCAGCAGTGCCAAGAGCTTC
* *
34958498 GGATAGTTTGCTCCAGTC
1 GGACAGTTTGTTCCAGTC
34958516 CGAGGGGTCG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.28
Consensus pattern (36 bp):
GGACAGTTTGTTCCAGTCAGCAGTGCCAAGAGCTTC
Found at i:34961156 original size:210 final size:209
Alignment explanation
Indices: 34960795--34961213 Score: 766
Period size: 210 Copynumber: 2.0 Consensus size: 209
34960785 CACAAAGCTA
*
34960795 TACACAATAATACCAAAAACTCCACGATCACATGCGAAAGCAACAAACAAAAGCAAAAAAGAAAG
1 TACACAATAATACCAAAAACTCCACGATCACATACGAAAGCAACAAACAAAAGCAAAAAAGAAAG
* *
34960860 AAAAAGATTCTGAAGTTCATTGAATGAAATGAAATTTAAGCTCCCAACAGTTAAAAAAGCAAATG
66 AAAAAGATTCTCAAGTTCAGTGAATGAAATGAAATTTAAGCTCCCAACAGTTAAAAAAGCAAATG
34960925 TCAAAGCATAAACAGTTCATCTCCCAAATCTATCACGTTACCATTATTCAAAAGAAAATACACAC
131 TCAAAGCATAAACAGTTCATCTCCCAAATCTATCACGTTACCATTATTCAAAAGAAAATACACAC
34960990 TAAGTGCCGCTTAG
196 TAAGTGCCGCTTAG
* * *
34961004 TACACAATAATACCAAAACCTCCACGGATCACATATGAAAGCAACAAACAAAAGCGAAAAAGAAA
1 TACACAATAATACCAAAAACTCCAC-GATCACATACGAAAGCAACAAACAAAAGCAAAAAAGAAA
34961069 GAAAAAGATTCTCAAGTTCAGTGAATGAAATGAAATTTAAGCTCCCAACAGTTAAAAAAGCAAAT
65 GAAAAAGATTCTCAAGTTCAGTGAATGAAATGAAATTTAAGCTCCCAACAGTTAAAAAAGCAAAT
34961134 GTCAAAGCATAAACAGTTCATCTCCCAAATCTATCACGTTACCATTATTCAAAAGAAAATACACA
130 GTCAAAGCATAAACAGTTCATCTCCCAAATCTATCACGTTACCATTATTCAAAAGAAAATACACA
*
34961199 CTAAGTGCTGCTTAG
195 CTAAGTGCCGCTTAG
34961214 CTTGCACATC
Statistics
Matches: 202, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
209 24 0.12
210 178 0.88
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.20
Consensus pattern (209 bp):
TACACAATAATACCAAAAACTCCACGATCACATACGAAAGCAACAAACAAAAGCAAAAAAGAAAG
AAAAAGATTCTCAAGTTCAGTGAATGAAATGAAATTTAAGCTCCCAACAGTTAAAAAAGCAAATG
TCAAAGCATAAACAGTTCATCTCCCAAATCTATCACGTTACCATTATTCAAAAGAAAATACACAC
TAAGTGCCGCTTAG
Found at i:34963534 original size:29 final size:29
Alignment explanation
Indices: 34963476--34963540 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
34963466 AGAACAGTGC
* * *
34963476 TAATAAATAAGTAAATAAATAAAATTAAT
1 TAATTAATAAGGAAATAAATAAAATAAAT
34963505 TAATTAATAAGGAAATAAAT-AAATAAAAT
1 TAATTAATAAGGAAATAAATAAAAT-AAAT
34963534 TAATTAA
1 TAATTAA
34963541 GCAGCGAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.31
Consensus pattern (29 bp):
TAATTAATAAGGAAATAAATAAAATAAAT
Found at i:34963752 original size:21 final size:21
Alignment explanation
Indices: 34963712--34963752 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
34963702 ATTTTTTATT
*
34963712 ATTTTTTAAGAATTTCAATAC
1 ATTTTTTAAGAATTTAAATAC
34963733 ATTTTTTAA-AATTTTAAATA
1 ATTTTTTAAGAA-TTTAAATA
34963753 TCTTCAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTTTTTAAGAATTTAAATAC
Found at i:34963797 original size:17 final size:18
Alignment explanation
Indices: 34963759--34963832 Score: 71
Period size: 18 Copynumber: 4.1 Consensus size: 18
34963749 AATATCTTCA
*
34963759 ATAAATTT-TATTACTCTT
1 ATAAATTTATATTAAT-TT
*
34963777 ATAAATTTTTA-TAATTT
1 ATAAATTTATATTAATTT
34963794 ATAAATTTATATTAATTTT
1 ATAAATTTATATTAA-TTT
* *
34963813 AATAACTTTATATCAATTT
1 -ATAAATTTATATTAATTT
34963832 A
1 A
34963833 GTTTTTTCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
17 12 0.25
18 15 0.31
19 8 0.17
20 13 0.27
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (18 bp):
ATAAATTTATATTAATTT
Found at i:34963822 original size:20 final size:20
Alignment explanation
Indices: 34963777--34963831 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
34963767 TATTACTCTT
*
34963777 ATAAATTTTTAT-AA-TTT-
1 ATAAATTTATATCAATTTTA
*
34963794 ATAAATTTATATTAATTTTA
1 ATAAATTTATATCAATTTTA
*
34963814 ATAACTTTATATCAATTT
1 ATAAATTTATATCAATTT
34963832 AGTTTTTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 11 0.34
18 2 0.06
19 3 0.09
20 16 0.50
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (20 bp):
ATAAATTTATATCAATTTTA
Found at i:34964587 original size:19 final size:19
Alignment explanation
Indices: 34964546--34964588 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
34964536 AAAATAATCG
*
34964546 AAAATCCAACAACAAATTT
1 AAAATCCAACAACAAATTA
*
34964565 AAAATCCAATCAAGAAA-TA
1 AAAATCCAA-CAACAAATTA
34964584 AAAAT
1 AAAAT
34964589 TAAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.63, C:0.16, G:0.02, T:0.19
Consensus pattern (19 bp):
AAAATCCAACAACAAATTA
Found at i:34967254 original size:22 final size:20
Alignment explanation
Indices: 34967228--34967270 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
34967218 AATATTAAAA
34967228 ATATACATTTAATTGATATTTT
1 ATATACATTTAATT-A-ATTTT
**
34967250 ATATATTTTTAATTAATTTT
1 ATATACATTTAATTAATTTT
34967270 A
1 A
34967271 AATTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 1 0.05
22 12 0.63
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
ATATACATTTAATTAATTTT
Found at i:34967690 original size:31 final size:31
Alignment explanation
Indices: 34967647--34967721 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 31
34967637 GAATGGGGCC
*
34967647 TTTTTATTTAAGT-ATTTGAACTATTCAAAAG
1 TTTTTATTTAAGTCA-CTGAACTATTCAAAAG
* *
34967678 TTTTTATCTAAGTCACTGAACTATTCGAAAG
1 TTTTTATTTAAGTCACTGAACTATTCAAAAG
34967709 TTTTTATTTAAGT
1 TTTTTATTTAAGT
34967722 TATTGGGTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 38 0.97
32 1 0.03
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (31 bp):
TTTTTATTTAAGTCACTGAACTATTCAAAAG
Found at i:34970683 original size:12 final size:11
Alignment explanation
Indices: 34970663--34970694 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
34970653 TTGTATAAAA
34970663 ATTATTTTATT
1 ATTATTTTATT
34970674 ATTAATTTTATT
1 ATT-ATTTTATT
34970686 ATTATTTTA
1 ATTATTTTA
34970695 AAGGCATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:34970711 original size:30 final size:30
Alignment explanation
Indices: 34970675--34970734 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
34970665 TATTTTATTA
34970675 TTAATTTTATTATTATTTTAAAGGCATTTG
1 TTAATTTTATTATTATTTTAAAGGCATTTG
* * * *
34970705 TTAATTTTGTTATTTTTTTAGAGGTATTTG
1 TTAATTTTATTATTATTTTAAAGGCATTTG
34970735 CTTGTTAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.25, C:0.02, G:0.13, T:0.60
Consensus pattern (30 bp):
TTAATTTTATTATTATTTTAAAGGCATTTG
Found at i:34974750 original size:16 final size:16
Alignment explanation
Indices: 34974729--34974764 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
34974719 TTTTAAACAC
*
34974729 ATTTAAAGAACAAATA
1 ATTTAAAGAAAAAATA
34974745 ATTTAAAGAAAAAATA
1 ATTTAAAGAAAAAATA
34974761 ATTT
1 ATTT
34974765 GCTTTCCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (16 bp):
ATTTAAAGAAAAAATA
Found at i:34974992 original size:17 final size:17
Alignment explanation
Indices: 34974970--34975022 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
34974960 ATATACAAAA
34974970 ATAA-TTTATAATATAAT
1 ATAATTTTA-AATATAAT
*
34974987 ATAATTTTAAATTTAAT
1 ATAATTTTAAATATAAT
* *
34975004 ATAAATATAAATAT-AT
1 ATAATTTTAAATATAAT
34975020 ATA
1 ATA
34975023 TTTAATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 5 0.16
17 22 0.71
18 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAATTTTAAATATAAT
Found at i:34975013 original size:33 final size:33
Alignment explanation
Indices: 34974979--34975038 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
34974969 AATAATTTAT
34974979 AATAT-AATATA-AT-TTTAA-AT-TTAATATA
1 AATATAAATATATATATTTAATATATTAATATA
34975007 AATATAAATATATATATTTAATATATTAATAT
1 AATATAAATATATATATTTAATATATTAATAT
34975039 TTTTCATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 5 0.19
29 6 0.22
30 2 0.07
31 5 0.19
32 2 0.07
33 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
AATATAAATATATATATTTAATATATTAATATA
Found at i:34975423 original size:9 final size:9
Alignment explanation
Indices: 34975411--34975441 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
34975401 AAATATAAGA
*
34975411 AAAATCATT
1 AAAATTATT
34975420 AAAATTATT
1 AAAATTATT
34975429 AAAATTATT
1 AAAATTATT
34975438 AAAA
1 AAAA
34975442 ACGTATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAATTATT
Found at i:34984539 original size:132 final size:131
Alignment explanation
Indices: 34984301--34984568 Score: 436
Period size: 132 Copynumber: 2.0 Consensus size: 131
34984291 TCAGATCATA
*
34984301 GTTTCTGCTTTTGATTTTATAACTATATGTTAAATGAAGCTTTCGATGGTTTATTTTATCGTAGT
1 GTTTCTGCTTTTGATTTTATAACTATATGTTAAATAAAGCTTTCGATGGTTTATTTTATCGTAGT
34984366 TTGATATTTCTATATTTTCATGATTCTACAAATGTTTATTAATGGAAGCCGACCAGTATAATTTA
66 TTGATATTTC-ATATTTTCATGATTCTACAAATGTTTATTAATGGAAGCCGACCAGTATAATTTA
34984431 CT
130 CT
34984433 GTTTCTGCTTTTGATTTTAATAACTATATGTTAAATAAAGCTTTC-AGTGGTTTATTTTATCGTG
1 GTTTCTGCTTTTGATTTT-ATAACTATATGTTAAATAAAGCTTTCGA-TGGTTTATTTTATC--G
*
34984497 TAGTATT-ATATTTC-TA-TTTCATGATTCTACAAATGTTTATTAATGGAAGCTGACCAGTATAA
62 TAGT-TTGATATTTCATATTTTCATGATTCTACAAATGTTTATTAATGGAAGCCGACCAGTATAA
34984559 TTTACT
126 TTTACT
34984565 GTTT
1 GTTT
34984569 TAATACTCTT
Statistics
Matches: 129, Mismatches: 2, Indels: 10
0.91 0.01 0.07
Matches are distributed among these distances:
132 74 0.57
133 41 0.32
135 12 0.09
136 2 0.02
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (131 bp):
GTTTCTGCTTTTGATTTTATAACTATATGTTAAATAAAGCTTTCGATGGTTTATTTTATCGTAGT
TTGATATTTCATATTTTCATGATTCTACAAATGTTTATTAATGGAAGCCGACCAGTATAATTTAC
T
Found at i:34985116 original size:186 final size:186
Alignment explanation
Indices: 34984802--34985174 Score: 710
Period size: 186 Copynumber: 2.0 Consensus size: 186
34984792 TGCGTGGGTG
34984802 TTTTCTAGCTTTGTTAATTTAAGTACATTCTTTGAGGTTATGATTTTTACTTCAATTTTAACAAT
1 TTTTCTAGCTTTGTTAATTTAAGTACATTCTTTGAGGTTATGATTTTTACTTCAATTTTAACAAT
* *
34984867 TGTAGTTTGTATCTGTAGAACCCTATATTAAACATGAGTCCTTGGTACCCTGGCAATCTTTAAGT
66 TGTAGTTTGTATCTATAGAACCCTATATTAAACATGAGTCCTTGGGACCCTGGCAATCTTTAAGT
34984932 TCTGTATCCTTTTTTTTATCTTTTCATGTACGAGGAGAGCTCAGATTTAAGATTTT
131 TCTGTATCCTTTTTTTTATCTTTTCATGTACGAGGAGAGCTCAGATTTAAGATTTT
*
34984988 TTTTCTAGCTTTGTTAATTTAAGTACATTCTTTGAGTTTATGATTTTTACTTCAATTTTAACAAT
1 TTTTCTAGCTTTGTTAATTTAAGTACATTCTTTGAGGTTATGATTTTTACTTCAATTTTAACAAT
*
34985053 TGTAGTTTGTATCTATAGAACCCTATATTAAACATGAGTCCTTGGGACCTTGGCAATCTTTAAGT
66 TGTAGTTTGTATCTATAGAACCCTATATTAAACATGAGTCCTTGGGACCCTGGCAATCTTTAAGT
34985118 TCTGTATCCTTTTTTTTATCTTTTCATGTACGAGGAGAGCTCAGATTTAAGATTTT
131 TCTGTATCCTTTTTTTTATCTTTTCATGTACGAGGAGAGCTCAGATTTAAGATTTT
34985174 T
1 T
34985175 ATCCTAACCC
Statistics
Matches: 183, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
186 183 1.00
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (186 bp):
TTTTCTAGCTTTGTTAATTTAAGTACATTCTTTGAGGTTATGATTTTTACTTCAATTTTAACAAT
TGTAGTTTGTATCTATAGAACCCTATATTAAACATGAGTCCTTGGGACCCTGGCAATCTTTAAGT
TCTGTATCCTTTTTTTTATCTTTTCATGTACGAGGAGAGCTCAGATTTAAGATTTT
Found at i:34987518 original size:39 final size:39
Alignment explanation
Indices: 34987459--34987542 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
34987449 GAAGTTTACA
*
34987459 TTCTGGTATGCAGATTTTGCCTTTACACACAGGACATAT
1 TTCTAGTATGCAGATTTTGCCTTTACACACAGGACATAT
*
34987498 TTCTAGTATGCAGATTTTGCCTTTACACATAGGACATAT
1 TTCTAGTATGCAGATTTTGCCTTTACACACAGGACATAT
34987537 TTCTAG
1 TTCTAG
34987543 CGTATACCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (39 bp):
TTCTAGTATGCAGATTTTGCCTTTACACACAGGACATAT
Found at i:34988423 original size:9 final size:9
Alignment explanation
Indices: 34988409--34988438 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
34988399 TCAAATTCGT
34988409 ATAACTCGA
1 ATAACTCGA
34988418 ATAACTCGA
1 ATAACTCGA
*
34988427 ATAATTCGA
1 ATAACTCGA
34988436 ATA
1 ATA
34988439 TCAAACTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.27
Consensus pattern (9 bp):
ATAACTCGA
Found at i:34988686 original size:30 final size:31
Alignment explanation
Indices: 34988652--34988711 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
34988642 AAACCTTTTA
*
34988652 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
34988682 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
34988712 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:34992671 original size:2 final size:2
Alignment explanation
Indices: 34992664--34992694 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
34992654 CTAATGCAAT
*
34992664 TC TC TC TC TC TC TC TC GC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
34992695 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.03, T:0.48
Consensus pattern (2 bp):
TC
Found at i:34996044 original size:55 final size:54
Alignment explanation
Indices: 34995951--34996119 Score: 234
Period size: 55 Copynumber: 3.1 Consensus size: 54
34995941 AACGAAAATG
* * *
34995951 AAAAAAAGGGTGTTAGATGTAGAAAAAAAATCTGAAATAAATGAGATTAAATGAAA
1 AAAAAAAGGGTGTTAGATGTAG-GAAAAAAT-TTAAATAAATGAGATTGAATGAAA
34996007 AAAAAAAGGGTGTTAGATGTAGGAAAAAATTTAAAATAAATGAGATTGAATG--A
1 AAAAAAAGGGTGTTAGATGTAGGAAAAAATTT-AAATAAATGAGATTGAATGAAA
* *
34996060 AAAAAAACGGTGTTAGATGTAGGAAAAAAAATTTAAATAAATGAGACTGAATGAAA
1 AAAAAAAGGGTGTTAGATGTAGG--AAAAAATTTAAATAAATGAGATTGAATGAAA
34996116 AAAA
1 AAAA
34996120 GAGTGTGTCA
Statistics
Matches: 103, Mismatches: 5, Indels: 10
0.87 0.04 0.08
Matches are distributed among these distances:
53 23 0.22
54 19 0.18
55 34 0.33
56 27 0.26
ACGTcount: A:0.56, C:0.02, G:0.20, T:0.22
Consensus pattern (54 bp):
AAAAAAAGGGTGTTAGATGTAGGAAAAAATTTAAATAAATGAGATTGAATGAAA
Found at i:34998361 original size:13 final size:13
Alignment explanation
Indices: 34998343--34998367 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34998333 GATCGCGACA
34998343 ATTTTAATTTTTT
1 ATTTTAATTTTTT
34998356 ATTTTAATTTTT
1 ATTTTAATTTTT
34998368 ACTTTCTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTAATTTTTT
Found at i:35005954 original size:22 final size:23
Alignment explanation
Indices: 35005901--35005956 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
35005891 CCCTTTTTTA
* * *
35005901 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
35005924 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
35005946 ATTAAAATTAA
1 ATTAAAATTAA
35005957 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:35005969 original size:16 final size:16
Alignment explanation
Indices: 35005932--35005971 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
35005922 TTAATAAAAT
* *
35005932 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
35005948 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
35005964 TAAAATTA
1 TAAAATTA
35005972 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:35006050 original size:59 final size:61
Alignment explanation
Indices: 35005981--35006160 Score: 274
Period size: 68 Copynumber: 2.9 Consensus size: 61
35005971 ATCAAATTAT
*
35005981 TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC--A--A
35006046 TTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC-A
1 -TAA-T-TATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
35006109 -AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
35006161 ACAAACTTGA
Statistics
Matches: 111, Mismatches: 1, Indels: 11
0.90 0.01 0.09
Matches are distributed among these distances:
59 49 0.44
60 1 0.01
61 2 0.02
63 1 0.01
66 3 0.03
67 1 0.01
68 54 0.49
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.46
Consensus pattern (61 bp):
TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
Found at i:35006077 original size:9 final size:9
Alignment explanation
Indices: 35006044--35006071 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
35006034 TTTATCAAAT
35006044 TATTAATTG
1 TATTAATTG
35006053 TATTAATTG
1 TATTAATTG
35006062 TATTAATTG
1 TATTAATTG
35006071 T
1 T
35006072 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:35006081 original size:68 final size:68
Alignment explanation
Indices: 35005960--35006130 Score: 319
Period size: 68 Copynumber: 2.5 Consensus size: 68
35005950 AAATTAATTG
*
35005960 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
35006023 TGA
66 TGA
35006026 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
35006091 TGA
66 TGA
35006094 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
35006131 TGTAATAAAA
Statistics
Matches: 102, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
66 26 0.25
68 76 0.75
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:35006193 original size:59 final size:60
Alignment explanation
Indices: 35005994--35006194 Score: 218
Period size: 68 Copynumber: 3.2 Consensus size: 60
35005984 TTGTTAATTG
35005994 TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTGTATTAA
1 TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA--TATCAAATTATT--TT-TATT-A
35006059 TT
60 -T
* *
35006061 GTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTA--TTAATT-G
1 -TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA--TATCAAATTATTTTTATTAT
35006121 TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA-A-CAAACTTGATGTTTTATTAT
1 TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATATCAAA-TT-AT-TTTTATTAT
35006182 TATT-ATT-TTGTAA
1 TATTAATTGTTGTAA
35006195 CACTAGTTAA
Statistics
Matches: 123, Mismatches: 4, Indels: 21
0.83 0.03 0.14
Matches are distributed among these distances:
55 4 0.03
56 3 0.02
57 1 0.01
59 46 0.37
60 8 0.07
61 4 0.03
63 3 0.02
64 2 0.02
68 52 0.42
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (60 bp):
TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATATCAAATTATTTTTATTAT
Found at i:35008199 original size:57 final size:57
Alignment explanation
Indices: 35008130--35008244 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
35008120 AAAATCAATT
35008130 TTTAGTTTAAAAAAAAAGGAAAAGGGGGAAAATAAACCTTGAAAGGTCTCCCATGGA
1 TTTAGTTTAAAAAAAAAGGAAAAGGGGGAAAATAAACCTTGAAAGGTCTCCCATGGA
35008187 TTTAGTTTAAAAAAAAAGGAAAAGGGGGAAAATAAACCTTGAAAGGTCTCCCATGGA
1 TTTAGTTTAAAAAAAAAGGAAAAGGGGGAAAATAAACCTTGAAAGGTCTCCCATGGA
35008244 T
1 T
35008245 AAACAAGGCC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.22
Consensus pattern (57 bp):
TTTAGTTTAAAAAAAAAGGAAAAGGGGGAAAATAAACCTTGAAAGGTCTCCCATGGA
Found at i:35010214 original size:13 final size:12
Alignment explanation
Indices: 35010178--35010214 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
35010168 TAATTATGTC
35010178 AAAATTTAAATA
1 AAAATTTAAATA
35010190 AAAATTTAAAATA
1 AAAATTT-AAATA
35010203 AAAATTATAAAT
1 AAAATT-TAAAT
35010215 TATTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 15 0.65
14 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTTAAATA
Found at i:35020335 original size:29 final size:29
Alignment explanation
Indices: 35020301--35020396 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
35020291 ACAAAATTGA
*
35020301 ATAGTTGAATGACCATGTTATAATTTTTC
1 ATAGTTGAATGACCATATTATAATTTTTC
* ** * ** *
35020330 ATAGTTGAGTGACCATAAAAGAAAGTTACTA
1 ATAGTTGAATGACCATATTA-TAA-TTTTTC
* *
35020361 ATAGTCGAATGACCATTTTATAATTTTTC
1 ATAGTTGAATGACCATATTATAATTTTTC
35020390 ATAGTTG
1 ATAGTTG
35020397 GGATAACAAA
Statistics
Matches: 47, Mismatches: 18, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
29 25 0.53
30 4 0.09
31 18 0.38
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (29 bp):
ATAGTTGAATGACCATATTATAATTTTTC
Found at i:35024936 original size:16 final size:16
Alignment explanation
Indices: 35024915--35024945 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35024905 TTCTAAATTT
*
35024915 TCACCAACATACAATG
1 TCACCAACACACAATG
35024931 TCACCAACACACAAT
1 TCACCAACACACAAT
35024946 TGTTGCTGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.35, G:0.03, T:0.16
Consensus pattern (16 bp):
TCACCAACACACAATG
Found at i:35043169 original size:168 final size:166
Alignment explanation
Indices: 35042817--35043298 Score: 493
Period size: 168 Copynumber: 2.9 Consensus size: 166
35042807 TTTCTGCTGG
* ** * *
35042817 TACTTTTTACAAACACATTGACTACATTCCAT-TTTTATATCCAATTCAAAATAACACCTAAACA
1 TACTTTTTACAAACACATTGACTACATTGCATATTGCACAT--AATTCAAAATAACAACT-AA-A
* * * * * * *
35042881 AAAGACTAACGGG-TTCTTCACATACATCCAAGAGATAAAATTCATGAAACGGGCATCACAAAAA
62 ATA-ACTAA-GGGCTTCTTCACATACATTCAAGAGATCAAATTCATGAAATGGGTATAAGAAAAA
* * * * * *
35042945 TTGAGATTTTACACGTAAAATAATAGAACCACTGTCTGTTAA
125 CTGACATTTTACACGTAAAAGAATAGAAACACTGTCCGTCAA
*
35042987 TACTTTTTACAAACACATTGACTACATTGCATATCTGCACATAATTCAAAATAACGAGCTAAAAT
1 TACTTTTTACAAACACATTGACTACATTGCATAT-TGCACATAATTCAAAATAAC-AACTAAAAT
* * *
35043052 AACTAAGGGCTTCTTAACATACATTCAAGAGATCAAATTCATAAAATGGGTATTAGAGAAAA-TG
64 AACTAAGGGCTTCTTCACATACATTCAAGAGATCAAATTCATGAAATGGGTATAAGA-AAAACTG
** * * *
35043116 ACATTTTATGCGTAAACGCATAGAAACACTTTCCGTCAA
128 ACATTTTACACGTAAAAGAATAGAAACACTGTCCGTCAA
*
35043155 TACTTTTTACAAACACATTGACTACATTGCATAGTTGCACCTAATTC----TAA-AAC--AAATA
1 TACTTTTTACAAACACATTGACTACATTGCATA-TTGCACATAATTCAAAATAACAACTAAAATA
*
35043213 ACTAATGGCTTCTTCACATACATTCACA-AGA-CAAAATTCATGAAATGGGTATAAGAAAAACTG
65 ACTAAGGGCTTCTTCACATACATTCA-AGAGATC-AAATTCATGAAATGGGTATAAGAAAAACTG
* *
35043276 ATATTTTACACGTAAATGAATAG
128 ACATTTTACACGTAAAAGAATAG
35043299 TATCAATCGG
Statistics
Matches: 268, Mismatches: 35, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
159 5 0.02
160 73 0.27
161 1 0.00
162 2 0.01
164 3 0.01
167 3 0.01
168 119 0.44
169 8 0.03
170 46 0.17
171 4 0.01
172 4 0.01
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.29
Consensus pattern (166 bp):
TACTTTTTACAAACACATTGACTACATTGCATATTGCACATAATTCAAAATAACAACTAAAATAA
CTAAGGGCTTCTTCACATACATTCAAGAGATCAAATTCATGAAATGGGTATAAGAAAAACTGACA
TTTTACACGTAAAAGAATAGAAACACTGTCCGTCAA
Found at i:35049290 original size:2 final size:2
Alignment explanation
Indices: 35049283--35049325 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
35049273 CTTTAACATT
35049283 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
35049325 T
1 T
35049326 AATCAATCAC
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:35055167 original size:31 final size:31
Alignment explanation
Indices: 35055132--35055203 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
35055122 TTTGATGGAT
*
35055132 TTTGACTTAAGCAACTAGTTATCTGATTTAA
1 TTTGACTTAAGCAACTAATTATCTGATTTAA
*
35055163 TTTGACTTAAGTAACTAATTATCTGATTTAA
1 TTTGACTTAAGCAACTAATTATCTGATTTAA
35055194 TTTGACTTAA
1 TTTGACTTAA
35055204 TTATTCACTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (31 bp):
TTTGACTTAAGCAACTAATTATCTGATTTAA
Found at i:35063809 original size:42 final size:42
Alignment explanation
Indices: 35063750--35063838 Score: 171
Period size: 42 Copynumber: 2.1 Consensus size: 42
35063740 TTTTAACAAT
35063750 CATTTTCATCCCAACACCAATAAGAATGTGAAATGTGGCATA
1 CATTTTCATCCCAACACCAATAAGAATGTGAAATGTGGCATA
35063792 CATTTTCATCCCAACACCAATAAGAATGTGAAATGTGGCATA
1 CATTTTCATCCCAACACCAATAAGAATGTGAAATGTGGCATA
35063834 C-TTTT
1 CATTTT
35063839 ACCGGATGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 4 0.09
42 43 0.91
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.29
Consensus pattern (42 bp):
CATTTTCATCCCAACACCAATAAGAATGTGAAATGTGGCATA
Found at i:35068091 original size:30 final size:30
Alignment explanation
Indices: 35068057--35068121 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
35068047 ATTTGGACTG
** *
35068057 ATTGATTCTTTTTAATAGTACAGGGACTAA
1 ATTGATTCCATTTAATAATACAGGGACTAA
*
35068087 ATTGA-TCCATTTAATAATAGAGGGACTAA
1 ATTGATTCCATTTAATAATACAGGGACTAA
*
35068116 TTTGAT
1 ATTGAT
35068122 CCAGTCACTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.38
Consensus pattern (30 bp):
ATTGATTCCATTTAATAATACAGGGACTAA
Found at i:35068099 original size:29 final size:29
Alignment explanation
Indices: 35068067--35068142 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
35068057 ATTGATTCTT
*
35068067 TTTAATAGTACAGGGACTAAATTGATCCA
1 TTTAATAATACAGGGACTAAATTGATCCA
* *
35068096 TTTAATAATAGAGGGACTAATTTGATCCA
1 TTTAATAATACAGGGACTAAATTGATCCA
* *
35068125 GTCACTATAATACAGGGA
1 TTTA--ATAATACAGGGA
35068143 TTTCCCAGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 28 0.72
31 11 0.28
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (29 bp):
TTTAATAATACAGGGACTAAATTGATCCA
Found at i:35070898 original size:3 final size:3
Alignment explanation
Indices: 35070892--35070918 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
35070882 TATTTTTTTA
35070892 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
35070919 TTTCCGTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:35077921 original size:616 final size:619
Alignment explanation
Indices: 35076746--35078108 Score: 2480
Period size: 616 Copynumber: 2.2 Consensus size: 619
35076736 TTCAGAGAGT
35076746 GATCTTATTCAACTAGTACAACTATTGGTTAAAGCCTAAATTACCCTTCACACATACGGATATTT
1 GATCTTATTCAACTAGTACAACTATTGGTTAAAGCCTAAATTACCCTTCACACATACGGATATTT
35076811 GTAGCCTAATATTCAACCAAAATTGTTAAAAATCAATCTCCCAAATCCCTAAGACACTCCAAAAC
66 GTAGCCTAATATTCAACCAAAATTGTTAAAAATCAATCTCCCAAATCCCTAAGACACTCCAAAAC
35076876 TTGTCACTAATGCGCGTCAATCAAGCCTATTTACAAGGTGATACAAACAAGCCCTTTAACAAAAT
131 TTGTCACTAATGCGCGTCAATCAAGCCTATTTACAAGGTGATACAAACAAGCCCTTTAACAAAAT
35076941 TTTGATAAACTTTAAACTCCCATTTAAAAATTGATTTTATTTCTTAAAATATCTTCAAAGATTAT
196 TTTGATAAACTTTAAACTCCCATTTAAAAATTGATTTTATTTCTTAAAATATCTTCAAAGATTAT
35077006 TCCATAAAGGCCTTTATAATCTAGTTTTTTTTTAAACGGCTTAAAATACTTCAAAGATAAGGATA
261 TCCATAAAGGCCTTTATAATCTAGTTTTTTTTTAAACGGCTTAAAATACTTCAAAGATAAGGATA
35077071 AAGAAAAGACTCTTCAAGGTAGAAGTATCATAAAAGGCCATTATACTAAGAATTGGATGGCATTT
326 AAGAAAAGACTCTTCAAGGTAGAAGTATCATAAAAGGCCATTATACTAAGAATTGGATGGCATTT
35077136 TGTCCCCTCGACTCAAAAACTGAGTAAATTAGTCATTATATGTTAGATCAAATAGCAAATTGGTC
391 TGTCCCCTCGACTCAAAAACTGAGTAAATTAGTCATTATATGTTAGATCAAATAGCAAATTGGTC
35077201 ATTTTGTTAAAAATTCGATCTATTTTTATTGTTAAAAACTAGTTCTTGTAGGTTAGCATAAGGTA
456 ATTTTGTTAAAAATTCGATCTATTTTTATTGTTAAAAACTAGTTCTTGTAGGTTAGCATAAGGTA
35077266 CATGTAGCATGCCACATGTAACCGTTTGATTATTTCGTCAACCACGCCAATTTATTCTTTAAAGT
521 CATGTAGCATGCCACATGTAACCGTTTGATTATTTCGTCAACCACGCCAATTTATTCTTTAAAGT
35077331 AATGAATAGGGACTAATTTGCTTATTTTTTCAA-
586 AATGAATAGGGACTAATTTGCTTATTTTTTCAAC
35077364 GATCTTATTCAACTAGTACAACTATTGGTTAAAGCCTAAATTACCCTTCACACATACGGATATTT
1 GATCTTATTCAACTAGTACAACTATTGGTTAAAGCCTAAATTACCCTTCACACATACGGATATTT
35077429 GTAGCCTAATATTCAACCAAAATTGTTAAAAATCAATCTCCCAAATCCCTAAGACACTCCAAAAC
66 GTAGCCTAATATTCAACCAAAATTGTTAAAAATCAATCTCCCAAATCCCTAAGACACTCCAAAAC
35077494 TTGTCACTAATGCGCGTCAATCAAGCCTATTTACAAGGTGATACAAACAAG-CCTTTAACAAAAT
131 TTGTCACTAATGCGCGTCAATCAAGCCTATTTACAAGGTGATACAAACAAGCCCTTTAACAAAAT
35077558 TTTGATAAACTTT-AACTCCCATTTAAAAATTGATTTTATTTCTTAAAATATCTTCAAAGATTAT
196 TTTGATAAACTTTAAACTCCCATTTAAAAATTGATTTTATTTCTTAAAATATCTTCAAAGATTAT
35077622 TCCATAAAGGCCTTTATAATCTAGTTTTTTTTTAAACGGCTTAAAATACTTCAAAGATAAGGATA
261 TCCATAAAGGCCTTTATAATCTAGTTTTTTTTTAAACGGCTTAAAATACTTCAAAGATAAGGATA
35077687 AAGAAAAGACTCTTCAAGGTAGAAGTATCATAAAAGGCCATTATACTAAGAATTGGATGGCATTT
326 AAGAAAAGACTCTTCAAGGTAGAAGTATCATAAAAGGCCATTATACTAAGAATTGGATGGCATTT
35077752 TGTCCCCTCGACTCAAAAACTGAGTAAATTAGTCATTATATGTTAGATCAAATAGCAAATTGGTC
391 TGTCCCCTCGACTCAAAAACTGAGTAAATTAGTCATTATATGTTAGATCAAATAGCAAATTGGTC
35077817 ATTTTGTTAAAAATTCGATCTATTTTTATTGTTAAAAACTAGTTCTTGTAGGTTAGCATAAGGTA
456 ATTTTGTTAAAAATTCGATCTATTTTTATTGTTAAAAACTAGTTCTTGTAGGTTAGCATAAGGTA
35077882 CATGTAGCATGCCACATGTAACCGTTTGATTATTTCGTCAACCACGCCAATTTATTCTTTAAAGT
521 CATGTAGCATGCCACATGTAACCGTTTGATTATTTCGTCAACCACGCCAATTTATTCTTTAAAGT
35077947 AATGAATAGGGACTAATTTGCTTATTTTTTCAAC
586 AATGAATAGGGACTAATTTGCTTATTTTTTCAAC
* ** * * * * ** ** * *
35077981 AAAATGGA-CCAA--AATGCAA-T-TT-G---ACTCCTAATAAAACCAACTCCGTCACATACGGA
1 GATCT-TATTCAACTAGTACAACTATTGGTTAAAGCCTAA-ATTACC--CTTC-ACACATACGGA
35078037 TATTTGTAGCCTAATATTCAACCAAAATTGTTAAAAATCAATCTCCCAAATCCCTAAGACACTCC
61 TATTTGTAGCCTAATATTCAACCAAAATTGTTAAAAATCAATCTCCCAAATCCCTAAGACACTCC
35078102 AAAACTT
126 AAAACTT
35078109 ACGAAATTCT
Statistics
Matches: 726, Mismatches: 13, Indels: 17
0.96 0.02 0.02
Matches are distributed among these distances:
609 6 0.01
610 4 0.01
612 4 0.01
613 84 0.12
614 1 0.00
615 5 0.01
616 409 0.56
617 31 0.04
618 182 0.25
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (619 bp):
GATCTTATTCAACTAGTACAACTATTGGTTAAAGCCTAAATTACCCTTCACACATACGGATATTT
GTAGCCTAATATTCAACCAAAATTGTTAAAAATCAATCTCCCAAATCCCTAAGACACTCCAAAAC
TTGTCACTAATGCGCGTCAATCAAGCCTATTTACAAGGTGATACAAACAAGCCCTTTAACAAAAT
TTTGATAAACTTTAAACTCCCATTTAAAAATTGATTTTATTTCTTAAAATATCTTCAAAGATTAT
TCCATAAAGGCCTTTATAATCTAGTTTTTTTTTAAACGGCTTAAAATACTTCAAAGATAAGGATA
AAGAAAAGACTCTTCAAGGTAGAAGTATCATAAAAGGCCATTATACTAAGAATTGGATGGCATTT
TGTCCCCTCGACTCAAAAACTGAGTAAATTAGTCATTATATGTTAGATCAAATAGCAAATTGGTC
ATTTTGTTAAAAATTCGATCTATTTTTATTGTTAAAAACTAGTTCTTGTAGGTTAGCATAAGGTA
CATGTAGCATGCCACATGTAACCGTTTGATTATTTCGTCAACCACGCCAATTTATTCTTTAAAGT
AATGAATAGGGACTAATTTGCTTATTTTTTCAAC
Found at i:35090992 original size:31 final size:31
Alignment explanation
Indices: 35090956--35091018 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
35090946 AAGAATTGTT
*
35090956 ATTGAATTATTCAAAAGTTTTCATTTAAGTC
1 ATTGAACTATTCAAAAGTTTTCATTTAAGTC
** * *
35090987 ATTGAACTATTTGACAGTTTTTATTTAAGTC
1 ATTGAACTATTCAAAAGTTTTCATTTAAGTC
35091018 A
1 A
35091019 CCGGGTTGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (31 bp):
ATTGAACTATTCAAAAGTTTTCATTTAAGTC
Found at i:35101259 original size:5 final size:5
Alignment explanation
Indices: 35101239--35101275 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
35101229 TCTAAATTAC
*
35101239 ATAAT AT-AT A-AAT ATAAT ATAAT ATAAT ATATT ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
35101276 ACTTAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
4 6 0.21
5 22 0.79
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:35105213 original size:229 final size:234
Alignment explanation
Indices: 35104799--35105243 Score: 630
Period size: 229 Copynumber: 1.9 Consensus size: 234
35104789 CAAGATATTA
*
35104799 AAAAAGGTTAAATTACTAAAGAAGCCCTTAAACTAGTTTTTTTTAAAAATAAGCCTCTAAACTTT
1 AAAAAGGTCAAATTACTAAAGAAGCCCTTAAACTAGTTTTTTTTAAAAATAAGCCTCTAAACTTT
* * *
35104864 TGTTGCAACTCAAATAAACCCTTATGTTTTGATTTGTATTTAAATTAGCTCTTAAATAATGATTT
66 TGTTGCAACTCAAATAAACCCGTATATTTTG--TTGTATTTAAATTAGCCCTTAAATAATGATTT
*
35104929 ATATTAAGAATTTTATTTAAGTTTAAACTAAAGGATAGAGGCTTATTTAGATACAAGTT-AAAGA
129 ATATTAAGAATTTTATTTAAGTATAAACTAAAGGATAGAGGCTTATTTAGATACAAGTTAAAAGA
35104993 TTAAGAGCTTATTTGGTTTTTAAGGGTTTATACAAATCATT
194 TTAAGAGCTTATTTGGTTTTTAAGGGTTTATACAAATCATT
* * *
35105034 AAAAAGGTCAAATTACTACAGAAGCCCTTAAACTAG-TTTTTTTAAAAATATGCTTCTAAACTTT
1 AAAAAGGTCAAATTACTAAAGAAGCCCTTAAACTAGTTTTTTTTAAAAATAAGCCTCTAAACTTT
* *
35105098 TTTTGTAACTCAAATAAACCCGTATATTTTG-T-T-TTTAAATTAGCCCTTAAATAATGATTTAT
66 TGTTGCAACTCAAATAAACCCGTATATTTTGTTGTATTTAAATTAGCCCTTAAATAATGATTTAT
* * ** ** * * *
35105160 ATTGAGAATTTTATTTAGGTATAAGTTGCAGTATAGATGCTTATTTGGATACAAGTTAAAAAAAG
131 ATTAAGAATTTTATTTAAGTATAAACTAAAGGATAGAGGCTTATTTAGATACAAGTT---AAAAG
*
35105225 ATTAAGAGCTTCTTTGGTT
193 ATTAAGAGCTTATTTGGTT
35105244 ACCAATTAAA
Statistics
Matches: 186, Mismatches: 20, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
229 75 0.40
230 1 0.01
231 1 0.01
233 22 0.12
234 53 0.28
235 34 0.18
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (234 bp):
AAAAAGGTCAAATTACTAAAGAAGCCCTTAAACTAGTTTTTTTTAAAAATAAGCCTCTAAACTTT
TGTTGCAACTCAAATAAACCCGTATATTTTGTTGTATTTAAATTAGCCCTTAAATAATGATTTAT
ATTAAGAATTTTATTTAAGTATAAACTAAAGGATAGAGGCTTATTTAGATACAAGTTAAAAGATT
AAGAGCTTATTTGGTTTTTAAGGGTTTATACAAATCATT
Found at i:35107157 original size:16 final size:17
Alignment explanation
Indices: 35107136--35107182 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
35107126 TGCCCAACAC
*
35107136 TAATTT-TTTTTCTTTT
1 TAATTTATTTTTATTTT
35107152 TAATTTATTTTTATTTT
1 TAATTTATTTTTATTTT
*
35107169 T-ATTTAATTTTATT
1 TAATTTATTTTTATT
35107183 GCTAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 18 0.64
17 10 0.36
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (17 bp):
TAATTTATTTTTATTTT
Found at i:35117086 original size:16 final size:15
Alignment explanation
Indices: 35117061--35117091 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
35117051 AGAATCTTTT
35117061 ATTTAATTAATTTAA
1 ATTTAATTAATTTAA
35117076 ATTTAAATTAATTTAA
1 ATTT-AATTAATTTAA
35117092 CCATAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTAATTAATTTAA
Found at i:35128937 original size:15 final size:15
Alignment explanation
Indices: 35128917--35128963 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
35128907 TATGGTGAAA
*
35128917 ATATTATTAATAAAT
1 ATATTAATAATAAAT
*
35128932 ATATTAATAAAAAATT
1 ATATTAATAATAAA-T
*
35128948 ATATTAAGAATAAAT
1 ATATTAATAATAAAT
35128963 A
1 A
35128964 AAGTTTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
ATATTAATAATAAAT
Found at i:35128962 original size:16 final size:16
Alignment explanation
Indices: 35128925--35128962 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
35128915 AAATATTATT
*
35128925 AATAAA-TATATTAAT
1 AATAAATTATATTAAG
*
35128940 AAAAAATTATATTAAG
1 AATAAATTATATTAAG
35128956 AATAAAT
1 AATAAAT
35128963 AAAGTTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
AATAAATTATATTAAG
Found at i:35128993 original size:14 final size:14
Alignment explanation
Indices: 35128971--35129009 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
35128961 ATAAAGTTTT
*
35128971 AATTGAAATGTTAA
1 AATTAAAATGTTAA
*
35128985 AATTAAAATCTTAA
1 AATTAAAATGTTAA
35128999 AATTTAAAATG
1 AA-TTAAAATG
35129010 ACAAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (14 bp):
AATTAAAATGTTAA
Found at i:35138040 original size:15 final size:16
Alignment explanation
Indices: 35138008--35138040 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35137998 ACAATGAGTT
*
35138008 TTTTTTTTTTTAATAA
1 TTTTATTTTTTAATAA
35138024 TTTTATTTTTTAA-AA
1 TTTTATTTTTTAATAA
35138039 TT
1 TT
35138041 GTAATAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTATTTTTTAATAA
Found at i:35139271 original size:21 final size:22
Alignment explanation
Indices: 35139247--35139288 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
35139237 CCGCCACCGC
*
35139247 TTCCGCCGTCTCC-GCCTCCAT
1 TTCCGCCGTCCCCGGCCTCCAT
35139268 TTCCGCCGTCCCCGGCCTCCA
1 TTCCGCCGTCCCCGGCCTCCA
35139289 CTCCCTCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.05, C:0.55, G:0.17, T:0.24
Consensus pattern (22 bp):
TTCCGCCGTCCCCGGCCTCCAT
Found at i:35140239 original size:4 final size:4
Alignment explanation
Indices: 35140230--35140255 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
35140220 GAAGAAGAAG
35140230 AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
35140256 TGGGGTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:35153541 original size:9 final size:9
Alignment explanation
Indices: 35153527--35153558 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
35153517 TTTTGGTTAA
35153527 GAATTAACC
1 GAATTAACC
*
35153536 GAATTACCC
1 GAATTAACC
35153545 GAATTAACC
1 GAATTAACC
35153554 GAATT
1 GAATT
35153559 GAATCACTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (9 bp):
GAATTAACC
Found at i:35156077 original size:24 final size:25
Alignment explanation
Indices: 35156045--35156096 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
35156035 ACATAAGTAA
35156045 ATTA-AATTATTTTTAAAT-TAAAT
1 ATTAGAATTATTTTTAAATGTAAAT
35156068 ATTAGAATTATTTTTAAATGTAAAT
1 ATTAGAATTATTTTTAAATGTAAAT
35156093 -TTAG
1 ATTAG
35156097 TAATACGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 4 0.15
24 18 0.67
25 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (25 bp):
ATTAGAATTATTTTTAAATGTAAAT
Found at i:35160120 original size:271 final size:273
Alignment explanation
Indices: 35159629--35160140 Score: 769
Period size: 271 Copynumber: 1.9 Consensus size: 273
35159619 ATAATTTATT
* ** *
35159629 TATTTTAAACAAATCAGTTTAATATAATGCCACTGGGGAAAATAATTAAATGATTTATTTGTTTG
1 TATTTTAAACAAATCAGTTTAATATAATACCACTGCAGAAAATAATTAAATGA--TATTTGTTTA
* * *
35159694 TTTCTATTTTAGGTACGACAACAGATTTGGAGGAAAAACGTAATGAAGAATCGAAAGGTAAAAAC
64 TTTCTATTTTAGGTACGACAACAGATTTGGAGAAAAAACGTAATGAAGAACCAAAAGGTAAAAAC
* * * *
35159759 TCTAATCTATATGTCTAAAAAATAAATTATTTTAGCCGAATTTATATTGTTAAAAATTTGAATTA
129 TCTAATCTACACGTCTAAAAAATAAATTATTTTAGCCGAATATACATTGTTAAAAATTTGAATTA
*
35159824 AAATTCTCATATCATATTACATATTAAATAAAAAATAAAAATTGTTTAACCAGTGAAGATGAAAT
194 AAATTCTCATATCATATTACATATTAAATAAAAAAGAAAAA-TGTTTAACCAGTGAAGATGAAAT
35159889 TATTTAAAAAAAAACA
258 TATTTAAAAAAAAACA
* * *
35159905 TATTTTAGACAAATCAGTTTAATATGATATCACTGCAGAAAATAATTAAAT-A-ATTT-TTTATT
1 TATTTTAAACAAATCAGTTTAATATAATACCACTGCAGAAAATAATTAAATGATATTTGTTTATT
* * * * * *
35159967 TTTATTTTAGGTATGACTACAGGTTTGGAGAAAAAACGTAATGAAGAACCAAAAGGTAAATACTT
66 TCTATTTTAGGTACGACAACAGATTTGGAGAAAAAACGTAATGAAGAACCAAAAGGTAAAAACTC
35160032 TAATCTACACGTCTAAAAAATAAATTATTTTAGCCGAATATACATTGTTAAAAATTTGAATTAAA
131 TAATCTACACGTCTAAAAAATAAATTATTTTAGCCGAATATACATTGTTAAAAATTTGAATTAAA
* *
35160097 ATTCTCATATCATATTGCATATTAAATCAAAAAGAAAAATGTTT
196 ATTCTCATATCATATTACATATTAAATAAAAAAGAAAAATGTTT
35160141 TAAATCAAAA
Statistics
Matches: 213, Mismatches: 23, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
270 5 0.02
271 158 0.74
272 4 0.02
275 1 0.00
276 45 0.21
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (273 bp):
TATTTTAAACAAATCAGTTTAATATAATACCACTGCAGAAAATAATTAAATGATATTTGTTTATT
TCTATTTTAGGTACGACAACAGATTTGGAGAAAAAACGTAATGAAGAACCAAAAGGTAAAAACTC
TAATCTACACGTCTAAAAAATAAATTATTTTAGCCGAATATACATTGTTAAAAATTTGAATTAAA
ATTCTCATATCATATTACATATTAAATAAAAAAGAAAAATGTTTAACCAGTGAAGATGAAATTAT
TTAAAAAAAAACA
Found at i:35160802 original size:155 final size:155
Alignment explanation
Indices: 35160187--35160812 Score: 779
Period size: 155 Copynumber: 4.0 Consensus size: 155
35160177 ATGGTATCAC
* * * *
35160187 TAGAGAAAATAATTGAATGATTTACTTATTTATTTATCCATTTTTATTTTAGGCAAGACTACAGG
1 TAGAGAAAATAATTGAATGATTTACTTATTTATTTATCCGTTTTTATTTTAGGTACGACTACAAG
* * ** * * *
35160252 TTCGGAAGAAAAATGTAATGAGGAACCGAAAGGTAAAGACCTTAATCTACAAGTATAAAAAATAA
66 TTCGGAAGAAAAACGTAATGAAGAACTAAAAGGTAAAGACCTTAATCTACACGTCTAAAGAATAA
*
35160317 TTTATTTTAGCC-AATTTTACATTGT
131 ATTATTTTAGCCGAA-TTTACATTGT
* *
35160342 TAGAGAAAATAATTGAATGATTTATTTATTTATTTAGTTGTCCGTTTTTATTTTAGGTACAACTA
1 TAGAGAAAATAATTGAATGATTTACTTATTTATTTA----TCCGTTTTTATTTTAGGTACGACTA
* * * * * * *
35160407 CAAGTTCGGAAGGAAAACGCAACGAAGAACAAAAAGGTAAAGAACTTAATCTACATGTCCAATA-
62 CAAGTTCGGAAGAAAAACGTAATGAAGAACTAAAAGGTAAAGACCTTAATCTACACGTCTAA-AG
* *
35160471 ATTAAATTATTTTAGCCAAATTTACATTGT
126 AATAAATTATTTTAGCCGAATTTACATTGT
* *
35160501 TAGAGAAAATAATTGAATGATTTACTTATTTATTTATCCGTTTTTATTTTAGGTACGACTATAGG
1 TAGAGAAAATAATTGAATGATTTACTTATTTATTTATCCGTTTTTATTTTAGGTACGACTACAAG
* * * * * *
35160566 TTCGGAAGAAAAACGTAATCAACAACTAAAAGGTAAAGGCTTTAATCTACACATCTAAAGAATAC
66 TTCGGAAGAAAAACGTAATGAAGAACTAAAAGGTAAAGACCTTAATCTACACGTCTAAAGAATAA
*
35160631 ATTATTTTAGCCGAATTTATATTGT
131 ATTATTTTAGCCGAATTTACATTGT
* * ** * * *
35160656 TAGAGAAAATATTTGAATGATTTATTTATTTATCCATTCGTTTTTATTTCAGGTATGACTACAAG
1 TAGAGAAAATAATTGAATGATTTACTTATTTATTTATCCGTTTTTATTTTAGGTACGACTACAAG
* * *
35160721 TTCGGAAGAAAAACGTAATGAGGAATTGAAAGGTAAAGACCTTAATCTACACGTCTAAAGAATAA
66 TTCGGAAGAAAAACGTAATGAAGAACTAAAAGGTAAAGACCTTAATCTACACGTCTAAAGAATAA
** *
35160786 ATTATTTTAGTTGAATTTAGATTGT
131 ATTATTTTAGCCGAATTTACATTGT
35160811 TA
1 TA
35160813 AAAAATTGAA
Statistics
Matches: 404, Mismatches: 60, Indels: 14
0.85 0.13 0.03
Matches are distributed among these distances:
154 1 0.00
155 269 0.67
159 131 0.32
160 3 0.01
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (155 bp):
TAGAGAAAATAATTGAATGATTTACTTATTTATTTATCCGTTTTTATTTTAGGTACGACTACAAG
TTCGGAAGAAAAACGTAATGAAGAACTAAAAGGTAAAGACCTTAATCTACACGTCTAAAGAATAA
ATTATTTTAGCCGAATTTACATTGT
Found at i:35162679 original size:286 final size:281
Alignment explanation
Indices: 35162048--35163047 Score: 1099
Period size: 286 Copynumber: 3.6 Consensus size: 281
35162038 ACAAAAATGG
* * * * * * * * *
35162048 TTAAAATAAACATTTTTTGAACAAATCAATCTAATTTGATATCATTGGATAAAGTAATTAAATGA
1 TTAAAAAAAACATATTTT-AACAAATCAGTTTAATATGATATCACTAGAGAAAATAATTAAATGA
* * * *
35162113 TTTA-TT-TGT-T-TGTTTTTATTTTAGGTACTG-CAACAGATTCGAAGAAAAAACTTAATGAAG
65 TTTATTTATTTATCTGTTTTTATTTTAGGTAC-GACAACAGGTTCGAAGGAAAAACGTAATGAAG
* *
35162173 AACCGAAAGGTAAAGACCTTAACCTACATGTGTAAAAAATAAATTATTTTAGTCGAAG-TTACAT
129 AACCGAAAGGTAAAAACCTTAACCTACATG-ATAAAAAATAAATTATTTTAGTC--AGTTTACAT
* *
35162237 TGTT-AAAATTTTGAATTAAAATTCTCATCTCATATTGC-A-T---ACTAAATCAAAAATAAAAA
191 TGTTAAAAATTTTGAATTAAAATTCTCATATCATATTGCAATTAAAAC-AAAACAAAAATAAAAA
*
35162296 TTGTTTAACCAGGTGAAGATGAAATTA
255 TTGTTTAACTAGGTGAAGATGAAATTA
* * * * *
35162323 TAAAAAAAAACATGTTTTAAACAAATCAGTTTAATATGATATTAGTGGAGAAAATAATTAAATGA
1 TTAAAAAAAACATATTTT-AACAAATCAGTTTAATATGATATCACTAGAGAAAATAATTAAATGA
* * *
35162388 TTTATTTATTTATCTGTTTTTATTTTAGGTGCGACAACAGGTTCAAAGGAAAAACGTAATGATGA
65 TTTATTTATTTATCTGTTTTTATTTTAGGTACGACAACAGGTTCGAAGGAAAAACGTAATGAAGA
**
35162453 ACCGAAAGGTAAAAATTTTAACCTACATGACTAAAAAATAAATTATTTTAGTCAGTTTTACATTG
130 ACCGAAAGGTAAAAACCTTAACCTACATGA-TAAAAAATAAATTATTTTAGTCAG-TTTACATTG
* *
35162518 TTAAAAATTTTGAATTAAAATTCTCTTATCATATTGCATATTAAAACGAAAACAAAAACAAAAAT
193 TTAAAAATTTTGAATTAAAATTCTCATATCATATTGCA-ATTAAAAC-AAAACAAAAATAAAAAT
35162583 TGTTTAACTAGGTGAAGATGAAATTA
256 TGTTTAACTAGGTGAAGATGAAATTA
*
35162609 TTAAAAAAAACATATTTTCAACAAATCAGTTTAATATGATATCACTAGAGAAAATAATTAAATAA
1 TTAAAAAAAACATATTTT-AACAAATCAGTTTAATATGATATCACTAGAGAAAATAATTAAATGA
* * **
35162674 TTTATTTATTTATCTATTATTATTTTTTAGGTACGATGACAGGTTCGAAGGAAAAAC-TCAATGA
65 TTTATTTATTTATCTGTT-TT-TATTTTAGGTACGACAACAGGTTCGAAGGAAAAACGT-AATGA
* * * * * * *
35162738 AGAACCGAAAGGTAAAGACCTTAATCTACACGTATAAAAAATAAATTATTGTAGCCGAATTAACA
127 AGAACCGAAAGGTAAAAACCTTAACCTACATG-ATAAAAAATAAATTATTTTAGTC-AGTTTACA
* * * *
35162803 TTGTCAAAAA-TTTGAATTAAAATTCTCATATCATATTACACATTAAATCAAAAAATAAAATTAA
190 TTGTTAAAAATTTTGAATTAAAATTCTCATATCATATTGCA-ATTAAAACAAAACA-AAAA-TAA
35162867 AAA-TGTTTTAACTAGGTGAAGATGAAATTA
252 AAATTG-TTTAACTAGGTGAAGATGAAATTA
* * * * * * * *
35162897 TTTAAAAAGA-TTATATTTAACTAAT-TGTTTAATATGATATTACTAGAGAAAATAATTGAACGA
1 TTAAAAAAAACATAT-TTTAACAAATCAGTTTAATATGATATCACTAGAGAAAATAATTAAATGA
** * *
35162960 TTTATTTATTTATC---CATT-TTTTAGGTACGACTACAGGTTCGGAA-GAAAAATGTAATGAAG
65 TTTATTTATTTATCTGTTTTTATTTTAGGTACGACAACAGGTTC-GAAGGAAAAACGTAATGAAG
* *
35163020 AACTGAAAGGTAAAAACCTTAATCTACA
129 AACCGAAAGGTAAAAACCTTAACCTACA
35163048 CTTTACGTTG
Statistics
Matches: 625, Mismatches: 74, Indels: 47
0.84 0.10 0.06
Matches are distributed among these distances:
275 58 0.09
276 2 0.00
277 4 0.01
278 2 0.00
279 101 0.16
280 91 0.15
281 5 0.01
282 2 0.00
283 1 0.00
286 169 0.27
287 53 0.08
288 135 0.22
289 2 0.00
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (281 bp):
TTAAAAAAAACATATTTTAACAAATCAGTTTAATATGATATCACTAGAGAAAATAATTAAATGAT
TTATTTATTTATCTGTTTTTATTTTAGGTACGACAACAGGTTCGAAGGAAAAACGTAATGAAGAA
CCGAAAGGTAAAAACCTTAACCTACATGATAAAAAATAAATTATTTTAGTCAGTTTACATTGTTA
AAAATTTTGAATTAAAATTCTCATATCATATTGCAATTAAAACAAAACAAAAATAAAAATTGTTT
AACTAGGTGAAGATGAAATTA
Found at i:35163345 original size:550 final size:556
Alignment explanation
Indices: 35162654--35163924 Score: 1691
Period size: 574 Copynumber: 2.3 Consensus size: 556
35162644 ATGATATCAC
* * * *
35162654 TAGAGAAAATAATTAAATAATTTATTTATTTATCTATTATTATTTTTTAGGTACGA-TGACAGGT
1 TAGAGAAAATAATTGAATGATTT-TTTATTTATCTGTT-TT-TATTTTAGGTACGACT-ACAGGT
* * *
35162718 TCGAAGGAAAAA-CTCAATGAAGAACCGAAAGGTAAAGACCTTAATCTACACGTATAAAAAATAA
62 TCAAAAGAAAAACCT-AATGAAGAACCGAAAGGTAAAGACCTTAATCTACACGTCTAAAAAATAA
* *
35162782 ATTATTGTAGCCGAATTAACATTGTCAAAAATTTGAATTAAAATTCTCATATCATATTACACATT
126 ATTATTTTAGCCGAATTTACATTGTCAAAAATTTGAATTAAAATTCTCATATCATATTACACATT
* * **
35162847 AAATCAAAAAATAAAATTAAAAATGTTTTAACTAGGTGAAGATGAAATTATTTAAAAAGATTATA
191 AAATC-AAAAATAAAATTAAAAATGTTTTAACTAGGTAAAGATGAAATTATTTAAAAACAACATA
* *
35162912 TTTAACTAATTGTTTAATATGATATTACTAGAGAAAATAATTGAACGATTTATTTATTTATCCAT
255 TTTAACTAATTATTTAATATGATATCACTAGAGAAAATAATTGAACGATTTATTTATTTAT-C--
* * *
35162977 TTTTTAGGTACGACTACAGGTTCGGAAGAAAAATGTAATGAAGAACTGAAAGG-TA-AA-A-AC-
317 TCTTTAGGTACGACTACAAGTTCGGAAGAAAAACGTAATGAAGAACTGAAAGGATATAATACACG
* *
35163037 CT-T-A-A-TCTA-C-ACTTTACGTTGTTAGAGAAAATAATTGAATGATTTATTTACCCGTTTTT
382 CTATAATATTCTACCAAATTTACATTGTTAGAGAAAATAATTGAATGATTTATTTACCCGTTTTT
* * * *
35163096 ATTTTTGATACGACTACAGGTACAAAAGAAAAACGTAATGAAGAACTGAAAGGTAAA-GACCTTA
447 ATTTTAGATACGACTACAAGTACAAAAGAAAAACGTAATGAAGAACCGAAAGGCAAATG-CCTTA
*
35163160 ACCTACACGTCTAAAAAATAAATTATTTTAGCCGAATTTACATTGT
511 AACTACACGTCTAAAAAATAAATTATTTTAGCCGAATTTACATTGT
*
35163206 TAGAGAAAATAATTGAATGATTTGTTTATTTATCTGTTTTTATTTTAGATACGACTACAGGTTCA
1 TAGAGAAAATAATTGAATGATTT-TTTATTTATCTGTTTTTATTTTAGGTACGACTACAGGTTCA
* *
35163271 AAAGAAAAACCTAATGAGGAACCGAAAGGTAAAGACCTTAATCTACATGTCTAAAAAATAAATTA
65 AAAGAAAAACCTAATGAAGAACCGAAAGGTAAAGACCTTAATCTACACGTCTAAAAAATAAATTA
* * *
35163336 TTTTAGCCGAATTTATATTGTCAAAAATTTGAATTAAAATTCTCATATCATGTTACATATTAAAT
130 TTTTAGCCGAATTTACATTGTCAAAAATTTGAATTAAAATTCTCATATCATATTACACATTAAAT
* *
35163401 CAAAAATGAAATTAAAAATGTTTTAACTAGGTAAAGCTGAAATTATTTAAAAACAACATATTTAA
195 CAAAAATAAAATTAAAAATGTTTTAACTAGGTAAAGATGAAATTATTTAAAAACAACATATTTAA
* *
35163466 TTGATTATTTAATATGATATCACTAGAGAAAATAATTGAACGATTTATTTATTTATCTCTTTAGG
260 CTAATTATTTAATATGATATCACTAGAGAAAATAATTGAACGATTTATTTATTTATCTCTTTAGG
35163531 TACGACTACAAGTTCGGAAGAAAAACGTAATGAAGAACTGAAAGGTAAAAATATTAATCTACACG
325 TACGACTACAAGTTCGGAAGAAAAACGTAATGAAGAACTGAAAGG-----ATA-TAA--TACACG
*
35163596 TCTAAAAAATAAATTATTTTAGCCAAATTTACATTGTTAGAGAAAATAATTGAATGATTTATTTA
382 -CT-----AT-AA-TATTCTA-CCAAATTTACATTGTTAGAGAAAATAATTGAATGATTTATTTA
* * * *
35163661 TCCGTTTTTATTTTAGGTTCGACTACAAGTTCAAAAGAAAAACGTAATGAAGAACCGAAAGGCAA
438 CCCGTTTTTATTTTAGATACGACTACAAGTACAAAAGAAAAACGTAATGAAGAACCGAAAGGCAA
35163726 ATGCCTTAAACTACACGTCTAAAAAATAAATTATTTTAGCCGAATTTACATTGT
503 ATGCCTTAAACTACACGTCTAAAAAATAAATTATTTTAGCCGAATTTACATTGT
* * * *
35163780 TAAAGAAAATAATTGAATGA---TTTATTTATCCGTTTTTATTTTAGGTACGACTACAGATACAA
1 TAGAGAAAATAATTGAATGATTTTTTATTTATCTGTTTTTATTTTAGGTACGACTACAGGTTCAA
* * * * *
35163842 AAGAAAAACGTAATGAAGAACCAAAAGGTAAATG--CTTAACCTACACCTCTAAAAAA-ATATTA
66 AAGAAAAACCTAATGAAGAACCGAAAGGTAAA-GACCTTAATCTACACGTCTAAAAAATAAATTA
*
35163904 TTTTAGCCAAATTTACATTGT
130 TTTTAGCCGAATTTACATTGT
35163925 TAGAGAAAAT
Statistics
Matches: 632, Mismatches: 55, Indels: 48
0.86 0.07 0.07
Matches are distributed among these distances:
546 50 0.08
548 1 0.00
549 110 0.17
550 139 0.22
551 5 0.01
552 36 0.06
554 2 0.00
557 1 0.00
558 2 0.00
560 2 0.00
566 1 0.00
568 25 0.04
569 19 0.03
570 68 0.11
571 4 0.01
573 1 0.00
574 165 0.26
575 1 0.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (556 bp):
TAGAGAAAATAATTGAATGATTTTTTATTTATCTGTTTTTATTTTAGGTACGACTACAGGTTCAA
AAGAAAAACCTAATGAAGAACCGAAAGGTAAAGACCTTAATCTACACGTCTAAAAAATAAATTAT
TTTAGCCGAATTTACATTGTCAAAAATTTGAATTAAAATTCTCATATCATATTACACATTAAATC
AAAAATAAAATTAAAAATGTTTTAACTAGGTAAAGATGAAATTATTTAAAAACAACATATTTAAC
TAATTATTTAATATGATATCACTAGAGAAAATAATTGAACGATTTATTTATTTATCTCTTTAGGT
ACGACTACAAGTTCGGAAGAAAAACGTAATGAAGAACTGAAAGGATATAATACACGCTATAATAT
TCTACCAAATTTACATTGTTAGAGAAAATAATTGAATGATTTATTTACCCGTTTTTATTTTAGAT
ACGACTACAAGTACAAAAGAAAAACGTAATGAAGAACCGAAAGGCAAATGCCTTAAACTACACGT
CTAAAAAATAAATTATTTTAGCCGAATTTACATTGT
Found at i:35163709 original size:147 final size:147
Alignment explanation
Indices: 35163489--35164084 Score: 713
Period size: 147 Copynumber: 4.0 Consensus size: 147
35163479 ATGATATCAC
* * * **
35163489 TAGAGAAAATAATTGAACGATTTATTTAT---TTATCT-CTTTAGGTACGACTACAAGTTCGGAA
1 TAGAGAAAATAATTGAATGATTTATTTATCCGTT-TTTATTTTAGGTACGACTACAAGTTCAAAA
** **
35163550 GAAAAACGTAATGAAGAACTGAAAGGTAAAAATATTAATCTACACGTCTAAAAAATAAATTATTT
65 GAAAAACGTAATGAAGAACCAAAAGGTAAAAACCTTAATCTACACGTCTAAAAAATAAATTATTT
35163615 TAGCCAAATTTACATTGT
130 TAGCCAAATTTACATTGT
*
35163633 TAGAGAAAATAATTGAATGATTTATTTATCCGTTTTTATTTTAGGTTCGACTACAAGTTCAAAAG
1 TAGAGAAAATAATTGAATGATTTATTTATCCGTTTTTATTTTAGGTACGACTACAAGTTCAAAAG
* * ** *
35163698 AAAAACGTAATGAAGAACCGAAAGGCAAATGCCTTAAACTACACGTCTAAAAAATAAATTATTTT
66 AAAAACGTAATGAAGAACCAAAAGGTAAAAACCTTAATCTACACGTCTAAAAAATAAATTATTTT
*
35163763 AGCCGAATTTACATTGT
131 AGCCAAATTTACATTGT
* *
35163780 TAAAGAAAATAATTGAATGATTTATTTATCCGTTTTTATTTTAGGTACGACTAC-AGATACAAAA
1 TAGAGAAAATAATTGAATGATTTATTTATCCGTTTTTATTTTAGGTACGACTACAAG-TTCAAAA
** * * *
35163844 GAAAAACGTAATGAAGAACCAAAAGGT-AAATGCTTAACCTACACCTCTAAAAAA-ATATTATTT
65 GAAAAACGTAATGAAGAACCAAAAGGTAAAAACCTTAATCTACACGTCTAAAAAATAAATTATTT
35163907 TAGCCAAATTTACATTGT
130 TAGCCAAATTTACATTGT
* * *
35163925 TAGAGAAAATGATTGAATGATTTATTAATTTATTTACTTATTCGTTTTTATTTTAGATACGGCTA
1 TAGAGAAAATAATTGAATGA--T-TT-ATTTA--T-C-----CGTTTTTATTTTAGGTACGACTA
* * * * *
35163990 CAGGTTTAGAAGAAAAACGTAATGAGGAACCAAAAGGTAAAGACCTTAATCTACACGTCT-AAAA
54 CAAGTTCAAAAGAAAAACGTAATGAAGAACCAAAAGGTAAAAACCTTAATCTACACGTCTAAAAA
**
35164054 ATAAATTATTTTAGCTGAATTTACATTGT
119 ATAAATTATTTTAGCCAAATTTACATTGT
35164083 TA
1 TA
35164085 AAATTTTGAA
Statistics
Matches: 389, Mismatches: 43, Indels: 26
0.85 0.09 0.06
Matches are distributed among these distances:
144 28 0.07
145 43 0.11
146 26 0.07
147 183 0.47
148 2 0.01
149 5 0.01
151 1 0.00
152 1 0.00
157 57 0.15
158 43 0.11
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (147 bp):
TAGAGAAAATAATTGAATGATTTATTTATCCGTTTTTATTTTAGGTACGACTACAAGTTCAAAAG
AAAAACGTAATGAAGAACCAAAAGGTAAAAACCTTAATCTACACGTCTAAAAAATAAATTATTTT
AGCCAAATTTACATTGT
Done.