Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 329 of 343
Found at i:105621940 original size:11 final size:11
Alignment explanation
Indices: 105621877--105621940 Score: 65
Period size: 11 Copynumber: 5.7 Consensus size: 11
105621867 CCCAGCAGAG
105621877 AAAAAAAAGAA
1 AAAAAAAAGAA
*
105621888 AAGAAAAAGAA
1 AAAAAAAAGAA
* *
105621899 GAAAAAGAGAA
1 AAAAAAAAGAA
**
105621910 GGAAAAAAGAA
1 AAAAAAAAGAA
*
105621921 GGAAAAAAAGAA
1 -AAAAAAAAGAA
105621933 AAAAAAAA
1 AAAAAAAA
105621941 AAGAGGTTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
11 34 0.77
12 10 0.23
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:105622110 original size:16 final size:17
Alignment explanation
Indices: 105622084--105622121 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
105622074 TTATATTTAT
105622084 ATTTTTAATTTAATTTG
1 ATTTTTAATTTAATTTG
* *
105622101 ATTTTT-ATTTTATTTT
1 ATTTTTAATTTAATTTG
105622117 ATTTT
1 ATTTT
105622122 AAATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTTTAATTTAATTTG
Found at i:105622318 original size:18 final size:17
Alignment explanation
Indices: 105622275--105622797 Score: 180
Period size: 17 Copynumber: 29.8 Consensus size: 17
105622265 CAATAATCCC
105622275 CGTGCTTTT-AAAAATTCT
1 CGTG-TTTTCAAAAATT-T
*
105622293 CATG-TTTCAAAAATCTT
1 CGTGTTTTCAAAAAT-TT
105622310 CGTGTTTTC-AAAATTCT
1 CGTGTTTTCAAAAATT-T
*
105622327 AGTG-TTTCAAAAATTTT
1 CGTGTTTTCAAAAA-TTT
*
105622344 CTTGTTTTCAGAAAAAAATTT
1 CGTGTTTTC----AAAAATTT
*
105622365 CGTGTTTT-ATAAATTT
1 CGTGTTTTCAAAAATTT
* **
105622381 CCGTATTTTCAAAAAAAT
1 -CGTGTTTTCAAAAATTT
* *
105622399 CATGCCTTTCAAAAATTTT
1 CGTG-TTTTCAAAAA-TTT
* **
105622418 CGTATTTTCAAAAAAAAT
1 CGTGTTTTC-AAAAATTT
105622436 -GACTGTGTTTCAAAAATTT
1 CG--TGT-TTTCAAAAATTT
***
105622455 CCGTGTTAAAAAAAAATCTT
1 -CGTGTT-TTCAAAAAT-TT
*
105622475 CGTATTTTCAAAAAATTTT
1 CGTGTTTTC-AAAAA-TTT
105622494 CGTG-TTTCAAAAATCTT
1 CGTGTTTTCAAAAAT-TT
105622511 CGTGTTTTCAAAAATTT
1 CGTGTTTTCAAAAATTT
*
105622528 CG-GTGTTTCAAAGATTTT
1 CGTGT-TTTCAAA-AATTT
* *
105622546 CGTGTTTTCAAAAACTC
1 CGTGTTTTCAAAAATTT
* **
105622563 CGGTGATTTTAAGAAAAAAAT
1 C-GTG-TTTT--CAAAAATTT
*
105622584 CGT-TTTCTAAAAAATTT
1 CGTGTTT-TCAAAAATTT
105622601 CCGTG-TTTCAAAAATTTT
1 -CGTGTTTTCAAAAA-TTT
105622619 CGTGTTTT-AAAAATTT
1 CGTGTTTTCAAAAATTT
* *
105622635 TGTGTTTTTAAAAATTCT
1 CGTGTTTTCAAAAATT-T
*
105622653 CGTATTTT---AAATTT
1 CGTGTTTTCAAAAATTT
* *
105622667 --T-TTTTAAGAAAAAAATT
1 CGTGTTTT---CAAAAATTT
*
105622684 -GTG-TTTCAAAAAAATGT
1 CGTGTTTTC--AAAAATTT
*
105622701 CTTGTTTT-AAAAA-TT
1 CGTGTTTTCAAAAATTT
* *
105622716 CTTGTGTTTCAAAAAATGT
1 CGTGT-TTTC-AAAAATTT
105622735 CGTGTTTT-AAAAATTTT
1 CGTGTTTTCAAAAA-TTT
**
105622752 CGTG-TTTCTGAAATTT
1 CGTGTTTTCAAAAATTT
105622768 CCGTG-TTT-AAAAATTCT
1 -CGTGTTTTCAAAAATT-T
105622785 CGTGTTTT-AAAAA
1 CGTGTTTTCAAAAA
105622798 AAACTTTCAT
Statistics
Matches: 383, Mismatches: 60, Indels: 125
0.67 0.11 0.22
Matches are distributed among these distances:
11 4 0.01
12 1 0.00
14 1 0.00
15 11 0.03
16 56 0.15
17 125 0.33
18 99 0.26
19 55 0.14
20 9 0.02
21 17 0.04
22 5 0.01
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (17 bp):
CGTGTTTTCAAAAATTT
Found at i:105622336 original size:16 final size:16
Alignment explanation
Indices: 105622285--105622338 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
105622275 CGTGCTTTTA
105622285 AAAATTCTCA-TGTTTC
1 AAAATTCT-AGTGTTTC
* *
105622301 AAAAATCTTCGTGTTTTC
1 AAAATTC-TAGTG-TTTC
105622319 AAAATTCTAGTGTTTC
1 AAAATTCTAGTGTTTC
105622335 AAAA
1 AAAA
105622339 ATTTTCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 14 0.45
17 7 0.23
18 10 0.32
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAATTCTAGTGTTTC
Found at i:105622379 original size:38 final size:38
Alignment explanation
Indices: 105622284--105622458 Score: 131
Period size: 38 Copynumber: 4.8 Consensus size: 38
105622274 CCGTGCTTTT
*
105622284 AAAAATTCTCA-TGTTTCAAAAATCTT-CGTGTTTTC---
1 AAAAATTCT-AGTGTTTCAAAAAT-TTCCGTATTTTCAAA
* * *
105622319 -AAAATTCTAGTGTTTCAAAAATTTTCTTGTTTTCAGAA
1 AAAAATTCTAGTGTTTCAAAAATTTCCGTATTTTCA-AA
* * *
105622357 AAAAATT-TCGTGTTTTATAAATTTCCGTATTTTC-AA
1 AAAAATTCTAGTGTTTCAAAAATTTCCGTATTTTCAAA
*
105622393 AAAAA-TC-A-TGCCTTTCAAAAATTTTCGTATTTTCAAA
1 AAAAATTCTAGTG--TTTCAAAAATTTCCGTATTTTCAAA
*
105622430 AAAAATGACT-GTGTTTCAAAAATTTCCGT
1 AAAAAT-TCTAGTGTTTCAAAAATTTCCGT
105622459 GTTAAAAAAA
Statistics
Matches: 112, Mismatches: 13, Indels: 27
0.74 0.09 0.18
Matches are distributed among these distances:
33 3 0.03
34 30 0.27
35 1 0.01
36 26 0.23
37 7 0.06
38 36 0.32
39 7 0.06
40 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (38 bp):
AAAAATTCTAGTGTTTCAAAAATTTCCGTATTTTCAAA
Found at i:105622469 original size:74 final size:74
Alignment explanation
Indices: 105622331--105622470 Score: 174
Period size: 74 Copynumber: 1.9 Consensus size: 74
105622321 AATTCTAGTG
* * ** * * ***
105622331 TTTCAAAAATTTTCTTGTTTTCAGAAAAAAATTTCGTGTTTTATAAATTTCCGTATTTTCAAAAA
1 TTTCAAAAATTTTCGTATTTTCAGAAAAAAATGACGTGTTTCAAAAATTTCCGTATTAAAAAAAA
105622396 AATCATGCC
66 AATCATGCC
*
105622405 TTTCAAAAATTTTCGTATTTTCA-AAAAAAATGACTGTGTTTCAAAAATTTCCGTGTTAAAAAAA
1 TTTCAAAAATTTTCGTATTTTCAGAAAAAAATGAC-GTGTTTCAAAAATTTCCGTATTAAAAAAA
105622469 AA
65 AA
105622471 TCTTCGTATT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
73 9 0.16
74 46 0.84
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (74 bp):
TTTCAAAAATTTTCGTATTTTCAGAAAAAAATGACGTGTTTCAAAAATTTCCGTATTAAAAAAAA
AATCATGCC
Found at i:105622680 original size:99 final size:99
Alignment explanation
Indices: 105622569--105622754 Score: 243
Period size: 99 Copynumber: 1.9 Consensus size: 99
105622559 ACTCCGGTGA
* * *
105622569 TTTTAAGAAAAAAATCGT-TTTCTAAAAAATTTCCGTGTTTCAAAAATT-TTCGTGTTT-TAAAA
1 TTTTAAGAAAAAAATCGTGTTTCAAAAAAATGT-CGTGTTTCAAAAATTCTT-GTGTTTCAAAAA
* *
105622631 ATTTTGTGTTTTTAAAAATTCTCGTATTTTAAATTTT
64 ATGTCGTG-TTTTAAAAATTCTCGTATTTTAAATTTT
* * *
105622668 TTTTAAGAAAAAAATTGTGTTTCAAAAAAATGTCTTGTTTTAAAAATTCTTGTGTTTCAAAAAAT
1 TTTTAAGAAAAAAATCGTGTTTCAAAAAAATGTCGTGTTTCAAAAATTCTTGTGTTTCAAAAAAT
*
105622733 GTCGTGTTTTAAAAATTTTCGT
66 GTCGTGTTTTAAAAATTCTCGT
105622755 GTTTCTGAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
99 51 0.68
100 24 0.32
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (99 bp):
TTTTAAGAAAAAAATCGTGTTTCAAAAAAATGTCGTGTTTCAAAAATTCTTGTGTTTCAAAAAAT
GTCGTGTTTTAAAAATTCTCGTATTTTAAATTTT
Found at i:105622836 original size:20 final size:20
Alignment explanation
Indices: 105622776--105622828 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
105622766 TTCCGTGTTT
105622776 AAAAATTCTCGTGTTTTAAAA
1 AAAAATT-TCGTGTTTTAAAA
* * *
105622797 AAAACTTTCATTTTTTAAAA
1 AAAAATTTCGTGTTTTAAAA
105622817 AAAAATTTCGTG
1 AAAAATTTCGTG
105622829 CTTCAAAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (20 bp):
AAAAATTTCGTGTTTTAAAA
Found at i:105624199 original size:118 final size:118
Alignment explanation
Indices: 105624034--105624250 Score: 353
Period size: 118 Copynumber: 1.8 Consensus size: 118
105624024 TTATTTATTT
* *
105624034 TCGGTTAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCA
1 TCGGCTAGCGGAGTTTTACCCAACACGTCACACAACCTTCTGACGCGAAGTAGAATGACAACCCA
*
105624099 AGCACCCTACCCCGGTTACTCAGTCAGTCACGATTTGAGCCATACTCATAACC
66 AGCACCCTACCCCGATTACTCAGTCAGTCACGATTTGAGCCATACTCATAACC
**** *
105624152 TCGGCTAGCGGAGTTTTACTTGTCACGTCACACAACCTTCTGACGCGAAGTAGAATGACAACCTA
1 TCGGCTAGCGGAGTTTTACCCAACACGTCACACAACCTTCTGACGCGAAGTAGAATGACAACCCA
*
105624217 AGCACCCTACCCTGATTACTCAGTCAGTCACGAT
66 AGCACCCTACCCCGATTACTCAGTCAGTCACGAT
105624251 CTAAGTTGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
118 90 1.00
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.23
Consensus pattern (118 bp):
TCGGCTAGCGGAGTTTTACCCAACACGTCACACAACCTTCTGACGCGAAGTAGAATGACAACCCA
AGCACCCTACCCCGATTACTCAGTCAGTCACGATTTGAGCCATACTCATAACC
Found at i:105625206 original size:7 final size:7
Alignment explanation
Indices: 105625194--105625255 Score: 58
Period size: 7 Copynumber: 8.9 Consensus size: 7
105625184 AAATAAAATA
105625194 AAATAAT
1 AAATAAT
105625201 AAATAAT
1 AAATAAT
105625208 AAATAAT
1 AAATAAT
105625215 AAAATAA-
1 -AAATAAT
* *
105625222 AAGAAAGAA
1 AA-ATA-AT
105625231 AAATAAT
1 AAATAAT
105625238 AAATAA-
1 AAATAAT
105625244 AAATAA-
1 AAATAAT
105625250 AAATAA
1 AAATAA
105625256 AGATTGGGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
6 14 0.29
7 23 0.48
8 9 0.19
9 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (7 bp):
AAATAAT
Found at i:105625235 original size:27 final size:27
Alignment explanation
Indices: 105625184--105625251 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
105625174 TATTTAACTA
* *
105625184 AAATAAAATAAAATAATAAATAATAA-
1 AAATAAAATAAAAGAATAAAAAATAAT
105625210 ATAATAAAATAAAAGAA-AGAAAAATAAT
1 A-AATAAAATAAAAGAATA-AAAAATAAT
105625238 AAATAAAAATAAAA
1 AAAT-AAAATAAAA
105625252 ATAAAGATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
26 2 0.06
27 24 0.67
28 10 0.28
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (27 bp):
AAATAAAATAAAAGAATAAAAAATAAT
Found at i:105630513 original size:26 final size:26
Alignment explanation
Indices: 105630476--105630559 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
105630466 TGATACAAAT
* *
105630476 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
105630502 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
105630528 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
105630554 TGATAA
1 TGATAA
105630560 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:105632106 original size:26 final size:25
Alignment explanation
Indices: 105632054--105632106 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
105632044 TTTACAGTTT
105632054 TACCCCTAGGAGATAAATTACCGAAA
1 TACCCCTA-GAGATAAATTACCGAAA
*
105632080 TACCCCTA-AGATTAAATTGACCTAAA
1 TACCCCTAGAGA-TAAATT-ACCGAAA
105632106 T
1 T
105632107 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 3 0.12
25 6 0.25
26 15 0.62
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.25
Consensus pattern (25 bp):
TACCCCTAGAGATAAATTACCGAAA
Found at i:105635287 original size:3 final size:3
Alignment explanation
Indices: 105635279--105635323 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
105635269 TATGTCTAAA
* **
105635279 AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AGC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
105635324 GTAAATATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:105635460 original size:26 final size:24
Alignment explanation
Indices: 105635407--105635483 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 24
105635397 ATAGCAATAG
*
105635407 TAATAATA-TAATAATAAAGTAAAA
1 TAATAATAGTAATAATTAA-TAAAA
105635431 -AATAATAGTAATACATTAATAAGAA
1 TAATAATAGTAATA-ATTAATAA-AA
105635456 TAATAATAGT-AT-ATTAATAACAA
1 TAATAATAGTAATAATTAATAA-AA
105635479 TAATA
1 TAATA
105635484 GAAAATAATG
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
23 22 0.47
24 8 0.17
25 8 0.17
26 9 0.19
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (24 bp):
TAATAATAGTAATAATTAATAAAA
Found at i:105635669 original size:3 final size:3
Alignment explanation
Indices: 105635402--105635639 Score: 59
Period size: 3 Copynumber: 79.7 Consensus size: 3
105635392 TGATGATAGC
* * *
105635402 AAT AGT AAT AAT -AT AAT AAT AA- AGT AA- AA- AAT AAT AGT AAT ACATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T
* * * * *
105635448 AAT AAG AAT AAT AAT AGT -AT ATT AAT AAC AAT AAT AGAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
** * * * * *
105635493 GACG AGAT AGT AAT AAT AAT AAT AA- ACT AA- AGAGT ACT AAT AGT ACT
1 -AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT AAT
* * * * *
105635540 AAC AAT AAT -AT AAAT AAT AAT GAA- AAC AAC AAG AGA- AAT AAT AAC
1 AAT AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT A-AT AAT AAT AAT
* * * * **
105635585 AAT AA- CAG AAT AAA AAT AAT GAT AAT AAT AAT AGC AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
105635631 AATT AAT AA
1 AA-T AAT AA
105635640 ATAAATATAA
Statistics
Matches: 168, Mismatches: 45, Indels: 44
0.65 0.18 0.17
Matches are distributed among these distances:
2 18 0.11
3 134 0.80
4 13 0.08
5 3 0.02
ACGTcount: A:0.61, C:0.05, G:0.08, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:105636782 original size:6 final size:6
Alignment explanation
Indices: 105636771--105636800 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
105636761 TTCTAAGTAA
105636771 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
105636801 ATCCCTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TCTTTT
Found at i:105637814 original size:68 final size:69
Alignment explanation
Indices: 105637705--105637847 Score: 279
Period size: 68 Copynumber: 2.1 Consensus size: 69
105637695 ATTGTTGTGA
105637705 AAGTGGGTGGACAAGGCCCACTCAAGGAGTAGGAGGCCTGAGTTCTTTGCTGAGAGCAAGGGGAG
1 AAGTGGGTGGACAAGGCCCACTCAAGGAGTAGGAGGCCTGAGTTCTTTGCTGAGAGCAAGGGGAG
105637770 GG-T
66 GGTT
105637773 AAGTGGGTGGACAAGGCCCACTCAAGGAGTAGGAGGCCTGAGTTCTTTGCTGAGAGCAAGGGGAG
1 AAGTGGGTGGACAAGGCCCACTCAAGGAGTAGGAGGCCTGAGTTCTTTGCTGAGAGCAAGGGGAG
105637838 GGTT
66 GGTT
105637842 AAGTGG
1 AAGTGG
105637848 AGAGAGAGCG
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
68 67 0.91
69 7 0.09
ACGTcount: A:0.25, C:0.15, G:0.41, T:0.18
Consensus pattern (69 bp):
AAGTGGGTGGACAAGGCCCACTCAAGGAGTAGGAGGCCTGAGTTCTTTGCTGAGAGCAAGGGGAG
GGTT
Found at i:105642529 original size:13 final size:13
Alignment explanation
Indices: 105642511--105642544 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
105642501 TTATTTTCCC
*
105642511 TTTCATTTATTAT
1 TTTCATCTATTAT
105642524 TTTCATCTATTAT
1 TTTCATCTATTAT
*
105642537 TTACATCT
1 TTTCATCT
105642545 TGCTATTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTCATCTATTAT
Found at i:105646063 original size:31 final size:31
Alignment explanation
Indices: 105646028--105646093 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
105646018 TTAATATGCT
105646028 ATTTGGTATCTTAA-TTTAACTTCAATGCTCA
1 ATTTGGTA-CTTAAGTTTAACTTCAATGCTCA
* **
105646059 ATTTGGTACTTAAGTTTGACTTCAATTTTCA
1 ATTTGGTACTTAAGTTTAACTTCAATGCTCA
105646090 ATTT
1 ATTT
105646094 AGTGTCTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.48
Consensus pattern (31 bp):
ATTTGGTACTTAAGTTTAACTTCAATGCTCA
Found at i:105646607 original size:27 final size:25
Alignment explanation
Indices: 105646577--105646634 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 25
105646567 ACCATGCACA
*
105646577 ATTTTTATTTTATA-ATATTTTACTATG
1 ATTTTT-TTTTATATATA-TATACTA-G
105646604 ATTTCTTTTTTATATATATATACTAG
1 ATTT-TTTTTTATATATATATACTAG
105646630 ATTTT
1 ATTTT
105646635 ATAGGTAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
25 1 0.04
26 5 0.18
27 17 0.61
28 5 0.18
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.62
Consensus pattern (25 bp):
ATTTTTTTTTATATATATATACTAG
Found at i:105647262 original size:39 final size:39
Alignment explanation
Indices: 105647180--105647264 Score: 118
Period size: 39 Copynumber: 2.2 Consensus size: 39
105647170 TTAAGTCAAT
**
105647180 TGTAAATTTTAAATTTATTTGCATCAATATGGTTACACA
1 TGTAAATTTTAAATTTATTTGCATCAATATGACTACACA
* *
105647219 TGTAAATTTTAAATTTATTTGCATCAATGT-ACTGCACA
1 TGTAAATTTTAAATTTATTTGCATCAATATGACTACACA
105647257 GTGTAAAT
1 -TGTAAAT
105647265 GAAAAGACAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 5 0.12
39 36 0.88
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (39 bp):
TGTAAATTTTAAATTTATTTGCATCAATATGACTACACA
Found at i:105652435 original size:84 final size:84
Alignment explanation
Indices: 105652257--105652436 Score: 220
Period size: 84 Copynumber: 2.1 Consensus size: 84
105652247 ATTCCTCTTC
* ** * *
105652257 AAAAATGAAAAAGTTTCAATTTAGTCATCTTATAAATAGAGAAATTATAAATTAATATATAGTGA
1 AAAAATGAAAAAGTTTCAATTCAAACATCTTATAAATAAAGAAATTATAAATTAATATATAGTAA
** *
105652322 AATAGAACTTTGGCTCTCT
66 AATAGAACTTTACCCCTCT
* *
105652341 CAAAATGAAAAATTTTCAATTCAAACATCTTATAAATAAAGAAATTATAAATTAATATATAGTAA
1 AAAAATGAAAAAGTTTCAATTCAAACATCTTATAAATAAAGAAATTATAAATTAATATATAGTAA
*
105652406 AATTA-CACTTTAACCCCT-T
66 AA-TAGAACTTT-ACCCCTCT
*
105652425 AAAAAAGAAAAA
1 AAAAATGAAAAA
105652437 AATTATGTTT
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
84 76 0.94
85 5 0.06
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.32
Consensus pattern (84 bp):
AAAAATGAAAAAGTTTCAATTCAAACATCTTATAAATAAAGAAATTATAAATTAATATATAGTAA
AATAGAACTTTACCCCTCT
Found at i:105653246 original size:47 final size:47
Alignment explanation
Indices: 105653195--105653360 Score: 181
Period size: 47 Copynumber: 3.5 Consensus size: 47
105653185 TCGACCAGAT
* * * *
105653195 AATACTCTAATAACTCACGTCTTATTTTAATCCCACATTCACTAAAG
1 AATACTTTAATAGCTTACATCTTATTTTAATCCCACATTCACTAAAG
* * * * * *
105653242 AATACTTCAATAGCTTACTTCTTTACTATTAATCTCACA-TCTACTAGAT
1 AATACTTTAATAGCTTACATC-TTA-TTTTAATCCCACATTC-ACTAAAG
* *
105653291 CATACTTTAATAGCTTACATTTTATTTTAATCCCACATTCACTAAAG
1 AATACTTTAATAGCTTACATCTTATTTTAATCCCACATTCACTAAAG
*
105653338 AATACTTTAATAGCTTACTTCTT
1 AATACTTTAATAGCTTACATCTT
105653361 TACTATTTTT
Statistics
Matches: 95, Mismatches: 20, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
47 52 0.55
48 10 0.11
49 33 0.35
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (47 bp):
AATACTTTAATAGCTTACATCTTATTTTAATCCCACATTCACTAAAG
Found at i:105653281 original size:49 final size:49
Alignment explanation
Indices: 105653221--105653367 Score: 201
Period size: 49 Copynumber: 3.0 Consensus size: 49
105653211 ACGTCTTATT
*
105653221 TTAATCCCACATTCACTAAAGAATACTTCAATAGCTTACTTCTTTACTA
1 TTAATCCCACATTCACTAAAGAATACTTTAATAGCTTACTTCTTTACTA
* * ** * *
105653270 TTAATCTCACA-TCTACTAGATCATACTTTAATAGCTTACAT-TTTA-TT
1 TTAATCCCACATTC-ACTAAAGAATACTTTAATAGCTTACTTCTTTACTA
105653317 TTAATCCCACATTCACTAAAGAATACTTTAATAGCTTACTTCTTTACTA
1 TTAATCCCACATTCACTAAAGAATACTTTAATAGCTTACTTCTTTACTA
105653366 TT
1 TT
105653368 TTTATTAAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
47 34 0.42
48 12 0.15
49 35 0.43
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (49 bp):
TTAATCCCACATTCACTAAAGAATACTTTAATAGCTTACTTCTTTACTA
Found at i:105653953 original size:15 final size:16
Alignment explanation
Indices: 105653927--105653956 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
105653917 AATTATTTTA
105653927 ATTTATTTATTAAATG
1 ATTTATTTATTAAATG
105653943 ATTTA-TTATTAAAT
1 ATTTATTTATTAAAT
105653957 TCAAAATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
ATTTATTTATTAAATG
Found at i:105660133 original size:22 final size:22
Alignment explanation
Indices: 105660105--105660150 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
105660095 AATTGATTTA
105660105 TTCTTTAAGTGATACGCCATTG
1 TTCTTTAAGTGATACGCCATTG
105660127 TTCTTTAAGTGATACGCCATTG
1 TTCTTTAAGTGATACGCCATTG
105660149 TT
1 TT
105660151 GTTCTGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.43
Consensus pattern (22 bp):
TTCTTTAAGTGATACGCCATTG
Found at i:105661150 original size:22 final size:22
Alignment explanation
Indices: 105661119--105661164 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
105661109 TTAAAATATA
*
105661119 TAAAAGTATTAAAATGAAGCTT
1 TAAAAATATTAAAATGAAGCTT
*
105661141 TAAAAATATTTAAATGAAGCTT
1 TAAAAATATTAAAATGAAGCTT
105661163 TA
1 TA
105661165 GTTGAGTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.35
Consensus pattern (22 bp):
TAAAAATATTAAAATGAAGCTT
Found at i:105663233 original size:24 final size:20
Alignment explanation
Indices: 105663188--105663237 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 20
105663178 AAATATTCTA
105663188 AAAATAATATAAAATAAGTT
1 AAAATAATATAAAATAAGTT
*
105663208 AATAATAATAGTATAAATAAATTT
1 AA-AATAATA-TA-AAAT-AAGTT
105663232 AAAATA
1 AAAATA
105663238 TTTAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 2 0.08
21 7 0.28
22 2 0.08
23 8 0.32
24 6 0.24
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (20 bp):
AAAATAATATAAAATAAGTT
Found at i:105680061 original size:3 final size:3
Alignment explanation
Indices: 105680055--105680097 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
105680045 AAAAAAAAAG
105680055 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
105680098 AGGCTTTGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:105681641 original size:119 final size:119
Alignment explanation
Indices: 105681489--105681723 Score: 443
Period size: 119 Copynumber: 2.0 Consensus size: 119
105681479 TTGAAAAATG
*
105681489 AGGAATAGTTAAAGTACCAAGTTGCATATTAACCCATAAAAAAATGGGGTAAATAAGTCAAAACC
1 AGGAATAGTTAAAGTACCAAGTTGCATATTAACCCATAAAAAAATGGGGCAAATAAGTCAAAACC
*
105681554 GAAAACCCTCCATTTAGGTTTGGTTATTGTATAGCCTACACTACAGTGCAAACT
66 AAAAACCCTCCATTTAGGTTTGGTTATTGTATAGCCTACACTACAGTGCAAACT
105681608 AGGAATAGTTAAAGTACCAAGTTGCATATTAACCCATAAAAAAATGGGGCAAATAAGTCAAAACC
1 AGGAATAGTTAAAGTACCAAGTTGCATATTAACCCATAAAAAAATGGGGCAAATAAGTCAAAACC
*
105681673 AAAAACCCTTCATTTAGGTTTGGTTATTGTATAGCCTACACTACAGTGCAA
66 AAAAACCCTCCATTTAGGTTTGGTTATTGTATAGCCTACACTACAGTGCAA
105681724 GCTATCTCCT
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
119 113 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (119 bp):
AGGAATAGTTAAAGTACCAAGTTGCATATTAACCCATAAAAAAATGGGGCAAATAAGTCAAAACC
AAAAACCCTCCATTTAGGTTTGGTTATTGTATAGCCTACACTACAGTGCAAACT
Found at i:105687530 original size:29 final size:31
Alignment explanation
Indices: 105687469--105687531 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
105687459 AAAATTATAT
*
105687469 ATGAATTTTGATTTAATGTTCAATTTGATAC
1 ATGAATTTTGATTTAATGTTCAATTTGACAC
*
105687500 ATGAATTTT-ATTT-TTGTTCAATTAT-ACAC
1 ATGAATTTTGATTTAATGTTCAATT-TGACAC
105687529 ATG
1 ATG
105687532 GTATTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 15 0.52
30 5 0.17
31 9 0.31
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (31 bp):
ATGAATTTTGATTTAATGTTCAATTTGACAC
Found at i:105700556 original size:32 final size:32
Alignment explanation
Indices: 105700517--105700584 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
105700507 GTTAAATTTC
* * * *
105700517 TAATTAATACTAATTTTTTCGAGGCTTTGTAT
1 TAATTAATACTAATATATTCAAGGATTTGTAT
*
105700549 TAATTAATCCTAATATATTCAAGGATTTGTAT
1 TAATTAATACTAATATATTCAAGGATTTGTAT
105700581 TAAT
1 TAAT
105700585 CGACCTCTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (32 bp):
TAATTAATACTAATATATTCAAGGATTTGTAT
Found at i:105702261 original size:32 final size:33
Alignment explanation
Indices: 105702190--105702261 Score: 78
Period size: 32 Copynumber: 2.2 Consensus size: 33
105702180 GAAATCTTCT
* * *
105702190 TGAAATCCCTAAAATTTTTACGAATCAAATCAT
1 TGAAATCCCTAAAACTATTACGAATCAAATCAG
*
105702223 TG-AATCCCTAAAACTATTAGGAA-CAAAATC-G
1 TGAAATCCCTAAAACTATTACGAATC-AAATCAG
105702254 TGAAATCC
1 TGAAATCC
105702262 TTTAGAACCA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
31 3 0.09
32 28 0.85
33 2 0.06
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28
Consensus pattern (33 bp):
TGAAATCCCTAAAACTATTACGAATCAAATCAG
Found at i:105702274 original size:23 final size:23
Alignment explanation
Indices: 105702243--105702286 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
105702233 AAACTATTAG
105702243 GAACAAAATCGTGAAATCCTTTA
1 GAACAAAATCGTGAAATCCTTTA
*
105702266 GAACCAAATCGTGAAATCCTT
1 GAACAAAATCGTGAAATCCTT
105702287 AATCTTTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (23 bp):
GAACAAAATCGTGAAATCCTTTA
Found at i:105703267 original size:22 final size:22
Alignment explanation
Indices: 105703237--105703278 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
105703227 TAAGCATATG
*
105703237 ATTTGGATAAATGTACTTTACA
1 ATTTCGATAAATGTACTTTACA
105703259 ATTTCGATAAATGTACTTTA
1 ATTTCGATAAATGTACTTTA
105703279 TAAAAGCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.43
Consensus pattern (22 bp):
ATTTCGATAAATGTACTTTACA
Found at i:105704358 original size:40 final size:40
Alignment explanation
Indices: 105704305--105704385 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
105704295 GGAAAAAAGT
105704305 AAGCTTTCTTGTAGGTATCAATGTGATAATATTCATGCAA
1 AAGCTTTCTTGTAGGTATCAATGTGATAATATTCATGCAA
105704345 AAGCTTTCTTGTAGGTATCAATGTGATAATATTCATGCAA
1 AAGCTTTCTTGTAGGTATCAATGTGATAATATTCATGCAA
105704385 A
1 A
105704386 TATTCATCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.37
Consensus pattern (40 bp):
AAGCTTTCTTGTAGGTATCAATGTGATAATATTCATGCAA
Found at i:105706170 original size:51 final size:51
Alignment explanation
Indices: 105706094--105706246 Score: 243
Period size: 51 Copynumber: 3.0 Consensus size: 51
105706084 CTACGTGTAG
* * *
105706094 CAGCAACATTATCTAGTCCATCTGATGTTGCAAAGTCACCAGCATATTCAT
1 CAGCAACATTATCCACTCCATCTGATGTTGCAAAATCACCAGCATATTCAT
* * *
105706145 CAGCAACATTATCCACTCTATCTGATGTTACAAAATCACCAACATATTCAT
1 CAGCAACATTATCCACTCCATCTGATGTTGCAAAATCACCAGCATATTCAT
*
105706196 CAGCAACATTATCCACTCCATCTGATGTTGCAAAATCACTAGCATATTCAT
1 CAGCAACATTATCCACTCCATCTGATGTTGCAAAATCACCAGCATATTCAT
105706247 TACCAGCAAC
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 92 1.00
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.29
Consensus pattern (51 bp):
CAGCAACATTATCCACTCCATCTGATGTTGCAAAATCACCAGCATATTCAT
Found at i:105706411 original size:33 final size:33
Alignment explanation
Indices: 105706374--105706443 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
105706364 CATCAGCTTG
* *
105706374 TACCTTTCCTACATCACCCTCCTCACCAGATTC
1 TACCTTTCCTAAATCACCCTCATCACCAGATTC
* * *
105706407 TACCTTTTCTAAATCACCTTCATCATCAGATTC
1 TACCTTTCCTAAATCACCCTCATCACCAGATTC
105706440 TACC
1 TACC
105706444 ACTTTATCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.39, G:0.03, T:0.34
Consensus pattern (33 bp):
TACCTTTCCTAAATCACCCTCATCACCAGATTC
Found at i:105707314 original size:117 final size:117
Alignment explanation
Indices: 105707105--105707315 Score: 316
Period size: 117 Copynumber: 1.8 Consensus size: 117
105707095 GGTAACAGAA
* ** * * *
105707105 ATCAACATCATCAGGACCACTGTCTCATCACAAATCGACAAAACAAACCCTACATTCTAGCACTG
1 ATCAACAACATCAGGACCACCATCGCATCAAAAATCGACAAAACAAACCCTACATTCTAGCACTC
*
105707170 AAATTGCAATAATAAATCACAATTAACCATCTACAATTTTTACAACAGTTTT
66 AAATTGCAATAATAAATCACAAATAACCATCTACAATTTTTACAACAGTTTT
* *
105707222 ATCAACAACATTAGGACCACCATCGCATCAAAAATCGACAAAACAAACCCTACATTTTCA-CACT
1 ATCAACAACATCAGGACCACCATCGCATCAAAAATCGACAAAACAAACCCTACATTCT-AGCACT
*
105707286 CAAATTGCAATAGTAAATCACAAATAACCA
65 CAAATTGCAATAATAAATCACAAATAACCA
105707316 ACTAATCAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
117 82 0.99
118 1 0.01
ACGTcount: A:0.44, C:0.27, G:0.07, T:0.23
Consensus pattern (117 bp):
ATCAACAACATCAGGACCACCATCGCATCAAAAATCGACAAAACAAACCCTACATTCTAGCACTC
AAATTGCAATAATAAATCACAAATAACCATCTACAATTTTTACAACAGTTTT
Found at i:105707527 original size:18 final size:16
Alignment explanation
Indices: 105707484--105707519 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
105707474 GAATGCTATC
* *
105707484 GATTTAGGTATTTGAA
1 GATTTAGGGACTTGAA
105707500 GATTTAGGGACTTGAA
1 GATTTAGGGACTTGAA
105707516 GATT
1 GATT
105707520 GTTAGGGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.39
Consensus pattern (16 bp):
GATTTAGGGACTTGAA
Found at i:105708852 original size:318 final size:323
Alignment explanation
Indices: 105708272--105708882 Score: 957
Period size: 318 Copynumber: 1.9 Consensus size: 323
105708262 CCTAACATCT
* *
105708272 TGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTTGAATCCCAG
1 TGTGGCTGTAGTTTAGTGGTAAGAATTCCAAGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCAG
* *
105708337 CAGCCACACAAAGAAAAAAGTTTTTACCTTCATTTTCGCAACCTCTGTTTTTAGGCTCTGTTCCT
66 CAGCCACACAAAGAAAAAAGTTTTTACCTTCATTTCCGCAACCTCTGTTTCTAGGCTCTGTTCCT
* * *
105708402 TTGGGCCTACTTATAGTTTAAAAAAGAACCCAAAACGCAAGTCGTTTTGTTTCCTAAATCGTTGC
131 TTGGGCCAACTTATAGTTTAAAAAAGAACCCAAAACGCAAGTCGTTTCGTTTCCTAAACCGTTGC
105708467 TACGAACTACACAAATTCTAAAAAACCATCGACTTGAAAAAAACGTATTCTTGTTTTCCGCTTTT
196 TACGAACTACACAAATTCTAAAAAACCATCGACTT-AAAAAAACGTATTCTTGTTTTCCGCTTTT
105708532 CAG-CTTT-GTCATTTTTCC-CCTTGAGATCTAGTGATTATGGATTTGGCTACGATGAATATCC
260 CAGTCTTTCGTCATTTTTCCTCCTTGAGATCTAGTGATTATGGATTTGGCTACGATGAATATCC
105708593 TGTGGCTGTAGTTTAGTGGTAAGAATTCCAAGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCAG
1 TGTGGCTGTAGTTTAGTGGTAAGAATTCCAAGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCAG
* * * *
105708658 CAGCCACACTAA-TAAATA-TTTTT-TCTTCATTTCCGCAACCTCTGTTTCTAGGCTCTGTTCCT
66 CAGCCACACAAAGAAAAAAGTTTTTACCTTCATTTCCGCAACCTCTGTTTCTAGGCTCTGTTCCT
* * *
105708720 TTGGGCCAACTTCTTGTTTAAAAAAGAACCCAAAATGCAAGTCGTTTCGTTTCCTAAAACCGTTG
131 TTGGGCCAACTTATAGTTTAAAAAAGAACCCAAAACGCAAGTCGTTTCGTTTCCT-AAACCGTTG
* * * * *
105708785 CTACGAACTACACAAATTCTGAAAAACCATTGACTT-CAAAAACGTTTTTTTTGTTTTCCGCTTT
195 CTACGAACTACACAAATTCTAAAAAACCATCGACTTAAAAAAACG-TATTCTTGTTTTCCGCTTT
* *
105708849 TCAGTTTTTCGTCATTTTTCCTCCTTGATATCTA
259 TCAGTCTTTCGTCATTTTTCCTCCTTGAGATCTA
105708883 CTCATTGTTT
Statistics
Matches: 264, Mismatches: 21, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
317 7 0.03
318 107 0.41
319 50 0.19
320 15 0.06
321 85 0.32
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.35
Consensus pattern (323 bp):
TGTGGCTGTAGTTTAGTGGTAAGAATTCCAAGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCAG
CAGCCACACAAAGAAAAAAGTTTTTACCTTCATTTCCGCAACCTCTGTTTCTAGGCTCTGTTCCT
TTGGGCCAACTTATAGTTTAAAAAAGAACCCAAAACGCAAGTCGTTTCGTTTCCTAAACCGTTGC
TACGAACTACACAAATTCTAAAAAACCATCGACTTAAAAAAACGTATTCTTGTTTTCCGCTTTTC
AGTCTTTCGTCATTTTTCCTCCTTGAGATCTAGTGATTATGGATTTGGCTACGATGAATATCC
Found at i:105710427 original size:124 final size:128
Alignment explanation
Indices: 105710204--105710528 Score: 442
Period size: 124 Copynumber: 2.5 Consensus size: 128
105710194 TGTAAAACCG
*
105710204 TGTGTAAATGGTTCTCAAAGCATGAGCTAGTTAATATGAATAGAATTGGATGAAATGAAGTAATT
1 TGTGTAAATAGTTCTCAAAGCATGAGCTAGTTAATATGAATAGAATTGGATGAAATGAAGTAATT
* * *
105710269 TTAGACCTGAATAAACGAATGACGGCCCTCTTAGTTTACTGATAA-ACTGCTA-ATG-GT-AA
66 TTAGACCCGAATAAACGAATGACAGCCCTCTTAGTTTACTGATAATACTGATACATGTGTAAA
* *
105710328 TGTGTAAATAGTTCTCAAAGCATGAGCTAGTTGATATGAATAGAAATGGATGAAATGAAGTAATT
1 TGTGTAAATAGTTCTCAAAGCATGAGCTAGTTAATATGAATAGAATTGGATGAAATGAAGTAATT
* * * *
105710393 TTGGACCCGAATAAACGAATGACATCCCTTTTAGTTTACTGATAATTTCTGATACTATGTGTAAA
66 TTAGACCCGAATAAACGAATGACAGCCCTCTTAGTTTACTGATAA-TACTGATAC-ATGTGT---
105710458 ACAA
126 A-AA
* * * *
105710462 TGTGTAAATAGTTCTCGAACCATGAGCTAATTAATATGAATAGAGTTGGATGAAATGAAGTAATT
1 TGTGTAAATAGTTCTCAAAGCATGAGCTAGTTAATATGAATAGAATTGGATGAAATGAAGTAATT
105710527 TT
66 TT
105710529 TAGTGTTGAA
Statistics
Matches: 175, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
124 102 0.58
126 5 0.03
128 3 0.02
129 2 0.01
134 63 0.36
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (128 bp):
TGTGTAAATAGTTCTCAAAGCATGAGCTAGTTAATATGAATAGAATTGGATGAAATGAAGTAATT
TTAGACCCGAATAAACGAATGACAGCCCTCTTAGTTTACTGATAATACTGATACATGTGTAAA
Found at i:105713404 original size:2 final size:2
Alignment explanation
Indices: 105713399--105713431 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
105713389 CAAAAATATT
105713399 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
105713432 TTAAACCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:105715137 original size:29 final size:31
Alignment explanation
Indices: 105715075--105715142 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 31
105715065 AGTTTCATAC
* *
105715075 ATACATTTGAACCACAATCAAAGTTTCACGT
1 ATACAATTGCACCACAATCAAAGTTTCACGT
* * *
105715106 ATATAATTGCACCA-AATTAAAG-TTCATGT
1 ATACAATTGCACCACAATCAAAGTTTCACGT
105715135 ATACAATT
1 ATACAATT
105715143 ACACATTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 13 0.42
30 7 0.23
31 11 0.35
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (31 bp):
ATACAATTGCACCACAATCAAAGTTTCACGT
Found at i:105715543 original size:29 final size:29
Alignment explanation
Indices: 105715501--105715559 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
105715491 AATATAAGAG
105715501 ATAAATAACTAAAGTTTAGGCTTAGGACC
1 ATAAATAACTAAAGTTTAGGCTTAGGACC
105715530 ATAAATAACTAAAGTTTAGGCTTAGGACC
1 ATAAATAACTAAAGTTTAGGCTTAGGACC
105715559 A
1 A
105715560 AAGTTAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (29 bp):
ATAAATAACTAAAGTTTAGGCTTAGGACC
Found at i:105718849 original size:2 final size:2
Alignment explanation
Indices: 105718842--105718866 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
105718832 AAACACTCAC
105718842 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 A
105718867 ATTCAACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:105726908 original size:21 final size:22
Alignment explanation
Indices: 105726882--105726928 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
105726872 CTCTGCTCAA
*
105726882 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
105726903 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
105726925 ACTC
1 ACTC
105726929 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:105733721 original size:18 final size:20
Alignment explanation
Indices: 105733698--105733739 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
105733688 TAGGTGGCTT
105733698 AATTAAA-ATTTAA-AAAAA
1 AATTAAAGATTTAATAAAAA
*
105733716 AATTAAAGATTTAATGAAAA
1 AATTAAAGATTTAATAAAAA
105733736 AATT
1 AATT
105733740 TTAGAACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 6 0.29
20 8 0.38
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (20 bp):
AATTAAAGATTTAATAAAAA
Found at i:105734472 original size:21 final size:20
Alignment explanation
Indices: 105734446--105734485 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
105734436 TTAATTGATA
* *
105734446 AATCAATATAAATTAAAAATT
1 AATCAAAAT-AATGAAAAATT
105734467 AATCAAAATAATGAAAAAT
1 AATCAAAATAATGAAAAAT
105734486 AATATTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (20 bp):
AATCAAAATAATGAAAAATT
Found at i:105734497 original size:20 final size:21
Alignment explanation
Indices: 105734474--105734513 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
105734464 ATTAATCAAA
*
105734474 ATAATGAAAAAT-AATATTAT
1 ATAACGAAAAATAAATATTAT
105734494 ATAACGAAAAATAAATATTA
1 ATAACGAAAAATAAATATTA
105734514 GATTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (21 bp):
ATAACGAAAAATAAATATTAT
Found at i:105735595 original size:16 final size:16
Alignment explanation
Indices: 105735574--105735605 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
105735564 TCAGTAATAC
105735574 GATAAAAAAATTATAT
1 GATAAAAAAATTATAT
105735590 GATAAAAAAATTATAT
1 GATAAAAAAATTATAT
105735606 TTCTGTTAGT
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:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
GATAAAAAAATTATAT
Found at i:105736175 original size:12 final size:13
Alignment explanation
Indices: 105736147--105736195 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
105736137 TCGAGTCCGT
105736147 AGATATTAAATAG
1 AGATATTAAATAG
*
105736160 AGATATTTAA-AG
1 AGATATTAAATAG
* *
105736172 AGATATTATATTG
1 AGATATTAAATAG
*
105736185 ATATATTAAAT
1 AGATATTAAAT
105736196 TTTGATTAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (13 bp):
AGATATTAAATAG
Found at i:105741320 original size:19 final size:19
Alignment explanation
Indices: 105741283--105741322 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
105741273 ATATTATAAA
*
105741283 ATTTATTTAAATCTTAATT
1 ATTTATTTAAATCTAAATT
105741302 ATTTATTTTAAAT-TAAATT
1 ATTTA-TTTAAATCTAAATT
105741321 AT
1 AT
105741323 GATTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTATTTAAATCTAAATT
Found at i:105741459 original size:21 final size:21
Alignment explanation
Indices: 105741433--105741474 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
105741423 TGAAATTTAA
*
105741433 ATAATTTA-AAATAATAATAT
1 ATAAATTATAAATAATAATAT
*
105741453 ATAAATTATAAATTATAATAT
1 ATAAATTATAAATAATAATAT
105741474 A
1 A
105741475 ATATATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAAATTATAAATAATAATAT
Found at i:105743764 original size:23 final size:21
Alignment explanation
Indices: 105743733--105743778 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
105743723 TATTAAAGAT
*
105743733 ATGTACATAATAATAGTATTAAA
1 ATGTACAT-ATAATA-TATAAAA
*
105743756 ATGTGCATATAATATATAAAA
1 ATGTACATATAATATATAAAA
105743777 AT
1 AT
105743779 ATAGTGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 6 0.29
23 7 0.33
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (21 bp):
ATGTACATATAATATATAAAA
Found at i:105745773 original size:38 final size:40
Alignment explanation
Indices: 105745724--105745811 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 40
105745714 AAAATTATAC
* * *
105745724 TTAATACAATAAAATA-TTTATTATATTTAT-TAGTGTTT
1 TTAATATAATAAAACATTTTATTATATCTATGTAGTGTTT
*
105745762 TTAATATAATAAAACATTTTATTATATCTATGGTAGTTTTT
1 TTAATATAATAAAACATTTTATTATATCTAT-GTAGTGTTT
105745803 TTAATATAA
1 TTAATATAA
105745812 ATATTTTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 14 0.33
39 13 0.30
41 16 0.37
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (40 bp):
TTAATATAATAAAACATTTTATTATATCTATGTAGTGTTT
Found at i:105748168 original size:27 final size:27
Alignment explanation
Indices: 105748121--105748185 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
105748111 GTTGCTCTAT
*
105748121 TTTATTATTATTATTACTATATTTATCA
1 TTTATTATTATTATTACTATACTTAT-A
*
105748149 -TTATTATTATTA-TATTTATACTTATA
1 TTTATTATTATTATTA-CTATACTTATA
105748175 TTTATT-TTATT
1 TTTATTATTATT
105748186 CTAATGCCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 8 0.24
27 25 0.76
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTATTATTATTATTACTATACTTATA
Found at i:105748173 original size:21 final size:21
Alignment explanation
Indices: 105748117--105748167 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
105748107 ATTGGTTGCT
*
105748117 CTAT-TTTATTATTATTATTA
1 CTATATTTATCATTATTATTA
105748137 CTATATTTATCATTATTATTA
1 CTATATTTATCATTATTATTA
*
105748158 TTATATTTAT
1 CTATATTTAT
105748168 ACTTATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (21 bp):
CTATATTTATCATTATTATTA
Found at i:105748654 original size:18 final size:18
Alignment explanation
Indices: 105748627--105748671 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
105748617 CTGTATTTAC
105748627 TTAT-ATTATGACTAATA
1 TTATCATTATGACTAATA
* *
105748644 TTATCATTATGATTACTA
1 TTATCATTATGACTAATA
*
105748662 TTGTCATTAT
1 TTATCATTAT
105748672 TATTTGTTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (18 bp):
TTATCATTATGACTAATA
Found at i:105748675 original size:3 final size:3
Alignment explanation
Indices: 105748642--105748724 Score: 51
Period size: 3 Copynumber: 27.0 Consensus size: 3
105748632 TTATGACTAA
* * * * * *
105748642 TAT TAT CAT TAT GAT TAC TAT TGT CAT TAT TATT TGT TACCT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA--T TAT TAT
* * *
105748690 TAC TAT TAT TAC TAC TAT TA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
105748725 ATTTTACCCA
Statistics
Matches: 60, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
2 2 0.03
3 53 0.88
4 2 0.03
5 3 0.05
ACGTcount: A:0.30, C:0.10, G:0.04, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:105748698 original size:9 final size:9
Alignment explanation
Indices: 105748684--105748724 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
105748674 TTTGTTACCT
105748684 TATTATTAC
1 TATTATTAC
105748693 TATTATTAC
1 TATTATTAC
*
105748702 TACTATTA-
1 TATTATTAC
*
105748710 TATTATTAT
1 TATTATTAC
105748719 TATTAT
1 TATTAT
105748725 ATTTTACCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 7 0.24
9 22 0.76
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATTAC
Found at i:105754245 original size:20 final size:21
Alignment explanation
Indices: 105754208--105754246 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
105754198 TTTTTGAAAA
*
105754208 TTTTAAAAATATTTATATTAT
1 TTTTAAAAATATTAATATTAT
*
105754229 TTTTAATAAT-TTAATATT
1 TTTTAAAAATATTAATATT
105754247 TTTCATTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTAAAAATATTAATATTAT
Found at i:105754906 original size:38 final size:38
Alignment explanation
Indices: 105754864--105754940 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
105754854 TTCTATTCAA
105754864 ATCTCTACAACATTTTTCCACTTCTTCCATGGGAGACG
1 ATCTCTACAACATTTTTCCACTTCTTCCATGGGAGACG
105754902 ATCTCTACAACATTTTTCCACTTCTTCCATGGGAGACG
1 ATCTCTACAACATTTTTCCACTTCTTCCATGGGAGACG
105754940 A
1 A
105754941 CGATGCTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.34
Consensus pattern (38 bp):
ATCTCTACAACATTTTTCCACTTCTTCCATGGGAGACG
Found at i:105758962 original size:18 final size:18
Alignment explanation
Indices: 105758939--105758973 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
105758929 TTCTTATTAT
105758939 TAAT-AATAATATTTAAAA
1 TAATAAATAA-ATTTAAAA
105758957 TAATAAATAAATTTAAA
1 TAATAAATAAATTTAAA
105758974 TATCATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATAAATAAATTTAAAA
Found at i:105762124 original size:3 final size:3
Alignment explanation
Indices: 105762106--105762156 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
105762096 TCAAGCCCTT
* * * *
105762106 TGA TGA TGG TGT TGA TGA TGA TGA TGA TGA GGA TGG TGA TGA TGA TG-
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
105762153 TGA T
1 TGA T
105762157 AGGTCCAAGA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.25, C:0.00, G:0.39, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:105763248 original size:21 final size:22
Alignment explanation
Indices: 105763216--105763259 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
105763206 TTTAAAAATA
105763216 AAAATAGATAATTT-TTTTAAT
1 AAAATAGATAATTTATTTTAAT
105763237 AAAA-AGACTAATTTAATTTTAAT
1 AAAATAGA-TAATTT-ATTTTAAT
105763260 TTAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.15
21 10 0.50
23 7 0.35
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (22 bp):
AAAATAGATAATTTATTTTAAT
Found at i:105764592 original size:29 final size:29
Alignment explanation
Indices: 105764550--105764608 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
105764540 AAAGGCCTCT
105764550 ATGATTCTTTTACCCCAATACATACCAAC
1 ATGATTCTTTTACCCCAATACATACCAAC
105764579 ATGATTCTTTTACCCCAATACATACCAAC
1 ATGATTCTTTTACCCCAATACATACCAAC
105764608 A
1 A
105764609 GAAATCATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.31
Consensus pattern (29 bp):
ATGATTCTTTTACCCCAATACATACCAAC
Found at i:105770292 original size:15 final size:14
Alignment explanation
Indices: 105770272--105770314 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
105770262 CATGATTATA
105770272 ATTTTTATTATTGTT
1 ATTTTTATTATT-TT
*
105770287 ATTTTTATTCCTTTT
1 ATTTTTATT-ATTTT
105770302 ATTATTTATTATT
1 ATT-TTTATTATT
105770315 AATATATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (14 bp):
ATTTTTATTATTTT
Found at i:105771426 original size:17 final size:17
Alignment explanation
Indices: 105771404--105771437 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
105771394 ATCCACTAAT
*
105771404 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
105771421 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
105771438 AATCCACTAC
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:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:105776055 original size:17 final size:17
Alignment explanation
Indices: 105776033--105776066 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
105776023 ATCCACTAAT
*
105776033 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
105776050 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
105776067 AATCCACTAC
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:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:105782633 original size:16 final size:17
Alignment explanation
Indices: 105782608--105782639 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
105782598 AAATTAATAT
105782608 TTATATAAATTTAGCAC
1 TTATATAAATTTAGCAC
105782625 TTATA-AAATTTAGCA
1 TTATATAAATTTAGCA
105782640 ATAAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (17 bp):
TTATATAAATTTAGCAC
Found at i:105782648 original size:14 final size:16
Alignment explanation
Indices: 105782609--105782650 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
105782599 AATTAATATT
*
105782609 TATATAAATTTAGCACT
1 TATA-AAATTTAGCACA
105782626 TATAAAATTTAGCA-A
1 TATAAAATTTAGCACA
105782641 TA-AAAATTTA
1 TATAAAATTTA
105782651 ATATTACATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 8 0.33
15 2 0.08
16 10 0.42
17 4 0.17
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (16 bp):
TATAAAATTTAGCACA
Found at i:105783318 original size:5 final size:5
Alignment explanation
Indices: 105783308--105783341 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
105783298 AGAAAATAAG
105783308 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
105783342 TTACAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:105786863 original size:13 final size:12
Alignment explanation
Indices: 105786847--105786888 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
105786837 TAAATTTTAC
105786847 AAAAAATACATA
1 AAAAAATACATA
*
105786859 AAAAAAGACACTA
1 AAAAAATACA-TA
*
105786872 AAAATATACATA
1 AAAAAATACATA
105786884 AAAAA
1 AAAAA
105786889 GACACTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.74, C:0.10, G:0.02, T:0.14
Consensus pattern (12 bp):
AAAAAATACATA
Found at i:105786886 original size:24 final size:25
Alignment explanation
Indices: 105786847--105786900 Score: 94
Period size: 24 Copynumber: 2.2 Consensus size: 25
105786837 TAAATTTTAC
105786847 AAAAA-ATACATAAAAAAAGACACT
1 AAAAATATACATAAAAAAAGACACT
105786871 AAAAATATACAT-AAAAAAGACACT
1 AAAAATATACATAAAAAAAGACACT
105786895 AAAAAT
1 AAAAAT
105786901 TGGGAGGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 23 0.79
25 6 0.21
ACGTcount: A:0.70, C:0.11, G:0.04, T:0.15
Consensus pattern (25 bp):
AAAAATATACATAAAAAAAGACACT
Found at i:105786897 original size:12 final size:12
Alignment explanation
Indices: 105786859--105786899 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
105786849 AAAATACATA
105786859 AAAAAAGACACT
1 AAAAAAGACACT
*
105786871 AAAAATATACA-T
1 AAAAA-AGACACT
105786883 AAAAAAGACACT
1 AAAAAAGACACT
105786895 AAAAA
1 AAAAA
105786900 TTGGGAGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 4 0.16
12 17 0.68
13 4 0.16
ACGTcount: A:0.71, C:0.12, G:0.05, T:0.12
Consensus pattern (12 bp):
AAAAAAGACACT
Found at i:105791713 original size:21 final size:21
Alignment explanation
Indices: 105791687--105791727 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
105791677 AGACGAGCAA
* *
105791687 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
105791708 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
105791728 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:105796671 original size:22 final size:22
Alignment explanation
Indices: 105796643--105796687 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
105796633 ATACATCAAC
105796643 ATTCTCAAGGCTTAACAAAATT
1 ATTCTCAAGGCTTAACAAAATT
105796665 ATTCTCAAGGCTTAACAAAATT
1 ATTCTCAAGGCTTAACAAAATT
105796687 A
1 A
105796688 AGAGTTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (22 bp):
ATTCTCAAGGCTTAACAAAATT
Found at i:105798865 original size:3 final size:3
Alignment explanation
Indices: 105798859--105798886 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
105798849 TATGTCGATG
105798859 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
105798887 CCATATGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:105799014 original size:15 final size:15
Alignment explanation
Indices: 105798994--105799038 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
105798984 TGACTAAATT
*
105798994 ATAATGATAGTAATA
1 ATAATGATAATAATA
*
105799009 ATAATGATAATGATA
1 ATAATGATAATAATA
*
105799024 ATAATGAGAATAATA
1 ATAATGATAATAATA
105799039 TATGTAGTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (15 bp):
ATAATGATAATAATA
Found at i:105802255 original size:28 final size:29
Alignment explanation
Indices: 105802223--105802278 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
105802213 TTATTATTCC
* *
105802223 GAATATAAAAATAGATGA-TAATAAAAAT
1 GAATAGAAAAATAGATAATTAATAAAAAT
* *
105802251 GAATAGAATAATAGTTAATTAATAAAAA
1 GAATAGAAAAATAGATAATTAATAAAAA
105802279 AATAACATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (29 bp):
GAATAGAAAAATAGATAATTAATAAAAAT
Found at i:105807037 original size:127 final size:127
Alignment explanation
Indices: 105806730--105807037 Score: 357
Period size: 127 Copynumber: 2.4 Consensus size: 127
105806720 AAAAACCGAC
* * * *
105806730 ACCCAGCACGGTAGGGCACGTTTCATCGAATTTCCAAACATTGAACATTGCCTCGCTCTAGCATT
1 ACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACATTGAACATTGCCTTGCTCTAGCATT
* * *
105806795 TAGAAAATATGAATGAAATTCTAAAGGAATAACCAAATATTTTGAGCAAACCGGAAATCGAA
66 TAGAAAACATGAATGAAATTCTAAAGGAATAACCAAATATTTTAAACAAACCGGAAATCGAA
* * * * * * * *
105806857 ACCCAACACGATTGGGCACGATTCCCCAAATTTCCAAGCGTTGAATATTGCCTTG-TCTTAGTAT
1 ACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACATTGAACATTGCCTTGCTC-TAGCAT
* * * ** * * *
105806921 TTTGAAGACATGAGTGAAATTCTAAAGGAATATTCGATTATTTTAAACAAACGGGAAATCGAA
65 TTAGAAAACATGAATGAAATTCTAAAGGAATAACCAAATATTTTAAACAAACCGGAAATCGAA
* * **
105806984 ACCCGGCACGATAGGACACGATTCCTCGAATTTCCAAACATCAAACATTGCCTT
1 ACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACATTGAACATTGCCTT
105807038 TGGTTTGGGG
Statistics
Matches: 146, Mismatches: 34, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
126 2 0.01
127 144 0.99
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (127 bp):
ACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACATTGAACATTGCCTTGCTCTAGCATT
TAGAAAACATGAATGAAATTCTAAAGGAATAACCAAATATTTTAAACAAACCGGAAATCGAA
Found at i:105808932 original size:26 final size:26
Alignment explanation
Indices: 105808903--105809012 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
105808893 TGGTACAAAT
105808903 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
105808929 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
105808955 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
105808981 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
105809007 TGATAA
1 TGATAA
105809013 GAATTTAATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:105810665 original size:27 final size:27
Alignment explanation
Indices: 105810624--105810736 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 27
105810614 GAGGAAGCGT
*
105810624 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
105810651 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
105810678 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
105810706 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
105810732 TCTGG
1 TCTGG
105810737 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
26 5 0.07
27 55 0.73
28 15 0.20
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:105810729 original size:54 final size:54
Alignment explanation
Indices: 105810622--105810736 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
105810612 TGGAGGAAGC
*
105810622 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * *
105810676 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
105810730 GTTCTGG
1 GTTCTGG
105810737 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:105812189 original size:10 final size:8
Alignment explanation
Indices: 105812159--105812184 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
105812149 AAAGAAAAGT
105812159 GGAGAAGG
1 GGAGAAGG
105812167 GGAGAAGG
1 GGAGAAGG
105812175 GGAGAAGG
1 GGAGAAGG
105812183 GG
1 GG
105812185 GGAGAGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (8 bp):
GGAGAAGG
Found at i:105820722 original size:131 final size:131
Alignment explanation
Indices: 105820488--105820868 Score: 539
Period size: 131 Copynumber: 2.9 Consensus size: 131
105820478 CATTTGTTCA
* * *
105820488 AAAATTCTTTAAAACAAAAACGAGATTCGATGTTTGGCGATTCGTGGAAGCGTGCCCTAACGTGT
1 AAAATTCTTTAAAACAAAGACGAGATTCGATGTTTGGCGATTCGCGGAATCGTGCCCTAACGTGT
***
105820553 TGGGTTGCAATTTTATGTTTGCTCAAAATAATCGAATATCGCTTCGAAATTTCACTCACGTCTTC
66 TGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCGCTTCGAAATTTCACTCACGTCTTC
105820618 T
131 T
* * *
105820619 AAAATTCTTTAAAACGAAGACGAGATTCGATGTTTGGTGATTCACGGAATCGTGCCCTAACGTGT
1 AAAATTCTTTAAAACAAAGACGAGATTCGATGTTTGGCGATTCGCGGAATCGTGCCCTAACGTGT
*
105820684 TGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCGCTTCGAAATTTTACTCACGTCTTC
66 TGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCGCTTCGAAATTTCACTCACGTCTTC
105820749 T
131 T
* * * * ** * * * * *
105820750 AAAATTCTTCAAAATAAAGACGAGGTTTGATAATTAGCAATTTGCAGAATCGTGACCTAACGTGT
1 AAAATTCTTTAAAACAAAGACGAGATTCGATGTTTGGCGATTCGCGGAATCGTGCCCTAACGTGT
* *
105820815 TGGGTTGCAATTTCGCGTTTGCTCAAAATAATC-AAGTATCCCTTCAAAATTTCA
66 TGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAA-TATCGCTTCGAAATTTCA
105820869 TTCATATCTT
Statistics
Matches: 222, Mismatches: 27, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
130 2 0.01
131 220 0.99
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (131 bp):
AAAATTCTTTAAAACAAAGACGAGATTCGATGTTTGGCGATTCGCGGAATCGTGCCCTAACGTGT
TGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCGCTTCGAAATTTCACTCACGTCTTC
T
Found at i:105821738 original size:15 final size:15
Alignment explanation
Indices: 105821718--105821760 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
105821708 CTATAAAATT
105821718 TTCAAATTAATCTCA
1 TTCAAATTAATCTCA
* *
105821733 TTCAAATACAATTTCA
1 TTCAAAT-TAATCTCA
*
105821749 TTCAATTTAATC
1 TTCAAATTAATC
105821761 CAACAACATA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.42
Consensus pattern (15 bp):
TTCAAATTAATCTCA
Found at i:105824367 original size:64 final size:63
Alignment explanation
Indices: 105824231--105824374 Score: 225
Period size: 64 Copynumber: 2.3 Consensus size: 63
105824221 TCAATCTTAT
* * * * *
105824231 TTTGGAAAATTGAAAATGAAATTAACCACAACTAGGCAAAAATCTAATTAGTTGGGCCCATAT
1 TTTGGAAAATTGAGAATGAAATTAACCACAACTAGGCAAAAATCAAATTAGCTGGGCCCACAA
*
105824294 TTTGGAAAATTGAGAATGAAATTAATCACAACTAGAGCAAAAATCAAATTAGCTGGGCCCACAA
1 TTTGGAAAATTGAGAATGAAATTAACCACAACTAG-GCAAAAATCAAATTAGCTGGGCCCACAA
105824358 TTTGGAAAATTGAGAAT
1 TTTGGAAAATTGAGAAT
105824375 CATAGTTGTG
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
63 33 0.45
64 41 0.55
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (63 bp):
TTTGGAAAATTGAGAATGAAATTAACCACAACTAGGCAAAAATCAAATTAGCTGGGCCCACAA
Found at i:105827735 original size:23 final size:24
Alignment explanation
Indices: 105827691--105827757 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 24
105827681 TTTAGCTTAT
* *
105827691 TTACATTAAATTTTCAAAACCC-AC
1 TTACATTAAA-CTCCAAAACCCAAC
105827715 TTACATTAAACTCCAAAACCCAAC
1 TTACATTAAACTCCAAAACCCAAC
*
105827739 --ACATTAAACACCCAAAACC
1 TTACATTAAAC-TCCAAAACC
105827758 TAATAGCCTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
22 9 0.24
23 17 0.45
24 12 0.32
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.22
Consensus pattern (24 bp):
TTACATTAAACTCCAAAACCCAAC
Found at i:105829225 original size:118 final size:120
Alignment explanation
Indices: 105828935--105829272 Score: 383
Period size: 118 Copynumber: 2.8 Consensus size: 120
105828925 TCGTTATTAT
*
105828935 TATTATTAT-TATATATTAGTGCATATTTGTTATATACGTGCATGTATATGTATATATATATAGT
1 TATTATTATATATATATTAGTGTATATTT-TT-TAT-CGTGC--GTATATGTATATATATATAGT
* * *
105828999 AGTG--TTTTTCATTATTTTATTTTAATATTTTATTATATTTGCTTTTTTTTTCATCGCAA
61 AGTGCTTTTTTTATTATTTTATTTTAATATTTTATTATATTTGC-TTTTATTGCATCGCAA
* * *
105829058 TATTATTATATATATATTA--GTATATTTTTT-TCATACATATATGCATATATATATATAGTAGT
1 TATTATTATATATATATTAGTGTATATTTTTTATCGTGCGTATATG--TATATATATATAGTAGT
* *
105829120 GCTCTTTTTTATTACTTTATTTTAATATTTTATTATATTTGC-TTTATTGCATTGC-A
64 GCT-TTTTTTATTATTTTATTTTAATATTTTATTATATTTGCTTTTATTGCATCGCAA
* **
105829176 TATTATTATATATATATTAGTGTATATTTTTTAT-GTGCGTATATGTATATCTAT-TTTTA-TAG
1 TATTATTATATATATATTAGTGTATATTTTTTATCGTGCGTATATGTATATATATATAGTAGT-G
*
105829238 CTTTTTTTATTATTTTATTTCAATATTTTTATTAT
65 CTTTTTTTATTATTTTATTTTAATA-TTTTATTAT
105829273 GCGTGCTTTT
Statistics
Matches: 187, Mismatches: 17, Indels: 28
0.81 0.07 0.12
Matches are distributed among these distances:
116 28 0.15
117 15 0.08
118 49 0.26
119 11 0.06
120 20 0.11
121 39 0.21
122 7 0.04
123 9 0.05
124 9 0.05
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (120 bp):
TATTATTATATATATATTAGTGTATATTTTTTATCGTGCGTATATGTATATATATATAGTAGTGC
TTTTTTTATTATTTTATTTTAATATTTTATTATATTTGCTTTTATTGCATCGCAA
Found at i:105829301 original size:3 final size:3
Alignment explanation
Indices: 105829293--105829319 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
105829283 TGTATTTTGC
105829293 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
105829320 ACAATAGCGT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:105829514 original size:3 final size:3
Alignment explanation
Indices: 105829508--105829568 Score: 56
Period size: 3 Copynumber: 21.3 Consensus size: 3
105829498 TTTAATTACT
* * * *
105829508 TTA TTA TTT TTA TTA -TA TT- TTA TTA TTC TTT TTA TT- TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
105829553 TTA CTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
105829569 CATTGTTAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
2 6 0.13
3 40 0.87
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:105829521 original size:28 final size:28
Alignment explanation
Indices: 105829490--105829554 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 28
105829480 ATATATATAG
105829490 TATTATTTTTTAATTA-CTTTATTATTTT-
1 TATTATTTTTT-ATTATCTTT-TTATTTTA
*
105829518 TATTATATTTTATTATTCTTTTTATTTTAA
1 TATTATTTTTTATTA-TCTTTTTATTTT-A
105829548 TATTATT
1 TATTATT
105829555 ACTATTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 4 0.13
28 17 0.55
29 4 0.13
30 6 0.19
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (28 bp):
TATTATTTTTTATTATCTTTTTATTTTA
Found at i:105829545 original size:17 final size:19
Alignment explanation
Indices: 105829507--105829551 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
105829497 TTTTAATTAC
*
105829507 TTTATTATTTTTATTATAT
1 TTTATTATTCTTATTATAT
105829526 TTTATTATTCTT-TT-TAT
1 TTTATTATTCTTATTATAT
*
105829543 TTTAATATT
1 TTTATTATT
105829552 ATTACTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 11 0.46
18 2 0.08
19 11 0.46
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTATTCTTATTATAT
Found at i:105830043 original size:3 final size:3
Alignment explanation
Indices: 105830035--105830060 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
105830025 ACTTTGGATT
105830035 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
105830061 TTGTTTCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:105835966 original size:30 final size:29
Alignment explanation
Indices: 105835918--105835974 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
105835908 CCCAAACACA
105835918 AAACCCAAATACCTCAGACCCGTTACAGC
1 AAACCCAAATACCTCAGACCCGTTACAGC
*
105835947 AAACCCAAAATAGCC-CAGACCTGTTACA
1 AAACCC-AAATA-CCTCAGACCCGTTACA
105835975 CCCTACCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 6 0.24
30 17 0.68
31 2 0.08
ACGTcount: A:0.40, C:0.35, G:0.11, T:0.14
Consensus pattern (29 bp):
AAACCCAAATACCTCAGACCCGTTACAGC
Found at i:105837235 original size:12 final size:12
Alignment explanation
Indices: 105837220--105837252 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
105837210 TATTTTTAAT
105837220 TTATTATATATA
1 TTATTATATATA
105837232 TTATT-TATTATA
1 TTATTATA-TATA
105837244 TTATTATAT
1 TTATTATAT
105837253 TTTCAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.11
12 15 0.79
13 2 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTATTATATATA
Found at i:105837239 original size:16 final size:15
Alignment explanation
Indices: 105837218--105837250 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
105837208 CTTATTTTTA
105837218 ATTTATTATATATATT
1 ATTTATTATAT-TATT
105837234 ATTTATTATATTATT
1 ATTTATTATATTATT
105837249 AT
1 AT
105837251 ATTTTCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTATTATATTATT
Found at i:105837285 original size:7 final size:7
Alignment explanation
Indices: 105837268--105837416 Score: 57
Period size: 7 Copynumber: 21.4 Consensus size: 7
105837258 AAATTTGTAA
105837268 ATTAT-T
1 ATTATAT
105837274 ATTATAT
1 ATTATAT
105837281 ATTATAT
1 ATTATAT
105837288 -TT-TA-
1 ATTATAT
105837292 ACTTATAT
1 A-TTATAT
105837300 ATCTTATAT
1 A--TTATAT
*
105837309 ATTTATTT
1 A-TTATAT
105837317 ATT-TAT
1 ATTATAT
*
105837323 ATTATAC
1 ATTATAT
105837330 ATTAT-T
1 ATTATAT
*
105837336 -TTA-AA
1 ATTATAT
*
105837341 ACTTACAT
1 A-TTATAT
*
105837349 -TTTTAT
1 ATTATAT
105837355 ATTATAT
1 ATTATAT
*
105837362 ATTATAA
1 ATTATAT
*
105837369 ATTATTT
1 ATTATAT
105837376 CATT-TATT
1 -ATTATA-T
*
105837384 ATTATTT
1 ATTATAT
*
105837391 TTATATACT
1 AT-TATA-T
105837400 ATTATAT
1 ATTATAT
*
105837407 ATTATCT
1 ATTATAT
105837414 ATT
1 ATT
105837417 TTAAAATTCA
Statistics
Matches: 107, Mismatches: 19, Indels: 33
0.67 0.12 0.21
Matches are distributed among these distances:
5 5 0.05
6 18 0.17
7 54 0.50
8 20 0.19
9 10 0.09
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTATAT
Found at i:105837409 original size:26 final size:28
Alignment explanation
Indices: 105837380--105837446 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
105837370 TTATTTCATT
* * *
105837380 TATTATTATTTTTATA-T-ACTATTATA
1 TATTATTATTTTAAAATTCACTATTAAA
105837406 TATTATCTATTTTAAAATTCACTATTAAA
1 TATTAT-TATTTTAAAATTCACTATTAAA
105837435 TATTA-TATTTTA
1 TATTATTATTTTA
105837447 TGTATTATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 6 0.17
27 15 0.43
28 1 0.03
29 13 0.37
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (28 bp):
TATTATTATTTTAAAATTCACTATTAAA
Found at i:105837470 original size:16 final size:17
Alignment explanation
Indices: 105837356--105837471 Score: 51
Period size: 17 Copynumber: 6.7 Consensus size: 17
105837346 CATTTTTATA
105837356 TTATATATTA-TAAATTAT
1 TTATATATTATTAAA-T-T
* *
105837374 TTCATTTATTATT-ATTT
1 TT-ATATATTATTAAATT
* * *
105837391 TTATATACTATTATATA
1 TTATATATTATTAAATT
* *
105837408 TTATCTATT-TTAAAAT
1 TTATATATTATTAAATT
* * *
105837424 TCACTATTAAATATTATATT
1 TTA-TA-T-ATTATTAAATT
*
105837444 TTATGTATTATTAAATT
1 TTATATATTATTAAATT
105837461 TT-TATATTATT
1 TTATATATTATT
105837472 TGATATAATA
Statistics
Matches: 69, Mismatches: 22, Indels: 16
0.64 0.21 0.15
Matches are distributed among these distances:
16 22 0.32
17 23 0.33
18 5 0.07
19 11 0.16
20 8 0.12
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (17 bp):
TTATATATTATTAAATT
Found at i:105841369 original size:15 final size:15
Alignment explanation
Indices: 105841340--105841382 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
105841330 CTTTTTGTAT
105841340 TCATGCATTTGCATC
1 TCATGCATTTGCATC
105841355 TCATAGCATTT-CATC
1 TCAT-GCATTTGCATC
*
105841370 ACAT-CATTTGCAT
1 TCATGCATTTGCAT
105841383 TCAAAGTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.20
14 3 0.12
15 11 0.44
16 6 0.24
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.40
Consensus pattern (15 bp):
TCATGCATTTGCATC
Found at i:105844476 original size:500 final size:499
Alignment explanation
Indices: 105843535--105844532 Score: 1784
Period size: 500 Copynumber: 2.0 Consensus size: 499
105843525 GTTGAGAAAG
* * *
105843535 AGAAAGAGATTGGAATACCCATCAATGAGCCAGTAAATGAGTAGAAGGCTAAGGAGTTCTTAAAG
1 AGAAAGAGACTGAAATACCCATCAATGAGCCAGTAAATGAGGAGAAGGCTAAGGAGTTCTTAAAG
* *
105843600 TTCCTTAAGCATAGCGAGTATAGTGTGGTCGAGCAGTTGCGTAAGCAGCCAGTGTGTATATCAGA
66 TTCCTTAAGCATAGCGAGTATAGTGTGGTCGAGCAGTTGCGTAAGCAGCCAGCGCGTATATCAGA
* *
105843665 ATTAGCCCTGTTTCTGAGTTCTGAGGTGCATCGGGATGCATTATTGAATGTGCTTAACGAAACAT
131 ATTAGCCCTGCTTCTGAGTTCTGAGGTGCATCGGGATGCATTATTGAAGGTGCTTAACGAAACAT
*
105843730 ATGTCACCCACGACATATCCATTAACAAATTGGATCGGTTGGTAAATAACATCAGTGCTGACAAT
196 ATGTCACCCACGACATATCCATTAACAAATTGGATCGGTTGGTAAATAACATCAGTGCTAACAAT
105843795 TTCATCTATTTCAATGATGATAAAATTCCACTTGAGGGTATAGGGTCAACCAAAGCCTTGCACAT
261 TTCATCTATTTCAATGATGATAAAATTCCACTTGAGGGTATAGGGTCAACCAAAGCCTTGCACAT
*
105843860 CACTACTCGGTGCAAAGGATACACGCTGCCAAGTGCACTCGTTGATAATGGGTCTGCTTTGAACG
326 CACTACTCGGTGCAAAGGATACACGCTGCCAAGTGCACTCATTGATAATGGGTCTGCTTTGAACG
*
105843925 TCCTGCCATTATCCACCTTGAACAGATTACCCATTGATAGTTCGCATATGAAAACATGTCATAAT
391 TCCTGCCATTATCCACCTTGAACAGATTACCCATTGACAGTTCGCATATGAAAACATGTCATAAT
105843990 GTGGTAAGAGCCTTTGATAGAATTGAAAAAAAAAGTGATGGGACA
456 GTGGTAAGAGCCTTTGATAGAATTG-AAAAAAAAGTGATGGGACA
* *
105844035 AGAAAGAGACTGAAATACCCATCAATGAGCCAGTAAATTAGGAGGAGGCTAAGGAGTTCTTAAAG
1 AGAAAGAGACTGAAATACCCATCAATGAGCCAGTAAATGAGGAGAAGGCTAAGGAGTTCTTAAAG
*
105844100 TTCCTTAAGCATAGCGAGTATAGTGTGGTCGAGCAGTTGCGTAAGCAGCCAGCGCGTATATCAGT
66 TTCCTTAAGCATAGCGAGTATAGTGTGGTCGAGCAGTTGCGTAAGCAGCCAGCGCGTATATCAGA
*
105844165 ATTAGCCTTGCTTCTGAGTTCTGAGGTGCATCGGGATGCATTATT-ACAGGTGCTTAACGAAACA
131 ATTAGCCCTGCTTCTGAGTTCTGAGGTGCATCGGGATGCATTATTGA-AGGTGCTTAACGAAACA
105844229 TATGTCACCCACGACATATCCATTAACAAATTGGATCGGTTGGTAAATAACATCAGTGCTAACAA
195 TATGTCACCCACGACATATCCATTAACAAATTGGATCGGTTGGTAAATAACATCAGTGCTAACAA
* *
105844294 TTTCATCTATTTCAATGATGATGAAATTCCA-TCTGGGGGTATAGGGTCAACCAAAGCCTTGCAC
260 TTTCATCTATTTCAATGATGATAAAATTCCACT-TGAGGGTATAGGGTCAACCAAAGCCTTGCAC
*
105844358 ATCACTACTCGGTGCAAAGGATATACGCTGCCAAGTGCACTCATTGATAATGGGTCTGCTTTGAA
324 ATCACTACTCGGTGCAAAGGATACACGCTGCCAAGTGCACTCATTGATAATGGGTCTGCTTTGAA
105844423 CGTCCTGCCATTATCCACCTTGAACAGATTACCCATTGACAGTTCGCATATGAAAACATGTCATA
389 CGTCCTGCCATTATCCACCTTGAACAGATTACCCATTGACAGTTCGCATATGAAAACATGTCATA
* *
105844488 ATGTGGTAAGAGCCTTTGATGGAATTGAAAGAAAAGTGATGGGAC
454 ATGTGGTAAGAGCCTTTGATAGAATTGAAAAAAAAGTGATGGGAC
105844533 GAATCGACAT
Statistics
Matches: 477, Mismatches: 19, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
499 19 0.04
500 458 0.96
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (499 bp):
AGAAAGAGACTGAAATACCCATCAATGAGCCAGTAAATGAGGAGAAGGCTAAGGAGTTCTTAAAG
TTCCTTAAGCATAGCGAGTATAGTGTGGTCGAGCAGTTGCGTAAGCAGCCAGCGCGTATATCAGA
ATTAGCCCTGCTTCTGAGTTCTGAGGTGCATCGGGATGCATTATTGAAGGTGCTTAACGAAACAT
ATGTCACCCACGACATATCCATTAACAAATTGGATCGGTTGGTAAATAACATCAGTGCTAACAAT
TTCATCTATTTCAATGATGATAAAATTCCACTTGAGGGTATAGGGTCAACCAAAGCCTTGCACAT
CACTACTCGGTGCAAAGGATACACGCTGCCAAGTGCACTCATTGATAATGGGTCTGCTTTGAACG
TCCTGCCATTATCCACCTTGAACAGATTACCCATTGACAGTTCGCATATGAAAACATGTCATAAT
GTGGTAAGAGCCTTTGATAGAATTGAAAAAAAAGTGATGGGACA
Found at i:105852725 original size:26 final size:26
Alignment explanation
Indices: 105852689--105852798 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
105852679 TATGAAATTC
*
105852689 TTATCATGAAACATTTACCTAACCGA
1 TTATCATGAAACATTTACCTAACCTA
*
105852715 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
105852741 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
105852767 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
105852793 TTATCA
1 TTATCA
105852799 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:105853871 original size:30 final size:29
Alignment explanation
Indices: 105853823--105853879 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
105853813 CCCAAACACA
105853823 AAACCCAAATACCTCAGACCCGTTACAGC
1 AAACCCAAATACCTCAGACCCGTTACAGC
*
105853852 AAACCCAAAATAGCC-CAGACCTGTTACA
1 AAACCC-AAATA-CCTCAGACCCGTTACA
105853880 CCCTACCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 6 0.24
30 17 0.68
31 2 0.08
ACGTcount: A:0.40, C:0.35, G:0.11, T:0.14
Consensus pattern (29 bp):
AAACCCAAATACCTCAGACCCGTTACAGC
Found at i:105855141 original size:16 final size:15
Alignment explanation
Indices: 105855122--105855154 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
105855112 ACTTATTTTA
105855122 ATTTATTATATATATT
1 ATTTATTATAT-TATT
105855138 ATTTATTATATTATT
1 ATTTATTATATTATT
105855153 AT
1 AT
105855155 ATTTTCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTATTATATTATT
Found at i:105855189 original size:7 final size:7
Alignment explanation
Indices: 105855172--105855316 Score: 53
Period size: 7 Copynumber: 21.4 Consensus size: 7
105855162 AAATTTGTAA
105855172 ATTAT-T
1 ATTATAT
105855178 ATTATAT
1 ATTATAT
105855185 ATTATAT
1 ATTATAT
105855192 -TT-TA-
1 ATTATAT
105855196 ACTTATAT
1 A-TTATAT
105855204 ATCT-TAT
1 AT-TATAT
*
105855211 A-TATTT
1 ATTATAT
105855217 ATT-TAT
1 ATTATAT
*
105855223 ATTATAC
1 ATTATAT
105855230 ATTAT-T
1 ATTATAT
* *
105855236 -TTAAAA
1 ATTATAT
*
105855242 ACTTACAT
1 A-TTATAT
*
105855250 -TTTTAT
1 ATTATAT
105855256 ATTATAT
1 ATTATAT
*
105855263 ATTATAA
1 ATTATAT
*
105855270 ATTATTT
1 ATTATAT
105855277 CATT-TATT
1 -ATTATA-T
105855285 ATTAT-T
1 ATTATAT
*
105855291 TTATATACT
1 AT-TATA-T
105855300 ATTATAT
1 ATTATAT
*
105855307 ATTATCT
1 ATTATAT
105855314 ATT
1 ATT
105855317 TTAAAATTCA
Statistics
Matches: 102, Mismatches: 18, Indels: 37
0.65 0.11 0.24
Matches are distributed among these distances:
5 6 0.06
6 23 0.23
7 56 0.55
8 15 0.15
9 2 0.02
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTATAT
Found at i:105861149 original size:18 final size:19
Alignment explanation
Indices: 105861128--105861169 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
105861118 ACAATATGTG
105861128 TATATAA-ATGTAAAATAA
1 TATATAATATGTAAAATAA
* *
105861146 TATATAATTTTTAAAATAA
1 TATATAATATGTAAAATAA
105861165 TATAT
1 TATAT
105861170 GATAATAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TATATAATATGTAAAATAA
Found at i:105861181 original size:50 final size:51
Alignment explanation
Indices: 105861127--105861223 Score: 133
Period size: 52 Copynumber: 1.9 Consensus size: 51
105861117 TACAATATGT
* * *
105861127 GTATATAAATGTAAAATAATA-TATAATTTTTAAAATAATATATGATAATA
1 GTATACAAATGTAAAATAATACTATAATATATAAAATAATATATGATAATA
* *
105861177 GTATACAAGTTTAAAATAATACTTATAATATATAAAATAATATATGA
1 GTATACAAATGTAAAATAATAC-TATAATATATAAAATAATATATGA
105861224 AAAGTAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 18 0.45
52 22 0.55
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (51 bp):
GTATACAAATGTAAAATAATACTATAATATATAAAATAATATATGATAATA
Found at i:105862373 original size:13 final size:13
Alignment explanation
Indices: 105862355--105862379 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
105862345 CTAGATTCGA
105862355 GGCCTGGAATCAT
1 GGCCTGGAATCAT
105862368 GGCCTGGAATCA
1 GGCCTGGAATCA
105862380 CTGCAAGACA
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:0.24, G:0.32, T:0.20
Consensus pattern (13 bp):
GGCCTGGAATCAT
Found at i:105865219 original size:24 final size:26
Alignment explanation
Indices: 105865192--105865239 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
105865182 TATGAATACG
105865192 TACAT-ATAATATA-ATAT-TAAAATA
1 TACATAAT-ATATACATATATAAAATA
105865216 TACATAATATATACATATATAAAA
1 TACATAATATATACATATATAAAA
105865240 CATGTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 10 0.48
25 6 0.29
26 5 0.24
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (26 bp):
TACATAATATATACATATATAAAATA
Found at i:105866218 original size:11 final size:11
Alignment explanation
Indices: 105866202--105866231 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
105866192 TAGGGGGCCG
105866202 GTCACCGGTCC
1 GTCACCGGTCC
105866213 GTCACCGGTCC
1 GTCACCGGTCC
105866224 GTCACCGG
1 GTCACCGG
105866232 ACCCTCGCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.43, G:0.30, T:0.17
Consensus pattern (11 bp):
GTCACCGGTCC
Found at i:105867610 original size:88 final size:85
Alignment explanation
Indices: 105867498--105867800 Score: 337
Period size: 88 Copynumber: 3.5 Consensus size: 85
105867488 ACTTGAGTAA
* * *
105867498 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAATAGAATTTGCCAAACAGATTTTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATA-AA-TTG-AAAACAAATTTTG
105867563 AAAATACCTCAGCATGTGACCCG
63 AAAATACCTCAGCATGTGACCCG
* * *
105867586 AGGCTCAACTCACCTCTTGTAATATGAGTTGATTCTTGAAAAGCATAAATTGAAAA-AACATTAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAA--ATAAATTGAAAACAA-ATT--
105867650 TTGAAAATACCTCAGC--GTG-CCTCG
60 TTGAAAATACCTCAGCATGTGACC-CG
**
105867674 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGACGAACATAAATTGAAAAACAAAAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA--AA-ATAAATTG-AAAACAAATTTT
* **
105867738 GAAAAGACCTCAGCATGTGAGTCG
62 GAAAATACCTCAGCATGTGACCCG
*
105867762 AGGCTCAACTCACCTCTCGCGATATGAGTTGATTTTTGA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
105867801 CAAACAAAAA
Statistics
Matches: 185, Mismatches: 15, Indels: 29
0.81 0.07 0.13
Matches are distributed among these distances:
86 16 0.09
87 16 0.09
88 118 0.64
89 14 0.08
90 18 0.10
91 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (85 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATAAATTGAAAACAAATTTTGAAA
ATACCTCAGCATGTGACCCG
Found at i:105867873 original size:75 final size:75
Alignment explanation
Indices: 105867722--105868053 Score: 269
Period size: 75 Copynumber: 4.3 Consensus size: 75
105867712 CGAACATAAA
* *
105867722 TTGAAAAACAAAAATTGAAAAGACCTCAGCATGTGAGTCGAGGCTCAACTCACCTCTCGCGATAT
1 TTGAAAAACAAAAATTGAAAAGACCTCAGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATAT
105867787 GAGTTGATTT
66 GAGTTGATTT
* ** * *
105867797 TTGACAAACAAAAATTGAAATTACCTCAGCGTGT-CCT-GAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAAAAATTGAAAAGACCTCAGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATAT
105867860 GAGTTGATTTTT
66 GAGTTGA--TTT
* * * ** ** * *
105867872 TTGAAGAGCAGAAATTGGAAAGCAGAAATCGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCAC
1 TTGAAAAACAAAAATT-GAAA--AGACCTC-AGCAT--GTGA-C-T---C-GAGGCTCAACTCAC
105867937 CTCTCGCAATATGAGTTGATTTTT
54 CTCTCGCAATATGAGTTGA--TTT
* * ** * *
105867961 TTGACAAACATAAATTGAAATTACCTCAGCGTGT-CCT-GAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAAAAATTGAAAAGACCTCAGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATAT
105868024 GAGTTGA-TT
66 GAGTTGATTT
* *
105868033 TTGACAAACAGAAATTGAAAA
1 TTGAAAAACAAAAATTGAAAA
105868054 ACAGAAATTG
Statistics
Matches: 206, Mismatches: 35, Indels: 35
0.75 0.13 0.13
Matches are distributed among these distances:
72 21 0.10
73 32 0.16
74 1 0.00
75 78 0.38
76 4 0.02
78 3 0.01
79 2 0.01
80 1 0.00
81 2 0.01
83 2 0.01
84 1 0.00
85 2 0.01
86 3 0.01
88 4 0.02
89 50 0.24
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (75 bp):
TTGAAAAACAAAAATTGAAAAGACCTCAGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTT
Found at i:105867976 original size:89 final size:89
Alignment explanation
Indices: 105867808--105867977 Score: 279
Period size: 89 Copynumber: 1.9 Consensus size: 89
105867798 TGACAAACAA
* * *
105867808 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATCGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
*
105867873 TGAAGAGCAGAAATTGGAAAGCAG
66 TGAAGAACAGAAATTGGAAAGCAG
105867897 AAATCGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATCGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
*
105867962 TGACA-AACATAAATTG
66 TGA-AGAACAGAAATTG
105867978 AAATTACCTC
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
89 74 0.99
90 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (89 bp):
AAATCGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
TGAAGAACAGAAATTGGAAAGCAG
Found at i:105868055 original size:14 final size:14
Alignment explanation
Indices: 105868033--105868067 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
105868023 TGAGTTGATT
*
105868033 TTGACAAACAGAAA
1 TTGAAAAACAGAAA
105868047 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
105868061 TTGAAAA
1 TTGAAAA
105868068 GACCTCAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.60, C:0.09, G:0.14, T:0.17
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:105868145 original size:161 final size:161
Alignment explanation
Indices: 105867641--105868304 Score: 930
Period size: 161 Copynumber: 4.1 Consensus size: 161
105867631 TAAATTGAAA
* *
105867641 AAACATTAATTGAAAATACCTCAGCGTG-CCTCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAACATAAATTGAAATTACCTCAGCGTGTCCT-GAGGCTCAACTCACCTCTCGCAATATGAGTTG
* * * * **
105867705 A-TTTTGACGAACATAAATTGAAAAACAAAAATTGAAAAGACCTCAGCATGTG-AGTCGAGGCTC
65 ATTTTTGAAGAACAGAAATTGAAAAACAGAAATCGAAAAGACCTCAGC--GTGCCCT-GAGGCTC
*
105867768 AACTCACCTCTCGCGATATGAGTTGA-TTTTTGAC
127 AACTCACCTCTCGCAATATGAGTTGATTTTTTGAC
*
105867802 AAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* * * *
105867867 TTTTTTTGAAGAGCAGAAATTGGAAAGCAGAAATCGAAAATACCTCAGCGTGCCCTGAGGCTCAA
66 --TTTTTGAAGAACAGAAATTGAAAAACAGAAATCGAAAAGACCTCAGCGTGCCCTGAGGCTCAA
105867932 CTCACCTCTCGCAATATGAGTTGATTTTTTTGAC
129 CTCACCTCTCGCAATATGAGTTGA-TTTTTTGAC
105867966 AAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* **
105868031 -TTTTGACA-AACAGAAATTGAAAAACAGAAATTGAAAAGACCTCAGCATGTG-AGTCGAGGCTC
66 TTTTTGA-AGAACAGAAATTGAAAAACAGAAATCGAAAAGACCTCAGC--GTGCCCT-GAGGCTC
*
105868093 AACTCACCTCTCGCGATATGAGTTGA-TTTTTGAC
127 AACTCACCTCTCGCAATATGAGTTGATTTTTTGAC
*
105868127 AAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* * * * *
105868192 TTTTTTTGAAGAGCAAAAATTGGAAAGCAGAAATCGAAAATACCTCAGCGTGCCCTGAGGCTCAA
66 --TTTTTGAAGAACAGAAATTGAAAAACAGAAATCGAAAAGACCTCAGCGTGCCCTGAGGCTCAA
105868257 CTCACCTCTCGCAATATGAGTTGATTTTTTTGAC
129 CTCACCTCTCGCAATATGAGTTGA-TTTTTTGAC
105868291 AAACATAAATTGAA
1 AAACATAAATTGAA
105868305 GAAAACAAAA
Statistics
Matches: 451, Mismatches: 34, Indels: 33
0.87 0.07 0.06
Matches are distributed among these distances:
161 169 0.37
162 75 0.17
163 38 0.08
164 169 0.37
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (161 bp):
AAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
TTTTTGAAGAACAGAAATTGAAAAACAGAAATCGAAAAGACCTCAGCGTGCCCTGAGGCTCAACT
CACCTCTCGCAATATGAGTTGATTTTTTGAC
Found at i:105868185 original size:73 final size:75
Alignment explanation
Indices: 105868047--105868196 Score: 223
Period size: 73 Copynumber: 2.0 Consensus size: 75
105868037 CAAACAGAAA
* *
105868047 TTGAAAAACAGAAATTGAAAAGACCTCAGCATGTGAGTCGAGGCTCAACTCACCTCTCGCGATAT
1 TTGAAAAACAGAAATTGAAAAGACCTCAGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATAT
105868112 GAGTTGATTT
66 GAGTTGATTT
* ** * *
105868122 TTGACAAACAGAAATTGAAATTACCTCAGCGTGT-CCT-GAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAAGACCTCAGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATAT
105868185 GAGTTGATTT
66 GAGTTGATTT
105868195 TT
1 TT
105868197 TTGAAGAGCA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
73 37 0.54
74 1 0.01
75 30 0.44
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (75 bp):
TTGAAAAACAGAAATTGAAAAGACCTCAGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTT
Done.