Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 5 of 126
Found at i:1347838 original size:31 final size:31
Alignment explanation
Indices: 1347803--1347861 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1347793 TTTAAAATTA
* *
1347803 AAAAAATATAAAAATTAAAATTAATCAATAC
1 AAAAAATACAAAAAATAAAATTAATCAATAC
*
1347834 AAAAAATACAAAAAATAAAATTGATCAA
1 AAAAAATACAAAAAATAAAATTAATCAA
1347862 ATTAAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.22
Consensus pattern (31 bp):
AAAAAATACAAAAAATAAAATTAATCAATAC
Found at i:1348996 original size:22 final size:23
Alignment explanation
Indices: 1348949--1348996 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1348939 AAATGTATAG
* * *
1348949 ATACTAAAAATACCAAATTACTA
1 ATACAAAAAATACAAAATTACAA
1348972 ATACAAAAAATACAAAATTA-AA
1 ATACAAAAAATACAAAATTACAA
1348994 ATA
1 ATA
1348997 AGGGAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (23 bp):
ATACAAAAAATACAAAATTACAA
Found at i:1352195 original size:22 final size:22
Alignment explanation
Indices: 1352170--1352216 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1352160 CAAAAGCATT
1352170 TCAACAAACACTTGAGGAGCAC
1 TCAACAAACACTTGAGGAGCAC
*
1352192 TCAACAAACACTTGGGGAGCAC
1 TCAACAAACACTTGAGGAGCAC
1352214 TCA
1 TCA
1352217 TACATACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.28, G:0.19, T:0.15
Consensus pattern (22 bp):
TCAACAAACACTTGAGGAGCAC
Found at i:1374873 original size:21 final size:21
Alignment explanation
Indices: 1374840--1374903 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
1374830 ATTTAATTGT
1374840 ATTATCTTCATATCTTTTTTTA
1 ATTATCTT-ATATCTTTTTTTA
* *
1374862 A-TATTCTTATATATTTTATTA
1 ATTA-TCTTATATCTTTTTTTA
1374883 ATTATCTT-TATCTTATTTTTA
1 ATTATCTTATATCTT-TTTTTA
1374904 GTCCCTTGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
20 5 0.14
21 23 0.66
22 7 0.20
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTATCTTATATCTTTTTTTA
Found at i:1377225 original size:2 final size:2
Alignment explanation
Indices: 1377220--1377256 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1377210 TAAAAAATTA
1377220 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
1377257 AAAAGATAGG
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:1381978 original size:133 final size:132
Alignment explanation
Indices: 1381738--1382118 Score: 529
Period size: 130 Copynumber: 2.9 Consensus size: 132
1381728 AAACAAGAAC
* * * *
1381738 CGAAGATTAGCAGAGAAGAGAGAACAACTTCGAACGCTGGTAATCACTTCAAAGTTATTGAAATT
1 CGAAGATTAGCAGAGAAGAGAGAACAATTTCG-ACGCTCGTAATCACTACAAAGCTATTGAAATT
1381803 CGATCAAACGAACTT-CATAATTCGACTATAAAACAATCATCCATCACCAAAAAAAAAAAATTCA
65 CGATCAAACGAACTTGCATAATTCGACTATAAAACAA-CATCCATCACCAAAAAAAAAAAATTCA
*
1381867 AAGG
129 AAAG
* * * *
1381871 CGAAGATTAGCAGAGAAGAGATAACGATTTCGACGCTCGTAATCTCTCCAAAGCTATTGAAATTC
1 CGAAGATTAGCAGAGAAGAGAGAACAATTTCGACGCTCGTAATCACTACAAAGCTATTGAAATTC
*
1381936 GATCAAACGAACTTGCATAATTCGACTATAAAACAACGATCCATCA-C--AAAAAAAAATTTCAA
66 GATCAAACGAACTTGCATAATTCGACTATAAAACAAC-ATCCATCACCAAAAAAAAAAAATTCAA
1381998 AAG
130 AAG
* * **
1382001 CGAAGATTAGCACAGCAGAGAGAACAATTTCGACGCTCGTAATCACTACAACTCTATCT-AAATT
1 CGAAGATTAGCAGAGAAGAGAGAACAATTTCGACGCTCGTAATCACTACAAAGCTAT-TGAAATT
* * *
1382065 TGATCAAACGAACTTGCATAATCCGACTATAAAACAACAATTCATCACCAAAAA
65 CGATCAAACGAACTTGCATAATTCGACTATAAAACAAC-ATCCATCACCAAAAA
1382119 GATTCAAAAA
Statistics
Matches: 221, Mismatches: 21, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
130 113 0.51
131 2 0.01
132 45 0.20
133 61 0.28
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.22
Consensus pattern (132 bp):
CGAAGATTAGCAGAGAAGAGAGAACAATTTCGACGCTCGTAATCACTACAAAGCTATTGAAATTC
GATCAAACGAACTTGCATAATTCGACTATAAAACAACATCCATCACCAAAAAAAAAAAATTCAAA
AG
Found at i:1385974 original size:53 final size:53
Alignment explanation
Indices: 1385894--1385999 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
1385884 TAGATAATAA
1385894 TAATCCTGGACAGGATCTACATGTGTAAGGGTGAATTCATAAATACTTTTAAG
1 TAATCCTGGACAGGATCTACATGTGTAAGGGTGAATTCATAAATACTTTTAAG
1385947 TAATCCTGGACAGGATCTACATGTGTAAGGGTGAATTCATAAATACTTTTAAG
1 TAATCCTGGACAGGATCTACATGTGTAAGGGTGAATTCATAAATACTTTTAAG
1386000 GAGTTCAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (53 bp):
TAATCCTGGACAGGATCTACATGTGTAAGGGTGAATTCATAAATACTTTTAAG
Found at i:1393283 original size:13 final size:12
Alignment explanation
Indices: 1393265--1393298 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
1393255 ACATTAAGAA
1393265 TATATAAAAATAT
1 TATATAAAAA-AT
1393278 TATATAAAAAAT
1 TATATAAAAAAT
1393290 TAATATAAA
1 T-ATATAAA
1393299 CAAACTAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 3 0.15
13 17 0.85
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TATATAAAAAAT
Found at i:1402973 original size:18 final size:18
Alignment explanation
Indices: 1402939--1402987 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
1402929 TTAAAAATTA
1402939 TTTCCATT-TT-CTTTTT
1 TTTCCATTATTCCTTTTT
1402955 TTT-C-TTATTTCCTTTTT
1 TTTCCATTA-TTCCTTTTT
1402972 TTTCCATTATTCCTTT
1 TTTCCATTATTCCTTT
1402988 CTTCTTCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.07
15 1 0.04
16 5 0.18
17 9 0.32
18 8 0.29
19 3 0.11
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTCCATTATTCCTTTTT
Found at i:1404919 original size:61 final size:61
Alignment explanation
Indices: 1404843--1404968 Score: 191
Period size: 61 Copynumber: 2.1 Consensus size: 61
1404833 TCCAATAATT
* *
1404843 AAATAATGATCCACGTCTTAATAATTTAGCTTTTCAATTTGATAAATAAATT-TTTTAGTGA
1 AAATAATGATACACGTCATAATAATTTAGCTTTTCAATTTGATAAAT-AATTATTTTAGTGA
* * *
1404904 AAATGATGATACACGTGATAATATTTTAGCTTTTCAATTTGATAAATAATTATTTTAGTGA
1 AAATAATGATACACGTCATAATAATTTAGCTTTTCAATTTGATAAATAATTATTTTAGTGA
1404965 AAAT
1 AAAT
1404969 TATAAGGTGT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 4 0.07
61 55 0.93
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (61 bp):
AAATAATGATACACGTCATAATAATTTAGCTTTTCAATTTGATAAATAATTATTTTAGTGA
Found at i:1407546 original size:8 final size:8
Alignment explanation
Indices: 1407535--1407565 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1407525 TTATTTATTT
*
1407535 AATAAATA
1 AATAAAAA
1407543 AATAAAAA
1 AATAAAAA
1407551 AATAAAAA
1 AATAAAAA
1407559 AATAAAA
1 AATAAAA
1407566 TTTGGGTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (8 bp):
AATAAAAA
Found at i:1408155 original size:40 final size:40
Alignment explanation
Indices: 1408111--1408718 Score: 432
Period size: 40 Copynumber: 15.2 Consensus size: 40
1408101 TCATGGTCGA
* *
1408111 GGTAAAAGATCTGATGGTCTTCAATCTGCCCTTTGGTTAG
1 GGTAAAAGATCTGATGGTCTTCAATCTGCCCTATGATTAG
* * * **
1408151 GGTAAAAGAT-TAGAT-TTCTTCAATCTACCCCATGATCGG
1 GGTAAAAGATCT-GATGGTCTTCAATCTGCCCTATGATTAG
* * * *
1408190 GGTAAAAGATCGGATGGTCTTTAATCTTACCCTCTGATTAG
1 GGTAAAAGATCTGATGGTCTTCAATC-TGCCCTATGATTAG
* * **
1408231 GGTAAAAGAT-TAGAT-TTCTTCAATCTGCCCCCATGATCGG
1 GGTAAAAGATCT-GATGGTCTTCAATCTG-CCCTATGATTAG
* * *
1408271 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAG
1 GGTAAAAGATCTGATGGTCTTCAATC-TGCCCTATGATTAG
* * * **
1408312 GGTAAAAGAT-TGGAT-TTCTTCAATCTACCCCATGATCGG
1 GGTAAAAGATCT-GATGGTCTTCAATCTGCCCTATGATTAG
* * *
1408351 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAG
1 GGTAAAAGATCTGATGGTCTTCAATC-TGCCCTATGATTAG
* * **
1408392 GGTAAAAGAT-TGGAT-TTCTTCAATCTGCCCCATGATCGG
1 GGTAAAAGATCT-GATGGTCTTCAATCTGCCCTATGATTAG
* * *
1408431 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAG
1 GGTAAAAGATCTGATGGTCTTCAATC-TGCCCTATGATTAG
* **
1408472 GGTAAAAGAT-TGGAT-TTCTTCAATCTGCCC-ATGATCGG
1 GGTAAAAGATCT-GATGGTCTTCAATCTGCCCTATGATTAG
* *
1408510 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTCG-TTAG
1 GGTAAAAGATCTGATGGTCTTCAATC-TGCCCTAT-GATTAG
* * * * **
1408551 GGTAAAAGAT-TGGAT-TTTTTCAATTTGCCCCATGATCGG
1 GGTAAAAGATCT-GATGGTCTTCAATCTGCCCTATGATTAG
*
1408590 GGTAAAAG-TC-GATTGGTCTTCAATCTTGCCCTCT-AGTTAG
1 GGTAAAAGATCTGA-TGGTCTTCAATC-TGCCCTATGA-TTAG
* * **
1408630 GGTAAAAGAT-TGAAT-TTCTTCAATCTGCCCCATGATCGG
1 GGTAAAAGATCTG-ATGGTCTTCAATCTGCCCTATGATTAG
*
1408669 GGTAAAAG-TC-GATTGGTCTTCAATCTTGCCCTCT-AGTTAG
1 GGTAAAAGATCTGA-TGGTCTTCAATC-TGCCCTATGA-TTAG
1408709 GGTAAAAGAT
1 GGTAAAAGAT
1408719 TGGAGGTTGT
Statistics
Matches: 433, Mismatches: 95, Indels: 79
0.71 0.16 0.13
Matches are distributed among these distances:
37 3 0.01
38 23 0.05
39 139 0.32
40 149 0.34
41 115 0.27
42 4 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (40 bp):
GGTAAAAGATCTGATGGTCTTCAATCTGCCCTATGATTAG
Found at i:1408253 original size:80 final size:80
Alignment explanation
Indices: 1408071--1408722 Score: 1039
Period size: 79 Copynumber: 8.2 Consensus size: 80
1408061 ATAACTTTAG
* * * * * *
1408071 GGGTAAAAGATTAGATTGT-TTCAATTTGCCTCATGGTCGAGGTAAAAGATCTGATGGTCTTCAA
1 GGGTAAAAGATTGGATT-TCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
*
1408135 TC-TGCCCTTTGGTTA
65 TCTTGCCCTCTGGTTA
* * *
1408150 GGGTAAAAGATTAGATTTCTTCAATCTACCCCATGATCGGGGTAAAAGATCGGATGGTCTTTAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
* *
1408215 CTTACCCTCTGATTA
66 CTTGCCCTCTGGTTA
*
1408230 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
1 GGGTAAAAGATTGGATTTCTTCAATCTG-CCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
1408295 TCTTGCCCTCTGGTTA
65 TCTTGCCCTCTGGTTA
*
1408311 GGGTAAAAGATTGGATTTCTTCAATCTACCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1408376 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
1408391 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1408456 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
1408471 GGGTAAAAGATTGGATTTCTTCAATCTG-CCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
1408535 CTTGCCCTCTCGTTA
66 CTTGCCCTCTGGTTA
* *
1408550 GGGTAAAAGATTGGATTTTTTCAATTTGCCCCATGATCGGGGTAAAAG-TC-GATTGGTCTTCAA
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGA-TGGTCTTCAA
*
1408613 TCTTGCCCTCTAGTTA
65 TCTTGCCCTCTGGTTA
*
1408629 GGGTAAAAGATTGAATTTCTTCAATCTGCCCCATGATCGGGGTAAAAG-TC-GATTGGTCTTCAA
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGA-TGGTCTTCAA
*
1408692 TCTTGCCCTCTAGTTA
65 TCTTGCCCTCTGGTTA
1408708 GGGTAAAAGATTGGA
1 GGGTAAAAGATTGGA
1408723 GGTTGTAACT
Statistics
Matches: 543, Mismatches: 25, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
78 3 0.01
79 250 0.46
80 215 0.40
81 75 0.14
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (80 bp):
GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
CTTGCCCTCTGGTTA
Found at i:1416976 original size:8 final size:8
Alignment explanation
Indices: 1416957--1416987 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
1416947 AATGTATGAT
1416957 AATGCAATG
1 AATGC-ATG
1416966 AATGCATG
1 AATGCATG
1416974 AATGCATG
1 AATGCATG
1416982 AATGCA
1 AATGCA
1416988 AATGCAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.77
9 5 0.23
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.23
Consensus pattern (8 bp):
AATGCATG
Found at i:1422911 original size:15 final size:15
Alignment explanation
Indices: 1422879--1422912 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1422869 TTTTAATATT
*
1422879 TTAATATTATTACGC
1 TTAATATTATTAAGC
*
1422894 TTAATATTATTAATC
1 TTAATATTATTAAGC
1422909 TTAA
1 TTAA
1422913 GCTTAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (15 bp):
TTAATATTATTAAGC
Found at i:1423360 original size:12 final size:12
Alignment explanation
Indices: 1423331--1423378 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
1423321 TTTTTTTTAC
*
1423331 TGTTTTGGTTGT
1 TGTTTTTGTTGT
* *
1423343 T-ATTTTCTTGT
1 TGTTTTTGTTGT
*
1423354 TGTTTTTGTTGC
1 TGTTTTTGTTGT
1423366 TGTTTTTGTTGT
1 TGTTTTTGTTGT
1423378 T
1 T
1423379 TTTAATGTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.02, C:0.04, G:0.23, T:0.71
Consensus pattern (12 bp):
TGTTTTTGTTGT
Found at i:1423433 original size:43 final size:43
Alignment explanation
Indices: 1423357--1423446 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 43
1423347 TTCTTGTTGT
* * * *
1423357 TTTTGTTGCTGTTTTTGTTGTTTTTAATGTTGTTTTGCTATTA
1 TTTTGTTGCTGTTTTGGTTGTTTTTAATATTGTTTGGATATTA
*
1423400 TTTTGTTGCTGTTTTGGTTGTTATTT-TTATTGTTTGGATATTA
1 TTTTGTTGCTGTTTTGGTTGTT-TTTAATATTGTTTGGATATTA
1423443 TTTT
1 TTTT
1423447 TTATGTGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
43 38 0.93
44 3 0.07
ACGTcount: A:0.10, C:0.03, G:0.19, T:0.68
Consensus pattern (43 bp):
TTTTGTTGCTGTTTTGGTTGTTTTTAATATTGTTTGGATATTA
Found at i:1425367 original size:25 final size:25
Alignment explanation
Indices: 1425339--1425387 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1425329 TGAAATTAAA
*
1425339 ATAAGGTAAG-TTAAAAAAGTATGAG
1 ATAAAGTAAGATTAAAAAA-TATGAG
*
1425364 ATAAATTAAGATTAAAAAATATGA
1 ATAAAGTAAGATTAAAAAATATGA
1425388 TGTGATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.16, T:0.27
Consensus pattern (25 bp):
ATAAAGTAAGATTAAAAAATATGAG
Found at i:1426300 original size:28 final size:28
Alignment explanation
Indices: 1426269--1426326 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1426259 TCTTTAATTT
*
1426269 TTAAATTTAGAAG-GATTAAAT-TTTAAAA
1 TTAAAATTA-AAGAGATT-AATCTTTAAAA
1426297 TTAAAATTAAAGAGATTAATCTTTAAAA
1 TTAAAATTAAAGAGATTAATCTTTAAAA
1426325 TT
1 TT
1426327 TCAAAGAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.40
Consensus pattern (28 bp):
TTAAAATTAAAGAGATTAATCTTTAAAA
Found at i:1430204 original size:13 final size:13
Alignment explanation
Indices: 1430186--1430212 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1430176 AAATGTTGTA
1430186 ATTCTTTGAACAT
1 ATTCTTTGAACAT
1430199 ATTCTTTGAACAT
1 ATTCTTTGAACAT
1430212 A
1 A
1430213 ACATGGATAC
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:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (13 bp):
ATTCTTTGAACAT
Found at i:1431957 original size:11 final size:11
Alignment explanation
Indices: 1431927--1431959 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
1431917 CAATTTAATT
1431927 TAATATATTT-
1 TAATATATTTA
1431937 TAAT-TATTTA
1 TAATATATTTA
1431947 TAATATATTTA
1 TAATATATTTA
1431958 TA
1 TA
1431960 GTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.24
10 8 0.38
11 8 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TAATATATTTA
Found at i:1432986 original size:31 final size:31
Alignment explanation
Indices: 1432951--1433011 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1432941 CAACCTAATA
* *
1432951 ACTTAAATAAAAATTTTTGAATAATTCAATG
1 ACTTAAATAAAAAATTTCGAATAATTCAATG
*
1432982 ACTTAGATAAAAAATTTCGAATAATTCAAT
1 ACTTAAATAAAAAATTTCGAATAATTCAAT
1433012 AATCATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (31 bp):
ACTTAAATAAAAAATTTCGAATAATTCAATG
Found at i:1437559 original size:17 final size:18
Alignment explanation
Indices: 1437520--1437563 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
1437510 TTTTTTTTTA
*
1437520 TTTTTATTTTTTGTGAAC
1 TTTTTATTTGTTGTGAAC
* *
1437538 CTTTTATTTGTT-TGAAT
1 TTTTTATTTGTTGTGAAC
1437555 TTTTTATTT
1 TTTTTATTT
1437564 TTAAAATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.16, C:0.05, G:0.09, T:0.70
Consensus pattern (18 bp):
TTTTTATTTGTTGTGAAC
Found at i:1442330 original size:4 final size:4
Alignment explanation
Indices: 1442321--1442363 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
1442311 TAAAAAATAT
* *
1442321 TTTA TTTA TTTA TTTA -TTA GTTA TTTA TTTA TTTA CTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1442364 CATTGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
3 3 0.09
4 32 0.91
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:1442346 original size:15 final size:16
Alignment explanation
Indices: 1442321--1442363 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
1442311 TAAAAAATAT
*
1442321 TTTATTTATTTATTTA
1 TTTACTTATTTATTTA
*
1442337 -TTAGTTATTTATTTA
1 TTTACTTATTTATTTA
1442352 TTTACTTATTTA
1 TTTACTTATTTA
1442364 CATTGTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (16 bp):
TTTACTTATTTATTTA
Found at i:1443062 original size:15 final size:15
Alignment explanation
Indices: 1443042--1443071 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1443032 AAGAATCGAT
1443042 CATGTGCGAGGGTGC
1 CATGTGCGAGGGTGC
*
1443057 CATGTGCGGGGGTGC
1 CATGTGCGAGGGTGC
1443072 TTTGTAGTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.20, G:0.50, T:0.20
Consensus pattern (15 bp):
CATGTGCGAGGGTGC
Found at i:1447955 original size:20 final size:20
Alignment explanation
Indices: 1447917--1447955 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1447907 TATATCAAAT
*
1447917 AAACTTAAAAACATTAAAAC
1 AAACTTAAAAACATAAAAAC
1447937 AAACGTTAAAAA-ATAAAAA
1 AAAC-TTAAAAACATAAAAA
1447956 ATTTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.69, C:0.10, G:0.03, T:0.18
Consensus pattern (20 bp):
AAACTTAAAAACATAAAAAC
Found at i:1448180 original size:24 final size:24
Alignment explanation
Indices: 1448111--1448180 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
1448101 AAACAACCAA
* *
1448111 AATAACAACAAAAA-TAATAAAAAT
1 AATAACAA-AAAAAGCAAAAAAAAT
* * * *
1448135 AGTAACAAAAACAGTAACAAAAAT
1 AATAACAAAAAAAGCAAAAAAAAT
*
1448159 AATAGCAAAAAAAGCAAAAAAA
1 AATAACAAAAAAAGCAAAAAAA
1448181 CAAAAATAAC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 4 0.11
24 33 0.89
ACGTcount: A:0.73, C:0.10, G:0.06, T:0.11
Consensus pattern (24 bp):
AATAACAAAAAAAGCAAAAAAAAT
Found at i:1448230 original size:30 final size:32
Alignment explanation
Indices: 1448174--1448243 Score: 99
Period size: 30 Copynumber: 2.2 Consensus size: 32
1448164 CAAAAAAAGC
*
1448174 AAAAAAACAAAAATAACAACATCAAAACAGTAA
1 AAAAAAACAAAAACAACAACA-CAAAACAGTAA
*
1448207 AAAAAAAC-AAAACAACAAC-CAAAATAGTAA
1 AAAAAAACAAAAACAACAACACAAAACAGTAA
1448237 AAAAAAA
1 AAAAAAA
1448244 ATACCAAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
30 17 0.49
32 10 0.29
33 8 0.23
ACGTcount: A:0.76, C:0.14, G:0.03, T:0.07
Consensus pattern (32 bp):
AAAAAAACAAAAACAACAACACAAAACAGTAA
Found at i:1459698 original size:24 final size:24
Alignment explanation
Indices: 1459665--1459732 Score: 102
Period size: 24 Copynumber: 2.9 Consensus size: 24
1459655 ATTTAAGAAA
1459665 TAATT-TTTCAGTTAAACTCTGTT
1 TAATTGTTTCAGTTAAACTCTGTT
1459688 TAATTGTTTCAGTTAAACTCTGTT
1 TAATTGTTTCAGTTAAACTCTGTT
* * *
1459712 TATTTGTTTGAGTCAAACTCT
1 TAATTGTTTCAGTTAAACTCT
1459733 TATTACTCTA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 5 0.12
24 36 0.88
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.50
Consensus pattern (24 bp):
TAATTGTTTCAGTTAAACTCTGTT
Found at i:1461745 original size:24 final size:24
Alignment explanation
Indices: 1461662--1461748 Score: 111
Period size: 24 Copynumber: 3.6 Consensus size: 24
1461652 AGAAATAATT
* * *
1461662 TTTCAATTAAACTCTATTTAATTG
1 TTTCAGTTAAACTCTGTTTATTTG
*
1461686 TTTCAGTTAAACTCTGTCTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
*
1461710 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
1461734 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
1461749 TATTACTCTA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTG
Found at i:1464674 original size:58 final size:58
Alignment explanation
Indices: 1464555--1464675 Score: 156
Period size: 58 Copynumber: 2.1 Consensus size: 58
1464545 ATGAGTTTTA
* * **
1464555 TTTAGGAATAAAATTATATTTGGGTTTAAAAATATTTAGGTTTAGTTTATGAGTGTTT
1 TTTAAGAATAAAATTATATTTGGGTTTAAAAATATTTAGGTTTAATTTATGAGTGGGT
* *
1464613 TTTAAGAATGAAATTATATTTGGGTTTAAAAATATTT-GAGTTTAATTTGTTGA-TGGGT
1 TTTAAGAATAAAATTATATTTGGGTTTAAAAATATTTAG-GTTTAATTT-ATGAGTGGGT
1464671 TTTAA
1 TTTAA
1464676 ATATTAGGAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
57 1 0.02
58 51 0.93
59 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (58 bp):
TTTAAGAATAAAATTATATTTGGGTTTAAAAATATTTAGGTTTAATTTATGAGTGGGT
Found at i:1479928 original size:39 final size:39
Alignment explanation
Indices: 1479883--1479987 Score: 149
Period size: 39 Copynumber: 2.7 Consensus size: 39
1479873 TTCTATGAAA
*
1479883 AGCAGCTTTAGTCAGCTCATCTTCATCACCATCACTTTC
1 AGCAGCTTTAGTCAACTCATCTTCATCACCATCACTTTC
*
1479922 AGCAGCTTTAGTCAACTCATCTTCATCGCCATCACTTTC
1 AGCAGCTTTAGTCAACTCATCTTCATCACCATCACTTTC
* * *
1479961 AGCTGCATTAG-CATCTTCATCTTCATC
1 AGCAGCTTTAGTCAAC-TCATCTTCATC
1479988 TTCATCTTCA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 3 0.05
39 57 0.95
ACGTcount: A:0.23, C:0.32, G:0.10, T:0.34
Consensus pattern (39 bp):
AGCAGCTTTAGTCAACTCATCTTCATCACCATCACTTTC
Found at i:1479981 original size:6 final size:6
Alignment explanation
Indices: 1479972--1479999 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1479962 GCTGCATTAG
1479972 CATCTT CATCTT CATCTT CATCTT CATC
1 CATCTT CATCTT CATCTT CATCTT CATC
1480000 CTCAAGATTC
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:0.18, C:0.36, G:0.00, T:0.46
Consensus pattern (6 bp):
CATCTT
Found at i:1483256 original size:31 final size:31
Alignment explanation
Indices: 1483221--1483286 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
1483211 ATTTAATTAA
* *
1483221 AAAAAGTTACAATTTAA-TTATTAAATTATTC
1 AAAAAGTTAC-ATTTAAGTCATTAAACTATTC
* *
1483252 AAAAATTTTCATTTAAGTCATTAAACTATTC
1 AAAAAGTTACATTTAAGTCATTAAACTATTC
1483283 AAAA
1 AAAA
1483287 GTATTTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.39
Consensus pattern (31 bp):
AAAAAGTTACATTTAAGTCATTAAACTATTC
Found at i:1483297 original size:31 final size:31
Alignment explanation
Indices: 1483232--1483302 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
1483222 AAAAGTTACA
* *
1483232 ATTTAA-TTATTAAATTATTCAAAAATTTTC
1 ATTTAAGTCATTAAACTATTCAAAAATTTTC
*
1483262 ATTTAAGTCATTAAACTATTCAAAAGTATTT-
1 ATTTAAGTCATTAAACTATTCAAAAAT-TTTC
1483293 ATTTAAGTCA
1 ATTTAAGTCA
1483303 CTGGACTGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.17
31 27 0.75
32 3 0.08
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.45
Consensus pattern (31 bp):
ATTTAAGTCATTAAACTATTCAAAAATTTTC
Found at i:1486113 original size:21 final size:22
Alignment explanation
Indices: 1486089--1486132 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1486079 CCCACCGTCC
*
1486089 CTTTCTCCACC-CCTACAAACT
1 CTTTATCCACCTCCTACAAACT
1486110 CTTTATCCACCTCCTACAAACT
1 CTTTATCCACCTCCTACAAACT
1486132 C
1 C
1486133 AAATCAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.25, C:0.45, G:0.00, T:0.30
Consensus pattern (22 bp):
CTTTATCCACCTCCTACAAACT
Found at i:1489255 original size:15 final size:15
Alignment explanation
Indices: 1489212--1489264 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1489202 ATTGTTCGGG
*
1489212 TTTTTAAAATTTTAG
1 TTTTTAAAATTTTAA
*** *
1489227 TCTTTTATGTTTTTAC
1 T-TTTTAAAATTTTAA
1489243 TTTTTAAAATTTTAA
1 TTTTTAAAATTTTAA
1489258 TTTTTAA
1 TTTTTAA
1489265 TAAATTATGT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (15 bp):
TTTTTAAAATTTTAA
Found at i:1490960 original size:6 final size:6
Alignment explanation
Indices: 1490941--1490971 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1490931 AAGGATTTAA
*
1490941 TATATG TATTTG TATATG TATATG TATATG T
1 TATATG TATATG TATATG TATATG TATATG T
1490972 GAATCTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (6 bp):
TATATG
Found at i:1495911 original size:23 final size:20
Alignment explanation
Indices: 1495864--1495902 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1495854 TCTCGATTCA
*
1495864 TTAAAATATAATATTATTAT
1 TTAAAATATAAAATTATTAT
1495884 TTAAAATAATAAAATTATT
1 TTAAAAT-ATAAAATTATT
1495903 TAATTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAAATATAAAATTATTAT
Found at i:1498201 original size:14 final size:14
Alignment explanation
Indices: 1498180--1498217 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1498170 AATCATATTT
1498180 TTTAATA-TTTATA
1 TTTAATATTTTATA
1498193 TTATAATATTTTATA
1 TT-TAATATTTTATA
1498208 TTTAAT-TTTT
1 TTTAATATTTT
1498218 GTATGATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTAATATTTTATA
Found at i:1501197 original size:70 final size:70
Alignment explanation
Indices: 1501043--1501216 Score: 152
Period size: 70 Copynumber: 2.5 Consensus size: 70
1501033 TTTAATTGAT
* * * * * * * * * * *
1501043 ACCCTAATATGATTACTAGATATCGTAAAATTTCATATTAGTATATAGTTTAACCTCAAATTTAG
1 ACCCTAATATAATTACCAAATATCGGAAAATTTCAGAATAATATATAGCTCAACATCAAATTGAG
*
1501108 TCGAA
66 TCAAA
* * * *
1501113 GCACTAACACAATTACCAAATA-CGAGAAAATTTCAGAATAATATATAGCTCAACATCAAATTGA
1 ACCCTAATATAATTACCAAATATCG-GAAAATTTCAGAATAATATATAGCTCAACATCAAATTGA
1501177 GTCAAA
65 GTCAAA
** *
1501183 ACCCTAATATAATTATTAAATATACCGAAAATTT
1 ACCCTAATATAATTACCAAATAT-CGGAAAATTT
1501217 TCAAATTAAT
Statistics
Matches: 78, Mismatches: 23, Indels: 5
0.74 0.22 0.05
Matches are distributed among these distances:
69 2 0.03
70 67 0.86
71 8 0.10
72 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (70 bp):
ACCCTAATATAATTACCAAATATCGGAAAATTTCAGAATAATATATAGCTCAACATCAAATTGAG
TCAAA
Found at i:1502690 original size:8 final size:8
Alignment explanation
Indices: 1502677--1502731 Score: 56
Period size: 8 Copynumber: 6.8 Consensus size: 8
1502667 TTCTCCTTAA
*
1502677 GCATGCAT
1 GCATGTAT
*
1502685 GCATGCAT
1 GCATGTAT
1502693 GCATGTAT
1 GCATGTAT
*
1502701 GTATGTAT
1 GCATGTAT
*
1502709 GTATGTAT
1 GCATGTAT
*
1502717 GCATGAATT
1 GCATGTA-T
1502726 GCATGT
1 GCATGT
1502732 GATGTATGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
8 35 0.85
9 6 0.15
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (8 bp):
GCATGTAT
Found at i:1502694 original size:12 final size:12
Alignment explanation
Indices: 1502677--1502721 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
1502667 TTCTCCTTAA
*
1502677 GCATGCATGCAT
1 GCATGCATGTAT
1502689 GCATGCATGTAT
1 GCATGCATGTAT
* *
1502701 GTATGTATGTAT
1 GCATGCATGTAT
*
1502713 GTATGCATG
1 GCATGCATG
1502722 AATTGCATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (12 bp):
GCATGCATGTAT
Found at i:1503800 original size:57 final size:57
Alignment explanation
Indices: 1503736--1503853 Score: 236
Period size: 57 Copynumber: 2.1 Consensus size: 57
1503726 AAGTTTCACC
1503736 CTATCTTTTTAATTTCAAGCATAAATTTACATTAATTATTCTTTATTTTATATCTAA
1 CTATCTTTTTAATTTCAAGCATAAATTTACATTAATTATTCTTTATTTTATATCTAA
1503793 CTATCTTTTTAATTTCAAGCATAAATTTACATTAATTATTCTTTATTTTATATCTAA
1 CTATCTTTTTAATTTCAAGCATAAATTTACATTAATTATTCTTTATTTTATATCTAA
1503850 CTAT
1 CTAT
1503854 TTTAAAACAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.53
Consensus pattern (57 bp):
CTATCTTTTTAATTTCAAGCATAAATTTACATTAATTATTCTTTATTTTATATCTAA
Found at i:1504729 original size:5 final size:5
Alignment explanation
Indices: 1504719--1504747 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1504709 CTTTGCCACG
1504719 CCTCC CCTCC CCTCC CCTCC CCTCC CCTC
1 CCTCC CCTCC CCTCC CCTCC CCTCC CCTC
1504748 ATCCCCATGC
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:0.00, C:0.79, G:0.00, T:0.21
Consensus pattern (5 bp):
CCTCC
Found at i:1505412 original size:69 final size:71
Alignment explanation
Indices: 1505323--1505502 Score: 204
Period size: 71 Copynumber: 2.6 Consensus size: 71
1505313 ATAGGTCTTG
** * * * *
1505323 ACTTTAAATTTAATTGAAACCTTAATATAATTATTGGATAT-C-AAAAATTTCAAAATAATATAT
1 ACTTTAAATTTAATCAAAACCCTAATATAATTATTAGATATACAAAAAATTTCAAAATAATACAC
*
1505386 AGCTCC
66 AACTCC
* * * *
1505392 ACTTTAAATTCAATCAAAACCCTAAAATGATT-TTAGATATACATAAAAATTTCAAATTAATACA
1 ACTTTAAATTTAATCAAAACCCTAATATAATTATTAGATATACA-AAAAATTTCAAAATAATACA
**
1505456 CAACTTG
65 CAACTCC
*
1505463 ATTTTAAATTTAATCAAAACCCTAATATAATTATTAGATA
1 ACTTTAAATTTAATCAAAACCCTAATATAATTATTAGATA
1505503 CCGGAGAATT
Statistics
Matches: 90, Mismatches: 17, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
68 7 0.08
69 27 0.30
71 49 0.54
72 7 0.08
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (71 bp):
ACTTTAAATTTAATCAAAACCCTAATATAATTATTAGATATACAAAAAATTTCAAAATAATACAC
AACTCC
Found at i:1507409 original size:15 final size:14
Alignment explanation
Indices: 1507373--1507416 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
1507363 CAATCAAAAC
*
1507373 TTTATTTTAATTTT
1 TTTATTTTAATATT
1507387 GATTTATTTTATATATT
1 --TTTATTTTA-ATATT
1507404 TTTATTTTAATAT
1 TTTATTTTAATAT
1507417 ACACAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 4 0.15
15 9 0.35
16 9 0.35
17 4 0.15
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTATTTTAATATT
Found at i:1508264 original size:27 final size:27
Alignment explanation
Indices: 1508212--1508263 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
1508202 GTCTGAGATC
1508212 TTTAAACATTGATAATGTTTTATTTTA
1 TTTAAACATTGATAATGTTTTATTTTA
*
1508239 TTTAAA-ATT-ATAATGATTTTTTTTT
1 TTTAAACATTGATAATG-TTTTATTTT
1508264 TTTCATTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 6 0.26
26 11 0.48
27 6 0.26
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.60
Consensus pattern (27 bp):
TTTAAACATTGATAATGTTTTATTTTA
Found at i:1509348 original size:5 final size:5
Alignment explanation
Indices: 1509338--1509401 Score: 128
Period size: 5 Copynumber: 12.8 Consensus size: 5
1509328 CTAAAAGATA
1509338 TATAG TATAG TATAG TATAG TATAG TATAG TATAG TATAG TATAG TATAG
1 TATAG TATAG TATAG TATAG TATAG TATAG TATAG TATAG TATAG TATAG
1509388 TATAG TATAG TATA
1 TATAG TATAG TATA
1509402 AAATAACTAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 59 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (5 bp):
TATAG
Found at i:1510485 original size:5 final size:5
Alignment explanation
Indices: 1510475--1510503 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1510465 CTCACATCAA
1510475 TGGTG TGGTG TGGTG TGGTG TGGTG -GGTG
1 TGGTG TGGTG TGGTG TGGTG TGGTG TGGTG
1510504 GGTAAGGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.00, C:0.00, G:0.62, T:0.38
Consensus pattern (5 bp):
TGGTG
Found at i:1523420 original size:17 final size:18
Alignment explanation
Indices: 1523398--1523431 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1523388 AGACACTGAT
1523398 AATATATAC-ATATAAAA
1 AATATATACAATATAAAA
*
1523415 AATATATTCAATATAAA
1 AATATATACAATATAAA
1523432 CATTTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (18 bp):
AATATATACAATATAAAA
Found at i:1526726 original size:21 final size:24
Alignment explanation
Indices: 1526682--1526727 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1526672 CACCGGTACT
1526682 GCACCAAATCTCTGCACGTAAATTA
1 GCACCAAATCTC-GCACGTAAATTA
1526707 GCACCAAATC-C-CAC-TAAATTA
1 GCACCAAATCTCGCACGTAAATTA
1526728 ATAACCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 7 0.33
22 3 0.14
24 1 0.05
25 10 0.48
ACGTcount: A:0.39, C:0.30, G:0.09, T:0.22
Consensus pattern (24 bp):
GCACCAAATCTCGCACGTAAATTA
Found at i:1531396 original size:21 final size:20
Alignment explanation
Indices: 1531357--1531396 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1531347 ATTGGAAGAA
*
1531357 AATTGAATAAGTAACAAATC
1 AATTGAATAAGTAAAAAATC
*
1531377 AATTGAAATGAGTAAAAAAT
1 AATTG-AATAAGTAAAAAAT
1531397 GATTAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.25
Consensus pattern (20 bp):
AATTGAATAAGTAAAAAATC
Found at i:1535864 original size:18 final size:16
Alignment explanation
Indices: 1535831--1535866 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
1535821 AATTAATATA
1535831 TAAATAAATAAATTAT
1 TAAATAAATAAATTAT
1535847 TAAATAAAATATAATTAT
1 TAAAT-AAATA-AATTAT
1535865 TA
1 TA
1535867 TAATTGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
18 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATAAATAAATTAT
Found at i:1537447 original size:42 final size:42
Alignment explanation
Indices: 1537392--1537476 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
1537382 TCACACATTA
* *
1537392 ATTAAGAGAGAGAAGGTGGAAGGAGGGAACAACCATTGACAC
1 ATTAAGAGAGAGAAAGTGGAAGAAGGGAACAACCATTGACAC
* **
1537434 ATTAAGAGAGAGAAAGTGGATGAAGGGAACCGCCATTGACAC
1 ATTAAGAGAGAGAAAGTGGAAGAAGGGAACAACCATTGACAC
1537476 A
1 A
1537477 ATAACTGGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.42, C:0.13, G:0.32, T:0.13
Consensus pattern (42 bp):
ATTAAGAGAGAGAAAGTGGAAGAAGGGAACAACCATTGACAC
Found at i:1553805 original size:20 final size:19
Alignment explanation
Indices: 1553780--1553817 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1553770 TGTTCAAATG
1553780 ATTAATCGAATTGAATTAAT
1 ATTAATCGAATT-AATTAAT
*
1553800 ATTAATTGAATTAATTAA
1 ATTAATCGAATTAATTAA
1553818 ATTTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (19 bp):
ATTAATCGAATTAATTAAT
Found at i:1563344 original size:19 final size:17
Alignment explanation
Indices: 1563313--1563347 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
1563303 TAAGTTTGTG
1563313 ATTTAAAAAAATATTTT
1 ATTTAAAAAAATATTTT
1563330 ATTTATAAAATAATATTT
1 ATTTA-AAAA-AATATTT
1563348 AATAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 4 0.25
19 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTAAAAAAATATTTT
Found at i:1563947 original size:31 final size:31
Alignment explanation
Indices: 1563883--1563949 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1563873 TAAATTACAG
* *
1563883 AAAAATGAAAGTAAAAATATTTTTAAAAAAT
1 AAAAATGAAAGTAAAAAGATATTTAAAAAAT
*
1563914 AAAATATGAAAGTAAAAAGA-ATTTAAAATAT
1 AAAA-ATGAAAGTAAAAAGATATTTAAAAAAT
1563945 AAAAA
1 AAAAA
1563950 ATACAAGGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 17 0.53
32 14 0.44
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.25
Consensus pattern (31 bp):
AAAAATGAAAGTAAAAAGATATTTAAAAAAT
Found at i:1564152 original size:21 final size:20
Alignment explanation
Indices: 1564123--1564166 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1564113 GGAAAACATA
* *
1564123 AAAAAAAATTACATGACAAAT
1 AAAAAAAATAAAATG-CAAAT
*
1564144 AAAATAAATAAAATGCAAAT
1 AAAAAAAATAAAATGCAAAT
1564164 AAA
1 AAA
1564167 TGACTATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAAAAAATAAAATGCAAAT
Found at i:1566271 original size:21 final size:21
Alignment explanation
Indices: 1566247--1566287 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1566237 TAATTTTTTA
1566247 TTAAATAAAATT-ATAAAATAG
1 TTAAAT-AAATTCATAAAATAG
1566268 TTAAATAAATTCATAAAATA
1 TTAAATAAATTCATAAAATA
1566288 AAATAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
TTAAATAAATTCATAAAATAG
Found at i:1568184 original size:31 final size:30
Alignment explanation
Indices: 1568149--1568265 Score: 104
Period size: 31 Copynumber: 4.0 Consensus size: 30
1568139 TTGGTAGTTG
1568149 AACTTGACACTTTTTCTTAATTTGGTATCTA
1 AACTTGACACTTTTTCTTAATTTGGTA-CTA
* *
1568180 AACTT-----TTTTTGGTCCAATTTGGTACTCA
1 AACTTGACACTTTTT-CT-TAATTTGGTACT-A
*
1568208 AACTTGACACTTTTTCCTAATTTGGTACCTA
1 AACTTGACACTTTTTCTTAATTTGGTA-CTA
*
1568239 AACTTGACAC-TTTT-TTAAGTTGGTACT
1 AACTTGACACTTTTTCTTAATTTGGTACT
1568266 TGAACCTTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 21
0.71 0.07 0.21
Matches are distributed among these distances:
26 5 0.07
27 3 0.04
28 17 0.24
29 9 0.13
30 4 0.06
31 25 0.36
32 2 0.03
33 5 0.07
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (30 bp):
AACTTGACACTTTTTCTTAATTTGGTACTA
Found at i:1570611 original size:2 final size:2
Alignment explanation
Indices: 1570600--1570628 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1570590 ATCTTAAATT
1570600 TA TA -A 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
1570629 ACAAGTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1570812 original size:15 final size:16
Alignment explanation
Indices: 1570780--1570820 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
1570770 TGAATAATAA
1570780 TAATAATATTATTATTT
1 TAATAAT-TTATTATTT
1570797 TAATAATTTA-TATTT
1 TAATAATTTATTATTT
*
1570812 TTATAATTT
1 TAATAATTT
1570821 TAATAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.57
16 3 0.13
17 7 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TAATAATTTATTATTT
Found at i:1570820 original size:24 final size:24
Alignment explanation
Indices: 1570788--1570848 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
1570778 AATAATAATA
* *
1570788 TTATTATTTTAATAATTTATATTT
1 TTATAATTTTAATAATTTATATCT
1570812 TTATAATTTTAATAATTTATATCT
1 TTATAATTTTAATAATTTATATCT
1570836 TTATAAATTTTAA
1 TTAT-AATTTTAA
1570849 AGGATCAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 26 0.76
25 8 0.24
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
TTATAATTTTAATAATTTATATCT
Found at i:1579530 original size:34 final size:34
Alignment explanation
Indices: 1579485--1579549 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
1579475 ATTATTATTA
*
1579485 TTTTAAAAGTTTATATCTTTATATTTTTTAATCT
1 TTTTAAAAGTTTATATCTTTATAATTTTTAATCT
*
1579519 TTTTAATAGTTTATATCTTTATAATTTTTAA
1 TTTTAAAAGTTTATATCTTTATAATTTTTAA
1579550 AGGATCAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (34 bp):
TTTTAAAAGTTTATATCTTTATAATTTTTAATCT
Found at i:1579536 original size:18 final size:18
Alignment explanation
Indices: 1579492--1579543 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 18
1579482 TTATTTTAAA
1579492 AGTTTATATCTTTAT-AT
1 AGTTTATATCTTTATAAT
** *
1579509 TTTTTA-ATCTTTTTAAT
1 AGTTTATATCTTTATAAT
1579526 AGTTTATATCTTTATAAT
1 AGTTTATATCTTTATAAT
1579544 TTTTAAAGGA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
16 7 0.26
17 10 0.37
18 10 0.37
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.62
Consensus pattern (18 bp):
AGTTTATATCTTTATAAT
Found at i:1582459 original size:31 final size:31
Alignment explanation
Indices: 1582391--1582452 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1582381 ATGGTCATTG
*
1582391 AACTATTTAAAAGATTTCATTTAAGTCACTA
1 AACTATTCAAAAGATTTCATTTAAGTCACTA
* *
1582422 AACTATTCAAAAGTTTTTATTTAAGTCACTA
1 AACTATTCAAAAGATTTCATTTAAGTCACTA
1582453 TGCTATTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.40
Consensus pattern (31 bp):
AACTATTCAAAAGATTTCATTTAAGTCACTA
Found at i:1591311 original size:5 final size:5
Alignment explanation
Indices: 1591303--1591357 Score: 57
Period size: 5 Copynumber: 11.8 Consensus size: 5
1591293 TTATAAAAAA
*
1591303 ATTAT ATTA- ATTAT A-TAT ATTA- AATA- ATTAT -TATAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT-TAT ATTAT ATTAT
1591349 ATTAT ATTA
1 ATTAT ATTA
1591358 AATCACTAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
4 15 0.35
5 27 0.63
6 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (5 bp):
ATTAT
Found at i:1591352 original size:20 final size:19
Alignment explanation
Indices: 1591303--1591353 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
1591293 TTATAAAAAA
1591303 ATTATATTAATTA-TATAT
1 ATTATATTAATTATTATAT
*
1591321 ATTA-AATAATTATTATAT
1 ATTATATTAATTATTATAT
1591339 ATTATATTATATTAT
1 ATTATATTA-ATTAT
1591354 ATTAAATCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 7 0.25
18 13 0.46
19 3 0.11
20 5 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTATATTAATTATTATAT
Found at i:1596264 original size:29 final size:28
Alignment explanation
Indices: 1596232--1596294 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
1596222 AAAAAACAAA
* *
1596232 TAAATTGAACTGAATTTATCCCCAAAACC
1 TAAATTAAACTGAATTTAACCCC-AAACC
* * *
1596261 TAAATCAAATTGAATTTAACTCCAAACC
1 TAAATTAAACTGAATTTAACCCCAAACC
1596289 TAAATT
1 TAAATT
1596295 TTATATTTTG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.30
Consensus pattern (28 bp):
TAAATTAAACTGAATTTAACCCCAAACC
Found at i:1598374 original size:268 final size:268
Alignment explanation
Indices: 1597874--1598406 Score: 804
Period size: 268 Copynumber: 2.0 Consensus size: 268
1597864 ACAAGTACCC
*
1597874 TATCCCTGTTAAGAGTGTAGTCCCCATAATATGTACTTACTCTGGTACGGGTCGGCGGGATCTTG
1 TATCCCTGTTAAGAGTGTAGTCCCCATAATATGTACTCACTCTGGTACGGGTCGGCGGGATCTTG
*
1597939 TTCTAGCGGTTGACTTTAACTTGCGGGGCATCTCGAAAGATTGGCAGCTTGTTAGATGAACCCGC
66 TTCTAGCGGTTGACTGTAACTTGCGGGGCATCTCGAAAGATTGGCAGCTTGTTAGATGAACCCGC
*
1598004 GAGTTCTATGTCTAACAAAATCGACCCTTAAACTATTTCCAATTCTCGTTTTGTCTCATTTTGTG
131 GAGTTCTATGTCTAACAAAATCGACCCTTAAACTATTTCCAATTCTCGTCTTGTCTCATTTTGTG
* * * *
1598069 TCTAAATTGTCAATTGTCTTATTTTACTAGAAAAAAAATTGGA-CGTCGTATGGCATCTGTTGTT
196 TCTAAATTGTCAATTGTCTCATTTTACGAGAAAAAAAATT-GACCGTCGTATGGCATCCGTGGTT
1598133 CTTATCGAT
260 CTTATCGAT
* * * *
1598142 TATCCCTGTTAAGGGTGTGGTCTCCATAATATGTACTCAC-CTTGGTACGGGTTGGCGGGATCTT
1 TATCCCTGTTAAGAGTGTAGTCCCCATAATATGTACTCACTC-TGGTACGGGTCGGCGGGATCTT
* *
1598206 GTTCTAG-GAGTTGACTGTAACTTGCGGGGCATCTCGCAAGATTGGCAGCTTGTTAGATGAACCT
65 GTTCTAGCG-GTTGACTGTAACTTGCGGGGCATCTCGAAAGATTGGCAGCTTGTTAGATGAACCC
* * * * * *
1598270 GCGAGTTGTATGTCTAACAAAATTGACCCTT-AACTGTTTTCGATTCTCGTCTTGTCTCGTTTTG
129 GCGAGTTCTATGTCTAACAAAATCGACCCTTAAACTATTTCCAATTCTCGTCTTGTCTCATTTTG
* *
1598334 TGTTTAAATTGTCAATTTTGTCTCATTTTACGAGAAAAAAAATTGACCGTTGTATGGCATCCGTG
194 TGTCTAAATTGTCAA--TTGTCTCATTTTACGAGAAAAAAAATTGACCGTCGTATGGCATCCGTG
1598399 GTTCTTAT
257 GTTCTTAT
1598407 TGACTATTAG
Statistics
Matches: 239, Mismatches: 21, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
267 44 0.18
268 147 0.62
269 48 0.20
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.37
Consensus pattern (268 bp):
TATCCCTGTTAAGAGTGTAGTCCCCATAATATGTACTCACTCTGGTACGGGTCGGCGGGATCTTG
TTCTAGCGGTTGACTGTAACTTGCGGGGCATCTCGAAAGATTGGCAGCTTGTTAGATGAACCCGC
GAGTTCTATGTCTAACAAAATCGACCCTTAAACTATTTCCAATTCTCGTCTTGTCTCATTTTGTG
TCTAAATTGTCAATTGTCTCATTTTACGAGAAAAAAAATTGACCGTCGTATGGCATCCGTGGTTC
TTATCGAT
Found at i:1602828 original size:138 final size:136
Alignment explanation
Indices: 1602657--1602922 Score: 322
Period size: 138 Copynumber: 1.9 Consensus size: 136
1602647 TAAGAAATTT
*
1602657 AATAATAAATAAACAAATACTGAAAATAAAAAAACCAGGTTATTGATTCAATA-CC-GTACAACT
1 AATAATAAATAAACAAATACTGAAAATAAAAAAACAAGGTTATTGATTCAATATCCTGT--AACT
* * * *
1602720 TCACAGCAGTTAGTAAAATAACAAAATCCTAGCATATCATAAGCTAACATCTCATTATATCAGGA
64 CCACAGAAATTA-AAAAATAACAAAAT-CTAGCATATCATAAGCTAACATCTCATTATATCAGGA
1602785 AACTGAAATC
127 AACTGAAATC
* ** * * *
1602795 AATAAT-AATCAAACAAATCCTGAAAATCCAAAAATAAGGTTATTGATTCTATATCCTGTATCTC
1 AATAATAAAT-AAACAAATACTGAAAATAAAAAAACAAGGTTATTGATTCAATATCCTGTAACTC
* * * * *
1602859 CGCAGAAATTAAAAAATAACAAAATCTAGCTTATCATAAGCTACCATCTCGTTCTATCAGGAAA
65 CACAGAAATTAAAAAATAACAAAATCTAGCATATCATAAGCTAACATCTCATTATATCAGGAAA
1602923 TCAACTTCCG
Statistics
Matches: 109, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
136 35 0.32
137 16 0.15
138 54 0.50
139 2 0.02
140 2 0.02
ACGTcount: A:0.46, C:0.18, G:0.09, T:0.26
Consensus pattern (136 bp):
AATAATAAATAAACAAATACTGAAAATAAAAAAACAAGGTTATTGATTCAATATCCTGTAACTCC
ACAGAAATTAAAAAATAACAAAATCTAGCATATCATAAGCTAACATCTCATTATATCAGGAAACT
GAAATC
Found at i:1603056 original size:163 final size:155
Alignment explanation
Indices: 1602818--1603216 Score: 532
Period size: 163 Copynumber: 2.5 Consensus size: 155
1602808 CAAATCCTGA
* *
1602818 AAATCCAAAAATAAGGTTATTGATTCTATATCCTGTATCTCCGCAGAAATT-AAAAAATAACAAA
1 AAATCCAAAAA-AAGGTTATTGATTCTATATCCTGTAACTGCGCAGAAATTGAAAAAATAACAAA
* * **
1602882 ATCTAGCTTATCATAAGCTACCATCTCGTTCTATCAGGAAATCAACTTCCGGATTTAATTTTGGA
65 ATATAGCTTATCATAAGCTACCATCTCGTTCTATCAGGAAATCAACTTCCAGATTTAA-TAAGGA
*
1602947 TTTTAATAATAAATAAACAAATACTGTAAAT
129 ATTTAATAATAAAT--A-AAA-ACTGTAAAT
* *
1602978 AAATCCAAAAAACCAGGTTATTGATTCAATATACTGTAACTGCGCAGAAATTAGAAAAAATAACA
1 AAATCCAAAAAA--AGGTTATTGATTCTATATCCTGTAACTGCGCAGAAATT-GAAAAAATAACA
* *
1603043 AAATTTAGCTTATCATAAGCTACCATCTCGTTCTATCTGGAAATCAACTTCCAGATTTAATAAGG
63 AAATATAGCTTATCATAAGCTACCATCTCGTTCTATCAGGAAATCAACTTCCAGATTTAATAAGG
1603108 AATTTAATAATAAATAAAAACTGTAAAT
128 AATTTAATAATAAATAAAAACTGTAAAT
* * * *
1603136 AAATCCAAAAAAAGGTTATT-ATTCTATATCCTGCAACTGTGCAGCAATTGGAAAAAATGAAAAA
1 AAATCCAAAAAAAGGTTATTGATTCTATATCCTGTAACTGCGCAGAAATT-GAAAAAAT-AACAA
* *
1603200 AATATAGCGTATAATAA
64 AATATAGCTTATCATAA
1603217 ATGATACTAT
Statistics
Matches: 214, Mismatches: 20, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
155 32 0.15
156 26 0.12
158 21 0.10
159 4 0.02
160 12 0.06
161 34 0.16
162 17 0.08
163 68 0.32
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (155 bp):
AAATCCAAAAAAAGGTTATTGATTCTATATCCTGTAACTGCGCAGAAATTGAAAAAATAACAAAA
TATAGCTTATCATAAGCTACCATCTCGTTCTATCAGGAAATCAACTTCCAGATTTAATAAGGAAT
TTAATAATAAATAAAAACTGTAAAT
Found at i:1606713 original size:159 final size:162
Alignment explanation
Indices: 1606367--1606729 Score: 375
Period size: 159 Copynumber: 2.3 Consensus size: 162
1606357 CTCTTGAAAG
* * ** *
1606367 TTTTCACAGATTCACTCAAAGGAAATATAG-AAAGAGCAAAAGGGTATCAGAATTGGTTTCCATT
1 TTTTCACAAATT-ACTC-AAGGAAATACAGCAAA-AGCAAAAGGACATCAGAATTGGTCTCCA-T
* * * * *
1606431 CATGCAAATTCCAAGAAAATTTTAACAAATTCCTCAACGAAATGCAGCATAGAGCAAAAGGGTGT
62 CATGCAAATTCCAAGAAAATTTTAACAAATTACTAAACGAAATACAGCATAAAGCAAAAGGGTAT
* *
1606496 GAAAATTGGTTTCCTCTTGCAAAATTCCCAGAAAAA
127 GAAAATTGATTTCCCCTTGCAAAATTCCCAGAAAAA
* * ** *
1606532 -ATTCACACAGAACT-AAGGAAATACAGCAAAAGCAAAAGGACATCA-AATTTGGTCTCC-TCTT
1 TTTTCACAAATTACTCAAGGAAATACAGCAAAAGCAAAAGGACATCAGAA-TTGGTCTCCATCAT
* * * * *
1606593 GCAAATTCCCAGAAAATTTTCACAAATTACTAAAGGAAATACAGGA-AAAGCAAAAGGGTAT-CA
65 GCAAATTCCAAGAAAATTTTAACAAATTACTAAACGAAATACAGCATAAAGCAAAAGGGTATGAA
1606656 AATTGATTTCTCCCATT-C-AAATTCCCAGAAAAA
130 AATTGATTTC-CCC-TTGCAAAATTCCCAGAAAAA
* * *
1606689 TTTTCACAAATTACTCAAGCAAATACAACAAGAGCAAAAGG
1 TTTTCACAAATTACTCAAGGAAATACAGCAAAAGCAAAAGG
1606730 GTACCTAGCC
Statistics
Matches: 164, Mismatches: 28, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
157 25 0.15
158 26 0.16
159 66 0.40
160 2 0.01
161 32 0.20
162 3 0.02
163 3 0.02
164 7 0.04
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.23
Consensus pattern (162 bp):
TTTTCACAAATTACTCAAGGAAATACAGCAAAAGCAAAAGGACATCAGAATTGGTCTCCATCATG
CAAATTCCAAGAAAATTTTAACAAATTACTAAACGAAATACAGCATAAAGCAAAAGGGTATGAAA
ATTGATTTCCCCTTGCAAAATTCCCAGAAAAA
Found at i:1606725 original size:80 final size:78
Alignment explanation
Indices: 1606362--1606807 Score: 328
Period size: 79 Copynumber: 5.6 Consensus size: 78
1606352 TTTTCCTCTT
* * *
1606362 GAAAGTTTTCACAGATTCACTCAAAGGAAATATAGA-AAGAGCAAAAGGGTATCAGAATTGGTTT
1 GAAAATTTTCACAAATT-ACTC-AAGGAAATACA-ACAAGAGCAAAAGGGTATCA-AATTGGTTT
* * *
1606426 CCATTCATGCAAATTCCAA
62 CC--CCATTCAAATTCCCA
* * * * * * *
1606445 GAAAATTTTAACAAATTCCTCAACGAAATGCAGCATAGAGCAAAAGGGTGTGAAAATTGGTTTCC
1 GAAAATTTTCACAAATTACTCAAGGAAATACAACA-AGAGCAAAAGGGTAT-CAAATTGGTTTCC
*
1606510 TC-TTGCAAAATTCCCA
64 CCATT-C-AAATTCCCA
** * ** * * ** * *
1606526 GAAAAAATTCACACAGAACT-AAGGAAATACAGCAAAAGCAAAAGGACATCAAATTTGGTCTCCT
1 GAAAATTTTCACAAATTACTCAAGGAAATACAACAAGAGCAAAAGGGTATCAAA-TTGGTTTCCC
1606590 C-TTGCAAATTCCCA
65 CATT-CAAATTCCCA
* ** * *
1606604 GAAAATTTTCACAAATTACTAAAGGAAATACAGGAAAAGCAAAAGGGTATCAAATTGATTTCTCC
1 GAAAATTTTCACAAATTACTCAAGGAAATACAACAAGAGCAAAAGGGTATCAAATTGGTTTC-CC
1606669 CATTCAAATTCCCA
65 CATTCAAATTCCCA
* * **** *
1606683 GAAAAATTTTCACAAATTACTCAAGCAAATACAACAAGAGCAAAAGGGTACCTAGCCAGTTTTCC
1 G-AAAATTTTCACAAATTACTCAAGGAAATACAACAAGAGCAAAAGGGTATC-AAATTGGTTTCC
*
1606748 CTCACTCAAATTCCCA
64 C-CATTCAAATTCCCA
* *
1606764 GAAAA-TTTCACAAACTACTCAA-GAAAAACACATCAAGAGCAAAA
1 GAAAATTTTCACAAATTACTCAAGGAAATACA-A-CAAGAGCAAAA
1606808 AAGGGTATTG
Statistics
Matches: 296, Mismatches: 53, Indels: 31
0.78 0.14 0.08
Matches are distributed among these distances:
78 39 0.13
79 86 0.29
80 78 0.26
81 50 0.17
82 28 0.09
83 15 0.05
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (78 bp):
GAAAATTTTCACAAATTACTCAAGGAAATACAACAAGAGCAAAAGGGTATCAAATTGGTTTCCCC
ATTCAAATTCCCA
Found at i:1607581 original size:14 final size:14
Alignment explanation
Indices: 1607543--1607582 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1607533 ACTTCATAAA
*
1607543 TTTAAAATTTAATT
1 TTTAAAATTTTATT
* *
1607557 TTTATATTTTTATT
1 TTTAAAATTTTATT
1607571 TTTAAAATTTTA
1 TTTAAAATTTTA
1607583 ATCATATTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTAAAATTTTATT
Found at i:1611831 original size:14 final size:15
Alignment explanation
Indices: 1611807--1611835 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1611797 ACAAACTCAC
1611807 ACCCAAAAAAGAAAA
1 ACCCAAAAAAGAAAA
1611822 ACCC-AAAAAGAAAA
1 ACCCAAAAAAGAAAA
1611836 TAACCGCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.72, C:0.21, G:0.07, T:0.00
Consensus pattern (15 bp):
ACCCAAAAAAGAAAA
Found at i:1614534 original size:150 final size:150
Alignment explanation
Indices: 1614349--1615083 Score: 650
Period size: 150 Copynumber: 4.9 Consensus size: 150
1614339 AGGAAGTAAC
* ****
1614349 AAAAAACAAGGCAATTAGAGTAAAGGGTATCGAAATAAATTTTTTTTTAAAAAAACACAAACCCA
1 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAA-TTTTAAAAAAAAAAAC-CAAACCCA
* *
1614414 GAGTCAAGAACACCATGAAAGATCAAATGCTCAAGCGAATAACCAATAAAACAGA-GATTTTCAG
64 GAGCCAAGAACACCATGAAAGATCAAATGCTCAAGCGAACAACCAATAAAACA-ATGATTTTCAG
1614478 CAAAATTAGAGATATGAAG-TT-
128 CAAAATTAGAGATATGAAGATTA
* * * *
1614499 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATTTGAAAAAAAAAAACCTAACTCATA
1 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATTTTAAAAAAAAAAACCAAACCCAGA
* * *
1614564 GCCAAGAACAACATGAAAGATCAGATGCTCAAACGAACAACCAATAAAACAATGATTTTCAGCAA
66 GCCAAGAACACCATGAAAGATCAAATGCTCAAGCGAACAACCAATAAAACAATGATTTTCAGCAA
* * * *
1614629 AA-TCGAGCTAGGAAGTTTTAAAAA
131 AATTAGAGATATGAAG-ATT----A
* * * * ** *
1614653 AAAAAACGAGGCAATTAGACTAAAGAGTATTGAGATAAAATTGAAAAAAAAAAAACCTAACCCAG
1 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAAT-AAATTTTAAAAAAAAAAACCAAACCCAG
* * * *
1614718 AGCCAAAAACACCATGAAAGATCAAATGCTCAAGCGAATAACCAATAAAACAATGGTTTTCAGCG
65 AGCCAAGAACACCATGAAAGATCAAATGCTCAAGCGAACAACCAATAAAACAATGATTTTCAGCA
* * **
1614783 AAATCA-A-ACTAAGAAGAAAAA
130 AAATTAGAGA-TATGAAG-ATTA
* * * * *
1614804 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAAAAAATTTGAAAAAAAAACACAAAAACCTAG
1 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATTTTAAAAAAAAAAAC-CAAACCCAG
* *** * * *
1614869 AGCCAAGAATC-TCACCCAAGCTCGAATGCTCATA-TGAACAACCAATAAAACAATGATTTTCAG
65 AGCCAAGAA-CACCATGAAAGATCAAATGCTCA-AGCGAACAACCAATAAAACAATGATTTTCAG
* * *
1614932 C-AAATTCGAGCTATG-AGTGTTA
128 CAAAATTAGAGATATGAAG-ATTA
* * * * ** * * * *
1614954 AAAAAACAAGGCAATTATACTAAAGGGAATTGAAATAAA-ATCGAAAAAACACA-CTAACCCAAA
1 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATTTTAAAAAAAAAAACCAAACCCAGA
* ** * * *
1615017 GCCAAGAATC-TCACCAAAGCTCAAATGCTCAAACGAACAACCAAAAACAACAATGATTTTCAGC
66 GCCAAGAA-CACCATGAAAGATCAAATGCTCAAGCGAACAACCAATAA-AACAATGATTTTCAGC
1615081 AAA
129 AAA
1615084 TTCTAGCTGG
Statistics
Matches: 481, Mismatches: 85, Indels: 39
0.80 0.14 0.06
Matches are distributed among these distances:
146 1 0.00
147 58 0.12
148 83 0.17
149 25 0.05
150 96 0.20
151 92 0.19
152 2 0.00
154 32 0.07
155 92 0.19
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.18
Consensus pattern (150 bp):
AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATTTTAAAAAAAAAAACCAAACCCAGA
GCCAAGAACACCATGAAAGATCAAATGCTCAAGCGAACAACCAATAAAACAATGATTTTCAGCAA
AATTAGAGATATGAAGATTA
Found at i:1614613 original size:148 final size:150
Alignment explanation
Indices: 1614349--1615083 Score: 693
Period size: 151 Copynumber: 4.9 Consensus size: 150
1614339 AGGAAGTAAC
* ***** *
1614349 AAAAAACAAGGCAATTAGAGTAAAGGGTATCGAAATAAATTTTTTTTTAAAAAAACACAAACCCA
1 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAA-TTTGAAAAAAAAAAAC-CTAACCCA
* * *
1614414 GAGTCAAGAACACCATGAAAGATCAAATGCTCAAGCGAATAACCAATAAAACAGA-GATTTTCAG
64 GAGCCAAGAACACCATGAAAGATCAAATGCTCAAACGAACAACCAATAAAACA-ATGATTTTCAG
1614478 CAAAATTAGAGATATGAAG-TT-
128 CAAAATTAGAGATATGAAGATTA
* *
1614499 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATTTGAAAAAAAAAAACCTAACTCATA
1 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATTTGAAAAAAAAAAACCTAACCCAGA
* *
1614564 GCCAAGAACAACATGAAAGATCAGATGCTCAAACGAACAACCAATAAAACAATGATTTTCAGCAA
66 GCCAAGAACACCATGAAAGATCAAATGCTCAAACGAACAACCAATAAAACAATGATTTTCAGCAA
* * * *
1614629 AA-TCGAGCTAGGAAGTTTTAAAAA
131 AATTAGAGATATGAAG-ATT----A
* * * * *
1614653 AAAAAACGAGGCAATTAGACTAAAGAGTATTGAGATAAAATTGAAAAAAAAAAAACCTAACCCAG
1 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATTTG-AAAAAAAAAAACCTAACCCAG
* * * * *
1614718 AGCCAAAAACACCATGAAAGATCAAATGCTCAAGCGAATAACCAATAAAACAATGGTTTTCAGCG
65 AGCCAAGAACACCATGAAAGATCAAATGCTCAAACGAACAACCAATAAAACAATGATTTTCAGCA
* * **
1614783 AAATCA-A-ACTAAGAAGAAAAA
130 AAATTAGAGA-TATGAAG-ATTA
* * ** *
1614804 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAAAAAATTTGAAAAAAAAACACAAAAACCTAG
1 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATTTGAAAAAAAAAAAC-CTAACCCAG
* *** * * * *
1614869 AGCCAAGAATC-TCACCCAAGCTCGAATGCTCATATGAACAACCAATAAAACAATGATTTTCAGC
65 AGCCAAGAA-CACCATGAAAGATCAAATGCTCAAACGAACAACCAATAAAACAATGATTTTCAGC
* * *
1614933 -AAATTCGAGCTATG-AGTGTTA
129 AAAATTAGAGATATGAAG-ATTA
* * * * * * * *
1614954 AAAAAACAAGGCAATTATACTAAAGGGAATTGAAATAAAATCG-AAAAAACACA-CTAACCCAAA
1 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATTTGAAAAAAAAAAACCTAACCCAGA
* ** * *
1615017 GCCAAGAATC-TCACCAAAGCTCAAATGCTCAAACGAACAACCAAAAACAACAATGATTTTCAGC
66 GCCAAGAA-CACCATGAAAGATCAAATGCTCAAACGAACAACCAATAA-AACAATGATTTTCAGC
1615081 AAA
129 AAA
1615084 TTCTAGCTGG
Statistics
Matches: 483, Mismatches: 85, Indels: 35
0.80 0.14 0.06
Matches are distributed among these distances:
147 59 0.12
148 83 0.17
149 24 0.05
150 93 0.19
151 98 0.20
152 1 0.00
154 38 0.08
155 87 0.18
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.18
Consensus pattern (150 bp):
AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATTTGAAAAAAAAAAACCTAACCCAGA
GCCAAGAACACCATGAAAGATCAAATGCTCAAACGAACAACCAATAAAACAATGATTTTCAGCAA
AATTAGAGATATGAAGATTA
Found at i:1617344 original size:14 final size:14
Alignment explanation
Indices: 1617325--1617352 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1617315 ATCCAATCGT
1617325 GTTCTAATAACACA
1 GTTCTAATAACACA
1617339 GTTCTAATAACACA
1 GTTCTAATAACACA
1617353 TGACAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (14 bp):
GTTCTAATAACACA
Found at i:1619457 original size:2 final size:2
Alignment explanation
Indices: 1619450--1619477 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1619440 TTTGATTTTG
1619450 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
1619478 CCTCTTCCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1626308 original size:31 final size:31
Alignment explanation
Indices: 1626250--1626311 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1626240 TCGGTTAAAA
* * *
1626250 ATAATTAAATTTCAATTAATATTTATATTTT
1 ATAATTAAATTTCAATAAAAATATATATTTT
1626281 ATAATTAAA-TTCAAGTAAAAATATATATTTT
1 ATAATTAAATTTCAA-TAAAAATATATATTTT
1626312 CTAAATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (31 bp):
ATAATTAAATTTCAATAAAAATATATATTTT
Found at i:1627878 original size:30 final size:28
Alignment explanation
Indices: 1627839--1627920 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 28
1627829 AGAATTGAAT
*
1627839 CAAAACAAAATTTTACATATAAAATTACA
1 CAAAACAAAA-TTCACATATAAAATTACA
*
1627868 CAAAATCAAAATTCACGTATAAAATTACA
1 CAAAA-CAAAATTCACATATAAAATTACA
*
1627897 CATTAAACTAAAATTCATATATAA
1 CA--AAAC-AAAATTCACATATAA
1627921 TTTTAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 23 0.51
30 6 0.13
31 16 0.36
ACGTcount: A:0.56, C:0.15, G:0.01, T:0.28
Consensus pattern (28 bp):
CAAAACAAAATTCACATATAAAATTACA
Found at i:1631916 original size:235 final size:235
Alignment explanation
Indices: 1631211--1632041 Score: 1023
Period size: 234 Copynumber: 3.6 Consensus size: 235
1631201 AGACTACCCC
* *
1631211 TTCAAGATTTTGTTGTCCATACATAACCATGAATTTAGCCTTTATTTATTTCCCCC-----TAAA
1 TTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTA-TTCCCCCTAAAATAAA
* * *
1631271 ATCAGTCAAAATTCATAGAAAGTCCCTCTATTATTTGTATTTTTCACAAATTTTAGTCTCTCTAC
65 ATCGGTCAAATTTCATAGAAAGTCCCTCTATTAATTGT-TTTTTCACAAA-TTTAGTCTCTCTAC
* * * * * *
1631336 TATAATTTGATCATTTCTTGGGTGAGTGGAGAGCATCGAGTCAAGTTACAATTCAGGAGAGTGGA
128 TATAATTTGATCATTTTTTTGGTGAATGGAGAGTATCGAGTCAAGTTACAGTTCAGGAGAGTGGG
* *
1631401 ATTGTATCAACAAAATTTGAATAATGGTCATTGAGAGTGCCCT
193 ATTATATCAACAAAGTTTGAATAATGGTCATTGAGAGTGCCCT
* *
1631444 TTCAAGATTTTGTTGTCCAAATATAACCATTAATTTAGCATTTATTTA-TCCCCCTATATAATAA
1 TTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTATTCCCCCTA-A-AATAA
* *
1631508 AATCGGTCAAATTTCATAGAAACTCCCTCTATT-ATT-TTCTTTCACAAATTTAGTCTCTCTACT
64 AATCGGTCAAATTTCATAGAAAGTCCCTCTATTAATTGTTTTTTCACAAATTTAGTCTCTCTACT
** * * * *
1631571 ATTGTTTGATTA-TTTCTTGGATGAATGGAGAGTATCGAGTCAAGTTACAGTTCAAGAGAGTGAG
129 ATAATTTGATCATTTTTTTGG-TGAATGGAGAGTATCGAGTCAAGTTACAGTTCAGGAGAGTGGG
* *
1631635 ATTATATCAACAAAGTTTGAACAATGGTCATTTAGAGTGCCCT
193 ATTATATCAACAAAGTTTGAATAATGGTCATTGAGAGTGCCCT
*** * *
1631678 TTCAAGATTTTGTTGTCCATGGATAGCCATGAATTTAGCCTTTATTTACT-CCCCTATATAATAA
1 TTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTATTCCCCCTA-A-AATAA
*
1631742 AATGGGTCAAATTTCATAGAAAGTCCCTCTATTAATT-TTTTTTCACAAATTTAGTCTCTCTACT
64 AATCGGTCAAATTTCATAGAAAGTCCCTCTATTAATTGTTTTTTCACAAATTTAGTCTCTCTACT
* * * *
1631806 ATAATTTAATCATTTTTTTGGTGAATGGAGGGTACCGAATCAAGTTACAGTTCAGGAGAGTGGGA
129 ATAATTTGATCATTTTTTTGGTGAATGGAGAGTATCGAGTCAAGTTACAGTTCAGGAGAGTGGGA
1631871 TTATATCAACAAAGTTTGAATAATGGTCATTGAGAGT-CTCCT
194 TTATATCAACAAAGTTTGAATAATGGTCATTGAGAGTGC-CCT
* * * * *
1631913 TTCAAAATTTTGTTGTTCAAATATAACCGTGAATTTAGCCTTCATGTATT-CCCC-----TAAAA
1 TTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTATTCCCCCTAAAATAAAA
* * * * * * * *
1631972 TCGATCAAATTTCATAAAAAGTCCCTCTATTATTTGTTTTTTTACGAATTTAATCTCTTTACTGT
66 TCGGTCAAATTTCATAGAAAGTCCCTCTATTAATTGTTTTTTCACAAATTTAGTCTCTCTACTAT
1632037 AATTT
131 AATTT
1632042 TTTTGAGGGT
Statistics
Matches: 520, Mismatches: 65, Indels: 30
0.85 0.11 0.05
Matches are distributed among these distances:
228 36 0.07
229 29 0.06
231 6 0.01
233 49 0.09
234 188 0.36
235 169 0.32
236 8 0.02
237 2 0.00
238 33 0.06
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (235 bp):
TTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTATTCCCCCTAAAATAAAA
TCGGTCAAATTTCATAGAAAGTCCCTCTATTAATTGTTTTTTCACAAATTTAGTCTCTCTACTAT
AATTTGATCATTTTTTTGGTGAATGGAGAGTATCGAGTCAAGTTACAGTTCAGGAGAGTGGGATT
ATATCAACAAAGTTTGAATAATGGTCATTGAGAGTGCCCT
Found at i:1651818 original size:2 final size:2
Alignment explanation
Indices: 1651811--1651837 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1651801 TTCTGCTTTC
1651811 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 T
1651838 TAGTCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1658467 original size:24 final size:24
Alignment explanation
Indices: 1658422--1658470 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1658412 TTAAAAAATT
*
1658422 AAATTAATTTTTATCACTTTTAAA
1 AAATTAATTTTTATCACATTTAAA
*
1658446 AAATTATATTTTTATTA-ATTTAAA
1 AAATTA-ATTTTTATCACATTTAAA
1658470 A
1 A
1658471 TTTAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATTAATTTTTATCACATTTAAA
Found at i:1663132 original size:16 final size:16
Alignment explanation
Indices: 1663085--1663132 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1663075 CGAGTAATTT
*
1663085 TTTTAAAAAAAAAT-A
1 TTTTATAAAAAAATAA
* *
1663100 TTCTTATAATAATATAA
1 TT-TTATAAAAAAATAA
1663117 TTTTATAAAAAAATAA
1 TTTTATAAAAAAATAA
1663133 GATTATTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 2 0.08
16 21 0.81
17 3 0.12
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
TTTTATAAAAAAATAA
Found at i:1663327 original size:21 final size:18
Alignment explanation
Indices: 1663289--1663327 Score: 51
Period size: 21 Copynumber: 2.0 Consensus size: 18
1663279 TAAATAACAC
1663289 AAATATCAATTTTTTTTT
1 AAATATCAATTTTTTTTT
1663307 AAATAATCACATTTATTTTTT
1 AAAT-ATCA-ATTT-TTTTTT
1663328 TTACTCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 4 0.22
21 6 0.33
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATATCAATTTTTTTTT
Found at i:1664888 original size:24 final size:24
Alignment explanation
Indices: 1664861--1664922 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
1664851 TAAAACTCAC
* *
1664861 ATATGCGTAATTGTCTATGATGGA
1 ATATGCGCAATTATCTATGATGGA
* *
1664885 ATATACACAATTATCTATGATGGA
1 ATATGCGCAATTATCTATGATGGA
*
1664909 ACATGCGCAATTAT
1 ATATGCGCAATTAT
1664923 ACATAGGAGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (24 bp):
ATATGCGCAATTATCTATGATGGA
Found at i:1685623 original size:42 final size:42
Alignment explanation
Indices: 1685548--1685629 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
1685538 AAAATTACCA
* *
1685548 AATTTCATACATAATGTGACTAGAAATTGGAATAGATCTAAAC
1 AATTTCATACATAATGTGACTAGAAACTAGAATA-ATCTAAAC
*
1685591 AATTT-ATACATGATGTGACTTA-AAACTAGAATAATCTAA
1 AATTTCATACATAATGTGAC-TAGAAACTAGAATAATCTAA
1685630 GGGCAAAGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 6 0.17
42 22 0.63
43 7 0.20
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (42 bp):
AATTTCATACATAATGTGACTAGAAACTAGAATAATCTAAAC
Found at i:1689796 original size:27 final size:28
Alignment explanation
Indices: 1689745--1689799 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
1689735 ACTCTATCAC
*
1689745 TAAAGAAATCTAAATTTAGGGACTAAAT
1 TAAAAAAATCTAAATTTAGGGACTAAAT
* *
1689773 TAAAAAAATC-AAATTTTGGTACTAAAT
1 TAAAAAAATCTAAATTTAGGGACTAAAT
1689800 GATGCTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (28 bp):
TAAAAAAATCTAAATTTAGGGACTAAAT
Found at i:1696092 original size:15 final size:15
Alignment explanation
Indices: 1696072--1696105 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1696062 GTTCAAAAAA
1696072 ATATTAAAATATTTT
1 ATATTAAAATATTTT
* *
1696087 ATATTAAATTTTTTT
1 ATATTAAAATATTTT
1696102 ATAT
1 ATAT
1696106 ATTTCTATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTAAAATATTTT
Found at i:1703491 original size:100 final size:100
Alignment explanation
Indices: 1703318--1703511 Score: 352
Period size: 100 Copynumber: 1.9 Consensus size: 100
1703308 ACATTTAGGA
*
1703318 CACCAAAGTCCCAAACTATCTCATGGATTTTAAATTGGTCCCAAAACTTCATAAAGTTCTAAGTC
1 CACCAAAGTCCCAAACTATCTCATGGATTTTAAATTGGTCCCAAAACTTCAAAAAGTTCTAAGTC
1703383 AATTATCAAGCATTTGTGTTGTATCAAATTAATTG
66 AATTATCAAGCATTTGTGTTGTATCAAATTAATTG
* *
1703418 CACCAAAGTCCCAAACTATCTCATGGATTTTAAATTGGTCTCAAAACTTCAAAAAGTTTTAAGTC
1 CACCAAAGTCCCAAACTATCTCATGGATTTTAAATTGGTCCCAAAACTTCAAAAAGTTCTAAGTC
*
1703483 AATTATCAAGTATTTGTGTTGTATCAAAT
66 AATTATCAAGCATTTGTGTTGTATCAAAT
1703512 AAGTCCTTTT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 90 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.35
Consensus pattern (100 bp):
CACCAAAGTCCCAAACTATCTCATGGATTTTAAATTGGTCCCAAAACTTCAAAAAGTTCTAAGTC
AATTATCAAGCATTTGTGTTGTATCAAATTAATTG
Found at i:1718286 original size:3 final size:3
Alignment explanation
Indices: 1718273--1718304 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1718263 CTAACTCAAG
*
1718273 TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1718305 CATGTTAAGC
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:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1719923 original size:29 final size:29
Alignment explanation
Indices: 1719874--1719930 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1719864 TTATAGAGAT
*
1719874 TGGATCGAATTAATCAATATATTATTAAA
1 TGGATCGAATTAATCAATATACTATTAAA
**
1719903 TGGATCG-ATGTAATCCTTATACTATTAA
1 TGGATCGAAT-TAATCAATATACTATTAA
1719931 TAATACAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TGGATCGAATTAATCAATATACTATTAAA
Found at i:1724236 original size:18 final size:17
Alignment explanation
Indices: 1724213--1724258 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
1724203 AAGGATAACA
1724213 TCATCT-TTATTTGTTTTT
1 TCATCTCTT-TTT-TTTTT
1724231 TCATCTCTTTTTTTTTT
1 TCATCTCTTTTTTTTTT
*
1724248 T-ATCCCTTTTT
1 TCATCTCTTTTT
1724259 ATCTTATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 9 0.35
17 6 0.23
18 9 0.35
19 2 0.08
ACGTcount: A:0.09, C:0.17, G:0.02, T:0.72
Consensus pattern (17 bp):
TCATCTCTTTTTTTTTT
Found at i:1725897 original size:132 final size:129
Alignment explanation
Indices: 1725591--1725983 Score: 491
Period size: 132 Copynumber: 3.0 Consensus size: 129
1725581 TGGAGTGAGC
* * *
1725591 CCAGTAATTAATCTTTCGCATTCTATAGGGCCATTAAGGGGTTAGATGTTGACCACGAGTTTTAA
1 CCAGTAACTAATCTTTCGCATTCTATA-GGCCATTAAGGGGATAGATGTTGGCCACGAGTTTTAA
* * *
1725656 AGCTGCTCCATACCCAAGGCGATAATCAAACCCTCGATCATTGGTTGAT-GTAGGAAAGAACCTT
65 AGCTGCTCCATACCCAAGGCGATGATCAAA-CCTCGACCATT-GTT-ATGGTAGGAAAG-ATCTT
1725720 GCCA
126 GCCA
* * *
1725724 CCAATAACTAATCATCCGCATTCTATAGGCCCATTAAGGGGATAGATGTTGGCCACGAGTTTTAA
1 CCAGTAACTAATCTTTCGCATTCTATAGG-CCATTAAGGGGATAGATGTTGGCCACGAGTTTTAA
** * * * * *
1725789 AATTGCTTCATACCTAATGTGAGGATCAAACCTCGACCATTAGTTATGGTAGGAAAGATCTTAGC
65 AGCTGCTCCATACCCAAGGCGATGATCAAACCTCGACCATT-GTTATGGTAGGAAAGATCTT-GC
1725854 CA
128 CA
* * * *
1725856 CCAGTAACTAATCTTTCACATTGTGTAGGCTCATTAAGGGGATAGATGTTGGTCACGAGTTTTAA
1 CCAGTAACTAATCTTTCGCATTCTATAGGC-CATTAAGGGGATAGATGTTGGCCACGAGTTTTAA
*
1725921 AGCTGCTCCATACCCAAGGCGATGATCAAACTCTCGACCATTGATTAAGGTAGGAAAGATCTT
65 AGCTGCTCCATACCCAAGGCGATGATCAAAC-CTCGACCATTG-TTATGGTAGGAAAGATCTT
1725984 TGTTATCTCA
Statistics
Matches: 222, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
131 7 0.03
132 109 0.49
133 106 0.48
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (129 bp):
CCAGTAACTAATCTTTCGCATTCTATAGGCCATTAAGGGGATAGATGTTGGCCACGAGTTTTAAA
GCTGCTCCATACCCAAGGCGATGATCAAACCTCGACCATTGTTATGGTAGGAAAGATCTTGCCA
Found at i:1727480 original size:25 final size:25
Alignment explanation
Indices: 1727434--1727484 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
1727424 AAATGTTTGA
1727434 TTGAATTCAAGTCAAGCATCGAGCT
1 TTGAATTCAAGTCAAGCATCGAGCT
*
1727459 TTGAATTTCATGTCAAGC-TCGAGCT
1 TTGAA-TTCAAGTCAAGCATCGAGCT
1727484 T
1 T
1727485 AGCTCGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (25 bp):
TTGAATTCAAGTCAAGCATCGAGCT
Found at i:1737135 original size:20 final size:21
Alignment explanation
Indices: 1737093--1737135 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
1737083 AACGTATTAA
*
1737093 AAATATTTGAAAGTAAAAGAG
1 AAATATTTGAAAGCAAAAGAG
* *
1737114 AAATTTTTG-AAGCAAAATAG
1 AAATATTTGAAAGCAAAAGAG
1737134 AA
1 AA
1737136 GAAGAAGAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.16, T:0.26
Consensus pattern (21 bp):
AAATATTTGAAAGCAAAAGAG
Found at i:1737140 original size:3 final size:3
Alignment explanation
Indices: 1737132--1737160 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1737122 GAAGCAAAAT
1737132 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1737161 GCCTTGGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1738323 original size:17 final size:18
Alignment explanation
Indices: 1738301--1738338 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1738291 TAGTTTCAAA
*
1738301 TATTATATTTTA-TTATT
1 TATTATATGTTATTTATT
1738318 TATTATATGTTATTTATT
1 TATTATATGTTATTTATT
1738336 TAT
1 TAT
1738339 ACATGCACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATATGTTATTTATT
Found at i:1743917 original size:20 final size:20
Alignment explanation
Indices: 1743881--1743922 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1743871 TTATTTTAAT
*
1743881 AAAATTTGAAAGTAAAAGAG
1 AAAATTTGAAAGCAAAAGAG
*
1743901 AAAATTTTG-AAGCAAAATAG
1 AAAA-TTTGAAAGCAAAAGAG
1743921 AA
1 AA
1743923 GAAGAAGCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.60, C:0.02, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAATTTGAAAGCAAAAGAG
Found at i:1748372 original size:31 final size:31
Alignment explanation
Indices: 1748337--1748396 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1748327 AAAAAATCTT
* *
1748337 AACAACTCAGTGACTTAAATAAAAACTTTTG
1 AACAACTCAATAACTTAAATAAAAACTTTTG
* *
1748368 AACAAGTCAATAACTTAAATGAAAACTTT
1 AACAACTCAATAACTTAAATAAAAACTTT
1748397 CGAAAACCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.28
Consensus pattern (31 bp):
AACAACTCAATAACTTAAATAAAAACTTTTG
Found at i:1749199 original size:31 final size:30
Alignment explanation
Indices: 1749161--1749256 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
1749151 TAGTTTACCC
*
1749161 AAAAATTTAAGGAATTTAATTAAAATTTTTGA
1 AAAAATTT-AGGAATTTAATTAAAA-TTTTCA
* ** *
1749193 AAAATTTTAGGGGTTTCA-TAAGAATTTTCA
1 AAAAATTTAGGAATTTAATTAA-AATTTTCA
1749223 AAAAATTTA-GAAGGTTTAATTAAAATTTTCA
1 AAAAATTTAGGAA--TTTAATTAAAATTTTCA
1749254 AAA
1 AAA
1749257 CTTTTGAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
29 1 0.02
30 16 0.31
31 24 0.47
32 10 0.20
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (30 bp):
AAAAATTTAGGAATTTAATTAAAATTTTCA
Found at i:1749232 original size:30 final size:31
Alignment explanation
Indices: 1749175--1749256 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
1749165 ATTTAAGGAA
* * *
1749175 TTTAATTAAAATTTTTGAAAAATTTTAG-GGG
1 TTTAATTAAAA-TTTTCAAAAAATTTAGAAGG
*
1749206 TTTCA-TAAGAATTTTCAAAAAATTTAGAAGG
1 TTTAATTAA-AATTTTCAAAAAATTTAGAAGG
1749237 TTTAATTAAAATTTTCAAAA
1 TTTAATTAAAATTTTCAAAA
1749257 CTTTTGAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
30 17 0.40
31 23 0.53
32 3 0.07
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.41
Consensus pattern (31 bp):
TTTAATTAAAATTTTCAAAAAATTTAGAAGG
Found at i:1749320 original size:29 final size:30
Alignment explanation
Indices: 1749277--1749341 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
1749267 GCTTAATTGG
**
1749277 AATTTCTAAAAATTTTGGGGGC-TAATAAA
1 AATTTCTAAAAATTTAAGGGGCATAATAAA
1749306 AATTT-TAAAACATTTAAGGGGCATAATAAA
1 AATTTCTAAAA-ATTTAAGGGGCATAATAAA
1749336 AATTTC
1 AATTTC
1749342 AAACTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 5 0.16
29 14 0.45
30 12 0.39
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.34
Consensus pattern (30 bp):
AATTTCTAAAAATTTAAGGGGCATAATAAA
Found at i:1749780 original size:18 final size:18
Alignment explanation
Indices: 1749753--1749787 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1749743 TTCCTTTTAC
*
1749753 CATAATTTATGCATAATA
1 CATAACTTATGCATAATA
1749771 CATAACTTATGCATAAT
1 CATAACTTATGCATAAT
1749788 GCAGGGACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (18 bp):
CATAACTTATGCATAATA
Found at i:1762279 original size:2 final size:2
Alignment explanation
Indices: 1762272--1762314 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1762262 GTGAAAGGGG
1762272 GT GT GT GT GT GT GT GT 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 GT GT GT GT GT GT GT GT
1762314 G
1 G
1762315 GTGATTTTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:1764180 original size:31 final size:30
Alignment explanation
Indices: 1764145--1764206 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
1764135 TTAGTGATTT
*
1764145 AAATAAAATCTTTCAAATAGTTCAATTACTA
1 AAATAAAATCTTTCAAATAATTCAA-TACTA
* **
1764176 AAATAAAATTTTTTGAATAATTCAATACTA
1 AAATAAAATCTTTCAAATAATTCAATACTA
1764206 A
1 A
1764207 TTTTGTAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 6 0.22
31 21 0.78
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.37
Consensus pattern (30 bp):
AAATAAAATCTTTCAAATAATTCAATACTA
Found at i:1764916 original size:11 final size:11
Alignment explanation
Indices: 1764902--1764936 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1764892 ATATCCAAAC
1764902 AATAACAACAA
1 AATAACAACAA
* *
1764913 AATAATAGCAA
1 AATAACAACAA
1764924 AATAACAACAA
1 AATAACAACAA
1764935 AA
1 AA
1764937 AAGGAAGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.71, C:0.14, G:0.03, T:0.11
Consensus pattern (11 bp):
AATAACAACAA
Found at i:1767458 original size:31 final size:29
Alignment explanation
Indices: 1767423--1767485 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
1767413 TCATTTATAT
1767423 TTTTATAATTTATAAAAAAATTAAATTAAAA
1 TTTTATAATTT-TAAAAAAA-TAAATTAAAA
* * *
1767454 TTTTATCATTTTTAAAAAATAAATTATAA
1 TTTTATAATTTTAAAAAAATAAATTAAAA
1767483 TTT
1 TTT
1767486 GTTTATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 12 0.41
30 7 0.24
31 10 0.34
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTTATAATTTTAAAAAAATAAATTAAAA
Found at i:1767484 original size:29 final size:31
Alignment explanation
Indices: 1767417--1767485 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1767407 GACTATTCAT
*
1767417 TTATATTTTTATAATTTATAAAAAAATTAAA
1 TTATAATTTTATAATTTATAAAAAAATTAAA
* * *
1767448 TTAAAATTTTATCATTT-TTAAAAAA-TAAA
1 TTATAATTTTATAATTTATAAAAAAATTAAA
1767477 TTATAATTT
1 TTATAATTT
1767486 GTTTATATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 12 0.36
30 7 0.21
31 14 0.42
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (31 bp):
TTATAATTTTATAATTTATAAAAAAATTAAA
Found at i:1770861 original size:104 final size:104
Alignment explanation
Indices: 1770681--1770874 Score: 370
Period size: 104 Copynumber: 1.9 Consensus size: 104
1770671 ATCAAAATTC
*
1770681 AAAATAATTTTATTCTCCAATTTCCAACAATAACCGTCAAATCGATGAAGATCTAAAATATGTTT
1 AAAATAATTTTATTCTCCAATTTCCAACAATAACCGTCAAATCGATGAAAATCTAAAATATGTTT
*
1770746 CTATCCGTCAATGAGATTTGATCTAAAATATGAAGATCT
66 CTATCCGTCAATGAGAATTGATCTAAAATATGAAGATCT
1770785 AAAATAATTTTATTCTCCAATTTCCAACAATAACCGTCAAATCGATGAAAATCTAAAATATGTTT
1 AAAATAATTTTATTCTCCAATTTCCAACAATAACCGTCAAATCGATGAAAATCTAAAATATGTTT
1770850 CTATCCGTCAATGAGAATTGATCTA
66 CTATCCGTCAATGAGAATTGATCTA
1770875 TTGTACCAAT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 88 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.34
Consensus pattern (104 bp):
AAAATAATTTTATTCTCCAATTTCCAACAATAACCGTCAAATCGATGAAAATCTAAAATATGTTT
CTATCCGTCAATGAGAATTGATCTAAAATATGAAGATCT
Found at i:1775262 original size:23 final size:23
Alignment explanation
Indices: 1775229--1775273 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1775219 GAGCTTGCTA
*
1775229 GGTGTACGTATAAAAATATATAT
1 GGTGTAAGTATAAAAATATATAT
*
1775252 GGTGTAAGTATAACAATATATA
1 GGTGTAAGTATAAAAATATATA
1775274 CACACGCACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.33
Consensus pattern (23 bp):
GGTGTAAGTATAAAAATATATAT
Found at i:1779970 original size:16 final size:17
Alignment explanation
Indices: 1779931--1779971 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1779921 ATAATAAAAA
1779931 TATAATTTTATTATTTT
1 TATAATTTTATTATTTT
*
1779948 AAT-ATTTTA-TATTTT
1 TATAATTTTATTATTTT
1779963 TATAATTTT
1 TATAATTTT
1779972 TAAAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 8 0.38
16 11 0.52
17 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATAATTTTATTATTTT
Found at i:1789583 original size:26 final size:26
Alignment explanation
Indices: 1789543--1789594 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1789533 TACGGATACC
*
1789543 TTAATTATAGTTTCTTATTCTACAAG
1 TTAATTATAGATTCTTATTCTACAAG
* *
1789569 TTAATTTTAGATTCTTGTTCTACAAG
1 TTAATTATAGATTCTTATTCTACAAG
1789595 ACTAAAACCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.50
Consensus pattern (26 bp):
TTAATTATAGATTCTTATTCTACAAG
Found at i:1795687 original size:28 final size:27
Alignment explanation
Indices: 1795653--1795715 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
1795643 TATTTCTTAA
1795653 ATTTTTTAAAATAT-ATATTTATATTAT
1 ATTTTTTAAAATATGATATTTATA-TAT
* * *
1795680 ATTATTTTAATATTTGATATTTTTATAT
1 ATT-TTTTAAAATATGATATTTATATAT
1795708 ATTTTTTA
1 ATTTTTTA
1795716 TTTATTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 8 0.26
28 15 0.48
29 8 0.26
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
ATTTTTTAAAATATGATATTTATATAT
Found at i:1800356 original size:22 final size:22
Alignment explanation
Indices: 1800317--1800359 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1800307 CCACTCTGAC
*
1800317 TCTTTCCTTCCTATTCCTTCCT
1 TCTTTCCTTCCTACTCCTTCCT
1800339 TCTTTCCTTCACT-CTCCTTCC
1 TCTTTCCTTC-CTACTCCTTCC
1800360 ATTTCCTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.05, C:0.44, G:0.00, T:0.51
Consensus pattern (22 bp):
TCTTTCCTTCCTACTCCTTCCT
Found at i:1802012 original size:17 final size:17
Alignment explanation
Indices: 1801990--1802024 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1801980 ATAAAAAAAG
1801990 TATGAGTTTTGTATCAT
1 TATGAGTTTTGTATCAT
1802007 TATGAGTTTTGTATCAT
1 TATGAGTTTTGTATCAT
1802024 T
1 T
1802025 CTCCTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (17 bp):
TATGAGTTTTGTATCAT
Done.