Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 27 of 203
Found at i:8955236 original size:23 final size:22
Alignment explanation
Indices: 8955196--8955247 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 22
8955186 GGCGAAGTGT
*
8955196 AATTTTATAATTATTAATTTAA
1 AATTTTATAATTAGTAATTTAA
8955218 AATTTTATAAATTAGTAATTTAA
1 AATTTTAT-AATTAGTAATTTAA
8955241 AATTTTA
1 AATTTTA
8955248 GAGGGGACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 8 0.29
23 20 0.71
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AATTTTATAATTAGTAATTTAA
Found at i:8975849 original size:31 final size:31
Alignment explanation
Indices: 8975803--8975866 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
8975793 TTACTATAAT
*
8975803 TTGGTCAATTCTAGTCTCTTTACTTTTCGAA
1 TTGGTCAATTCTAGTCTCTGTACTTTTCGAA
* * * *
8975834 TTGGTCGATTTTAGTCTCTGTATTTTTTGAA
1 TTGGTCAATTCTAGTCTCTGTACTTTTCGAA
8975865 TT
1 TT
8975867 TCAAAATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.17, C:0.14, G:0.16, T:0.53
Consensus pattern (31 bp):
TTGGTCAATTCTAGTCTCTGTACTTTTCGAA
Found at i:8979494 original size:3 final size:3
Alignment explanation
Indices: 8979486--8979516 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
8979476 TTTTACGTTG
8979486 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
8979517 ACATGAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:8984832 original size:26 final size:25
Alignment explanation
Indices: 8984784--8984832 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
8984774 GAGTAAACTG
*
8984784 ATTTTTTCTGTTAAAAATTACATTC
1 ATTTTTTCTGTTAAAAATAACATTC
8984809 ATTTTTAT-TGTTAAAAACTAACAT
1 ATTTTT-TCTGTTAAAAA-TAACAT
8984833 AATTGACAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.49
Consensus pattern (25 bp):
ATTTTTTCTGTTAAAAATAACATTC
Found at i:8997432 original size:177 final size:174
Alignment explanation
Indices: 8997136--8997484 Score: 617
Period size: 177 Copynumber: 2.0 Consensus size: 174
8997126 AAATTATCCA
*
8997136 AAACAACAAAGAATCAAAGTACATCCAAACAAAATATCTACTTTGGCATTAAGGATACATAGCAA
1 AAACAACAAAGAATCAAAGTACATCCAAACAAAATATCTACTTTGACATTAAGGATACATAGCAA
8997201 TAGCATACAAACAGGGGTGAAACCAAGGGACAGGCAGGCCTTCGGTAAATGGAAAATTTGCATTT
66 TAGCATACAAACAGGGGTGAAACCAAGGGACAGGCAGGCCTTCGGTAAATGGAAAATTTGCATTT
8997266 TAGGCCCTCCCAAGAATTAAAATTTCAATTTAAGACCCTTTTAACAG
131 T-GGCCCTCCCAAGAATTAAAATTTCAATTTAAGA--CTTTTAACAG
* * *
8997313 AAACAACAAAGAATCAAAGTTCATCCAAACAAAATATCTACTTTTACATTAAGGATACGTAGCAA
1 AAACAACAAAGAATCAAAGTACATCCAAACAAAATATCTACTTTGACATTAAGGATACATAGCAA
* *
8997378 TAGCATACAAACAGGGGTGAAACCAAGGGACAGGCAGGCCTTTGGTAAATGGAAATTTTGCATTT
66 TAGCATACAAACAGGGGTGAAACCAAGGGACAGGCAGGCCTTCGGTAAATGGAAAATTTGCATTT
8997443 TGGCCCTCCCAAGAATTAAAATTTCAATTTAAGACTTTTAAC
131 TGGCCCTCCCAAGAATTAAAATTTCAATTTAAGACTTTTAAC
8997485 GCAAAATTCA
Statistics
Matches: 166, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
174 8 0.05
176 33 0.20
177 125 0.75
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (174 bp):
AAACAACAAAGAATCAAAGTACATCCAAACAAAATATCTACTTTGACATTAAGGATACATAGCAA
TAGCATACAAACAGGGGTGAAACCAAGGGACAGGCAGGCCTTCGGTAAATGGAAAATTTGCATTT
TGGCCCTCCCAAGAATTAAAATTTCAATTTAAGACTTTTAACAG
Found at i:9009211 original size:195 final size:192
Alignment explanation
Indices: 9008872--9009261 Score: 627
Period size: 195 Copynumber: 2.0 Consensus size: 192
9008862 CATCCAATCA
* *
9008872 AACAGCTGCAAAAAAATTATCCAAAACAACAAAGAATCAAAGTCCATTCAAACAAAATATCTACT
1 AACAGCAGCAAAAAAATTATCCAAAACAACAAAGAATCAAAGTCCATCCAAACAAAATATCTACT
9008937 TTGACATTAAGGATACATAGCAATAGCATACAAACAAGGGTGAAACCAAGGGACAGAAAGGCCTT
66 TTGACATTAAGGATACATAGCAATAGCATACAAACAAGGGTGAAACCAAGGGACAGAAAGGCCTT
9009002 CGGGAAATGGAAAATTTGCATTTTAGGCCCTCCCAAGAATTAAAATTTCAATTTAAGACCCTTTT
131 CGGGAAATGGAAAATTTGCATTTT-GGCCCTCCCAAGAATTAAAATTTCAATTTAAGA--CTTTT
* * * *
9009067 AACAGCAGCAAAAAATTTATTCGAAACAACAAAGAATCAAAGTTCATCCAAACAAAATATCTACT
1 AACAGCAGCAAAAAAATTATCCAAAACAACAAAGAATCAAAGTCCATCCAAACAAAATATCTACT
* * **
9009132 TTGACATTAAGGATACGTAGCAATAGCATACAAACAGGGGTGAAACCAAGGGACAGGCAGGCCTT
66 TTGACATTAAGGATACATAGCAATAGCATACAAACAAGGGTGAAACCAAGGGACAGAAAGGCCTT
* * * *
9009197 TGGTAAATGGAAAATTTGCATTTTGGTCCTCCCAATAATTAAAATTTCAATTTAAGACTTTT
131 CGGGAAATGGAAAATTTGCATTTTGGCCCTCCCAAGAATTAAAATTTCAATTTAAGACTTTT
9009259 AAC
1 AAC
9009262 GCAAAATTCA
Statistics
Matches: 181, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
192 8 0.04
194 31 0.17
195 142 0.78
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (192 bp):
AACAGCAGCAAAAAAATTATCCAAAACAACAAAGAATCAAAGTCCATCCAAACAAAATATCTACT
TTGACATTAAGGATACATAGCAATAGCATACAAACAAGGGTGAAACCAAGGGACAGAAAGGCCTT
CGGGAAATGGAAAATTTGCATTTTGGCCCTCCCAAGAATTAAAATTTCAATTTAAGACTTTT
Found at i:9018254 original size:20 final size:20
Alignment explanation
Indices: 9018229--9018266 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9018219 CTATAAATAT
9018229 TTTTGAAATTTTGAAGATAG
1 TTTTGAAATTTTGAAGATAG
*
9018249 TTTTGAAATTTTGTAGAT
1 TTTTGAAATTTTGAAGAT
9018267 TTTATAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (20 bp):
TTTTGAAATTTTGAAGATAG
Found at i:9019337 original size:5 final size:5
Alignment explanation
Indices: 9019295--9019363 Score: 50
Period size: 5 Copynumber: 12.8 Consensus size: 5
9019285 GACCCTTTCT
* * *
9019295 TTTTC TTTTC TTTTA TTATTA -TTTA TTTCCTT TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TT-TTA TTTTA TTT--TA TTTTA TTTTA TTTTA
9019342 TTTTA TTATTA CTATTTA TTTT
1 TTTTA TT-TTA -T-TTTA TTTT
9019364 TTAATATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
4 3 0.06
5 35 0.65
6 7 0.13
7 8 0.15
8 1 0.02
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:9023117 original size:39 final size:39
Alignment explanation
Indices: 9023069--9023182 Score: 186
Period size: 39 Copynumber: 3.1 Consensus size: 39
9023059 TTCCGACTCT
9023069 TCACAACACTTCACCCTGATTGATACCACCACATCTTCC
1 TCACAACACTTCACCCTGATTGATACCACCACATCTTCC
9023108 TCACAACACTTCACCCTGATTGATACCACCACATCTTCC
1 TCACAACACTTCACCCTGATTGATACCACCACATCTTCC
9023147 TCACAACAC-T-----TGATTGATACCACCACATCTTCC
1 TCACAACACTTCACCCTGATTGATACCACCACATCTTCC
9023180 TCA
1 TCA
9023183 GTACTCTTTC
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
33 26 0.35
38 1 0.01
39 48 0.64
ACGTcount: A:0.29, C:0.39, G:0.05, T:0.26
Consensus pattern (39 bp):
TCACAACACTTCACCCTGATTGATACCACCACATCTTCC
Found at i:9025358 original size:25 final size:25
Alignment explanation
Indices: 9025330--9025381 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
9025320 ATGTAAAGGC
* *
9025330 AAACAAAACCGTAACTAATAGTAAA
1 AAACAAAACCATAACTAAAAGTAAA
*
9025355 AAACAAAACCATATCTAAAAGTAAA
1 AAACAAAACCATAACTAAAAGTAAA
9025380 AA
1 AA
9025382 GTAAATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.63, C:0.15, G:0.06, T:0.15
Consensus pattern (25 bp):
AAACAAAACCATAACTAAAAGTAAA
Found at i:9029002 original size:23 final size:23
Alignment explanation
Indices: 9028976--9029050 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
9028966 ATAAGTGCCA
9028976 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
9028999 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
9029021 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
9029044 CACTGAT
1 CACTGAT
9029051 CAATAACACT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 20 0.43
23 26 0.57
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:9041829 original size:21 final size:23
Alignment explanation
Indices: 9041803--9041850 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
9041793 ATGGATTCAT
9041803 AATTTA-AA-AAAAAAAACCCAA
1 AATTTAGAAGAAAAAAAACCCAA
*
9041824 AATTTAGAAGGAAAAAGAACCCAA
1 AATTTAGAA-GAAAAAAAACCCAA
9041848 AAT
1 AAT
9041851 AAAGGGAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 6 0.26
22 2 0.09
24 15 0.65
ACGTcount: A:0.65, C:0.12, G:0.08, T:0.15
Consensus pattern (23 bp):
AATTTAGAAGAAAAAAAACCCAA
Found at i:9044406 original size:17 final size:18
Alignment explanation
Indices: 9044369--9044407 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
9044359 GGTAGTTAAA
9044369 AAATTAATTTTCAAAATT
1 AAATTAATTTTCAAAATT
* *
9044387 AAATTTATTTT-AATATT
1 AAATTAATTTTCAAAATT
9044404 AAAT
1 AAAT
9044408 AAATCTCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATTAATTTTCAAAATT
Found at i:9057541 original size:8 final size:8
Alignment explanation
Indices: 9057528--9057554 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
9057518 AAAAAAACAT
9057528 AAATTTAA
1 AAATTTAA
9057536 AAATTTAA
1 AAATTTAA
9057544 AAATTTAA
1 AAATTTAA
9057552 AAA
1 AAA
9057555 ATAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAATTTAA
Found at i:9058940 original size:19 final size:19
Alignment explanation
Indices: 9058918--9058964 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
9058908 TTTTACAACA
*
9058918 TTCATTTTTCTTTAAAGTT
1 TTCATTTTCCTTTAAAGTT
9058937 TTCATTTTCCTTTAAAGTT
1 TTCATTTTCCTTTAAAGTT
9058956 TTCATTTTC
1 TTCATTTTC
9058965 AATTATGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.04, T:0.62
Consensus pattern (19 bp):
TTCATTTTCCTTTAAAGTT
Found at i:9064594 original size:33 final size:33
Alignment explanation
Indices: 9064554--9064624 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
9064544 AGTTTATACC
9064554 TTTATAATTTTTAGAGAATTAAATAAAAATTTT
1 TTTATAATTTTTAGAGAATTAAATAAAAATTTT
9064587 TTTATAATTTTTAGAGAATTAAATAAAAATTTT
1 TTTATAATTTTTAGAGAATTAAATAAAAATTTT
*
9064620 ATTAT
1 TTTAT
9064625 TTAAGAGGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (33 bp):
TTTATAATTTTTAGAGAATTAAATAAAAATTTT
Found at i:9067902 original size:22 final size:20
Alignment explanation
Indices: 9067871--9067911 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
9067861 TAGTTTTTAA
9067871 TAATACAAATGGATGAAATTTT
1 TAATACAAAT-GAT-AAATTTT
*
9067893 TAATAGAAATGATAAATTT
1 TAATACAAATGATAAATTT
9067912 GCTTTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 9 0.50
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (20 bp):
TAATACAAATGATAAATTTT
Found at i:9071218 original size:31 final size:30
Alignment explanation
Indices: 9071180--9071256 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 30
9071170 AATCTTAAAA
*
9071180 TTATACATAAATTTTGGCTTAGTGTGTAATT
1 TTATACATAAATTTTGGATT-GTGTGTAATT
* *
9071211 TTATACATAAACTTT-GATTTTGTGTAATT
1 TTATACATAAATTTTGGATTGTGTGTAATT
*
9071240 TTATATATGAAATTTTG
1 TTATACAT-AAATTTTG
9071257 ATTTGATCCA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 16 0.41
30 9 0.23
31 14 0.36
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (30 bp):
TTATACATAAATTTTGGATTGTGTGTAATT
Found at i:9076480 original size:9 final size:9
Alignment explanation
Indices: 9076466--9076493 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
9076456 TTTTGTTACA
9076466 ACAATTAAT
1 ACAATTAAT
9076475 ACAATTAAT
1 ACAATTAAT
9076484 ACAATTAAT
1 ACAATTAAT
9076493 A
1 A
9076494 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:9076515 original size:68 final size:66
Alignment explanation
Indices: 9076436--9076577 Score: 248
Period size: 68 Copynumber: 2.1 Consensus size: 66
9076426 TCAAGTTTGT
*
9076436 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
9076501 AAA
64 AAA
9076504 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
9076569 T
66 A
9076570 TTTACTAA
1 TTTACTAA
9076578 CAATTAATTT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 27 0.38
67 1 0.01
68 44 0.61
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:9076587 original size:16 final size:16
Alignment explanation
Indices: 9076566--9076607 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
9076556 AATAATTTGA
*
9076566 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
9076582 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
9076598 TAGTTTTAAT
1 TAATTTTAAT
9076608 TTTATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:9076591 original size:22 final size:23
Alignment explanation
Indices: 9076581--9076642 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
9076571 TTACTAACAA
* * *
9076581 TTAATTTTA-ATAACAATTAGTT
1 TTAATTTTATATAAAAAATAATT
*
9076603 TTAATTTTATTTAAAAAATAATT
1 TTAATTTTATATAAAAAATAATT
*
9076626 TTAATTTTA-ATTAAAAA
1 TTAATTTTATATAAAAAA
9076643 CGGGTCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TTAATTTTATATAAAAAATAATT
Found at i:9076596 original size:59 final size:66
Alignment explanation
Indices: 9076436--9076599 Score: 216
Period size: 68 Copynumber: 2.5 Consensus size: 66
9076426 TCAAGTTTGT
*
9076436 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTT-ATACAACAATTAATACAATTAATACAATTAATAATTTGAT
9076501 AAA
64 AAA
9076504 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTTA-TACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
9076567 AAT
64 AAA
*
9076570 TTTACTAA-C-AA-TTA-ATTTTA-ATAACAATTA
1 TTTACTAATCAAAGTTAGATTTTATACAACAATTA
9076600 GTTTTAATTT
Statistics
Matches: 92, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
59 9 0.10
61 6 0.07
62 3 0.03
64 2 0.02
65 1 0.01
66 27 0.29
67 1 0.01
68 43 0.47
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAAGTTAGATTTTATACAACAATTAATACAATTAATACAATTAATAATTTGATAA
A
Found at i:9083764 original size:29 final size:29
Alignment explanation
Indices: 9083731--9083803 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
9083721 ATGGGGACTA
9083731 GATCAAATAAGTCGCTCTAT-TATT-AAAAG
1 GATCAAATAAGTC-CT-TATATATTAAAAAG
* *
9083760 GATCAATTTAGTCCTTATAATATTAAAAAG
1 GATCAAATAAGTCCTTAT-ATATTAAAAAG
9083790 GATCAAATAAGTCC
1 GATCAAATAAGTCC
9083804 AAATTGTAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 3 0.08
28 2 0.05
29 15 0.41
30 17 0.46
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (29 bp):
GATCAAATAAGTCCTTATATATTAAAAAG
Found at i:9093498 original size:36 final size:34
Alignment explanation
Indices: 9093451--9093522 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 34
9093441 CATTTTATTG
9093451 TTTTATAATT-AATTATAAATATAAAAATAATTTTA
1 TTTTATAATTAAATT-TAAATA-AAAAATAATTTTA
* *
9093486 TTTTAATAATTAAATTTAAATAAAAATTATTTTTA
1 TTTT-ATAATTAAATTTAAATAAAAAATAATTTTA
9093521 TT
1 TT
9093523 AAAATTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 17 0.52
36 12 0.36
37 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
TTTTATAATTAAATTTAAATAAAAAATAATTTTA
Found at i:9094981 original size:18 final size:19
Alignment explanation
Indices: 9094950--9094986 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
9094940 AATTAGATTT
*
9094950 TTTATATTTTTATTCTTGA
1 TTTATATTTATATTCTTGA
9094969 TTTA-ATTTATATTCTTGA
1 TTTATATTTATATTCTTGA
9094987 GTCAGTAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTATATTTATATTCTTGA
Found at i:9095242 original size:18 final size:18
Alignment explanation
Indices: 9095219--9095254 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9095209 AATGATTTTC
*
9095219 TGTCTTAACCTATAATGA
1 TGTCTTAACCTAGAATGA
*
9095237 TGTCTTAATCTAGAATGA
1 TGTCTTAACCTAGAATGA
9095255 GATACTCCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (18 bp):
TGTCTTAACCTAGAATGA
Found at i:9098545 original size:3 final size:3
Alignment explanation
Indices: 9098539--9098570 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
9098529 AACCATATAC
*
9098539 TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
9098571 ACCTACAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:9117648 original size:32 final size:32
Alignment explanation
Indices: 9117607--9117667 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
9117597 GGGGTTAAGA
*
9117607 AATTTATAGCATTAAGGTCTCACTAATCTTGT
1 AATTTATAGCATTAAGGTCCCACTAATCTTGT
9117639 AATTTATAGCATTAAGGTCCCACTAATCT
1 AATTTATAGCATTAAGGTCCCACTAATCT
9117668 CATTTTTCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (32 bp):
AATTTATAGCATTAAGGTCCCACTAATCTTGT
Found at i:9133265 original size:2 final size:2
Alignment explanation
Indices: 9133253--9133282 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
9133243 TAAAGTATCA
9133253 AT AT CAT 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 A
9133283 AAGGGGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9133508 original size:81 final size:81
Alignment explanation
Indices: 9133414--9133663 Score: 374
Period size: 81 Copynumber: 3.1 Consensus size: 81
9133404 TGGAGCATGT
* * *
9133414 AGCATGTGCCTTCTTAATGGGACTTTATTAATTGGACCAACGCATGGAACTGCAAAAAAGTTGAA
1 AGCATGTGCCTTCTTAATGGGAGTTTATTAATTGGACCAACGCATGGAACTGCAAAAGAGTTGGA
*
9133479 ATCAACACAACATTAG
66 ATCAACACAACATTGG
* *
9133495 AGCATGTGCCTTCTTAATGGGAGTTTATTAATTGGACCAACACATGGAACTTCAAAAGAGTTGGA
1 AGCATGTGCCTTCTTAATGGGAGTTTATTAATTGGACCAACGCATGGAACTGCAAAAGAGTTGGA
*
9133560 ATCAACACAACAATGG
66 ATCAACACAACATTGG
* * * * *
9133576 CGCATGGGCCTTCTTAATGGGAGTTTATTAATTGGACCAACGCTTGGAATTGCAATAGAGTTGGA
1 AGCATGTGCCTTCTTAATGGGAGTTTATTAATTGGACCAACGCATGGAACTGCAAAAGAGTTGGA
*
9133641 ATCAACATAACATTGG
66 ATCAACACAACATTGG
*
9133657 AGTATGT
1 AGCATGT
9133664 AGCATCTGCC
Statistics
Matches: 150, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 150 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.28
Consensus pattern (81 bp):
AGCATGTGCCTTCTTAATGGGAGTTTATTAATTGGACCAACGCATGGAACTGCAAAAGAGTTGGA
ATCAACACAACATTGG
Found at i:9133646 original size:162 final size:164
Alignment explanation
Indices: 9133358--9133663 Score: 438
Period size: 162 Copynumber: 1.9 Consensus size: 164
9133348 GCATGAAGTT
* *
9133358 TTGGACCAACCATGGAACTACAAAAGAGTTGGAATCAACACAACATTGGAGCATGTAGCATGTGC
1 TTGGACCAACCATGGAACTACAAAAGAGTTGGAATCAACACAACAATGGAGC----AGCATGGGC
9133423 CTTCTTAATGGGACTTTATTAATTGGACCAACGCATGGAACTGCAAAAAAGTTGAAATCAACACA
62 CTTCTTAATGGGACTTTATTAATTGGACCAACGCATGGAACTGCAAAAAAGTTGAAATCAACACA
9133488 ACATTAGAGCATGTGCCTTCTTAATGGGAGTTTATTAA
127 ACATTAGAGCATGTGCCTTCTTAATGGGAGTTTATTAA
*
9133526 TTGGACCAACACATGGAACTTCAAAAGAGTTGGAATCAACACAACAAT-G-GC-GCATGGGCCTT
1 TTGGACCAAC-CATGGAACTACAAAAGAGTTGGAATCAACACAACAATGGAGCAGCATGGGCCTT
* * * * * * *
9133588 CTTAATGGGAGTTTATTAATTGGACCAACGCTTGGAATTGCAATAGAGTTGGAATCAACATAACA
65 CTTAATGGGACTTTATTAATTGGACCAACGCATGGAACTGCAAAAAAGTTGAAATCAACACAACA
* *
9133653 TTGGAGTATGT
130 TTAGAGCATGT
9133664 AGCATCTGCC
Statistics
Matches: 125, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
162 77 0.62
167 2 0.02
168 11 0.09
169 35 0.28
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (164 bp):
TTGGACCAACCATGGAACTACAAAAGAGTTGGAATCAACACAACAATGGAGCAGCATGGGCCTTC
TTAATGGGACTTTATTAATTGGACCAACGCATGGAACTGCAAAAAAGTTGAAATCAACACAACAT
TAGAGCATGTGCCTTCTTAATGGGAGTTTATTAA
Found at i:9140417 original size:2 final size:2
Alignment explanation
Indices: 9140412--9140437 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9140402 ATGTGTATGC
9140412 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
9140438 ATGTACGTAT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:9143173 original size:14 final size:14
Alignment explanation
Indices: 9143133--9143174 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
9143123 AATGGGTCCT
9143133 AAATATGTGGTCTG
1 AAATATGTGGTCTG
*
9143147 AAA-ATGATTGTCTG
1 AAATATG-TGGTCTG
9143161 AAATATGTGGTCTG
1 AAATATGTGGTCTG
9143175 TCAGCCACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 3 0.12
14 18 0.75
15 3 0.12
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.36
Consensus pattern (14 bp):
AAATATGTGGTCTG
Found at i:9148566 original size:25 final size:25
Alignment explanation
Indices: 9148538--9148612 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
9148528 CGGACACACC
*
9148538 ACAGTTCACATGAGCTTCCCGTTAT
1 ACAGTTCGCATGAGCTTCCCGTTAT
* *
9148563 ACAGCTCGCATGAGCTTCCCATTAT
1 ACAGTTCGCATGAGCTTCCCGTTAT
* *
9148588 TCAGCTT-GCATGAGCTTTCCGTTAT
1 ACAG-TTCGCATGAGCTTCCCGTTAT
9148613 TCAGCTCGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
25 41 0.98
26 1 0.02
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.33
Consensus pattern (25 bp):
ACAGTTCGCATGAGCTTCCCGTTAT
Found at i:9148613 original size:25 final size:25
Alignment explanation
Indices: 9148546--9148629 Score: 114
Period size: 25 Copynumber: 3.4 Consensus size: 25
9148536 CCACAGTTCA
*
9148546 CATGAGCTTCCCGTTATACAGCTCG
1 CATGAGCTTCCCGTTATTCAGCTCG
* *
9148571 CATGAGCTTCCCATTATTCAGCTTG
1 CATGAGCTTCCCGTTATTCAGCTCG
*
9148596 CATGAGCTTTCCGTTATTCAGCTCG
1 CATGAGCTTCCCGTTATTCAGCTCG
* *
9148621 AAAGAGCTT
1 CATGAGCTT
9148630 ACTGTTTACA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.32
Consensus pattern (25 bp):
CATGAGCTTCCCGTTATTCAGCTCG
Found at i:9151130 original size:22 final size:21
Alignment explanation
Indices: 9151105--9151150 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
9151095 AAAAAATTTG
9151105 AATTAAGAAAAAAAAAACAGAA
1 AATTAA-AAAAAAAAAACAGAA
* * *
9151127 AATTTAAAGAAAAAAAGAGAA
1 AATTAAAAAAAAAAAACAGAA
9151148 AAT
1 AAT
9151151 GATAACATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.13
Consensus pattern (21 bp):
AATTAAAAAAAAAAAACAGAA
Found at i:9154592 original size:54 final size:54
Alignment explanation
Indices: 9154528--9154633 Score: 203
Period size: 54 Copynumber: 2.0 Consensus size: 54
9154518 ACGATGATCG
*
9154528 GCAATATTTTTTAAACCGGATTGATAATTAAATCGATCAAATCACTAATTTACC
1 GCAATATTTTTTAAACCGGATCGATAATTAAATCGATCAAATCACTAATTTACC
9154582 GCAATATTTTTTAAACCGGATCGATAATTAAATCGATCAAATCACTAATTTA
1 GCAATATTTTTTAAACCGGATCGATAATTAAATCGATCAAATCACTAATTTA
9154634 TCGATCTGAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (54 bp):
GCAATATTTTTTAAACCGGATCGATAATTAAATCGATCAAATCACTAATTTACC
Found at i:9154661 original size:29 final size:29
Alignment explanation
Indices: 9154627--9154683 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
9154617 ATCAAATCAC
*
9154627 TAATTTATCGATCTGATCAATCTGATAAT
1 TAATTTACCGATCTGATCAATCTGATAAT
9154656 TAATTTACCGATCTGATCAATCTGATAA
1 TAATTTACCGATCTGATCAATCTGATAA
9154684 AAAATTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (29 bp):
TAATTTACCGATCTGATCAATCTGATAAT
Found at i:9160327 original size:11 final size:11
Alignment explanation
Indices: 9160311--9160341 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
9160301 AGAAACAGAT
9160311 AAATAATATAA
1 AAATAATATAA
9160322 AAATAATATAA
1 AAATAATATAA
*
9160333 AAATGATAT
1 AAATAATAT
9160342 TCTAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
AAATAATATAA
Found at i:9164412 original size:28 final size:29
Alignment explanation
Indices: 9164352--9164424 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 29
9164342 ATGTAATAAA
* *
9164352 AAATTATAAAAAAAATCAATAAAAATTATT
1 AAATTTTAATAAAAAT-AATAAAAATTATT
9164382 AAATTTTAATAAAAAT-ATAAAAA-TATCT
1 AAATTTTAATAAAAATAATAAAAATTAT-T
*
9164410 AAATTTTATTAAAAA
1 AAATTTTAATAAAAA
9164425 CTAGAAACTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
27 3 0.08
28 22 0.56
30 14 0.36
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (29 bp):
AAATTTTAATAAAAATAATAAAAATTATT
Found at i:9164518 original size:21 final size:21
Alignment explanation
Indices: 9164492--9164556 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
9164482 TAAATACGAA
*
9164492 TCTTTTACGAATTTTAT-ATTT
1 TCTTTTAC-ATTTTTATAATTT
9164513 TCTTTTACATTATTTATAATTT
1 TCTTTTACATT-TTTATAATTT
*
9164535 T-TTTTACTATTTTTATGATTT
1 TCTTTTAC-ATTTTTATAATTT
9164556 T
1 T
9164557 TATAAAGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 2 0.05
21 29 0.74
22 8 0.21
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.66
Consensus pattern (21 bp):
TCTTTTACATTTTTATAATTT
Found at i:9164829 original size:50 final size:50
Alignment explanation
Indices: 9164726--9164830 Score: 147
Period size: 50 Copynumber: 2.1 Consensus size: 50
9164716 ATTAATGATC
* * *
9164726 AAAAAATTTTTTTTATGCATTTTAATAATTTAAGTACACAATTAAGTGTA
1 AAAAAACTTTTTTGATGCATTTTAATAATTTAAGTACACAATTAAGTGAA
** * *
9164776 AAAAAACTTTTTTGATGCATTTTAATAATTTAAGTACGTACTTGAGTGAA
1 AAAAAACTTTTTTGATGCATTTTAATAATTTAAGTACACAATTAAGTGAA
9164826 AAAAA
1 AAAAA
9164831 TTAATGGGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (50 bp):
AAAAAACTTTTTTGATGCATTTTAATAATTTAAGTACACAATTAAGTGAA
Found at i:9168831 original size:9 final size:9
Alignment explanation
Indices: 9168802--9168838 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
9168792 TGAGTTTTCG
9168802 AATTCGAAT
1 AATTCGAAT
*
9168811 AACTCGAAT
1 AATTCGAAT
9168820 AATTCGAAT
1 AATTCGAAT
*
9168829 AATTAGAAT
1 AATTCGAAT
9168838 A
1 A
9168839 TTAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:9169343 original size:9 final size:9
Alignment explanation
Indices: 9169321--9169384 Score: 55
Period size: 9 Copynumber: 7.2 Consensus size: 9
9169311 TAGTAATAAT
9169321 TTTAT-TTA
1 TTTATATTA
*
9169329 TATATATTA
1 TTTATATTA
9169338 TTTATATTA
1 TTTATATTA
*
9169347 -TTAAATTAAA
1 TTTATATT--A
9169357 TTT-TA-TA
1 TTTATATTA
9169364 TTTTATATTA
1 -TTTATATTA
9169374 TTTATATTA
1 TTTATATTA
9169383 TT
1 TT
9169385 AAATTGTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
7 1 0.02
8 13 0.29
9 25 0.56
10 4 0.09
11 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTATATTA
Found at i:9170762 original size:28 final size:30
Alignment explanation
Indices: 9170722--9170784 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
9170712 ACAGTTATAA
*
9170722 AAAAATAATAAAAATTA-TTAAATTTTATT
1 AAAAATAATAAAAAATATTTAAATTTTATT
9170751 AAAAAT-ATAAAAAATATTTAAATTTTATT
1 AAAAATAATAAAAAATATTTAAATTTTATT
9170780 AAAAA
1 AAAAA
9170785 CTAGGAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 9 0.28
29 23 0.72
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (30 bp):
AAAAATAATAAAAAATATTTAAATTTTATT
Found at i:9170896 original size:10 final size:10
Alignment explanation
Indices: 9170881--9170998 Score: 60
Period size: 10 Copynumber: 12.7 Consensus size: 10
9170871 TTCCTTTCAC
9170881 ATTTTTTATA
1 ATTTTTTATA
9170891 ATTTTTT-TA
1 ATTTTTTATA
* *
9170900 CTATTTTTATG
1 AT-TTTTTATA
9170911 A-TTTTTATA
1 ATTTTTTATA
**
9170920 AAATTTTATA
1 ATTTTTTATA
9170930 A--TTTT-TA
1 ATTTTTTATA
*
9170937 A-TTTTTA-C
1 ATTTTTTATA
9170945 ATTTTTCT-TA
1 ATTTTT-TATA
*
9170955 ATTTTTAAT-
1 ATTTTTTATA
*
9170964 A-TTTTAAT-
1 ATTTTTTATA
*
9170972 ATTTTTAATA
1 ATTTTTTATA
*
9170982 AATTTTTATA
1 ATTTTTTATA
9170992 ATTTTTT
1 ATTTTTT
9170999 TATTAAAAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 22
0.72 0.09 0.18
Matches are distributed among these distances:
7 3 0.03
8 17 0.20
9 23 0.27
10 42 0.49
11 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.66
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:9170906 original size:9 final size:8
Alignment explanation
Indices: 9170894--9171002 Score: 58
Period size: 9 Copynumber: 12.2 Consensus size: 8
9170884 TTTTATAATT
9170894 TTTTTACTA
1 TTTTTA-TA
9170903 TTTTTATGA
1 TTTTTAT-A
9170912 TTTTTATAAA
1 TTTTTAT--A
*
9170922 ATTTTATAA
1 TTTTTAT-A
9170931 TTTTTA-A
1 TTTTTATA
*
9170938 TTTTTACA
1 TTTTTATA
*
9170946 TTTTTCTTAA
1 TTTTT-AT-A
9170956 TTTTTAATA
1 TTTTT-ATA
*
9170965 TTTTAATA
1 TTTTTATA
9170973 TTTTTAATAAA
1 TTTTT-AT--A
9170984 TTTTTATAA
1 TTTTTAT-A
*
9170993 TTTTTTTA
1 TTTTTATA
9171001 TT
1 TT
9171003 AAAAAAGATT
Statistics
Matches: 82, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
7 7 0.09
8 17 0.21
9 36 0.44
10 16 0.20
11 6 0.07
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (8 bp):
TTTTTATA
Found at i:9170908 original size:20 final size:19
Alignment explanation
Indices: 9170883--9170997 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
9170873 CCTTTCACAT
* *
9170883 TTTTTATAATTTTTTTACTA
1 TTTTTATAATTTTTATA-AA
*
9170903 TTTTTATGATTTTTATAAA
1 TTTTTATAATTTTTATAAA
* *
9170922 ATTTTATAATTTTTAATTTTTACA
1 TTTTTATAATTTTT-A----TAAA
* *
9170946 TTTTTCTTAATTTTTA-ATA
1 TTTTT-ATAATTTTTATAAA
*
9170965 TTTTAAT-ATTTTTAATAAA
1 TTTTTATAATTTTT-ATAAA
9170984 TTTTTATAATTTTT
1 TTTTTATAATTTTT
9170998 TTATTAAAAA
Statistics
Matches: 73, Mismatches: 13, Indels: 18
0.70 0.12 0.17
Matches are distributed among these distances:
17 6 0.08
18 2 0.03
19 27 0.37
20 22 0.30
24 8 0.11
25 8 0.11
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (19 bp):
TTTTTATAATTTTTATAAA
Found at i:9170968 original size:18 final size:18
Alignment explanation
Indices: 9170913--9170981 Score: 56
Period size: 17 Copynumber: 4.0 Consensus size: 18
9170903 TTTTTATGAT
* *
9170913 TTTTATAAAATTTT-ATA
1 TTTTATTAATTTTTAATA
*
9170930 ATTT-TTAATTTTTACAT-
1 TTTTATTAATTTTTA-ATA
*
9170947 TTTTCTTAATTTTTAATA
1 TTTTATTAATTTTTAATA
*
9170965 TTTTAAT-ATTTTTAATA
1 TTTTATTAATTTTTAATA
9170982 AATTTTTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
16 7 0.17
17 18 0.43
18 17 0.40
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTATTAATTTTTAATA
Found at i:9174618 original size:25 final size:25
Alignment explanation
Indices: 9174570--9174618 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
9174560 TAGCTGCGTC
**
9174570 AGTTTTTAACAGTAAAAATGAATTA
1 AGTTTTTAACAGTAAAAACCAATTA
9174595 AGTTTTTAACAG-AAAAGACCAATT
1 AGTTTTTAACAGTAAAA-ACCAATT
9174619 TGCTCTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (25 bp):
AGTTTTTAACAGTAAAAACCAATTA
Found at i:9177463 original size:55 final size:55
Alignment explanation
Indices: 9177402--9177512 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
9177392 GGTATCGGTT
*
9177402 TGCTACAGAGAATCATAATAATAAAGCACATAAATAATACAGTTTCTTATCGTAA
1 TGCTACAGAGAATCATAATAATAAAGCACATAAATAATACAGTTTCTTATCATAA
*
9177457 TGCTACAGAGAATCATAATAATAAAGCACGTAAATAATACAGTTTCTTATCATAA
1 TGCTACAGAGAATCATAATAATAAAGCACATAAATAATACAGTTTCTTATCATAA
9177512 T
1 T
9177513 AACCGTGATA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (55 bp):
TGCTACAGAGAATCATAATAATAAAGCACATAAATAATACAGTTTCTTATCATAA
Found at i:9180362 original size:16 final size:18
Alignment explanation
Indices: 9180323--9180356 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9180313 AGTTTATATA
9180323 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
9180340 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
9180357 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:9180867 original size:5 final size:5
Alignment explanation
Indices: 9180857--9180885 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
9180847 ATTTATAATT
9180857 AATAA AATAA AATAA AATAA AATAA AATA
1 AATAA AATAA AATAA AATAA AATAA AATA
9180886 TTTCCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:9188520 original size:23 final size:24
Alignment explanation
Indices: 9188480--9188527 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
9188470 CTTCATCATG
9188480 AGTGAAATAAAAAACCCCATAAAA
1 AGTGAAATAAAAAACCCCATAAAA
*
9188504 AGTGAAAT-TAAAACCCCATAAAA
1 AGTGAAATAAAAAACCCCATAAAA
9188527 A
1 A
9188528 CTTGTCATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.60, C:0.17, G:0.08, T:0.15
Consensus pattern (24 bp):
AGTGAAATAAAAAACCCCATAAAA
Found at i:9201808 original size:24 final size:25
Alignment explanation
Indices: 9201758--9201810 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
9201748 ATTATTTTTT
* *
9201758 ATATATATTTTAGAATTTTTTAAAA
1 ATATAAATTTTAGAAATTTTTAAAA
*
9201783 ATATAAATTTT-GAAATTTTTATAA
1 ATATAAATTTTAGAAATTTTTAAAA
9201807 ATAT
1 ATAT
9201811 TTTGAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (25 bp):
ATATAAATTTTAGAAATTTTTAAAA
Found at i:9201820 original size:19 final size:19
Alignment explanation
Indices: 9201789--9201860 Score: 92
Period size: 20 Copynumber: 3.7 Consensus size: 19
9201779 AAAAATATAA
9201789 ATTTTGAAATTTTTATAAA-T
1 ATTTTG-AATTTTTA-AAACT
* *
9201809 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTTAAAACT
9201828 ATTTTGAATTTTTGAAAACT
1 ATTTTGAATTTTT-AAAACT
9201848 ATTTTGAATTTTT
1 ATTTTGAATTTTT
9201861 TTTGTAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
18 3 0.06
19 20 0.43
20 24 0.51
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.56
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAACT
Found at i:9201851 original size:39 final size:41
Alignment explanation
Indices: 9201753--9201859 Score: 123
Period size: 39 Copynumber: 2.6 Consensus size: 41
9201743 AAAATATTAT
*
9201753 TTTTTATATATATTTTAGAATTTTTTAAAAATATAAATTTTGAAA
1 TTTTTATAAATATTTT-GAA--TTTTAAAAATAT-AATTTTGAAA
9201798 TTTTTATAAATATTTTGAATTTTAAAAAT-T-ATTTTG-AA
1 TTTTTATAAATATTTTGAATTTTAAAAATATAATTTTGAAA
9201836 TTTTTGA-AAACTATTTTGAATTTT
1 TTTTT-ATAAA-TATTTTGAATTTT
9201860 TTTTGTAATT
Statistics
Matches: 59, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
38 10 0.17
39 20 0.34
41 1 0.02
42 10 0.17
44 3 0.05
45 15 0.25
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (41 bp):
TTTTTATAAATATTTTGAATTTTAAAAATATAATTTTGAAA
Found at i:9213721 original size:30 final size:30
Alignment explanation
Indices: 9213687--9213745 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
9213677 AATGGAGCAA
*
9213687 GTGTGGCTAGTGGATTTGGTGGTGGAAAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
9213717 GTGTGGCTAGTGGAGTTGGTGGTGGAAAA
1 GTGTGGCTAGTGGAGTTGGTGGTGGAAAA
9213746 AGCTAAGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.20, C:0.03, G:0.47, T:0.29
Consensus pattern (30 bp):
GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
Found at i:9220804 original size:33 final size:33
Alignment explanation
Indices: 9220767--9220837 Score: 76
Period size: 33 Copynumber: 2.2 Consensus size: 33
9220757 CCCGAACCAT
9220767 GAACCCTAG-ACCCGAA-CCTAAACCA-TGAACCCC
1 GAACCCTAGCA-CCGAATCCTAAA-CATTGAA-CCC
* *
9220800 GAACCTTAGCATCGAATCCTAAACATTGAACCC
1 GAACCCTAGCACCGAATCCTAAACATTGAACCC
9220833 GAACC
1 GAACC
9220838 GCGAACCCCG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
33 22 0.67
34 11 0.33
ACGTcount: A:0.37, C:0.37, G:0.13, T:0.14
Consensus pattern (33 bp):
GAACCCTAGCACCGAATCCTAAACATTGAACCC
Found at i:9224408 original size:4 final size:4
Alignment explanation
Indices: 9224401--9224446 Score: 69
Period size: 4 Copynumber: 12.0 Consensus size: 4
9224391 CCAAGGTAGG
*
9224401 TACA TACA TACA CACA TACA T--A TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
9224447 CTCTTTCATG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
4 36 0.95
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
TACA
Found at i:9224427 original size:18 final size:18
Alignment explanation
Indices: 9224404--9224440 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
9224394 AGGTAGGTAC
9224404 ATACATACACACATACAT
1 ATACATACACACATACAT
*
9224422 ATACATACATACATACAT
1 ATACATACACACATACAT
9224440 A
1 A
9224441 CATACACTCT
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:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (18 bp):
ATACATACACACATACAT
Found at i:9224429 original size:22 final size:22
Alignment explanation
Indices: 9224401--9224444 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
9224391 CCAAGGTAGG
9224401 TACATACATACACACATACATA
1 TACATACATACACACATACATA
*
9224423 TACATACATACATACATACATA
1 TACATACATACACACATACATA
9224445 CACTCTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (22 bp):
TACATACATACACACATACATA
Found at i:9226160 original size:21 final size:21
Alignment explanation
Indices: 9226114--9226153 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9226104 AACGCTGTTG
*
9226114 TTTTGTTGTTATTTTTTCATA
1 TTTTGTTGTTATTTTCTCATA
*
9226135 TTTTGTTGTTGTTTTCTCA
1 TTTTGTTGTTATTTTCTCA
9226154 CTTTTTGCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.07, G:0.12, T:0.70
Consensus pattern (21 bp):
TTTTGTTGTTATTTTCTCATA
Found at i:9234746 original size:31 final size:30
Alignment explanation
Indices: 9234679--9234735 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
9234669 TTTAAACCAT
*
9234679 AATCAAATTTTCATGTATATAATTGCACGA
1 AATCAAAATTTCATGTATATAATTGCACGA
9234709 AATCAAAATTT-ATGTATCA-AATTGCAC
1 AATCAAAATTTCATGTAT-ATAATTGCAC
9234736 ATTAAATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (30 bp):
AATCAAAATTTCATGTATATAATTGCACGA
Found at i:9238662 original size:8 final size:8
Alignment explanation
Indices: 9238649--9238674 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
9238639 TTAAAATTAA
9238649 TTCGAATT
1 TTCGAATT
9238657 TTCGAATT
1 TTCGAATT
9238665 TTCGAATT
1 TTCGAATT
9238673 TT
1 TT
9238675 TTCAACATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.54
Consensus pattern (8 bp):
TTCGAATT
Found at i:9238932 original size:16 final size:16
Alignment explanation
Indices: 9238901--9238933 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9238891 ATGTATATTT
9238901 ATTTTAAAATGATATA
1 ATTTTAAAATGATATA
9238917 ATTTGTAAAATG-TATA
1 ATTT-TAAAATGATATA
9238933 A
1 A
9238934 AAATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (16 bp):
ATTTTAAAATGATATA
Found at i:9242681 original size:86 final size:83
Alignment explanation
Indices: 9242441--9242745 Score: 330
Period size: 86 Copynumber: 3.6 Consensus size: 83
9242431 TTTAGATGTG
* *
9242441 TATGAAAGCATTGGTTTATGGTTGAAATAGGAGAAAAGGGTTGTTGGAAATGTTGATATTCGAAT
1 TATGAAA-CATTGG-TTATGGTTGAAATAGGAG-AAAGGGTTGTTGTAAATGTTGAGATTCGAAT
* * * *
9242506 CTTAGACTTACGAAAGT-TGTG
63 ATTGGACTTACGAAAATATG-A
* * * * * *
9242527 TATCAAACATTGGTTTTGGTTGAAATAAGAGAAAGGGGTTCTTGTAAATGTTGAGAGTCGAATGT
1 TATGAAACATTGGTTATGGTTGAAATAGGAGAAA-GGGTTGTTGTAAATGTTGAGATTCGAATAT
**
9242592 TGGACTTATTAAAATATGAA
65 TGGACTTACGAAAATATG-A
* * *
9242612 TATGACACATTAGTTATGATTGAAATAGGAGAAAGGGTTGGGTTGTAAATGTTGAGATTCGAATA
1 TATGAAACATTGGTTATGGTTGAAATAGGAGAAAGGGTT--GTTGTAAATGTTGAGATTCGAATA
*
9242677 TTGGATTTACGAAAAGCTAT-A
64 TTGGACTTACGAAAA--TATGA
9242698 TATGAAACATTGGTTATGGTTGAAATAGGAGAAAGGG--GTTGTAAATGT
1 TATGAAACATTGGTTATGGTTGAAATAGGAGAAAGGGTTGTTGTAAATGT
9242746 CAAAATTCTA
Statistics
Matches: 184, Mismatches: 29, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
82 11 0.06
83 3 0.02
84 57 0.31
85 36 0.20
86 74 0.40
88 3 0.02
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (83 bp):
TATGAAACATTGGTTATGGTTGAAATAGGAGAAAGGGTTGTTGTAAATGTTGAGATTCGAATATT
GGACTTACGAAAATATGA
Found at i:9242815 original size:24 final size:24
Alignment explanation
Indices: 9242788--9242835 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
9242778 ATATCAAGGG
9242788 TGGTTGATGAATCAATTGAGTTAA
1 TGGTTGATGAATCAATTGAGTTAA
9242812 TGGTTGATGAATCAATTGAGTTAA
1 TGGTTGATGAATCAATTGAGTTAA
9242836 GTCCCGAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (24 bp):
TGGTTGATGAATCAATTGAGTTAA
Found at i:9245274 original size:4 final size:4
Alignment explanation
Indices: 9245265--9245357 Score: 127
Period size: 4 Copynumber: 23.8 Consensus size: 4
9245255 GCTAAGAAGG
* * *
9245265 TACA TACA TACA TACA TAC- -ACA TACC TACA TACA TGCA TACC TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* *
9245311 TACA TACA TACA TACA TACA TACA TACA TACA TACG CACA TACA TAC
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC
9245358 GAATCCGAAG
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.03
4 75 0.97
ACGTcount: A:0.45, C:0.29, G:0.02, T:0.24
Consensus pattern (4 bp):
TACA
Found at i:9248112 original size:21 final size:21
Alignment explanation
Indices: 9248088--9248149 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
9248078 GTAAGCTTTT
9248088 AAGAAGAAATGAAGCATCTAA
1 AAGAAGAAATGAAGCATCTAA
* * **
9248109 AAGATG--ACG-AGC-T-TTT
1 AAGAAGAAATGAAGCATCTAA
9248125 AAGAAGAAATGAAGCATCTAA
1 AAGAAGAAATGAAGCATCTAA
9248146 AAGA
1 AAGA
9248150 TGACGAAGTA
Statistics
Matches: 28, Mismatches: 8, Indels: 10
0.61 0.17 0.22
Matches are distributed among these distances:
16 6 0.21
17 1 0.04
18 5 0.18
19 5 0.18
20 1 0.04
21 10 0.36
ACGTcount: A:0.52, C:0.10, G:0.21, T:0.18
Consensus pattern (21 bp):
AAGAAGAAATGAAGCATCTAA
Found at i:9248123 original size:37 final size:37
Alignment explanation
Indices: 9248081--9248155 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
9248071 GGTTTAAGTA
9248081 AGCTTTTAAGAAGAAATGAAGCATCTAAAAGATGACG
1 AGCTTTTAAGAAGAAATGAAGCATCTAAAAGATGACG
9248118 AGCTTTTAAGAAGAAATGAAGCATCTAAAAGATGACG
1 AGCTTTTAAGAAGAAATGAAGCATCTAAAAGATGACG
9248155 A
1 A
9248156 AGTATACAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (37 bp):
AGCTTTTAAGAAGAAATGAAGCATCTAAAAGATGACG
Found at i:9252860 original size:25 final size:25
Alignment explanation
Indices: 9252809--9252860 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
9252799 AAATACTATC
* * *
9252809 AAAATCAATCCATTAATCAATATAA
1 AAAAACAATCAATTAATCAATAAAA
* *
9252834 AAAAACAATCAATTAATTATTAAAA
1 AAAAACAATCAATTAATCAATAAAA
9252859 AA
1 AA
9252861 TTCATCACCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.27
Consensus pattern (25 bp):
AAAAACAATCAATTAATCAATAAAA
Found at i:9256158 original size:29 final size:30
Alignment explanation
Indices: 9256101--9256165 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
9256091 TAATCTTATG
* * * *
9256101 AAAAAAGTTGACTTTGACCATTAACCTTTT
1 AAAAAAGTTAAATTTAACCATCAACCTTTT
9256131 AAAAAAGTTAAATTTAACCATCAA-CTTTT
1 AAAAAAGTTAAATTTAACCATCAACCTTTT
*
9256160 CAAAAA
1 AAAAAA
9256166 TAGTCGATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.32
Consensus pattern (30 bp):
AAAAAAGTTAAATTTAACCATCAACCTTTT
Found at i:9257807 original size:188 final size:188
Alignment explanation
Indices: 9257586--9257963 Score: 666
Period size: 188 Copynumber: 2.0 Consensus size: 188
9257576 AAATAATATT
9257586 ATTTTGAAGGTGTTTTTTATGACTGGTCCATATACATCCGAATGAGTTACACGTGTTTTTTATGC
1 ATTTTGAAGGTGTTTTTTATGACTGGTCCATATACATCCGAATGAGTTACACGTGTTTTTTATGC
* *
9257651 CAATCACGCTAGTTTTTAATAGCAAAAATGGTTGAAATTTTAACAAAAAGGACAAATTAACTATT
66 CAATCACGCTAGTTTTTAACAGCAAAAATGGTTAAAATTTTAACAAAAAGGACAAATTAACTATT
* *
9257716 TGATCCAACATATAATGACCTCTAATTTATTTATTTTTAAGTAAAGAGGCAATATGTA
131 TGATCCAACATATAAGGACCTCTAATTTATTTATTTTTAAGCAAAGAGGCAATATGTA
* *
9257774 ATTTTGAAGGTGTTTTTTATGACTGGTCCATATAGATCCGAATGAGTTACACGTGTTTTTTATGT
1 ATTTTGAAGGTGTTTTTTATGACTGGTCCATATACATCCGAATGAGTTACACGTGTTTTTTATGC
*
9257839 CAATCACGCTAGTTTTTAACAGCAAAAATGGTTAAAATTTTAACAAAAATGACAAATTAACTATT
66 CAATCACGCTAGTTTTTAACAGCAAAAATGGTTAAAATTTTAACAAAAAGGACAAATTAACTATT
** *
9257904 TGATCTGACATATAAGGACCTCTAATTTATTTATTTTTAAGCAAAGAGTCAATATGTA
131 TGATCCAACATATAAGGACCTCTAATTTATTTATTTTTAAGCAAAGAGGCAATATGTA
9257962 AT
1 AT
9257964 CTTACTTCTA
Statistics
Matches: 180, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
188 180 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (188 bp):
ATTTTGAAGGTGTTTTTTATGACTGGTCCATATACATCCGAATGAGTTACACGTGTTTTTTATGC
CAATCACGCTAGTTTTTAACAGCAAAAATGGTTAAAATTTTAACAAAAAGGACAAATTAACTATT
TGATCCAACATATAAGGACCTCTAATTTATTTATTTTTAAGCAAAGAGGCAATATGTA
Found at i:9265727 original size:24 final size:24
Alignment explanation
Indices: 9265685--9265747 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
9265675 AACCGATTTA
* **
9265685 TAAACTAATAAATGCTAAATATAT
1 TAAAATAATAAATATTAAATATAT
* *
9265709 TATAATAATAAATATTAAATATTT
1 TAAAATAATAAATATTAAATATAT
*
9265733 TAAAAT-ATATATATT
1 TAAAATAATAAATATT
9265748 TTATTTAACT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 8 0.25
24 24 0.75
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (24 bp):
TAAAATAATAAATATTAAATATAT
Found at i:9274148 original size:22 final size:21
Alignment explanation
Indices: 9274117--9274166 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
9274107 CCAATTATGG
*
9274117 AATAAATTTATTGCTTTGTAA
1 AATAAATTTATTGCTTTATAA
*
9274138 AATAATATTTATTTCTTTATAA
1 AATAA-ATTTATTGCTTTATAA
9274160 AATAAAT
1 AATAAAT
9274167 GAGTTTTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (21 bp):
AATAAATTTATTGCTTTATAA
Found at i:9278009 original size:15 final size:16
Alignment explanation
Indices: 9277972--9278013 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
9277962 AAGTTTGAAC
9277972 AACTCGAACACAAAAT
1 AACTCGAACACAAAAT
*
9277988 AATCTCGAATA-AAAAT
1 AA-CTCGAACACAAAAT
9278004 AACTCGAACA
1 AACTCGAACA
9278014 AGTAATTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.30
16 9 0.39
17 7 0.30
ACGTcount: A:0.55, C:0.21, G:0.07, T:0.17
Consensus pattern (16 bp):
AACTCGAACACAAAAT
Found at i:9279549 original size:42 final size:43
Alignment explanation
Indices: 9279426--9279556 Score: 119
Period size: 42 Copynumber: 3.0 Consensus size: 43
9279416 CAGTGAAATT
*
9279426 ATAAAGCCTTGCCTCCCTCAGTTGCAGTGGAGCA-AGT-TAAAG
1 ATAAAGCCTTGCCTCCCTCAGTTGCAGTGGAGCAGA-TCGAAAG
** * * * *
9279468 ATAGCAAATCTTGCCTTCCTGCA-TCGACAGCGAAGCAGATCGAAA-
1 ATA--AAGCCTTGCCTCCCT-CAGTTG-CAGTGGAGCAGATCGAAAG
9279513 ATAAAGCCTTGCCTCCCTCAGTTGCAGTGGAGCAGATC-AAAG
1 ATAAAGCCTTGCCTCCCTCAGTTGCAGTGGAGCAGATCGAAAG
9279555 AT
1 AT
9279557 GGTGTATTTT
Statistics
Matches: 68, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
41 3 0.04
42 19 0.28
43 14 0.21
44 14 0.21
45 14 0.21
46 4 0.06
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (43 bp):
ATAAAGCCTTGCCTCCCTCAGTTGCAGTGGAGCAGATCGAAAG
Found at i:9279699 original size:132 final size:131
Alignment explanation
Indices: 9279538--9280303 Score: 1201
Period size: 132 Copynumber: 5.8 Consensus size: 131
9279528 CCTCAGTTGC
*
9279538 AGTGGAGCAGATCAAAGATGGT-GTATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCC
1 AGTGGAGCAGATCGAAGATGGTAG-ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCC
* *
9279602 AGTAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTATAGATCTTATCTCCCTCAGC
65 AGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCT-AGC
9279667 AGT
129 AGT
**
9279670 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCA
1 AGTGGAGCAGATCGAAGATGGTAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCA
*
9279735 ATAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCA
66 GTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCT-AGCA
9279800 GT
130 GT
*
9279802 AGTGGAGCAGATCGAAGATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCA
1 AGTGGAGCAGATCGAAGATGGTAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCA
9279867 GTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCA
66 GTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCT-AGCA
9279932 GT
130 GT
* * * *
9279934 AGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCTTGAGGTTACAGTGGAGCACATTGAAGCCA
1 AGTGGAGCAGATCGAAGATGGTAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCA
* * * *
9279999 GTAATTCTATCTCCCTGGGCAACAGTGGAATATATTGAATATTACATATCTTATCTCCCTAGACA
66 GTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAG-CA
9280064 GT
130 GT
* * *
9280066 GGTGGAGTAGATCGAAGATGGTAGATTTTACCTCCCTGAGGTTACAATGGAGTACATTGAAGCCA
1 AGTGGAGCAGATCGAAGATGGTAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCA
* * *
9280131 GTAATTTTATCTCCCTAGGCAGCAGTGGAATAGATTGAATATTACAGATCTTATCTCCCTAGACA
66 GTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAG-CA
9280196 GT
130 GT
* * **
9280198 AGTGGAGTAGATCGAAGATGGTAGATTTTACCTCTCTGAGGTTACAGTGGAGTATGTTGAAGCCA
1 AGTGGAGCAGATCGAAGATGGTAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCA
* * * * *
9280263 GTAATTCTAACTCCCTGGTCGGCAGTGGAATCGATCGAAGA
66 GTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGA
9280304 AAGCAGATAT
Statistics
Matches: 590, Mismatches: 42, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
131 2 0.00
132 587 0.99
133 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.28
Consensus pattern (131 bp):
AGTGGAGCAGATCGAAGATGGTAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCA
GTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAGCAG
T
Found at i:9280159 original size:88 final size:89
Alignment explanation
Indices: 9279536--9280165 Score: 258
Period size: 88 Copynumber: 7.2 Consensus size: 89
9279526 TCCCTCAGTT
* *
9279536 GCAGTGGAGCAGATCAAAGATGGT-GTATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAG
1 GCAGTGGAGTAGATCGAAGATGGTAG-ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAG
* *
9279600 CCAGTA-ATTCTATCTCCCTGGGCA
65 CCAGTACATTTTATCTCCCTAGGCA
* * * ** * * * * * *
9279624 ACAGTGGAATAGATTGAAGATTATAGATCTTATCTCCCTCAGCAG-T--AGTGGAGCAGATCGAA
1 GCAGTGGAGTAGATCGAAGATGGTAGATTTTACCTCCCTGAG--GTTACAGTGGAGTACATTGAA
*** *** * *
9279686 GATGGCGGATTTTACCTCCCTGAGGTTA
64 GCCAGTACATTTTATCTCCCT-AGG-CA
* * **** * * * * *
9279714 -CAGTGGAGTACATTGAAGCCAATA-ATTCTATCTCCCTG-GG-CAGCAGTGGAATAGATTGAAG
1 GCAGTGGAGTAGATCGAAGATGGTAGATTTTACCTCCCTGAGGTTA-CAGTGGAGTACATTGAAG
* * *
9279775 --ATTACAGATCTTATCTCCCTAAGCA
65 CCAGTAC--ATTTTATCTCCCTAGGCA
* * *
9279800 GTAGTGGAGCAGATCGAAGATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGC
1 GCAGTGGAGTAGATCGAAGATGGTAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGC
* *
9279865 CAGTA-ATTCTATCTCCCTGGGCA
66 CAGTACATTTTATCTCCCTAGGCA
* * *** * * * * * **
9279888 GCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAG-T--AGTGGAGCAGATCAAA
1 GCAGTGGAGTAGATCGAAGATGGTAGATTTTACCTCCCTGAG--GTTACAGTGGAGTACATTGAA
*** * * * * *
9279950 GATGGCAGATTTTACCTCCTTGAGGTTA
64 GCCAGTACATTTTATCTCCCT-AGG-CA
* * * *** * * ** * *
9279978 -CAGTGGAGCACATTGAAGCCAGTA-ATTCTATCTCCCTG-GGCAACAGTGGAATATATTGAA--
1 GCAGTGGAGTAGATCGAAGATGGTAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGC
* * *
9280038 TATTACATATCTTATCTCCCTAGACA
66 CAGTACAT-T-TTATCTCCCTAGGCA
** *
9280064 GTGGTGGAGTAGATCGAAGATGGTAGATTTTACCTCCCTGAGGTTACAATGGAGTACATTGAAGC
1 GCAGTGGAGTAGATCGAAGATGGTAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGC
9280129 CAGTA-ATTTTATCTCCCTAGGCA
66 CAGTACATTTTATCTCCCTAGGCA
*
9280152 GCAGTGGAATAGAT
1 GCAGTGGAGTAGAT
9280166 TGAATATTAC
Statistics
Matches: 378, Mismatches: 132, Indels: 64
0.66 0.23 0.11
Matches are distributed among these distances:
85 2 0.01
86 6 0.02
87 68 0.18
88 211 0.56
89 78 0.21
90 7 0.02
91 6 0.02
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (89 bp):
GCAGTGGAGTAGATCGAAGATGGTAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGC
CAGTACATTTTATCTCCCTAGGCA
Found at i:9280358 original size:44 final size:44
Alignment explanation
Indices: 9280295--9280480 Score: 228
Period size: 44 Copynumber: 4.2 Consensus size: 44
9280285 CAGTGGAATC
* *
9280295 GATCGAAGAAAGCAGATATTGTCTTCATGTATTGGCGTGAAATA
1 GATCGAAGAAAGCAGATATTGTCTTCATGTATTGGCATGAAGTA
* *
9280339 GATCGAAGAAAGCAAATATTGTCTTCATGTATTGGCATGGAGTA
1 GATCGAAGAAAGCAGATATTGTCTTCATGTATTGGCATGAAGTA
* * *
9280383 AATCGAAGAAAGCAGATCTTGTCTTCTTGTATTGGCATGAAGTA
1 GATCGAAGAAAGCAGATATTGTCTTCATGTATTGGCATGAAGTA
* * * *** **
9280427 GATCAAAGAGAGCAGATCTTGTCTTCCCATATTGGTGGTGAAGTA
1 GATCGAAGAAAGCAGATATTGTCTTCATGTATTGG-CATGAAGTA
9280472 GATCGAAGA
1 GATCGAAGA
9280481 TACAAGTCTT
Statistics
Matches: 123, Mismatches: 18, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
44 108 0.88
45 15 0.12
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (44 bp):
GATCGAAGAAAGCAGATATTGTCTTCATGTATTGGCATGAAGTA
Found at i:9280711 original size:124 final size:125
Alignment explanation
Indices: 9280487--9280732 Score: 370
Period size: 124 Copynumber: 2.0 Consensus size: 125
9280477 AAGATACAAG
* * * *
9280487 TCTTGTCTCCCTGAAGTTGCAGTGGAGCAGACAGAAATAACCGGTCCTATCTCTTTGGAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAATAACCAGTCCTATCTCCTTGAAGTTGCA
* * *
9280552 ATGGAGTGGATTAAAACTGCTGATCTTATCTCTCTGA-AGTTGCAG-AGAGCAGATCATA
66 ATGGAGTGGATTAAAACTACGGATCTCATCTCTCTGATAGTTGCAGTAGAGCAGATCATA
* * *
9280610 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGTGACCAAGTCTTATCTCCTTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAATAACC-AGTCCTATCTCCTTGAAGTTGC
*
9280675 AATGGAGTGGATTAAAACTACGGATCTCATCTCTCTGATATTTGCAGTAGAGCAGATC
65 AATGGAGTGGATTAAAACTACGGATCTCATCTCTCTGATAGTTGCAGTAGAGCAGATC
9280733 GCATCAGATT
Statistics
Matches: 109, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
123 39 0.36
124 53 0.49
125 7 0.06
126 10 0.09
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (125 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAATAACCAGTCCTATCTCCTTGAAGTTGCA
ATGGAGTGGATTAAAACTACGGATCTCATCTCTCTGATAGTTGCAGTAGAGCAGATCATA
Found at i:9282199 original size:15 final size:15
Alignment explanation
Indices: 9282174--9282223 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
9282164 TCCCATTATT
*
9282174 TATTA-TTATTGTTA
1 TATTATTTATTGTCA
9282188 TATTATTTATTGTCA
1 TATTATTTATTGTCA
9282203 TCATTA-TTATT-TC-
1 T-ATTATTTATTGTCA
9282216 TATTATTT
1 TATTATTT
9282224 TTATATTGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.12
13 3 0.09
14 7 0.22
15 14 0.44
16 4 0.12
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (15 bp):
TATTATTTATTGTCA
Found at i:9283961 original size:15 final size:16
Alignment explanation
Indices: 9283924--9283965 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
9283914 AAGTTTGCGC
9283924 AACTCGAACACAAAAT
1 AACTCGAACACAAAAT
*
9283940 AATCTCGAATA-AAAAT
1 AA-CTCGAACACAAAAT
9283956 AACTCGAACA
1 AACTCGAACA
9283966 AGTAATTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.30
16 9 0.39
17 7 0.30
ACGTcount: A:0.55, C:0.21, G:0.07, T:0.17
Consensus pattern (16 bp):
AACTCGAACACAAAAT
Found at i:9286436 original size:6 final size:6
Alignment explanation
Indices: 9286427--9286467 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
9286417 TTAAGGTTTT
* * *
9286427 GTATAC GTATAC GTATAC GTATTC GTATAT GTATAT GTATA
1 GTATAC GTATAC GTATAC GTATAC GTATAC GTATAC GTATA
9286468 TCTTTGATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (6 bp):
GTATAC
Found at i:9288083 original size:21 final size:20
Alignment explanation
Indices: 9288057--9288108 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
9288047 AGCAGTGACA
* *
9288057 GTGAGATTAATTATTGTAGTG
1 GTGAGATTAA-TACTGTAGCG
9288078 GTGAGATTCAATACTGTAGCG
1 GTGAGATT-AATACTGTAGCG
9288099 GTGAGATTAA
1 GTGAGATTAA
9288109 AAACAACGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.35
Consensus pattern (20 bp):
GTGAGATTAATACTGTAGCG
Found at i:9289606 original size:21 final size:21
Alignment explanation
Indices: 9289582--9289631 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 21
9289572 ATGTTTTCTT
9289582 ACTTATCCATAGTACTAATTA
1 ACTTATCCATAGTACTAATTA
9289603 ACTTATCCATAGTACTAATTA
1 ACTTATCCATAGTACTAATTA
9289624 ACTGTATC
1 ACT-TATC
9289632 GGTTATCGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (21 bp):
ACTTATCCATAGTACTAATTA
Found at i:9292016 original size:24 final size:24
Alignment explanation
Indices: 9291989--9292037 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
9291979 AATGATGTGC
*
9291989 TTAATTATTTTTAATTGTTCACTT
1 TTAATTATTCTTAATTGTTCACTT
*
9292013 TTAATTATTCTTAATTGTTGACTT
1 TTAATTATTCTTAATTGTTCACTT
9292037 T
1 T
9292038 AAAAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.08, G:0.06, T:0.61
Consensus pattern (24 bp):
TTAATTATTCTTAATTGTTCACTT
Found at i:9305563 original size:11 final size:11
Alignment explanation
Indices: 9305547--9305571 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9305537 CAAACAAGGG
9305547 AAAATGCCTGT
1 AAAATGCCTGT
9305558 AAAATGCCTGT
1 AAAATGCCTGT
9305569 AAA
1 AAA
9305572 TGTACTTGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (11 bp):
AAAATGCCTGT
Found at i:9309647 original size:2 final size:2
Alignment explanation
Indices: 9309642--9309667 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9309632 CGCGCGCGCG
9309642 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
9309668 GACATACATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:9309676 original size:4 final size:4
Alignment explanation
Indices: 9309669--9309731 Score: 126
Period size: 4 Copynumber: 15.8 Consensus size: 4
9309659 ACACACACAG
9309669 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
9309717 ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACA
9309732 GTCTATGTTG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:9312896 original size:3 final size:3
Alignment explanation
Indices: 9312888--9312920 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
9312878 TTGTTGCTTC
9312888 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9312921 TCAAGCTCAA
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):
AAT
Found at i:9313480 original size:5 final size:5
Alignment explanation
Indices: 9313472--9313498 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
9313462 TTCTCTGGTC
9313472 TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TT
9313499 AACTACTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:9315854 original size:16 final size:15
Alignment explanation
Indices: 9315808--9315857 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
9315798 TTTTTATTTC
9315808 TTTTCGTATTTTATT
1 TTTTCGTATTTTATT
* *
9315823 TTTTCGTAAATATATT
1 TTTTCGT-ATTTTATT
9315839 TTTTCGGTATTTTATT
1 TTTTC-GTATTTTATT
9315855 TTT
1 TTT
9315858 AATACTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 7 0.24
16 20 0.69
17 2 0.07
ACGTcount: A:0.18, C:0.06, G:0.08, T:0.68
Consensus pattern (15 bp):
TTTTCGTATTTTATT
Found at i:9315857 original size:17 final size:16
Alignment explanation
Indices: 9315799--9315857 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
9315789 TATTTTTATT
9315799 TTTTATTTCTTTTCGTA
1 TTTTATTT-TTTTCGTA
9315816 TTTTA-TTTTTTCGTA
1 TTTTATTTTTTTCGTA
**
9315831 -AATATATTTTTTCGGTA
1 TTTTAT-TTTTTTC-GTA
9315848 TTTTATTTTT
1 TTTTATTTTT
9315858 AATACTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 2 0.06
15 8 0.24
16 9 0.26
17 12 0.35
18 3 0.09
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.69
Consensus pattern (16 bp):
TTTTATTTTTTTCGTA
Found at i:9317635 original size:13 final size:13
Alignment explanation
Indices: 9317617--9317643 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9317607 CGTTAATTTT
9317617 TAAATCTAAAAAA
1 TAAATCTAAAAAA
9317630 TAAATCTAAAAAA
1 TAAATCTAAAAAA
9317643 T
1 T
9317644 TTCGACCCAA
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:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAATCTAAAAAA
Found at i:9318577 original size:19 final size:18
Alignment explanation
Indices: 9318542--9318577 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
9318532 ATTATTGTTT
*
9318542 TATTTTTTATTTTTAATA
1 TATTTTTTATTTATAATA
9318560 TATTTTTTAGTTTATAAT
1 TATTTTTTA-TTTATAAT
9318578 TATCCTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TATTTTTTATTTATAATA
Found at i:9322956 original size:16 final size:16
Alignment explanation
Indices: 9322935--9322979 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
9322925 CTAATAAACA
*
9322935 AAAATATCTCAAACTT
1 AAAATAACTCAAACTT
* *
9322951 AAAATAACTCGAATTT
1 AAAATAACTCAAACTT
9322967 AAAATAA-TCAAAC
1 AAAATAACTCAAAC
9322980 AAGAAATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.27
Consensus pattern (16 bp):
AAAATAACTCAAACTT
Found at i:9323933 original size:20 final size:20
Alignment explanation
Indices: 9323882--9323929 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
9323872 TACAAAATAA
9323882 TCAAAATAATTTTCATAAAT
1 TCAAAATAATTTTCATAAAT
* *
9323902 TTAAAATAATTTTTA-AAAT
1 TCAAAATAATTTTCATAAAT
9323921 TCAAAATAA
1 TCAAAATAA
9323930 ATTTAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (20 bp):
TCAAAATAATTTTCATAAAT
Found at i:9337747 original size:25 final size:26
Alignment explanation
Indices: 9337688--9337747 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
9337678 GTTACTTAAT
* *
9337688 AAATAATTATTATTTTTGTTTACCAAA
1 AAATAATTATTATTTTTG-TAAACAAA
*
9337715 ATAA-AATTATTATTTTTG-AAAGAAA
1 A-AATAATTATTATTTTTGTAAACAAA
9337740 AAATAATT
1 AAATAATT
9337748 TAGTAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 2 0.07
25 9 0.32
27 15 0.54
28 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (26 bp):
AAATAATTATTATTTTTGTAAACAAA
Found at i:9338996 original size:4 final size:4
Alignment explanation
Indices: 9338980--9339039 Score: 93
Period size: 4 Copynumber: 15.0 Consensus size: 4
9338970 AAAAGGCTAA
* * *
9338980 TATG TACG TATG TATG TATG TATG AATG TATG AATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9339028 TATG TATG TATG
1 TATG TATG TATG
9339040 AAACAATGCA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.28, C:0.02, G:0.25, T:0.45
Consensus pattern (4 bp):
TATG
Found at i:9339189 original size:4 final size:4
Alignment explanation
Indices: 9339180--9339220 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
9339170 CCTCTCTCAG
*
9339180 GTAT GTAT GTAT GTAT GTAT GTAT GTAT ATAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
9339221 CGCGCGCGCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:9339291 original size:4 final size:4
Alignment explanation
Indices: 9339271--9339312 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
9339261 TCTGTCTGTG
* * *
9339271 TGTA TGTG TGCA TGTA TGTA TGTA TGTA CGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
9339313 AATGAATGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.21, C:0.05, G:0.29, T:0.45
Consensus pattern (4 bp):
TGTA
Found at i:9339696 original size:4 final size:4
Alignment explanation
Indices: 9339689--9339731 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
9339679 GTAATATTTC
9339689 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
9339732 CTTACAAGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:9342815 original size:4 final size:4
Alignment explanation
Indices: 9342806--9342833 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
9342796 AAAAGGCTAA
9342806 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
9342834 AAACAATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:9342983 original size:4 final size:4
Alignment explanation
Indices: 9342974--9343014 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
9342964 CCTCTCTCAG
*
9342974 GTAT GTAT GTAT GTAT GTAT GTAT GTAT ATAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
9343015 CGCGCGCGCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:9343085 original size:4 final size:4
Alignment explanation
Indices: 9343065--9343106 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
9343055 TCTGTCTGTG
* * *
9343065 TGTA TGTG TGCA TGTA TGTA TGTA TGTA CGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
9343107 AATGAATGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.21, C:0.05, G:0.29, T:0.45
Consensus pattern (4 bp):
TGTA
Found at i:9343490 original size:4 final size:4
Alignment explanation
Indices: 9343483--9343525 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
9343473 GTAATATTTC
9343483 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
9343526 CTTACAAGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:9351022 original size:15 final size:15
Alignment explanation
Indices: 9350991--9351024 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9350981 AATTATGGTG
9350991 CTTTTTTTTTTCTTT
1 CTTTTTTTTTTCTTT
9351006 CTTTCTTTTTTTC-TT
1 CTTT-TTTTTTTCTTT
9351021 CTTT
1 CTTT
9351025 AAGAGTTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
CTTTTTTTTTTCTTT
Found at i:9373737 original size:41 final size:41
Alignment explanation
Indices: 9373691--9373774 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
9373681 TAAAAAATAT
* * *
9373691 TTATATTAAAAAACATTACCATTAATATAATAAATGTTTTA
1 TTATATTAAAAAACACTACCATAAATATAATAAATATTTTA
9373732 TTATATTAAAAAACACTACCATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACTACCATAAATATAATAAATATTTTA
9373773 TT
1 TT
9373775 GTATCAAACA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.40
Consensus pattern (41 bp):
TTATATTAAAAAACACTACCATAAATATAATAAATATTTTA
Found at i:9377525 original size:38 final size:38
Alignment explanation
Indices: 9377482--9377559 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
9377472 TATGAGGATT
9377482 AATTTCCACATCCCTTTACAATTCGTTATGAGCAAATC
1 AATTTCCACATCCCTTTACAATTCGTTATGAGCAAATC
9377520 AATTTCCACATCCCTTTACAATTCGTTATGAGCAAATC
1 AATTTCCACATCCCTTTACAATTCGTTATGAGCAAATC
9377558 AA
1 AA
9377560 AGTTTCACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.33, C:0.26, G:0.08, T:0.33
Consensus pattern (38 bp):
AATTTCCACATCCCTTTACAATTCGTTATGAGCAAATC
Found at i:9393353 original size:10 final size:10
Alignment explanation
Indices: 9393335--9393367 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
9393325 TTTTCAATTC
*
9393335 TCATACAATA
1 TCATCCAATA
9393345 TCATCCAATA
1 TCATCCAATA
9393355 TCATCCAATA
1 TCATCCAATA
9393365 TCA
1 TCA
9393368 ATCATAGCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.30
Consensus pattern (10 bp):
TCATCCAATA
Found at i:9416394 original size:103 final size:103
Alignment explanation
Indices: 9416215--9416417 Score: 388
Period size: 103 Copynumber: 2.0 Consensus size: 103
9416205 AGTAATATGT
9416215 ACATACATATTATCAGTTGAAAACACTGACCTCTCTAGCAACGGAAGTGGCAACCATATTGGAAG
1 ACATACATATTATCAGTTGAAAACACTGACCTCTCTAGCAACGGAAGTGGCAACCATATTGGAAG
*
9416280 TAGGAACAGAAAGGAACATAAAAACATAGCTCATACAA
66 TAGCAACAGAAAGGAACATAAAAACATAGCTCATACAA
*
9416318 ACATACATATTATCAGTTGAAAACACTGACCTCTCTAGCAAGGGAAGTGGCAACCATATTGGAAG
1 ACATACATATTATCAGTTGAAAACACTGACCTCTCTAGCAACGGAAGTGGCAACCATATTGGAAG
9416383 TAGCAACAGAAAGGAACATAAAAACATAGCTCATA
66 TAGCAACAGAAAGGAACATAAAAACATAGCTCATA
9416418 TAATCACAAA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.20
Consensus pattern (103 bp):
ACATACATATTATCAGTTGAAAACACTGACCTCTCTAGCAACGGAAGTGGCAACCATATTGGAAG
TAGCAACAGAAAGGAACATAAAAACATAGCTCATACAA
Found at i:9422845 original size:31 final size:31
Alignment explanation
Indices: 9422810--9422878 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 31
9422800 ACCAAAAAAA
*
9422810 TATTAAGTGT-AGTAGAGCACGCTAAAATTAG
1 TATTAAGTGTAAG-AGAGCACACTAAAATTAG
* * *
9422841 TATTAATTTTAAAGAGTGCACACTAAAATTAG
1 TATTAAGTGT-AAGAGAGCACACTAAAATTAG
9422873 TATTAA
1 TATTAA
9422879 AATTTACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 8 0.25
32 22 0.69
33 2 0.06
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (31 bp):
TATTAAGTGTAAGAGAGCACACTAAAATTAG
Found at i:9427046 original size:15 final size:16
Alignment explanation
Indices: 9427026--9427056 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9427016 TCTTCTCCAT
9427026 CACATG-ATAGATAAA
1 CACATGAATAGATAAA
9427041 CACATGAATAGATAAA
1 CACATGAATAGATAAA
9427057 ATCAGGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.55, C:0.13, G:0.13, T:0.19
Consensus pattern (16 bp):
CACATGAATAGATAAA
Found at i:9430300 original size:7 final size:7
Alignment explanation
Indices: 9430290--9430328 Score: 69
Period size: 7 Copynumber: 5.4 Consensus size: 7
9430280 GACTTGGGAC
9430290 TTTGGTA
1 TTTGGTA
9430297 TTTGGTA
1 TTTGGTA
9430304 TTTGGTA
1 TTTGGTA
9430311 TTTGGTA
1 TTTGGTA
9430318 TTTGGATA
1 TTTGG-TA
9430326 TTT
1 TTT
9430329 CTATTTCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 26 0.84
8 5 0.16
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (7 bp):
TTTGGTA
Found at i:9430333 original size:14 final size:14
Alignment explanation
Indices: 9430290--9430334 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
9430280 GACTTGGGAC
*
9430290 TTTGGTATTTGGTA
1 TTTGGTATTTGCTA
*
9430304 TTTGGTATTTGGTA
1 TTTGGTATTTGCTA
9430318 TTTGGATATTT-CTA
1 TTTGG-TATTTGCTA
9430332 TTT
1 TTT
9430335 CAAACTCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 24 0.83
15 5 0.17
ACGTcount: A:0.16, C:0.02, G:0.22, T:0.60
Consensus pattern (14 bp):
TTTGGTATTTGCTA
Found at i:9430333 original size:21 final size:21
Alignment explanation
Indices: 9430290--9430334 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
9430280 GACTTGGGAC
*
9430290 TTTGGTATTTGGTATTTGGTA
1 TTTGGTATTTGGTATTTGCTA
9430311 TTTGGTATTTGGATATTT-CTA
1 TTTGGTATTTGG-TATTTGCTA
9430332 TTT
1 TTT
9430335 CAAACTCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.16, C:0.02, G:0.22, T:0.60
Consensus pattern (21 bp):
TTTGGTATTTGGTATTTGCTA
Found at i:9433217 original size:6 final size:6
Alignment explanation
Indices: 9433206--9433236 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
9433196 TCAAGTATAC
9433206 ATACAT ATACAT ATACAT ATACAT ATACAT A
1 ATACAT ATACAT ATACAT ATACAT ATACAT A
9433237 ACCCAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ATACAT
Done.