Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 12 of 378
Found at i:3444808 original size:64 final size:64
Alignment explanation
Indices: 3444600--3444810 Score: 164
Period size: 64 Copynumber: 3.2 Consensus size: 64
3444590 TCTGAATAAG
**
3444600 GGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACTGTTACCCAAAT
1 GGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACTGTTACCTGAAT
* ** * * * * *
3444664 GGGCT--TGCATATGTTTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCA-T---ACTGTT
1 GGGCTAAGGCCCA-GTTT-A---T---TGTAATCTGAAAAGGG-CTCTGGCCCAGTACCACTGTT
*
3444723 ATCTGAAT
57 ACCTGAAT
3444731 AAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACTGTTACCTGA
1 ---GGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACTGTTACCTGA
3444796 AT
63 AT
*
3444798 GGGCTTAGGCCCA
1 GGGCTAAGGCCCA
3444811 ATAGGCTTGA
Statistics
Matches: 108, Mismatches: 21, Indels: 36
0.65 0.13 0.22
Matches are distributed among these distances:
62 3 0.03
63 12 0.11
64 32 0.30
67 26 0.24
70 20 0.19
71 12 0.11
72 3 0.03
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (64 bp):
GGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACTGTTACCTGAAT
Found at i:3447821 original size:132 final size:132
Alignment explanation
Indices: 3447584--3447826 Score: 364
Period size: 132 Copynumber: 1.8 Consensus size: 132
3447574 TTGCCTCACC
* * * * * *
3447584 TTAGAAAACATGAATGAAATTCTGAAGGGATATTCGATTATTTTGAACAAATGGGAGATTGCAAC
1 TTAGAAAACACGAATGAAATTCTAAAGAGATATTCGATTATTTTGAACAAACGAGAAATTGCAAC
* *
3447649 CCAGCACGATAGGGCACTATTCCTCAAATTGCTAAACATCGAACATTTCCTTCATTTTAAAAAGT
66 CCAGCACGATAGGGCACGATTCCCCAAATTGCTAAACATCGAACATTTCCTTCATTTTAAAAAGT
3447714 TT
131 TT
*
3447716 TTAGAAAACACGAATGAAATTCTAAAGAGATATTCGATTATTTTGAGCAAACGAGAAATTGCAAC
1 TTAGAAAACACGAATGAAATTCTAAAGAGATATTCGATTATTTTGAACAAACGAGAAATTGCAAC
*
3447781 CCAGCAC-AGTAGGGCACGATTCCCCGAATTG-TCAAACATCGAACAT
66 CCAGCACGA-TAGGGCACGATTCCCCAAATTGCT-AAACATCGAACAT
3447827 CGCCTCCGTC
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
131 2 0.02
132 97 0.98
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (132 bp):
TTAGAAAACACGAATGAAATTCTAAAGAGATATTCGATTATTTTGAACAAACGAGAAATTGCAAC
CCAGCACGATAGGGCACGATTCCCCAAATTGCTAAACATCGAACATTTCCTTCATTTTAAAAAGT
TT
Found at i:3448505 original size:2 final size:2
Alignment explanation
Indices: 3448498--3448541 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3448488 TTACAAATCG
3448498 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3448540 TA
1 TA
3448542 AATTTAGAAT
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):
TA
Found at i:3455220 original size:2 final size:2
Alignment explanation
Indices: 3455213--3455238 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3455203 CCTTCTATTC
3455213 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
3455239 TAAGGTTTCT
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:3468599 original size:3 final size:3
Alignment explanation
Indices: 3468593--3468624 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3468583 CTTTTTGTAT
3468593 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3468625 CTTGAGCAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3469207 original size:27 final size:26
Alignment explanation
Indices: 3469172--3469232 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
3469162 CTAATTTAAC
*
3469172 ATATTATTTATTTGAAATTTGCTTTAT
1 ATATTATTTATTTCAAA-TTGCTTTAT
*
3469199 ATATTATTTTATTTCAAATTGTTTTAT
1 ATATTA-TTTATTTCAAATTGCTTTAT
*
3469226 ATTTTAT
1 ATATTAT
3469233 CCATGTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 19 0.63
28 10 0.33
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (26 bp):
ATATTATTTATTTCAAATTGCTTTAT
Found at i:3471484 original size:13 final size:13
Alignment explanation
Indices: 3471466--3471490 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3471456 ATAGAAATAC
3471466 AATACTTAAAGAA
1 AATACTTAAAGAA
3471479 AATACTTAAAGA
1 AATACTTAAAGA
3471491 TATTTCGCCC
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:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (13 bp):
AATACTTAAAGAA
Found at i:3476858 original size:17 final size:17
Alignment explanation
Indices: 3476806--3476860 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
3476796 GAATTTTTAT
* *
3476806 TTTTAACTCAAAGA-AA
1 TTTTAACTCAAATATTA
*
3476822 TTTTAA-TGAAAT-TTA
1 TTTTAACTCAAATATTA
3476837 CTTTTAACTCAAATATTA
1 -TTTTAACTCAAATATTA
3476855 TTTTAA
1 TTTTAA
3476861 TAATTATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 11 0.35
18 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (17 bp):
TTTTAACTCAAATATTA
Found at i:3481884 original size:18 final size:19
Alignment explanation
Indices: 3481828--3481887 Score: 68
Period size: 18 Copynumber: 3.0 Consensus size: 19
3481818 ATAAAATTTT
3481828 TAAAATAAAATTCTAAAGAATA
1 TAAAA-AAAATTC-AAA-AATA
*
3481850 TAAAAAGAAATTAAAAAATA
1 TAAAAA-AAATTCAAAAATA
3481870 T-AAAAAAATTCAAAAATA
1 TAAAAAAAATTCAAAAATA
3481888 ATAATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 12 0.34
19 4 0.11
20 5 0.14
21 4 0.11
22 10 0.29
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (19 bp):
TAAAAAAAATTCAAAAATA
Found at i:3484972 original size:2 final size:2
Alignment explanation
Indices: 3484965--3484993 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3484955 AGTTAAGATT
3484965 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
3484994 TATCATTAAT
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:3488335 original size:25 final size:25
Alignment explanation
Indices: 3488301--3488350 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3488291 TTTTCTACCA
3488301 TAAAAAATACAACACTATCTGCATT
1 TAAAAAATACAACACTATCTGCATT
3488326 TAAAAAATACAACACTATCTGCATT
1 TAAAAAATACAACACTATCTGCATT
3488351 CTCAATTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.20, G:0.04, T:0.28
Consensus pattern (25 bp):
TAAAAAATACAACACTATCTGCATT
Found at i:3489727 original size:11 final size:11
Alignment explanation
Indices: 3489713--3489755 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
3489703 ATATTACAAT
3489713 TATTTATTAAA
1 TATTTATTAAA
3489724 TATTTATTAAA
1 TATTTATTAAA
* *
3489735 -ATTATAATATA
1 TATT-TATTAAA
3489746 TATTTATTAA
1 TATTTATTAA
3489756 TATAATTGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 3 0.12
11 20 0.77
12 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TATTTATTAAA
Found at i:3493899 original size:22 final size:24
Alignment explanation
Indices: 3493857--3493900 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
3493847 TAATTATATG
*
3493857 TATTTTTATAGATTTATTCTTATA
1 TATTTTTATAGATATATTCTTATA
3493881 TATTTTT-T-GATATATTCTTA
1 TATTTTTATAGATATATTCTTA
3493901 CTATCAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 1 0.05
24 7 0.37
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.64
Consensus pattern (24 bp):
TATTTTTATAGATATATTCTTATA
Found at i:3496294 original size:23 final size:23
Alignment explanation
Indices: 3496262--3496310 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3496252 TATCTTTCTC
*
3496262 TTTTAGAAATTTAATCTTTTA-AT
1 TTTTAGAAATTCAAT-TTTTAGAT
*
3496285 TTTTATAAATTCAATTTTTAGAT
1 TTTTAGAAATTCAATTTTTAGAT
3496308 TTT
1 TTT
3496311 AAAAATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (23 bp):
TTTTAGAAATTCAATTTTTAGAT
Found at i:3502477 original size:2 final size:2
Alignment explanation
Indices: 3502470--3502523 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
3502460 AAGTCCTCCC
3502470 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
3502512 AT AT AT AT -T AT A
1 AT AT AT AT AT AT A
3502524 AAATTAAGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3502659 original size:32 final size:32
Alignment explanation
Indices: 3502618--3502683 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
3502608 ACTGCTCCTT
3502618 TATGCTATTGACTATGTATATGGGAAGGGATC
1 TATGCTATTGACTATGTATATGGGAAGGGATC
3502650 TATGCTATTGACTATGTATATGGGAAGGGATC
1 TATGCTATTGACTATGTATATGGGAAGGGATC
3502682 TA
1 TA
3502684 CTTACATCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.29, C:0.09, G:0.27, T:0.35
Consensus pattern (32 bp):
TATGCTATTGACTATGTATATGGGAAGGGATC
Found at i:3514566 original size:9 final size:9
Alignment explanation
Indices: 3514544--3514578 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
3514534 AGTACTTATT
*
3514544 TTTTTCTTCT
1 TTTTT-TTCA
3514554 TTTTTTTCA
1 TTTTTTTCA
3514563 TTTTTTTCA
1 TTTTTTTCA
3514572 TTTTTTT
1 TTTTTTT
3514579 AAATTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 19 0.79
10 5 0.21
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:3515734 original size:5 final size:5
Alignment explanation
Indices: 3515724--3515811 Score: 61
Period size: 5 Copynumber: 15.8 Consensus size: 5
3515714 AATATTTAAC
* *
3515724 TAAAA TAAAA TAAAA TAATAAA TAATAA TAATAA TAAAA GAAAA GAAAGA
1 TAAAA TAAAA TAAAA T-A-AAA TAA-AA TAA-AA TAAAA TAAAA TAAA-A
3515774 -AAAA TAATAAA TAAAAA TAAAAA TAAAA TAAAAA TAAA
1 TAAAA T-A-AAA T-AAAA T-AAAA TAAAA T-AAAA TAAA
3515812 GATTGGGTTG
Statistics
Matches: 74, Mismatches: 1, Indels: 16
0.81 0.01 0.18
Matches are distributed among these distances:
4 1 0.01
5 33 0.45
6 30 0.41
7 10 0.14
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:3515758 original size:16 final size:15
Alignment explanation
Indices: 3515732--3515810 Score: 56
Period size: 16 Copynumber: 5.1 Consensus size: 15
3515722 ACTAAAATAA
3515732 AATAAAATAATAAAT
1 AATAAAATAATAAAT
*
3515747 AATAATAATAATAAAAG
1 AATAA-AATAAT-AAAT
* *
3515764 AAAAGAAAGAA-AAAT
1 AATA-AAATAATAAAT
*
3515779 AATAAATAAAAATAAA-
1 AAT-AA-AATAATAAAT
3515795 AATAAAATAA-AAAT
1 AATAAAATAATAAAT
3515809 AA
1 AA
3515811 AGATTGGGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
13 3 0.06
14 6 0.12
15 13 0.26
16 14 0.28
17 13 0.26
18 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (15 bp):
AATAAAATAATAAAT
Found at i:3515790 original size:23 final size:24
Alignment explanation
Indices: 3515747--3515811 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
3515737 AATAATAAAT
3515747 AATAATAATAATAAA-AGAAAAGAAA
1 AATAA-AATAATAAATA-AAAAGAAA
* *
3515772 GA-AAAATAATAAATAAAAATAAA
1 AATAAAATAATAAATAAAAAGAAA
3515795 AATAAAATAA-AAATAAA
1 AATAAAATAATAAATAAA
3515812 GATTGGGTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
23 24 0.69
24 10 0.29
25 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (24 bp):
AATAAAATAATAAATAAAAAGAAA
Found at i:3515793 original size:6 final size:6
Alignment explanation
Indices: 3515725--3515811 Score: 81
Period size: 6 Copynumber: 14.3 Consensus size: 6
3515715 ATATTTAACT
* * * *
3515725 AAAAT- AAAAT- AAAATA ATAAATA ATAATA ATAATA AAAGAAA AGAAAGA
1 AAAATA AAAATA AAAATA A-AAATA AAAATA AAAATA AAA-ATA A-AAATA
3515774 AAAATA ATAAATA AAAATA AAAAT- AAAATA AAAATA AA
1 AAAATA A-AAATA AAAATA AAAATA AAAATA AAAATA AA
3515812 GATTGGGTTG
Statistics
Matches: 71, Mismatches: 5, Indels: 11
0.82 0.06 0.13
Matches are distributed among these distances:
5 15 0.21
6 36 0.51
7 18 0.25
8 2 0.03
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:3524140 original size:35 final size:33
Alignment explanation
Indices: 3524101--3524184 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 33
3524091 AAACCCTCCC
*
3524101 AAAAAAACCTAACCCCCCCAAAAAAAAGAAAAA
1 AAAAAAACCTAACCCACCCAAAAAAAAGAAAAA
** * *
3524134 AGAAAAAGA-AAAACCTAACCCAAAAAAAAGAAGAA
1 A-AAAAA-ACCTAACC-CACCCAAAAAAAAGAAAAA
3524169 AAAAAAACCTAACCCA
1 AAAAAAACCTAACCCA
3524185 AAAAAAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
33 3 0.08
34 18 0.46
35 18 0.46
ACGTcount: A:0.68, C:0.23, G:0.06, T:0.04
Consensus pattern (33 bp):
AAAAAAACCTAACCCACCCAAAAAAAAGAAAAA
Found at i:3524161 original size:29 final size:29
Alignment explanation
Indices: 3524129--3524191 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
3524119 CAAAAAAAAG
*
3524129 AAAAAAGAA-AAAGAAAAACCTAACCCAA
1 AAAAAAGAAGAAAAAAAAACCTAACCCAA
3524157 AAAAAAGAAGAAAAAAAAACCTAACCCAA
1 AAAAAAGAAGAAAAAAAAACCTAACCCAA
3524186 AAAAAA
1 AAAAAA
3524192 AAAACCTAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 9 0.27
29 24 0.73
ACGTcount: A:0.75, C:0.16, G:0.06, T:0.03
Consensus pattern (29 bp):
AAAAAAGAAGAAAAAAAAACCTAACCCAA
Found at i:3524194 original size:35 final size:34
Alignment explanation
Indices: 3524117--3524195 Score: 96
Period size: 29 Copynumber: 2.4 Consensus size: 34
3524107 ACCTAACCCC
*
3524117 CCCAAAAAAAAGAAAAAAGAAAAAGAAAAACCTAA
1 CCCAAAAAAAA-AAAAAAGAAAAAAAAAAACCTAA
*
3524152 CCC---AAAAAAAAGAAG--AAAAAAAAACCTAA
1 CCCAAAAAAAAAAAAAAGAAAAAAAAAAACCTAA
3524181 CCCAAAAAAAAAAAA
1 CCCAAAAAAAAAAAA
3524196 CCTAGCCACC
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
29 16 0.42
31 6 0.16
32 13 0.34
35 3 0.08
ACGTcount: A:0.75, C:0.16, G:0.06, T:0.03
Consensus pattern (34 bp):
CCCAAAAAAAAAAAAAAGAAAAAAAAAAACCTAA
Found at i:3524430 original size:18 final size:17
Alignment explanation
Indices: 3524391--3524429 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3524381 CCTAAAGGTG
*
3524391 ATTTTATCTTCTTTATT
1 ATTTTATCTTATTTATT
3524408 ATTTTACTCTTATTT-TT
1 ATTTTA-TCTTATTTATT
3524425 ATTTT
1 ATTTT
3524430 TTATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTATCTTATTTATT
Found at i:3524958 original size:21 final size:23
Alignment explanation
Indices: 3524932--3524974 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3524922 ATACTTCTTG
*
3524932 TATATT-TC-CATGTATATACTT
1 TATATTGTCTCATGTACATACTT
3524953 TATATTGTCTCATGTACATACT
1 TATATTGTCTCATGTACATACT
3524975 CCGAAATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 2 0.11
23 11 0.58
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (23 bp):
TATATTGTCTCATGTACATACTT
Found at i:3529416 original size:10 final size:10
Alignment explanation
Indices: 3529398--3529436 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
3529388 GACAGTCATG
*
3529398 AAAAGAAAAA
1 AAAACAAAAA
3529408 AAAACAAAAA
1 AAAACAAAAA
3529418 AAAACAAAAA
1 AAAACAAAAA
*
3529428 GAAA-AAAAA
1 AAAACAAAAA
3529437 GGACAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 5 0.19
10 22 0.81
ACGTcount: A:0.90, C:0.05, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAACAAAAA
Found at i:3529433 original size:26 final size:25
Alignment explanation
Indices: 3529398--3529457 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 25
3529388 GACAGTCATG
3529398 AAAAGAAAAAAAA-ACAAAAAAAAACA
1 AAAAGAAAAAAAAGAC-AAAAAAAA-A
*
3529424 AAAAGAAAAAAAAGGACAAGAAAAAA
1 AAAAGAAAAAAAA-GACAAAAAAAAA
3529450 AAAAGAAA
1 AAAAGAAA
3529458 TCAAATGCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 22 0.71
27 7 0.23
28 2 0.06
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (25 bp):
AAAAGAAAAAAAAGACAAAAAAAAA
Found at i:3530531 original size:33 final size:33
Alignment explanation
Indices: 3530489--3530555 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
3530479 TTTCAAGCAT
3530489 TTCGCATTGAAATAATGATTAATAGACTAATCA
1 TTCGCATTGAAATAATGATTAATAGACTAATCA
*
3530522 TTCGCATTGAAATAATGATTAATGGACTAATCA
1 TTCGCATTGAAATAATGATTAATAGACTAATCA
3530555 T
1 T
3530556 ACTTTTATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (33 bp):
TTCGCATTGAAATAATGATTAATAGACTAATCA
Found at i:3531636 original size:116 final size:117
Alignment explanation
Indices: 3531428--3531647 Score: 309
Period size: 116 Copynumber: 1.9 Consensus size: 117
3531418 TCAAGAATCA
*
3531428 ACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAACTCATATTGC
* *
3531493 GAGAAGTGAGTTGAGCCTCGGGGCACGCTGACGTATTTTTAGTTTTAAATTG
66 GAGAAGTGAGTCGAGCCTCAGGGCACGCTGACGTATTTTTAGTTTTAAATTG
* ** * *
3531545 ACTCATATTGCGAGAGGTGAGTT-AAGCCTTTTTATTT-TTGTTTTTTAAAATTAACTCATATTG
1 ACTCATATTGCGAGAGGTGAGTTGAA-CCTTTTAATTTCTACTTTTTCAAAATCAACTCATATTG
* * * *
3531608 CTAGAGGTGAGTCGAGCCTCAGGTCACGCTGAGGTATTTT
65 CGAGAAGTGAGTCGAGCCTCAGGGCACGCTGACGTATTTT
3531648 CAATTTTTGT
Statistics
Matches: 90, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
116 58 0.64
117 32 0.36
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.37
Consensus pattern (117 bp):
ACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAACTCATATTGC
GAGAAGTGAGTCGAGCCTCAGGGCACGCTGACGTATTTTTAGTTTTAAATTG
Found at i:3531818 original size:87 final size:84
Alignment explanation
Indices: 3531667--3532077 Score: 318
Period size: 87 Copynumber: 4.8 Consensus size: 84
3531657 TGTTTTAATT
* * * **
3531667 TCAACTCATATTGCGAGAGGTAAGTTGAGCCTTGAGTTACATA-TCGAGGTATTTTCAAAATCTG
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTG-GTCACACACT-GAGGTATTTTCAATTTCTG
3531731 TTTTTCAAGTTAAGTTTCAAAAA
64 TTTTT-AAGTT-AGTTTCAAAAA
* * * * * *
3531754 TCAACTCTTATTGCGAGAGGTGAGTTGAGCATTGGCTTACGCGCTGAGCTATTTTCAATTTCTGT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGG-TCACACACTGAGGTATTTTCAATTTCTGT
* * * *
3531819 TTTTAATGTCTATTTTTAGAGAG
65 TTTTAA-GT-TAGTTTCA-AAAA
* ** * * * ** **
3531842 TCAATTCATATTGCGA-AAATGAGTTGA-ACTTCAGATCACACACTGAGGTGTTTT-TTTTTCAA
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTT--GGTCACACACTGAGGTATTTTCAATTTCTG
*
3531904 TTTAT-A-TT--TTTCAAAAA
64 TTTTTAAGTTAGTTTCAAAAA
* * *
3531921 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGAGTCACATATTGAGGTATTTTCAAAATT-TG
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTG-GTCACACACTGAGGTATTTTC-AATTTCTG
*
3531985 CTTTTCAAGTTAAGTTTCAAAAA
64 -TTTTTAAGTT-AGTTTCAAAAA
* * * *
3532008 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCACTGAGCTATTTTCAATGTCTAT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGG-TCACACACTGAGGTATTTTCAATTTCTGT
3532073 TTTTA
65 TTTTA
3532078 GAGAGTCAAT
Statistics
Matches: 248, Mismatches: 56, Indels: 41
0.72 0.16 0.12
Matches are distributed among these distances:
79 18 0.07
80 29 0.12
81 3 0.01
82 6 0.02
83 2 0.01
84 2 0.01
85 1 0.00
86 22 0.09
87 146 0.59
88 19 0.08
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (84 bp):
TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGTCACACACTGAGGTATTTTCAATTTCTGTT
TTTAAGTTAGTTTCAAAAA
Found at i:3532840 original size:31 final size:33
Alignment explanation
Indices: 3532782--3532858 Score: 122
Period size: 32 Copynumber: 2.4 Consensus size: 33
3532772 ACCCCCCCAA
3532782 AAAAAAGAAAAAAGAAAAAGAAAAACCTAA-CCC
1 AAAAAA-AAAAAAGAAAAAGAAAAACCTAACCCC
*
3532815 AAAAAAAAAGAAGAAAAA-AAAAACCTAACCCC
1 AAAAAAAAAAAAGAAAAAGAAAAACCTAACCCC
3532847 AAAAAAAAAAAA
1 AAAAAAAAAAAA
3532859 ACCTAGCCAC
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
31 10 0.24
32 25 0.61
33 6 0.15
ACGTcount: A:0.77, C:0.14, G:0.06, T:0.03
Consensus pattern (33 bp):
AAAAAAAAAAAAGAAAAAGAAAAACCTAACCCC
Found at i:3533094 original size:18 final size:17
Alignment explanation
Indices: 3533055--3533093 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3533045 CCTAAAGGTG
*
3533055 ATTTTATCTTCTTTATT
1 ATTTTATCTTATTTATT
3533072 ATTTTACTCTTATTT-TT
1 ATTTTA-TCTTATTTATT
3533089 ATTTT
1 ATTTT
3533094 TTATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTATCTTATTTATT
Found at i:3533622 original size:21 final size:23
Alignment explanation
Indices: 3533596--3533638 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3533586 ATACTTCTTG
*
3533596 TATATT-TC-CATGTATATACTT
1 TATATTGTCTCATGTACATACTT
3533617 TATATTGTCTCATGTACATACT
1 TATATTGTCTCATGTACATACT
3533639 CCGAAATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 2 0.11
23 11 0.58
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (23 bp):
TATATTGTCTCATGTACATACTT
Found at i:3534858 original size:2 final size:2
Alignment explanation
Indices: 3534846--3534876 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
3534836 AATAACATTA
3534846 AT AT CAT 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
3534877 GGCGAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3535761 original size:13 final size:13
Alignment explanation
Indices: 3535743--3535769 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3535733 TCACCTCTCT
3535743 CTTATTTGTACAA
1 CTTATTTGTACAA
3535756 CTTATTTGTACAA
1 CTTATTTGTACAA
3535769 C
1 C
3535770 ATGCATACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (13 bp):
CTTATTTGTACAA
Found at i:3544211 original size:20 final size:20
Alignment explanation
Indices: 3544178--3544232 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
3544168 CGATCTGACT
3544178 CAAATGTATCGATACCCTTAA
1 CAAA-GTATCGATACCCTTAA
* * *
3544199 CAAAGTATTGATACCTTTCA
1 CAAAGTATCGATACCCTTAA
3544219 CAAAAGTATCGATA
1 C-AAAGTATCGATA
3544233 TCATGCCTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (20 bp):
CAAAGTATCGATACCCTTAA
Found at i:3544588 original size:12 final size:12
Alignment explanation
Indices: 3544571--3544596 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3544561 CATACAATTT
3544571 AACAATTTTAAA
1 AACAATTTTAAA
3544583 AACAATTTTAAA
1 AACAATTTTAAA
3544595 AA
1 AA
3544597 TATTATGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (12 bp):
AACAATTTTAAA
Found at i:3546843 original size:13 final size:13
Alignment explanation
Indices: 3546825--3546857 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
3546815 TTAAAAATTT
3546825 ATATAAATACTAA
1 ATATAAATACTAA
3546838 ATATAAATACTAA
1 ATATAAATACTAA
3546851 ATATAAA
1 ATATAAA
3546858 AATAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (13 bp):
ATATAAATACTAA
Found at i:3547181 original size:2 final size:2
Alignment explanation
Indices: 3547174--3547224 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
3547164 AATTGATAAT
*
3547174 TA TA TA TA TC 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
3547216 TA TA TA TA T
1 TA TA TA TA T
3547225 CTAAATGAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3548229 original size:21 final size:22
Alignment explanation
Indices: 3548194--3548246 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
3548184 TTCGAAACTT
* *
3548194 TTTTTTTAGATAATT-ACATTTA
1 TTTTTTTA-AAAATTAACAGTTA
*
3548216 TTTTTTTAAAAATTAAGAGTTA
1 TTTTTTTAAAAATTAACAGTTA
3548238 TTTTTTTAA
1 TTTTTTTAA
3548247 TTGCATGTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (22 bp):
TTTTTTTAAAAATTAACAGTTA
Found at i:3548992 original size:36 final size:36
Alignment explanation
Indices: 3548951--3549021 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
3548941 AAAAGAAGGG
*
3548951 GTGAATTGCATATTAATAATTAAGAAACAAAATATT
1 GTGAATTGCATATTAAAAATTAAGAAACAAAATATT
*
3548987 GTGAATTGCATATTAAAAATTAATAAACAAAATAT
1 GTGAATTGCATATTAAAAATTAAGAAACAAAATAT
3549022 CTTGGTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.32
Consensus pattern (36 bp):
GTGAATTGCATATTAAAAATTAAGAAACAAAATATT
Found at i:3549070 original size:20 final size:20
Alignment explanation
Indices: 3549028--3549071 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
3549018 ATATCTTGGT
* * *
3549028 TTTTTAGTTAAAATTACATA
1 TTTTTAATTAAAATAACAAA
*
3549048 TTTTTAATTAAAATAATAAA
1 TTTTTAATTAAAATAACAAA
3549068 TTTT
1 TTTT
3549072 ACAAGGAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
TTTTTAATTAAAATAACAAA
Found at i:3549995 original size:3 final size:3
Alignment explanation
Indices: 3549989--3550021 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3549979 ATCAACCACC
3549989 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3550022 CACTCTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3552834 original size:28 final size:29
Alignment explanation
Indices: 3552799--3552864 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
3552789 TTTAATTAGT
* * *
3552799 AATGATAAAAGTGTATTTTAAT-TTTAAA
1 AATGATAAAAATGTAATTAAATATTTAAA
*
3552827 AATGATAAAAATTTAATTAAATATTTAAA
1 AATGATAAAAATGTAATTAAATATTTAAA
*
3552856 AATTATAAA
1 AATGATAAA
3552865 GATAAATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (29 bp):
AATGATAAAAATGTAATTAAATATTTAAA
Found at i:3552874 original size:23 final size:24
Alignment explanation
Indices: 3552844--3552888 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3552834 AAAATTTAAT
*
3552844 TAAATATT-TAAAAATTATAAAGA
1 TAAATATTATAAAAATAATAAAGA
*
3552867 TAAATATTATTAAAATAATAAA
1 TAAATATTATAAAAATAATAAA
3552889 ATTATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
TAAATATTATAAAAATAATAAAGA
Found at i:3577625 original size:73 final size:72
Alignment explanation
Indices: 3577418--3577653 Score: 312
Period size: 73 Copynumber: 3.2 Consensus size: 72
3577408 TGATATTTTT
* * * *
3577418 ATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT
1 ATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCTGAGGT
3577483 ATTTTCA
66 ATTTTCA
**
3577490 ATTTCCT-TCTCTAAAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCT
1 ATTT-CTGT-T-T--TCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCT
*
3577554 GAGGTAATTTCA
61 GAGGTATTTTCA
* * *
3577566 ATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGGGCACGCTGAGG
1 ATTTCTGTTT-TCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCTGAGG
3577631 TATTTTCA
65 TATTTTCA
3577639 ATTTCTGCTTTTCAA
1 ATTTCTG-TTTTCAA
3577654 TTTTTGCTTT
Statistics
Matches: 143, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
72 5 0.03
73 70 0.49
74 5 0.03
75 3 0.02
76 60 0.42
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (72 bp):
ATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCTGAGGT
ATTTTCA
Found at i:3577652 original size:14 final size:14
Alignment explanation
Indices: 3577633--3577667 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
3577623 CGCTGAGGTA
3577633 TTTTCAATTTCTGC
1 TTTTCAATTTCTGC
*
3577647 TTTTCAATTTTTGC
1 TTTTCAATTTCTGC
3577661 TTTTCAA
1 TTTTCAA
3577668 AAAAATCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.06, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGC
Found at i:3577714 original size:89 final size:89
Alignment explanation
Indices: 3577579--3577742 Score: 283
Period size: 89 Copynumber: 1.8 Consensus size: 89
3577569 TCTGTTTGTC
* * * *
3577579 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGGGCACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCAAAAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
3577644 TGCTTTTCAATTTTTGCTTTTCAA
66 TGCTTTTCAATTTTTGCTTTTCAA
3577668 AAAAATCAACTCATATTGCAAAAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCAAAAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
*
3577733 TGTTTTTCAA
66 TGCTTTTCAA
3577743 AAAATCAATT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 70 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (89 bp):
AAAAATCAACTCATATTGCAAAAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
TGCTTTTCAATTTTTGCTTTTCAA
Found at i:3577841 original size:238 final size:240
Alignment explanation
Indices: 3577430--3577890 Score: 621
Period size: 238 Copynumber: 1.9 Consensus size: 240
3577420 TTCTGTTTTC
* *
3577430 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
**
3577495 CTTCTCTAAAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCTGAGGTA
66 CTTCTCTAAAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCCAAGGTA
* *** * **
3577560 ATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTC-AG-GGCA
131 ATTTCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCACA
*
3577623 CGCTGAGGTATTTTCAATTTCTGCTTTTCAATTTTTGCTTTTCAA
196 CGCTGAGGTATTTTCAATTCCTGCTTTTCAATTTTTGCTTTTCAA
*
3577668 AAAAATCAACTCATATTGC-A-AAAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAAA--TGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATT
*** * * * * *
3577731 T-CTGT-T-TTTCAAAAAATCAATTCATATTGCTAGAGGTGAGTTGAGCCTCGGGTCACATGCCA
64 TCCT-TCTCTAAAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGG--ACACGCCA
*
3577793 AGGTATTTTCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG
126 AGGTAATTTCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG
*
3577858 TCACACGCTGAGGTATTTTCAATTCCTGTTTTT
191 TCACACGCTGAGGTATTTTCAATTCCTGCTTTT
3577891 TAAAAAAAGT
Statistics
Matches: 193, Mismatches: 23, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
236 42 0.22
237 4 0.02
238 117 0.61
239 2 0.01
240 28 0.15
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (240 bp):
AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
CTTCTCTAAAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCCAAGGTA
ATTTCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCACA
CGCTGAGGTATTTTCAATTCCTGCTTTTCAATTTTTGCTTTTCAA
Found at i:3577931 original size:78 final size:77
Alignment explanation
Indices: 3577647--3577971 Score: 426
Period size: 75 Copynumber: 4.3 Consensus size: 77
3577637 CAATTTCTGC
* * * * *
3577647 TTTTCAATTTTTGCTTTTCAAAAAAATCAACTCATATTGCAAAAGGTGAGTTGAGCCTC-AG-GA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCA
*
3577710 CACGCTGAGGTA
66 CACGCCGAGGTA
* * **
3577722 TTTTCAATTTCTGTTTTTC-AAAAAATCAATTCATATTGCTAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCA
* *
3577786 CATGCCAAGGTA
66 CACGCCGAGGTA
*
3577798 TTTTCAATTTATG--TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCA
*
3577861 CACGCTGAGGTA
66 CACGCCGAGGTA
* * * * *
3577873 TTTTCAATTCCTGTTTTTTAAAAAAAGTCAACTCGTATTGCGAGAGGTGAGTTAAGCCTCAGGTC
1 TTTTCAATTTCTGTTTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTC
3577938 ACACGCCGAGGTA
65 ACACGCCGAGGTA
*
3577951 TTTTCAATTTCTATTTTTCAA
1 TTTTCAATTTCTGTTTTTCAA
3577972 CTTATGTTTC
Statistics
Matches: 216, Mismatches: 28, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
74 40 0.19
75 79 0.37
76 22 0.10
77 10 0.05
78 65 0.30
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (77 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCA
CACGCCGAGGTA
Found at i:3577958 original size:153 final size:150
Alignment explanation
Indices: 3577647--3577960 Score: 459
Period size: 153 Copynumber: 2.1 Consensus size: 150
3577637 CAATTTCTGC
* *
3577647 TTTTCAATTTTTGCTTTTCAAAAAAATCAACTCATATTGCAAAAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTATGC-TTTCAAAAAAATCAACTCATATTGCAAAAGGTGAGTTGAGCCTCAGCACA
* * * * *
3577712 CGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAATCAATTCATATTGCTAGAGGTGAGTTGAGC
65 CGCTGAGGTATTTTCAATTCCTGTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGC
* *
3577777 CTCGGGTCACATGCCAAGGTA
130 CTCAGGTCACACGCCAAGGTA
* *
3577798 TTTTCAATTTATG-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCAC
1 TTTTCAATTTATGCTTTCAAAAAAATCAACTCATATTGCAAAAGGTGAGTTGAGCCTC-AG-CAC
*
3577862 ACGCTGAGGTATTTTCAATTCCTGTTTTTTAAAAAAAGTCAACTCGTATTGCGAGAGGTGAGTTA
64 ACGCTGAGGTATTTTCAATTCCTG-TTTTTAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTA
*
3577927 AGCCTCAGGTCACACGCCGAGGTA
127 AGCCTCAGGTCACACGCCAAGGTA
3577951 TTTTCAATTT
1 TTTTCAATTT
3577961 CTATTTTTCA
Statistics
Matches: 146, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
149 42 0.29
150 2 0.01
151 37 0.25
152 11 0.08
153 54 0.37
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (150 bp):
TTTTCAATTTATGCTTTCAAAAAAATCAACTCATATTGCAAAAGGTGAGTTGAGCCTCAGCACAC
GCTGAGGTATTTTCAATTCCTGTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCC
TCAGGTCACACGCCAAGGTA
Found at i:3578042 original size:29 final size:29
Alignment explanation
Indices: 3578009--3578065 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
3577999 TTGCGAGAAA
*
3578009 TGAGTTGAG-CTTCAGGTCATACGCTGAGG
1 TGAGTTGAGCCTTCA-GTCACACGCTGAGG
*
3578038 TGAGTTGAGCCTTGAGTCACACGCTGAG
1 TGAGTTGAGCCTTCAGTCACACGCTGAG
3578066 AATAAAGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.26
Consensus pattern (29 bp):
TGAGTTGAGCCTTCAGTCACACGCTGAGG
Found at i:3579943 original size:9 final size:9
Alignment explanation
Indices: 3579924--3579958 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
3579914 TTTCTAATAC
3579924 ATATA-TAT
1 ATATATTAT
3579932 ATATATTAT
1 ATATATTAT
*
3579941 ATATTTTAT
1 ATATATTAT
3579950 ATATATTAT
1 ATATATTAT
3579959 GTACATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 5 0.21
9 19 0.79
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATATATTAT
Found at i:3579950 original size:22 final size:22
Alignment explanation
Indices: 3579925--3579969 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
3579915 TTCTAATACA
*
3579925 TATATATATATAT-TATATATTT
1 TATATATAT-TATGTACATATTT
3579947 TATATATATTATGTACATATTT
1 TATATATATTATGTACATATTT
3579969 T
1 T
3579970 TAATGTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
TATATATATTATGTACATATTT
Found at i:3580246 original size:21 final size:21
Alignment explanation
Indices: 3580222--3580382 Score: 95
Period size: 21 Copynumber: 7.6 Consensus size: 21
3580212 TCATATAGTG
3580222 TTATATTTATTATTAT-ACTTA
1 TTAT-TTTATTATTATGACTTA
3580243 TTATTTTCATTATTATGACTTA
1 TTATTTT-ATTATTATGACTTA
* *
3580265 TTATTTTATTATTGTG---TG
1 TTATTTTATTATTATGACTTA
** * *
3580283 TTATTTGGTGTA-CATACATCTTA
1 TTATTTTAT-TATTAT-GA-CTTA
*
3580306 TTATTATTATTATTATTA-TTA
1 TTATT-TTATTATTATGACTTA
*
3580327 TTATTATTATTATTATTA-TTA
1 TTATT-TTATTATTATGACTTA
*
3580348 TTATTATTATTATTATTA-TTA
1 TTATT-TTATTATTATGACTTA
*
3580369 TTATTATTGTTATT
1 TTATT-TTATTATT
3580383 GTTAGTATAT
Statistics
Matches: 117, Mismatches: 13, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
18 9 0.08
19 2 0.02
20 3 0.03
21 78 0.67
22 12 0.10
23 9 0.08
24 4 0.03
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.63
Consensus pattern (21 bp):
TTATTTTATTATTATGACTTA
Found at i:3580311 original size:3 final size:3
Alignment explanation
Indices: 3580303--3580382 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
3580293 TACATACATC
3580303 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3580351 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3580383 GTTAGTATAT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3580428 original size:21 final size:21
Alignment explanation
Indices: 3580388--3580428 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3580378 TTATTGTTAG
* *
3580388 TATATATGTATATATCTTTAA
1 TATATATCTATATATATTTAA
*
3580409 TATATATCTGTATATATTTA
1 TATATATCTATATATATTTA
3580429 TGCAATACTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (21 bp):
TATATATCTATATATATTTAA
Found at i:3580664 original size:19 final size:18
Alignment explanation
Indices: 3580636--3580672 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
3580626 CATTCGTTTG
*
3580636 ATATTATTATGTGTATAT
1 ATATTATTATGTATATAT
3580654 ATATATATTATGTATATAT
1 ATAT-TATTATGTATATAT
3580673 TTGGTACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (18 bp):
ATATTATTATGTATATAT
Found at i:3584845 original size:20 final size:20
Alignment explanation
Indices: 3584820--3584857 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3584810 TTGTTATTTT
3584820 TTGAAAGTTGAGTGACTGAA
1 TTGAAAGTTGAGTGACTGAA
3584840 TTGAAAGTTGAGTGACTG
1 TTGAAAGTTGAGTGACTG
3584858 TTTTGTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.32
Consensus pattern (20 bp):
TTGAAAGTTGAGTGACTGAA
Found at i:3587015 original size:6 final size:6
Alignment explanation
Indices: 3587004--3587031 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3586994 TAATGGGGTG
3587004 CATATA CATATA CATATA CATATA CATA
1 CATATA CATATA CATATA CATATA CATA
3587032 GAGAGTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (6 bp):
CATATA
Found at i:3591250 original size:2 final size:2
Alignment explanation
Indices: 3591243--3591279 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3591233 ATGTAGAATA
3591243 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3591280 AAGTAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3592240 original size:23 final size:21
Alignment explanation
Indices: 3592202--3592244 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
3592192 TCAAAACATA
3592202 AATATTCAAACATACAATCTTC
1 AATATTCAAACATAC-ATCTTC
3592224 AATATTTCAAA-ACTACATCTT
1 AATA-TTCAAACA-TACATCTT
3592245 TCAACCCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (21 bp):
AATATTCAAACATACATCTTC
Found at i:3592686 original size:35 final size:35
Alignment explanation
Indices: 3592636--3592852 Score: 174
Period size: 35 Copynumber: 6.3 Consensus size: 35
3592626 AGTGCCACGA
**
3592636 TTCACAACTCAGTATGGTTAATACCATACCTACGT
1 TTCACAACTCAGTATGGGAAATACCATACCTACGT
**
3592671 TTCACAACTTGGTATGGGAAATACCATACCTACGT
1 TTCACAACTCAGTATGGGAAATACCATACCTACGT
* * * *
3592706 ATT-ATAGCTCAATAT-GGAAATACCATACCTATGT
1 -TTCACAACTCAGTATGGGAAATACCATACCTACGT
* * * *
3592740 ATCATAGCTCAATAT-GGATAATACCATACCTACGT
1 TTCACAACTCAGTATGGGA-AATACCATACCTACGT
* * * *
3592775 ATCATAGCTCAGTAT-GAAAATACCATACCTACGT
1 TTCACAACTCAGTATGGGAAATACCATACCTACGT
* * * *
3592809 ATCATAGCTCAGTAT-GGATAATACCATACTTACGT
1 TTCACAACTCAGTATGGGA-AATACCATACCTACGT
* *
3592844 GTCATAACT
1 TTCACAACT
3592853 TTGCCATGGA
Statistics
Matches: 160, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
33 1 0.01
34 66 0.41
35 91 0.57
36 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (35 bp):
TTCACAACTCAGTATGGGAAATACCATACCTACGT
Found at i:3592730 original size:34 final size:34
Alignment explanation
Indices: 3592655--3592849 Score: 246
Period size: 35 Copynumber: 5.6 Consensus size: 34
3592645 CAGTATGGTT
* * * ***
3592655 AATACCATACCTACGTTTCACAACTTGGTATGGGA
1 AATACCATACCTACGTATCATAGCTCAATAT-GGA
*
3592690 AATACCATACCTACGTATTATAGCTCAATATGGA
1 AATACCATACCTACGTATCATAGCTCAATATGGA
*
3592724 AATACCATACCTATGTATCATAGCTCAATATGGA
1 AATACCATACCTACGTATCATAGCTCAATATGGA
* *
3592758 TAATACCATACCTACGTATCATAGCTCAGTATGAA
1 -AATACCATACCTACGTATCATAGCTCAATATGGA
*
3592793 AATACCATACCTACGTATCATAGCTCAGTATGGA
1 AATACCATACCTACGTATCATAGCTCAATATGGA
* *
3592827 TAATACCATACTTACGTGTCATA
1 -AATACCATACCTACGTATCATA
3592850 ACTTTGCCAT
Statistics
Matches: 143, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
34 68 0.48
35 75 0.52
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (34 bp):
AATACCATACCTACGTATCATAGCTCAATATGGA
Found at i:3592766 original size:69 final size:69
Alignment explanation
Indices: 3592655--3592849 Score: 257
Period size: 69 Copynumber: 2.8 Consensus size: 69
3592645 CAGTATGGTT
* * * *** *
3592655 AATACCATACCTACGTTTCACAACTTGGTATGGGA-AATACCATACCTACGTATTATAGCTCAAT
1 AATACCATACCTACGTATCATAGCTCAATAT-GGATAATACCATACCTACGTATCATAGCTCAAT
*
3592719 ATGGA
65 ATGAA
* *
3592724 AATACCATACCTATGTATCATAGCTCAATATGGATAATACCATACCTACGTATCATAGCTCAGTA
1 AATACCATACCTACGTATCATAGCTCAATATGGATAATACCATACCTACGTATCATAGCTCAATA
3592789 TGAA
66 TGAA
* * *
3592793 AATACCATACCTACGTATCATAGCTCAGTATGGATAATACCATACTTACGTGTCATA
1 AATACCATACCTACGTATCATAGCTCAATATGGATAATACCATACCTACGTATCATA
3592850 ACTTTGCCAT
Statistics
Matches: 111, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
68 3 0.03
69 108 0.97
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (69 bp):
AATACCATACCTACGTATCATAGCTCAATATGGATAATACCATACCTACGTATCATAGCTCAATA
TGAA
Found at i:3594886 original size:29 final size:29
Alignment explanation
Indices: 3594847--3594905 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3594837 TTCTTGAAGT
3594847 TTTTAATTTTAGCCTTTAAAAAAGTTGTC
1 TTTTAATTTTAGCCTTTAAAAAAGTTGTC
3594876 TTTTAATTTTAGCCTTTAAAAAAGTTGTC
1 TTTTAATTTTAGCCTTTAAAAAAGTTGTC
3594905 T
1 T
3594906 GTCTTTCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (29 bp):
TTTTAATTTTAGCCTTTAAAAAAGTTGTC
Found at i:3602119 original size:5 final size:5
Alignment explanation
Indices: 3602080--3602118 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
3602070 TTTAACCTGT
* *
3602080 CAATC CAATC CAATC CAATC CAATC CAATT CAATT CAAT
1 CAATC CAATC CAATC CAATC CAATC CAATC CAATC CAAT
3602119 TAATCTTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26
Consensus pattern (5 bp):
CAATC
Found at i:3602119 original size:10 final size:10
Alignment explanation
Indices: 3602079--3602123 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
3602069 ATTTAACCTG
3602079 TCAATCCAAT
1 TCAATCCAAT
*
3602089 CCAATCCAAT
1 TCAATCCAAT
*
3602099 CCAATCCAAT
1 TCAATCCAAT
*
3602109 TCAATTCAAT
1 TCAATCCAAT
3602119 T-AATC
1 TCAATC
3602124 TTTCTTTAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
9 3 0.10
10 28 0.90
ACGTcount: A:0.40, C:0.31, G:0.00, T:0.29
Consensus pattern (10 bp):
TCAATCCAAT
Found at i:3602735 original size:16 final size:18
Alignment explanation
Indices: 3602696--3602736 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3602686 AAAACATGTT
*
3602696 TTTAATTTAATGATATGA
1 TTTAAATTAATGATATGA
3602714 TCTTAAATTAAT-ATATG-
1 T-TTAAATTAATGATATGA
3602731 TTTAAA
1 TTTAAA
3602737 AAATTTCACT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 1 0.05
18 6 0.29
19 9 0.43
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (18 bp):
TTTAAATTAATGATATGA
Found at i:3605527 original size:14 final size:14
Alignment explanation
Indices: 3605508--3605541 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3605498 CTAAACCCGA
*
3605508 AGCCCAACTACCCT
1 AGCCCAACTACCCC
3605522 AGCCCAACTACCCC
1 AGCCCAACTACCCC
3605536 AGCCCA
1 AGCCCA
3605542 TCTGCAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.53, G:0.09, T:0.09
Consensus pattern (14 bp):
AGCCCAACTACCCC
Found at i:3606131 original size:22 final size:23
Alignment explanation
Indices: 3606106--3606148 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3606096 CCGGGGCTCC
3606106 CTCCCTCTC-CCCTTTCTTTTCT
1 CTCCCTCTCTCCCTTTCTTTTCT
* *
3606128 CTCCCTTTCTCTCTTTCTTTT
1 CTCCCTCTCTCCCTTTCTTTT
3606149 TTTTCTTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (23 bp):
CTCCCTCTCTCCCTTTCTTTTCT
Found at i:3606589 original size:3 final size:3
Alignment explanation
Indices: 3606583--3606643 Score: 86
Period size: 3 Copynumber: 20.0 Consensus size: 3
3606573 TTTTTCTTAT
* *
3606583 TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3606631 TTA CTA TGTA TTA
1 TTA TTA T-TA TTA
3606644 GTATACGTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3606859 original size:26 final size:29
Alignment explanation
Indices: 3606828--3606886 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
3606818 TTTAATATAG
3606828 TATTAT-CT-TTTT-ACTATTA-TATTTAT
1 TATTATCCTATTTTCACTATTATTA-TTAT
*
3606854 TATTATCCTATTTTCACTGTTATTATTAT
1 TATTATCCTATTTTCACTATTATTATTAT
3606883 TATT
1 TATT
3606887 TTCATCATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 6 0.21
27 2 0.07
28 4 0.14
29 14 0.50
30 2 0.07
ACGTcount: A:0.25, C:0.10, G:0.02, T:0.63
Consensus pattern (29 bp):
TATTATCCTATTTTCACTATTATTATTAT
Found at i:3606897 original size:21 final size:22
Alignment explanation
Indices: 3606850--3606900 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
3606840 ACTATTATAT
*
3606850 TTATTATTATCCTATTTTCACTG
1 TTATTATTAT-CTATTTTCACTA
3606873 TTATTATTAT-TATTTTCA-TCA
1 TTATTATTATCTATTTTCACT-A
3606894 TTATTAT
1 TTATTAT
3606901 ACATATATGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 15 0.58
23 10 0.38
ACGTcount: A:0.25, C:0.12, G:0.02, T:0.61
Consensus pattern (22 bp):
TTATTATTATCTATTTTCACTA
Found at i:3619615 original size:71 final size:71
Alignment explanation
Indices: 3619494--3619627 Score: 198
Period size: 71 Copynumber: 1.9 Consensus size: 71
3619484 GTTTTCCAAG
* * *
3619494 AAAATCAGCTCATATTGCGAAAGGTGAGTTGAGCCTTAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
3619559 GTTTCA
66 GTTTCA
* * *
3619565 AAAATCAACTCATATTGCGAGAA-GTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGA-AAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
3619628 CTGCTTTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
71 54 0.96
72 2 0.04
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
GTTTCA
Found at i:3619775 original size:71 final size:71
Alignment explanation
Indices: 3619654--3619787 Score: 214
Period size: 71 Copynumber: 1.9 Consensus size: 71
3619644 GTTTTCCAAG
* * *
3619654 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
3619719 GTTTCA
66 GTTTCA
* * *
3619725 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
3619788 CTGCTTTTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
GTTTCA
Found at i:3619896 original size:159 final size:160
Alignment explanation
Indices: 3619395--3619945 Score: 1059
Period size: 160 Copynumber: 3.5 Consensus size: 160
3619385 TGTCCTCCAG
3619395 TTATGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATT
1 TTATGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATT
*
3619460 TTCAATTTCTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAAAGGTGAGTTG
66 TTCAATTTCTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTG
*
3619525 AGCCTTAAGACACGTTGAGGTAATTTCAAT
131 AGCCTCAAGACACGTTGAGGTAATTTCAAT
3619555 TTATGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATT
1 TTATGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATT
3619620 TTCAATTTCTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTG
66 TTCAATTTCTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTG
3619685 AGCCTCAAGACACGTTGAGGTAATTTCAAT
131 AGCCTCAAGACACGTTGAGGTAATTTCAAT
3619715 TTATGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATT
1 TTATGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATT
3619780 TTCAATTTCTGC-TTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTG
66 TTCAATTTCTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTG
3619844 AGCCTCAAGACACGTTGAGGTAATTTCAAT
131 AGCCTCAAGACACGTTGAGGTAATTTCAAT
* *
3619874 TTATGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCAGGGCACGCTGAGGTAAT
1 TTATGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATT
3619939 TTCAATT
66 TTCAATT
3619946 CCTATTAAAT
Statistics
Matches: 387, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
159 152 0.39
160 235 0.61
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (160 bp):
TTATGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATT
TTCAATTTCTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTG
AGCCTCAAGACACGTTGAGGTAATTTCAAT
Found at i:3619934 original size:71 final size:72
Alignment explanation
Indices: 3619813--3619993 Score: 240
Period size: 71 Copynumber: 2.5 Consensus size: 72
3619803 GTTTTCCAAG
* * *
3619813 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATT-TA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGCTGAGGTAATTTCAATTCTA
*
3619877 TGT-TTCA
66 T-TAATCA
* * *
3619884 AAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCAGGGCACGCTGAGGTAATTTCAATTCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGCTGAGGTAATTTCAATT-CT
*
3619949 ATTAAATCT
65 ATT-AATCA
*
3619958 AAAATCAACTCATATTGCGAGAGGTGGGTTGAACCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCT
3619994 TTTAATTTCT
Statistics
Matches: 96, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
71 56 0.58
72 1 0.01
73 3 0.03
74 36 0.38
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Consensus pattern (72 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGCTGAGGTAATTTCAATTCTA
TTAATCA
Found at i:3620150 original size:56 final size:54
Alignment explanation
Indices: 3619958--3620158 Score: 255
Period size: 54 Copynumber: 3.7 Consensus size: 54
3619948 TATTAAATCT
* **
3619958 AAAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTC-
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTT-TTGTTTTTCA
* * *
3620012 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTGTTGTTTTTTA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTTTGTTTTTCA
*
3620066 AAAAGCAACTCATATTGCGAGAGGTGAGTT-ATACCTTTTAATTTTTGTTTTTCAA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGA-ACCTTTTAATTTTTGTTTTTC-A
* *
3620121 AAGAATCAA-TCCATATTGCGAGAAGTGAGTTGAGCCTT
1 AA-AATCAACT-CATATTGCGAGAGGTGAGTTGAACCTT
3620159 AGGTATTTTT
Statistics
Matches: 128, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
53 7 0.05
54 88 0.69
55 4 0.03
56 28 0.22
57 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (54 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTTTGTTTTTCA
Found at i:3620964 original size:14 final size:14
Alignment explanation
Indices: 3620945--3620978 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
3620935 CTAAACCCGA
3620945 AGCCCAACTACCCC
1 AGCCCAACTACCCC
3620959 AGCCCAACTACCCC
1 AGCCCAACTACCCC
3620973 AGCCCA
1 AGCCCA
3620979 TTTGCAACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.29, C:0.56, G:0.09, T:0.06
Consensus pattern (14 bp):
AGCCCAACTACCCC
Found at i:3621578 original size:14 final size:16
Alignment explanation
Indices: 3621547--3621576 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3621537 GGCTCCCTCC
3621547 CTCTCCCCTTTCTTTT
1 CTCTCCCCTTTCTTTT
3621563 CTCT-CCCTTTCTTT
1 CTCTCCCCTTTCTTT
3621577 CTTTCTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (16 bp):
CTCTCCCCTTTCTTTT
Found at i:3622026 original size:3 final size:3
Alignment explanation
Indices: 3622020--3622080 Score: 86
Period size: 3 Copynumber: 20.0 Consensus size: 3
3622010 TTTTTCTTAT
* *
3622020 TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3622068 TTA CTA TGTA TTA
1 TTA TTA T-TA TTA
3622081 GTATACGTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3622297 original size:26 final size:29
Alignment explanation
Indices: 3622266--3622324 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
3622256 TTTAATATAG
3622266 TATTAT-CT-TTTT-ACTATTA-TATTTAT
1 TATTATCCTATTTTCACTATTATTA-TTAT
*
3622292 TATTATCCTATTTTCACTGTTATTATTAT
1 TATTATCCTATTTTCACTATTATTATTAT
3622321 TATT
1 TATT
3622325 TTCATCATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 6 0.21
27 2 0.07
28 4 0.14
29 14 0.50
30 2 0.07
ACGTcount: A:0.25, C:0.10, G:0.02, T:0.63
Consensus pattern (29 bp):
TATTATCCTATTTTCACTATTATTATTAT
Found at i:3622335 original size:21 final size:22
Alignment explanation
Indices: 3622288--3622338 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
3622278 ACTATTATAT
*
3622288 TTATTATTATCCTATTTTCACTG
1 TTATTATTAT-CTATTTTCACTA
3622311 TTATTATTAT-TATTTTCA-TCA
1 TTATTATTATCTATTTTCACT-A
3622332 TTATTAT
1 TTATTAT
3622339 ACATATATGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 15 0.58
23 10 0.38
ACGTcount: A:0.25, C:0.12, G:0.02, T:0.61
Consensus pattern (22 bp):
TTATTATTATCTATTTTCACTA
Found at i:3624118 original size:17 final size:17
Alignment explanation
Indices: 3624096--3624130 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3624086 ATTCTTACTC
*
3624096 CTATTATTAGTGCATGT
1 CTATTATTAGTCCATGT
3624113 CTATTATTAGTCCATGT
1 CTATTATTAGTCCATGT
3624130 C
1 C
3624131 ATTGAACCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (17 bp):
CTATTATTAGTCCATGT
Found at i:3625276 original size:17 final size:17
Alignment explanation
Indices: 3625244--3625277 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3625234 ATTAAATCTA
**
3625244 TAAATATGATTTTATTT
1 TAAATATGATAATATTT
3625261 TAAATATGATAATATTT
1 TAAATATGATAATATTT
3625278 ATTTTATTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TAAATATGATAATATTT
Found at i:3626522 original size:88 final size:88
Alignment explanation
Indices: 3626368--3626547 Score: 342
Period size: 88 Copynumber: 2.0 Consensus size: 88
3626358 TCTCCGCTGT
3626368 ATGCAAGTTACGACTAAGAAACAAAGTTTTCATTGCATAATGAACTCCGGCCTAGTCCCTTCTCG
1 ATGCAAGTTACGACTAAGAAACAAAGTTTTCATTGCATAATGAACTCCGGCCTAGTCCCTTCTCG
3626433 AACTCTTACAATTCCTAAGTTAC
66 AACTCTTACAATTCCTAAGTTAC
* *
3626456 ATGCAAGTTACGACTAAGAAACAAAGTTTTCATTGCATAATGAACTCTGGCCTAGTCCCTTTTCG
1 ATGCAAGTTACGACTAAGAAACAAAGTTTTCATTGCATAATGAACTCCGGCCTAGTCCCTTCTCG
3626521 AACTCTTACAATTCCTAAGTTAC
66 AACTCTTACAATTCCTAAGTTAC
3626544 ATGC
1 ATGC
3626548 TGTCGAAACC
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 90 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (88 bp):
ATGCAAGTTACGACTAAGAAACAAAGTTTTCATTGCATAATGAACTCCGGCCTAGTCCCTTCTCG
AACTCTTACAATTCCTAAGTTAC
Found at i:3628671 original size:4 final size:4
Alignment explanation
Indices: 3628664--3628690 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3628654 CAAAATAAAT
3628664 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
3628691 ACTTAATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:3629896 original size:18 final size:18
Alignment explanation
Indices: 3629873--3629915 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3629863 GATATCTGGA
3629873 TTTTTATAATAT-TTATTG
1 TTTTTAT-ATATCTTATTG
* *
3629891 TTTTTATTTATCTTTTTG
1 TTTTTATATATCTTATTG
3629909 TTTTTAT
1 TTTTTAT
3629916 TCGGGCCGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (18 bp):
TTTTTATATATCTTATTG
Found at i:3634153 original size:16 final size:16
Alignment explanation
Indices: 3634134--3634185 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
3634124 TCCTTATTAT
3634134 ATAAAATCTAATTAGC
1 ATAAAATCTAATTAGC
*
3634150 ATAAAAATTCTTA-TA--
1 AT-AAAA-TCTAATTAGC
3634165 ATAAAATCTAATTAGC
1 ATAAAATCTAATTAGC
3634181 ATAAA
1 ATAAA
3634186 TTATAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 4 0.14
14 6 0.21
15 2 0.07
16 7 0.24
17 6 0.21
18 4 0.14
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (16 bp):
ATAAAATCTAATTAGC
Found at i:3634196 original size:31 final size:30
Alignment explanation
Indices: 3634127--3634198 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 30
3634117 AACCCAATCC
3634127 TTATTAT-ATAAAATCTAATTAGCATAAAAA
1 TTATTATAATAAAATCTAATTAGCAT-AAAA
*
3634157 TTCTTATAATAAAATCTAATTAGCAT-AAA
1 TTATTATAATAAAATCTAATTAGCATAAAA
3634186 TTATAATATAATA
1 TTAT--TATAATA
3634199 TACTATAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
29 6 0.16
30 6 0.16
31 25 0.68
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (30 bp):
TTATTATAATAAAATCTAATTAGCATAAAA
Found at i:3637209 original size:46 final size:46
Alignment explanation
Indices: 3636989--3637310 Score: 144
Period size: 46 Copynumber: 6.8 Consensus size: 46
3636979 GTCATTTGTG
* * * *
3636989 TGAGTTAGTGTAAGA-CACGTTTGGGACAT-GCATCGGCTAT-ATTA
1 TGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTATGA-GA
* *
3637033 TGAGAGCCAGTGTAAGACCATGCCTGGGACATGGCATCGGC-ATTGAGA
1 T--GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTA-TGAGA
* * ** * * *
3637081 CGAGTGTCAGTGTAA-AATATGTCTGGAACAT-GCATCGGCCT-CGGGA
1 TGAG-CT-AGTGTAAGACCATGTCTGGGACATGGCATCGG-CTATGAGA
* * * * * *
3637127 CGTAAGCCAATGTAAGA-CTTGTCTAGGACAT-ACATCGGCTATGAGA
1 --TGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTATGAGA
* * *
3637173 TGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACGGATA
1 TGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTA-TGAGA
* * * *
3637219 TACGAAAGTTAGTGTAAGACCATGTCTGGGACATGACATTGGCCTCGTTGATGA
1 T--G--AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CT--ATGA-GA
* * *
3637273 T-AGCTAGTGTAAGACCTTGTATGGGATATGGCATCGGC
1 TGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
3637311 ACACTGACCC
Statistics
Matches: 203, Mismatches: 49, Indels: 48
0.68 0.16 0.16
Matches are distributed among these distances:
44 12 0.06
45 15 0.07
46 61 0.30
47 26 0.13
48 21 0.10
49 31 0.15
50 32 0.16
51 1 0.00
53 2 0.01
54 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (46 bp):
TGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTATGAGA
Found at i:3640639 original size:7 final size:7
Alignment explanation
Indices: 3640627--3640674 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
3640617 GATTCATTCA
3640627 ATTTTTT
1 ATTTTTT
3640634 ATTTTTT
1 ATTTTTT
3640641 ATTTTTT
1 ATTTTTT
**
3640648 A-TTACT
1 ATTTTTT
3640654 A-TTTTT
1 ATTTTTT
3640660 ATTTATTT
1 ATTT-TTT
3640668 ATTTTTT
1 ATTTTTT
3640675 CTTCTCTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
6 8 0.23
7 20 0.57
8 7 0.20
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (7 bp):
ATTTTTT
Found at i:3640861 original size:3 final size:3
Alignment explanation
Indices: 3640853--3640941 Score: 99
Period size: 3 Copynumber: 29.0 Consensus size: 3
3640843 CTACTGCACG
*
3640853 TAT TAT TAT TAT TAT TAG TAT T-T GTAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
* * * *
3640898 TAT TAT TCAT CTTT TAT TAT TAT CAT TAT TAC TAT TAT CAT TAT
1 TAT TAT T-AT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3640942 ATTTATACTT
Statistics
Matches: 72, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
2 1 0.01
3 66 0.92
4 4 0.06
5 1 0.01
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:3641252 original size:26 final size:24
Alignment explanation
Indices: 3641194--3641261 Score: 59
Period size: 28 Copynumber: 2.7 Consensus size: 24
3641184 TTCCTTTTTA
3641194 TATTTA-TTTACTTGTTACTTCAT
1 TATTTATTTTACTTGTTACTTCAT
*
3641217 TACTAATTATTTTAACTTGTTATTATCAT
1 TA-T--TTATTTT-ACTTGTTACT-TCAT
3641246 TATTTATTGTTA-TTGT
1 TATTTATT-TTACTTGT
3641262 AAATATATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
23 2 0.05
24 1 0.03
25 4 0.11
26 9 0.24
27 5 0.14
28 10 0.27
29 6 0.16
ACGTcount: A:0.25, C:0.09, G:0.06, T:0.60
Consensus pattern (24 bp):
TATTTATTTTACTTGTTACTTCAT
Found at i:3641302 original size:9 final size:9
Alignment explanation
Indices: 3641290--3641419 Score: 65
Period size: 9 Copynumber: 15.9 Consensus size: 9
3641280 CTTATTTAAC
3641290 CTATTATTA
1 CTATTATTA
*
3641299 CTATTGTT-
1 CTATTATTA
*
3641307 -T-TTTTTA
1 CTATTATTA
3641314 CT-TTATTA
1 CTATTATTA
3641322 -T-T-ATTA
1 CTATTATTA
*
3641328 CTATTATCA
1 CTATTATTA
*
3641337 TTATTCATTA
1 CTATT-ATTA
3641347 CT-TTATTA
1 CTATTATTA
*
3641355 TTATTATTA
1 CTATTATTA
*
3641364 CTACTATTA
1 CTATTATTA
3641373 --A--ATTA
1 CTATTATTA
*
3641378 GTATTATTA
1 CTATTATTA
3641387 -TATT-TTA
1 CTATTATTA
3641394 CTATTATTA
1 CTATTATTA
*
3641403 -TTTGTATTA
1 CTAT-TATTA
3641412 CTATTATT
1 CTATTATT
3641420 TTAATCATTT
Statistics
Matches: 94, Mismatches: 12, Indels: 30
0.69 0.09 0.22
Matches are distributed among these distances:
5 4 0.04
6 8 0.09
7 9 0.10
8 22 0.23
9 45 0.48
10 6 0.06
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.60
Consensus pattern (9 bp):
CTATTATTA
Found at i:3641322 original size:3 final size:3
Alignment explanation
Indices: 3641316--3641419 Score: 74
Period size: 3 Copynumber: 35.7 Consensus size: 3
3641306 TTTTTTTACT
* * *
3641316 TTA TTA TTA TTA CTA TTA TCA TTA TTCA TTA CT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
* * * * *
3641361 TTA CTA CTA TTA -AA TTA GTA TTA TTA -TA TT- TTA CTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3641405 TGTA TTA CTA TTA TT
1 T-TA TTA TTA TTA TT
3641420 TTAATCATTT
Statistics
Matches: 78, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
2 7 0.09
3 67 0.86
4 4 0.05
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:3641399 original size:36 final size:38
Alignment explanation
Indices: 3641310--3641399 Score: 96
Period size: 39 Copynumber: 2.4 Consensus size: 38
3641300 TATTGTTTTT
* * * *
3641310 TTTACTTTATTATTATTACTATTATCATTATTCATTAC
1 TTTATTTTATTATTACTACTATTATAATTAGTCATTAC
3641348 TTTATTATTATTATTACTACTATTA-AATTAGT-ATTA-
1 TTTATT-TTATTATTACTACTATTATAATTAGTCATTAC
*
3641384 TTATATTTTACTATTA
1 TT-TATTTTATTATTA
3641400 TTATTTGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
36 10 0.22
37 8 0.18
38 10 0.22
39 17 0.38
ACGTcount: A:0.32, C:0.09, G:0.01, T:0.58
Consensus pattern (38 bp):
TTTATTTTATTATTACTACTATTATAATTAGTCATTAC
Found at i:3646333 original size:10 final size:10
Alignment explanation
Indices: 3646314--3646345 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
3646304 ATCAAATTCT
3646314 AAAAAA-AAA
1 AAAAAAGAAA
3646323 AAAAAAGAAA
1 AAAAAAGAAA
3646333 AAAAAAGAAA
1 AAAAAAGAAA
3646343 AAA
1 AAA
3646346 GGGTGCCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 6 0.27
10 16 0.73
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:3646336 original size:17 final size:17
Alignment explanation
Indices: 3646314--3646346 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3646304 ATCAAATTCT
3646314 AAAAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAAGA
*
3646331 AAAAAAAAGAAAAAAG
1 AAAAAAAAAAAAAAAG
3646347 GGTGCCAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAAGA
Found at i:3646453 original size:6 final size:6
Alignment explanation
Indices: 3646436--3646477 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
3646426 GGCACTATAT
*
3646436 GGCAAA GCCAAA GGCAAA GGCAAA GGCAAA GGCAAA GGCAAA
1 GGCAAA GGCAAA GGCAAA GGCAAA GGCAAA GGCAAA GGCAAA
3646478 AAAAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.50, C:0.19, G:0.31, T:0.00
Consensus pattern (6 bp):
GGCAAA
Found at i:3648244 original size:67 final size:66
Alignment explanation
Indices: 3648133--3648326 Score: 266
Period size: 67 Copynumber: 3.0 Consensus size: 66
3648123 ATTCATATGT
* *
3648133 CATTCATAACACATCTAATTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGAC
1 CATTCATAACATATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGAC
3648198 A
66 A
* *
3648199 CATTCATAACAATATCTAGTTAGGAGCATTTGATTCATTTTGATCATGGCATCCTAATTATTTGA
1 CATTCATAAC-ATATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGA
3648264 CA
65 CA
* ** * * * *
3648266 TAAGCATTACAT-T-TAGTTAGGAACATTTGATTCATTTCAATCATAGCGTCCTAATTATTTG
1 CATTCATAACATATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTG
3648327 GCATAAACAT
Statistics
Matches: 114, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
64 43 0.38
65 1 0.01
66 12 0.11
67 58 0.51
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (66 bp):
CATTCATAACATATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGAC
A
Found at i:3648443 original size:42 final size:43
Alignment explanation
Indices: 3648398--3648648 Score: 158
Period size: 43 Copynumber: 5.9 Consensus size: 43
3648388 GGAATCGGTG
*
3648398 AATTCAAAG-CCTTATCTCCCTAAGCAGTAGGGTAACAGGCTG
1 AATTCAAAGACCTTATCTCCCTAAGCAGTAGGGTAACAGGCTA
* * * * **
3648440 AATT-ACAGATCTTGTCTCCCTAAGCAGTAGTGG-AGCA-AATCA
1 AATTCAAAGACCTTATCTCCCTAAGCAGTAG-GGTAACAGGCT-A
* * ** ** * * *
3648482 AAGAT-GAAGGGCTT-TAACCCTAAGCAGTAGGATAACAAGCCA
1 AA-TTCAAAGACCTTATCTCCCTAAGCAGTAGGGTAACAGGCTA
* * * * *
3648524 AATTTACAGACCTTAAAC-CCCTAAGCAGTAGGGTAACAGGTTG
1 AATTCAAAGACCTT-ATCTCCCTAAGCAGTAGGGTAACAGGCTA
3648567 AATTCACAAG-CCTTATCTCCCTAAGCAGTAGGGTAACAGGCTA
1 AATTCA-AAGACCTTATCTCCCTAAGCAGTAGGGTAACAGGCTA
* * * * * *
3648610 AATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAG
1 AATTCAAAGACCTTATCTCCCTAAGCAGTAGGGTAACAG
3648649 ATCGAAGGCG
Statistics
Matches: 155, Mismatches: 42, Indels: 23
0.70 0.19 0.10
Matches are distributed among these distances:
41 6 0.04
42 57 0.37
43 90 0.58
44 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (43 bp):
AATTCAAAGACCTTATCTCCCTAAGCAGTAGGGTAACAGGCTA
Found at i:3648717 original size:44 final size:44
Alignment explanation
Indices: 3648495--3649239 Score: 320
Period size: 44 Copynumber: 17.0 Consensus size: 44
3648485 ATGAAGGGCT
* * * *
3648495 TTAA-CCCTAAGCAGTAGGATAACAAGC-CAA-ATTTACAGACC
1 TTAACCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATC
* * *
3648536 TTAAACCCCTAAGCAGTAGGGTAACAGGTTG-A-ATTCACA-AGCC
1 TT-AACCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGA-TC
*
3648579 TTATCTCCCTAAGCAGTAGGGTAACAGGCT-AA-ATTTACAGATC
1 TTAAC-CCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATC
* * *** ** *
3648622 TTAACCCCCTAAGCAGTAGGGAAACA-GATCGAAG-GCGATGGACC
1 TTAA-CCCCTAAGCAGTAGGGTAACAGGCT-GAAGATTTACAGATC
3648666 TTAAACCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATC
1 TT-AACCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATC
* * * * *
3648711 TTAACCCCCTAAGTAGTAGGGAAACA-GATCGAAGATGATT--GGCT-
1 TTAA-CCCCTAAGCAGTAGGGTAACAGGCT-GAAGAT--TTACAGATC
* *
3648755 TTAACCCCCTAATCAGTAGGGTAGCAGGCTGAAGATTTACAGATC
1 TTAA-CCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATC
* * * * * * * * **
3648800 TTGACCCCCTAAGTAGTAAGGAAACA-GATCAAAGA-TGA-TGGCC
1 TT-AACCCCTAAGCAGTAGGGTAACAGGCT-GAAGATTTACAGATC
* * * * * *
3648843 TTTAACACTCTAAGCAATAGGGTAACAAGCCG-A-ATTTATA-AGCC
1 -TTAAC-CCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGA-TC
3648887 TTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATC
1 TTAA-CCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATC
* * * * **
3648932 TTAACCCCCTAAGCAGTAGGGAAACA-GATCGAAGA-TGA-TGGGC
1 TTAA-CCCCTAAGCAGTAGGGTAACAGGCT-GAAGATTTACAGATC
* * *
3648975 TTTAACCCCCTAAGCAGTAGGGTAAAAAGCTG-A-ATTTACCAG-CC
1 -TTAA-CCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTA-CAGATC
* * ** * * *
3649019 TTAGCACCCTAAGCAGTAGGGAAACAGATTGAAG-GTGAC-GAGTT
1 TTAAC-CCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGA-TC
* * * *
3649063 TTGACCCCCTAAGCAGTAGGGTAACAAGCTGAAG-TTCATAGATC
1 TT-AACCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATC
* * * *
3649107 TTATCACCCTAAGCAGTAGGGAAACA-GATCGAAGA--TA-ATGAGC
1 TTAAC-CCCTAAGCAGTAGGGTAACAGGCT-GAAGATTTACA-GATC
* * *
3649150 TTTAACCCCCTAAGCAGTAGGGTAACAAGC-CAA-ATTTACAGACC
1 -TTAA-CCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATC
* * * * *
3649194 ATAAATCCCTAAGCAGTAGGGTAATAGTCTGAA-AATTACAGATC
1 -TTAACCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATC
3649238 TT
1 TT
3649240 GTCTCTCTGA
Statistics
Matches: 527, Mismatches: 119, Indels: 114
0.69 0.16 0.15
Matches are distributed among these distances:
41 2 0.00
42 15 0.03
43 176 0.33
44 221 0.42
45 109 0.21
46 2 0.00
47 2 0.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (44 bp):
TTAACCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATC
Found at i:3648729 original size:89 final size:87
Alignment explanation
Indices: 3648415--3648913 Score: 478
Period size: 89 Copynumber: 5.7 Consensus size: 87
3648405 AGCCTTATCT
** * *
3648415 CCCTAAGCAGTAGGGTAACAGGCTG-AA-TTACAGATCTTGTCTCCCTAAGCAGTAGTGG-AGCA
1 CCCTAAGCAGTAGGGTAACAGGCTGAAATTTACAGATCTTAACCCCCTAAGCAGTAG-GGAAACA
* * * * *
3648477 AATCAAAGATGAAGGGCTTTAA-
65 GATCGAAGATGATGGCCTTAAAC
* * * * * *
3648499 CCCTAAGCAGTAGGATAACAAGC-CAAATTTACAGACCTTAAACCCCTAAGCAGTAGGGTAACAG
1 CCCTAAGCAGTAGGGTAACAGGCTGAAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAG
* * * * ** *
3648563 GTTGAA-TTCACAAGCCTT-ATC
66 ATCGAAGATGA-TGGCCTTAAAC
3648584 TCCCTAAGCAGTAGGGTAACAGGCT-AAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACA
1 -CCCTAAGCAGTAGGGTAACAGGCTGAAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACA
**
3648648 GATCGAAGGCGATGGACCTTAAAC
65 GATCGAAGATGATGG-CCTTAAAC
*
3648672 CCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATCTTAACCCCCTAAGTAGTAGGGAAACA
1 CCCTAAGCAGTAGGGTAACAGGCTGAA-ATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACA
* *
3648737 GATCGAAGATGATTGGCTTTAACC
65 GATCGAAGATGA-TGGCCTTAAAC
* * * * *
3648761 CCCTAATCAGTAGGGTAGCAGGCTGAAGATTTACAGATCTTGACCCCCTAAGTAGTAAGGAAACA
1 CCCTAAGCAGTAGGGTAACAGGCTGAA-ATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACA
* *
3648826 GATCAAAGATGATGGCCTTTAAC
65 GATCGAAGATGATGGCCTTAAAC
* * * * * * *
3648849 ACTCTAAGCAATAGGGTAACAAGCCG-AATTTATA-AGCCTTAACCCCCTAAGCAGTAGGGTAAC
1 -CCCTAAGCAGTAGGGTAACAGGCTGAAATTTACAGA-TCTTAACCCCCTAAGCAGTAGGGAAAC
3648912 AG
64 AG
3648914 GCTGAAGATT
Statistics
Matches: 344, Mismatches: 56, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
84 28 0.08
85 34 0.10
86 64 0.19
87 59 0.17
88 13 0.04
89 143 0.42
90 3 0.01
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (87 bp):
CCCTAAGCAGTAGGGTAACAGGCTGAAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAG
ATCGAAGATGATGGCCTTAAAC
Found at i:3649052 original size:132 final size:132
Alignment explanation
Indices: 3648755--3649088 Score: 429
Period size: 132 Copynumber: 2.5 Consensus size: 132
3648745 ATGATTGGCT
* * * * *
3648755 TTAACCCCCTAATCAGTAGGGTAGCAGGCTGAAGATTTACAGATCTTGACCCCCTAAGTAGTAAG
1 TTAACACCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATCTTGACCCCCTAAGCAGTAGG
* * *
3648820 GAAACAGATCAAAGATGATGGCCTTTAACACTCTAAGCAATAGGGTAACAAGCCGAATTTATAAG
66 GAAACAGATCAAAGATGATGGCCTTTAACACCCTAAGCAATAGGGTAAAAAGCCGAATTTACAAG
3648885 CC
131 CC
* *
3648887 TTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATCTTAACCCCCTAAGCAGTAGG
1 TTAACACCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATCTTGACCCCCTAAGCAGTAGG
* * * * * *
3648952 GAAACAGATCGAAGATGATGGGCTTTAACCCCCTAAGCAGTAGGGTAAAAAGCTGAATTTACCAG
66 GAAACAGATCAAAGATGATGGCCTTTAACACCCTAAGCAATAGGGTAAAAAGCCGAATTTACAAG
3649017 CC
131 CC
* * ** * * *
3649019 TTAGCACCCTAAGCAGTAGGGAAACAGATTGAAG-GTGAC-GAGTTTTGACCCCCTAAGCAGTAG
1 TTAACACCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGA-TCTTGACCCCCTAAGCAGTAG
*
3649082 GGTAACA
65 GGAAACA
3649089 AGCTGAAGTT
Statistics
Matches: 177, Mismatches: 24, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
130 2 0.01
131 28 0.16
132 147 0.83
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (132 bp):
TTAACACCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATCTTGACCCCCTAAGCAGTAGG
GAAACAGATCAAAGATGATGGCCTTTAACACCCTAAGCAATAGGGTAAAAAGCCGAATTTACAAG
CC
Found at i:3649137 original size:175 final size:176
Alignment explanation
Indices: 3648890--3649214 Score: 503
Period size: 175 Copynumber: 1.9 Consensus size: 176
3648880 ATAAGCCTTA
* * *
3648890 ACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATCTTAACCCCCTAAGCAGTAGGGAA
1 ACCCCCTAAGCAGTAGGGTAACAAGCTGAAGATTCACAGATCTTAACACCCTAAGCAGTAGGGAA
* * **
3648955 ACAGATCGAAGATGATGGGCTTTAACCCCCTAAGCAGTAGGGTAAAAAGCTGAATTTACCAG-CC
66 ACAGATCGAAGATAATGAGCTTTAACCCCCTAAGCAGTAGGGTAAAAAGCCAAATTTA-CAGACC
* *
3649019 TTAGCA-CCCTAAGCAGTAGGGAAACAGATTGAAGGTGACGAGTTTTG
130 ATA-AATCCCTAAGCAGTAGGGAAACAGATTGAAGGTGACGAGTTTTG
* *
3649066 ACCCCCTAAGCAGTAGGGTAACAAGCTGAAG-TTCATAGATCTTATCACCCTAAGCAGTAGGGAA
1 ACCCCCTAAGCAGTAGGGTAACAAGCTGAAGATTCACAGATCTTAACACCCTAAGCAGTAGGGAA
*
3649130 ACAGATCGAAGATAATGAGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAGACCA
66 ACAGATCGAAGATAATGAGCTTTAACCCCCTAAGCAGTAGGGTAAAAAGCCAAATTTACAGACCA
3649195 TAAATCCCTAAGCAGTAGGG
131 TAAATCCCTAAGCAGTAGGG
3649215 TAATAGTCTG
Statistics
Matches: 135, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
174 4 0.03
175 101 0.75
176 30 0.22
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (176 bp):
ACCCCCTAAGCAGTAGGGTAACAAGCTGAAGATTCACAGATCTTAACACCCTAAGCAGTAGGGAA
ACAGATCGAAGATAATGAGCTTTAACCCCCTAAGCAGTAGGGTAAAAAGCCAAATTTACAGACCA
TAAATCCCTAAGCAGTAGGGAAACAGATTGAAGGTGACGAGTTTTG
Found at i:3649158 original size:88 final size:88
Alignment explanation
Indices: 3648887--3649214 Score: 430
Period size: 87 Copynumber: 3.7 Consensus size: 88
3648877 TTTATAAGCC
* *
3648887 TTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATCTTAACCCCCTAAGCAGTAGG
1 TTAACCCCCTAAGCAGTAGGGTAACAAGCTGAAG-TTTACAGATCTTAACACCCTAAGCAGTAGG
*
3648952 GAAACAGATCGAAGATGATGGGCT
65 GAAACAGATCGAAGATGATGAGCT
* * *
3648976 TTAACCCCCTAAGCAGTAGGGTAAAAAGCTGAA-TTTACCAG-CCTTAGCACCCTAAGCAGTAGG
1 TTAACCCCCTAAGCAGTAGGGTAACAAGCTGAAGTTTA-CAGATCTTAACACCCTAAGCAGTAGG
* * * *
3649039 GAAACAGATTGAAGGTGACGAGTT
65 GAAACAGATCGAAGATGATGAGCT
* * * *
3649063 TTGACCCCCTAAGCAGTAGGGTAACAAGCTGAAGTTCATAGATCTTATCACCCTAAGCAGTAGGG
1 TTAACCCCCTAAGCAGTAGGGTAACAAGCTGAAGTTTACAGATCTTAACACCCTAAGCAGTAGGG
*
3649128 AAACAGATCGAAGATAATGAGCT
66 AAACAGATCGAAGATGATGAGCT
* * * *
3649151 TTAACCCCCTAAGCAGTAGGGTAACAAGC-CAAATTTACAGACCATAA-ATCCCTAAGCAGTAGG
1 TTAACCCCCTAAGCAGTAGGGTAACAAGCTGAAGTTTACAGATCTTAACA-CCCTAAGCAGTAGG
3649214 G
65 G
3649215 TAATAGTCTG
Statistics
Matches: 206, Mismatches: 29, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
86 1 0.00
87 101 0.49
88 73 0.35
89 31 0.15
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (88 bp):
TTAACCCCCTAAGCAGTAGGGTAACAAGCTGAAGTTTACAGATCTTAACACCCTAAGCAGTAGGG
AAACAGATCGAAGATGATGAGCT
Found at i:3649164 original size:132 final size:132
Alignment explanation
Indices: 3648529--3649176 Score: 408
Period size: 132 Copynumber: 4.9 Consensus size: 132
3648519 AGCCAAATTT
* * * * * * *
3648529 ACAGACCTTAAACCCCTAAGCAGTAGGGTAACAGGTTGAA-TTCACA-AGCCTTATCTCCCTAAG
1 ACAGATCTTAACCCCCTAAGCAGTAGGGTAACAAGATGAAGTTCATAGA-CCTTAACACCCTAAG
* * * * *
3648592 CAGTAGGGTAACAG-GCTAAATTTACA-GA-TCTTAACCCCCTAAGCAGTAGGGAAACAGA-TCG
65 CAGTAGGGAAACAGATCGAAA--TA-ATGAGCCTTAACCCCCTAAGCAGTAGGGTAACAGACT-G
*
3648653 AAG-GCG
126 AAGAGTG
** * * * * * * * *
3648659 ATGGACCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATCTTAACCCCCTAAG
1 ACAGATCTTAACCCCCTAAGCAGTAGGGTAACAAGATGAAG-TTCATAGACCTTAACACCCTAAG
* * * * * *
3648724 TAGTAGGGAAACAGATCGAAGATGATTG-GCTTTAACCCCCTAATCAGTAGGGTAGCAGGCTGAA
65 CAGTAGGGAAACAGATCGAA-AT-AATGAGCCTTAACCCCCTAAGCAGTAGGGTAACAGACTGAA
* *
3648788 GATTT
128 GAGTG
* * * * * * * * *
3648793 ACAGATCTTGACCCCCTAAGTAGTAAGGAAAC-AGATCAAAGATGAT-GGCCTTTAACACTCTAA
1 ACAGATCTTAACCCCCTAAGCAGTAGGGTAACAAGAT-GAAGTTCATAGACC-TTAACACCCTAA
* * * * * * *
3648856 GCAATAGGGTAACA-AGCCGAATTTATAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAA
64 GCAGTAGGGAAACAGA-TCGAAATAATGAGCCTTAACCCCCTAAGCAGTAGGGTAACAGACTGAA
* *
3648920 GATTT
128 GAGTG
* * * * * * *
3648925 ACAGATCTTAACCCCCTAAGCAGTAGGGAAAC-AGATCGAAGATGATGGGCTTTAACCCCCTAAG
1 ACAGATCTTAACCCCCTAAGCAGTAGGGTAACAAGAT-GAAGTTCATAGACCTTAACACCCTAAG
* * * * ** * * * *
3648989 CAGTAGGGTAAAAAGCT-GAATTTACCAGCCTTAGCACCCTAAGCAGTAGGGAAACAGATTGAAG
65 CAGTAGGG-AAACAGATCGAAATAATGAGCCTTAACCCCCTAAGCAGTAGGGTAACAGACTGAAG
3649053 -GTG
129 AGTG
* * * * *
3649056 AC-GAGTTTTGACCCCCTAAGCAGTAGGGTAACAAGCTGAAGTTCATAGATCTTATCACCCTAAG
1 ACAGA-TCTTAACCCCCTAAGCAGTAGGGTAACAAGATGAAGTTCATAGACCTTAACACCCTAAG
*
3649120 CAGTAGGGAAACAGATCGAAGATAATGAGCTTTAACCCCCTAAGCAGTAGGGTAACA
65 CAGTAGGGAAACAGATCGAA-ATAATGAGCCTTAACCCCCTAAGCAGTAGGGTAACA
3649177 AGCCAAATTT
Statistics
Matches: 404, Mismatches: 93, Indels: 40
0.75 0.17 0.07
Matches are distributed among these distances:
130 45 0.11
131 58 0.14
132 203 0.50
133 69 0.17
134 29 0.07
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.21
Consensus pattern (132 bp):
ACAGATCTTAACCCCCTAAGCAGTAGGGTAACAAGATGAAGTTCATAGACCTTAACACCCTAAGC
AGTAGGGAAACAGATCGAAATAATGAGCCTTAACCCCCTAAGCAGTAGGGTAACAGACTGAAGAG
TG
Found at i:3649500 original size:36 final size:36
Alignment explanation
Indices: 3649443--3649512 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
3649433 TAAGATGATT
* *
3649443 TGGCATCTCTATATTGTCAGAGAACAAATCGAAGTC
1 TGGCATCTCCATATTGACAGAGAACAAATCGAAGTC
* * *
3649479 TGGCATCTCCATTTTGACAGAGAGCAGATCGAAG
1 TGGCATCTCCATATTGACAGAGAACAAATCGAAG
3649513 ATATCAACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (36 bp):
TGGCATCTCCATATTGACAGAGAACAAATCGAAGTC
Found at i:3650964 original size:7 final size:7
Alignment explanation
Indices: 3650952--3650999 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
3650942 GATTCATTCA
3650952 ATTTTTT
1 ATTTTTT
3650959 ATTTTTT
1 ATTTTTT
3650966 ATTTTTT
1 ATTTTTT
**
3650973 A-TTACT
1 ATTTTTT
3650979 A-TTTTT
1 ATTTTTT
3650985 ATTTATTT
1 ATTT-TTT
3650993 ATTTTTT
1 ATTTTTT
3651000 CTTCTCTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
6 8 0.23
7 20 0.57
8 7 0.20
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (7 bp):
ATTTTTT
Found at i:3651186 original size:3 final size:3
Alignment explanation
Indices: 3651178--3651257 Score: 81
Period size: 3 Copynumber: 26.0 Consensus size: 3
3651168 CTACTGCACG
*
3651178 TAT TAT TAT TAT TAT TAG TAT T-T GTAT TAT TAT TAT TAT TAT TCAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT T-AT
* * * *
3651224 CTTT TAT TAT TAT CAT TAT TAC TAT TAT CAT TAT
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3651258 ATTTATACTT
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
2 1 0.02
3 57 0.90
4 4 0.06
5 1 0.02
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3651568 original size:26 final size:24
Alignment explanation
Indices: 3651510--3651577 Score: 59
Period size: 28 Copynumber: 2.7 Consensus size: 24
3651500 TTCCTTTTTA
3651510 TATTTA-TTTACTTGTTACTTCAT
1 TATTTATTTTACTTGTTACTTCAT
*
3651533 TACTAATTATTTTAACTTGTTATTATCAT
1 TA-T--TTATTTT-ACTTGTTACT-TCAT
3651562 TATTTATTGTTA-TTGT
1 TATTTATT-TTACTTGT
3651578 AAATATATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
23 2 0.05
24 1 0.03
25 4 0.11
26 9 0.24
27 5 0.14
28 10 0.27
29 6 0.16
ACGTcount: A:0.25, C:0.09, G:0.06, T:0.60
Consensus pattern (24 bp):
TATTTATTTTACTTGTTACTTCAT
Found at i:3651618 original size:9 final size:9
Alignment explanation
Indices: 3651606--3651735 Score: 65
Period size: 9 Copynumber: 15.9 Consensus size: 9
3651596 CTTATTTAAC
3651606 CTATTATTA
1 CTATTATTA
*
3651615 CTATTGTT-
1 CTATTATTA
*
3651623 -T-TTTTTA
1 CTATTATTA
3651630 CT-TTATTA
1 CTATTATTA
3651638 -T-T-ATTA
1 CTATTATTA
*
3651644 CTATTATCA
1 CTATTATTA
*
3651653 TTATTCATTA
1 CTATT-ATTA
3651663 CT-TTATTA
1 CTATTATTA
*
3651671 TTATTATTA
1 CTATTATTA
*
3651680 CTACTATTA
1 CTATTATTA
3651689 --A--ATTA
1 CTATTATTA
*
3651694 GTATTATTA
1 CTATTATTA
3651703 -TATT-TTA
1 CTATTATTA
3651710 CTATTATTA
1 CTATTATTA
*
3651719 -TTTGTATTA
1 CTAT-TATTA
3651728 CTATTATT
1 CTATTATT
3651736 TTAATCATTT
Statistics
Matches: 94, Mismatches: 12, Indels: 30
0.69 0.09 0.22
Matches are distributed among these distances:
5 4 0.04
6 8 0.09
7 9 0.10
8 22 0.23
9 45 0.48
10 6 0.06
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.60
Consensus pattern (9 bp):
CTATTATTA
Found at i:3651638 original size:3 final size:3
Alignment explanation
Indices: 3651632--3651735 Score: 74
Period size: 3 Copynumber: 35.7 Consensus size: 3
3651622 TTTTTTTACT
* * *
3651632 TTA TTA TTA TTA CTA TTA TCA TTA TTCA TTA CT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
* * * * *
3651677 TTA CTA CTA TTA -AA TTA GTA TTA TTA -TA TT- TTA CTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3651721 TGTA TTA CTA TTA TT
1 T-TA TTA TTA TTA TT
3651736 TTAATCATTT
Statistics
Matches: 78, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
2 7 0.09
3 67 0.86
4 4 0.05
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:3651715 original size:36 final size:38
Alignment explanation
Indices: 3651626--3651715 Score: 96
Period size: 39 Copynumber: 2.4 Consensus size: 38
3651616 TATTGTTTTT
* * * *
3651626 TTTACTTTATTATTATTACTATTATCATTATTCATTAC
1 TTTATTTTATTATTACTACTATTATAATTAGTCATTAC
3651664 TTTATTATTATTATTACTACTATTA-AATTAGT-ATTA-
1 TTTATT-TTATTATTACTACTATTATAATTAGTCATTAC
*
3651700 TTATATTTTACTATTA
1 TT-TATTTTATTATTA
3651716 TTATTTGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
36 10 0.22
37 8 0.18
38 10 0.22
39 17 0.38
ACGTcount: A:0.32, C:0.09, G:0.01, T:0.58
Consensus pattern (38 bp):
TTTATTTTATTATTACTACTATTATAATTAGTCATTAC
Found at i:3653532 original size:2 final size:2
Alignment explanation
Indices: 3653525--3653557 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3653515 TATCCCTCCC
3653525 TA TA 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 TA TA T
3653558 TTTAAATTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3663230 original size:53 final size:53
Alignment explanation
Indices: 3663150--3663255 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
3663140 ACCGACAAAA
*
3663150 ATCATCTGAGCTCAAGATAGATAATGCAGACACCAAACATATAAAAAGGCAAC
1 ATCATCTGAGCTCAAGATAGATAATGCAGACACCAAACATATAAAAAGACAAC
3663203 ATCATCTGAGCTCAAGATAGATAATGCAGACACCAAACATATAAAAAGACAAC
1 ATCATCTGAGCTCAAGATAGATAATGCAGACACCAAACATATAAAAAGACAAC
3663256 CAGGTCGTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (53 bp):
ATCATCTGAGCTCAAGATAGATAATGCAGACACCAAACATATAAAAAGACAAC
Found at i:3666461 original size:15 final size:15
Alignment explanation
Indices: 3666438--3666474 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
3666428 ATACTAATTA
*
3666438 AAATGTTAAATTTTT
1 AAATATTAAATTTTT
3666453 AAATATTAAATTTTT
1 AAATATTAAATTTTT
3666468 AAATATT
1 AAATATT
3666475 GCAGTTTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
AAATATTAAATTTTT
Done.