Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 9 of 106
Found at i:4303545 original size:18 final size:18
Alignment explanation
Indices: 4303504--4303545 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
4303494 AATTATATTA
* *
4303504 AAAATAAAAAATAAGATT
1 AAAATAAAAAATAAAAAT
*
4303522 ATAATAAAAAATAAAAAT
1 AAAATAAAAAATAAAAAT
4303540 AAAATA
1 AAAATA
4303546 TATGATATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (18 bp):
AAAATAAAAAATAAAAAT
Found at i:4318870 original size:3 final size:3
Alignment explanation
Indices: 4318864--4318913 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
4318854 CATTATTAGC
* * * *
4318864 TGG TGG TGG TGG TGG TGG TGA TGG TGG TGG TGA TGG TGG CGA TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
4318912 TG
1 TG
4318914 ATGATGATGA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.06, C:0.02, G:0.60, T:0.32
Consensus pattern (3 bp):
TGG
Found at i:4318919 original size:12 final size:12
Alignment explanation
Indices: 4318873--4318922 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
4318863 CTGGTGGTGG
*
4318873 TGGTGGTGGTGA
1 TGGTGGTGATGA
*
4318885 TGGTGGTGGTGA
1 TGGTGGTGATGA
* *
4318897 TGGTGGCGATGG
1 TGGTGGTGATGA
*
4318909 TGGTGATGATGA
1 TGGTGGTGATGA
4318921 TG
1 TG
4318923 ACGAGGGCGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.12, C:0.02, G:0.54, T:0.32
Consensus pattern (12 bp):
TGGTGGTGATGA
Found at i:4330880 original size:2 final size:2
Alignment explanation
Indices: 4330873--4330901 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4330863 AACATTTCCT
4330873 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4330902 GTATGTCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4332195 original size:19 final size:19
Alignment explanation
Indices: 4332171--4332211 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
4332161 ACATAATATT
* *
4332171 TTTAAAAAAATTTAAATTA
1 TTTAAAAAAATTCAAATAA
*
4332190 TTTAAAAATATTCAAATAA
1 TTTAAAAAAATTCAAATAA
4332209 TTT
1 TTT
4332212 TTATTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTAAAAAAATTCAAATAA
Found at i:4333584 original size:29 final size:28
Alignment explanation
Indices: 4333527--4333585 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
4333517 ATGAGAAAAA
* **
4333527 TATTTTAAAATAAAATATTATTAGTTAT
1 TATTTTAAAATAAAATAATATTAAATAT
*
4333555 TATTTTTAAATAAAATAATATTAAAATAT
1 TATTTTAAAATAAAATAATATT-AAATAT
4333584 TA
1 TA
4333586 ATATTTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
TATTTTAAAATAAAATAATATTAAATAT
Found at i:4334478 original size:17 final size:16
Alignment explanation
Indices: 4334441--4334498 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 16
4334431 GTAAGGGAAG
*
4334441 AAAAGAGAGGAAAAAAA
1 AAAAGAGA-AAAAAAAA
4334458 AAAAGAGAAAAAAAATA
1 AAAAGAGAAAAAAAA-A
* *
4334475 AAAAAATAAAATAAAAA
1 AAAAGAGAAAA-AAAAA
4334492 AAAAGAG
1 AAAAGAG
4334499 GAGTAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
16 6 0.18
17 24 0.71
18 4 0.12
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (16 bp):
AAAAGAGAAAAAAAAA
Found at i:4334485 original size:13 final size:12
Alignment explanation
Indices: 4334451--4334495 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 12
4334441 AAAAGAGAGG
4334451 AAAAAAAAAAA-
1 AAAAAAAAAAAT
* *
4334462 GAGAAAAAAAAT
1 AAAAAAAAAAAT
4334474 AAAAAAATAAAAT
1 AAAAAAA-AAAAT
4334487 AAAAAAAAA
1 AAAAAAAAA
4334496 GAGGAGTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
11 9 0.32
12 7 0.25
13 12 0.43
ACGTcount: A:0.89, C:0.00, G:0.04, T:0.07
Consensus pattern (12 bp):
AAAAAAAAAAAT
Found at i:4334491 original size:23 final size:23
Alignment explanation
Indices: 4334451--4334495 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4334441 AAAAGAGAGG
4334451 AAAAAAAAAAAGAGAAAAAAAAT
1 AAAAAAAAAAAGAGAAAAAAAAT
*
4334474 AAAAAAATAAAATA-AAAAAAAA
1 AAAAAAA-AAAAGAGAAAAAAAA
4334496 GAGGAGTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.89, C:0.00, G:0.04, T:0.07
Consensus pattern (23 bp):
AAAAAAAAAAAGAGAAAAAAAAT
Found at i:4335232 original size:62 final size:62
Alignment explanation
Indices: 4335123--4335369 Score: 195
Period size: 62 Copynumber: 4.0 Consensus size: 62
4335113 ATATTTGATT
* * * *
4335123 TAAAAAGGGA-ACTTGAAGCCCCGATTTATATATGGTGGTATGAGTAGTTTCCACGAGTAGG
1 TAAAAAGGGAGTCTTGAAGCCTCGATTTATATATGGTGGCATGGGTAGTTTCCACGAGTAGG
* * * * * * *
4335184 TAAAAAGGGAGTCTTGAAGCCTCGATTTAAATATAGTGGCGTGGGTAGTTCCCGCAAGTAGA
1 TAAAAAGGGAGTCTTGAAGCCTCGATTTATATATGGTGGCATGGGTAGTTTCCACGAGTAGG
* * * *
4335246 TAAAAAGAGG-GATC-TAAAGTCTCAATTTATATATGGTGGCATGGGTAG-TTCTCACGAGGAGG
1 TAAAAAG-GGAG-TCTTGAAGCCTCGATTTATATATGGTGGCATGGGTAGTTTC-CACGAGTAGG
* * * * * *
4335308 TAAAATAGGGAGACCTT-AAGCCCCGA-TT-CATCTGGTGGCACGGGCAG-TTCTCACGAGTAGG
1 TAAAA-AGGGAG-TCTTGAAGCCTCGATTTATATATGGTGGCATGGGTAGTTTC-CACGAGTAGG
4335369 T
1 T
4335370 GATGATGTTA
Statistics
Matches: 148, Mismatches: 31, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
61 41 0.28
62 91 0.61
63 15 0.10
64 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (62 bp):
TAAAAAGGGAGTCTTGAAGCCTCGATTTATATATGGTGGCATGGGTAGTTTCCACGAGTAGG
Found at i:4337830 original size:78 final size:78
Alignment explanation
Indices: 4337721--4338415 Score: 758
Period size: 78 Copynumber: 8.9 Consensus size: 78
4337711 GACAAATTGT
* * * * *
4337721 TTCTTTTTTTTAAGGTCAACATTGTCAGTGTAAGCACTAACACTTGGCCTCGGCTTGAAATCATT
1 TTCTTTTCTTTAAGGCCAACATCGTCAGTGTAAGCAGTAACACTTGGCCTCGGCTCGAAATCATT
4337786 AGCAAATGACAAC
66 AGCAAATGACAAC
* * * * *
4337799 TCCTTTTTTTTTAGGCCAACATCGTCGGTGTAAGCAGAAACACTTGGCCTCGGCTCGAAATCATT
1 TTCTTTTCTTTAAGGCCAACATCGTCAGTGTAAGCAGTAACACTTGGCCTCGGCTCGAAATCATT
*
4337864 AGCAAATGCCAAC
66 AGCAAATGACAAC
* *
4337877 TTCTTTTTTTTAAGGCCAACATCGTCAGTGTAAGCACTAACACTTGGCCTCGGCTCGAAATCATT
1 TTCTTTTCTTTAAGGCCAACATCGTCAGTGTAAGCAGTAACACTTGGCCTCGGCTCGAAATCATT
*
4337942 TGCAAAT---AAC
66 AGCAAATGACAAC
** * *
4337952 TTCTTTTCTTTAAGGCCAACATCGTCAACGTAAGTAGTAACACTTGGCCTCGGCTCGAAATCTTT
1 TTCTTTTCTTTAAGGCCAACATCGTCAGTGTAAGCAGTAACACTTGGCCTCGGCTCGAAATCATT
*
4338017 AGCAAATGCCAAC
66 AGCAAATGACAAC
* * *
4338030 TTCTTTTCTTTAAGACCAACATCGTCTGTGTAAGCAGTAACACCTGGCCTCGGCTCGAAATCATT
1 TTCTTTTCTTTAAGGCCAACATCGTCAGTGTAAGCAGTAACACTTGGCCTCGGCTCGAAATCATT
*
4338095 AGCAAATGACAGC
66 AGCAAATGACAAC
* * * * * *
4338108 TTCTTTTCTCTAAGGCCAACATCGTCGGTGTAAGCAGTAGCACTTGGTCTCGGTTCAAAATCATT
1 TTCTTTTCTTTAAGGCCAACATCGTCAGTGTAAGCAGTAACACTTGGCCTCGGCTCGAAATCATT
* *
4338173 AACAAATGCCAAC
66 AGCAAATGACAAC
* * * * * * * *
4338186 TTCTCTTCTTTAAGGTCGACATTGTCAGTGTAAGTAGTAACGCTTGGCCTTGGTTCGAAATCATT
1 TTCTTTTCTTTAAGGCCAACATCGTCAGTGTAAGCAGTAACACTTGGCCTCGGCTCGAAATCATT
*
4338251 AGCAATTGACAAC
66 AGCAAATGACAAC
* * * * * ** * * * *
4338264 TTC---TCTTT-AGAACCAACATCATCAGTATAAGCTGTAGCACTTGGTTTGGGTTC-AAAGCTT
1 TTCTTTTCTTTAAG-GCCAACATCGTCAGTGTAAGCAGTAACACTTGGCCTCGGCTCGAAATC-A
*
4338324 TTAGCAAATGATGACAAT
64 TTAGC-AA--ATGACAAC
* * * * * * *
4338342 TTCTTCTCTTTAAGGCCAACATCGTCAGTGTGAGCAGTAGCACTGGGCCTCTGTTCGAAATCGTT
1 TTCTTTTCTTTAAGGCCAACATCGTCAGTGTAAGCAGTAACACTTGGCCTCGGCTCGAAATCATT
4338407 AGCAAATGA
66 AGCAAATGA
4338416 TGACTTTTCT
Statistics
Matches: 518, Mismatches: 86, Indels: 26
0.82 0.14 0.04
Matches are distributed among these distances:
74 6 0.01
75 107 0.21
76 2 0.00
78 353 0.68
80 2 0.00
81 42 0.08
82 6 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (78 bp):
TTCTTTTCTTTAAGGCCAACATCGTCAGTGTAAGCAGTAACACTTGGCCTCGGCTCGAAATCATT
AGCAAATGACAAC
Found at i:4338281 original size:231 final size:229
Alignment explanation
Indices: 4337729--4338415 Score: 763
Period size: 231 Copynumber: 3.0 Consensus size: 229
4337719 GTTTCTTTTT
* *
4337729 TTTAAGGTCAACATTGTCAGTGTAAGCACTAACACTTGGCCTCGGCTT-GAAATCATTAGCAAAT
1 TTTAAGGTCAACATTGTCAGTGTAAGTAGTAACACTTGGCCTCGG-TTCGAAATCATTAGCAAAT
* * * * *
4337793 GACAACTCCTTTTTTTTTAG-GCCAACATCGTCGGTGTAAGCAGAAACACTTGGCCTCGGCTCGA
65 GACAA---C-TTCTCTTTAGAACCAACATCGTCAGTGTAAGCAGTAACACTTGGCCTCGGCTCGA
* * * *
4337857 AATCATTAGCAAATGCCAACTTCTTTTTTTTAAGGCCAACATCGTCAGTGTAAGCACTAACACTT
126 AATCATTAGCAAATGACAACTTCTTTTCTTTAAGGCCAACATCGTCAGTGTAAGCAGTAGCACTT
* * *
4337922 GGCCTCGGCTCGAAATCATTTGCAAAT-AACTTCTTTTC
191 GGCCTCGGTTCGAAATCATTAGCAAATGAACTTCTCTTC
* * ** * *
4337960 TTTAAGGCCAACATCGTCAACGTAAGTAGTAACACTTGGCCTCGGCTCGAAATCTTTAGCAAATG
1 TTTAAGGTCAACATTGTCAGTGTAAGTAGTAACACTTGGCCTCGGTTCGAAATCATTAGCAAATG
* * *
4338025 CCAACTTCTTTTCTTTA-AGACCAACATCGTCTGTGTAAGCAGTAACACCTGGCCTCGGCTCGAA
66 ACAACTTC---TCTTTAGA-ACCAACATCGTCAGTGTAAGCAGTAACACTTGGCCTCGGCTCGAA
* * *
4338089 ATCATTAGCAAATGACAGCTTCTTTTCTCTAAGGCCAACATCGTCGGTGTAAGCAGTAGCACTTG
127 ATCATTAGCAAATGACAACTTCTTTTCTTTAAGGCCAACATCGTCAGTGTAAGCAGTAGCACTTG
* * *
4338154 GTCTCGGTTCAAAATCATTAACAAATGCCAACTTCTCTTC
192 GCCTCGGTTCGAAATCATTAGCAAATG--AACTTCTCTTC
* * * *
4338194 TTTAAGGTCGACATTGTCAGTGTAAGTAGTAACGCTTGGCCTTGGTTCGAAATCATTAGCAATTG
1 TTTAAGGTCAACATTGTCAGTGTAAGTAGTAACACTTGGCCTCGGTTCGAAATCATTAGCAAATG
* * * * ** * * *
4338259 ACAACTTCTCTTTAGAACCAACATCATCAGTATAAGCTGTAGCACTTGGTTTGGGTTC-AAAGCT
66 ACAACTTCTCTTTAGAACCAACATCGTCAGTGTAAGCAGTAACACTTGGCCTCGGCTCGAAATC-
* * * * *
4338323 TTTAGCAAATGATGACAATTTCTTCTCTTTAAGGCCAACATCGTCAGTGTGAGCAGTAGCACTGG
130 ATTAGC-AA--ATGACAACTTCTTTTCTTTAAGGCCAACATCGTCAGTGTAAGCAGTAGCACTTG
* *
4338388 GCCTCTGTTCGAAATCGTTAGCAAATGA
192 GCCTCGGTTCGAAATCATTAGCAAATGA
4338416 TGACTTTTCT
Statistics
Matches: 379, Mismatches: 63, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
227 2 0.01
228 1 0.00
230 10 0.03
231 221 0.58
232 4 0.01
234 141 0.37
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (229 bp):
TTTAAGGTCAACATTGTCAGTGTAAGTAGTAACACTTGGCCTCGGTTCGAAATCATTAGCAAATG
ACAACTTCTCTTTAGAACCAACATCGTCAGTGTAAGCAGTAACACTTGGCCTCGGCTCGAAATCA
TTAGCAAATGACAACTTCTTTTCTTTAAGGCCAACATCGTCAGTGTAAGCAGTAGCACTTGGCCT
CGGTTCGAAATCATTAGCAAATGAACTTCTCTTC
Found at i:4349445 original size:154 final size:153
Alignment explanation
Indices: 4349116--4349524 Score: 628
Period size: 154 Copynumber: 2.7 Consensus size: 153
4349106 ATAAAAATAC
* *
4349116 AAATGGAGCCATATATTAGCTTTATTCTAATTGCTTTCAAAGGTACTTTGATAGTTATAATATAT
1 AAATGGAGCCATATATTAGCTTTAATCTAATTGCTTTCAAAGATACTTTGATAGTTATAATATAT
* *
4349181 ACTT-ATTAAATAATACATTTGAAATGGAGCCATACAATTATCAAAGTATACATAAATATATACT
66 ACTTGATTAAATAATACATTTGAAATGGAGCCATATAACTATCAAAGTATACATAAATATATACT
4349245 TTATATTATAAATAATACATTTG
131 TTATATTATAAATAATACATTTG
* *
4349268 AAATGGTA-CCATACATTAGCTTTAATCTAATTGCTTTCAGAGATACTTTGATAGTTATAATATA
1 AAATGG-AGCCATATATTAGCTTTAATCTAATTGCTTTCAAAGATACTTTGATAGTTATAATATA
* *
4349332 TACTTGATTAAATAATACATTTGAAATGAAGCCATATAGCTATCAAAGTATACATATAATATATA
65 TACTTGATTAAATAATACATTTGAAATGGAGCCATATAACTATCAAAGTATACATA-AATATATA
4349397 -TTGTATATTATAAATAATACATTTG
129 CTT-TATATTATAAATAATACATTTG
* * *
4349422 AAATGGAGCCATATATTAACTTT-ATGCTAATTGCTTTCAAAGATATTTTGATAGATATAATATA
1 AAATGGAGCCATATATTAGCTTTAAT-CTAATTGCTTTCAAAGATACTTTGATAGTTATAATATA
* *
4349486 TAATTTGGTTAAATAATACATTTGAAATGGAGCCATATA
65 T-ACTTGATTAAATAATACATTTGAAATGGAGCCATATA
4349525 TTAACTTTAT
Statistics
Matches: 234, Mismatches: 16, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
152 63 0.27
153 52 0.22
154 85 0.36
155 34 0.15
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (153 bp):
AAATGGAGCCATATATTAGCTTTAATCTAATTGCTTTCAAAGATACTTTGATAGTTATAATATAT
ACTTGATTAAATAATACATTTGAAATGGAGCCATATAACTATCAAAGTATACATAAATATATACT
TTATATTATAAATAATACATTTG
Found at i:4349519 original size:88 final size:87
Alignment explanation
Indices: 4349407--4349608 Score: 332
Period size: 88 Copynumber: 2.3 Consensus size: 87
4349397 TTGTATATTA
*
4349407 TAAATAATACATTTGAAATGGAGCCATATATTAACTTTATGCTAATTGCTTTCAAAGATATTTTG
1 TAAATAATACATTTGAAATGGAGCCATATATTAACTTTATGCTAATTGCTTTCAAAGATACTTTG
* *
4349472 ATAGATATAATATATAATTTGGT
66 ATAGATATAATATAT-ACTTGAT
* *
4349495 TAAATAATACATTTGAAATGGAGCCATATATTAACTTTATGCTAATTGCTTTTAAAGGTACTTTG
1 TAAATAATACATTTGAAATGGAGCCATATATTAACTTTATGCTAATTGCTTTCAAAGATACTTTG
*
4349560 ATAGTTATAATATATACTTGAT
66 ATAGATATAATATATACTTGAT
*
4349582 TAAATAATGCATTTGAAATGGAGCCAT
1 TAAATAATACATTTGAAATGGAGCCAT
4349609 GTAACTATCA
Statistics
Matches: 107, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
87 31 0.29
88 76 0.71
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (87 bp):
TAAATAATACATTTGAAATGGAGCCATATATTAACTTTATGCTAATTGCTTTCAAAGATACTTTG
ATAGATATAATATATACTTGAT
Found at i:4356431 original size:20 final size:20
Alignment explanation
Indices: 4356406--4356446 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
4356396 ATAAAATATA
*
4356406 TATCTATATGTAGT-CTGCAT
1 TATCTATA-GTAATGCTGCAT
4356426 TATCTATAGTAATGCTGCAT
1 TATCTATAGTAATGCTGCAT
4356446 T
1 T
4356447 CAGTTCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
TATCTATAGTAATGCTGCAT
Found at i:4365297 original size:22 final size:21
Alignment explanation
Indices: 4365258--4365299 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
4365248 ATGAAAATAC
**
4365258 TTTTTATTAAAATTTAAAAAT
1 TTTTTATTAAAAAATAAAAAT
4365279 TTTTTAATTAAAAAATAAAAA
1 TTTTT-ATTAAAAAATAAAAA
4365300 AACTATGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTTTATTAAAAAATAAAAAT
Found at i:4365464 original size:23 final size:22
Alignment explanation
Indices: 4365435--4365504 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 22
4365425 ATAAACATAG
4365435 TTTTATTATAATTTAATAATAT
1 TTTTATTATAATTTAATAATAT
* ** *
4365457 TTTGTATTAGAAGATAATTAA-ACC
1 TTT-TATTATAATTTAA-TAATA-T
*
4365481 TTTTATTATAATTAAATAATAT
1 TTTTATTATAATTTAATAATAT
4365503 TT
1 TT
4365505 AATATTAAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
22 8 0.23
23 21 0.60
24 6 0.17
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (22 bp):
TTTTATTATAATTTAATAATAT
Found at i:4365616 original size:36 final size:36
Alignment explanation
Indices: 4365570--4365683 Score: 114
Period size: 36 Copynumber: 3.3 Consensus size: 36
4365560 CTTTATTACA
*
4365570 TTTATTATATTCAAATAATAATATTAAGTAATATGC
1 TTTATAATATTCAAATAATAATATTAAGTAATATGC
* ** * *
4365606 TTTATAATATTTAAAT-AT--T-TT-CNTTAT-TAC
1 TTTATAATATTCAAATAATAATATTAAGTAATATGC
*
4365636 ATTTATTATATTCAAATAATAATATTAAGTAATATGC
1 -TTTATAATATTCAAATAATAATATTAAGTAATATGC
4365673 TTTATAATATT
1 TTTATAATATT
4365684 TATTATAGTG
Statistics
Matches: 58, Mismatches: 13, Indels: 14
0.68 0.15 0.16
Matches are distributed among these distances:
30 2 0.03
31 17 0.29
32 4 0.07
33 1 0.02
34 1 0.02
35 4 0.07
36 27 0.47
37 2 0.03
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.49
Consensus pattern (36 bp):
TTTATAATATTCAAATAATAATATTAAGTAATATGC
Found at i:4371245 original size:24 final size:23
Alignment explanation
Indices: 4371212--4371259 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
4371202 ATTGAATTTT
* *
4371212 ATATTAAATAGCTTCATTCTAGA
1 ATATTAAATAGCCTAATTCTAGA
4371235 ATATTCAAATAGCCTAATTCTAGA
1 ATATT-AAATAGCCTAATTCTAGA
4371259 A
1 A
4371260 CATTTAGTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATTAAATAGCCTAATTCTAGA
Found at i:4371760 original size:11 final size:12
Alignment explanation
Indices: 4371740--4371771 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
4371730 AACTCTTAAA
4371740 AAATAATAAAAT
1 AAATAATAAAAT
4371752 AAA-AAT-AAAT
1 AAATAATAAAAT
4371762 AAATAATAAA
1 AAATAATAAA
4371772 TATTTACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 7 0.39
11 6 0.33
12 5 0.28
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
AAATAATAAAAT
Found at i:4371772 original size:11 final size:11
Alignment explanation
Indices: 4371736--4371773 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
4371726 ATATAACTCT
4371736 TAAA-AAATAA
1 TAAATAAATAA
4371746 TAAAATAAA-AA
1 T-AAATAAATAA
4371757 TAAATAAATAA
1 TAAATAAATAA
4371768 TAAATA
1 TAAATA
4371774 TTTACAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 8 0.32
11 14 0.56
12 3 0.12
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:4375569 original size:16 final size:17
Alignment explanation
Indices: 4375550--4375620 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 17
4375540 ATCAACTATC
4375550 ATATAAA-ATAAAAATA
1 ATATAAAGATAAAAATA
*
4375566 ATATAATA-ATATAATAAAA
1 ATATAA-AGATA-AA-AATA
* *
4375585 ATNTAAAGAAAAAAAT-
1 ATATAAAGATAAAAATA
*
4375601 ATATAAAGATTAAAATA
1 ATATAAAGATAAAAATA
4375618 ATA
1 ATA
4375621 GTACTTAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
16 19 0.44
17 9 0.21
18 5 0.12
19 10 0.23
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (17 bp):
ATATAAAGATAAAAATA
Found at i:4380673 original size:13 final size:13
Alignment explanation
Indices: 4380653--4380684 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4380643 ATTATTAAAA
4380653 TCTATTTTTATTT
1 TCTATTTTTATTT
*
4380666 TTTATTTTTATTT
1 TCTATTTTTATTT
4380679 TCTATT
1 TCTATT
4380685 GTAAGTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (13 bp):
TCTATTTTTATTT
Found at i:4380677 original size:40 final size:39
Alignment explanation
Indices: 4380584--4380662 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 39
4380574 AAACTTAAAC
4380584 ATTAA-TAATTTATTATTAAATTATTAAAATCATTTTTA
1 ATTAATTAATTTATTATTAAATTATTAAAATCATTTTTA
4380622 NATTAATTAATTTATTATTAAATTATTAAAATCTATTTTTA
1 -ATTAATTAATTTATTATTAAATTATTAAAATC-ATTTTTA
4380663 TTTTTTATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 5 0.13
40 26 0.68
41 7 0.18
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (39 bp):
ATTAATTAATTTATTATTAAATTATTAAAATCATTTTTA
Found at i:4380678 original size:112 final size:112
Alignment explanation
Indices: 4380431--4380680 Score: 260
Period size: 112 Copynumber: 2.2 Consensus size: 112
4380421 AAATTCTTCT
* *
4380431 TTTTTAATCTTTTAATTTTATTTTCATTAAAACTTTAAAACATTAATAATTTATTATTAAATTAT
1 TTTTTAATTTTTTATTTTTATTTTCATTAAAACTTTAAAACATTAATAATTTATTATTAAATTAT
* ** * * ** ** *
4380496 TAATATGTTTTTTATTTTAATCTCTTTTTTTCTATTTGTATTTGTAC
66 TAAAATCATTTTTATATTAATCTATTTTTTTAAATTTGTAAATCTAC
* *
4380543 TTTTTAATCTTTTAATTTCTATTTTCATTAAAAAC-TT-AAACATTAATAATTTATTATTAAATT
1 TTTTTAAT-TTTTTATTTTTATTTTCATT-AAAACTTTAAAACATTAATAATTTATTATTAAATT
*
4380606 ATTAAAATCATTTTTANATTAAT-TAATTTATTATTAAATTAT-TAAAATCTA-
64 ATTAAAATCATTTTTATATTAATCT-ATTT-TT-TTAAATT-TGT-AAATCTAC
4380657 TTTTT-ATTTTTTATTTTTATTTTC
1 TTTTTAATTTTTTATTTTTATTTTC
4380681 TATTGTAAGT
Statistics
Matches: 114, Mismatches: 17, Indels: 14
0.79 0.12 0.10
Matches are distributed among these distances:
111 1 0.01
112 70 0.61
113 22 0.19
114 16 0.14
115 5 0.04
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.58
Consensus pattern (112 bp):
TTTTTAATTTTTTATTTTTATTTTCATTAAAACTTTAAAACATTAATAATTTATTATTAAATTAT
TAAAATCATTTTTATATTAATCTATTTTTTTAAATTTGTAAATCTAC
Found at i:4397648 original size:62 final size:62
Alignment explanation
Indices: 4397551--4397675 Score: 214
Period size: 62 Copynumber: 2.0 Consensus size: 62
4397541 AGGATAATGC
4397551 TAGGAAGATGGTTTAGAACTGATAATCCACTCAACAGTCTATATGAGCACGCACACAAGTTT
1 TAGGAAGATGGTTTAGAACTGATAATCCACTCAACAGTCTATATGAGCACGCACACAAGTTT
* * * *
4397613 TAGGAAGATGGTTTCGAACTGATAATCCACTCAACAGTCTATATGAGCATGCGCACGAGTTT
1 TAGGAAGATGGTTTAGAACTGATAATCCACTCAACAGTCTATATGAGCACGCACACAAGTTT
4397675 T
1 T
4397676 GTATTTTAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (62 bp):
TAGGAAGATGGTTTAGAACTGATAATCCACTCAACAGTCTATATGAGCACGCACACAAGTTT
Found at i:4408659 original size:35 final size:35
Alignment explanation
Indices: 4408601--4408709 Score: 146
Period size: 35 Copynumber: 3.1 Consensus size: 35
4408591 TATTATATAG
* * * *
4408601 AGAACAACCAGAACAAGTAAAGTGTTACTTCACGC
1 AGAATAACTAGAACAAGTGAAGTGCTACTTCACGC
*
4408636 AGAATAACTAGAACAAGTGAAGTGCTACTTCACGT
1 AGAATAACTAGAACAAGTGAAGTGCTACTTCACGC
* * *
4408671 AGAATAACTGGAATAAGTGAAGCGCTACTTCACGC
1 AGAATAACTAGAACAAGTGAAGTGCTACTTCACGC
4408706 AGAA
1 AGAA
4408710 CAAGTGAAGC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.19
Consensus pattern (35 bp):
AGAATAACTAGAACAAGTGAAGTGCTACTTCACGC
Found at i:4409074 original size:29 final size:29
Alignment explanation
Indices: 4409003--4409083 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 29
4408993 TGTTCTCGTA
* * *
4409003 TACCTATTCATGAACAGCTTATTCTCTTG
1 TACCTATTCATGTACATCTTTTTCTCTTG
* *
4409032 TACTTGTTCATGTACATCTTTTTCTCTTG
1 TACCTATTCATGTACATCTTTTTCTCTTG
* *
4409061 TACCTATTCTTGTAAATCTTTTT
1 TACCTATTCATGTACATCTTTTT
4409084 TCTATTACCT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.20, C:0.21, G:0.09, T:0.51
Consensus pattern (29 bp):
TACCTATTCATGTACATCTTTTTCTCTTG
Found at i:4409314 original size:13 final size:13
Alignment explanation
Indices: 4409296--4409320 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4409286 ACTTGAGAGC
4409296 TTCTCTCTCTAAA
1 TTCTCTCTCTAAA
4409309 TTCTCTCTCTAA
1 TTCTCTCTCTAA
4409321 TTATCTTGTA
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:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCTCTCTCTAAA
Found at i:4416331 original size:13 final size:13
Alignment explanation
Indices: 4416313--4416337 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4416303 ACTTGAGAGC
4416313 TTCTCTCTCTAAA
1 TTCTCTCTCTAAA
4416326 TTCTCTCTCTAA
1 TTCTCTCTCTAA
4416338 TTATCTTGTA
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:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCTCTCTCTAAA
Found at i:4416907 original size:15 final size:15
Alignment explanation
Indices: 4416876--4416934 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
4416866 GTTTGGTACT
4416876 TTATAATATAATATGA
1 TTATAA-ATAATATGA
* *
4416892 TTATAAGTAATGTGA
1 TTATAAATAATATGA
*
4416907 TTGTAAATAATATGA
1 TTATAAATAATATGA
* *
4416922 TTACAAATGATAT
1 TTATAAATAATAT
4416935 AATTGCAAAG
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
15 29 0.83
16 6 0.17
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.41
Consensus pattern (15 bp):
TTATAAATAATATGA
Found at i:4416994 original size:23 final size:22
Alignment explanation
Indices: 4416968--4417010 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
4416958 AATGTTCGGT
* *
4416968 ATATAAATAAAGTAATGATTAAA
1 ATATAAAAAAACTAAT-ATTAAA
4416991 ATATAAAAAAACTAATATTA
1 ATATAAAAAAACTAATATTA
4417011 CAACATTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (22 bp):
ATATAAAAAAACTAATATTAAA
Found at i:4417203 original size:33 final size:33
Alignment explanation
Indices: 4417161--4417243 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
4417151 TAATGTTATG
*
4417161 TATTTTATTTTTATTTCTTATTATAATCTCATA
1 TATTTTATTTTTATTTCTTAATATAATCTCATA
* * **
4417194 TATTTTATTTTTATTTTTTAATATAATTTTTTA
1 TATTTTATTTTTATTTCTTAATATAATCTCATA
*
4417227 CATTTTATATTTTATTT
1 TATTTTAT-TTTTATTT
4417244 AAATTTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 35 0.81
34 8 0.19
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.69
Consensus pattern (33 bp):
TATTTTATTTTTATTTCTTAATATAATCTCATA
Found at i:4417655 original size:70 final size:69
Alignment explanation
Indices: 4417542--4417673 Score: 183
Period size: 70 Copynumber: 1.9 Consensus size: 69
4417532 ATTATTGCTA
* *
4417542 TTGTTTCTGTTCTGGACGGAAAGAGTAACTAGTCGTCGCTTGGGAGGGCAGGTTTGTCCATATCG
1 TTGTTTCTGTTCTGCAAGGAAAGAGTAACTAGTCGTCGCTTGGGAGGG-AGGTTTGTCCATATCG
4417607 TGCGT
65 TGCGT
* * * * * *
4417612 TTGTTTCTGTTTTGCAAGGGAAGTGTACCTAGTCGTCTCTTGGGAGGGAGGTTTGTCTATAT
1 TTGTTTCTGTTCTGCAAGGAAAGAGTAACTAGTCGTCGCTTGGGAGGGAGGTTTGTCCATAT
4417674 TATGTAGGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
69 13 0.24
70 41 0.76
ACGTcount: A:0.17, C:0.15, G:0.32, T:0.36
Consensus pattern (69 bp):
TTGTTTCTGTTCTGCAAGGAAAGAGTAACTAGTCGTCGCTTGGGAGGGAGGTTTGTCCATATCGT
GCGT
Found at i:4420123 original size:12 final size:12
Alignment explanation
Indices: 4420106--4420139 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4420096 TTACCTGACT
* *
4420106 GAGAGATAGTGG
1 GAGAGAGAGAGG
4420118 GAGAGAGAGAGG
1 GAGAGAGAGAGG
4420130 GAGAGAGAGA
1 GAGAGAGAGA
4420140 TGGATCCAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.53, T:0.06
Consensus pattern (12 bp):
GAGAGAGAGAGG
Found at i:4427240 original size:438 final size:437
Alignment explanation
Indices: 4426420--4428613 Score: 3475
Period size: 438 Copynumber: 5.0 Consensus size: 437
4426410 ACCCCAATTT
* * *
4426420 ATATCACCTCCATCATTGCACCTTATGTGGAAATTTCATGACATCAAAACATTGTAACACACTTT
1 ATATCACCTCCATCATTGCACCTGATGTGGAAATGTCATGTCATCAAAACATTGTAACACAC-TT
** * * *
4426485 TTTGTCTTTACCCAACAGTGAGTCCTCTTTTTGTTTGTGTCAAATACTCGACATATTCTCTATAC
65 TTTGTCTTCGCCCGACAGTGAGTCCTCTTTTTGTTTGTGTCAAATACTCGAGATATTCTCTATCC
*
4426550 TTAATATGCTTTACCAAATTCAGCCAACTTTCCCTTCTCACTGGTCATCCACTCCTAGCCTCCTT
130 TTAATATGC-TTACCAAATTCAGCCAACTTTCCCTTCTTACTGGTCATCCACTCCTAGCCTCCTT
*
4426615 TTTTTTGTCTTGCTTCTAATATCAAATCTAGAATTTAATCTTATTCGCATAAAATTACTTTGAAA
194 TTTTTTGCCTTGCTTCTAATATCAAATCTAGAATTTAATCTTATTCGCATAAAATTACTTTGAAA
* *
4426680 CTCAAACCTAAGAATAAAATCCAAAAATCAAACTAAACACTTACAAGAGTTCATGAAAGGAAATA
259 CTCAAACCCAAGAATAAAATCCAAAAATCAAACTAAACACTAACAAGAGTTCATGAAAGGAAATA
* * * * *
4426745 AGAGTGTCTAGCCTCTAGCATACTCTACGTTAGGGAAACAGCCTGACCAAGAAATGCTCGAAGCT
324 AGAGTGTCTAGCCTCTAGCATACTCTACCTTAGGAAAATAGCCTGACCAACAAATGCTCAAAGCT
* *
4426810 CGAGACACCTATCAATCACCTATTTCACCCGCAAATAATCCATAACCAA
389 CTAGACACCTATCAATCACCTATTTCACCCGCAAATAATCCATACCCAA
* * *
4426859 ATATCACCTCCATCATTGCACCTGATGTGGAAATGTGATGTCATCAAAACACTGTAGCACACTTT
1 ATATCACCTCCATCATTGCACCTGATGTGGAAATGTCATGTCATCAAAACATTGTAACACACTTT
* * * *
4426924 TTGGTCTTTGCTCAACAATGAGTCCTCTTTTTGTTTGTGTCAAATACTCGAGATATTCTCTATCC
66 TT-GTCTTCGCCCGACAGTGAGTCCTCTTTTTGTTTGTGTCAAATACTCGAGATATTCTCTATCC
4426989 TTAATATGCTTACCAAATTCAGCCAACTTTCCCTTCTTACTGGTCATCCACTCCTAGCCTCCTTT
130 TTAATATGCTTACCAAATTCAGCCAACTTTCCCTTCTTACTGGTCATCCACTCCTAGCCTCCTTT
*
4427054 TTTTTGCCTTGCTTCTAATATCAAATCTAGAATTTAATCTTATTCGCATAAAATTAC-CTGAAAC
195 TTTTTGCCTTGCTTCTAATATCAAATCTAGAATTTAATCTTATTCGCATAAAATTACTTTGAAAC
* * **
4427118 TCAAGCCCAAGAATAAAATCCAAAAATAAAACTAAACACTAACAAAGAGTTTGTGAAAGGAAATA
260 TCAAACCCAAGAATAAAATCCAAAAATCAAACTAAACACTAAC-AAGAGTTCATGAAAGGAAATA
*
4427183 AGAGTGTTTAGCCTCTAGCATACTCTACCTTAGGAAAATAGCCTGACCAACAAATGCTC-AAGCT
324 AGAGTGTCTAGCCTCTAGCATACTCTACCTTAGGAAAATAGCCTGACCAACAAATGCTCAAAGCT
* *
4427247 CTAGACACCTATCAGTCACCTATTTCACCCGCGAATAATCCATACCCAA
389 CTAGACACCTATCAATCACCTATTTCACCCGCAAATAATCCATACCCAA
4427296 ATATCACCTCCATCATTGCACCTGATGTGGAAATGTCATGTCATCAAAACATTGTAACACACGTT
1 ATATCACCTCCATCATTGCACCTGATGTGGAAATGTCATGTCATCAAAACATTGTAACACAC-TT
*
4427361 TTTGTCTTCACCCGACAGTGAGTCCTCTTTTTGTTTGTGTCAAATACTCGAGATATTCTCTATCC
65 TTTGTCTTCGCCCGACAGTGAGTCCTCTTTTTGTTTGTGTCAAATACTCGAGATATTCTCTATCC
*
4427426 TTAATATGCTTACCAAATTCAGCCAACTTTCCCTTCTTATTGGTCATCCACTCCTAGCCT-CTTT
130 TTAATATGCTTACCAAATTCAGCCAACTTTCCCTTCTTACTGGTCATCCACTCCTAGCCTCCTTT
*** * * *
4427490 TGTTACAACCTTGCTTCTAATATTAAATCTAGAATTTAATCTTATTTGCATAAACTTACTTTGAA
195 T-TT-TTGCCTTGCTTCTAATATCAAATCTAGAATTTAATCTTATTCGCATAAAATTACTTTGAA
* * *
4427555 ACTCAAACTCAAGAATAAAATCCAAAAGTCAAACTAAACACTTACAAGAGTTCATGAAAGGAAAT
258 ACTCAAACCCAAGAATAAAATCCAAAAATCAAACTAAACACTAACAAGAGTTCATGAAAGGAAAT
*
4427620 AAGAGTGTCTAGCCTCTAGCATACTCTAACTTAGG--AATAGCCTGACCAACAAATGCTCAAAGC
323 AAGAGTGTCTAGCCTCTAGCATACTCTACCTTAGGAAAATAGCCTGACCAACAAATGCTCAAAGC
* *
4427683 TCTAGACACCTATAAATCACCTATTTCACCTGCAAATAATCCATACCCAA
388 TCTAGACACCTATCAATCACCTATTTCACCCGCAAATAATCCATACCCAA
* * * *
4427733 ATATCACCTCCATCATTGCACCTGATGTGGAAAAGTCGTGTCATCGAAACATAGTAACACACTTT
1 ATATCACCTCCATCATTGCACCTGATGTGGAAATGTCATGTCATCAAAACATTGTAACACAC-TT
* *
4427798 TTTGTCTTCG-CCGACAGTGAGTCCTCTTTTTGTTTATGTCAAATACTCGAGATATTCTCTATTC
65 TTTGTCTTCGCCCGACAGTGAGTCCTCTTTTTGTTTGTGTCAAATACTCGAGATATTCTCTATCC
* * *
4427862 TTAATATGCTTACCAAATTCAACCAACTTTCCCTTCTTAATGGTCATCCACTCCTAGCCTCCTCT
130 TTAATATGCTTACCAAATTCAGCCAACTTTCCCTTCTTACTGGTCATCCACTCCTAGCCTCCTTT
* *
4427927 TTTGTGCCTTGCTTCTAATATCAAATCTAGTATTTAATCTTATTCGCATAAAATTACTTTGAAAC
195 TTTTTGCCTTGCTTCTAATATCAAATCTAGAATTTAATCTTATTCGCATAAAATTACTTTGAAAC
*
4427992 TCAAACCCAAGAATAAAATCCAAAAAATCAAACTAAACACTAACAAGAGTTCATAAAAGGAAATA
260 TCAAACCCAAGAATAAAATCC-AAAAATCAAACTAAACACTAACAAGAGTTCATGAAAGGAAATA
* * ** *
4428057 AGAGCGTCTAGCCTCTGGCATACTCTACCTTACTAAAATAGCCTGACCAAGAAATGCTCAAAGCT
324 AGAGTGTCTAGCCTCTAGCATACTCTACCTTAGGAAAATAGCCTGACCAACAAATGCTCAAAGCT
* * ** *
4428122 CTGGACACCCATCAATTGCCTATTTCACCCGCAAATAATCCATAACCAA
389 CTAGACACCTATCAATCACCTATTTCACCCGCAAATAATCCATACCCAA
* *
4428171 ATATCACCTCCATCATTGCACCTGATATGGAAATGTCATGTCATCGAAACATTGTAACACACTTC
1 ATATCACCTCCATCATTGCACCTGATGTGGAAATGTCATGTCATCAAAACATTGTAACACACTT-
*
4428236 TTTGTCTTCGCCCGACAGTGAGTCATCTTTTTGTTTGTGTCAAATACTCG-GCATATTCTCTATC
65 TTTGTCTTCGCCCGACAGTGAGTCCTCTTTTTGTTTGTGTCAAATACTCGAG-ATATTCTCTATC
* * * *
4428300 CTTAATATGCTTACCAAATTCAGCCAACATTCCATTCTTACCGGTCATCCACTCCTTGCCTCCTT
129 CTTAATATGCTTACCAAATTCAGCCAACTTTCCCTTCTTACTGGTCATCCACTCCTAGCCTCCTT
* * * *
4428365 GTTTTTGCCTTGCTTCTTATATCAAATCTAGGATTTAATCTTATTTGCATAAAATTACTTTGAAA
194 TTTTTTGCCTTGCTTCTAATATCAAATCTAGAATTTAATCTTATTCGCATAAAATTACTTTGAAA
*
4428430 CTCAAACCCAAGAATAAAATCCAAAAATCAAACTAAACACTAACAAGAGTTCATGAAAGGAAGTA
259 CTCAAACCCAAGAATAAAATCCAAAAATCAAACTAAACACTAACAAGAGTTCATGAAAGGAAATA
*
4428495 AGAGTGTCTAGCCTCTAGCATACTCTACCTTAGGAAAATAGCCTGACCAACAAATGCACAAAGCT
324 AGAGTGTCTAGCCTCTAGCATACTCTACCTTAGGAAAATAGCCTGACCAACAAATGCTCAAAGCT
* *
4428560 CTAGACACCTATCAATAACCTATTTCACCCACAAATAATCCATACCCAA
389 CTAGACACCTATCAATCACCTATTTCACCCGCAAATAATCCATACCCAA
4428609 ATATC
1 ATATC
4428614 CCAAGTCAAA
Statistics
Matches: 1615, Mismatches: 126, Indels: 29
0.91 0.07 0.02
Matches are distributed among these distances:
435 75 0.05
436 209 0.13
437 397 0.25
438 580 0.36
439 354 0.22
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (437 bp):
ATATCACCTCCATCATTGCACCTGATGTGGAAATGTCATGTCATCAAAACATTGTAACACACTTT
TTGTCTTCGCCCGACAGTGAGTCCTCTTTTTGTTTGTGTCAAATACTCGAGATATTCTCTATCCT
TAATATGCTTACCAAATTCAGCCAACTTTCCCTTCTTACTGGTCATCCACTCCTAGCCTCCTTTT
TTTTGCCTTGCTTCTAATATCAAATCTAGAATTTAATCTTATTCGCATAAAATTACTTTGAAACT
CAAACCCAAGAATAAAATCCAAAAATCAAACTAAACACTAACAAGAGTTCATGAAAGGAAATAAG
AGTGTCTAGCCTCTAGCATACTCTACCTTAGGAAAATAGCCTGACCAACAAATGCTCAAAGCTCT
AGACACCTATCAATCACCTATTTCACCCGCAAATAATCCATACCCAA
Found at i:4428378 original size:874 final size:872
Alignment explanation
Indices: 4426420--4428613 Score: 3502
Period size: 874 Copynumber: 2.5 Consensus size: 872
4426410 ACCCCAATTT
* * *
4426420 ATATCACCTCCATCATTGCACCTTATGTGGAAATTTCATGACATCAAAACATTGTAACACACTTT
1 ATATCACCTCCATCATTGCACCTGATGTGGAAATGTCATGTCATCAAAACATTGTAACACAC-TT
* * * *
4426485 TTTGTCTTTACCCAACAGTGAGTCCTCTTTTTGTTTGTGTCAAATACTCGACATATTCTCTATAC
65 TTTGTCTTCACCCGACAGTGAGTCCTCTTTTTGTTTGTGTCAAATACTCGGCATATTCTCTATCC
*
4426550 TTAATATGCTTTACCAAATTCAGCCAACTTTCCCTTCTCACTGGTCATCCACTCCTAGCCTCCTT
130 TTAATATGC-TTACCAAATTCAGCCAACTTTCCCTTCTTACTGGTCATCCACTCCTAGCCTCCTT
* * *
4426615 TTTTTTGTCTTGCTTCTAATATCAAATCTAGAATTTAATCTTATTCGCATAAAATTACTTTGAAA
194 GTTTTTGCCTTGCTTCTAATATCAAATCTAGAATTTAATCTTATTTGCATAAAATTACTTTGAAA
4426680 CTCAAACCTAAGAATAAAATCCAAAAATCAAACTAAACACTTACAAGAGTTCATGAAAGGAAATA
259 CTCAAACC-AAGAATAAAATCCAAAAATCAAACTAAACACTTACAAGAGTTCATGAAAGGAAATA
* * *
4426745 AGAGTGTCTAGCCTCTAGCATACTCT-ACGTTAGGGAAACAGCCTGACCAAGAAATGCTCGAAGC
323 AGAGTGTCTAGCCTCTAGCATACTCTAAC-TTA-GGAAATAGCCTGACCAACAAATGCTCAAAGC
* *
4426809 TCGAGACACCTATCAATCACCTATTTCACCCGCAAATAATCCATAACCAAATATCACCTCCATCA
386 TCTAGACACCTATCAATCACCTATTTCACCCGCAAATAATCCATACCCAAATATCACCTCCATCA
* * *
4426874 TTGCACCTGATGTGGAAATGTGATGTCATCAAAACACTGTAGCACACTTTTTGGTCTTTGCTCAA
451 TTGCACCTGATGTGGAAAAGTGATGTCATCAAAACACTGTAACACACTTTTTGGTCTTCGCTCAA
*
4426939 CAATGAGTCCTCTTTTTGTTTGTGTCAAATACTCGAGATATTCTCTATCCTTAATATGCTTACCA
516 CAATGAGTCCTCTTTTTGTTTATGTCAAATACTCGAGATATTCTCTATCCTTAATATGCTTACCA
* * * *
4427004 AATTCAGCCAACTTTCCCTTCTTACTGGTCATCCACTCCTAGCCTCCTTTTTTTTGCCTTGCTTC
581 AATTCAACCAACTTTCCCTTCTTAATGGTCATCCACTCCTAGCCTCCTCTTTTGTGCCTTGCTTC
*
4427069 TAATATCAAATCTAGAATTTAATCTTATTCGCATAAAATTACCTGAAACTCAAGCCCAAGAATAA
646 TAATATCAAATCTAGAATTTAATCTTATTCGCATAAAATTACCTGAAACTCAAACCCAAGAATAA
** * * *
4427134 AATCCAAAAATAAAACTAAACACTAACAAAGAGTTTGTGAAAGGAAATAAGAGTGTTTAGCCTCT
711 AATCCAAAAATAAAACTAAACACTAACAAAGAGTTCATAAAAGGAAATAAGAGCGTCTAGCCTCT
* * *
4427199 AGCATACTCTACCTTAGGAAAATAGCCTGACCAACAAATGCTCAAGCTCTAGACACCTATCAGTC
776 AGCATACTCTACCTTACGAAAATAGCCTGACCAACAAATGCTCAAGCTCTAGACACCCATCAATC
* *
4427264 ACCTATTTCACCCGCGAATAATCCATACCCAA
841 ACCTATTTCACCCGCAAATAATCCATAACCAA
4427296 ATATCACCTCCATCATTGCACCTGATGTGGAAATGTCATGTCATCAAAACATTGTAACACACGTT
1 ATATCACCTCCATCATTGCACCTGATGTGGAAATGTCATGTCATCAAAACATTGTAACACAC-TT
4427361 TTTGTCTTCACCCGACAGTGAGTCCTCTTTTTGTTTGTGTCAAATACTCGAG-ATATTCTCTATC
65 TTTGTCTTCACCCGACAGTGAGTCCTCTTTTTGTTTGTGTCAAATACTCG-GCATATTCTCTATC
* *
4427425 CTTAATATGCTTACCAAATTCAGCCAACTTTCCCTTCTTATTGGTCATCCACTCCTAGCCTCTTT
129 CTTAATATGCTTACCAAATTCAGCCAACTTTCCCTTCTTACTGGTCATCCACTCCTAGCCTC-CT
**** * *
4427490 TGTTACAACCTTGCTTCTAATATTAAATCTAGAATTTAATCTTATTTGCATAAACTTACTTTGAA
193 TGTTTTTGCCTTGCTTCTAATATCAAATCTAGAATTTAATCTTATTTGCATAAAATTACTTTGAA
*
4427555 ACTCAAACTCAAGAATAAAATCCAAAAGTCAAACTAAACACTTACAAGAGTTCATGAAAGGAAAT
258 ACTCAAAC-CAAGAATAAAATCCAAAAATCAAACTAAACACTTACAAGAGTTCATGAAAGGAAAT
4427620 AAGAGTGTCTAGCCTCTAGCATACTCTAACTTAGG-AATAGCCTGACCAACAAATGCTCAAAGCT
322 AAGAGTGTCTAGCCTCTAGCATACTCTAACTTAGGAAATAGCCTGACCAACAAATGCTCAAAGCT
* *
4427684 CTAGACACCTATAAATCACCTATTTCACCTGCAAATAATCCATACCCAAATATCACCTCCATCAT
387 CTAGACACCTATCAATCACCTATTTCACCCGCAAATAATCCATACCCAAATATCACCTCCATCAT
* * *
4427749 TGCACCTGATGTGGAAAAGTCG-TGTCATCGAAACA-TAGTAACACACTTTTTTGTCTTCGC-CG
452 TGCACCTGATGTGGAAAAGT-GATGTCATCAAAACACT-GTAACACACTTTTTGGTCTTCGCTCA
* *
4427811 ACAGTGAGTCCTCTTTTTGTTTATGTCAAATACTCGAGATATTCTCTATTCTTAATATGCTTACC
515 ACAATGAGTCCTCTTTTTGTTTATGTCAAATACTCGAGATATTCTCTATCCTTAATATGCTTACC
4427876 AAATTCAACCAACTTTCCCTTCTTAATGGTCATCCACTCCTAGCCTCCTCTTTTGTGCCTTGCTT
580 AAATTCAACCAACTTTCCCTTCTTAATGGTCATCCACTCCTAGCCTCCTCTTTTGTGCCTTGCTT
* *
4427941 CTAATATCAAATCTAGTATTTAATCTTATTCGCATAAAATTACTTTGAAACTCAAACCCAAGAAT
645 CTAATATCAAATCTAGAATTTAATCTTATTCGCATAAAATTAC-CTGAAACTCAAACCCAAGAAT
*
4428006 AAAATCCAAAAAATCAAACTAAACACTAAC-AAGAGTTCATAAAAGGAAATAAGAGCGTCTAGCC
709 AAAATCC-AAAAATAAAACTAAACACTAACAAAGAGTTCATAAAAGGAAATAAGAGCGTCTAGCC
* * * *
4428070 TCTGGCATACTCTACCTTACTAAAATAGCCTGACCAAGAAATGCTCAAAGCTCTGGACACCCATC
773 TCTAGCATACTCTACCTTACGAAAATAGCCTGACCAACAAATGCTC-AAGCTCTAGACACCCATC
**
4428135 AATTGCCTATTTCACCCGCAAATAATCCATAACCAA
837 AATCACCTATTTCACCCGCAAATAATCCATAACCAA
* *
4428171 ATATCACCTCCATCATTGCACCTGATATGGAAATGTCATGTCATCGAAACATTGTAACACACTTC
1 ATATCACCTCCATCATTGCACCTGATGTGGAAATGTCATGTCATCAAAACATTGTAACACACTT-
* *
4428236 TTTGTCTTCGCCCGACAGTGAGTCATCTTTTTGTTTGTGTCAAATACTCGGCATATTCTCTATCC
65 TTTGTCTTCACCCGACAGTGAGTCCTCTTTTTGTTTGTGTCAAATACTCGGCATATTCTCTATCC
* * * *
4428301 TTAATATGCTTACCAAATTCAGCCAACATTCCATTCTTACCGGTCATCCACTCCTTGCCTCCTTG
130 TTAATATGCTTACCAAATTCAGCCAACTTTCCCTTCTTACTGGTCATCCACTCCTAGCCTCCTTG
* *
4428366 TTTTTGCCTTGCTTCTTATATCAAATCTAGGATTTAATCTTATTTGCATAAAATTACTTTGAAAC
195 TTTTTGCCTTGCTTCTAATATCAAATCTAGAATTTAATCTTATTTGCATAAAATTACTTTGAAAC
* *
4428431 TCAAACCCAAGAATAAAATCCAAAAATCAAACTAAACACTAACAAGAGTTCATGAAAGGAAGTAA
260 TCAAA-CCAAGAATAAAATCCAAAAATCAAACTAAACACTTACAAGAGTTCATGAAAGGAAATAA
* *
4428496 GAGTGTCTAGCCTCTAGCATACTCTACCTTAGGAAAATAGCCTGACCAACAAATGCACAAAGCTC
324 GAGTGTCTAGCCTCTAGCATACTCTAACTTAGG-AAATAGCCTGACCAACAAATGCTCAAAGCTC
* *
4428561 TAGACACCTATCAATAACCTATTTCACCCACAAATAATCCATACCCAAATATC
388 TAGACACCTATCAATCACCTATTTCACCCGCAAATAATCCATACCCAAATATC
4428614 CCAAGTCAAA
Statistics
Matches: 1216, Mismatches: 88, Indels: 28
0.91 0.07 0.02
Matches are distributed among these distances:
873 167 0.14
874 390 0.32
875 299 0.25
876 357 0.29
877 3 0.00
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (872 bp):
ATATCACCTCCATCATTGCACCTGATGTGGAAATGTCATGTCATCAAAACATTGTAACACACTTT
TTGTCTTCACCCGACAGTGAGTCCTCTTTTTGTTTGTGTCAAATACTCGGCATATTCTCTATCCT
TAATATGCTTACCAAATTCAGCCAACTTTCCCTTCTTACTGGTCATCCACTCCTAGCCTCCTTGT
TTTTGCCTTGCTTCTAATATCAAATCTAGAATTTAATCTTATTTGCATAAAATTACTTTGAAACT
CAAACCAAGAATAAAATCCAAAAATCAAACTAAACACTTACAAGAGTTCATGAAAGGAAATAAGA
GTGTCTAGCCTCTAGCATACTCTAACTTAGGAAATAGCCTGACCAACAAATGCTCAAAGCTCTAG
ACACCTATCAATCACCTATTTCACCCGCAAATAATCCATACCCAAATATCACCTCCATCATTGCA
CCTGATGTGGAAAAGTGATGTCATCAAAACACTGTAACACACTTTTTGGTCTTCGCTCAACAATG
AGTCCTCTTTTTGTTTATGTCAAATACTCGAGATATTCTCTATCCTTAATATGCTTACCAAATTC
AACCAACTTTCCCTTCTTAATGGTCATCCACTCCTAGCCTCCTCTTTTGTGCCTTGCTTCTAATA
TCAAATCTAGAATTTAATCTTATTCGCATAAAATTACCTGAAACTCAAACCCAAGAATAAAATCC
AAAAATAAAACTAAACACTAACAAAGAGTTCATAAAAGGAAATAAGAGCGTCTAGCCTCTAGCAT
ACTCTACCTTACGAAAATAGCCTGACCAACAAATGCTCAAGCTCTAGACACCCATCAATCACCTA
TTTCACCCGCAAATAATCCATAACCAA
Found at i:4443767 original size:2 final size:2
Alignment explanation
Indices: 4443760--4443788 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4443750 AATGTGTAGA
4443760 TG TG 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 TG TG T
4443789 ACAAGCACGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4478037 original size:17 final size:17
Alignment explanation
Indices: 4478015--4478050 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
4478005 ATGCGGCTGT
*
4478015 TAGGCCCACTTTATGGG
1 TAGGCCAACTTTATGGG
4478032 TAGGCCAACTTTATGGG
1 TAGGCCAACTTTATGGG
4478049 TA
1 TA
4478051 TATACCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (17 bp):
TAGGCCAACTTTATGGG
Found at i:4498141 original size:86 final size:86
Alignment explanation
Indices: 4497996--4498168 Score: 276
Period size: 86 Copynumber: 2.0 Consensus size: 86
4497986 AGGGATTGAG
** * *
4497996 ACTAAGAAAAGTGTTCCTTGGATTCTTTGAATTATGTAATATAATGCAATCAATAAATCTTATGA
1 ACTAAGAAAAGTGCACCTTCGATTCTTTGAATTATGTAATATAATGCAATCAATAAATCTTACGA
*
4498061 AGAAATCAGAGAAAAACATTA
66 AGAAATCACAGAAAAACATTA
4498082 ACTAAGAAAAGTGCACCTTCGATTC-TTGAAATTATGTAATATAATGCAATCAATAAATCTTACG
1 ACTAAGAAAAGTGCACCTTCGATTCTTTG-AATTATGTAATATAATGCAATCAATAAATCTTACG
*
4498146 AAGAAATCACAGATAAACATTA
65 AAGAAATCACAGAAAAACATTA
4498168 A
1 A
4498169 TTGTTTGATT
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
85 3 0.04
86 77 0.96
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (86 bp):
ACTAAGAAAAGTGCACCTTCGATTCTTTGAATTATGTAATATAATGCAATCAATAAATCTTACGA
AGAAATCACAGAAAAACATTA
Found at i:4500094 original size:29 final size:29
Alignment explanation
Indices: 4500062--4500138 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
4500052 ATTTAAAAAT
* *
4500062 TTTAAATAAATTATTATTTTTTTATTATA
1 TTTAAATAAATTTTTATATTTTTATTATA
* * *
4500091 TTTAATTAATTTTTTATATTTTTATTTTA
1 TTTAAATAAATTTTTATATTTTTATTATA
4500120 TATTAAATAAATTTTTATA
1 T-TTAAATAAATTTTTATA
4500139 ATTAATATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 25 0.62
30 15 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTAAATAAATTTTTATATTTTTATTATA
Found at i:4500121 original size:31 final size:31
Alignment explanation
Indices: 4500076--4500135 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
4500066 AATAAATTAT
* *
4500076 TATTTTTTTATTATATTTAATTAATTTTTTA
1 TATTTTTTTATTATATTAAATAAATTTTTTA
4500107 TATTTTTATT-TTATATTAAATAAATTTTT
1 TATTTTT-TTATTATATTAAATAAATTTTT
4500136 ATAATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (31 bp):
TATTTTTTTATTATATTAAATAAATTTTTTA
Found at i:4500148 original size:31 final size:31
Alignment explanation
Indices: 4500086--4500148 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
4500076 TATTTTTTTA
* * **
4500086 TTATATTTAATTAATTTTTTATATTTTTATT
1 TTATATTAAATAAATTTTTTATATTAATATT
4500117 TTATATTAAATAAA-TTTTTATAATTAATATT
1 TTATATTAAATAAATTTTTTAT-ATTAATATT
4500148 T
1 T
4500149 AACTAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (31 bp):
TTATATTAAATAAATTTTTTATATTAATATT
Found at i:4504635 original size:6 final size:7
Alignment explanation
Indices: 4504618--4504642 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4504608 GGGGAACGTA
4504618 AAAAAAG
1 AAAAAAG
4504625 AAAAAAG
1 AAAAAAG
4504632 AAAAAAG
1 AAAAAAG
4504639 AAAA
1 AAAA
4504643 GGAATCATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:4505506 original size:15 final size:15
Alignment explanation
Indices: 4505488--4505519 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4505478 TTCTTCTTCT
4505488 TCTTCTTCCTCTGCA
1 TCTTCTTCCTCTGCA
*
4505503 TCTTCTTCCTTTGCA
1 TCTTCTTCCTCTGCA
4505518 TC
1 TC
4505520 CCCATCTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.38, G:0.06, T:0.50
Consensus pattern (15 bp):
TCTTCTTCCTCTGCA
Found at i:4508522 original size:12 final size:12
Alignment explanation
Indices: 4508505--4508537 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
4508495 GTATTACAAG
4508505 CTTTTTGTTTTT
1 CTTTTTGTTTTT
4508517 CTTTTT-TTTTT
1 CTTTTTGTTTTT
4508528 -TTTTTGTTTT
1 CTTTTTGTTTT
4508538 ATGGAGATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.25
11 9 0.45
12 6 0.30
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (12 bp):
CTTTTTGTTTTT
Found at i:4512241 original size:46 final size:45
Alignment explanation
Indices: 4512181--4512298 Score: 134
Period size: 46 Copynumber: 2.6 Consensus size: 45
4512171 AAATAAAAAC
** *
4512181 ATAT-TTTTATTATAATTTAATAATATTTTGTATTAGAAGATAATTA
1 ATATATTTTATTATAATTTAATAATATTTAATATTAAAAGATAA--A
*
4512227 A-ATATTTTATTATAATTAAATAATATTTAATATTAAAAGATAAA
1 ATATATTTTATTATAATTTAATAATATTTAATATTAAAAGATAAA
4512271 ATATATTCTTCATTA-AATTTAAATAATA
1 ATATATT-TT-ATTATAATTT-AATAATA
4512299 CTAAATAATT
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
44 2 0.03
45 7 0.11
46 42 0.68
47 11 0.18
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (45 bp):
ATATATTTTATTATAATTTAATAATATTTAATATTAAAAGATAAA
Found at i:4512260 original size:23 final size:21
Alignment explanation
Indices: 4512185--4512254 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 21
4512175 AAAAACATAT
*
4512185 TTTTATTATAATTTAATAATA
1 TTTTATTATAATTAAATAATA
* * *
4512206 TTTTGTATTAGAAGATAATTAAATA
1 -TTT-TATTATAA-TTAAAT-AATA
4512231 TTTTATTATAATTAAATAATA
1 TTTTATTATAATTAAATAATA
4512252 TTT
1 TTT
4512255 AATATTAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
21 7 0.18
22 7 0.18
23 14 0.37
24 6 0.16
25 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTATTATAATTAAATAATA
Found at i:4512358 original size:45 final size:45
Alignment explanation
Indices: 4512292--4512393 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 45
4512282 ATTAAATTTA
* ** *
4512292 AATAATACTAAATAATTTTCTTTATTACATTTATTATA-TTCAAAT
1 AATAATATTAAATAAGATTCTTTATAACATTTATTATAGTT-AAAT
4512337 AATAATATTAAATAAGATTCTTTATAACATTTATTATAGTTAAAT
1 AATAATATTAAATAAGATTCTTTATAACATTTATTATAGTTAAAT
4512382 AAT-AT-TTAAATA
1 AATAATATTAAATA
4512394 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
43 7 0.13
44 2 0.04
45 41 0.79
46 2 0.04
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (45 bp):
AATAATATTAAATAAGATTCTTTATAACATTTATTATAGTTAAAT
Found at i:4531726 original size:36 final size:36
Alignment explanation
Indices: 4531679--4531939 Score: 291
Period size: 36 Copynumber: 7.3 Consensus size: 36
4531669 CACAAGGTGG
* * * *
4531679 GAATTATGGGCAGGGACCAAGTTCTGGCTATGGGCA
1 GAATTATGGGCAAGGAGCAAATCCTGGCTATGGGCA
* *
4531715 GAATTTTGGGCAAGGGGCAAATCCTGGCTATGGGCA
1 GAATTATGGGCAAGGAGCAAATCCTGGCTATGGGCA
4531751 GAATT-TCGGGCAAGGAGCAAATCCTGGCTATGGGCA
1 GAATTAT-GGGCAAGGAGCAAATCCTGGCTATGGGCA
*
4531787 GAATTATGGGC-A--AGCAAATCCTGGTTATGGGCA
1 GAATTATGGGCAAGGAGCAAATCCTGGCTATGGGCA
*
4531820 GAATTATGGGCAAGGAGCAAATCCTGGCTATGGACA
1 GAATTATGGGCAAGGAGCAAATCCTGGCTATGGGCA
* * * *
4531856 GAGTTATGGGCAAGGATCAAATCCT-GCGTCTGGTCA
1 GAATTATGGGCAAGGAGCAAATCCTGGC-TATGGGCA
* * * *
4531892 GAACTATGGGCCAGGAGCAACTGCTGGC-ACTGGGCA
1 GAATTATGGGCAAGGAGCAAATCCTGGCTA-TGGGCA
**
4531928 GGGTTATGGGCA
1 GAATTATGGGCA
4531940 GAGAACAAAT
Statistics
Matches: 191, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
33 31 0.16
34 1 0.01
35 4 0.02
36 152 0.80
37 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.34, T:0.21
Consensus pattern (36 bp):
GAATTATGGGCAAGGAGCAAATCCTGGCTATGGGCA
Found at i:4531894 original size:105 final size:105
Alignment explanation
Indices: 4531702--4531902 Score: 289
Period size: 105 Copynumber: 1.9 Consensus size: 105
4531692 GGACCAAGTT
* * *
4531702 CTGGCTATGGGCAGAATTTTGGGCAAGGGGCAAATCCTGGCTATGGGCAGAATTTCGGGCAAGGA
1 CTGGCTATGGGCAGAATTATGGGCAAGGAGCAAATCCTGGCTATGGACAGAATTTCGGGCAAGGA
*
4531767 GCAAATCCTGGCTATGGGCAGAATTATGGGCAAGCAAATC
66 GCAAATCCTGGCTATGGGCAGAACTATGGGCAAGCAAATC
* *
4531807 CTGGTTATGGGCAGAATTATGGGCAAGGAGCAAATCCTGGCTATGGACAGAGTTAT-GGGCAAGG
1 CTGGCTATGGGCAGAATTATGGGCAAGGAGCAAATCCTGGCTATGGACAGAATT-TCGGGCAAGG
* * *
4531871 ATCAAATCCT-GCGTCTGGTCAGAACTATGGGC
65 AGCAAATCCTGGC-TATGGGCAGAACTATGGGC
4531903 CAGGAGCAAC
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
104 2 0.02
105 82 0.96
106 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.33, T:0.22
Consensus pattern (105 bp):
CTGGCTATGGGCAGAATTATGGGCAAGGAGCAAATCCTGGCTATGGACAGAATTTCGGGCAAGGA
GCAAATCCTGGCTATGGGCAGAACTATGGGCAAGCAAATC
Found at i:4531935 original size:141 final size:141
Alignment explanation
Indices: 4531679--4531939 Score: 321
Period size: 141 Copynumber: 1.9 Consensus size: 141
4531669 CACAAGGTGG
* * * * * *
4531679 GAATTATGGGCAGGGACCAAGTTCTGGCTATGGGCAGAATTTTGGGCAAGGGGCAAATCCTGGCT
1 GAATTATGGGCAAGGACCAAATCCTGGCTATGGACAGAATTATGGGCAAGGAGCAAATCCTGGCT
*
4531744 ATGGGCAGAATTTCGGGCAAGGAGCAAATCCTGGCTATGGGCAGAATTATGGGCAAGCAAATCCT
66 ATGGGCAGAATATCGGGCAAGGAGCAAATCCTGGCTATGGGCAGAATTATGGGCAAGCAAATCCT
4531809 GGTTATGGGCA
131 GGTTATGGGCA
* * *
4531820 GAATTATGGGCAAGGAGCAAATCCTGGCTATGGACAGAGTTATGGGCAAGGATCAAATCCT-GCG
1 GAATTATGGGCAAGGACCAAATCCTGGCTATGGACAGAATTATGGGCAAGGAGCAAATCCTGGC-
* * * * * **
4531884 TCTGGTCAGAACTAT-GGGCCAGGAGCAACTGCTGGC-ACTGGGCAGGGTTATGGGCA
65 TATGGGCAGAA-TATCGGGCAAGGAGCAAATCCTGGCTA-TGGGCAGAATTATGGGCA
4531940 GAGAACAAAT
Statistics
Matches: 100, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
140 3 0.03
141 95 0.95
142 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.34, T:0.21
Consensus pattern (141 bp):
GAATTATGGGCAAGGACCAAATCCTGGCTATGGACAGAATTATGGGCAAGGAGCAAATCCTGGCT
ATGGGCAGAATATCGGGCAAGGAGCAAATCCTGGCTATGGGCAGAATTATGGGCAAGCAAATCCT
GGTTATGGGCA
Found at i:4547223 original size:24 final size:25
Alignment explanation
Indices: 4547191--4547277 Score: 70
Period size: 25 Copynumber: 3.3 Consensus size: 25
4547181 AATAAAATAT
*
4547191 ATAATATAAA-AATAAAAAATTAAA
1 ATAAAATAAACAATAAAAAATTAAA
* *
4547215 ATAAAATAAACTATAAGAAATTAAA
1 ATAAAATAAACAATAAAAAATTAAA
*
4547240 ATTTATATAATATAAGTAA-AAAAAATTAAA
1 A--TA-A-AATA-AA-CAATAAAAAATTAAA
4547270 ATAAAATA
1 ATAAAATA
4547278 TATAATATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
24 9 0.18
25 13 0.26
26 4 0.08
27 3 0.06
28 3 0.06
29 4 0.08
30 13 0.26
31 1 0.02
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.28
Consensus pattern (25 bp):
ATAAAATAAACAATAAAAAATTAAA
Found at i:4547326 original size:29 final size:29
Alignment explanation
Indices: 4547267--4547328 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
4547257 AAAAAAAATT
* * * *
4547267 AAAATAAAATATATAATATATTATATTGA
1 AAAATAAAAAATATAAGATATAATATAGA
4547296 AAAATAAAAAATATAAGATTATAATA-AGA
1 AAAATAAAAAATATAAGA-TATAATATAGA
4547325 AAAA
1 AAAA
4547329 AAATATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (29 bp):
AAAATAAAAAATATAAGATATAATATAGA
Found at i:4555590 original size:3 final size:3
Alignment explanation
Indices: 4555582--4555610 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4555572 GTTCTTAGTT
4555582 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
4555611 CATTTAAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:4561197 original size:26 final size:26
Alignment explanation
Indices: 4561120--4561200 Score: 117
Period size: 26 Copynumber: 3.1 Consensus size: 26
4561110 AAGATAGTTT
* * *
4561120 GGTGCGTGCTGGTTTTCAATGAATTT
1 GGTGTGTGCTGGTTTTCAATCAATTA
*
4561146 GGTGTGTGCTGGTTTTCACTCAATTA
1 GGTGTGTGCTGGTTTTCAATCAATTA
*
4561172 GGTGTGTGCTAGTTTTCAATCAATTA
1 GGTGTGTGCTGGTTTTCAATCAATTA
4561198 GGT
1 GGT
4561201 ACCCTCTTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.17, C:0.12, G:0.28, T:0.42
Consensus pattern (26 bp):
GGTGTGTGCTGGTTTTCAATCAATTA
Found at i:4570654 original size:15 final size:15
Alignment explanation
Indices: 4570634--4570666 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
4570624 ATATATTTTT
4570634 ATTTTA-AATTAAATA
1 ATTTTATAATT-AATA
4570649 ATTTTATAATTAATA
1 ATTTTATAATTAATA
4570664 ATT
1 ATT
4570667 AATTAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTTATAATTAATA
Found at i:4572905 original size:2 final size:2
Alignment explanation
Indices: 4572898--4572923 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4572888 GGAAGCTAAA
4572898 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
4572924 GGATCTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4582835 original size:25 final size:24
Alignment explanation
Indices: 4582807--4582884 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 24
4582797 AAATATTATT
4582807 AATATATATTTGACTATTATATATA
1 AATATA-ATTTGACTATTATATATA
* * ** *
4582832 AATATAATTTTATTAAAAAAATATA
1 AATATAATTTGACT-ATTATATATA
*
4582857 AATATAA-TTGACTATTATAAATA
1 AATATAATTTGACTATTATATATA
4582880 AATAT
1 AATAT
4582885 TTACTATTTA
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
23 11 0.27
24 10 0.24
25 20 0.49
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (24 bp):
AATATAATTTGACTATTATATATA
Found at i:4582892 original size:20 final size:19
Alignment explanation
Indices: 4582853--4582910 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
4582843 ATTAAAAAAA
*
4582853 TATAAATATAATTGACTAT
1 TATAAATAAAATTGACTAT
*
4582872 TATAAATAAATATTTACTAT
1 TATAAATAAA-ATTGACTAT
* * *
4582892 T-TATATATAATAGACTAT
1 TATAAATAAAATTGACTAT
4582910 T
1 T
4582911 CTCTTTCTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 8 0.25
19 15 0.47
20 9 0.28
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (19 bp):
TATAAATAAAATTGACTAT
Found at i:4585355 original size:20 final size:20
Alignment explanation
Indices: 4585332--4585373 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
4585322 TCTTCCTTTC
4585332 TCTCCCTAT-CTCTTTCTTCT
1 TCTCCCT-TCCTCTTTCTTCT
*
4585352 TCTCTCTTCCTCTTTCTTCT
1 TCTCCCTTCCTCTTTCTTCT
4585372 TC
1 TC
4585374 AGATTTTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.57
Consensus pattern (20 bp):
TCTCCCTTCCTCTTTCTTCT
Found at i:4587537 original size:23 final size:21
Alignment explanation
Indices: 4587509--4587560 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
4587499 ATTCAAAAAA
4587509 ATATATAAATATAATTGACTA-TT
1 ATATATAAATAT--TT-ACTATTT
4587532 ATATATAAATATTTACTATTT
1 ATATATAAATATTTACTATTT
4587553 ATATATAA
1 ATATATAA
4587561 TAGACTGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.14
21 12 0.43
23 12 0.43
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (21 bp):
ATATATAAATATTTACTATTT
Found at i:4594906 original size:105 final size:105
Alignment explanation
Indices: 4594787--4595010 Score: 315
Period size: 105 Copynumber: 2.1 Consensus size: 105
4594777 CTTATTTAGC
* *
4594787 CTTTAGAGAGAAAACTAAAAAATAATTGCTTTTTAGTGTCATATATAATTGA-AGTGATGTGAGC
1 CTTTAGAGAGAAAACTAAAAAATAATTGCTTTTTAGTGTCATATATAATCGAGA-TAATGTGAGC
*
4594851 ATTATATCAATTAATTTGTTAATTGTCTATAAAATTGATGT
65 ATTATATCAATTAATTTGTTAATTGTCTATAAAATTAATGT
* * * * * * * *
4594892 CTTTAGAGATAAAACTGAAAATTAATTGTTTTTTAGTGTTATCTATAATCGGGATAATGTGATCA
1 CTTTAGAGAGAAAACTAAAAAATAATTGCTTTTTAGTGTCATATATAATCGAGATAATGTGAGCA
* *
4594957 TTATATCGATTAATTTGTTAGTTGTCTATAAAATTAATGT
66 TTATATCAATTAATTTGTTAATTGTCTATAAAATTAATGT
4594997 CTTTAGAGAGAAAA
1 CTTTAGAGAGAAAA
4595011 AAATAATTGA
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
105 103 0.99
106 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.41
Consensus pattern (105 bp):
CTTTAGAGAGAAAACTAAAAAATAATTGCTTTTTAGTGTCATATATAATCGAGATAATGTGAGCA
TTATATCAATTAATTTGTTAATTGTCTATAAAATTAATGT
Found at i:4597377 original size:19 final size:17
Alignment explanation
Indices: 4597339--4597396 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
4597329 AATGAAATAT
*
4597339 TATTATATATAATTGGC
1 TATTATATATAATTGAC
4597356 TATTATATATGAATATGAC
1 TATTATATAT-AAT-TGAC
4597375 TATT-TATATAATTGAC
1 TATTATATATAATTGAC
*
4597391 TGTTAT
1 TATTAT
4597397 CTTTCTTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
16 7 0.19
17 14 0.39
18 8 0.22
19 7 0.19
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.48
Consensus pattern (17 bp):
TATTATATATAATTGAC
Found at i:4600403 original size:147 final size:147
Alignment explanation
Indices: 4600166--4600447 Score: 385
Period size: 147 Copynumber: 1.9 Consensus size: 147
4600156 TTCTGAAATT
* * * *
4600166 TTTTTTTCTTTTTTTTCCTTAGCTCATCTAGCCCAATTTTGGAATTAATTTTCTTTTAATTTTTT
1 TTTTTTCCTTTTTTTTCCTTACCTCACCTAGCCCAATTTTGAAATTAATTTTCTTTTAATTTTTT
*
4600231 TCTTTTTTTTCCTTAACTCAACTTTTGATAT-TAAAGATGGATTTAATTATTCAAG-TTAATGAT
66 TCCTTTTTTTCCTTAACTCAACTTTTGAT-TCTAAAGATGGATTTAATTATTCAAGCTTAATGAT
*
4600294 TTTGAAATTATTTTTTTC
130 ATTGAAATTATTTTTTTC
*
4600312 TTTTTTCCTTTTTTTT-CTTACCTCACCTAGGCCCAAATTTTGAAATT-ATTTTCCTTTT-CTTT
1 TTTTTTCCTTTTTTTTCCTTACCTCACCTA-GCCC-AATTTTGAAATTAATTTT-CTTTTAATTT
* * * *
4600374 TTTTCCCTTTTTTTCCTTAATTCATCTTTTGATTCTAGAGATGGATTTAATTATTCAAGCTTGAT
63 TTTT-CCTTTTTTTCCTTAACTCAACTTTTGATTCTAAAGATGGATTTAATTATTCAAGCTTAAT
4600439 GATATTGAA
127 GATATTGAA
4600448 CTTGATATTA
Statistics
Matches: 119, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
145 11 0.09
146 32 0.27
147 64 0.54
148 12 0.10
ACGTcount: A:0.22, C:0.15, G:0.08, T:0.55
Consensus pattern (147 bp):
TTTTTTCCTTTTTTTTCCTTACCTCACCTAGCCCAATTTTGAAATTAATTTTCTTTTAATTTTTT
TCCTTTTTTTCCTTAACTCAACTTTTGATTCTAAAGATGGATTTAATTATTCAAGCTTAATGATA
TTGAAATTATTTTTTTC
Found at i:4602677 original size:29 final size:29
Alignment explanation
Indices: 4602635--4602690 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
4602625 CAATTTACCG
4602635 AGCAAGCAAGACTTTGACTGAGCATTCTC
1 AGCAAGCAAGACTTTGACTGAGCATTCTC
*
4602664 AGCAAGCAAGACTTTGACTTAGCATTC
1 AGCAAGCAAGACTTTGACTGAGCATTC
4602691 ACTGGAACGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (29 bp):
AGCAAGCAAGACTTTGACTGAGCATTCTC
Found at i:4606134 original size:2 final size:2
Alignment explanation
Indices: 4606127--4606152 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4606117 TCTTTGTGTA
4606127 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4606153 GAGAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4610986 original size:42 final size:42
Alignment explanation
Indices: 4610924--4611014 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 42
4610914 GTTCTTTTAT
* * *
4610924 ACTTTTTTCTCTTATTTTATTTTTTTATATATTTTCACGTAC
1 ACTTTTTTCTCTTATCTTATTCTTTTATACATTTTCACGTAC
* * *
4610966 ACTTTTTTCTCTTATCTTATTCTTTTGTACCTTTTGACGTAC
1 ACTTTTTTCTCTTATCTTATTCTTTTATACATTTTCACGTAC
*
4611008 AATTTTT
1 ACTTTTT
4611015 ACTTTTACCT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.18, C:0.16, G:0.04, T:0.62
Consensus pattern (42 bp):
ACTTTTTTCTCTTATCTTATTCTTTTATACATTTTCACGTAC
Found at i:4612829 original size:32 final size:32
Alignment explanation
Indices: 4612793--4612857 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
4612783 AATTTTTTTG
4612793 TTGTTTGGATAAACTATCAAAAATATTTTTCA
1 TTGTTTGGATAAACTATCAAAAATATTTTTCA
*** *
4612825 TTGTTTGGATATTTTATGAAAAATATTTTTCA
1 TTGTTTGGATAAACTATCAAAAATATTTTTCA
4612857 T
1 T
4612858 CATGGTAGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (32 bp):
TTGTTTGGATAAACTATCAAAAATATTTTTCA
Found at i:4613408 original size:22 final size:22
Alignment explanation
Indices: 4613355--4613410 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
4613345 TTTAAATATT
4613355 AATTTTTAA-ATTAATTTTTTA
1 AATTTTTAATATTAATTTTTTA
** *
4613376 AAAATTAAATATTAATTTTTTA
1 AATTTTTAATATTAATTTTTTA
**
4613398 TTTTTTTAATATT
1 AATTTTTAATATT
4613411 TTAAGTTAAA
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
AATTTTTAATATTAATTTTTTA
Found at i:4622808 original size:75 final size:75
Alignment explanation
Indices: 4622707--4622857 Score: 234
Period size: 75 Copynumber: 2.0 Consensus size: 75
4622697 GAATACTACT
*
4622707 CCATCTGCGTTGGGTATTCCTTGGTCTTAAGATACGAA-GGGAATTCACATT-CAAATGTTCATG
1 CCATCTGCGTTAGGTATTCCTTGGTCTTAAGATAC-AACGGGAATTCACATTGC-AATGTTCATG
4622770 TATATAATCTGG
64 TATATAATCTGG
* * *
4622782 CCATCTGCGTTATGTATTTCTTGGTCTTCAGATACAACGGGAATTCACATTGCAATGTTCATGTA
1 CCATCTGCGTTAGGTATTCCTTGGTCTTAAGATACAACGGGAATTCACATTGCAATGTTCATGTA
4622847 TATAATCTGG
66 TATAATCTGG
4622857 C
1 C
4622858 AGCTTCAGAG
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
74 2 0.03
75 67 0.96
76 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (75 bp):
CCATCTGCGTTAGGTATTCCTTGGTCTTAAGATACAACGGGAATTCACATTGCAATGTTCATGTA
TATAATCTGG
Found at i:4629954 original size:130 final size:130
Alignment explanation
Indices: 4629708--4629963 Score: 381
Period size: 130 Copynumber: 2.0 Consensus size: 130
4629698 GATTGGGTAT
* *
4629708 TACTCAACACTGATTGGTCAAACTCGAAAACTACTTTACATATCAAGCATAATTATGAAATATTT
1 TACTCAACACTGATTGATCAAACTCGAAAACTACTTTACATATCAAGCAGAATTATGAAATATTT
* ** * *
4629773 ATTGGAGTTTGCCAATGGGATGGGATGAGGGATGTTGTACAGTGATGTTGGCTATGAACAACTTC
66 ATTGGAGTTTGCCAATGGGATGAGATGAGGGATGTCATACAGCGATATTGGCTATGAACAACTTC
* * *
4629838 TACTCAACATTGATTGATCAAACTCGAAAACTATTTTACATATCAAGCAGAATTATGAAATGTTT
1 TACTCAACACTGATTGATCAAACTCGAAAACTACTTTACATATCAAGCAGAATTATGAAATATTT
*
4629903 ATT-GAGGTTTGCCAATGGG-TCGAGATGAGGGATGTCATATAGCGATATTGGCTATGAACAA
66 ATTGGA-GTTTGCCAATGGGAT-GAGATGAGGGATGTCATACAGCGATATTGGCTATGAACAA
4629964 TAAAATCGTT
Statistics
Matches: 113, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
129 3 0.03
130 110 0.97
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (130 bp):
TACTCAACACTGATTGATCAAACTCGAAAACTACTTTACATATCAAGCAGAATTATGAAATATTT
ATTGGAGTTTGCCAATGGGATGAGATGAGGGATGTCATACAGCGATATTGGCTATGAACAACTTC
Found at i:4634636 original size:3 final size:3
Alignment explanation
Indices: 4634628--4634652 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4634618 AAAAATTAAA
4634628 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
4634653 CTGAAGAAAT
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4634917 original size:2 final size:2
Alignment explanation
Indices: 4634910--4634940 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4634900 TTAAGTGCTC
*
4634910 AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4634941 TACTCAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4635278 original size:10 final size:10
Alignment explanation
Indices: 4635236--4635280 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
4635226 CTCCCCTGCT
*
4635236 TGTTTTTTAG
1 TGTTTTTTTG
4635246 TGTTTTTTT-
1 TGTTTTTTTG
*
4635255 T-TTTTTTTC
1 TGTTTTTTTG
4635264 T-TTTTTTTG
1 TGTTTTTTTG
4635273 TGTTTTTT
1 TGTTTTTT
4635281 NCCCACCAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 7 0.23
9 10 0.32
10 14 0.45
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.84
Consensus pattern (10 bp):
TGTTTTTTTG
Found at i:4639956 original size:1 final size:1
Alignment explanation
Indices: 4639950--4639979 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
4639940 TTAAGGGACC
4639950 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4639980 CATCAACTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4646558 original size:18 final size:18
Alignment explanation
Indices: 4646535--4646571 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
4646525 TCTCTCCTTT
4646535 GACTGGGACCACATATGC
1 GACTGGGACCACATATGC
*
4646553 GACTGGGACCAGATATGC
1 GACTGGGACCACATATGC
4646571 G
1 G
4646572 TTTCCCATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.32, T:0.16
Consensus pattern (18 bp):
GACTGGGACCACATATGC
Found at i:4647211 original size:46 final size:46
Alignment explanation
Indices: 4647149--4647236 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
4647139 GAGCAGAACC
* * *
4647149 AGAATCCACAATTCCTAGGCGACTTTAGTATGTTTCTTGCCAAACT
1 AGAAACCACAATTCCTACGCAACTTTAGTATGTTTCTTGCCAAACT
*
4647195 AGAAACCACGATTCCTACGCAACTTTAGTATGTTTCTTGCCA
1 AGAAACCACAATTCCTACGCAACTTTAGTATGTTTCTTGCCA
4647237 TGAAGATCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (46 bp):
AGAAACCACAATTCCTACGCAACTTTAGTATGTTTCTTGCCAAACT
Found at i:4656258 original size:12 final size:12
Alignment explanation
Indices: 4656241--4656265 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4656231 TCAGATTGAC
4656241 TATTCTTTGCGG
1 TATTCTTTGCGG
4656253 TATTCTTTGCGG
1 TATTCTTTGCGG
4656265 T
1 T
4656266 GGATGAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.24, T:0.52
Consensus pattern (12 bp):
TATTCTTTGCGG
Found at i:4660495 original size:33 final size:33
Alignment explanation
Indices: 4660457--4660536 Score: 160
Period size: 33 Copynumber: 2.4 Consensus size: 33
4660447 TATCAGGCCA
4660457 CCAGCACCTAAGAACCCAACTCGGGAGCCACCC
1 CCAGCACCTAAGAACCCAACTCGGGAGCCACCC
4660490 CCAGCACCTAAGAACCCAACTCGGGAGCCACCC
1 CCAGCACCTAAGAACCCAACTCGGGAGCCACCC
4660523 CCAGCACCTAAGAA
1 CCAGCACCTAAGAA
4660537 GCCGACTCCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.33, C:0.44, G:0.17, T:0.06
Consensus pattern (33 bp):
CCAGCACCTAAGAACCCAACTCGGGAGCCACCC
Found at i:4660681 original size:21 final size:21
Alignment explanation
Indices: 4660657--4660993 Score: 183
Period size: 21 Copynumber: 14.8 Consensus size: 21
4660647 GAGGGGTCCG
*
4660657 CTCACCTCCACCACCAGTCTA
1 CTCACCACCACCACCAGTCTA
* *
4660678 CTCACCACCCCCACCCGTGC-A
1 CTCACCACCACCACCAGT-CTA
* *
4660699 CTCACCCCCGCCACCAGTCTA
1 CTCACCACCACCACCAGTCTA
* *
4660720 TTCACCACCGCCACCACCAGTCCATT
1 CTCACCA---CCACCACCAGT-C-TA
*
4660746 CTCCACCACCACCACCAGTTTA
1 CT-CACCACCACCACCAGTCTA
*
4660768 TTCTCCACCACCACCTCCACCTGTCTA
1 --CT-CACCACCA---CCACCAGTCTA
*
4660795 CTCACCACCCCCACCAGT-TCA
1 CTCACCACCACCACCAGTCT-A
* *
4660816 CTCGCCACCTCCACCAGTCTA
1 CTCACCACCACCACCAGTCTA
4660837 CTCACCCCCACCACCACCACCTGTCTATTCA
1 CTCA---CCACCACCACCA---GTCT----A
*
4660868 CCATCACCACCACCACCAGTCCA
1 -C-TCACCACCACCACCAGTCTA
* * *
4660891 TTCACCACCACCTCCTGTCTA
1 CTCACCACCACCACCAGTCTA
*
4660912 CTCCCCACCACCACCAGTCTA
1 CTCACCACCACCACCAGTCTA
* * * * *
4660933 CTCCCCTCCACCACCTGCCCA
1 CTCACCACCACCACCAGTCTA
*
4660954 TTCACCACCACCACCACCCGTCTA
1 CTCACCACCACCACCA---GTCTA
*
4660978 CTCTCCACCACCACCA
1 CTCACCACCACCACCA
4660994 CCACCACCCG
Statistics
Matches: 244, Mismatches: 42, Indels: 57
0.71 0.12 0.17
Matches are distributed among these distances:
20 2 0.01
21 128 0.52
22 3 0.01
23 1 0.00
24 67 0.27
25 3 0.01
26 2 0.01
27 21 0.09
30 12 0.05
31 1 0.00
32 1 0.00
33 3 0.01
ACGTcount: A:0.22, C:0.55, G:0.05, T:0.17
Consensus pattern (21 bp):
CTCACCACCACCACCAGTCTA
Found at i:4660760 original size:27 final size:27
Alignment explanation
Indices: 4660722--4660902 Score: 95
Period size: 27 Copynumber: 7.3 Consensus size: 27
4660712 CCAGTCTATT
*
4660722 CACCACCGCCACCACCAGTCCATTCT-
1 CACCACCACCACCACCAGTCCATTCTC
**
4660748 --CCACCACCACCACCAGTTTATTCTC
1 CACCACCACCACCACCAGTCCATTCTC
* * *
4660773 CACCACCACCTCCACCTGT-C-TACT-
1 CACCACCACCACCACCAGTCCATTCTC
*
4660797 CACCA-C-CC-CCACCAGTTCA--CT-
1 CACCACCACCACCACCAGTCCATTCTC
* * * * *
4660818 CGCCACC---TCCACCAGTCTACTCAC
1 CACCACCACCACCACCAGTCCATTCTC
* * * *
4660842 CCCCACCACCACCACCTGTCTATTCAC
1 CACCACCACCACCACCAGTCCATTCTC
* *
4660869 CATCACCACCACCACCAGTCCATTCAC
1 CACCACCACCACCACCAGTCCATTCTC
4660896 CACCACC
1 CACCACC
4660903 TCCTGTCTAC
Statistics
Matches: 121, Mismatches: 21, Indels: 25
0.72 0.13 0.15
Matches are distributed among these distances:
21 22 0.18
22 4 0.03
23 2 0.02
24 32 0.26
25 3 0.02
27 58 0.48
ACGTcount: A:0.24, C:0.54, G:0.05, T:0.17
Consensus pattern (27 bp):
CACCACCACCACCACCAGTCCATTCTC
Found at i:4660848 original size:96 final size:96
Alignment explanation
Indices: 4660680--4660947 Score: 258
Period size: 96 Copynumber: 2.8 Consensus size: 96
4660670 CCAGTCTACT
* * * * * * * *
4660680 CACCACCCCCACCCGTGCACTCACCCCCGCCACCAGTCTATTCACCACCGCCACCACCAGTCCA-
1 CACCACCACCACCAGTCCACTCACCACCACCACCAGTCTA--CTCC-CCACCACCACCAGTCTAC
* * *
4660744 T--TCTCCACCACCACCACCAGTTTATTCTCCAC
63 TCCCCTCCACCACCACCACCAGTCTATTCACCAC
* * * * * *
4660776 CACCACCTCCACCTGTCTACTCACCACCCCCACCAGT-TCACTCGCCACCTCCACCAGTCTACTC
1 CACCACCACCACCAGTCCACTCACCACCACCACCAGTCT-ACTCCCCACCACCACCAGTCTACTC
* *
4660840 ACCC-CCACCACCACCACCTGTCTATTCACCAT
65 -CCCTCCACCACCACCACCAGTCTATTCACCAC
* * *
4660872 CACCACCACCACCAGTCCATTCACCACCACCTCCTGTCTACTCCCCACCACCACCAGTCTACTCC
1 CACCACCACCACCAGTCCACTCACCACCACCACCAGTCTACTCCCCACCACCACCAGTCTACTCC
4660937 CCTCCACCACC
66 CCTCCACCACC
4660948 TGCCCATTCA
Statistics
Matches: 140, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
93 14 0.10
94 3 0.02
95 4 0.03
96 117 0.84
97 2 0.01
ACGTcount: A:0.22, C:0.55, G:0.06, T:0.17
Consensus pattern (96 bp):
CACCACCACCACCAGTCCACTCACCACCACCACCAGTCTACTCCCCACCACCACCAGTCTACTCC
CCTCCACCACCACCACCAGTCTATTCACCAC
Found at i:4660878 original size:69 final size:69
Alignment explanation
Indices: 4660751--4661043 Score: 197
Period size: 75 Copynumber: 4.2 Consensus size: 69
4660741 CCATTCTCCA
* * * * *
4660751 CCACCACCACCAGTTTATTCTCCACCACCACCTCCACCTGTCTACTCACCACCCCCACCAGTTCA
1 CCACCACCACCAGTCTACTCACCACCACCACCACCACCTGTCTACTCACCACCACCACCAGTTCA
4660816 CTCG
66 CTCG
* *
4660820 CCACCTCCACCAGTCTACTCACCCCCACCACCACCACCTGTCTATTCACCATCACCACCACCACC
1 CCACCACCACCAGTCTACTCACCACCACCACCACCACCTGTC---T-A-C-TCACCACCACCACC
* * *
4660885 AGTCCATTCA
60 AGTTCACTCG
* * * * *
4660895 CCACCACCTCCTGTCTACT--CC-CCACCACCACCA---GTCTACTCCCCTCCACCACCTGCCCA
1 CCACCACCACCAGTCTACTCACCACCACCACCACCACCTGTCTACTCACCACCACCACCAG----
*
4660954 TTCAC-CA
62 TTCACTCG
* * * * *
4660961 CCACCACCACCCGTCTACTCTCCACCACCACCACCACCACCCGTCCACTCTCCACCTCCACC-GC
1 CCACCACCACCAGTCTA--CT-CACCACCACCACCACCACCTGTCTACTCACCACCACCACCAG-
* *
4661025 TTTACTCA
62 TTCACTCG
4661033 CCACCACCACC
1 CCACCACCACC
4661044 TGTACGATCC
Statistics
Matches: 178, Mismatches: 26, Indels: 37
0.74 0.11 0.15
Matches are distributed among these distances:
63 13 0.07
64 1 0.01
65 1 0.01
66 18 0.10
67 3 0.02
68 2 0.01
69 39 0.22
71 6 0.03
72 38 0.21
73 3 0.02
74 2 0.01
75 52 0.29
ACGTcount: A:0.22, C:0.56, G:0.04, T:0.17
Consensus pattern (69 bp):
CCACCACCACCAGTCTACTCACCACCACCACCACCACCTGTCTACTCACCACCACCACCAGTTCA
CTCG
Found at i:4661031 original size:21 final size:21
Alignment explanation
Indices: 4660989--4661085 Score: 83
Period size: 21 Copynumber: 4.6 Consensus size: 21
4660979 TCTCCACCAC
**
4660989 CACCACCACCACC-CGTCCACT
1 CACCACCACCACCGC-TTTACT
* *
4661010 CTCCACCTCCACCGCTTTACT
1 CACCACCACCACCGCTTTACT
*
4661031 CACCACCACCA-C-CTGTACGAT
1 CACCACCACCACCGCTTTAC--T
* *
4661052 CCCCACCTCCACCGCTTTACT
1 CACCACCACCACCGCTTTACT
4661073 CACCACCACCACC
1 CACCACCACCACC
4661086 ACCAGTTCCA
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
19 5 0.08
20 1 0.02
21 46 0.78
22 2 0.03
23 5 0.08
ACGTcount: A:0.22, C:0.57, G:0.05, T:0.16
Consensus pattern (21 bp):
CACCACCACCACCGCTTTACT
Found at i:4661034 original size:18 final size:18
Alignment explanation
Indices: 4661013--4661082 Score: 50
Period size: 18 Copynumber: 3.6 Consensus size: 18
4661003 GTCCACTCTC
*
4661013 CACCTCCACCGCTTTACT
1 CACCACCACCGCTTTACT
* *
4661031 CACCACCACCACCTGTACGAT
1 CACCACCACC-GCTTTAC--T
*
4661052 CCCCACCTCCACCGCTTTACT
1 ---CACCACCACCGCTTTACT
4661073 CACCACCACC
1 CACCACCACC
4661083 ACCACCAGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
18 18 0.46
19 5 0.13
21 2 0.05
23 5 0.13
24 9 0.23
ACGTcount: A:0.21, C:0.54, G:0.06, T:0.19
Consensus pattern (18 bp):
CACCACCACCGCTTTACT
Found at i:4661058 original size:42 final size:42
Alignment explanation
Indices: 4660989--4661085 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
4660979 TCTCCACCAC
*
4660989 CACCACCACCACCCGTCCACTCTCCACCTCCACCGCTTTACT
1 CACCACCACCACCCGTCCACTCCCCACCTCCACCGCTTTACT
* *
4661031 CACCACCACCACCTGTACGA-TCCCCACCTCCACCGCTTTACT
1 CACCACCACCACCCGT-CCACTCCCCACCTCCACCGCTTTACT
4661073 CACCACCACCACC
1 CACCACCACCACC
4661086 ACCAGTTCCA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
42 49 0.96
43 2 0.04
ACGTcount: A:0.22, C:0.57, G:0.05, T:0.16
Consensus pattern (42 bp):
CACCACCACCACCCGTCCACTCCCCACCTCCACCGCTTTACT
Found at i:4661101 original size:117 final size:117
Alignment explanation
Indices: 4660652--4661101 Score: 350
Period size: 117 Copynumber: 3.8 Consensus size: 117
4660642 TGTTGGAGGG
* * * * * * *
4660652 GTCCGCTCACCTCCACCACCAGTCTACTCACCACCCCCACCCGTGCACTCACCC-CCGCCACCAG
1 GTCCACTCACCACCTCCACCTGTCTACTCACCACCACCACCAGT-CACTC-CCCACCTCCACCAG
* * ** ** **
4660716 -TCTATTCACCACCGCCACCACCAGTCCATTCTCCACCACCACCACCAGTTTATTC
64 CTCTACTCACCACCACCACCACCAGTCCACACTCCACCACCACCACCA--CCACCC
* *
4660771 -TCCAC-CACCACCTCCACCTGTCTACTCACCACCCCCACCAGTTCACTCGCCACCTCCACCAG-
1 GTCCACTCACCACCTCCACCTGTCTACTCACCACCACCACCAG-TCACTCCCCACCTCCACCAGC
* * * * *
4660833 TCTACTCACCCCCACCACCACCACCTGT-C-TA-TTCACCATCACCACCACCACCA
65 TCTACTCA---CCACCACCACCACCAGTCCACACTCCACCACCACCACCACCACCC
* * * * * * *
4660886 GTCCATTCACCACCACCTCCTGTCTACTCCCCACCACCACCAGTCTACTCCCCTCCACCACCTGC
1 GTCCACTCACCACCTCCACCTGTCTACTCACCACCACCACCAGTC-ACTCCCCACCTCCACCAGC
* * * * *
4660951 -CCATTCACCACCACCACCACCCGTCTACTCTCCACCACCACCACCACCACCC
65 TCTACTCACCACCACCACCACCAGTCCACACTCCACCACCACCACCACCACCC
* * *
4661003 GTCCACTCTCCACCTCCACC-GCTTTACTCACCACCACCACCTGT-ACGATCCCCACCTCCACC-
1 GTCCACTCACCACCTCCACCTG-TCTACTCACCACCACCACCAGTCAC--TCCCCACCTCCACCA
*
4661065 GCTTTACTCACCACCACCACCACCAGTTCCA-ACTCCA
63 GCTCTACTCACCACCACCACCACCAG-TCCACACTCCA
4661102 TCTCTTCCTC
Statistics
Matches: 263, Mismatches: 51, Indels: 36
0.75 0.15 0.10
Matches are distributed among these distances:
114 16 0.06
115 3 0.01
116 11 0.04
117 208 0.79
118 9 0.03
119 1 0.00
120 15 0.06
ACGTcount: A:0.22, C:0.55, G:0.06, T:0.17
Consensus pattern (117 bp):
GTCCACTCACCACCTCCACCTGTCTACTCACCACCACCACCAGTCACTCCCCACCTCCACCAGCT
CTACTCACCACCACCACCACCAGTCCACACTCCACCACCACCACCACCACCC
Found at i:4672487 original size:8 final size:8
Alignment explanation
Indices: 4672476--4672509 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
4672466 AGTATATATA
4672476 TTTATAAT
1 TTTATAAT
4672484 TTTATAAT
1 TTTATAAT
4672492 TTTATAA-
1 TTTATAAT
*
4672499 GTTATAAT
1 TTTATAAT
4672507 TTT
1 TTT
4672510 TGTAACGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (8 bp):
TTTATAAT
Found at i:4678463 original size:7 final size:7
Alignment explanation
Indices: 4678451--4678479 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
4678441 TTCGAATTAT
4678451 AAAAACA
1 AAAAACA
4678458 AAAAACA
1 AAAAACA
4678465 AAAAA-A
1 AAAAACA
4678471 AAAAACA
1 AAAAACA
4678478 AA
1 AA
4678480 GAAGTGATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:4690239 original size:36 final size:36
Alignment explanation
Indices: 4690192--4690316 Score: 124
Period size: 36 Copynumber: 3.7 Consensus size: 36
4690182 CTACTTTGAC
*
4690192 TCATATAAGGATTATTTAAAATCATTTTATTTCTAT
1 TCATATAAGGATTGTTTAAAATCATTTTATTTCTAT
*
4690228 TCATATAAGGATTGTTT----T--TTTT-TTT-TTT
1 TCATATAAGGATTGTTTAAAATCATTTTATTTCTAT
* * * *
4690256 TAATATAAGGATTGTTTAAAATCATTCTACTTCGACT
1 TCATATAAGGATTGTTTAAAATCATTTTATTTCTA-T
4690293 T-ATATAAGGATTGTTTAAAATCAT
1 TCATATAAGGATTGTTTAAAATCAT
4690317 AATAATAATA
Statistics
Matches: 73, Mismatches: 7, Indels: 18
0.74 0.07 0.18
Matches are distributed among these distances:
28 18 0.25
29 3 0.04
30 4 0.05
32 2 0.03
34 3 0.04
35 2 0.03
36 39 0.53
37 2 0.03
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.50
Consensus pattern (36 bp):
TCATATAAGGATTGTTTAAAATCATTTTATTTCTAT
Found at i:4690546 original size:22 final size:22
Alignment explanation
Indices: 4690518--4690560 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4690508 CAAATGATAC
*
4690518 AGAAAATTTCAAAATTTTATTA
1 AGAAAATTTCAAAAATTTATTA
4690540 AGAAAATTTCAAAAATTTATT
1 AGAAAATTTCAAAAATTTATT
4690561 TAGTTTAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (22 bp):
AGAAAATTTCAAAAATTTATTA
Found at i:4697540 original size:117 final size:117
Alignment explanation
Indices: 4697334--4697691 Score: 716
Period size: 117 Copynumber: 3.1 Consensus size: 117
4697324 GATTGTCATT
4697334 TGAAAGAGATGGAGGCTCAAAAAGGTGCCACCATTTTAGAAACTGAGTTGAAGGAGTTGCAAGAA
1 TGAAAGAGATGGAGGCTCAAAAAGGTGCCACCATTTTAGAAACTGAGTTGAAGGAGTTGCAAGAA
4697399 AAGGCATATATGTTGACTGAAGATAATAAACAGTTACATGAAAGGCTTGAAA
66 AAGGCATATATGTTGACTGAAGATAATAAACAGTTACATGAAAGGCTTGAAA
4697451 TGAAAGAGATGGAGGCTCAAAAAGGTGCCACCATTTTAGAAACTGAGTTGAAGGAGTTGCAAGAA
1 TGAAAGAGATGGAGGCTCAAAAAGGTGCCACCATTTTAGAAACTGAGTTGAAGGAGTTGCAAGAA
4697516 AAGGCATATATGTTGACTGAAGATAATAAACAGTTACATGAAAGGCTTGAAA
66 AAGGCATATATGTTGACTGAAGATAATAAACAGTTACATGAAAGGCTTGAAA
4697568 TGAAAGAGATGGAGGCTCAAAAAGGTGCCACCATTTTAGAAACTGAGTTGAAGGAGTTGCAAGAA
1 TGAAAGAGATGGAGGCTCAAAAAGGTGCCACCATTTTAGAAACTGAGTTGAAGGAGTTGCAAGAA
4697633 AAGGCATATATGTTGACTGAAGATAATAAACAGTTACATGAAAGGCTTGAAA
66 AAGGCATATATGTTGACTGAAGATAATAAACAGTTACATGAAAGGCTTGAAA
4697685 TGAAAGA
1 TGAAAGA
4697692 TGGGGAACTA
Statistics
Matches: 241, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 241 1.00
ACGTcount: A:0.41, C:0.11, G:0.26, T:0.22
Consensus pattern (117 bp):
TGAAAGAGATGGAGGCTCAAAAAGGTGCCACCATTTTAGAAACTGAGTTGAAGGAGTTGCAAGAA
AAGGCATATATGTTGACTGAAGATAATAAACAGTTACATGAAAGGCTTGAAA
Found at i:4719157 original size:2 final size:2
Alignment explanation
Indices: 4719145--4719189 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
4719135 TTTCAAGGTT
*
4719145 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4719187 TA T
1 TA T
4719190 GTCTTGTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4719234 original size:2 final size:2
Alignment explanation
Indices: 4719223--4719266 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
4719213 TGAANCTAGT
4719223 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4719264 TA T
1 TA T
4719267 GTCTTGTCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4719278 original size:77 final size:77
Alignment explanation
Indices: 4719144--4719293 Score: 284
Period size: 77 Copynumber: 1.9 Consensus size: 77
4719134 TTTTCAAGGT
4719144 TTATATAAATATATATATATATATATATATATATATATATATATATGTCTTGTCAACCAAGCAAT
1 TTATATAAATATATATATATATATATATATATATATATATATATATGTCTTGTCAACCAAGCAAT
4719209 GTCGTGAANCTAG
66 GTCGTGAA-CTAG
4719222 TTATAT-AATATATATATATATATATATATATATATATATATATATGTCTTGTCAACCAAGCAAT
1 TTATATAAATATATATATATATATATATATATATATATATATATATGTCTTGTCAACCAAGCAAT
4719286 GTCGTGAA
66 GTCGTGAA
4719294 ATCATGAAGC
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 66 0.92
78 6 0.08
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (77 bp):
TTATATAAATATATATATATATATATATATATATATATATATATATGTCTTGTCAACCAAGCAAT
GTCGTGAACTAG
Found at i:4722395 original size:1 final size:1
Alignment explanation
Indices: 4722389--4722424 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
4722379 ACTTAACTTC
**
4722389 TTTTTTTTTTTTTTTTTTTTTTTCCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4722425 GTAAAGATGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:4727479 original size:3 final size:3
Alignment explanation
Indices: 4727473--4727516 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
4727463 TGAGGAAGAA
4727473 GAG GAG GAG GAG GAG GAG GAG CG-G GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG -GAG GAG GAG GAG GAG GAG GAG GA
4727517 AGAAGTAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 1 0.03
3 37 0.95
4 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:4728750 original size:52 final size:52
Alignment explanation
Indices: 4728660--4728764 Score: 151
Period size: 52 Copynumber: 2.0 Consensus size: 52
4728650 CAAATTATTA
4728660 TGTATAAATGCAAAGTTGGTAAATTTTCTTATAAAAGGGGAT-CCTTGACTTT
1 TGTATAAATGCAAAGTTGGTAAATTTTCTTATAAAA-GGGATGCCTTGACTTT
* * *
4728712 TGTATAAATGCAAAGTTGGTAAGTTTTCTT-TAGGAAGGGATGCTTTGACTTT
1 TGTATAAATGCAAAGTTGGTAAATTTTCTTATA-AAAGGGATGCCTTGACTTT
4728764 T
1 T
4728765 CTATTCATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
51 7 0.15
52 41 0.85
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.40
Consensus pattern (52 bp):
TGTATAAATGCAAAGTTGGTAAATTTTCTTATAAAAGGGATGCCTTGACTTT
Found at i:4729569 original size:20 final size:20
Alignment explanation
Indices: 4729544--4729583 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4729534 ACCAGCTGAA
* *
4729544 AGATAATCTCTTTTTGTGTT
1 AGATAATATCTTTCTGTGTT
4729564 AGATAATATCTTTCTGTGTT
1 AGATAATATCTTTCTGTGTT
4729584 TTTTTTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.53
Consensus pattern (20 bp):
AGATAATATCTTTCTGTGTT
Found at i:4735424 original size:2 final size:2
Alignment explanation
Indices: 4735419--4735449 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4735409 CTTTTTTTGG
4735419 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4735450 AATCAAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:4736623 original size:26 final size:24
Alignment explanation
Indices: 4736594--4736641 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
4736584 AGAAGAAATT
*
4736594 TCAAAACTCATCTCATATTTTATTAA
1 TCAAAA-TC-TCTAATATTTTATTAA
*
4736620 TCAAAATCTGTAATATTTTATT
1 TCAAAATCTCTAATATTTTATT
4736642 TCATTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 2 0.10
26 6 0.30
ACGTcount: A:0.38, C:0.15, G:0.02, T:0.46
Consensus pattern (24 bp):
TCAAAATCTCTAATATTTTATTAA
Found at i:4755317 original size:3 final size:3
Alignment explanation
Indices: 4755286--4755331 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
4755276 ATCATGAACT
* * * *
4755286 ATC ATA ATC ATC AAC ATC ATT ATC TTC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
4755332 CTCTGAGATG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.37, C:0.28, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:4765311 original size:40 final size:40
Alignment explanation
Indices: 4765256--4765337 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
4765246 CATGTTATTG
*
4765256 TGCTTATAGAACCTTCTTCCTACACTTTGATATTTCAAGA
1 TGCTTATAAAACCTTCTTCCTACACTTTGATATTTCAAGA
**
4765296 TGCTTATAAAACCTTCTTGTTACACTTTGATATTTCAAGA
1 TGCTTATAAAACCTTCTTCCTACACTTTGATATTTCAAGA
4765336 TG
1 TG
4765338 GTGCTTCCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (40 bp):
TGCTTATAAAACCTTCTTCCTACACTTTGATATTTCAAGA
Found at i:4776092 original size:2 final size:2
Alignment explanation
Indices: 4776087--4776130 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4776077 AGTTCAATTA
4776087 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4776129 AT
1 AT
4776131 GACTTAGGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4778789 original size:2 final size:2
Alignment explanation
Indices: 4778782--4778836 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
4778772 NCTTTAGACA
4778782 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4778824 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
4778837 CTATTTTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4787000 original size:32 final size:33
Alignment explanation
Indices: 4786938--4787016 Score: 106
Period size: 32 Copynumber: 2.4 Consensus size: 33
4786928 TAAATTATAT
* * * *
4786938 AATATAAAAAATTATATTCAAAAATGAAAATAA
1 AATATATAACATTATAATCAAAAATAAAAATAA
4786971 AATATATAACATTATAAT-AAAAATAAAAATAA
1 AATATATAACATTATAATCAAAAATAAAAATAA
*
4787003 AATATATGACATTA
1 AATATATAACATTA
4787017 AAAATATATT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 26 0.63
33 15 0.37
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.29
Consensus pattern (33 bp):
AATATATAACATTATAATCAAAAATAAAAATAA
Found at i:4787245 original size:15 final size:15
Alignment explanation
Indices: 4787225--4787264 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
4787215 ATTTTCTCTG
**
4787225 CAATCACATTATTTA
1 CAATCACATTACCTA
4787240 CAATCACATTACCTA
1 CAATCACATTACCTA
*
4787255 TAATCACATT
1 CAATCACATT
4787265 GCATTATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (15 bp):
CAATCACATTACCTA
Found at i:4790660 original size:31 final size:31
Alignment explanation
Indices: 4790599--4790659 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
4790589 TAAAAATTCA
* * *
4790599 AATTAAAAAATATATAAATTTATCCATTTTT
1 AATTAAAAAATACATAAATTTAACAATTTTT
*
4790630 AATTAAAAATTACATAAA-TTAACAATTTTT
1 AATTAAAAAATACATAAATTTAACAATTTTT
4790660 TTCTTATAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.43
Consensus pattern (31 bp):
AATTAAAAAATACATAAATTTAACAATTTTT
Found at i:4790993 original size:37 final size:36
Alignment explanation
Indices: 4790943--4791015 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 36
4790933 TTTGATGAGT
* *
4790943 ATTAATATTTAACTTAATATATTAAAAAATATAAAAA
1 ATTAATATCTAACTTAAAATATTAAAAAAT-TAAAAA
*
4790980 ATTAATATCTAACTTAAAATATTAGAAAATTAAAAA
1 ATTAATATCTAACTTAAAATATTAAAAAATTAAAAA
4791016 TTTTTGACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 6 0.18
37 27 0.82
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (36 bp):
ATTAATATCTAACTTAAAATATTAAAAAATTAAAAA
Found at i:4792406 original size:29 final size:29
Alignment explanation
Indices: 4792374--4792459 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 29
4792364 CTTATTTTTG
* *
4792374 TATACCTGTTCACATATACCTTTTTCTCT
1 TATACCTATTCACATATACCTTCTTCTCT
** * *
4792403 TATATTTATTCATATATAGCTTCTTCTCT
1 TATACCTATTCACATATACCTTCTTCTCT
* *
4792432 TATACCTTTTCACGTATACC-TCTTCTCT
1 TATACCTATTCACATATACCTTCTTCTCT
4792460 ATTACTTTTT
Statistics
Matches: 45, Mismatches: 12, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
28 8 0.18
29 37 0.82
ACGTcount: A:0.21, C:0.26, G:0.03, T:0.50
Consensus pattern (29 bp):
TATACCTATTCACATATACCTTCTTCTCT
Found at i:4795364 original size:3 final size:3
Alignment explanation
Indices: 4795358--4795384 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4795348 ATTACTACTA
4795358 CTG CTG CTG CTG CTG CTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG
4795385 TTTGCAACGT
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:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
CTG
Found at i:4798162 original size:15 final size:18
Alignment explanation
Indices: 4798122--4798162 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
4798112 AATCTAATAT
4798122 ATATATATATATATAAAG
1 ATATATATATATATAAAG
4798140 -TATATATAT-TA-AAAG
1 ATATATATATATATAAAG
4798155 ATAT-TATA
1 ATATATATA
4798163 AATTAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 8 0.36
16 5 0.23
17 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
ATATATATATATATAAAG
Found at i:4799072 original size:337 final size:337
Alignment explanation
Indices: 4798457--4800307 Score: 3684
Period size: 337 Copynumber: 5.5 Consensus size: 337
4798447 ATAGAAAGAN
4798457 TCATCTCCAAGCTTTGAAAGAATTTCAATGGTTGATCTTTAATTGTTTTGGTTGTAATAAATCAA
1 TCATCTCCAAGCTTTGAAAGAATTTCAATGGTTGATCTTTAATTGTTTTGGTTGTAATAAATCAA
4798522 GTAAGTGACTTGATATCTCTTTAATATTTTCATTCTCTAAAAATCAACTTTAATATGAATTTTAC
66 GTAAGTGACTTGATATCTCTTTAATATTTTCATTCTCTAAAAATCAACTTTAATATGAATTTTAC
4798587 TATCATATAGTAAATATTATATTATGTCCCTTGATTTGTTCTTTTAAGTTATTTTTCATAACATG
131 TATCATATAGTAAATATTATATTATGTCCCTTGATTTGTTCTTTTAAGTTATTTTTCATAACATG
4798652 TTATCAGCACGATCCTCTTTGATCTCTCAAGTTTTGAAATTATTTTGTTTTCTTCATCTTCAAGT
196 TTATCAGCACGATCCTCTTTGATCTCTCAAGTTTTGAAATTATTTTGTTTTCTTCATCTTCAAGT
4798717 TTCAAAAAGATTTCAACGATTTGGTTTTGATTTATAGTTTAGCAAATCAGGTAACTATTGCTATT
261 TTCAAAAAGATTTCAACGATTTGGTTTTGATTTATAGTTTAGCAAATCAGGTAACTATTGCTATT
4798782 ATTTTGTTTTCA
326 ATTTTGTTTTCA
4798794 TCATCTCCAAGCTTTGAAAGAATTTCAATGGTTGATCTTTAATTGTTTTGGTTGTAATAAATCAA
1 TCATCTCCAAGCTTTGAAAGAATTTCAATGGTTGATCTTTAATTGTTTTGGTTGTAATAAATCAA
4798859 GTAAGTGACTTGATATCTCTTTAATATTTTCATTCTCTAAAAATCAACTTTAATATGAATTTTAC
66 GTAAGTGACTTGATATCTCTTTAATATTTTCATTCTCTAAAAATCAACTTTAATATGAATTTTAC
4798924 TATCATATAGTAAATATTATATTATGTCCCTTGATTTGTTCTTTTAAGTTATTTTTCATAACATG
131 TATCATATAGTAAATATTATATTATGTCCCTTGATTTGTTCTTTTAAGTTATTTTTCATAACATG
4798989 TTATCAGCACGATCCTCTTTGATCTCTCAAGTTTTGAAATTATTTTGTTTTCTTCATCTTCAAGT
196 TTATCAGCACGATCCTCTTTGATCTCTCAAGTTTTGAAATTATTTTGTTTTCTTCATCTTCAAGT
4799054 TTCAAAAAGATTTCAACGATTTGGTTTTGATTTATAGTTTAGCAAATCAGGTAACTATTGCTATT
261 TTCAAAAAGATTTCAACGATTTGGTTTTGATTTATAGTTTAGCAAATCAGGTAACTATTGCTATT
4799119 ATTTTGTTTTCA
326 ATTTTGTTTTCA
4799131 TCATCTCCAAGCTTTGAAAGAATTTCAATGGTTGATCTTTAATTGTTTTGGTTGTAATAAATCAA
1 TCATCTCCAAGCTTTGAAAGAATTTCAATGGTTGATCTTTAATTGTTTTGGTTGTAATAAATCAA
4799196 GTAAGTGACTTGATATCTCTTTAATATTTTCATTCTCTAAAAATCAACTTTAATATGAATTTTAC
66 GTAAGTGACTTGATATCTCTTTAATATTTTCATTCTCTAAAAATCAACTTTAATATGAATTTTAC
4799261 TATCATATAGTAAATATTATATTATGTCCCTTGATTTGTTCTTTTAAGTTATTTTTCATAACATG
131 TATCATATAGTAAATATTATATTATGTCCCTTGATTTGTTCTTTTAAGTTATTTTTCATAACATG
4799326 TTATCAGCACGATCCTCTTTGATCTCTCAAGTTTTGAAATTATTTTGTTTTCTTCATCTTCAAGT
196 TTATCAGCACGATCCTCTTTGATCTCTCAAGTTTTGAAATTATTTTGTTTTCTTCATCTTCAAGT
4799391 TTCAAAAAGATTTCAACGATTTGGTTTTGATTTATAGTTTAGCAAATCAGGTAACTATTGCTATT
261 TTCAAAAAGATTTCAACGATTTGGTTTTGATTTATAGTTTAGCAAATCAGGTAACTATTGCTATT
4799456 ATTTTGTTTTCA
326 ATTTTGTTTTCA
4799468 TCATCTCCAAGCTTTGAAAGAATTTCAATGGTTGATCTTTAATTGTTTTGGTTGTAATAAATCAA
1 TCATCTCCAAGCTTTGAAAGAATTTCAATGGTTGATCTTTAATTGTTTTGGTTGTAATAAATCAA
4799533 GTAAGTGACTTGATATCTCTTTAATATTTTCATTCTCTAAAAATCAACTTTAATATGAATTTTAC
66 GTAAGTGACTTGATATCTCTTTAATATTTTCATTCTCTAAAAATCAACTTTAATATGAATTTTAC
4799598 TATCATATAGTAAATATTATATTATGTCCCTTGATTTGTTCTTTTAAGTTATTTTTCATAACATG
131 TATCATATAGTAAATATTATATTATGTCCCTTGATTTGTTCTTTTAAGTTATTTTTCATAACATG
4799663 TTATCAGCACGATCCTCTTTGATCTCTCAAGTTTTGAAATTATTTTGTTTTCTTCATCTTCAAGT
196 TTATCAGCACGATCCTCTTTGATCTCTCAAGTTTTGAAATTATTTTGTTTTCTTCATCTTCAAGT
4799728 TTCAAAAAGATTTCAACGATTTGGTTTTGATTTATAGTTTAGCAAATCAGGTAACTATTGCTATT
261 TTCAAAAAGATTTCAACGATTTGGTTTTGATTTATAGTTTAGCAAATCAGGTAACTATTGCTATT
4799793 ATTTTGTTTTCA
326 ATTTTGTTTTCA
4799805 TCATCTCCAAGCTTTGAAAGAATTTCAATGGTTGATCTTTAATTGTTTTGGTTGTAATAAATCAA
1 TCATCTCCAAGCTTTGAAAGAATTTCAATGGTTGATCTTTAATTGTTTTGGTTGTAATAAATCAA
4799870 GTAAGTGACTTGATATCTCTTTAATATTTTCATTCTCTAAAAATCAACTTTAATATGAATTTTAC
66 GTAAGTGACTTGATATCTCTTTAATATTTTCATTCTCTAAAAATCAACTTTAATATGAATTTTAC
4799935 TATCATATAGTAAATATTATATTATGTCCCTTGATTTGTTCTTTTAAGTTATTTTTCATAACATG
131 TATCATATAGTAAATATTATATTATGTCCCTTGATTTGTTCTTTTAAGTTATTTTTCATAACATG
4800000 TTATCAGCACGATCCTCTTTGATCTCTCAAGTTTTGAAATTATTTTGTTTTCTTCATCTTCAAGT
196 TTATCAGCACGATCCTCTTTGATCTCTCAAGTTTTGAAATTATTTTGTTTTCTTCATCTTCAAGT
4800065 TTCAAAAAGATTTCAACGATTTGGTTTTGATTTATAGTTTAGCAAATCAGGTAACTATTGCTATT
261 TTCAAAAAGATTTCAACGATTTGGTTTTGATTTATAGTTTAGCAAATCAGGTAACTATTGCTATT
4800130 ATTTTGTTTTCA
326 ATTTTGTTTTCA
4800142 TCATCTCCAAGCTTTGAAAGAATTTCAATGGTTGATCTTTAATTGTTTTGGTTGTAATAAATCAA
1 TCATCTCCAAGCTTTGAAAGAATTTCAATGGTTGATCTTTAATTGTTTTGGTTGTAATAAATCAA
*
4800207 GTAAGTGACTTGATATCTCTTTAATATTTTTATTCTCTAAAAATCAACTTTAATATGAATTTTAC
66 GTAAGTGACTTGATATCTCTTTAATATTTTCATTCTCTAAAAATCAACTTTAATATGAATTTTAC
*
4800272 TATCATATAGTAAATATTATATTCTGTCCCTTGATT
131 TATCATATAGTAAATATTATATTATGTCCCTTGATT
4800308 AGAAAGTATA
Statistics
Matches: 1512, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
337 1512 1.00
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (337 bp):
TCATCTCCAAGCTTTGAAAGAATTTCAATGGTTGATCTTTAATTGTTTTGGTTGTAATAAATCAA
GTAAGTGACTTGATATCTCTTTAATATTTTCATTCTCTAAAAATCAACTTTAATATGAATTTTAC
TATCATATAGTAAATATTATATTATGTCCCTTGATTTGTTCTTTTAAGTTATTTTTCATAACATG
TTATCAGCACGATCCTCTTTGATCTCTCAAGTTTTGAAATTATTTTGTTTTCTTCATCTTCAAGT
TTCAAAAAGATTTCAACGATTTGGTTTTGATTTATAGTTTAGCAAATCAGGTAACTATTGCTATT
ATTTTGTTTTCA
Found at i:4801160 original size:18 final size:18
Alignment explanation
Indices: 4801116--4801152 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4801106 AATGAACTTA
4801116 ATAGTAATTGGTATATTT
1 ATAGTAATTGGTATATTT
4801134 ATAGTAATTGGTATATTT
1 ATAGTAATTGGTATATTT
4801152 A
1 A
4801153 GTATAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (18 bp):
ATAGTAATTGGTATATTT
Found at i:4804861 original size:17 final size:17
Alignment explanation
Indices: 4804841--4804876 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
4804831 TTCACTCGAA
*
4804841 TTTTTTCCCA-TGAGGT
1 TTTTTTCCCAGTAAGGT
4804857 TTTTTTCCCAGTAAGGT
1 TTTTTTCCCAGTAAGGT
4804874 TTT
1 TTT
4804877 AACGAGGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.14, C:0.17, G:0.17, T:0.53
Consensus pattern (17 bp):
TTTTTTCCCAGTAAGGT
Found at i:4817128 original size:2 final size:2
Alignment explanation
Indices: 4817123--4817158 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
4817113 TTTTTTTCCT
*
4817123 TC TC TC ATC TC TC TC TC TC TC TC TC TC TC TG TC TC T
1 TC TC TC -TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4817159 TACAACAGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.03, C:0.44, G:0.03, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4822038 original size:5 final size:5
Alignment explanation
Indices: 4822028--4822052 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4822018 GTCGCAACTC
4822028 CCCCA CCCCA CCCCA CCCCA CCCCA
1 CCCCA CCCCA CCCCA CCCCA CCCCA
4822053 AAAAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.80, G:0.00, T:0.00
Consensus pattern (5 bp):
CCCCA
Found at i:4829299 original size:6 final size:6
Alignment explanation
Indices: 4829290--4829315 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4829280 GGAGGAAGAC
4829290 GAAGGA GAAGGA GAAGGA GAAGGA GA
1 GAAGGA GAAGGA GAAGGA GAAGGA GA
4829316 GGAATTGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GAAGGA
Found at i:4829472 original size:15 final size:16
Alignment explanation
Indices: 4829454--4829491 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
4829444 AAAGCAGAGA
4829454 GGAAGGAGAGGAAG-G
1 GGAAGGAGAGGAAGTG
*
4829469 GGAAGGGGAGGAAGTG
1 GGAAGGAGAGGAAGTG
4829485 GG-AGGAG
1 GGAAGGAG
4829492 GCGAAGAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.34, C:0.00, G:0.63, T:0.03
Consensus pattern (16 bp):
GGAAGGAGAGGAAGTG
Done.