Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 3 of 344
Found at i:976292 original size:51 final size:50
Alignment explanation
Indices: 976232--976352 Score: 136
Period size: 51 Copynumber: 2.4 Consensus size: 50
976222 TTGCCTTAAA
*
976232 ATTTACACATTCTGTCAATTTTGTCCTGATTAAACAAATTTAACTCATAAT
1 ATTTACACATTCTGTCAATTTTATCCTGATTAAACAAATTTAAC-CATAAT
* * * * *
976283 ATTTACACATT-TCGCCCATTTTATTCTGATTTAACAAATTTAACCTTAAT
1 ATTTACACATTCT-GTCAATTTTATCCTGATTAAACAAATTTAACCATAAT
*
976333 ATTTATACATATCATGTCAA
1 ATTTACACAT-TC-TGTCAA
976353 CATTTACACG
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
50 15 0.26
51 38 0.67
52 3 0.05
53 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (50 bp):
ATTTACACATTCTGTCAATTTTATCCTGATTAAACAAATTTAACCATAAT
Found at i:977093 original size:3 final size:3
Alignment explanation
Indices: 977085--977109 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
977075 TTATTAAGGA
977085 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
977110 ATTCCAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:979405 original size:131 final size:131
Alignment explanation
Indices: 979263--979537 Score: 288
Period size: 131 Copynumber: 2.1 Consensus size: 131
979253 CCGAATATTG
* * * * *
979263 CCTTCGTTTTAACAGATTTTTAGA-AGACAC-GAGTGAAATTTTGAAGGGATATTTGATTATTTT
1 CCTTCGTTTTAACAGATTTTTA-ATA-AC-CGGAGTGAAATTCTAAAGGGACATTCGATTACTTT
* *
979326 AAGCAAACGAGAAATTGCAACTCAGCACATTAGGGCACGATTCCGTGAATTGCCAAATATCGCAA
63 AAGCAAACGAGAAATTGCAACCCAACACATTAGGGCACGATTCCGTGAATTGCCAAATATCGCAA
979391 ATCT
128 ATCT
** * * *
979395 CCTTCG-TTTAAGGGATTTTTAATAACCGTGGGTGAAATTCTAAAGGGACCTTCGATTACTTTGA
1 CCTTCGTTTTAACAGATTTTTAATAACCG-GAGTGAAATTCTAAAGGGACATTCGATTACTTTAA
* ** ** * * *
979459 GCAAACGAGGAATTGCAACCCAACATGTTAGGGCACGATTCCACGAATTACCAAGTATC-AAATA
65 GCAAACGAGAAATTGCAACCCAACACATTAGGGCACGATTCCGTGAATTGCCAAATATCGCAA-A
*
979523 TCG
129 TCT
979526 CCTTCGTTTTAA
1 CCTTCGTTTTAA
979538 AGGAAATTGT
Statistics
Matches: 117, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
129 1 0.01
130 5 0.04
131 100 0.85
132 11 0.09
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (131 bp):
CCTTCGTTTTAACAGATTTTTAATAACCGGAGTGAAATTCTAAAGGGACATTCGATTACTTTAAG
CAAACGAGAAATTGCAACCCAACACATTAGGGCACGATTCCGTGAATTGCCAAATATCGCAAATC
T
Found at i:984061 original size:13 final size:14
Alignment explanation
Indices: 984045--984080 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
984035 CAATCTCATA
984045 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
984058 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
984071 TCTC-ATTTCA
1 TCTCAATTTCA
984081 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:984070 original size:18 final size:19
Alignment explanation
Indices: 984032--984072 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
984022 TGGTTCATGT
984032 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
984051 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
984069 TTTC
1 TTTC
984073 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:984735 original size:15 final size:15
Alignment explanation
Indices: 984711--984763 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
984701 ATATATATAT
*
984711 TATAATTTCAATCAA
1 TATAAATTCAATCAA
984726 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* * *
984741 AATGATTTCAATCAA
1 TATAAATTCAATCAA
984756 TATAAATT
1 TATAAATT
984764 TGATAAATTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:985534 original size:15 final size:15
Alignment explanation
Indices: 985495--985541 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
985485 CCTGTTTCTT
985495 CTCTGTTTCGTTTCCA
1 CTCTGTTTC-TTTCCA
*
985511 CATTCTGTTTCTTTTCA
1 C--TCTGTTTCTTTCCA
985528 CTCTGTTTCTTTCC
1 CTCTGTTTCTTTCC
985542 TTTATTTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 12 0.44
16 1 0.04
17 6 0.22
18 8 0.30
ACGTcount: A:0.06, C:0.30, G:0.09, T:0.55
Consensus pattern (15 bp):
CTCTGTTTCTTTCCA
Found at i:988474 original size:17 final size:18
Alignment explanation
Indices: 988452--988488 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
988442 TAATTTTATA
*
988452 TTATTTATATAAAA-AAC
1 TTATTTAAATAAAATAAC
988469 TTATTTAAATAAAATAAC
1 TTATTTAAATAAAATAAC
988487 TT
1 TT
988489 TTGTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
TTATTTAAATAAAATAAC
Found at i:998914 original size:3 final size:3
Alignment explanation
Indices: 998906--998935 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
998896 AAGAGCAAAT
998906 ATA ATA ATA ATA ATA ATA ATA ATA TATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA AT
998936 GAGATAGACG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:1004994 original size:10 final size:10
Alignment explanation
Indices: 1004976--1005010 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1004966 TTTTGACTTT
*
1004976 ATTAGGTAAC
1 ATTATGTAAC
1004986 ATTATGTAAC
1 ATTATGTAAC
*
1004996 ATTTTGTAAC
1 ATTATGTAAC
1005006 ATTAT
1 ATTAT
1005011 CATAGTGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (10 bp):
ATTATGTAAC
Found at i:1015645 original size:23 final size:23
Alignment explanation
Indices: 1015616--1015661 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1015606 TTTAGAGCAT
1015616 ATAAACTCGATAAGGAGTAAGAC
1 ATAAACTCGATAAGGAGTAAGAC
1015639 ATAAACTCGATAAGGAGTAAGAC
1 ATAAACTCGATAAGGAGTAAGAC
1015662 GAGGCATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.13, G:0.22, T:0.17
Consensus pattern (23 bp):
ATAAACTCGATAAGGAGTAAGAC
Found at i:1018990 original size:19 final size:19
Alignment explanation
Indices: 1018968--1019050 Score: 71
Period size: 19 Copynumber: 4.2 Consensus size: 19
1018958 ACAAATATTA
1018968 AAAAAATC-AAAATAAATTT
1 AAAAAATCTAAAA-AAATTT
* *
1018987 AAAATATCTATAAAAATTT
1 AAAAAATCTAAAAAAATTT
*
1019006 AAAAAATCT-AGAAAATTCT
1 AAAAAATCTAAAAAAATT-T
*
1019025 AATAAATATTTAAAGAAAATTT
1 AA-AAA-ATCTAAA-AAAATTT
1019047 AAAA
1 AAAA
1019051 TAATAATTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
18 6 0.12
19 24 0.47
20 6 0.12
21 5 0.10
22 4 0.08
23 6 0.12
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAAATCTAAAAAAATTT
Found at i:1019051 original size:30 final size:28
Alignment explanation
Indices: 1018981--1019052 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 28
1018971 AAATCAAAAT
1018981 AAATTTAAAATATCTATAAAAATTTAAA
1 AAATTTAAAATATCTATAAAAATTTAAA
* *
1019009 AAATCTAGAAA-ATTCTAATAAATATTTAAAGA
1 AAATTTA-AAATA-TCT-ATAAAAATTT-AA-A
1019041 AAATTTAAAATA
1 AAATTTAAAATA
1019053 ATAATTTTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
28 7 0.20
29 6 0.17
30 9 0.26
31 5 0.14
32 8 0.23
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (28 bp):
AAATTTAAAATATCTATAAAAATTTAAA
Found at i:1037749 original size:23 final size:22
Alignment explanation
Indices: 1037716--1037759 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
1037706 TAAAATAAAT
1037716 AAAAATAAAAATATTAAAATAC
1 AAAAATAAAAATATTAAAATAC
*
1037738 AAAAATACAAAATTTTAAAATA
1 AAAAATA-AAAATATTAAAATA
1037760 TTAATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (22 bp):
AAAAATAAAAATATTAAAATAC
Found at i:1046826 original size:31 final size:31
Alignment explanation
Indices: 1046788--1046853 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1046778 AACAATCTAG
*
1046788 TGACTTAAATAAAAACTTTCGAATAATTCAA
1 TGACTTAAACAAAAACTTTCGAATAATTCAA
* * * *
1046819 TGACTTAAACGAAAACTTTTGAATAGTTTAA
1 TGACTTAAACAAAAACTTTCGAATAATTCAA
1046850 TGAC
1 TGAC
1046854 CATTTTGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (31 bp):
TGACTTAAACAAAAACTTTCGAATAATTCAA
Found at i:1050861 original size:168 final size:168
Alignment explanation
Indices: 1050561--1050893 Score: 467
Period size: 168 Copynumber: 2.0 Consensus size: 168
1050551 AGCCAAAGGG
* * * *
1050561 TCCCTTTGCTAAATAGAAAAATTCTTTATGGCTCCTCCTCGAAATTAAAAAAAAATTCAATTTAG
1 TCCCTTGGCTAAATAGAAAAATTCTTTATAGCCCCTCCTCAAAATTAAAAAAAAATTCAATTTAG
* *
1050626 TCTTTTTTAACCATTGATTAAATAAAAAATTTATAATTTAGCCCTTTTGAAAATTAATAATTTAA
66 TCTTTTTTAACCATTGAATAAATAAAAAAATTATAATTTAGCCCTTTTGAAAATTAATAATTTAA
*
1050691 TTTAAAGTATTTTTAATACAAGAATTTTAGCTTTGCCC
131 TTTAAAGCATTTTTAATACAAGAATTTTAGCTTTGCCC
* * * *
1050729 TCCCTTGGCTAAATGGAAAATTTGCTTTATATCCCCTCC-CAAAATT-AAAAAAGA-TCAATTTA
1 TCCCTTGGCTAAATAGAAAAATT-CTTTATAGCCCCTCCTCAAAATTAAAAAAAAATTCAATTTA
* *
1050791 GTAC-TTTTTAATCTTTGAATAAATAAAAAAATTATAATTTTAGCCCTTTTGAAAAATTAATAAT
65 GT-CTTTTTTAACCATTGAATAAATAAAAAAATTATAA-TTTAGCCCTTTTG-AAAATTAATAAT
* *
1050855 TTAATTTCAAGCATTTTTAATGCAAGAATTTTAGCTTTG
127 TTAATTTAAAGCATTTTTAATACAAGAATTTTAGCTTTG
1050894 GTCCCCCAAA
Statistics
Matches: 146, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
166 39 0.27
167 21 0.14
168 74 0.51
169 12 0.08
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (168 bp):
TCCCTTGGCTAAATAGAAAAATTCTTTATAGCCCCTCCTCAAAATTAAAAAAAAATTCAATTTAG
TCTTTTTTAACCATTGAATAAATAAAAAAATTATAATTTAGCCCTTTTGAAAATTAATAATTTAA
TTTAAAGCATTTTTAATACAAGAATTTTAGCTTTGCCC
Found at i:1052853 original size:52 final size:52
Alignment explanation
Indices: 1052775--1052879 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
1052765 TCATCCTAAA
* *
1052775 ACATCATGCCACTATCACTGTCAAGGGTATCAAATTAGACTTCCATGTTAGC
1 ACATCATGCCACTATCACTGTCAAGGGTATCAAATTAAACTTCCATATTAGC
*
1052827 ACATCATGCCACTATCACTGTCAAGGGTATCAAATTAAACTTTCATATTAGC
1 ACATCATGCCACTATCACTGTCAAGGGTATCAAATTAAACTTCCATATTAGC
1052879 A
1 A
1052880 ATCTTGGGAC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (52 bp):
ACATCATGCCACTATCACTGTCAAGGGTATCAAATTAAACTTCCATATTAGC
Found at i:1058023 original size:43 final size:43
Alignment explanation
Indices: 1057974--1058059 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
1057964 CATAAGAATT
*
1057974 AATTTTCTCTTTTTTTAAATAAAGAAAATAAAATACAATCTAA
1 AATTTTCTCTATTTTTAAATAAAGAAAATAAAATACAATCTAA
1058017 AATTTTCTCTATTTTTAAATAAAGAAAATAAAATACAATCTAA
1 AATTTTCTCTATTTTTAAATAAAGAAAATAAAATACAATCTAA
1058060 CTCATACTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.38
Consensus pattern (43 bp):
AATTTTCTCTATTTTTAAATAAAGAAAATAAAATACAATCTAA
Found at i:1063017 original size:31 final size:30
Alignment explanation
Indices: 1062977--1063063 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 30
1062967 AAATTCTAAA
* * *
1062977 TTAATAATAATAAAATTATACTTTGACCTCT
1 TTAAAAATAATAAAATTATAATTT-AACTCT
*
1063008 TTAAAAATAATAAAAATT-TAATTTAATTCT
1 TTAAAAATAAT-AAAATTATAATTTAACTCT
* *
1063038 TTAAAAATTATAAAAATATAAATTTA
1 TTAAAAATAATAAAATTAT-AATTTA
1063064 TAAAATTATA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
29 5 0.11
30 15 0.32
31 21 0.45
32 6 0.13
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAATAATAAAATTATAATTTAACTCT
Found at i:1063041 original size:30 final size:31
Alignment explanation
Indices: 1063005--1063063 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
1062995 TACTTTGACC
*
1063005 TCTTTAAAAATAATAAAAAT-TTAATTTAAT
1 TCTTTAAAAATAATAAAAATATAAATTTAAT
*
1063035 TCTTTAAAAATTATAAAAATATAAATTTA
1 TCTTTAAAAATAATAAAAATATAAATTTA
1063064 TAAAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (31 bp):
TCTTTAAAAATAATAAAAATATAAATTTAAT
Found at i:1063052 original size:8 final size:8
Alignment explanation
Indices: 1063041--1063080 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
1063031 TAATTCTTTA
1063041 AAAATTAT
1 AAAATTAT
*
1063049 AAAAATAT
1 AAAATTAT
*
1063057 AAATTTAT
1 AAAATTAT
1063065 AAAATTAT
1 AAAATTAT
1063073 AAAATTAT
1 AAAATTAT
1063081 TTTTTTACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
AAAATTAT
Found at i:1071851 original size:26 final size:26
Alignment explanation
Indices: 1071803--1071853 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1071793 ATTTAATGTT
*
1071803 TAATTTCATATATATATTATTTTATG
1 TAATTTCATATATAAATTATTTTATG
*
1071829 TAATTTTATATATTAAATT-TTTTAT
1 TAATTTCATATA-TAAATTATTTTAT
1071854 TTGATTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
TAATTTCATATATAAATTATTTTATG
Found at i:1077429 original size:59 final size:58
Alignment explanation
Indices: 1077319--1077465 Score: 156
Period size: 59 Copynumber: 2.5 Consensus size: 58
1077309 ACTTAATATT
* * *
1077319 TTTTTCTAATTTGGTACCTAAT-TTTTTTGGGTCCTATTTGGTACTCAAACTTGA-TAC
1 TTTTTCTAATTTGGTACCTAATCTTTTTTGGGTCCAATTTAGTACTCAAACTTAACT-C
* * * * *
1077376 TTTTTCTTAAGTTGGTACTTAATCTTTTTTGGGTTCAATTTATTAC-CTGAACTTAACTC
1 TTTTTC-TAATTTGGTACCTAATCTTTTTTGGGTCCAATTTAGTACTC-AAACTTAACTC
1077435 TTTTTCCTAATTTGGTACCTAATCATTTTTT
1 TTTTT-CTAATTTGGTACCTAATC-TTTTTT
1077466 TTGTTTGATT
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
57 6 0.08
58 15 0.20
59 45 0.61
60 8 0.11
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.52
Consensus pattern (58 bp):
TTTTTCTAATTTGGTACCTAATCTTTTTTGGGTCCAATTTAGTACTCAAACTTAACTC
Found at i:1086965 original size:37 final size:37
Alignment explanation
Indices: 1086915--1086989 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
1086905 AATCAGTCAA
1086915 ATTTGATAATTTTTTTAAAAGAAAATTGAGAGGATCG
1 ATTTGATAATTTTTTTAAAAGAAAATTGAGAGGATCG
1086952 ATTTGATAATTTTTTTAAAAGAAAATTGAGAGGATCG
1 ATTTGATAATTTTTTTAAAAGAAAATTGAGAGGATCG
1086989 A
1 A
1086990 AATGATGTTT
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:0.41, C:0.03, G:0.19, T:0.37
Consensus pattern (37 bp):
ATTTGATAATTTTTTTAAAAGAAAATTGAGAGGATCG
Found at i:1087002 original size:37 final size:37
Alignment explanation
Indices: 1086918--1087006 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 37
1086908 CAGTCAAATT
**
1086918 TGATAATTTTTTTAAAAGAAAATTGAGAGGATCGATT
1 TGATAATTTTTTTAAAAGAAAATTGAGAGGATCGAAA
1086955 TGATAATTTTTTTAAAAGAAAATTGAGAGGATCGAAA
1 TGATAATTTTTTTAAAAGAAAATTGAGAGGATCGAAA
**
1086992 TGATGTTTTTTTTAA
1 TGATAATTTTTTTAA
1087007 TGAGAATATT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.39, C:0.02, G:0.18, T:0.40
Consensus pattern (37 bp):
TGATAATTTTTTTAAAAGAAAATTGAGAGGATCGAAA
Found at i:1087950 original size:12 final size:12
Alignment explanation
Indices: 1087906--1087960 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
1087896 TAATAATTTT
*
1087906 ATATAAATATAA
1 ATATTAATATAA
* *
1087918 GT-TTAAT-TAT
1 ATATTAATATAA
1087928 ATATT-ATATAA
1 ATATTAATATAA
*
1087939 ATTTTAATATAA
1 ATATTAATATAA
1087951 ATATTAATAT
1 ATATTAATAT
1087961 GATAAAATGA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
10 5 0.15
11 12 0.36
12 16 0.48
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (12 bp):
ATATTAATATAA
Found at i:1093867 original size:59 final size:59
Alignment explanation
Indices: 1093753--1093867 Score: 133
Period size: 59 Copynumber: 1.9 Consensus size: 59
1093743 TGAACTGTTT
* * * * *
1093753 TTTGTCCAAGTTCATCTTTGAACTTGACAATTGTTCCCACATGATGGCTTGAACTTCTA
1 TTTGTCCAAGTTAATCCTTGAACTTGACAATTGTTCCCACATGAGGGCCTAAACTTCTA
* * * *
1093812 TTTGTCTAAGTTAATCCTTGTACTTGATAATTGTTCTCACATTG-GGGCCTAAACTT
1 TTTGTCCAAGTTAATCCTTGAACTTGACAATTGTTCCCACA-TGAGGGCCTAAACTT
1093868 TTTTTTTATC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
59 44 0.96
60 2 0.04
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (59 bp):
TTTGTCCAAGTTAATCCTTGAACTTGACAATTGTTCCCACATGAGGGCCTAAACTTCTA
Found at i:1102158 original size:19 final size:20
Alignment explanation
Indices: 1102134--1102189 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
1102124 TTATTTACGT
*
1102134 ATTTAAAATATATA-AATTA
1 ATTTAAAATATATATAATAA
1102153 ATTTAAAAGTAATATATAATAA
1 ATTTAAAA-T-ATATATAATAA
*
1102175 ATAATAAAATATATA
1 AT-TTAAAATATATA
1102190 GTTTAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 8 0.26
20 1 0.03
21 10 0.32
22 7 0.23
23 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
ATTTAAAATATATATAATAA
Found at i:1102524 original size:3 final size:3
Alignment explanation
Indices: 1102516--1102547 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1102506 TTAATCAAAT
1102516 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1102548 TAAATATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1105029 original size:17 final size:19
Alignment explanation
Indices: 1104988--1105031 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1104978 ATACCATTAA
*
1104988 AAATAATATAATATATAAT
1 AAATAATAAAATATATAAT
*
1105007 ATATAATAAAAT-TAT-AT
1 AAATAATAAAATATATAAT
1105024 AAATAATA
1 AAATAATA
1105032 TTTTTTAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 9 0.41
18 3 0.14
19 10 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATAATAAAATATATAAT
Found at i:1105846 original size:3 final size:3
Alignment explanation
Indices: 1105838--1105884 Score: 76
Period size: 3 Copynumber: 15.3 Consensus size: 3
1105828 TAGTTAATCC
*
1105838 TAA TAA TAA TAA TAA TAA TAG TAA TAAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
1105884 T
1 T
1105885 GTATAATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1105892 original size:22 final size:22
Alignment explanation
Indices: 1105838--1105884 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1105828 TAGTTAATCC
*
1105838 TAAT-AATAATAATAATAATAG
1 TAATAAATAATAATAATAATAA
1105859 TAATAAATAATAATAATAATAA
1 TAATAAATAATAATAATAATAA
1105881 TAAT
1 TAAT
1105885 GTATAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
TAATAAATAATAATAATAATAA
Found at i:1107600 original size:39 final size:39
Alignment explanation
Indices: 1107555--1107675 Score: 242
Period size: 39 Copynumber: 3.1 Consensus size: 39
1107545 GAATTGCATT
1107555 AAATGAAACGTAAATATTAAATTATTAGAAGAATAAAAA
1 AAATGAAACGTAAATATTAAATTATTAGAAGAATAAAAA
1107594 AAATGAAACGTAAATATTAAATTATTAGAAGAATAAAAA
1 AAATGAAACGTAAATATTAAATTATTAGAAGAATAAAAA
1107633 AAATGAAACGTAAATATTAAATTATTAGAAGAATAAAAA
1 AAATGAAACGTAAATATTAAATTATTAGAAGAATAAAAA
1107672 AAAT
1 AAAT
1107676 TCTTCCTATG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 82 1.00
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.26
Consensus pattern (39 bp):
AAATGAAACGTAAATATTAAATTATTAGAAGAATAAAAA
Found at i:1108499 original size:19 final size:19
Alignment explanation
Indices: 1108475--1108513 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1108465 AGCTAAAACT
1108475 TAAAATCATTTAACTCAAA
1 TAAAATCATTTAACTCAAA
1108494 TAAAATCATTTAACTCAAA
1 TAAAATCATTTAACTCAAA
1108513 T
1 T
1108514 TAACTCGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATCATTTAACTCAAA
Found at i:1108931 original size:25 final size:24
Alignment explanation
Indices: 1108895--1108942 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1108885 ACAGCAACTT
*
1108895 CAAAAAATAAAACAATTAATAAAC
1 CAAAAAATAAAACAATAAATAAAC
* *
1108919 CAAAAATTAAAAATAATAAATAAA
1 CAAAAAAT-AAAACAATAAATAAA
1108943 TAATCAGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (24 bp):
CAAAAAATAAAACAATAAATAAAC
Found at i:1111593 original size:75 final size:75
Alignment explanation
Indices: 1111481--1112450 Score: 891
Period size: 75 Copynumber: 13.0 Consensus size: 75
1111471 AACCAAACAC
* * * ** * * ** * * *
1111481 CTAAATTTCCCGAGCCTGAACCCCAAGCTATATCTTGTGAACCCACTGCAATTGACGTTTTTGGT
1 CTAAATTTCCCGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTTGGG
1111546 AAACAGGCTT
66 AAACAGGCTT
* * ** * ** * *
1111556 CTAAATTTCCCGAGCATGAACCTCAAGTGATGCCTTGTGAATCTGGTGGAATCAAGATGTTTGGT
1 CTAAATTTCCCGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTTGGG
*
1111621 AAGC-GGCCTT
66 AAACAGG-CTT
* * * *
1111631 CTAAATTTCCTGAACCTGAAACTCAA-CCAATGACGTGTGAACCTACTGGAATCAACATGTTTGG
1 CTAAATTTCCCGAACCTGAACCTCAAGCC-ATGCCTTGTGAACCTACTGGAATCAACATGTTTGG
*
1111695 GAAACGGGCTT
65 GAAACAGGCTT
* * * * *
1111706 CTAAATTTCCTGAACCTGAACCTCAAGGCATGCCTTGTGAACCTGCTGAAATCCACATGTTTGGG
1 CTAAATTTCCCGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTTGGG
*
1111771 AAGCAGGCTT
66 AAACAGGCTT
* * * * * * * * *
1111781 CTAAATTTGCTGAACCTGAACCTCGAGCCATACCTTGTGAACCCATTGGAATCGACGTGTTTGGA
1 CTAAATTTCCCGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTTGGG
1111846 AAACAGGCTT
66 AAACAGGCTT
* *
1111856 CTAAATTTCCCGAACCTGAACCTTTAAG-CATGCAC-TGTGAACCTGCTGGAATCAACATGTTT-
1 CTAAATTTCCCGAACCTGAACC-TCAAGCCATGC-CTTGTGAACCTACTGGAATCAACATGTTTG
1111918 GGAAAGCAGGCTT
64 GGAAA-CAGGCTT
* * * *
1111931 CTAAATTTCCCGAACCTGAAACTCAACCCGTGCAC-TGTGAACCAACTGGAATCAACATGTTT-G
1 CTAAATTTCCCGAACCTGAACCTCAAGCCATGC-CTTGTGAACCTACTGGAATCAACATGTTTGG
1111994 GAAAGCAGGCTT
65 GAAA-CAGGCTT
* * * * *
1112006 CTAAATTTCCTGAACCTGAAACTCAACCCATGCAC-TGTGAACCAACTGGAATCAACATTTTTGG
1 CTAAATTTCCCGAACCTGAACCTCAAGCCATGC-CTTGTGAACCTACTGGAATCAACATGTTTGG
*
1112070 GAAACAGGCTA
65 GAAACAGGCTT
* * * * * * *
1112081 CTAAATTTCCTGAACCCGAACCTCAAACCATGCCTTGTGGACCAACAGGAATCAACATG-TTCGG
1 CTAAATTTCCCGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTTGGG
* *
1112145 AAAGCAGCCAT
66 AAA-CAGGCTT
* *
1112156 CTAAATTT------CCTGACCCTCAAGCCATGCCTTGTGAATCC-ACTGGAATCAACAAT-TTCG
1 CTAAATTTCCCGAACCTGAACCTCAAGCCATGCCTTGTGAA-CCTACTGGAATCAAC-ATGTTTG
*
1112213 GGAAGCAGGCTT
64 GGAAACAGGCTT
* * * **
1112225 CTAAATTTCCCGAACCTGAACTTCGAA-CCATGTCTTGCGAACCTACCAGAATCAACAT-TTTCG
1 CTAAATTTCCCGAACCTGAACCTC-AAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTT-G
*
1112288 GGAAACAAGCTT
64 GGAAACAGGCTT
* * * * * *
1112300 CTAAATTTCCTGAACCTGAACCTCAAACCATACCTTGTGAACCCACTGGACTTAACATGTTTGGG
1 CTAAATTTCCCGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTTGGG
*
1112365 AAACAAGCTT
66 AAACAGGCTT
* ** * * * *
1112375 CTAAGTTTCTTGAACCTGAACAC-CAAGCCATACCTTGTGAACTTACTGGACTCAACATGTTCGG
1 CTAAATTTCCCGAACCTGAAC-CTCAAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTTGG
*
1112439 TAAACAGGCTT
65 GAAACAGGCTT
1112450 C
1 C
1112451 ATCTAGGCAA
Statistics
Matches: 748, Mismatches: 121, Indels: 52
0.81 0.13 0.06
Matches are distributed among these distances:
69 47 0.06
70 9 0.01
74 25 0.03
75 649 0.87
76 18 0.02
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (75 bp):
CTAAATTTCCCGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTTGGG
AAACAGGCTT
Found at i:1113905 original size:15 final size:15
Alignment explanation
Indices: 1113885--1113914 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1113875 GTAAAGATTA
1113885 AATTAATAATTATAC
1 AATTAATAATTATAC
1113900 AATTAATAATTATAC
1 AATTAATAATTATAC
1113915 CTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
AATTAATAATTATAC
Found at i:1123968 original size:174 final size:174
Alignment explanation
Indices: 1123656--1123971 Score: 413
Period size: 174 Copynumber: 1.8 Consensus size: 174
1123646 TCGTAATTTG
1123656 CTTTGAATTGCTATTATTGCTTGCTTCTGCTTGACAAAACTCCTCCTTAACTGCCAACCACGGAA
1 CTTTGAATTGCTATTATTGCTTGCTTCTGCTTGACAAAACTCCTCCTTAACTGCCAACCACGGAA
* * *
1123721 ATGACTTTGAATTTTTGTTGCAGCAAATGTCTGATTTTGAAGAGATCTACAGACAAATTCCTTCT
66 ATGACTCTGAATTTTAGTTGCAGCAAATGTCTGATTTTGAAGAGATCTACAAACAAATTCCTTCT
*
1123786 GAGCAATCTGAAAGGCCCACCAACACTTCAGCCGTCGAAAATTA
131 CAGCAATCTGAAAGGCCCACCAACACTTCAGCCGTCGAAAATTA
** * * * * * * * *
1123830 CTTTGAATTTTTATTATTTCTTGCTTCTGCTTTATAAAACTTCTCCTTAATTGCCAAGCTCGGTA
1 CTTTGAATTGCTATTATTGCTTGCTTCTGCTTGACAAAACTCCTCCTTAACTGCCAACCACGGAA
* * * * *
1123895 ATGGCTCTGAATTTTAGTTGCAGCATAA-GTCTGTTTTTGTAGATATCTGCAAACAAAGTT-CTT
66 ATGACTCTGAATTTTAGTTGCAGCA-AATGTCTGATTTTGAAGAGATCTACAAACAAA-TTCCTT
1123958 C-CATGCAATCTGAA
129 CTCA-GCAATCTGAA
1123972 TCTTGCTTGC
Statistics
Matches: 120, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
173 1 0.01
174 115 0.96
175 4 0.03
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.36
Consensus pattern (174 bp):
CTTTGAATTGCTATTATTGCTTGCTTCTGCTTGACAAAACTCCTCCTTAACTGCCAACCACGGAA
ATGACTCTGAATTTTAGTTGCAGCAAATGTCTGATTTTGAAGAGATCTACAAACAAATTCCTTCT
CAGCAATCTGAAAGGCCCACCAACACTTCAGCCGTCGAAAATTA
Found at i:1138562 original size:19 final size:20
Alignment explanation
Indices: 1138521--1138562 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1138511 TATTTTTTAA
**
1138521 TGATTTTTTTTAGAAATTTT
1 TGATTTTTTTTAGAAATGGT
*
1138541 TGATTTTTTTTA-CAATGGT
1 TGATTTTTTTTAGAAATGGT
1138560 TGA
1 TGA
1138563 ACCAGGGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (20 bp):
TGATTTTTTTTAGAAATGGT
Found at i:1149816 original size:11 final size:9
Alignment explanation
Indices: 1149782--1149811 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1149772 TTGAACCGGA
1149782 TTTT-ATAT
1 TTTTAATAT
1149790 TTTTAATAT
1 TTTTAATAT
1149799 TTTTAATAT
1 TTTTAATAT
1149808 TTTT
1 TTTT
1149812 TTAATTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTAATAT
Found at i:1154682 original size:44 final size:45
Alignment explanation
Indices: 1154610--1154717 Score: 119
Period size: 44 Copynumber: 2.4 Consensus size: 45
1154600 TGTCTTTGAC
** * * **
1154610 ATGGACTTACATGAATTATTCCTATCTCCAGTGCCATA-TATAAT
1 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATATTATAAT
* * *
1154654 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGTCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATA-TTATAAT
1154700 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
1154718 TTTCTGTTCT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 30 0.57
46 23 0.43
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (45 bp):
ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATATTATAAT
Found at i:1162107 original size:46 final size:44
Alignment explanation
Indices: 1162003--1162110 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
1161993 TGTCTTTGAC
** * * *
1162003 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
1162047 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
1162093 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
1162111 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:1166109 original size:46 final size:46
Alignment explanation
Indices: 1166056--1166148 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
1166046 TGAATGTTAG
*
1166056 TAATCTATGTAATTGAACTCACAACCTCGTACAGAAAGGAGTGCAT
1 TAATCTATGTAATTGAACTCACAACCTCATACAGAAAGGAGTGCAT
*
1166102 TAATCTATGTAATTGAACTCACAACCTCATATAGAAAGGAGTGCAT
1 TAATCTATGTAATTGAACTCACAACCTCATACAGAAAGGAGTGCAT
1166148 T
1 T
1166149 CTAAGTTCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (46 bp):
TAATCTATGTAATTGAACTCACAACCTCATACAGAAAGGAGTGCAT
Found at i:1170168 original size:21 final size:21
Alignment explanation
Indices: 1170142--1170182 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1170132 ATCTGCTCAA
* *
1170142 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1170163 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1170183 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1175031 original size:13 final size:13
Alignment explanation
Indices: 1175013--1175037 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1175003 AATGCCTCTT
1175013 CATGCATTCAAGA
1 CATGCATTCAAGA
1175026 CATGCATTCAAG
1 CATGCATTCAAG
1175038 GAAAGTAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (13 bp):
CATGCATTCAAGA
Found at i:1186381 original size:21 final size:21
Alignment explanation
Indices: 1186355--1186399 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1186345 AATTAAAAAT
*
1186355 TATTTAATATT-AAATATTAAA
1 TATTTAAAATTGAAATA-TAAA
*
1186376 TATTTAAAATTGGAATATAAA
1 TATTTAAAATTGAAATATAAA
1186397 TAT
1 TAT
1186400 CATAATCCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (21 bp):
TATTTAAAATTGAAATATAAA
Found at i:1186561 original size:21 final size:21
Alignment explanation
Indices: 1186520--1186578 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
1186510 CTATATATTT
* *
1186520 ATATAATTAAAAATAAA--AA
1 ATATATTTAAAATTAAATTAA
1186539 ATATATTTAAAATTAAATTAA
1 ATATATTTAAAATTAAATTAA
* * *
1186560 ATCTATTTGAATTTAAATT
1 ATATATTTAAAATTAAATT
1186579 TGTCGAATCG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 15 0.45
21 18 0.55
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
ATATATTTAAAATTAAATTAA
Found at i:1191447 original size:4 final size:4
Alignment explanation
Indices: 1191426--1191461 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1191416 GAAATTGAAT
* *
1191426 TACA TACA TTCA TTCA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA
1191462 GATCATAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (4 bp):
TACA
Found at i:1192372 original size:8 final size:8
Alignment explanation
Indices: 1192359--1192401 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
1192349 GGTCAAGACT
1192359 AAAATTTA
1 AAAATTTA
1192367 AAAATTTA
1 AAAATTTA
**
1192375 AAAAACT-
1 AAAATTTA
1192382 AAAATTTA
1 AAAATTTA
*
1192390 AAAACTTA
1 AAAATTTA
1192398 AAAA
1 AAAA
1192402 ATATAGAACT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
7 5 0.17
8 24 0.83
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (8 bp):
AAAATTTA
Found at i:1192382 original size:23 final size:23
Alignment explanation
Indices: 1192356--1192402 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1192346 TTGGGTCAAG
*
1192356 ACTAAAATTTAAAAATTTAAAAA
1 ACTAAAATTTAAAAACTTAAAAA
1192379 ACTAAAATTTAAAAACTTAAAAA
1 ACTAAAATTTAAAAACTTAAAAA
1192402 A
1 A
1192403 TATAGAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (23 bp):
ACTAAAATTTAAAAACTTAAAAA
Found at i:1193454 original size:18 final size:17
Alignment explanation
Indices: 1193418--1193457 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1193408 TAGTAAAAAT
1193418 ATAATTTTATCATTTTA
1 ATAATTTTATCATTTTA
1193435 ATAA-TTTAT-ATCTTT-
1 ATAATTTTATCAT-TTTA
1193450 ATAATTTT
1 ATAATTTT
1193458 TAAAGGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.29
16 11 0.52
17 4 0.19
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
ATAATTTTATCATTTTA
Found at i:1193576 original size:83 final size:82
Alignment explanation
Indices: 1193417--1193575 Score: 182
Period size: 83 Copynumber: 1.9 Consensus size: 82
1193407 ATAGTAAAAA
* * * * *
1193417 TATAATTTTATCATTTTAATAATTTATATCTTTATAATTTTTAAAGGATTAAATCAAAATTTTAT
1 TATAATTTTATCATTTTAAT-ATTAAAATCTTTATAAATTATAAAGGATTAAATCAAAATTTTAC
1193482 TATTCTTGGGGGCTCAAG
65 TATTCTTGGGGGCTCAAG
* *
1193500 TATAATTTTATCATTATTAAT-TTAAAAT-TTTATAAATTATAAAGGGTCTAAATAGAAAATTTT
1 TATAATTTTATCATT-TTAATATTAAAATCTTTATAAATTATAAAGGAT-TAAAT-CAAAATTTT
1193563 -CTATT-TTAGGGGG
63 ACTATTCTT-GGGGG
1193576 GTCAGGCCCC
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
81 18 0.28
82 19 0.29
83 23 0.35
84 5 0.08
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.47
Consensus pattern (82 bp):
TATAATTTTATCATTTTAATATTAAAATCTTTATAAATTATAAAGGATTAAATCAAAATTTTACT
ATTCTTGGGGGCTCAAG
Found at i:1202262 original size:18 final size:18
Alignment explanation
Indices: 1202239--1202326 Score: 131
Period size: 18 Copynumber: 4.9 Consensus size: 18
1202229 TCCGACTACT
1202239 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
* *
1202257 GTATACGTAAATAGTGCC
1 GTATACGTGAATAGTACC
*
1202275 GTATATGTGAATAGTACC
1 GTATACGTGAATAGTACC
*
1202293 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
1202311 GTATACATGAATAGTA
1 GTATACGTGAATAGTA
1202327 TCATAAACGG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:1202286 original size:36 final size:36
Alignment explanation
Indices: 1202239--1202326 Score: 149
Period size: 36 Copynumber: 2.4 Consensus size: 36
1202229 TCCGACTACT
1202239 GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
* *
1202275 GTATATGTGAATAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
*
1202311 GTATACATGAATAGTA
1 GTATACGTGAATAGTA
1202327 TCATAAACGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
Found at i:1205349 original size:12 final size:12
Alignment explanation
Indices: 1205332--1205365 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
1205322 CCGGCTCGCC
1205332 TATATTAATTTT
1 TATATTAATTTT
1205344 TATATTAA-TTT
1 TATATTAATTTT
1205355 TATA-TAATTTT
1 TATATTAATTTT
1205366 AAAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 10 0.48
12 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATATTAATTTT
Found at i:1205364 original size:10 final size:11
Alignment explanation
Indices: 1205332--1205366 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
1205322 CCGGCTCGCC
1205332 TATATTAATTTT
1 TATATTAA-TTT
1205344 TATATTAATTT
1 TATATTAATTT
1205355 TATA-TAATTT
1 TATATTAATTT
1205365 TA
1 TA
1205367 AAATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.35
11 7 0.30
12 8 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATATTAATTT
Found at i:1205523 original size:30 final size:30
Alignment explanation
Indices: 1205489--1205551 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1205479 ACTTAACAAG
1205489 CAAATGTCACTAAAATAATAACAAAATTAA
1 CAAATGTCACTAAAATAATAACAAAATTAA
**
1205519 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCACTAAAATAATAACAAAATTAA
1205549 CAA
1 CAA
1205552 TAAAATAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.59, C:0.13, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGTCACTAAAATAATAACAAAATTAA
Found at i:1205636 original size:22 final size:22
Alignment explanation
Indices: 1205580--1205628 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1205570 ATATCTAAAC
*
1205580 AATAACAATAAAATAGTAGCAA
1 AATAACAGTAAAATAGTAGCAA
* *
1205602 CATAACAGTAAAATGGTAGCAA
1 AATAACAGTAAAATAGTAGCAA
1205624 AATAA
1 AATAA
1205629 TGAGAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.59, C:0.10, G:0.12, T:0.18
Consensus pattern (22 bp):
AATAACAGTAAAATAGTAGCAA
Found at i:1206381 original size:8 final size:8
Alignment explanation
Indices: 1206362--1206407 Score: 60
Period size: 7 Copynumber: 5.8 Consensus size: 8
1206352 TATTTATAAT
1206362 TTTTTATA
1 TTTTTATA
1206370 -TTTTATA
1 TTTTTATA
1206377 TTTTTATA
1 TTTTTATA
1206385 -TTTTATA
1 TTTTTATA
1206392 TTTTTGAATA
1 TTTTT--ATA
1206402 TTTTTA
1 TTTTTA
1206408 AATTATTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 14 0.41
8 12 0.35
10 8 0.24
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (8 bp):
TTTTTATA
Found at i:1206405 original size:17 final size:15
Alignment explanation
Indices: 1206362--1206396 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1206352 TATTTATAAT
1206362 TTTTTATATTTTATA
1 TTTTTATATTTTATA
1206377 TTTTTATATTTTATA
1 TTTTTATATTTTATA
1206392 TTTTT
1 TTTTT
1206397 GAATATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTATATTTTATA
Found at i:1209609 original size:26 final size:26
Alignment explanation
Indices: 1209578--1209628 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
1209568 TTAAAAACAG
1209578 TGATTCAAGAAAGGCAAATAAACCTA
1 TGATTCAAGAAAGGCAAATAAACCTA
1209604 TGATTCAAGAAAGGCAAATAAACCT
1 TGATTCAAGAAAGGCAAATAAACCT
1209629 TTAAGTAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.20
Consensus pattern (26 bp):
TGATTCAAGAAAGGCAAATAAACCTA
Found at i:1212183 original size:17 final size:15
Alignment explanation
Indices: 1212161--1212195 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
1212151 TATTATATAT
1212161 ATTTTAAAATATTTACA
1 ATTTTAAAAT-TTTA-A
1212178 ATTTTAAAATTTTAA
1 ATTTTAAAATTTTAA
1212193 ATT
1 ATT
1212196 AATAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 4 0.22
17 10 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTTTAAAATTTTAA
Found at i:1214971 original size:100 final size:100
Alignment explanation
Indices: 1214778--1215025 Score: 255
Period size: 100 Copynumber: 2.5 Consensus size: 100
1214768 CAGAGTAAAT
* * * * * *
1214778 ATTAATTGACTAATTATTTTAAGTCACAACAAGACACATCAGGGTCGATATATGTGAAGATTTAT
1 ATTAATTGACTAATTATTTTATGTCACAACACGACACAACAAGATCGATATATGTGAAGACTTAT
** * * * *
1214843 GCCGTTACACATAAATTAATACACGTAGAATAAAC
66 GCCGCCACACACAAATGAATACACGTAGAACAAAA
*
1214878 GTTAATTGACTAATTATTTTATGTCACAACACGACACAACAAGATCGATATATGTGAAGACTTAT
1 ATTAATTGACTAATTATTTTATGTCACAACACGACACAACAAGATCGATATATGTGAAGACTTAT
** * * *
1214943 GTTGCCGCGCACAAATGAATGC-CTGTAGAACAAAA
66 GCCGCCACACACAAATGAATACAC-GTAGAACAAAA
* * * * * * *
1214978 ATCAATTGATTAATCATTTTATGTTACGACACGACACGAGAAGATCGA
1 ATTAATTGACTAATTATTTTATGTCACAACACGACACAACAAGATCGA
1215026 GTTGGATTGT
Statistics
Matches: 121, Mismatches: 26, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
99 1 0.01
100 120 0.99
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.29
Consensus pattern (100 bp):
ATTAATTGACTAATTATTTTATGTCACAACACGACACAACAAGATCGATATATGTGAAGACTTAT
GCCGCCACACACAAATGAATACACGTAGAACAAAA
Found at i:1215599 original size:21 final size:21
Alignment explanation
Indices: 1215581--1215641 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
1215571 CCTCACCAAG
1215581 ACCACCACCAGGACCACCAGC
1 ACCACCACCAGGACCACCAGC
* *
1215602 ACCAACACCAGGGCCACCAGC
1 ACCACCACCAGGACCACCAGC
*
1215623 AGCACCACCAGGACCACCA
1 ACCACCACCAGGACCACCA
1215642 TACTCTCCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.34, C:0.49, G:0.16, T:0.00
Consensus pattern (21 bp):
ACCACCACCAGGACCACCAGC
Found at i:1220587 original size:19 final size:18
Alignment explanation
Indices: 1220563--1220598 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1220553 AAAAATCAAA
*
1220563 AATAAAAATTTCAAAAAAT
1 AATAAAAA-CTCAAAAAAT
1220582 AATAAAAACTCAAAAAA
1 AATAAAAACTCAAAAAA
1220599 ATTAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.19
Consensus pattern (18 bp):
AATAAAAACTCAAAAAAT
Found at i:1226064 original size:34 final size:34
Alignment explanation
Indices: 1226025--1226126 Score: 104
Period size: 34 Copynumber: 3.1 Consensus size: 34
1226015 CAGATTAATT
1226025 TATAATTTATGTATTATTATATTAAAATTTTAAA
1 TATAATTTATGTATTATTATATTAAAATTTTAAA
* **
1226059 TATAATTTA-ATATT-TTAT-TTAAGCTTTTAAA
1 TATAATTTATGTATTATTATATTAAAATTTTAAA
* ** *
1226090 -ATATTTTATGTACAATTATATTAAATTATTTAAA
1 TATAATTTATGTATTATTATATTAAAAT-TTTAAA
1226124 TAT
1 TAT
1226127 CTTATAATTT
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
30 7 0.13
31 13 0.24
32 8 0.15
33 9 0.17
34 15 0.28
35 2 0.04
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (34 bp):
TATAATTTATGTATTATTATATTAAAATTTTAAA
Found at i:1227249 original size:30 final size:31
Alignment explanation
Indices: 1227215--1227272 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
1227205 TATTTTGACC
1227215 TAAATATC-AAAAATTAAAAA-A-TAAAAAGAT
1 TAAAT-TCTAAAAA-TAAAAATATTAAAAAGAT
1227245 TAAATTCTAAAAATAAAAATATTAAAAA
1 TAAATTCTAAAAATAAAAATATTAAAAA
1227273 AACATTGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
29 8 0.32
30 11 0.44
31 6 0.24
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (31 bp):
TAAATTCTAAAAATAAAAATATTAAAAAGAT
Found at i:1230632 original size:29 final size:31
Alignment explanation
Indices: 1230580--1230644 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
1230570 GTATTCTTCA
*
1230580 AATTTTAGAAATTTAGTCTCTTTA-TT-TTT
1 AATTTTAGAAATTTAATCTCTTTATTTGTTT
*
1230609 AATTTTAGAGATTTAAT-TCATTTATTTGTTT
1 AATTTTAGAAATTTAATCTC-TTTATTTGTTT
1230640 AATTT
1 AATTT
1230645 GAAAATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 2 0.06
29 19 0.61
30 2 0.06
31 8 0.26
ACGTcount: A:0.29, C:0.05, G:0.08, T:0.58
Consensus pattern (31 bp):
AATTTTAGAAATTTAATCTCTTTATTTGTTT
Found at i:1234313 original size:228 final size:229
Alignment explanation
Indices: 1233865--1234777 Score: 1005
Period size: 228 Copynumber: 4.0 Consensus size: 229
1233855 AGGCTTAGAA
* * * * * * * * *
1233865 CCCACCACG-AAGACGAAGAACAAGGTGAAGAGTGGACTCCTTTTGAATATTGTAATCAGCCAAA
1 CCCACCACGCAA-ACGAAGGACAAGATGGAGAGTTGACTCCTTCTGGATGTTGTAATCGGCCAAG
** * * * * * * * * * * * *
1233929 GTCCTTCCGTCTTCCAGTTGTTTCCCAGCAAAAATCA-ACCTTTGCTGATCTGGTGGAATTCCTT
65 GTCCGGCCGTCCTCAAGTTGTTTTCCGGCGAAGATGAGA-CGTTGCTGGTCTGGAGGGATGCCTT
* * * * * * * * * * * * * *
1233993 CTTTGTCCTGAATCTTCGCTTTCACGTTATCAATCGTATCCGAGCTCTCCACTTCTAAAGTAATC
129 CCTTGTCTTGGATTTTGGCTTTCACGTTGTCGATCGTGTCGGAGCTCTCGACCTCGAGAGTGATC
*
1234058 GTCTTACCGGTCAA-AGTCTTGACGAAGATCTGCAT
194 GTCTTGCCGGTCAAGAGTCTTGACGAAGATCTGCAT
* * * * * * * * *
1234093 CCCACCTCG-AAGACGCAGGACCAGATGAAGAGTCGATTCCTTCTGGATATTGTAATCGGCTAAA
1 CCCACCACGCAA-ACGAAGGACAAGATGGAGAGTTGACTCCTTCTGGATGTTGTAATCGGCCAAG
* * * *
1234157 GTCCGCCCGTCCTCGAGTTGCTTTCCGGCGAAGATGAGACGTTGCTGGTCTGGCGGGATGCCTTC
65 GTCCGGCCGTCCTCAAGTTGTTTTCCGGCGAAGATGAGACGTTGCTGGTCTGGAGGGATGCCTTC
*
1234222 CTTGTCTTGGATTTTGGCTTTCACGTTGTCGATCGTGTCAGAGCTCTCGACCTCGAGAGTGATCG
130 CTTGTCTTGGATTTTGGCTTTCACGTTGTCGATCGTGTCGGAGCTCTCGACCTCGAGAGTGATCG
* * * * *
1234287 TCTTTCCCGT-AAGCGTCTTAACGAAGATTTGCAT
195 TCTTGCCGGTCAAGAGTCTTGACGAAGATCTGCAT
* * *
1234321 CCCGCCACGCAAACGAAGGACAAGATGGAGCGTTGACTCCTTCTGGATGTTGTAGTCGGCCAAGG
1 CCCACCACGCAAACGAAGGACAAGATGGAGAGTTGACTCCTTCTGGATGTTGTAATCGGCCAAGG
* * *
1234386 TACGGCCGTCTTCAAGTTGTTTTCCGGCGAAGATGAGACGTTGCTGGTCTGGGGGGATGCCTTCC
66 TCCGGCCGTCCTCAAGTTGTTTTCCGGCGAAGATGAGACGTTGCTGGTCTGGAGGGATGCCTTCC
* * * * *
1234451 TTGTCTTGGATCTTCGCCTTAACGTTGTCGATCGTGTCGGAGCTCTCGACCTCGAGAGTGATTGT
131 TTGTCTTGGATTTTGGCTTTCACGTTGTCGATCGTGTCGGAGCTCTCGACCTCGAGAGTGATCGT
* * *
1234516 CTTGCCGGTCAAG-GTTTTCACGAAGATTTGCAT
196 CTTGCCGGTCAAGAGTCTTGACGAAGATCTGCAT
* * * * *
1234549 CCCACCGCGCAAACGGAGGACGAGGTGGAGAGTTGACTCCTTTTGGATGTTGTAATCGGCCAAGG
1 CCCACCACGCAAACGAAGGACAAGATGGAGAGTTGACTCCTTCTGGATGTTGTAATCGGCCAAGG
* * *
1234614 TCCGGCCGTCCTCAAGCTGTTTTCCGGCGAAGATCAGACGCTGCTGGTCTGGAGGGATGCCTTCC
66 TCCGGCCGTCCTCAAGTTGTTTTCCGGCGAAGATGAGACGTTGCTGGTCTGGAGGGATGCCTTCC
*
1234679 TTATCTTGGATTTTGG-TCTTCACGTTGTCGATCGTGTCGGAGCTCTCGACCTCGAGAGTGATCG
131 TTGTCTTGGATTTTGGCT-TTCACGTTGTCGATCGTGTCGGAGCTCTCGACCTCGAGAGTGATCG
*
1234743 TCTTGCCGGT-TAGAGTCTTGACGAAGATCTGCAT
195 TCTTGCCGGTCAAGAGTCTTGACGAAGATCTGCAT
1234777 C
1 C
1234778 TTTTTTGGCT
Statistics
Matches: 582, Mismatches: 97, Indels: 12
0.84 0.14 0.02
Matches are distributed among these distances:
227 4 0.01
228 572 0.98
229 6 0.01
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.29
Consensus pattern (229 bp):
CCCACCACGCAAACGAAGGACAAGATGGAGAGTTGACTCCTTCTGGATGTTGTAATCGGCCAAGG
TCCGGCCGTCCTCAAGTTGTTTTCCGGCGAAGATGAGACGTTGCTGGTCTGGAGGGATGCCTTCC
TTGTCTTGGATTTTGGCTTTCACGTTGTCGATCGTGTCGGAGCTCTCGACCTCGAGAGTGATCGT
CTTGCCGGTCAAGAGTCTTGACGAAGATCTGCAT
Found at i:1244728 original size:35 final size:35
Alignment explanation
Indices: 1244654--1244747 Score: 100
Period size: 35 Copynumber: 2.7 Consensus size: 35
1244644 AATGTGTTTT
* *
1244654 TAATGTAAACAGAACCACATCACCCTATACATGAT
1 TAATGTAAACAAAACCACATCACCCTATACATGAC
** * *
1244689 TAATGTAAACAAAACCACA-CTACGGTATATATGCC
1 TAATGTAAACAAAACCACATC-ACCCTATACATGAC
* *
1244724 TAATGTAAACAAAGCCACAACACC
1 TAATGTAAACAAAACCACATCACC
1244748 AGAGTCTAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
34 1 0.02
35 47 0.96
36 1 0.02
ACGTcount: A:0.45, C:0.26, G:0.10, T:0.20
Consensus pattern (35 bp):
TAATGTAAACAAAACCACATCACCCTATACATGAC
Found at i:1250970 original size:13 final size:16
Alignment explanation
Indices: 1250938--1250977 Score: 59
Period size: 13 Copynumber: 2.7 Consensus size: 16
1250928 TTCTCGGACC
1250938 TATTTTTATAATTAAT
1 TATTTTTATAATTAAT
1250954 TATTTTT-TAA-T-AT
1 TATTTTTATAATTAAT
1250967 TATTTTTATAA
1 TATTTTTATAA
1250978 AAAATCCTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.39
14 4 0.17
15 3 0.13
16 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTTATAATTAAT
Found at i:1254826 original size:20 final size:21
Alignment explanation
Indices: 1254789--1254827 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1254779 AAAATACCTT
*
1254789 AAAATATAAATTACTTTTAAA
1 AAAATATAAAGTACTTTTAAA
*
1254810 AAAATA-AAAGTATTTTTA
1 AAAATATAAAGTACTTTTA
1254828 TTTTTTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
AAAATATAAAGTACTTTTAAA
Found at i:1256820 original size:31 final size:29
Alignment explanation
Indices: 1256783--1256840 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
1256773 ATTTGAGAAG
*
1256783 TCCTTATTTGAATACATTTAAAAATATTTAA
1 TCCTTATTT-AAT-CATTTAAAAAGATTTAA
*
1256814 TCCTTATTTAATCATTTTAAAAGATTT
1 TCCTTATTTAATCATTTAAAAAGATTT
1256841 GATCTTCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 13 0.52
30 3 0.12
31 9 0.36
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.48
Consensus pattern (29 bp):
TCCTTATTTAATCATTTAAAAAGATTTAA
Found at i:1257875 original size:29 final size:30
Alignment explanation
Indices: 1257839--1257904 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 30
1257829 AAAAATGAAT
1257839 ATTTAGTTT-TTATATTT-TTA-ATTTTAGAA
1 ATTTAGTTTATT-TATTTATTATATTTTA-AA
*
1257868 ATTTAGTTTATTTATTTATTATGTTTTAAA
1 ATTTAGTTTATTTATTTATTATATTTTAAA
1257898 ATTTAGT
1 ATTTAGT
1257905 CTAATTATCC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
29 14 0.42
30 14 0.42
31 5 0.15
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (30 bp):
ATTTAGTTTATTTATTTATTATATTTTAAA
Found at i:1263465 original size:21 final size:21
Alignment explanation
Indices: 1263439--1263479 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1263429 ATCTGCTCAA
* *
1263439 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1263460 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1263480 TTGCTTGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1266838 original size:15 final size:15
Alignment explanation
Indices: 1266818--1266850 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1266808 AAAACAGACA
1266818 TGTGATAGATATACG
1 TGTGATAGATATACG
1266833 TGTGATAGATATACG
1 TGTGATAGATATACG
1266848 TGT
1 TGT
1266851 TTATAATTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.36
Consensus pattern (15 bp):
TGTGATAGATATACG
Found at i:1267099 original size:28 final size:28
Alignment explanation
Indices: 1267059--1267115 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1267049 GCAACGGACC
1267059 AATATTCAATACAGATAGAGAAAATTAA
1 AATATTCAATACAGATAGAGAAAATTAA
1267087 AATATTCAATACAGATAGAGAAAATTAA
1 AATATTCAATACAGATAGAGAAAATTAA
1267115 A
1 A
1267116 CCACTATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.58, C:0.07, G:0.11, T:0.25
Consensus pattern (28 bp):
AATATTCAATACAGATAGAGAAAATTAA
Found at i:1271237 original size:16 final size:16
Alignment explanation
Indices: 1271216--1271251 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1271206 ATTTACGTTA
1271216 ATTTTGAG-TTTAATTT
1 ATTTTGAGTTTTAA-TT
1271232 ATTTTGAGTTTTAATT
1 ATTTTGAGTTTTAATT
1271248 ATTT
1 ATTT
1271252 AAGTTTGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (16 bp):
ATTTTGAGTTTTAATT
Found at i:1272180 original size:20 final size:21
Alignment explanation
Indices: 1272164--1272208 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1272154 AAATTTAATC
1272164 TTTTTA-TTTTTATTTTAAAA
1 TTTTTATTTTTTATTTTAAAA
*
1272184 TTTTTATTTTTTATTTTTAAA
1 TTTTTATTTTTTATTTTAAAA
1272205 TTTT
1 TTTT
1272209 AAGTTTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTATTTTTTATTTTAAAA
Found at i:1274311 original size:23 final size:23
Alignment explanation
Indices: 1274284--1274328 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1274274 AGAAATAAAA
1274284 ATATAATTTTAT-TTCATATTAAC
1 ATATAATTTTATGTTCA-ATTAAC
1274307 ATATAATTTTATGTTCAATTAA
1 ATATAATTTTATGTTCAATTAA
1274329 GGTATGAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATAATTTTATGTTCAATTAAC
Found at i:1275577 original size:27 final size:28
Alignment explanation
Indices: 1275537--1275595 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
1275527 ATACTGGTTA
* * *
1275537 AAAAATTTTAAATTTTATAAAA-AAATAT
1 AAAAATTGTAAA-TTTAAAAAAGAAACAT
1275565 AAAAATTGT-AATTTAAAAAAGAAACAT
1 AAAAATTGTAAATTTAAAAAAGAAACAT
1275592 AAAA
1 AAAA
1275596 TAATGTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 8 0.30
27 11 0.41
28 8 0.30
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (28 bp):
AAAAATTGTAAATTTAAAAAAGAAACAT
Found at i:1287648 original size:18 final size:18
Alignment explanation
Indices: 1287625--1287693 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
1287615 CGTTTATGGT
*
1287625 ACTATTTACGTATACGGC
1 ACTATTCACGTATACGGC
* **
1287643 ACTATTCACATATACAAC
1 ACTATTCACGTATACGGC
*
1287661 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGGC
* *
1287679 ACTGTTCACATATAC
1 ACTATTCACGTATAC
1287694 AGTAGTTGGG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.32
Consensus pattern (18 bp):
ACTATTCACGTATACGGC
Found at i:1287672 original size:36 final size:36
Alignment explanation
Indices: 1287625--1287694 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
1287615 CGTTTATGGT
*
1287625 ACTATTTACGTATACGGCACTATTCACATATACAAC
1 ACTATTCACGTATACGGCACTATTCACATATACAAC
* *
1287661 ACTATTCACGTATACGGTACTGTTCACATATACA
1 ACTATTCACGTATACGGCACTATTCACATATACA
1287695 GTAGTTGGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.31
Consensus pattern (36 bp):
ACTATTCACGTATACGGCACTATTCACATATACAAC
Found at i:1295318 original size:13 final size:13
Alignment explanation
Indices: 1295300--1295324 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1295290 TTGCTGTGTT
1295300 ATTTAGTTAATTA
1 ATTTAGTTAATTA
1295313 ATTTAGTTAATT
1 ATTTAGTTAATT
1295325 TTAATTTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
ATTTAGTTAATTA
Found at i:1297096 original size:450 final size:450
Alignment explanation
Indices: 1296233--1297104 Score: 1399
Period size: 450 Copynumber: 1.9 Consensus size: 450
1296223 GTTAATGTTT
* *
1296233 ATCAATTTCCAGATAAACCAGTTTGGAGAGAGGATGTAGAGTTGATGATGATGGTGCTTCTATTT
1 ATCAATTTCCAGAGAAACCAGTTTGGAGAGAGGATGTAGAGTTGATGATGATGGTGCTTCTAGTT
*
1296298 TGGTGATCTTCAACTTCATTGTCTCTTGAAACGGCTTTAAGCTGGTATTATTCAACTTCAACGCT
66 TGGTCATCTTCAACTTCATTGTCTCTTGAAACGGCTTTAAGCTGGTATTATTCAACTTCAACGCT
*
1296363 TTAACAGATGGAAACAATGGCATAATGGTTAGATTAGGGCAATGCTCGATAGCTAAATGTAAAAG
131 TTAACAGATGGAAACAATGGCATAATGGTTAAATTAGGGCAATGCTCGATAGCTAAATGTAAAAG
* *
1296428 GCAAGGAAAGCACGGCAAGTGTAGATTTGAAGCTTCACCAACATCACCCTTCCACCATCCTTTGA
196 GCAAGGAAAGCACGGCAAGTGTAGATTTGAAGCTTCACCAACATCACCATTCCACCATCCTTTAA
* * *
1296493 GATTTGGACAATCTATTATACATAGTGTTTCCAATGTTGGAAGAAATATTGTTGTTGATTTCCCC
261 GATTTGGACAATCTATTATACATAGTGTTTCCAAGGATGGAAAAAATATTGTTGTTGATTTCCCC
*
1296558 GAAACCAACTCCTCTTGCATTTCAGTCTCCGAAACATTCTCCAAAGCTTCTAATCTTGAAAGCGT
326 GAAACCAACTCCTCTTGCATTTCAGTCTCCGAAACATTCTCCAAAGCTTCTAATCTTGAAAGCCT
* **
1296623 CATAACTCTGAGGGAGTACAACTGATGCAATGATGACAGAGAATCAAGATCTTTGACCTC
391 CATAAATCTGAGGGAACACAACTGATGCAATGATGACAGAGAATCAAGATCTTTGACCTC
** * * *
1296683 ATCAATTTCCAGAGATTCCGGTTTGGGGAGATGATGTAGAGTTGATGATGATGGTGCTTCTAGTT
1 ATCAATTTCCAGAGAAACCAGTTTGGAGAGAGGATGTAGAGTTGATGATGATGGTGCTTCTAGTT
* * * *
1296748 TGGTCATCTTCAACTTCATTGTCTCTTGAAATGGCTTTGAGCTGGTATTCTTCAACTTCAACGTT
66 TGGTCATCTTCAACTTCATTGTCTCTTGAAACGGCTTTAAGCTGGTATTATTCAACTTCAACGCT
* * * *
1296813 TTAACGGATGGAAACAATGGCATAGTGGTTAAATTAGGGCAATGCTCGATGGCTAAATGTGAAAG
131 TTAACAGATGGAAACAATGGCATAATGGTTAAATTAGGGCAATGCTCGATAGCTAAATGTAAAAG
*
1296878 GCAAGGAAAGCACGGCAAGTGT-GTATTTGAAGCTTCACCAACATCACCATTCCACCATCTTTTA
196 GCAAGGAAAGCACGGCAAGTGTAG-ATTTGAAGCTTCACCAACATCACCATTCCACCATCCTTTA
* *
1296942 AGATTTGGGCAATC-ATTTATATATAGTTGTTT-CAAGGATGGAAAAAATATTGTTGTTGATTTC
260 AGATTTGGACAATCTA-TTATACATAG-TGTTTCCAAGGATGGAAAAAATATTGTTGTTGATTTC
*
1297005 CCGGAAACCAACTCCTCTTGCATTTCAGTCTCCGAAACATTCTCCAAAGCTTCTAATCTTGAAAG
323 CCCGAAACCAACTCCTCTTGCATTTCAGTCTCCGAAACATTCTCCAAAGCTTCTAATCTTGAAAG
* * *
1297070 CCTTATAAATTTTAGGGAACACAACTGATGCAATG
388 CCTCATAAATCTGAGGGAACACAACTGATGCAATG
1297105 GTGGCAGATG
Statistics
Matches: 386, Mismatches: 33, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
449 2 0.01
450 379 0.98
451 5 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (450 bp):
ATCAATTTCCAGAGAAACCAGTTTGGAGAGAGGATGTAGAGTTGATGATGATGGTGCTTCTAGTT
TGGTCATCTTCAACTTCATTGTCTCTTGAAACGGCTTTAAGCTGGTATTATTCAACTTCAACGCT
TTAACAGATGGAAACAATGGCATAATGGTTAAATTAGGGCAATGCTCGATAGCTAAATGTAAAAG
GCAAGGAAAGCACGGCAAGTGTAGATTTGAAGCTTCACCAACATCACCATTCCACCATCCTTTAA
GATTTGGACAATCTATTATACATAGTGTTTCCAAGGATGGAAAAAATATTGTTGTTGATTTCCCC
GAAACCAACTCCTCTTGCATTTCAGTCTCCGAAACATTCTCCAAAGCTTCTAATCTTGAAAGCCT
CATAAATCTGAGGGAACACAACTGATGCAATGATGACAGAGAATCAAGATCTTTGACCTC
Found at i:1301135 original size:21 final size:21
Alignment explanation
Indices: 1301109--1301149 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1301099 ATCTGCTCAA
* *
1301109 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1301130 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1301150 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1305124 original size:49 final size:49
Alignment explanation
Indices: 1305071--1305179 Score: 200
Period size: 49 Copynumber: 2.2 Consensus size: 49
1305061 TTTATTTTTA
1305071 AAAATATTTAAAATATTAAATTTTTTAATATTATTAAACATACATATTT
1 AAAATATTTAAAATATTAAATTTTTTAATATTATTAAACATACATATTT
*
1305120 AAAATATTTAAAATATTATATTTTTTAATATTATTAAACATACATATTT
1 AAAATATTTAAAATATTAAATTTTTTAATATTATTAAACATACATATTT
1305169 AATAATATTTA
1 AA-AATATTTA
1305180 GTCATATAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
49 50 0.86
50 8 0.14
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.48
Consensus pattern (49 bp):
AAAATATTTAAAATATTAAATTTTTTAATATTATTAAACATACATATTT
Found at i:1305166 original size:26 final size:26
Alignment explanation
Indices: 1305090--1305177 Score: 94
Period size: 26 Copynumber: 3.5 Consensus size: 26
1305080 AAAATATTAA
*
1305090 ATTTTTTAATATTATTAAACATACAT
1 ATTTTATAATATTATTAAACATACAT
* *
1305116 A-TTTAAAATA-T-TTAAA-ATATTAT
1 ATTTTATAATATTATTAAACATA-CAT
*
1305139 ATTTTTTAATATTATTAAACATACAT
1 ATTTTATAATATTATTAAACATACAT
*
1305165 ATTTAATAATATT
1 ATTTTATAATATT
1305178 TAGTCATATA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
22 3 0.06
23 8 0.16
24 8 0.16
25 8 0.16
26 19 0.39
27 3 0.06
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTTTATAATATTATTAAACATACAT
Found at i:1305217 original size:38 final size:39
Alignment explanation
Indices: 1305163--1305241 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 39
1305153 TTAAACATAC
* *
1305163 ATATTTAATAATATTTAGTCA-TATAATAAATT-ATTAAT
1 ATATTAAATAAAATTTA-TCATTATAATAAATTAATTAAT
* *
1305201 ATATTAAATAAAATTTATTATTTTAATAAATTAATTAAT
1 ATATTAAATAAAATTTATCATTATAATAAATTAATTAAT
1305240 AT
1 AT
1305242 TTCAAATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 2 0.06
38 25 0.71
39 8 0.23
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (39 bp):
ATATTAAATAAAATTTATCATTATAATAAATTAATTAAT
Found at i:1305344 original size:15 final size:15
Alignment explanation
Indices: 1305324--1305380 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
1305314 ATTCAATATT
1305324 AATATTTTAATAATA
1 AATATTTTAATAATA
*
1305339 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
1305358 AATATATTAATAATA
1 AATATTTTAATAATA
1305373 AATATTTT
1 AATATTTT
1305381 GTAGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:1306531 original size:11 final size:11
Alignment explanation
Indices: 1306515--1306545 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1306505 TAGAATATAT
1306515 CCCATACCTTG
1 CCCATACCTTG
*
1306526 CCCATACCTTT
1 CCCATACCTTG
1306537 CCCATACCT
1 CCCATACCT
1306546 ACCTATACAT
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:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:1308170 original size:33 final size:33
Alignment explanation
Indices: 1308128--1308196 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
1308118 CAATACTAAG
1308128 GATTTCAAATTCAATTTGTCTTTCAAGTAAGTA
1 GATTTCAAATTCAATTTGTCTTTCAAGTAAGTA
1308161 GATTTCAAATTCAATTTGTCTTTCAAGTAAGTA
1 GATTTCAAATTCAATTTGTCTTTCAAGTAAGTA
1308194 GAT
1 GAT
1308197 CCCTGCTTCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (33 bp):
GATTTCAAATTCAATTTGTCTTTCAAGTAAGTA
Found at i:1313434 original size:16 final size:15
Alignment explanation
Indices: 1313409--1313456 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
1313399 CTATTTTAAG
1313409 TTTATTTTAATTTTA
1 TTTATTTTAATTTTA
1313424 TTTATTTTTAATTATTA
1 TTTA-TTTTAATT-TTA
1313441 -TTATTTTAGATTTTA
1 TTTATTTTA-ATTTTA
1313456 T
1 T
1313457 ATTAATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.41
16 14 0.48
17 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:1314391 original size:19 final size:19
Alignment explanation
Indices: 1314344--1314383 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1314334 TATTTTGTTA
1314344 TTTATTTTTATTTCATCTT
1 TTTATTTTTATTTCATCTT
1314363 TTTATTTTTATTTCATCTT
1 TTTATTTTTATTTCATCTT
1314382 TT
1 TT
1314384 ACTTTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTATTTTTATTTCATCTT
Found at i:1317248 original size:447 final size:447
Alignment explanation
Indices: 1316171--1317498 Score: 2227
Period size: 447 Copynumber: 3.0 Consensus size: 447
1316161 TAGAGAATAT
* * *
1316171 AGATCTTTGACCTTATCAATTTCCAGAGAATCCAGTTTGGAGAGAGGATGTAGAGTTGATGATGA
1 AGATCTTTGACCTCATCAATTTCCAGAGATTCCAGTTTGGAGAGAGGATGTAGA-AT--TGATGA
* *
1316236 TGGTGCTTCTATTTTGGTCATCTTCAACTTCATTGTCTCTTGAAATGGCTTTGAGCTGGTATTCT
63 TGGTGCTTCTATTTTTGTCATCTTCAACTTCATTGTCTCTTGGAATGGCTTTGAGCTGGTATTCT
* ** * *
1316301 TCAACTTCAACGT-TTTAACAGATGGAAACAATGGCATAGTGGTTAGATTAGGGCAATGCTCGAT
128 TCAACTCCAAC-TCCGTAACAGATGGAAACAATGGCATAGTGGTTAGATTAGGGCAATGATTGAT
* *
1316365 AGCTAAATGTGAAAGGCAAGGAAAGCACGGCAAGTGTGGATTTGAAGCTTCACCAACATCACCCT
192 AGTTAAACGTGAAAGGCAAGGAAAGCACGGCAAGTGTGGATTTGAAGCTTCACCAACATCACCCT
* * * *
1316430 TCCACCATCCTTTAAGATTTGGGCAATCTAT-TATATATAGTGT-TTCCAATGATGGAAGAAATA
257 TCCACCATCCTTTAAGATTTGGGCAATC-ATCTATCTGTAGT-TCTTCCAAGGATGGAAAAAATA
*
1316493 TTGTTGTTGATTTCCCCGAAACCAACTCCTCTTGCATTTCAGTCTCCGAAACATTCTCCAAAGCT
320 TTGTTGTTGATTTCCCCGAAACCAACTCCTCTTGCATTTCAGTCTTCGAAACATTCTCCAAAGCT
*
1316558 TCTAATCTTGAAAGCCAAATAAC--TGAGGGAATACAACTGATGCAATGATGACAGAGAATCA
385 TCTAATCTTGAAAGCCAAATAACTTTGAGGGAATACAACTGATGCAATGATGACAGAGAACCA
1316619 AGATCTTTGACCTCATCAATTTCCAGAGATTCCAGTTTGGAGAGAGGATGTAGAATTGATGATGG
1 AGATCTTTGACCTCATCAATTTCCAGAGATTCCAGTTTGGAGAGAGGATGTAGAATTGATGATGG
*
1316684 TGGTTCTATTTTTGTCATCTTCAACTTCATTGTCTCTTGGAATGGCTTTGAGCTGGTATTCTTCA
66 TGCTTCTATTTTTGTCATCTTCAACTTCATTGTCTCTTGGAATGGCTTTGAGCTGGTATTCTTCA
1316749 ACTCCAACTCCGTAACAGATGGAAACAATGGCATAGTGGTTAGATTAGGGCAATGATTGATAGTT
131 ACTCCAACTCCGTAACAGATGGAAACAATGGCATAGTGGTTAGATTAGGGCAATGATTGATAGTT
*
1316814 AAACATGAAAGGCAAGGAAAGCACGGCAAGTGTGGATTTGAAGCTTCACCAACATCACCCTTCCA
196 AAACGTGAAAGGCAAGGAAAGCACGGCAAGTGTGGATTTGAAGCTTCACCAACATCACCCTTCCA
1316879 CCATCCTTTAAGATTTGGGCAATCATCTATCTGTAGTTCTTCCAAGGATGGAAAAAATATTGTTG
261 CCATCCTTTAAGATTTGGGCAATCATCTATCTGTAGTTCTTCCAAGGATGGAAAAAATATTGTTG
*
1316944 TTGATTTCCCTGAAACCAACTCCTCTTGCATTTCAGTCTTCGAAACATTCTCCAAAGCTTCTAAT
326 TTGATTTCCCCGAAACCAACTCCTCTTGCATTTCAGTCTTCGAAACATTCTCCAAAGCTTCTAAT
* * *
1317009 CTTGAAAGCCTAATAACTTTTAGGGAATACAACTGATGCAATGATGACATAGAACCA
391 CTTGAAAGCCAAATAACTTTGAGGGAATACAACTGATGCAATGATGACAGAGAACCA
* * * * * *
1317066 AGATCTTTGACCTCATCAATGTACAGATATTCCAGTCTGGAGCGAGGATCTAGAATTGATGATGG
1 AGATCTTTGACCTCATCAATTTCCAGAGATTCCAGTTTGGAGAGAGGATGTAGAATTGATGATGG
* *
1317131 TGCTTCTATTTTTGTCAGCTTCAACTTCATTGTCTCTTGGAATGGCTTTGAGCTGGTATTTTTCA
66 TGCTTCTATTTTTGTCATCTTCAACTTCATTGTCTCTTGGAATGGCTTTGAGCTGGTATTCTTCA
1317196 ACTCCAACTCCGTAACAGATGGAAACAATGGCATAGTGGTTAGATTAGGGCAATGATTGATAGTT
131 ACTCCAACTCCGTAACAGATGGAAACAATGGCATAGTGGTTAGATTAGGGCAATGATTGATAGTT
1317261 AAACGTGAAAGGCAAGGAAAGCACGGCAAGTGTGGATTTGAAGCTTCACCAACATCACCCTTCCA
196 AAACGTGAAAGGCAAGGAAAGCACGGCAAGTGTGGATTTGAAGCTTCACCAACATCACCCTTCCA
*
1317326 CCATCCTTTAAAATTTGGGCAATCATCTATCTGTAGTTCTTCCAAGGATGGAAAAAATATTGTTG
261 CCATCCTTTAAGATTTGGGCAATCATCTATCTGTAGTTCTTCCAAGGATGGAAAAAATATTGTTG
* *
1317391 TTGATTTCCCCGAAACCAACTCTTCTTGCATTTCAGTC-TCTGAAACATTCTCTAAAGCTTCTAA
326 TTGATTTCCCCGAAACCAACTCCTCTTGCATTTCAGTCTTC-GAAACATTCTCCAAAGCTTCTAA
*
1317455 TCTTGAAAGCCGAATAACTTTGAGGGAATACAACTGATGCAATG
390 TCTTGAAAGCCAAATAACTTTGAGGGAATACAACTGATGCAATG
1317499 GTGGCAGATG
Statistics
Matches: 834, Mismatches: 40, Indels: 13
0.94 0.05 0.01
Matches are distributed among these distances:
444 4 0.00
445 326 0.39
446 2 0.00
447 450 0.54
448 52 0.06
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (447 bp):
AGATCTTTGACCTCATCAATTTCCAGAGATTCCAGTTTGGAGAGAGGATGTAGAATTGATGATGG
TGCTTCTATTTTTGTCATCTTCAACTTCATTGTCTCTTGGAATGGCTTTGAGCTGGTATTCTTCA
ACTCCAACTCCGTAACAGATGGAAACAATGGCATAGTGGTTAGATTAGGGCAATGATTGATAGTT
AAACGTGAAAGGCAAGGAAAGCACGGCAAGTGTGGATTTGAAGCTTCACCAACATCACCCTTCCA
CCATCCTTTAAGATTTGGGCAATCATCTATCTGTAGTTCTTCCAAGGATGGAAAAAATATTGTTG
TTGATTTCCCCGAAACCAACTCCTCTTGCATTTCAGTCTTCGAAACATTCTCCAAAGCTTCTAAT
CTTGAAAGCCAAATAACTTTGAGGGAATACAACTGATGCAATGATGACAGAGAACCA
Found at i:1324099 original size:31 final size:31
Alignment explanation
Indices: 1324052--1324128 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
1324042 TATAAAATTT
*
1324052 AAATTTAG-T-ATATATACTTTTATTTTTAG
1 AAATTTAGTTAATTTATACTTTTATTTTTAG
1324081 AAATTTAGTTAATTTATACTTTTATTTTTAG
1 AAATTTAGTTAATTTATACTTTTATTTTTAG
1324112 AAATTTAGTTAATTTAT
1 AAATTTAGTTAATTTAT
1324129 TTTTTAGGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 8 0.18
30 1 0.02
31 36 0.80
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (31 bp):
AAATTTAGTTAATTTATACTTTTATTTTTAG
Found at i:1324146 original size:30 final size:31
Alignment explanation
Indices: 1324052--1324148 Score: 103
Period size: 31 Copynumber: 3.2 Consensus size: 31
1324042 TATAAAATTT
* * *
1324052 AAATTTAG-T-ATATATACTTTTATTTTTAG
1 AAATTTAGTTAATTTATACTTTTAGTTTCAG
* *
1324081 AAATTTAGTTAATTTATACTTTTATTTTTAG
1 AAATTTAGTTAATTTATACTTTTAGTTTCAG
*
1324112 AAATTTAGTTAATTTAT-TTTTTAGGTTTCA-
1 AAATTTAGTTAATTTATACTTTTA-GTTTCAG
1324142 AAATTTA
1 AAATTTA
1324149 TATCTAATTG
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
29 8 0.13
30 13 0.21
31 40 0.66
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (31 bp):
AAATTTAGTTAATTTATACTTTTAGTTTCAG
Found at i:1329089 original size:26 final size:26
Alignment explanation
Indices: 1329044--1329094 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1329034 TTTCAATCTC
***
1329044 TAATTATTCTTATTTTTTAATCGAAA
1 TAATTATTCTTATACATTAATCGAAA
1329070 TAATTATTCTTATACATTAATCGAA
1 TAATTATTCTTATACATTAATCGAA
1329095 TCCTCAGGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.49
Consensus pattern (26 bp):
TAATTATTCTTATACATTAATCGAAA
Found at i:1330037 original size:27 final size:26
Alignment explanation
Indices: 1330007--1330068 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
1329997 AGATAATTAA
1330007 AATAAAATCCTAAAT-TTGAATAATCCT
1 AATAAAAT-CTAAATATT-AATAATCCT
* * *
1330034 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTAAATATTAATAATCCT
1330061 AATAAAAT
1 AATAAAAT
1330069 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 23 0.79
28 4 0.14
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (26 bp):
AATAAAATCTAAATATTAATAATCCT
Found at i:1331620 original size:48 final size:48
Alignment explanation
Indices: 1331555--1331653 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
1331545 TTATTAAGAA
1331555 AATTCCATCGGATAAGTTTGAGACGTCCTATTAGGGTCAATCGTTATG
1 AATTCCATCGGATAAGTTTGAGACGTCCTATTAGGGTCAATCGTTATG
1331603 AATTCCATCGGATAAGTTTGAGACGTCCTATTAGGGTCAATCGTTATG
1 AATTCCATCGGATAAGTTTGAGACGTCCTATTAGGGTCAATCGTTATG
1331651 AAT
1 AAT
1331654 CACGTTTAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.33
Consensus pattern (48 bp):
AATTCCATCGGATAAGTTTGAGACGTCCTATTAGGGTCAATCGTTATG
Found at i:1332206 original size:11 final size:12
Alignment explanation
Indices: 1332185--1332217 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1332175 TAAATTTTTA
1332185 TATAGAATATATT
1 TATA-AATATATT
1332198 TA-AAATATATT
1 TATAAATATATT
1332209 TATAAATAT
1 TATAAATAT
1332218 TTTGATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.53
12 7 0.37
13 2 0.11
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (12 bp):
TATAAATATATT
Found at i:1336576 original size:5 final size:5
Alignment explanation
Indices: 1336566--1336594 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1336556 ACTATTTGTG
1336566 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1336595 AACACACGGA
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:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1339812 original size:17 final size:17
Alignment explanation
Indices: 1339790--1339831 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1339780 AATGTAAGAG
* *
1339790 AATAATAAAATATTAAT
1 AATAATAAAATAGTAAA
*
1339807 AATAATTAAATAGTAAA
1 AATAATAAAATAGTAAA
1339824 AATAATAA
1 AATAATAA
1339832 TAGTAATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
AATAATAAAATAGTAAA
Found at i:1340039 original size:16 final size:17
Alignment explanation
Indices: 1340020--1340057 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1340010 AAAAGGAAAT
1340020 AATAATATGGTAA-AAA
1 AATAATATGGTAATAAA
*
1340036 AATAATATGTTAATAAA
1 AATAATATGGTAATAAA
1340053 AATAA
1 AATAA
1340058 CAGTAGTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (17 bp):
AATAATATGGTAATAAA
Found at i:1340073 original size:3 final size:3
Alignment explanation
Indices: 1340067--1340140 Score: 87
Period size: 3 Copynumber: 24.3 Consensus size: 3
1340057 ACAGTAGTAG
* * * *
1340067 TAA TAA TAA TAG TAA GAA TAA TAA TGA TAA T-A TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1340114 TAA TAA CTAAA TAA TAA TAA TAA TAA T
1 TAA TAA -T-AA TAA TAA TAA TAA TAA T
1340141 GTTAATGGTA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
2 2 0.03
3 54 0.90
4 2 0.03
5 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1340126 original size:20 final size:19
Alignment explanation
Indices: 1340067--1340139 Score: 89
Period size: 20 Copynumber: 3.9 Consensus size: 19
1340057 ACAGTAGTAG
* *
1340067 TAATAATAATAGTAAGAA-
1 TAATAATAATAATAATAAC
*
1340085 TAATAATGATAAT-ATAAC
1 TAATAATAATAATAATAAC
1340103 -AATAATAATAATAATAAC
1 TAATAATAATAATAATAAC
1340121 TAAATAATAATAATAATAA
1 T-AATAATAATAATAATAA
1340140 TGTTAATGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
17 14 0.30
18 16 0.34
20 17 0.36
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (19 bp):
TAATAATAATAATAATAAC
Found at i:1345972 original size:16 final size:15
Alignment explanation
Indices: 1345930--1345979 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
1345920 AGATGATTTT
1345930 ATAAA-AAAAT-ATA
1 ATAAATAAAATAATA
1345943 ATAAATAAAA-AATA
1 ATAAATAAAATAATA
*
1345957 TTAAATTAAAATAATA
1 ATAAA-TAAAATAATA
1345973 A-AAATAA
1 ATAAATAA
1345980 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
13 5 0.16
14 14 0.45
15 8 0.26
16 4 0.13
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAAATAAAATAATA
Found at i:1348857 original size:30 final size:30
Alignment explanation
Indices: 1348798--1348886 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 30
1348788 TTGGTTACTA
* *
1348798 TTTTTTTTAATTTGGTACTAAAAAACTTGACAC
1 TTTTTCTTAATTTGGTACT---AATCTTGACAC
1348831 TTTTTCTTAATTTGGTACTAATCTTGACAC
1 TTTTTCTTAATTTGGTACTAATCTTGACAC
* * *
1348861 TTTCTCTTAAATTAGTACTTAATCTT
1 TTTTTCTTAATTTGGTAC-TAATCTT
1348887 TTTGGGGTCC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
30 25 0.50
31 7 0.14
33 18 0.36
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.49
Consensus pattern (30 bp):
TTTTTCTTAATTTGGTACTAATCTTGACAC
Found at i:1349384 original size:60 final size:61
Alignment explanation
Indices: 1349319--1349472 Score: 181
Period size: 60 Copynumber: 2.6 Consensus size: 61
1349309 TTTAGGCACT
* * * * *
1349319 AAATTAGGAAAAAATGCCAAGTTCATGTACCAAATTGGG-TCCACAAAGAGTTT-AGGTACC
1 AAATTAGGAAAAAATGCCAAGTTCAAGTACCAAATTGGGCT-AAAAAAAAGTTTCAGATACC
* * *
1349379 CAATTAGG-AAAAGTGTCAAGTTCAAGTACCAAATTGGGCTAAAAAAAAGTTTCAGATACC
1 AAATTAGGAAAAAATGCCAAGTTCAAGTACCAAATTGGGCTAAAAAAAAGTTTCAGATACC
* *
1349439 AAATTA-AAAAAAATGCCAAGTTCAAATACCAAAT
1 AAATTAGGAAAAAATGCCAAGTTCAAGTACCAAAT
1349473 GCTATTTTAA
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
59 36 0.46
60 42 0.54
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (61 bp):
AAATTAGGAAAAAATGCCAAGTTCAAGTACCAAATTGGGCTAAAAAAAAGTTTCAGATACC
Found at i:1349813 original size:46 final size:47
Alignment explanation
Indices: 1349746--1349838 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 47
1349736 AATTCGTGCC
*
1349746 TTTAAAATTTTGAGATATTTTGGATTCGACATTTGGTT-ATTAGTAT
1 TTTAAAATTTTGAGATATTTTGGATTCGACATTTGATTGATTAGTAT
1349792 TTTAAAATTTTGAGATATTTTGGATTCGACATTTGATTGATTAGTAT
1 TTTAAAATTTTGAGATATTTTGGATTCGACATTTGATTGATTAGTAT
1349839 AAATTTGATT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 37 0.82
47 8 0.18
ACGTcount: A:0.29, C:0.04, G:0.17, T:0.49
Consensus pattern (47 bp):
TTTAAAATTTTGAGATATTTTGGATTCGACATTTGATTGATTAGTAT
Found at i:1349825 original size:24 final size:24
Alignment explanation
Indices: 1349752--1349825 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
1349742 TGCCTTTAAA
1349752 ATTTTGAGATATTTTGGATTCGAC
1 ATTTTGAGATATTTTGGATTCGAC
* * * ** *
1349776 A-TTTG-GTTA-TTAGTATTTTAAA
1 ATTTTGAGATATTTTGGA-TTCGAC
1349798 ATTTTGAGATATTTTGGATTCGAC
1 ATTTTGAGATATTTTGGATTCGAC
1349822 ATTT
1 ATTT
1349826 GATTGATTAG
Statistics
Matches: 34, Mismatches: 12, Indels: 8
0.63 0.22 0.15
Matches are distributed among these distances:
21 4 0.12
22 7 0.21
23 8 0.24
24 11 0.32
25 4 0.12
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (24 bp):
ATTTTGAGATATTTTGGATTCGAC
Found at i:1352228 original size:25 final size:26
Alignment explanation
Indices: 1352200--1352250 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1352190 CTTATTTCAT
*
1352200 TAAATAAAAAAT-TTTAAAAATATAA
1 TAAATAAAAAATATTTAAAAACATAA
* *
1352225 TAAATCAAATATATTTAAAAACATAA
1 TAAATAAAAAATATTTAAAAACATAA
1352251 AAACAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAATAAAAAATATTTAAAAACATAA
Found at i:1352243 original size:26 final size:24
Alignment explanation
Indices: 1352212--1352260 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
1352202 AATAAAAAAT
*
1352212 TTTAAAAATATAATAAATCAAATATA
1 TTTAAAAACATAA-AAA-CAAATATA
1352238 TTTAAAAACATAAAAACAAATAT
1 TTTAAAAACATAAAAACAAATAT
1352261 TAAGACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
TTTAAAAACATAAAAACAAATATA
Found at i:1359076 original size:18 final size:18
Alignment explanation
Indices: 1359053--1359087 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1359043 CCCAACTACT
1359053 GTATACGTGAACAGTACC
1 GTATACGTGAACAGTACC
*
1359071 GTATACGTGAATAGTAC
1 GTATACGTGAACAGTAC
1359088 GAACCTGGCT
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:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (18 bp):
GTATACGTGAACAGTACC
Found at i:1364173 original size:17 final size:17
Alignment explanation
Indices: 1364151--1364185 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1364141 ATCATATGGC
1364151 TTTTAAAACATTCATAT
1 TTTTAAAACATTCATAT
1364168 TTTTAAAACATTCATAT
1 TTTTAAAACATTCATAT
1364185 T
1 T
1364186 ATAAACATGT
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:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTAAAACATTCATAT
Found at i:1364193 original size:15 final size:17
Alignment explanation
Indices: 1364154--1364190 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1364144 ATATGGCTTT
*
1364154 TAAAACATTCATATTTT
1 TAAAACATTCATATTTA
1364171 TAAAACATTCATA-TTA
1 TAAAACATTCATATTTA
1364187 TAAA
1 TAAA
1364191 CATGTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAACATTCATATTTA
Found at i:1366820 original size:31 final size:31
Alignment explanation
Indices: 1366752--1366813 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1366742 ATAACCTTTA
1366752 TAATAAAACATAAAACCATTATATTTAATGG
1 TAATAAAACATAAAACCATTATATTTAATGG
*
1366783 TAATAAAATATAAAACCATTATATTTAATGG
1 TAATAAAACATAAAACCATTATATTTAATGG
1366814 CTATAAACGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.34
Consensus pattern (31 bp):
TAATAAAACATAAAACCATTATATTTAATGG
Found at i:1367003 original size:14 final size:15
Alignment explanation
Indices: 1366986--1367014 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1366976 ATACGAGAAT
1366986 TTCACACA-TATAAA
1 TTCACACATTATAAA
1367000 TTCACACATTATAAA
1 TTCACACATTATAAA
1367015 CACATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (15 bp):
TTCACACATTATAAA
Found at i:1374202 original size:21 final size:21
Alignment explanation
Indices: 1374176--1374216 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1374166 ATCTACTCAA
* *
1374176 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1374197 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1374217 TCGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1387722 original size:15 final size:15
Alignment explanation
Indices: 1387702--1387731 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1387692 GTTTTAGAAT
1387702 TTATCCCTTTTCAAA
1 TTATCCCTTTTCAAA
1387717 TTATCCCTTTTCAAA
1 TTATCCCTTTTCAAA
1387732 AGTATCTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATCCCTTTTCAAA
Done.