Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 8 of 228
Found at i:2790778 original size:3 final size:3
Alignment explanation
Indices: 2790770--2790800 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2790760 TACAAACTAC
2790770 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2790801 CAGCACACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2791723 original size:19 final size:19
Alignment explanation
Indices: 2791699--2791736 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2791689 TATCCTATCC
2791699 TATGTATGGTAGCCCTATT
1 TATGTATGGTAGCCCTATT
*
2791718 TATGTATGGTAGCCTTATT
1 TATGTATGGTAGCCCTATT
2791737 AAGTAATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.45
Consensus pattern (19 bp):
TATGTATGGTAGCCCTATT
Found at i:2798674 original size:3 final size:3
Alignment explanation
Indices: 2798666--2798704 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2798656 GAACTCTTAA
2798666 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2798705 TAACATAAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2803708 original size:21 final size:21
Alignment explanation
Indices: 2803682--2803722 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2803672 ATCTGCTCAA
* *
2803682 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2803703 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2803723 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2804139 original size:31 final size:31
Alignment explanation
Indices: 2804094--2804152 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2804084 ATTATTAAAT
2804094 TATTCGAAAATTTTTATTTAAGTCACTGAAC
1 TATTCGAAAATTTTTATTTAAGTCACTGAAC
2804125 TATTC-AAAACTTTTTATTTAAGTCACTG
1 TATTCGAAAA-TTTTTATTTAAGTCACTG
2804153 GAAGTTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (31 bp):
TATTCGAAAATTTTTATTTAAGTCACTGAAC
Found at i:2806347 original size:11 final size:11
Alignment explanation
Indices: 2806321--2806359 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
2806311 GCTCTAAAGT
2806321 TGAAAAAATCA
1 TGAAAAAATCA
*
2806332 T--AAAAATTA
1 TGAAAAAATCA
2806341 TGAAAAAATCA
1 TGAAAAAATCA
2806352 TGAAAAAA
1 TGAAAAAA
2806360 GCCTGGGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 8 0.33
11 16 0.67
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.21
Consensus pattern (11 bp):
TGAAAAAATCA
Found at i:2813019 original size:33 final size:32
Alignment explanation
Indices: 2812975--2813046 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 32
2812965 TCTTTTTTGT
*
2812975 AATTGTTGCTATTGATTCAAAAATGATTTAAA
1 AATTGTTGCTATTGATTCAAAAAAGATTTAAA
2813007 AACTTGTTGCTATTGATTCAAAAAAGATTTAAA
1 AA-TTGTTGCTATTGATTCAAAAAAGATTTAAA
2813040 AATTGTT
1 AATTGTT
2813047 ACCAACAAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 7 0.18
33 31 0.82
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (32 bp):
AATTGTTGCTATTGATTCAAAAAAGATTTAAA
Found at i:2831735 original size:74 final size:74
Alignment explanation
Indices: 2831648--2831791 Score: 270
Period size: 74 Copynumber: 1.9 Consensus size: 74
2831638 GCCTTGTGGT
* *
2831648 GAAGATGTCAAGTGAAGTGTCACCAAGGAAGCATAAGCCCCATCGGTTATATTCATCAACGTATC
1 GAAGATGTCAAGTGAAGTGCCACCAAGGAAGCATAAGCCCCATCGGTAATATTCATCAACGTATC
2831713 GTGTCTACC
66 GTGTCTACC
2831722 GAAGATGTCAAGTGAAGTGCCACCAAGGAAGCATAAGCCCCATCGGTAATATTCATCAACGTATC
1 GAAGATGTCAAGTGAAGTGCCACCAAGGAAGCATAAGCCCCATCGGTAATATTCATCAACGTATC
2831787 GTGTC
66 GTGTC
2831792 GACCTTTCTC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (74 bp):
GAAGATGTCAAGTGAAGTGCCACCAAGGAAGCATAAGCCCCATCGGTAATATTCATCAACGTATC
GTGTCTACC
Found at i:2837152 original size:10 final size:10
Alignment explanation
Indices: 2837123--2837152 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2837113 CCAACTAGAA
*
2837123 AGAGAGAGAG
1 AGAGAGAGAC
2837133 AGAGAGAGAC
1 AGAGAGAGAC
2837143 AGAGAGAGAC
1 AGAGAGAGAC
2837153 GTAGCAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.43, T:0.00
Consensus pattern (10 bp):
AGAGAGAGAC
Found at i:2837674 original size:21 final size:21
Alignment explanation
Indices: 2837631--2837671 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2837621 TTTTTTTAAA
*
2837631 AATTAATTACCAAAAAATAAT
1 AATTAATTAACAAAAAATAAT
*
2837652 AATTAAATTAACAATAAATA
1 AATT-AATTAACAAAAAATA
2837672 TAAATATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
AATTAATTAACAAAAAATAAT
Found at i:2840388 original size:25 final size:25
Alignment explanation
Indices: 2840354--2840402 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2840344 CTAGGATAAT
*
2840354 CAGAGTTTAAGTGGGA-AACTAAAAA
1 CAGAGTTTAACTGGGAGAA-TAAAAA
2840379 CAGAGTTTAACTGGGAGAATAAAA
1 CAGAGTTTAACTGGGAGAATAAAA
2840403 CCAAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.20
Consensus pattern (25 bp):
CAGAGTTTAACTGGGAGAATAAAAA
Found at i:2842135 original size:21 final size:21
Alignment explanation
Indices: 2842102--2842145 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2842092 AAGATGTGAC
**
2842102 TTGTATTGGATTGAATG-TAAA
1 TTGTATTAAATTG-ATGTTAAA
2842123 TTGTATTAAATTGATGTTAAA
1 TTGTATTAAATTGATGTTAAA
2842144 TT
1 TT
2842146 TACTCGTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (21 bp):
TTGTATTAAATTGATGTTAAA
Found at i:2842652 original size:26 final size:27
Alignment explanation
Indices: 2842604--2842654 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
2842594 GAGCGTCCCG
* *
2842604 TTATATGGCTCTTCGTGATCTTCCCAA
1 TTATATGGCTCTTCATGAACTTCCCAA
*
2842631 TTATA-GGCTCTTTATGAACTTCCC
1 TTATATGGCTCTTCATGAACTTCCC
2842655 GTTAATGCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (27 bp):
TTATATGGCTCTTCATGAACTTCCCAA
Found at i:2842755 original size:25 final size:26
Alignment explanation
Indices: 2842593--2842757 Score: 103
Period size: 25 Copynumber: 6.6 Consensus size: 26
2842583 GTAGCTCTTA
* *
2842593 TGAGCGTCCCGTTATATGGCTCTTCG
1 TGAGCTTCCCGTTATATGGCTCTTTG
* * *
2842619 TGATCTTCCCAATTATA-GGCTCTTTA
1 TGAGCTTCCC-GTTATATGGCTCTTTG
* **
2842645 TGAACTTCCCGTTA-AT-GCTCACT-
1 TGAGCTTCCCGTTATATGGCTCTTTG
* * *
2842668 TGAACTTCCCGTTATATGGCTATTCG
1 TGAGCTTCCCGTTATATGGCTCTTTG
* * *
2842694 -GTGCTTCCCGTTA-ATTGCTC-TTC
1 TGAGCTTCCCGTTATATGGCTCTTTG
* * * *
2842717 AGAGCTACCAGTTATA-AGCTCTTTG
1 TGAGCTTCCCGTTATATGGCTCTTTG
2842742 TGAGCTTCCCGTTATA
1 TGAGCTTCCCGTTATA
2842758 GTGCTTGAGA
Statistics
Matches: 104, Mismatches: 27, Indels: 17
0.70 0.18 0.11
Matches are distributed among these distances:
23 15 0.14
24 27 0.26
25 33 0.32
26 24 0.23
27 5 0.05
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (26 bp):
TGAGCTTCCCGTTATATGGCTCTTTG
Found at i:2843742 original size:45 final size:45
Alignment explanation
Indices: 2843693--2844046 Score: 573
Period size: 45 Copynumber: 7.9 Consensus size: 45
2843683 TCGGCCATGG
* * * * *
2843693 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
2843738 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
2843783 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
2843828 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* *
2843873 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTAGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
2843918 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
2843963 TGCTTCCTCAAATTCTTCCATGAATTATGCATAATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * * **
2844008 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
2844047 CCCACCTCTT
Statistics
Matches: 289, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 289 1.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:2844181 original size:16 final size:16
Alignment explanation
Indices: 2844160--2844191 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2844150 CATTCTGCAT
2844160 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
2844176 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
2844192 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:2848226 original size:33 final size:31
Alignment explanation
Indices: 2848180--2848253 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 31
2848170 TATTTTCATT
*
2848180 ATTTTTTTAATTATTTAACGACGT-TTTT-GTA
1 ATTTTTTTAATTA-TTAAC-ACATATTTTAGTA
2848211 ATTTTTTTCATATTATTAACACATAATTTTAGTA
1 ATTTTTTT-A-ATTATTAACACAT-ATTTTAGTA
2848245 ATTTTTTTA
1 ATTTTTTTA
2848254 CCCTAGATCT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
31 11 0.30
32 6 0.16
33 9 0.24
34 11 0.30
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (31 bp):
ATTTTTTTAATTATTAACACATATTTTAGTA
Found at i:2855868 original size:16 final size:16
Alignment explanation
Indices: 2855847--2855903 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
2855837 TTTGGTTCGC
*
2855847 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
2855863 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
2855879 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
2855895 TGTAATGGA
1 TGTAATGGA
2855904 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:2856170 original size:18 final size:17
Alignment explanation
Indices: 2856149--2856183 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2856139 TTATTATTAA
*
2856149 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
2856167 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
2856184 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:2856320 original size:16 final size:16
Alignment explanation
Indices: 2856283--2856324 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2856273 TTAATCATAT
*
2856283 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
2856299 TT-AAATATATTATAA
1 TTAAAATATATTATAA
2856314 TTAAAATATAT
1 TTAAAATATAT
2856325 AATTTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:2856321 original size:154 final size:156
Alignment explanation
Indices: 2856036--2856333 Score: 537
Period size: 154 Copynumber: 1.9 Consensus size: 156
2856026 TAGAATACCC
2856036 TTAGCAGAAATTTGTTTTGATAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGATAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-TA
*
2856101 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
65 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
2856166 TATATAATTTAATAAAATTCTTAATAA
130 TATATAATTTAATAAAATTCTTAATAA
* * *
2856193 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-A-
1 TTAGCAGAAATTTGTTTTGATAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
2856256 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
66 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
2856321 ATATAATTTAATA
131 ATATAATTTAATA
2856334 TGAATTTACT
Statistics
Matches: 137, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
154 77 0.56
155 1 0.01
157 59 0.43
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (156 bp):
TTAGCAGAAATTTGTTTTGATAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
ATATAATTTAATAAAATTCTTAATAA
Found at i:2856331 original size:14 final size:15
Alignment explanation
Indices: 2856292--2856426 Score: 70
Period size: 15 Copynumber: 8.9 Consensus size: 15
2856282 TTTAAACATA
*
2856292 ATTATTATTAAATAT
1 ATTATAATTAAATAT
2856307 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
2856321 A-TATAATTTAATAT
1 ATTATAATTAAATAT
*
2856335 GAATTTACTCAAATCATAATAT
1 --A-TTA-T--AATTA-AATAT
* *
2856357 ATGATACTGTAAA-AT
1 ATTATAAT-TAAATAT
2856372 A-TA-AATTAACATA-
1 ATTATAATTAA-ATAT
*
2856385 ATTATTATTAAATAT
1 ATTATAATTAAATAT
2856400 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
2856414 A-TATAATTTAATA
1 ATTATAATTAAATA
2856427 AAATTCTTAA
Statistics
Matches: 92, Mismatches: 12, Indels: 33
0.67 0.09 0.24
Matches are distributed among these distances:
12 3 0.03
13 22 0.24
14 16 0.17
15 30 0.33
16 5 0.05
17 1 0.01
18 3 0.03
19 3 0.03
20 1 0.01
21 3 0.03
22 5 0.05
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:2856390 original size:154 final size:155
Alignment explanation
Indices: 2856075--2856390 Score: 401
Period size: 154 Copynumber: 2.0 Consensus size: 155
2856065 ATTGTTATTG
2856075 TTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATAATTTAATCATATTTAAACATAAT
1 TTATTTAAATTTTAATAAGATTA-TATTATCAATAATAAATAATTTAATCATATTTAAACATAAT
* *
2856140 TATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCATAAATT
65 TATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA-TAGCATAAATA
** * * *** **
2856205 TGTTTTGGTAAATTATTATTGTTATTG
129 TGTACTGGTAAAATATAATTAACATAA
2856232 TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAACATAATT
1 TTATTTAAATTTTAATAAGATTATATTATCAATAATAAATAATTTAATCATATTTAAACATAATT
* * *
2856295 ATTATTAAATATATTATAATTAAAATATATAATTTAATATGAA-T-TTACTCAA-ATCATAATAT
66 ATTATTAAATATATTATAATTAAAATATATAATTTAATA-AAATTCTTAAT-AATAGCATAA-AT
2856357 ATGATACT-GTAAAATATAAATTAACATAA
128 ATG-TACTGGTAAAATAT-AATTAACATAA
2856386 TTATT
1 TTATT
2856391 ATTAAATATA
Statistics
Matches: 140, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
152 6 0.04
153 16 0.11
154 92 0.66
155 3 0.02
157 23 0.16
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (155 bp):
TTATTTAAATTTTAATAAGATTATATTATCAATAATAAATAATTTAATCATATTTAAACATAATT
ATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATAGCATAAATATG
TACTGGTAAAATATAATTAACATAA
Found at i:2856441 original size:44 final size:43
Alignment explanation
Indices: 2856352--2856442 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 43
2856342 CTCAAATCAT
* * *
2856352 AATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
* * *
2856395 AATATATTATAAT-TAAAATATATAATTTAATAAAATTCTTAATA
1 AATATATGATAATGTAAAATATA-AA-TTAACAAAATTATTAATA
2856439 AATA
1 AATA
2856443 AATTCTTCTA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 9 0.22
43 13 0.32
44 18 0.45
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (43 bp):
AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
Found at i:2856474 original size:119 final size:118
Alignment explanation
Indices: 2856332--2856549 Score: 343
Period size: 119 Copynumber: 1.8 Consensus size: 118
2856322 TATAATTTAA
* * *
2856332 TATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA-TT-AACATAATTATTATTA
1 TATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AAATTTCAA-ATAATTAATATTA
2856395 AATAT-ATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAAATTCTTC
64 AATATGATT-TAATT-AAATATATAATTTAATAAAATTCTTAATAAATAAATTCTTC
2856451 TATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATTTCAAATAATTAATATTAAA
1 TATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATTTCAAATAATTAATATTAAA
*
2856516 TATGATTTAATTAAATATATGATTTAATAAAATT
66 TATGATTTAATTAAATATATAATTTAATAAAATT
2856550 TAAAATTATT
Statistics
Matches: 92, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
118 24 0.26
119 63 0.68
120 5 0.05
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (118 bp):
TATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATTTCAAATAATTAATATTAAA
TATGATTTAATTAAATATATAATTTAATAAAATTCTTAATAAATAAATTCTTC
Found at i:2856530 original size:15 final size:15
Alignment explanation
Indices: 2856510--2856548 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
2856500 AATAATTAAT
2856510 ATTAAATATGATTTA
1 ATTAAATATGATTTA
2856525 ATTAAATATATGATTTA
1 ATT-AA-ATATGATTTA
*
2856542 ATAAAAT
1 ATTAAAT
2856549 TTAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.24
16 4 0.19
17 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (15 bp):
ATTAAATATGATTTA
Found at i:2856535 original size:17 final size:17
Alignment explanation
Indices: 2856515--2856548 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2856505 TTAATATTAA
*
2856515 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
2856532 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
2856549 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:2856691 original size:93 final size:92
Alignment explanation
Indices: 2856581--2856775 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
2856571 GATTATAGTT
* * *
2856581 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTAT-ATAATAATATATAATTTC
* *
2856644 ATAAAATTCTTGATAATAAAAATTTTCTTA
64 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
2856674 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
2856739 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTCTTA
2856766 TATGAATTTA
1 TATGAATTTA
2856776 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 21 0.23
93 68 0.73
94 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:2858189 original size:11 final size:11
Alignment explanation
Indices: 2858175--2858201 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2858165 AAAAATCAAT
2858175 ACAAAAGTTTC
1 ACAAAAGTTTC
2858186 ACAAAAGTTTC
1 ACAAAAGTTTC
2858197 ACAAA
1 ACAAA
2858202 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:2860783 original size:21 final size:21
Alignment explanation
Indices: 2860740--2860795 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
2860730 AAGCAGATGG
*
2860740 AGCCACTGCAAATAAATTATAT
1 AGCCACTGCAAA-CAATTATAT
*
2860762 AGCCACTGCAAACAATTGTAT
1 AGCCACTGCAAACAATTATAT
2860783 AGCCACTGCAAAC
1 AGCCACTGCAAAC
2860796 GGGGGAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.21
Consensus pattern (21 bp):
AGCCACTGCAAACAATTATAT
Found at i:2861905 original size:33 final size:33
Alignment explanation
Indices: 2861863--2861998 Score: 167
Period size: 33 Copynumber: 4.3 Consensus size: 33
2861853 AAAAATGGCA
*
2861863 AGAGGAACAAAACATGGTACAGAAACAGAAAAT
1 AGAGAAACAAAACATGGTACAGAAACAGAAAAT
**
2861896 AGAGAAACAAAA-A----ACCA-CTACAGAAAAT
1 AGAGAAACAAAACATGGTA-CAGAAACAGAAAAT
*
2861924 AGAGGAACAAAACATGGTACAGAAACAGAAAAT
1 AGAGAAACAAAACATGGTACAGAAACAGAAAAT
* *
2861957 AAAGAAACAAAACACGGTACAGAAACAGAAAAT
1 AGAGAAACAAAACATGGTACAGAAACAGAAAAT
2861990 AGAGAAACA
1 AGAGAAACA
2861999 TAAAGCAGAC
Statistics
Matches: 86, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
28 21 0.24
29 3 0.03
32 3 0.03
33 59 0.69
ACGTcount: A:0.61, C:0.14, G:0.18, T:0.07
Consensus pattern (33 bp):
AGAGAAACAAAACATGGTACAGAAACAGAAAAT
Found at i:2861982 original size:18 final size:17
Alignment explanation
Indices: 2861929--2861983 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
2861919 AAAATAGAGG
2861929 AACAAAACATGGTACAGA
1 AACAAAACA-GGTACAGA
*
2861947 AACAGAAA-A--TAAAGA
1 AACA-AAACAGGTACAGA
2861962 AACAAAACACGGTACAGA
1 AACAAAACA-GGTACAGA
2861980 AACA
1 AACA
2861984 GAAAATAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 3 0.10
15 10 0.33
18 14 0.47
19 3 0.10
ACGTcount: A:0.62, C:0.16, G:0.15, T:0.07
Consensus pattern (17 bp):
AACAAAACAGGTACAGA
Found at i:2863053 original size:22 final size:20
Alignment explanation
Indices: 2863022--2863075 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
2863012 TTTCCTAAAA
*
2863022 AAATAAAAAAAATCACTATTTT
1 AAATATAAAAAAT--CTATTTT
* *
2863044 AAATATAAAATATTTATTTT
1 AAATATAAAAAATCTATTTT
*
2863064 AATTATAAAAAA
1 AAATATAAAAAA
2863076 GATTCAATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 16 0.59
22 11 0.41
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATATAAAAAATCTATTTT
Found at i:2868627 original size:27 final size:27
Alignment explanation
Indices: 2868590--2868644 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2868580 GTATAATTGC
2868590 GCGCGCAGTCCTTCCACTCTGCAGCAT
1 GCGCGCAGTCCTTCCACTCTGCAGCAT
2868617 GCGCGCAGTCCTTCCACTCTGCAGCAT
1 GCGCGCAGTCCTTCCACTCTGCAGCAT
2868644 G
1 G
2868645 TTTCAATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.15, C:0.40, G:0.24, T:0.22
Consensus pattern (27 bp):
GCGCGCAGTCCTTCCACTCTGCAGCAT
Found at i:2871390 original size:18 final size:19
Alignment explanation
Indices: 2871347--2871395 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
2871337 CATTATGTAT
2871347 AATTTTATTGCTAGCATGAA
1 AATTTTA-TGCTAGCATGAA
* *
2871367 AGTTTTATGCTA-CTTGAA
1 AATTTTATGCTAGCATGAA
2871385 AATTTTATGCT
1 AATTTTATGCT
2871396 TAATTACTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 15 0.58
19 5 0.19
20 6 0.23
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (19 bp):
AATTTTATGCTAGCATGAA
Found at i:2873007 original size:45 final size:45
Alignment explanation
Indices: 2872958--2873050 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
2872948 TAAAGGGGCT
2872958 TGGATTTTGGCGTCGTCCCCCTTGAGTTAGTGCTTTATTTGGTAG
1 TGGATTTTGGCGTCGTCCCCCTTGAGTTAGTGCTTTATTTGGTAG
2873003 TGGATTTTGGCGTCGTCCCCCTTGAGTTAGTGCTTTATTTGGTAG
1 TGGATTTTGGCGTCGTCCCCCTTGAGTTAGTGCTTTATTTGGTAG
2873048 TGG
1 TGG
2873051 TTGAGGTACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.11, C:0.17, G:0.30, T:0.42
Consensus pattern (45 bp):
TGGATTTTGGCGTCGTCCCCCTTGAGTTAGTGCTTTATTTGGTAG
Found at i:2873501 original size:19 final size:19
Alignment explanation
Indices: 2873477--2873520 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
2873467 TAATTGAAAT
*
2873477 AAAAATTAATTTATATT-TA
1 AAAAATTAA-ATATATTCTA
2873496 AAAAA-TAAATATATTCTA
1 AAAAATTAAATATATTCTA
2873514 AAAAATT
1 AAAAATT
2873521 TGCGTTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.27
18 10 0.45
19 6 0.27
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATTAAATATATTCTA
Found at i:2884007 original size:8 final size:7
Alignment explanation
Indices: 2883988--2884017 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
2883978 ATCATGTTCA
2883988 AAATTTG
1 AAATTTG
2883995 AAATTTAG
1 AAATTT-G
2884003 AAATTTG
1 AAATTTG
2884010 AAATTTG
1 AAATTTG
2884017 A
1 A
2884018 GTTCAAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (7 bp):
AAATTTG
Found at i:2892894 original size:40 final size:40
Alignment explanation
Indices: 2892839--2892932 Score: 161
Period size: 40 Copynumber: 2.4 Consensus size: 40
2892829 CGTCAGCGCG
*
2892839 ATTTGCTGACGTGGACACAAATAGCGCCCTTTAGGACGCA
1 ATTTGCTGACGTGGACACAAATAGCGCCCTCTAGGACGCA
*
2892879 ATTTGCTGACGTGGACACAAATAGCGCCCTCTAGGACGCG
1 ATTTGCTGACGTGGACACAAATAGCGCCCTCTAGGACGCA
*
2892919 ATTTGTTGACGTGG
1 ATTTGCTGACGTGG
2892933 CATGAACAGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
ATTTGCTGACGTGGACACAAATAGCGCCCTCTAGGACGCA
Found at i:2893972 original size:13 final size:13
Alignment explanation
Indices: 2893956--2893982 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2893946 AGTTTAGTAT
2893956 TGTTTTTTAAAAG
1 TGTTTTTTAAAAG
2893969 TGTTTTTTAAAAG
1 TGTTTTTTAAAAG
2893982 T
1 T
2893983 ACTTTTCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (13 bp):
TGTTTTTTAAAAG
Found at i:2899729 original size:24 final size:24
Alignment explanation
Indices: 2899701--2899752 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2899691 TTAGTAAGTC
* *
2899701 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2899725 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2899749 AAAT
1 AAAT
2899753 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2901025 original size:51 final size:52
Alignment explanation
Indices: 2900963--2901183 Score: 238
Period size: 51 Copynumber: 4.3 Consensus size: 52
2900953 TTCGGTGGTT
* * *
2900963 TGCACATAGTACCACCCATGTGACCATTGTC-ATCCGATACATGTAGTAGCC
1 TGCACATAGTACTACACATGTGACCATTGTCTATCCGATACACGTAGTAGCC
* * * * * * * *
2901014 TACACATAGTACTACACACGTGATCA-AG-CTTTCTGGTTCACGTAGTAGCC
1 TGCACATAGTACTACACATGTGACCATTGTCTATCCGATACACGTAGTAGCC
* * *
2901064 TGCACATAGTACTACACATGTGACCAATG-CCATCC-AGTACACATAGTAGCC
1 TGCACATAGTACTACACATGTGACCATTGTCTATCCGA-TACACGTAGTAGCC
* *
2901115 TGCACATAGTACTACAAATGTGACCATTATCTAT-CGATACACGTAGTAGCC
1 TGCACATAGTACTACACATGTGACCATTGTCTATCCGATACACGTAGTAGCC
*
2901166 TGCACTTAGTACTACACA
1 TGCACATAGTACTACACA
2901184 CGTGTTCATA
Statistics
Matches: 137, Mismatches: 28, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
49 1 0.01
50 39 0.28
51 93 0.68
52 4 0.03
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (52 bp):
TGCACATAGTACTACACATGTGACCATTGTCTATCCGATACACGTAGTAGCC
Found at i:2901434 original size:21 final size:21
Alignment explanation
Indices: 2901410--2901471 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 21
2901400 TCAATACTAA
2901410 ATTTCTAATTGTTAAATAACT
1 ATTTCTAATTGTTAAATAACT
* *
2901431 ATTTC--A-TATTCAA-AA--
1 ATTTCTAATTGTTAAATAACT
2901446 ATTTCTAATTGTTAAATAACT
1 ATTTCTAATTGTTAAATAACT
2901467 ATTTC
1 ATTTC
2901472 ATATTCAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
15 5 0.16
17 3 0.10
18 10 0.32
19 3 0.10
21 10 0.32
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (21 bp):
ATTTCTAATTGTTAAATAACT
Found at i:2901487 original size:36 final size:36
Alignment explanation
Indices: 2901408--2901479 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
2901398 TATCAATACT
2901408 AAATTTCTAATTGTTAAATAACTATTTCATATTCAA
1 AAATTTCTAATTGTTAAATAACTATTTCATATTCAA
2901444 AAATTTCTAATTGTTAAATAACTATTTCATATTCAA
1 AAATTTCTAATTGTTAAATAACTATTTCATATTCAA
2901480 CCATTTCTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (36 bp):
AAATTTCTAATTGTTAAATAACTATTTCATATTCAA
Found at i:2904250 original size:44 final size:43
Alignment explanation
Indices: 2904187--2904303 Score: 148
Period size: 44 Copynumber: 2.7 Consensus size: 43
2904177 TATGAGTTAT
2904187 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGGGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATGTT-GGA-TTA
** *
2904231 CGTGTAAGACCTTGTCTGGGACAG-TGGCATCGATGTTTGATTA
1 CGTGTAAGACCACGTCTGGGAC-GTTGGCATCGATGTTGGATTA
* *
2904274 CATGTAAGACCACGTCTGAGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
2904304 TGCAAGAGCT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
42 1 0.02
43 27 0.43
44 32 0.51
45 3 0.05
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATGTTGGATTA
Found at i:2904359 original size:23 final size:23
Alignment explanation
Indices: 2904333--2904383 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
2904323 ATTCGAATAT
2904333 TGTAATATCC-CAAAAATTACTAC
1 TGTAATA-CCTCAAAAATTACTAC
2904356 TGTAATACCTCAAAAATTACTAC
1 TGTAATACCTCAAAAATTACTAC
*
2904379 AGTAA
1 TGTAA
2904384 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.29
Consensus pattern (23 bp):
TGTAATACCTCAAAAATTACTAC
Found at i:2907574 original size:27 final size:27
Alignment explanation
Indices: 2907542--2907597 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
2907532 AAATTCGATG
*
2907542 ATTGTAAGTAAGGTTATTTGTTTTGGT
1 ATTGTAAGTAAGGTCATTTGTTTTGGT
2907569 ATTGTAAGTAAGGTCATTTGTTTTGGT
1 ATTGTAAGTAAGGTCATTTGTTTTGGT
2907596 AT
1 AT
2907598 GTACATGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.23, C:0.02, G:0.25, T:0.50
Consensus pattern (27 bp):
ATTGTAAGTAAGGTCATTTGTTTTGGT
Found at i:2911078 original size:15 final size:15
Alignment explanation
Indices: 2911058--2911088 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2911048 TTTAATAATG
*
2911058 TTTATTCATTTTTTA
1 TTTATTAATTTTTTA
2911073 TTTATTAATTTTTTA
1 TTTATTAATTTTTTA
2911088 T
1 T
2911089 ATAATTATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATTAATTTTTTA
Found at i:2923386 original size:14 final size:14
Alignment explanation
Indices: 2923367--2923396 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2923357 AATGGTACAC
2923367 TTAGAAGTTGTCAA
1 TTAGAAGTTGTCAA
*
2923381 TTAGAAGTTGTGAA
1 TTAGAAGTTGTCAA
2923395 TT
1 TT
2923397 TTATAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.03, G:0.23, T:0.40
Consensus pattern (14 bp):
TTAGAAGTTGTCAA
Found at i:2924761 original size:3 final size:3
Alignment explanation
Indices: 2924755--2924790 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
2924745 CAGCCACCAC
* *
2924755 CTT CTT CTT CTT CTT CTT CTT ATT CTT CTT CCT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2924791 GGTGGTGTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:2929028 original size:22 final size:19
Alignment explanation
Indices: 2928997--2929036 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
2928987 TTAATCAACA
2928997 TTTTAATAAATCAATAAAATT
1 TTTTAATAAAT-AA-AAAATT
2929018 TTTTAAATAAATAAAAAAT
1 TTTT-AATAAATAAAAAAT
2929037 CAAATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTTAATAAATAAAAAATT
Found at i:2933047 original size:15 final size:15
Alignment explanation
Indices: 2933023--2933058 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2933013 ATCAATACGG
*
2933023 CCCAACTAGCCTAAA
1 CCCAATTAGCCTAAA
*
2933038 CCCAATTAGCCTAAG
1 CCCAATTAGCCTAAA
2933053 CCCAAT
1 CCCAAT
2933059 ACCCTAGCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.39, G:0.08, T:0.17
Consensus pattern (15 bp):
CCCAATTAGCCTAAA
Found at i:2934563 original size:3 final size:3
Alignment explanation
Indices: 2934555--2934597 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
2934545 AAACATGCGT
* * * *
2934555 ATA ATA ATA ATA ACA ATA ATA GTA ATA GTA GTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2934598 AGTCATAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:2944241 original size:29 final size:30
Alignment explanation
Indices: 2944199--2944259 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 30
2944189 TTAACAATTA
2944199 ATCCTAATGTGGGTGGATTTGGTAA-GGAG
1 ATCCTAATGTGGGTGGATTTGGTAAGGGAG
2944228 ATCCTAATGTGGGTGGATTTGGTAAGGGAG
1 ATCCTAATGTGGGTGGATTTGGTAAGGGAG
2944258 AT
1 AT
2944260 GCATAAATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.25, C:0.07, G:0.38, T:0.31
Consensus pattern (30 bp):
ATCCTAATGTGGGTGGATTTGGTAAGGGAG
Found at i:2949761 original size:6 final size:6
Alignment explanation
Indices: 2949752--2949781 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2949742 GATGGTGATG
*
2949752 ATATAT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT
2949782 TGAGCATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:2951895 original size:18 final size:18
Alignment explanation
Indices: 2951869--2951961 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
2951859 TACGACCGTT
*
2951869 TACGGCACTATTCATGTA
1 TACGGCACTATTCACGTA
*
2951887 TATGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
* *
2951905 TACAGTACTATTCACGTA
1 TACGGCACTATTCACGTA
*
2951923 TACGGAACTATTCACGTA
1 TACGGCACTATTCACGTA
* *
2951941 TACGGTACTGTTCACGTA
1 TACGGCACTATTCACGTA
2951959 TAC
1 TAC
2951962 AGTAGTTGGG
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (18 bp):
TACGGCACTATTCACGTA
Found at i:2959410 original size:23 final size:22
Alignment explanation
Indices: 2959363--2959408 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2959353 TATTTAATTA
* *
2959363 TTAATTTTTTCGATTTAACTAT
1 TTAATTTTTTCGAATTAAATAT
2959385 TTAA-TTTTTCGAGATTAAATAT
1 TTAATTTTTTCGA-ATTAAATAT
2959407 TT
1 TT
2959409 TAGTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (22 bp):
TTAATTTTTTCGAATTAAATAT
Found at i:2959836 original size:16 final size:17
Alignment explanation
Indices: 2959815--2959846 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2959805 GCACAAAGTA
2959815 AAATA-TTTAAAAAAAT
1 AAATATTTTAAAAAAAT
2959831 AAATATTTTAAAAAAA
1 AAATATTTTAAAAAAA
2959847 GAGACACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATATTTTAAAAAAAT
Found at i:2967249 original size:40 final size:40
Alignment explanation
Indices: 2967205--2967285 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
2967195 ATCATCAAAG
*
2967205 TGTGTTTATACATGAATGGTATGATCTTCAAATGAAACAA
1 TGTGTTTATACATGAATGGTATGATCTTCAAAGGAAACAA
2967245 TGTGTTTATACATGAATGGTATGATCTTCAAAGGAAACAA
1 TGTGTTTATACATGAATGGTATGATCTTCAAAGGAAACAA
2967285 T
1 T
2967286 CCAAGCATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.35
Consensus pattern (40 bp):
TGTGTTTATACATGAATGGTATGATCTTCAAAGGAAACAA
Found at i:2967644 original size:46 final size:46
Alignment explanation
Indices: 2967577--2967669 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
2967567 TAGCAAAAAG
2967577 AATTTTGAGATATGTCAAAGGTACGATAGATCAAGGTTTATTTCAT
1 AATTTTGAGATATGTCAAAGGTACGATAGATCAAGGTTTATTTCAT
2967623 AATTTTGAGATATGTCAAAGGTACGATAGATCAAGGTTTATTTCAT
1 AATTTTGAGATATGTCAAAGGTACGATAGATCAAGGTTTATTTCAT
2967669 A
1 A
2967670 CTCTCACAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (46 bp):
AATTTTGAGATATGTCAAAGGTACGATAGATCAAGGTTTATTTCAT
Found at i:2974675 original size:8 final size:8
Alignment explanation
Indices: 2974662--2974693 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
2974652 TTATCAACTC
2974662 TTATTATT
1 TTATTATT
2974670 TTATTATT
1 TTATTATT
2974678 TTATTATT
1 TTATTATT
2974686 TTATTATT
1 TTATTATT
2974694 CTAAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTATTATT
Found at i:2975179 original size:4 final size:4
Alignment explanation
Indices: 2975161--2975211 Score: 50
Period size: 4 Copynumber: 12.0 Consensus size: 4
2975151 CCAACCTTTG
*
2975161 ATTT ATTT -TTCT ATTT ATTT ATCTT AGTT ATTT AATTT ATTT ATTTT
1 ATTT ATTT ATT-T ATTT ATTT AT-TT ATTT ATTT -ATTT ATTT A-TTT
2975208 ATTT
1 ATTT
2975212 GACTTGGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
3 2 0.05
4 25 0.62
5 13 0.32
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:2975204 original size:13 final size:12
Alignment explanation
Indices: 2975161--2975211 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 12
2975151 CCAACCTTTG
2975161 ATTTATTT-TTCT
1 ATTTATTTATT-T
2975173 ATTTATTTATCTT
1 ATTTATTTAT-TT
*
2975186 AGTTATTTAATTT
1 ATTTATTT-ATTT
2975199 ATTTATTTTATTT
1 ATTTA-TTTATTT
2975212 GACTTGGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 8 0.24
13 19 0.58
14 6 0.18
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (12 bp):
ATTTATTTATTT
Found at i:2976063 original size:59 final size:59
Alignment explanation
Indices: 2975942--2976063 Score: 147
Period size: 59 Copynumber: 2.1 Consensus size: 59
2975932 TTGCATCCCG
** * **
2975942 AACAAAGTGACAATCCACCTCAATTGCAATATGTAAAGCAAATTGTTTATTGCATCTTA
1 AACAAAGTGACAATCCACCTCAATTGCAATATGTAAAGCAAATTGACTATGGCATCGAA
* * * *
2976001 AACAAAGTGACAATCCACTTCAATTGCAATTTGTAACA-CAGATTGACTATGGCCTCGAA
1 AACAAAGTGACAATCCACCTCAATTGCAATATGTAA-AGCAAATTGACTATGGCATCGAA
2976060 AACA
1 AACA
2976064 TTGTTCTTCT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 52 0.98
60 1 0.02
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.27
Consensus pattern (59 bp):
AACAAAGTGACAATCCACCTCAATTGCAATATGTAAAGCAAATTGACTATGGCATCGAA
Found at i:2976600 original size:21 final size:22
Alignment explanation
Indices: 2976574--2976630 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
2976564 AATAGGGAAT
* *
2976574 ATATATAATATTTTTCT-AAAG
1 ATATATAATATATTCCTAAAAG
2976595 ATATATAATATATTCCTAAAAG
1 ATATATAATATATTCCTAAAAG
2976617 ATATATAATATATT
1 ATATATAATATATT
2976631 TAGATATTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
21 15 0.45
22 18 0.55
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (22 bp):
ATATATAATATATTCCTAAAAG
Found at i:2980193 original size:3 final size:3
Alignment explanation
Indices: 2980185--2980209 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2980175 CATTATATCT
2980185 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
2980210 ATGTAATGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:2982829 original size:5 final size:5
Alignment explanation
Indices: 2982816--2982846 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
2982806 GACTAACCTT
*
2982816 GAAAG GAAAA GAAAA GAAAA GAAAA GAAAA G
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA G
2982847 GCAAGTATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:2987496 original size:29 final size:30
Alignment explanation
Indices: 2987433--2987511 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
2987423 AATTTCAAAA
*
2987433 TATACATAAACTTTGGTTTAATATGCAATTG
1 TATACATAAACTTTGATTT-ATATGCAATTG
* *
2987464 TATACATGAACTTTGATTT-TATGCAATTT
1 TATACATAAACTTTGATTTATATGCAATTG
* *
2987493 TATATATCAAATTTTGATT
1 TATACAT-AAACTTTGATT
2987512 CAAACCAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 15 0.37
30 9 0.22
31 17 0.41
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (30 bp):
TATACATAAACTTTGATTTATATGCAATTG
Found at i:2989018 original size:19 final size:20
Alignment explanation
Indices: 2988994--2989042 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
2988984 ATTTATTATA
*
2988994 AATTAATTATAC-TAATTTT
1 AATTAATTATACATAATATT
*
2989013 AATTAAAT-TACATAATATT
1 AATTAATTATACATAATATT
*
2989032 AATTATTTATA
1 AATTAATTATA
2989043 TTTGGTCAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.12
19 19 0.79
20 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTAATTATACATAATATT
Found at i:2992209 original size:11 final size:10
Alignment explanation
Indices: 2992179--2992213 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
2992169 ATTTCAGAAT
2992179 ATTTTTATAA
1 ATTTTTATAA
*
2992189 ATTTTAATAA
1 ATTTTTATAA
2992199 TATTTTTATAA
1 -ATTTTTATAA
2992210 ATTT
1 ATTT
2992214 ATACTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTTTTATAA
Found at i:3003106 original size:32 final size:32
Alignment explanation
Indices: 3003062--3003122 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
3003052 TAATTAGTAT
*
3003062 GAGTTATCAAATTAAATTAATTAATTTATCAC
1 GAGTTATCAAATTAAAGTAATTAATTTATCAC
* * *
3003094 GAGTTATTAAATTTAAGTAATTAGTTTAT
1 GAGTTATCAAATTAAAGTAATTAATTTAT
3003123 AAGTTTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (32 bp):
GAGTTATCAAATTAAAGTAATTAATTTATCAC
Found at i:3004395 original size:4 final size:4
Alignment explanation
Indices: 3004386--3004416 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3004376 CTATTTTGTT
3004386 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
3004417 TTAATATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:3011252 original size:4 final size:4
Alignment explanation
Indices: 3011243--3011268 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3011233 ATCATCGTGA
3011243 TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TA
3011269 GAGTTACCTT
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:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:3018004 original size:33 final size:32
Alignment explanation
Indices: 3017932--3018008 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
3017922 TATATACATG
* * * **
3017932 TGTAAGACCATAGCTGGGCTATGGCATTCTGA
1 TGTAAGACCATAACTAGGCTATGGCATACAAA
*
3017964 TGATAAGACCATAACTAGGTTATGGCACTACAAA
1 TG-TAAGACCATAACTAGGCTATGGCA-TACAAA
3017998 TGTAAGACCAT
1 TGTAAGACCAT
3018009 GGCAGGGTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.05
33 30 0.81
34 5 0.14
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (32 bp):
TGTAAGACCATAACTAGGCTATGGCATACAAA
Found at i:3018815 original size:11 final size:11
Alignment explanation
Indices: 3018799--3018836 Score: 67
Period size: 11 Copynumber: 3.4 Consensus size: 11
3018789 TATTTTTAAA
3018799 TTTTAAAATAT
1 TTTTAAAATAT
3018810 TTTTAAAATAT
1 TTTTAAAATAT
3018821 TTTTAAAATACT
1 TTTTAAAATA-T
3018833 TTTT
1 TTTT
3018837 TAATTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 21 0.81
12 5 0.19
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:3018856 original size:20 final size:20
Alignment explanation
Indices: 3018819--3018857 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3018809 TTTTTAAAAT
**
3018819 ATTTTTAAAATACTTTTTTA
1 ATTTTTAAAATAAATTTTTA
3018839 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
3018858 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTAAAATAAATTTTTA
Found at i:3022212 original size:2 final size:2
Alignment explanation
Indices: 3022207--3022231 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3022197 AACAAAACTT
3022207 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
3022232 TTCAATGCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3029429 original size:5 final size:6
Alignment explanation
Indices: 3029415--3029439 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3029405 ACTAAGCATT
3029415 AAAACA AAAACA AAAACA AAAACA A
1 AAAACA AAAACA AAAACA AAAACA A
3029440 CCCATTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:3034748 original size:12 final size:12
Alignment explanation
Indices: 3034723--3034759 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
3034713 GGTGGTTCAA
3034723 TTCTTT-TT-TT
1 TTCTTTCTTGTT
3034733 TTCTTTCTTGTT
1 TTCTTTCTTGTT
3034745 TTCTTTCTTGTT
1 TTCTTTCTTGTT
3034757 TTC
1 TTC
3034760 GTTTTTGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 6 0.24
11 2 0.08
12 17 0.68
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (12 bp):
TTCTTTCTTGTT
Found at i:3043379 original size:17 final size:16
Alignment explanation
Indices: 3043332--3043383 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
3043322 GTGCATTAAA
3043332 ATATTTTATTAATTTT
1 ATATTTTATTAATTTT
3043348 A-ATTTTAGTTAAATTTT
1 ATATTTTA-TT-AATTTT
*
3043365 CATATTTTACTAATTTT
1 -ATATTTTATTAATTTT
3043382 AT
1 AT
3043384 TGTCTATGCG
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
15 6 0.19
16 5 0.16
17 12 0.39
18 2 0.06
19 6 0.19
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (16 bp):
ATATTTTATTAATTTT
Found at i:3047247 original size:21 final size:21
Alignment explanation
Indices: 3047221--3047276 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
3047211 TTTTTTATTT
*
3047221 ATTTTTATTTTAAAATTTTTA
1 ATTTTTATTTTAAAATTTTAA
*
3047242 ATTTTTATATTTCAAATTTTAA
1 ATTTTTAT-TTTAAAATTTTAA
* *
3047264 AATTTAATTTTAA
1 ATTTTTATTTTAA
3047277 TTATTAGTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTTATTTTAAAATTTTAA
Found at i:3068080 original size:98 final size:98
Alignment explanation
Indices: 3067906--3068102 Score: 322
Period size: 98 Copynumber: 2.0 Consensus size: 98
3067896 GTACAATAAA
* * *
3067906 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGTACGATT
1 ACTTAAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* ** *
3067971 CCTTTAGAATCCCAAACTTGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCAGAATATTTCATTT
*
3068004 ACTTAAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTATGGCACAATT
1 ACTTAAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
3068069 CCTTTAAAATCCCAAACTCAGAATATTTCATTT
66 CCTTTAAAATCCCAAACTCAGAATATTTCATTT
3068102 A
1 A
3068103 TTATTTAAAA
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.29
Consensus pattern (98 bp):
ACTTAAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTTTAAAATCCCAAACTCAGAATATTTCATTT
Found at i:3069683 original size:14 final size:16
Alignment explanation
Indices: 3069646--3069683 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3069636 GAAAGAAAAG
3069646 AAAAAAACAATAGATA
1 AAAAAAACAATAGATA
*
3069662 AAATAAAACAA-ATATA
1 AAA-AAAACAATAGATA
3069678 AAAAAA
1 AAAAAA
3069684 CCTGTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 3 0.15
16 10 0.50
17 7 0.35
ACGTcount: A:0.79, C:0.05, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAAAACAATAGATA
Found at i:3081068 original size:29 final size:29
Alignment explanation
Indices: 3081026--3081086 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
3081016 ACCATCAAGC
* *
3081026 TAACACGGTGTTGTTCTATAATTATATAT
1 TAACACGATATTGTTCTATAATTATATAT
3081055 TAACACGATATTGTTCTATAATTATATAT
1 TAACACGATATTGTTCTATAATTATATAT
3081084 TAA
1 TAA
3081087 GCATTTGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (29 bp):
TAACACGATATTGTTCTATAATTATATAT
Found at i:3082549 original size:24 final size:23
Alignment explanation
Indices: 3082520--3082578 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
3082510 TATAATTTAA
*
3082520 TAAATTTTTTAATATAATTATTTT
1 TAAATTTTTTAATA-AATTATATT
* *
3082544 TTAATTTTTATACTAAATTATATT
1 TAAATTTTT-TAATAAATTATATT
*
3082568 TAAATATTTTA
1 TAAATTTTTTA
3082579 TTTTTATGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 2 0.07
24 23 0.79
25 4 0.14
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TAAATTTTTTAATAAATTATATT
Found at i:3086521 original size:31 final size:31
Alignment explanation
Indices: 3086447--3086521 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
3086437 TATAAAATAG
* *
3086447 TCACTTAACTATTTGAAAGTATTCATTTAAT
1 TCACTGAACTATTCGAAAGTATTCATTTAAT
* * *
3086478 TCATTGAACTATTCGAAAGTTTTTATTTAAGT
1 TCACTGAACTATTCGAAAGTATTCATTTAA-T
*
3086510 T-ACTGAGCTATT
1 TCACTGAACTATT
3086522 AAGTTTTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 34 0.94
32 2 0.06
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (31 bp):
TCACTGAACTATTCGAAAGTATTCATTTAAT
Found at i:3089097 original size:14 final size:14
Alignment explanation
Indices: 3089078--3089107 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3089068 GATATGTCGA
3089078 AACATATTAATACC
1 AACATATTAATACC
3089092 AACATATTAATACC
1 AACATATTAATACC
3089106 AA
1 AA
3089108 TACCAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (14 bp):
AACATATTAATACC
Found at i:3094106 original size:15 final size:15
Alignment explanation
Indices: 3094086--3094116 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3094076 CACTTTCAAC
3094086 ATTTTATTCTATTTT
1 ATTTTATTCTATTTT
*
3094101 ATTTTATTGTATTTT
1 ATTTTATTCTATTTT
3094116 A
1 A
3094117 AAATTTCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (15 bp):
ATTTTATTCTATTTT
Found at i:3096977 original size:19 final size:20
Alignment explanation
Indices: 3096945--3096982 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3096935 TTCTACTAAA
3096945 TTTTATATTATTTTAATATT
1 TTTTATATTATTTTAATATT
*
3096965 TTTTTTATT-TTTTAATAT
1 TTTTATATTATTTTAATAT
3096983 CTAAATATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTATATTATTTTAATATT
Found at i:3101308 original size:17 final size:18
Alignment explanation
Indices: 3101281--3101322 Score: 68
Period size: 17 Copynumber: 2.3 Consensus size: 18
3101271 TTACTGTTAA
3101281 TATAGTTTATATTTATA-T
1 TATA-TTTATATTTATATT
3101299 TATATTTATATTTATATT
1 TATATTTATATTTATATT
3101317 TATATT
1 TATATT
3101323 AGTCTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TATATTTATATTTATATT
Found at i:3101330 original size:23 final size:22
Alignment explanation
Indices: 3101281--3101337 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
3101271 TTACTGTTAA
*
3101281 TATAGTTTATATTTATATTATATT
1 TATA-TTTATATTTATATTATA-C
3101305 TATATTTATATTTATATTAGT-C
1 TATATTTATATTTATATTA-TAC
3101327 T-TATTTATATT
1 TATATTTATATT
3101338 ATTGTAGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 10 0.32
22 1 0.03
23 15 0.48
24 5 0.16
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.63
Consensus pattern (22 bp):
TATATTTATATTTATATTATAC
Found at i:3101337 original size:6 final size:6
Alignment explanation
Indices: 3101281--3101322 Score: 68
Period size: 6 Copynumber: 7.0 Consensus size: 6
3101271 TTACTGTTAA
3101281 TATAGTT TATATT TATA-T TATATT TATATT TATATT TATATT
1 TATA-TT TATATT TATATT TATATT TATATT TATATT TATATT
3101323 AGTCTTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.15
6 25 0.74
7 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (6 bp):
TATATT
Found at i:3102671 original size:31 final size:31
Alignment explanation
Indices: 3102610--3102675 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
3102600 AACAATCCAT
*
3102610 TGACTTAAATAAAAATTAGTGGATAATTCAA
1 TGACTTAAATAAAAATTAGTGAATAATTCAA
* * *
3102641 TGACTTCAATAAAAACTT-TTGAATAGTTCAA
1 TGACTTAAATAAAAA-TTAGTGAATAATTCAA
3102672 TGAC
1 TGAC
3102676 CACTTTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAATTAGTGAATAATTCAA
Found at i:3109366 original size:28 final size:28
Alignment explanation
Indices: 3109334--3109426 Score: 100
Period size: 28 Copynumber: 3.2 Consensus size: 28
3109324 GTTCAAACAC
3109334 ACTCATAATAAAAATCAGGGTAAACTAA
1 ACTCATAATAAAAATCAGGGTAAACTAA
* *
3109362 ACTCAAGGTGCACTAAATAATTA--GTAAACTAA
1 ACTC-A--T--AATAAA-AATCAGGGTAAACTAA
3109394 ACTCATAATAAAAATCAGGGTAAACTAA
1 ACTCATAATAAAAATCAGGGTAAACTAA
3109422 ACTCA
1 ACTCA
3109427 AGGTCACTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
26 4 0.08
27 5 0.09
28 18 0.34
29 2 0.04
31 2 0.04
32 13 0.25
33 5 0.09
34 4 0.08
ACGTcount: A:0.51, C:0.16, G:0.11, T:0.23
Consensus pattern (28 bp):
ACTCATAATAAAAATCAGGGTAAACTAA
Found at i:3109401 original size:60 final size:59
Alignment explanation
Indices: 3109334--3109448 Score: 221
Period size: 60 Copynumber: 1.9 Consensus size: 59
3109324 GTTCAAACAC
3109334 ACTCATAATAAAAATCAGGGTAAACTAAACTCAAGGTGCACTAAATAATTAGTAAACTAA
1 ACTCATAATAAAAATCAGGGTAAACTAAACTCAAGGT-CACTAAATAATTAGTAAACTAA
3109394 ACTCATAATAAAAATCAGGGTAAACTAAACTCAAGGTCACTAAATAATTAGTAAA
1 ACTCATAATAAAAATCAGGGTAAACTAAACTCAAGGTCACTAAATAATTAGTAAA
3109449 TTTACATTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 18 0.33
60 37 0.67
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.23
Consensus pattern (59 bp):
ACTCATAATAAAAATCAGGGTAAACTAAACTCAAGGTCACTAAATAATTAGTAAACTAA
Found at i:3109532 original size:31 final size:31
Alignment explanation
Indices: 3109491--3109556 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
3109481 CAAATGATTG
*
3109491 TTGAACTATTCAAAAGTTTTCATTTAAGTTA
1 TTGAACTATTCAAAAGTTTTCATTTAAGTCA
* *
3109522 TTGAATTATTCAAAAGTTTTTATTTAAGTCA
1 TTGAACTATTCAAAAGTTTTCATTTAAGTCA
3109553 TTGA
1 TTGA
3109557 GTTGTTAAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.47
Consensus pattern (31 bp):
TTGAACTATTCAAAAGTTTTCATTTAAGTCA
Found at i:3115837 original size:16 final size:16
Alignment explanation
Indices: 3115803--3115836 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3115793 AAAAAAGGCA
*
3115803 TTATATCAGATTAATT
1 TTATATCAAATTAATT
3115819 TTATCATCAAATTAATT
1 TTAT-ATCAAATTAATT
3115836 T
1 T
3115837 ACTTTATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (16 bp):
TTATATCAAATTAATT
Found at i:3119883 original size:27 final size:27
Alignment explanation
Indices: 3119853--3119916 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
3119843 TTTATCGAGG
*
3119853 TTATTAGTTTATCGATAAATTAATATT
1 TTATTAATTTATCGATAAATTAATATT
3119880 TTATTAATTTATCGATAAATTAATA-T
1 TTATTAATTTATCGATAAATTAATATT
*
3119906 TCATTAATTTA
1 TTATTAATTTA
3119917 GAGAATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 11 0.31
27 24 0.69
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (27 bp):
TTATTAATTTATCGATAAATTAATATT
Found at i:3120035 original size:34 final size:35
Alignment explanation
Indices: 3119995--3120065 Score: 110
Period size: 34 Copynumber: 2.0 Consensus size: 35
3119985 TGAATCAACG
3119995 TTAATTGGTTCATGTATA-AAAAA-AAAAGAGTTAA
1 TTAATTGGTTCATGTA-ACAAAAAGAAAAGAGTTAA
3120029 TTAATTGGTTCATGTAACCAAAAAGAAAAGAGTTAA
1 TTAATTGGTTCATGTAA-CAAAAAGAAAAGAGTTAA
3120065 T
1 T
3120066 GGTTTCAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 1 0.03
34 16 0.47
35 5 0.15
36 12 0.35
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (35 bp):
TTAATTGGTTCATGTAACAAAAAGAAAAGAGTTAA
Found at i:3142221 original size:14 final size:15
Alignment explanation
Indices: 3142201--3142242 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
3142191 ATAATGTAAC
3142201 ATATATTTTAATGTT
1 ATATATTTTAATGTT
* *
3142216 -TATATTGTAGTGTT
1 ATATATTTTAATGTT
3142230 ATATATTATTAAT
1 ATATATT-TTAAT
3142243 TTAATTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
14 12 0.57
15 6 0.29
16 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (15 bp):
ATATATTTTAATGTT
Found at i:3144105 original size:8 final size:8
Alignment explanation
Indices: 3144094--3144126 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
3144084 TAACCTTTTC
3144094 AAAAA-AA
1 AAAAACAA
3144101 AAAAACAA
1 AAAAACAA
3144109 AAAAACAA
1 AAAAACAA
3144117 AAAAACAA
1 AAAAACAA
3144125 AA
1 AA
3144127 CAACTAGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.20
8 20 0.80
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAACAA
Found at i:3148511 original size:23 final size:21
Alignment explanation
Indices: 3148472--3148518 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
3148462 ACAAATTCTA
* *
3148472 TATTATTATTGTTATTGCATTGT
1 TATTATTATTATAATTG-ATT-T
3148495 TATTATTATTATAATTGATTT
1 TATTATTATTATAATTGATTT
3148516 TAT
1 TAT
3148519 AGATATATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 3 0.14
23 15 0.68
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.62
Consensus pattern (21 bp):
TATTATTATTATAATTGATTT
Found at i:3148540 original size:22 final size:23
Alignment explanation
Indices: 3148515--3148560 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
3148505 ATAATTGATT
3148515 TTATAGATATATACATATA-TTA
1 TTATAGATATATACATATACTTA
* * *
3148537 TTATATATTTCTACATATACTTA
1 TTATAGATATATACATATACTTA
3148560 T
1 T
3148561 ACACATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (23 bp):
TTATAGATATATACATATACTTA
Found at i:3148568 original size:22 final size:22
Alignment explanation
Indices: 3148526--3148568 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3148516 TATAGATATA
* *
3148526 TACATATATTATTATATATTTC
1 TACATATATTATTACACATTTC
3148548 TACATATACTTA-TACACATTT
1 TACATATA-TTATTACACATTT
3148569 TTTTTGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (22 bp):
TACATATATTATTACACATTTC
Found at i:3148809 original size:27 final size:25
Alignment explanation
Indices: 3148778--3148841 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 25
3148768 ATGTGTCCCC
*
3148778 TTTTTATATAT-ATGTAAATCTCCATA
1 TTTTTATATATCATATAAAT-T-CATA
*
3148804 TATTTTACATATGCATATAAATTCATA
1 T-TTTTATATAT-CATATAAATTCATA
3148831 TTTTTATATAT
1 TTTTTATATAT
3148842 TTTATAATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 10 0.31
27 14 0.44
28 1 0.03
29 7 0.22
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (25 bp):
TTTTTATATATCATATAAATTCATA
Found at i:3149016 original size:5 final size:5
Alignment explanation
Indices: 3149001--3149030 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
3148991 TACATAAGTG
3149001 TTTTA -TTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
3149031 ATTGTTTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:3154887 original size:18 final size:18
Alignment explanation
Indices: 3154861--3154909 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 18
3154851 AATCTAAACT
*
3154861 TGAACCATGAACTTGAAA
1 TGAATCATGAACTTGAAA
3154879 TGAATCATGATGAACTTGAAA
1 TGAATC---ATGAACTTGAAA
3154900 TGAATCATGA
1 TGAATCATGA
3154910 TCCTTAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 9 0.33
21 18 0.67
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (18 bp):
TGAATCATGAACTTGAAA
Found at i:3154893 original size:21 final size:21
Alignment explanation
Indices: 3154867--3154910 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3154857 AACTTGAACC
3154867 ATGAACTTGAAATGAATCATG
1 ATGAACTTGAAATGAATCATG
3154888 ATGAACTTGAAATGAATCATG
1 ATGAACTTGAAATGAATCATG
3154909 AT
1 AT
3154911 CCTTAACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.30
Consensus pattern (21 bp):
ATGAACTTGAAATGAATCATG
Found at i:3155268 original size:11 final size:11
Alignment explanation
Indices: 3155252--3155276 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3155242 GATACAATAA
3155252 AATCTTAATTT
1 AATCTTAATTT
3155263 AATCTTAATTT
1 AATCTTAATTT
3155274 AAT
1 AAT
3155277 TGTTGAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (11 bp):
AATCTTAATTT
Found at i:3157217 original size:30 final size:31
Alignment explanation
Indices: 3157142--3157228 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
3157132 AAACTTAATG
*
3157142 GGTTTTAGTGAGAATTTTCAAAAATTTTGGTA
1 GGTTTTA-TGAAAATTTTCAAAAATTTTGGTA
* * * * *
3157174 GGTCTAATTAAAATTTTCAAAATTTTTTG-A
1 GGTTTTATGAAAATTTTCAAAAATTTTGGTA
*
3157204 GGTTTTATGAAAATTTATAAAAAAT
1 GGTTTTATGAAAATTT-TCAAAAAT
3157229 GAAGAGTCTA
Statistics
Matches: 43, Mismatches: 11, Indels: 3
0.75 0.19 0.05
Matches are distributed among these distances:
30 14 0.33
31 24 0.56
32 5 0.12
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (31 bp):
GGTTTTATGAAAATTTTCAAAAATTTTGGTA
Found at i:3160384 original size:33 final size:33
Alignment explanation
Indices: 3160347--3160409 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
3160337 CTTTTTTTGC
*
3160347 AGCATGTAATTACTAATTAGTATGTTCTTATGT
1 AGCATGTAATTACTAATCAGTATGTTCTTATGT
3160380 AGCATGTAATTACTAATCAGTATGTTCTTA
1 AGCATGTAATTACTAATCAGTATGTTCTTA
3160410 ATAACCAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (33 bp):
AGCATGTAATTACTAATCAGTATGTTCTTATGT
Found at i:3169511 original size:31 final size:30
Alignment explanation
Indices: 3169475--3169587 Score: 95
Period size: 31 Copynumber: 3.6 Consensus size: 30
3169465 GATTGACTAA
3169475 AATTTTTAAAAATTTTGAAGGTTTTAATGAG
1 AATTTTTAAAAATTTTGAAGG-TTTAATGAG
* * * *
3169506 AATTTTTAAACAATTTTGTATGTTAAACT-AA
1 AATTTTTAAA-AATTTTGAAGGTTTAA-TGAG
**
3169537 AACTTTCAAAAAAAATTTTGAAAGGTTTAATGAG
1 AA-TTT--TTAAAAATTTTG-AAGGTTTAATGAG
3169571 AA-TTTTAAAAATTTTGA
1 AATTTTTAAAAATTTTGA
3169588 GCGGGCTAAT
Statistics
Matches: 63, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
29 1 0.02
30 10 0.16
31 17 0.27
32 15 0.24
33 8 0.13
34 12 0.19
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.42
Consensus pattern (30 bp):
AATTTTTAAAAATTTTGAAGGTTTAATGAG
Found at i:3178745 original size:100 final size:102
Alignment explanation
Indices: 3178608--3178879 Score: 360
Period size: 100 Copynumber: 2.7 Consensus size: 102
3178598 AAAATTACAT
*
3178608 TAAAAAATCACAAAACAC-TAAACT-AACACTAACAATTTATATAACCTAATCATAAATTACAAA
1 TAAAAAATCACAAAACACAT-AACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAA
**
3178671 CAAAATAACTATAAAATTATTT-ATTAAA-TACATTAC
65 CAAAATAACTATAAAATTATTTAAAAAAAGTACATTAC
3178707 TAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAC
1 TAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAC
* * *
3178772 AAAATAATTATAAATTTTTTTAAAAAAAAGTTACATTAC
66 AAAATAACTATAAAATTATTT-AAAAAAAG-TACATTAC
* * *
3178811 TAAAAGATCACAAAAC-CATATACTAAACACTAACAA-TT-TGTAACCTAATCCCATAAATTATT
1 TAAAAAATCACAAAACACATA-ACTAAACACTAACAATTTATATAACCTAAT--CATAAATTACT
3178873 AACAAAA
63 AACAAAA
3178880 ATAAATAACT
Statistics
Matches: 155, Mismatches: 9, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
99 22 0.14
100 58 0.37
102 14 0.09
103 6 0.04
104 55 0.35
ACGTcount: A:0.54, C:0.17, G:0.01, T:0.28
Consensus pattern (102 bp):
TAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAC
AAAATAACTATAAAATTATTTAAAAAAAGTACATTAC
Found at i:3179152 original size:60 final size:60
Alignment explanation
Indices: 3179074--3179188 Score: 203
Period size: 60 Copynumber: 1.9 Consensus size: 60
3179064 TAAACTAAAC
*
3179074 ACAAAAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTACAAAT
1 ACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTACAAAT
* *
3179134 ACAACAATTTATAGCATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 ACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
3179189 TAAAAAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (60 bp):
ACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTACAAAT
Found at i:3179551 original size:26 final size:26
Alignment explanation
Indices: 3179515--3179603 Score: 90
Period size: 26 Copynumber: 3.4 Consensus size: 26
3179505 TATCTATGCA
* *
3179515 GCAGAGAGGCGTAGGGGGGCTGTATG
1 GCAGAGGGGCGTAGGGGGGCTGTACG
* *
3179541 GCAGAGGGGCGTAGGGGGACTGTGCG
1 GCAGAGGGGCGTAGGGGGGCTGTACG
* * *
3179567 GTAGAGGGGCGCA-GGGGGCTGTGCGGG
1 GCAGAGGGGCGTAGGGGGGCTGTAC--G
3179594 GCAGAGGGGC
1 GCAGAGGGGC
3179604 ACAAGGGGCA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
25 10 0.19
26 33 0.62
27 10 0.19
ACGTcount: A:0.16, C:0.15, G:0.58, T:0.11
Consensus pattern (26 bp):
GCAGAGGGGCGTAGGGGGGCTGTACG
Found at i:3179780 original size:25 final size:24
Alignment explanation
Indices: 3179736--3179785 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
3179726 TATATATTTA
3179736 AATATTTTAATAAAAATAAAATAAT
1 AATATTTTAATAAAAATAAAA-AAT
* * *
3179761 AATATTTTATTTAAAGTAAAAAAT
1 AATATTTTAATAAAAATAAAAAAT
3179785 A
1 A
3179786 TTTTAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
AATATTTTAATAAAAATAAAAAAT
Found at i:3180831 original size:37 final size:37
Alignment explanation
Indices: 3180783--3180948 Score: 314
Period size: 37 Copynumber: 4.5 Consensus size: 37
3180773 CACTTGTCCC
*
3180783 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
3180820 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
3180857 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
*
3180894 TGATCAGATAAGTGTAGCCACTTATCACTTTGTCTCT
1 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
3180931 TGATCAGATAAGTGTAGC
1 TGATCAGATAAGTGTAGC
3180949 TAAAGCTATC
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 127 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (37 bp):
TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
Found at i:3180991 original size:52 final size:52
Alignment explanation
Indices: 3180912--3181278 Score: 470
Period size: 52 Copynumber: 7.2 Consensus size: 52
3180902 TAAGTGTAGC
* * **
3180912 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
3180965 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
*
3181017 CAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* ** *
3181063 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
3181115 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* * *
3181161 CACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* ** *
3181213 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
3181265 CACTTTGTCACTTG
1 CACTTT-TCACTTG
3181279 ATCAGAAGTA
Statistics
Matches: 278, Mismatches: 23, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
46 84 0.30
49 1 0.00
52 178 0.64
53 15 0.05
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
Found at i:3181043 original size:98 final size:98
Alignment explanation
Indices: 3180912--3181270 Score: 529
Period size: 98 Copynumber: 3.6 Consensus size: 98
3180902 TAAGTGTAGC
* * *
3180912 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTCCACTT
3180977 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
3181010 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTCCACTT
** *
3181075 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* * *
3181108 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTCCACTT
*
3181173 GTCACTTGATCAGATAAGTATAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* * *
3181206 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTT
3181271 GTCACTTGAT
Statistics
Matches: 236, Mismatches: 19, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
98 192 0.81
100 1 0.00
104 43 0.18
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTCCACTT
GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:3181279 original size:150 final size:144
Alignment explanation
Indices: 3180923--3181284 Score: 571
Period size: 150 Copynumber: 2.4 Consensus size: 144
3180913 ACTTATCACT
* *
3180923 TTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTTGTCACTTGATC
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC---T---TTGTCACTTGATC
* *
3180988 AGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
60 AGATAAGTATAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGC
3181053 TATTACTTATCACTTTCCAC
125 TATTACTTATCACTTTCCAC
3181073 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAA
*
3181138 GTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGC
66 GTATAGCCGAAGCTATCACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGC
3181203 TATTACTTATCACTTTCCAC
125 TATTACTTATCACTTTCCAC
3181223 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
3181285 AGTACTCAAA
Statistics
Matches: 201, Mismatches: 5, Indels: 12
0.92 0.02 0.06
Matches are distributed among these distances:
144 43 0.21
146 1 0.00
147 1 0.00
150 156 0.78
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (144 bp):
TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAA
GTATAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTAC
TTATCACTTTCCAC
Done.