Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 4 of 425
Found at i:1052322 original size:31 final size:31
Alignment explanation
Indices: 1052287--1052352 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
1052277 AGGAAAATTC
* *
1052287 CATTTCCCCCTTGAAATTTTTAGAATATTTT
1 CATTTCCCCCTTGAAATTTTTAAAAAATTTT
* * *
1052318 CATTTCTCTCTTGAAGTTTTTAAAAAATTTT
1 CATTTCCCCCTTGAAATTTTTAAAAAATTTT
1052349 -ATTT
1 CATTT
1052353 AGGCCCCCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (31 bp):
CATTTCCCCCTTGAAATTTTTAAAAAATTTT
Found at i:1054161 original size:4 final size:4
Alignment explanation
Indices: 1054152--1054178 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1054142 ACATAGTGTA
1054152 CATC CATC CATC CATC CATC CATC CAT
1 CATC CATC CATC CATC CATC CATC CAT
1054179 TTATACATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.48, G:0.00, T:0.26
Consensus pattern (4 bp):
CATC
Found at i:1054215 original size:88 final size:89
Alignment explanation
Indices: 1054078--1054242 Score: 253
Period size: 88 Copynumber: 1.9 Consensus size: 89
1054068 ATCCATGCAA
* * *
1054078 CATCCATCCATTCATACATACACGTACATACATTATCTTAACCGTTTCACAAT-AGCTCGTCGTT
1 CATCCATCCATTCATACATACACG-ACATACATTACCCTAACCGTTTCACAATGA-CTCGCCGTT
1054142 ACATAGTGTACATCCATCCATCCATC
64 ACATAGTGTACATCCATCCATCCATC
* *
1054168 CATCCATCCATTTATACATACAC-ACATACATTACCCTAACCGTTTCACAATGACTGGCCGTTAC
1 CATCCATCCATTCATACATACACGACATACATTACCCTAACCGTTTCACAATGACTCGCCGTTAC
1054232 ATAGTGTACAT
66 ATAGTGTACAT
1054243 AAATTGAAAT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
88 46 0.67
89 1 0.01
90 22 0.32
ACGTcount: A:0.31, C:0.30, G:0.08, T:0.30
Consensus pattern (89 bp):
CATCCATCCATTCATACATACACGACATACATTACCCTAACCGTTTCACAATGACTCGCCGTTAC
ATAGTGTACATCCATCCATCCATC
Found at i:1060577 original size:21 final size:22
Alignment explanation
Indices: 1060552--1060601 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1060542 TTATCAATTT
*
1060552 TTTAAATAAAA-TAAAATTTAA
1 TTTAAATAAAATTAAAATTGAA
*
1060573 TTTAAA-AAAATTTAAATTGAA
1 TTTAAATAAAATTAAAATTGAA
*
1060594 ATTAAATA
1 TTTAAATA
1060602 TTTGTGCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 4 0.17
21 19 0.79
22 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
TTTAAATAAAATTAAAATTGAA
Found at i:1065235 original size:115 final size:115
Alignment explanation
Indices: 1065033--1065241 Score: 373
Period size: 115 Copynumber: 1.8 Consensus size: 115
1065023 TGCAAAAGTT
*
1065033 TAGCTTCCTTCTCCACATATTCCGAATTCTTGCTATATTATTAGTATCAACTCTCCATAAAAAAC
1 TAGCTTCCTTCTCCACATATTCCGAATTCTTGCTATATTATAAGTATCAACTCTCCATAAAAAAC
*
1065098 ACCTTGATCTTAGCAGGCACCAATGCATAATGGCATAATGGCCGTTGTAC
66 ACCTTGATCTTAGCAGGCACCAATACATAATGGCATAATGGCCGTTGTAC
* *
1065148 TAGCTTCCTTCTCCACATATTCCGAATTCTTGCTATATTATAAGTATGAATTCTCCATAAAAAAC
1 TAGCTTCCTTCTCCACATATTCCGAATTCTTGCTATATTATAAGTATCAACTCTCCATAAAAAAC
*
1065213 ACCTTGATTTTAGCAGGCACCAATACATA
66 ACCTTGATCTTAGCAGGCACCAATACATA
1065242 TCCACTTCCA
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
115 89 1.00
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.33
Consensus pattern (115 bp):
TAGCTTCCTTCTCCACATATTCCGAATTCTTGCTATATTATAAGTATCAACTCTCCATAAAAAAC
ACCTTGATCTTAGCAGGCACCAATACATAATGGCATAATGGCCGTTGTAC
Found at i:1069498 original size:2 final size:2
Alignment explanation
Indices: 1069493--1069542 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1069483 TATATATACT
1069493 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1069535 GA GA GA GA
1 GA GA GA GA
1069543 AATTTTAGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1071093 original size:25 final size:24
Alignment explanation
Indices: 1071057--1071131 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 24
1071047 TTTGTCTCTT
1071057 TTTTAAAACATTTAACACGTGGCA
1 TTTTAAAACATTTAACACGTGGCA
* **
1071081 TTTTATAATCATTGT-GTAC-T---A
1 TTTTA-AAACATT-TAACACGTGGCA
1071102 TCTTTAAAACATTTAACACGTGGCA
1 T-TTTAAAACATTTAACACGTGGCA
1071127 TTTTA
1 TTTTA
1071132 TAATCATTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
20 1 0.03
21 10 0.27
22 5 0.14
24 10 0.27
25 10 0.27
26 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (24 bp):
TTTTAAAACATTTAACACGTGGCA
Found at i:1071108 original size:46 final size:46
Alignment explanation
Indices: 1071058--1071150 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
1071048 TTGTCTCTTT
1071058 TTTAAAACATTTAACACGTGGCATTTTATAATCATTGTGTACTATC
1 TTTAAAACATTTAACACGTGGCATTTTATAATCATTGTGTACTATC
1071104 TTTAAAACATTTAACACGTGGCATTTTATAATCATTGTGTACTATC
1 TTTAAAACATTTAACACGTGGCATTTTATAATCATTGTGTACTATC
1071150 T
1 T
1071151 CCTTAAAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (46 bp):
TTTAAAACATTTAACACGTGGCATTTTATAATCATTGTGTACTATC
Found at i:1073719 original size:31 final size:32
Alignment explanation
Indices: 1073668--1073739 Score: 78
Period size: 34 Copynumber: 2.2 Consensus size: 32
1073658 TATTTATAAT
*
1073668 TTTTAAAAGATTAAATTAATTTT-T-TTATTA
1 TTTTAAAAGATAAAATTAATTTTATATTATTA
1073698 TTTTAAAAG-TAAAAGTATAATTTTATAATTATTA
1 TTTTAAAAGATAAAA-T-TAATTTTAT-ATTATTA
*
1073732 ATTTAAAA
1 TTTTAAAA
1073740 TTTTATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 4 0.11
30 10 0.29
31 7 0.20
32 1 0.03
34 13 0.37
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (32 bp):
TTTTAAAAGATAAAATTAATTTTATATTATTA
Found at i:1079647 original size:15 final size:15
Alignment explanation
Indices: 1079627--1079658 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1079617 TACTTGTTCA
*
1079627 ATACCTTGTGTTTTG
1 ATACCTTATGTTTTG
1079642 ATACCTTATGTTTTG
1 ATACCTTATGTTTTG
1079657 AT
1 AT
1079659 GTTCTGATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.16, T:0.53
Consensus pattern (15 bp):
ATACCTTATGTTTTG
Found at i:1082765 original size:19 final size:21
Alignment explanation
Indices: 1082741--1082784 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1082731 TAAAATTTTG
1082741 TTTAAA-TATATCCATATT-T
1 TTTAAAGTATATCCATATTAT
*
1082760 TTTAAAGTTATATCTATATTAT
1 TTTAAAG-TATATCCATATTAT
1082782 TTT
1 TTT
1082785 TAATTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
21 11 0.52
22 4 0.19
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTAAAGTATATCCATATTAT
Found at i:1088308 original size:118 final size:119
Alignment explanation
Indices: 1088021--1088316 Score: 380
Period size: 119 Copynumber: 2.5 Consensus size: 119
1088011 AAGTGCAACT
** * *
1088021 GCTATGCTAGTGCAATGAAGAACATATTGACATTGAACTTGAGATATGCAAAAGAATGACAACAT
1 GCTATGCTAGTGCAATGAAGAACATATCAACATTAAACTTGAGATATGCAAAAGAATAACAACAT
*
1088086 ATGCAGCAAATAGCATAAGAACCGGAAAGAACCATCACCAGTAAACATCAAACC
66 ATGCAGCAAATAGCATAAGAACCGGAAAGAACCATCACCAATAAACATCAAACC
* * * ** *
1088140 GCTATGCTAGTGCAATGAAGGACATATCACCATTAAAGTCAAGATATGCAAACA-AATAACATCA
1 GCTATGCTAGTGCAATGAAGAACATATCAACATTAAACTTGAGATATGCAAA-AGAATAACAACA
* ** * * * * * *
1088204 TATGCAGCAAATTGTGTAAGAACTGGAAAGAATCATCACTAATATACGTCGAA-C
65 TATGCAGCAAATAGCATAAGAACCGGAAAGAACCATCACCAATAAACATCAAACC
*
1088258 GCTATGCTAGTGCAATGAAGAACATATCAACATTAAACTTGAGATATGCAAATGAATAA
1 GCTATGCTAGTGCAATGAAGAACATATCAACATTAAACTTGAGATATGCAAAAGAATAA
1088317 TAAGTTAATA
Statistics
Matches: 149, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
118 53 0.36
119 95 0.64
120 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.22
Consensus pattern (119 bp):
GCTATGCTAGTGCAATGAAGAACATATCAACATTAAACTTGAGATATGCAAAAGAATAACAACAT
ATGCAGCAAATAGCATAAGAACCGGAAAGAACCATCACCAATAAACATCAAACC
Found at i:1089850 original size:3 final size:3
Alignment explanation
Indices: 1089842--1089866 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1089832 ATTGAAGATT
1089842 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
1089867 TACCATGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1094434 original size:54 final size:53
Alignment explanation
Indices: 1094336--1094444 Score: 141
Period size: 54 Copynumber: 2.0 Consensus size: 53
1094326 AGAAATCCAT
1094336 TTTAATAAATGTAATGTTTTTAAATAAAAAAACATATTTTTTAATTCA-TCATA
1 TTTAATAAATGTAATGTTTTTAAATAAAAAAACATATTTTTTAATT-ATTCATA
*** *
1094389 TTTAATAAACT-TAATGTTTTTTAAATAAAAATTTATGTTTTTTAATTATTCATA
1 TTTAATAAA-TGTAATG-TTTTTAAATAAAAAAACATATTTTTTAATTATTCATA
1094443 TT
1 TT
1094445 GGCTTCTACA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
53 15 0.31
54 34 0.69
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (53 bp):
TTTAATAAATGTAATGTTTTTAAATAAAAAAACATATTTTTTAATTATTCATA
Found at i:1094624 original size:31 final size:32
Alignment explanation
Indices: 1094561--1094625 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 32
1094551 TCTTAAATTT
* *
1094561 GTCATGAAAATATTTAAATTTTTTTTAATTAA
1 GTCATGAAAATATTTAAATGTTTTTCAATTAA
* * *
1094593 GTCATTAAAATATTTGAA-GTTTTTCATTTAA
1 GTCATGAAAATATTTAAATGTTTTTCAATTAA
1094624 GT
1 GT
1094626 TTCTTAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 12 0.43
32 16 0.57
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (32 bp):
GTCATGAAAATATTTAAATGTTTTTCAATTAA
Found at i:1099590 original size:1 final size:1
Alignment explanation
Indices: 1099584--1099611 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
1099574 TTAGGGAAGC
1099584 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1099612 ATGTGGTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1102838 original size:2 final size:2
Alignment explanation
Indices: 1102831--1102855 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1102821 TTGTGTTGCT
1102831 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 T
1102856 CATGGACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1103095 original size:27 final size:27
Alignment explanation
Indices: 1103057--1103113 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
1103047 GGATTTAGTA
*
1103057 CTTAAATTTAATTTGGTCATTCTAGCC
1 CTTAAATTTAATTTGGCCATTCTAGCC
*
1103084 CTTAAATTTAATTTGGCCATTCTAGTC
1 CTTAAATTTAATTTGGCCATTCTAGCC
1103111 CTT
1 CTT
1103114 GGTACTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.46
Consensus pattern (27 bp):
CTTAAATTTAATTTGGCCATTCTAGCC
Found at i:1110991 original size:29 final size:29
Alignment explanation
Indices: 1110949--1111035 Score: 147
Period size: 29 Copynumber: 3.0 Consensus size: 29
1110939 AACCATCTTT
*
1110949 TTCTTCCTCGGTGTAAACATATTAAATTA
1 TTCTTCCTCGGTGTAAACATACTAAATTA
*
1110978 TTCTTCCTCGGTGTAAAAATACTAAATTA
1 TTCTTCCTCGGTGTAAACATACTAAATTA
*
1111007 TTCTTCCTCGGTATAAACATACTAAATTA
1 TTCTTCCTCGGTGTAAACATACTAAATTA
1111036 CTGTTTAGGG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.39
Consensus pattern (29 bp):
TTCTTCCTCGGTGTAAACATACTAAATTA
Found at i:1123885 original size:26 final size:26
Alignment explanation
Indices: 1123846--1123981 Score: 218
Period size: 26 Copynumber: 5.2 Consensus size: 26
1123836 TGATACAAAT
* * *
1123846 TGATAATAGATTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
1123872 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
1123898 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
1123924 TGATAATGGATTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
1123950 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
1123976 TGATAA
1 TGATAA
1123982 GAATATCATG
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 101 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:1126012 original size:136 final size:137
Alignment explanation
Indices: 1125767--1126052 Score: 502
Period size: 136 Copynumber: 2.1 Consensus size: 137
1125757 GAGTAGTCTC
*
1125767 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGGCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* * *
1125832 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTTTGGCCCAGTATC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC
1125897 ACTGTTA
131 ACTGTTA
*
1125904 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1125968 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC
1126033 ACTGTTA
131 ACTGTTA
**
1126040 CCTGAATGGGCTT
1 CCCAAATGGGCTT
1126053 AGGCCCAATG
Statistics
Matches: 142, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
136 122 0.86
137 20 0.14
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:1127660 original size:28 final size:29
Alignment explanation
Indices: 1127612--1127667 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
1127602 TAAATACAAA
* *
1127612 ATCTAAGGCTTAGAATTA-TTTAATTTTG
1 ATCTAAGGCTTAAAATCATTTTAATTTTG
1127640 ATCTAATGG-TTAAAATCATTTTAATTTT
1 ATCTAA-GGCTTAAAATCATTTTAATTTT
1127668 TATGGTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (29 bp):
ATCTAAGGCTTAAAATCATTTTAATTTTG
Found at i:1128523 original size:101 final size:100
Alignment explanation
Indices: 1128348--1128723 Score: 480
Period size: 101 Copynumber: 3.8 Consensus size: 100
1128338 AAAAAAAAAC
*
1128348 ATACATATACATATAGTAATCATCATATAAAAAAACATATCAAACTAGCATATAGTGTTGATCAT
1 ATACATATACATATAGTAATCATCATATAAAAAAAC--ATCAAACTAGCATATAGTATTGATCAT
* *
1128413 AGATCCAATAAACTATGCATACACACACACATATTCAT
64 AGATTCAATAAACTATACATACACACACACATA-TCAT
* **
1128451 ATACATATACATATAGTAATCATCATTTCCAAAAACATCAAACTAGCATATAGTATTGATCATAG
1 ATACATATACATATAGTAATCATCATATAAAAAAACATCAAACTAGCATATAGTATTGATCATAG
* * *
1128516 ATTCAATAAACTATACATGCACATACACATACACAT
66 ATTCAATAAACTATACATACACACACACATA-TCAT
* *
1128552 ACACATATTCATATAGTAATCATCATATAAAAAAACATCAAACTAGCATATAGTATTGATCATAG
1 ATACATATACATATAGTAATCATCATATAAAAAAACATCAAACTAGCATATAGTATTGATCATAG
* *
1128617 ATTGAATAAACTATACATA-A-ACATACATAT-AT
66 ATTCAATAAACTATACATACACACACACATATCAT
* * * * *
1128649 ATACATAT--ATAGTAGTGATTAT-ATAGAAAAACAACATCAAACTAG--TATAGTACTGATCAA
1 ATACATATACATA-TAGTAATCATCATATAAAAA-AACATCAAACTAGCATATAGTATTGATCAT
1128709 AGATTCAATAAACTA
64 AGATTCAATAAACTA
1128724 AATAGATGTG
Statistics
Matches: 244, Mismatches: 27, Indels: 13
0.86 0.10 0.05
Matches are distributed among these distances:
94 27 0.11
95 11 0.05
96 21 0.09
97 9 0.04
99 7 0.03
100 1 0.00
101 135 0.55
103 33 0.14
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.29
Consensus pattern (100 bp):
ATACATATACATATAGTAATCATCATATAAAAAAACATCAAACTAGCATATAGTATTGATCATAG
ATTCAATAAACTATACATACACACACACATATCAT
Found at i:1128953 original size:4 final size:4
Alignment explanation
Indices: 1128946--1128973 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1128936 ACTAAGAAAC
1128946 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
1128974 TATATATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:1131352 original size:66 final size:66
Alignment explanation
Indices: 1131246--1131441 Score: 248
Period size: 66 Copynumber: 3.0 Consensus size: 66
1131236 TCTTTTTTAT
* * * * *
1131246 ACAATGTCTATAACTATACATAGCCCATTCCCAACCCTTAAATAAGAGGATAATGCGCTTCAGCA
1 ACAATGCCTATAACAATACATAACCCCTCCCCAACCCTTAAATAAGAGGATAATGCGCTTCAGCA
1131311 C
66 C
* * ** * *
1131312 ACAATGCTTATAACAATACATAGCTTCTCCCCAACCCTTAAATAAAAGGATAATGCGCTTCAGCG
1 ACAATGCCTATAACAATACATAACCCCTCCCCAACCCTTAAATAAGAGGATAATGCGCTTCAGCA
1131377 C
66 C
** ** *
1131378 ACAATGCCTATAACTTTACATAACCCCTCCTTAACCCTTAAATAAGAGGATAATGCGTTTCAGC
1 ACAATGCCTATAACAATACATAACCCCTCCCCAACCCTTAAATAAGAGGATAATGCGCTTCAGC
1131442 TCATTCGAAC
Statistics
Matches: 111, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 111 1.00
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.26
Consensus pattern (66 bp):
ACAATGCCTATAACAATACATAACCCCTCCCCAACCCTTAAATAAGAGGATAATGCGCTTCAGCA
C
Found at i:1131859 original size:17 final size:20
Alignment explanation
Indices: 1131837--1131888 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
1131827 CTAATTTTTT
1131837 TATATTTT-A-TTAATT-TA
1 TATATTTTAATTTAATTATA
1131854 TATATTTTAATTTTAATTATA
1 TATATTTTAA-TTTAATTATA
1131875 TATATTTTTAATTT
1 TATA-TTTTAATTT
1131889 CATAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.27
18 1 0.03
20 6 0.20
21 9 0.30
22 6 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TATATTTTAATTTAATTATA
Found at i:1131867 original size:23 final size:22
Alignment explanation
Indices: 1131846--1131888 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1131836 TTATATTTTA
1131846 TTAATT-TATATA-TTTTAATT
1 TTAATTATATATATTTTTAATT
1131866 TTAATTATATATATTTTTAATT
1 TTAATTATATATATTTTTAATT
1131888 T
1 T
1131889 CATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.29
21 6 0.29
22 9 0.43
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTAATTATATATATTTTTAATT
Found at i:1132067 original size:18 final size:18
Alignment explanation
Indices: 1132044--1132092 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 18
1132034 AAAAATGCTT
*
1132044 TTTTTATTAATTTATATA
1 TTTTTATTAATTTATAAA
1132062 TTTTTA--AAGTTT-TAAA
1 TTTTTATTAA-TTTATAAA
*
1132078 TTTTTTTTAATTTAT
1 TTTTTATTAATTTAT
1132093 GTCTGCCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
16 10 0.40
17 6 0.24
18 9 0.36
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTTATTAATTTATAAA
Found at i:1133406 original size:29 final size:30
Alignment explanation
Indices: 1133344--1133423 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 30
1133334 ATCCCAAAAC
* * *
1133344 TATACATGAACTATGGTTTAATGTGTAATTT
1 TATACATGAACTTTGATTT-ATGTGCAATTT
1133375 TATACATGAACTTTGATTT-TGTGCAATTT
1 TATACATGAACTTTGATTTATGTGCAATTT
*
1133404 TATACATGAAATTTTGATTT
1 TATACATG-AACTTTGATTT
1133424 GATCCAATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 17 0.39
30 10 0.23
31 17 0.39
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.47
Consensus pattern (30 bp):
TATACATGAACTTTGATTTATGTGCAATTT
Found at i:1133432 original size:30 final size:29
Alignment explanation
Indices: 1133370--1133432 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
1133360 TTTAATGTGT
*
1133370 AATTTTATACATGAACTTTGATTTTGTGC
1 AATTTTATACATGAACTTTGATTTTGTCC
*
1133399 AATTTTATACATGAAATTTTGA-TTTGATCC
1 AATTTTATACATG-AACTTTGATTTTG-TCC
1133429 AATT
1 AATT
1133433 CTTGTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.48
Consensus pattern (29 bp):
AATTTTATACATGAACTTTGATTTTGTCC
Found at i:1133650 original size:29 final size:30
Alignment explanation
Indices: 1133618--1133676 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
1133608 TCACGTGTAT
*
1133618 AATTG-CATCAAATTAAAGTTCATATATAC
1 AATTGACATCAAATTAAAATTCATATATAC
* *
1133647 AATTGCACATTAAATTAAAATTCATGTATA
1 AATTG-ACATCAAATTAAAATTCATATATA
1133677 ATTTTGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.20
31 20 0.80
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.36
Consensus pattern (30 bp):
AATTGACATCAAATTAAAATTCATATATAC
Found at i:1133679 original size:29 final size:27
Alignment explanation
Indices: 1133613--1133679 Score: 71
Period size: 31 Copynumber: 2.3 Consensus size: 27
1133603 GAGTTTCACG
*
1133613 TGTATAATTGCATCAAATTAAAGTTCA
1 TGTATAATTGCATCAAATTAAAATTCA
* *
1133640 TATATACAATTGCACATTAAATTAAAATTCA
1 TGTAT--AATTG--CATCAAATTAAAATTCA
1133671 TGTATAATT
1 TGTATAATT
1133680 TTGAATTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 4 0.12
29 9 0.28
31 19 0.59
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.39
Consensus pattern (27 bp):
TGTATAATTGCATCAAATTAAAATTCA
Found at i:1136098 original size:15 final size:16
Alignment explanation
Indices: 1136078--1136108 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1136068 TTACAATATC
1136078 TCAAATACAG-TAAAT
1 TCAAATACAGTTAAAT
1136093 TCAAATACAGTTAAAT
1 TCAAATACAGTTAAAT
1136109 ATATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (16 bp):
TCAAATACAGTTAAAT
Found at i:1139027 original size:20 final size:21
Alignment explanation
Indices: 1139004--1139048 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1138994 TTTTTTAGAT
*
1139004 AATT-ACATTTATTTTCTTTA
1 AATTAACAGTTATTTTCTTTA
* *
1139024 AATTAAGAGTTATTTTTTTTA
1 AATTAACAGTTATTTTCTTTA
1139045 AATT
1 AATT
1139049 TCATGTATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (21 bp):
AATTAACAGTTATTTTCTTTA
Found at i:1152920 original size:14 final size:15
Alignment explanation
Indices: 1152891--1152928 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
1152881 TTAATTTTAG
1152891 TTAAAATATGTAATT
1 TTAAAATATGTAATT
*
1152906 TTAAAAT-TTTAATT
1 TTAAAATATGTAATT
1152920 TTAAAATAT
1 TTAAAATAT
1152929 CTTTTATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TTAAAATATGTAATT
Found at i:1153356 original size:6 final size:6
Alignment explanation
Indices: 1153339--1153368 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
1153329 TAAAAATTTG
1153339 ATTTATT ATTTAT ATTTAT ATTTAT ATTTA
1 ATTTA-T ATTTAT ATTTAT ATTTAT ATTTA
1153369 AATCGATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTAT
Found at i:1155595 original size:22 final size:24
Alignment explanation
Indices: 1155564--1155613 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
1155554 ATCATTAAGA
1155564 TAAATATTGTTTATC-TTA-ATATT
1 TAAATATTG-TTATCATTAGATATT
*
1155587 TAAAT-TTGTTATCATTAGATTTT
1 TAAATATTGTTATCATTAGATATT
1155610 TAAA
1 TAAA
1155614 AATTATCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.21
22 6 0.25
23 13 0.54
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (24 bp):
TAAATATTGTTATCATTAGATATT
Found at i:1155776 original size:16 final size:17
Alignment explanation
Indices: 1155755--1155788 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1155745 AGAATTTTTT
1155755 TAAAA-TATTAAAAAAA
1 TAAAATTATTAAAAAAA
*
1155771 TAAAATTTTTAAAAAAA
1 TAAAATTATTAAAAAAA
1155788 T
1 T
1155789 TTGGTGAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAATTATTAAAAAAA
Found at i:1157110 original size:2 final size:2
Alignment explanation
Indices: 1157103--1157150 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1157093 TCAATGCAAA
1157103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1157145 AT AT AT
1 AT AT AT
1157151 GTGTGTGTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1160907 original size:31 final size:28
Alignment explanation
Indices: 1160869--1160964 Score: 79
Period size: 31 Copynumber: 3.3 Consensus size: 28
1160859 TTACTATATC
1160869 ATTTGGTACTTAAATTTAGTTTTAATGTTCA
1 ATTTGGTACTT-AATTT-GTTTTAAT-TTCA
* *
1160900 ATTTGGTACTTGATTT-TTTT-GTTTCA
1 ATTTGGTACTTAATTTGTTTTAATTTCA
* * *
1160926 ATTTGATACTTGAGTTTGGCTTTAATATTCA
1 ATTTGGTACTT-AATTT-GTTTTAAT-TTCA
1160957 ATTTGGTA
1 ATTTGGTA
1160965 TCCAAACCAA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
26 14 0.27
27 4 0.08
28 4 0.08
29 3 0.06
30 5 0.10
31 22 0.42
ACGTcount: A:0.24, C:0.07, G:0.16, T:0.53
Consensus pattern (28 bp):
ATTTGGTACTTAATTTGTTTTAATTTCA
Found at i:1161810 original size:9 final size:9
Alignment explanation
Indices: 1161792--1161839 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
1161782 TTTACTTGGC
*
1161792 TTTTAAGAT
1 TTTTATGAT
1161801 TTTTATGAT
1 TTTTATGAT
**
1161810 TTTT-TGGC
1 TTTTATGAT
*
1161818 TTTTAAGAT
1 TTTTATGAT
1161827 TTTTATGAT
1 TTTTATGAT
1161836 TTTT
1 TTTT
1161840 TAATTATTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
8 6 0.19
9 25 0.81
ACGTcount: A:0.21, C:0.02, G:0.12, T:0.65
Consensus pattern (9 bp):
TTTTATGAT
Found at i:1161818 original size:26 final size:26
Alignment explanation
Indices: 1161787--1161840 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1161777 CCAATTTTAC
1161787 TTGGCTTTTAAGATTTTTATGATTTT
1 TTGGCTTTTAAGATTTTTATGATTTT
1161813 TTGGCTTTTAAGATTTTTATGATTTT
1 TTGGCTTTTAAGATTTTTATGATTTT
1161839 TT
1 TT
1161841 AATTATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.19, C:0.04, G:0.15, T:0.63
Consensus pattern (26 bp):
TTGGCTTTTAAGATTTTTATGATTTT
Found at i:1166654 original size:3 final size:3
Alignment explanation
Indices: 1166640--1166688 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
1166630 GAAAAATGAA
*
1166640 AAG AACG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG
1 AAG AA-G AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1166686 AAG
1 AAG
1166689 GGAAGTGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1168984 original size:31 final size:31
Alignment explanation
Indices: 1168946--1169026 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
1168936 TTTGGGTGAC
*
1168946 TGATTTGTTATTTTTTAAAAAAATTAATAAT
1 TGATTTGTCATTTTTTAAAAAAATTAATAAT
* * * *
1168977 TGATTTGTCATTTTTCATAAACATTAATGAT
1 TGATTTGTCATTTTTTAAAAAAATTAATAAT
*
1169008 TGATTTATCA-TTTTTAAAA
1 TGATTTGTCATTTTTTAAAA
1169027 GTTTAATGAC
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 7 0.17
31 35 0.83
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (31 bp):
TGATTTGTCATTTTTTAAAAAAATTAATAAT
Found at i:1179275 original size:2 final size:2
Alignment explanation
Indices: 1179270--1179297 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1179260 GCTTTCACAC
1179270 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1179298 GGGGGCGTGC
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1183967 original size:15 final size:15
Alignment explanation
Indices: 1183947--1183975 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1183937 GCTTCTTTTA
1183947 ACCATCATCATCATC
1 ACCATCATCATCATC
1183962 ACCATCATCATCAT
1 ACCATCATCATCAT
1183976 ACTCAAGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.38, G:0.00, T:0.28
Consensus pattern (15 bp):
ACCATCATCATCATC
Found at i:1194058 original size:32 final size:33
Alignment explanation
Indices: 1194022--1194096 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 33
1194012 AGTTCAAGAA
* *
1194022 ATTTTGGATTTTG-TTTATTTTAGGTTCGGGTC
1 ATTTTGGATTTTGAATTATTTTAGGTTCAGGTC
* * *
1194054 ATTTT-GAGTTTGAATTGTTTTAGGTTTAGGTC
1 ATTTTGGATTTTGAATTATTTTAGGTTCAGGTC
*
1194086 ACTTTGGATTT
1 ATTTTGGATTT
1194097 GGATTAGTTC
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
31 6 0.18
32 24 0.71
33 4 0.12
ACGTcount: A:0.16, C:0.05, G:0.24, T:0.55
Consensus pattern (33 bp):
ATTTTGGATTTTGAATTATTTTAGGTTCAGGTC
Found at i:1195042 original size:19 final size:19
Alignment explanation
Indices: 1195003--1195042 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
1194993 TAAATTAATA
1195003 TTGAAAAAAATAATCTGAAC
1 TTGAAAAAAATAATC-GAAC
1195023 TTGAAAACAAATAATC-AAC
1 TTGAAAA-AAATAATCGAAC
1195042 T
1 T
1195043 AGTATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
21 8 0.42
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.25
Consensus pattern (19 bp):
TTGAAAAAAATAATCGAAC
Found at i:1198608 original size:132 final size:132
Alignment explanation
Indices: 1198369--1198612 Score: 398
Period size: 132 Copynumber: 1.8 Consensus size: 132
1198359 ATTGCCTCGC
* * * *
1198369 TTTAGAAAACACGAATGAAATTCCAAAGGGATATTCGATTATTTTGCGCAAACGAGAAGTTGCAA
1 TTTAGAAAACACGAACGAAATTCCAAAGAGACATTCGATTATTTTGCGCAAACGAGAAATTGCAA
1198434 CCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTTCCTTTGTTTTAAAAAG
66 CCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTTCCTTTGTTTTAAAAAG
1198499 TT
131 TT
* * *
1198501 TTTAGAAAACATGAACGAAATTCTAAAGAGACATTCGATTATTTTGGGCAAACGAGAAATTGCAA
1 TTTAGAAAACACGAACGAAATTCCAAAGAGACATTCGATTATTTTGCGCAAACGAGAAATTGCAA
* * *
1198566 CCTAGCACGATAGGGCACGATTCCCCGAATTGCTAAATATCGAACAT
66 CCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACAT
1198613 CATCTCCGTT
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
132 102 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (132 bp):
TTTAGAAAACACGAACGAAATTCCAAAGAGACATTCGATTATTTTGCGCAAACGAGAAATTGCAA
CCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTTCCTTTGTTTTAAAAAG
TT
Found at i:1199445 original size:2 final size:2
Alignment explanation
Indices: 1199438--1199505 Score: 77
Period size: 2 Copynumber: 35.0 Consensus size: 2
1199428 GCATGTACAC
* *
1199438 AT AT AT AT A- AT AT AT AA AA AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1199479 AT AT AT A- AT AT TT AT AA AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1199506 GGTATAATAT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
1 2 0.03
2 56 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1201176 original size:49 final size:46
Alignment explanation
Indices: 1201105--1201357 Score: 140
Period size: 49 Copynumber: 5.6 Consensus size: 46
1201095 TGATCTACTA
1201105 TACTGCAACTTCAGAGAGATAAGATCCGTAATTTAGTTCCAATCTGTTC
1 TACTGCAACTTCAG-GAGATAAGAT-C-TAATTTAGTTCCAATCTGTTC
* * * *
1201154 TACTGCAACTTCATGGAAATAAGAT-TTA-TT--TT-CAGTCTGCTC
1 TACTGCAACTTCA-GGAGATAAGATCTAATTTAGTTCCAATCTGTTC
* * * * * *
1201196 CACTGCAACTTCAGGGAGATAAGA-CT--TGTAACTTCGACT-TGTTT
1 TACTGCAACTTCA-GGAGATAAGATCTAAT-TTAGTTCCAATCTGTTC
* *
1201240 TACTGCAACTTCAGAGAGATAATATCCGTAATTTAGTTTCAATCTGTTC
1 TACTGCAACTTCAG-GAGATAAGAT-C-TAATTTAGTTCCAATCTGTTC
* * * * *
1201289 CACTGCAACTTCAGGGAAATAAGAT-TTA-TT--TT--GATCTGCTC
1 TACTGCAACTTCA-GGAGATAAGATCTAATTTAGTTCCAATCTGTTC
*
1201330 TACTGCAACTTCAGAGAGATGAGATCTA
1 TACTGCAACTTCAG-GAGATAAGATCTA
1201358 CTGAAACTTC
Statistics
Matches: 157, Mismatches: 30, Indels: 41
0.69 0.13 0.18
Matches are distributed among these distances:
40 1 0.01
41 27 0.17
42 32 0.20
43 5 0.03
44 25 0.16
45 6 0.04
46 5 0.03
47 1 0.01
48 6 0.04
49 47 0.30
50 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (46 bp):
TACTGCAACTTCAGGAGATAAGATCTAATTTAGTTCCAATCTGTTC
Found at i:1201267 original size:135 final size:134
Alignment explanation
Indices: 1201105--1201349 Score: 418
Period size: 135 Copynumber: 1.8 Consensus size: 134
1201095 TGATCTACTA
* *
1201105 TACTGCAACTTCAGAGAGATAAGATCCGTAATTTAGTTCCAATCTGTTCTACTGCAACTTCATGG
1 TACTGCAACTTCAGAGAGATAAGATCCGTAATTTAGTTCCAATCTGTTCCACTGCAACTTCAGGG
*
1201170 AAATAAGATTTATTTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCGACT
66 AAATAAGATTTATTTTCA-TCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTAACTTCGACT
1201235 TGTTT
130 TGTTT
* *
1201240 TACTGCAACTTCAGAGAGATAATATCCGTAATTTAGTTTCAATCTGTTCCACTGCAACTTCAGGG
1 TACTGCAACTTCAGAGAGATAAGATCCGTAATTTAGTTCCAATCTGTTCCACTGCAACTTCAGGG
* *
1201305 AAATAAGATTTATTTTGATCTGCTCTACTGCAACTTCAGAGAGAT
66 AAATAAGATTTATTTTCATCTGCTCCACTGCAACTTCAGAGAGAT
1201350 GAGATCTACT
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
134 25 0.24
135 78 0.76
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (134 bp):
TACTGCAACTTCAGAGAGATAAGATCCGTAATTTAGTTCCAATCTGTTCCACTGCAACTTCAGGG
AAATAAGATTTATTTTCATCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTAACTTCGACTT
GTTT
Found at i:1201298 original size:93 final size:90
Alignment explanation
Indices: 1201177--1201349 Score: 231
Period size: 93 Copynumber: 1.9 Consensus size: 90
1201167 TGGAAATAAG
* * * * *
1201177 ATTTATTTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCGA-CTTGTTTT
1 ATTTAGTTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGA-TT-T-ACTTCGATC-TGCTCT
1201241 ACTGCAACTTCAGAGAGATAATATCCGTA
62 ACTGCAACTTCAGAGAGATAATATCCGTA
* * *
1201270 ATTTAGTTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTATTTTGATCTGCTCTACTG
1 ATTTAGTTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTACTTCGATCTGCTCTACTG
1201335 CAACTTCAGAGAGAT
66 CAACTTCAGAGAGAT
1201350 GAGATCTACT
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
90 28 0.39
91 2 0.03
92 2 0.03
93 39 0.55
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (90 bp):
ATTTAGTTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTACTTCGATCTGCTCTACTG
CAACTTCAGAGAGATAATATCCGTA
Found at i:1213094 original size:120 final size:122
Alignment explanation
Indices: 1212947--1213227 Score: 296
Period size: 132 Copynumber: 2.2 Consensus size: 122
1212937 AGTAGGGCAT
* * * * * *
1212947 GATTCCTCGAATTTCCAGACGTTGAACATTGCC-TCG-CTTTAGAAAACACGAATGAAATTCCAA
1 GATTCCCCGAATTGCCAAACATCGAACATTGCCTTCGTCTTTAGAAAACACGAACGAAATTCCAA
* * *
1213010 AGGGATATTCGATTATTTTGCGCAAACGAGAAGTTGCAACCCAACACGATAGGACAC
66 AGAGACATTCGATTATTTTGCGCAAACGAGAAATTGCAACCCAACACGATAGGACAC
* * *
1213067 GATTCCCCGAATTGCCAAACATCGAACATTTCCTTCGTTTTAAAAATTTTTTAGAAAACATGAAC
1 GATTCCCCGAATTGCCAAACATCGAACATTGCCTTCG----------TCTTTAGAAAACACGAAC
* * * *
1213132 GAAATTCTAAAGAGACATTCGATTATTTTGGGCAAACGAGAAATTGCAACCCAGCACGATAGGGC
56 GAAATTCCAAAGAGACATTCGATTATTTTGCGCAAACGAGAAATTGCAACCCAACACGATAGGAC
1213197 AC
121 AC
* *
1213199 GATTCCCCGAATTGCTAAATATCGAACAT
1 GATTCCCCGAATTGCCAAACATCGAACAT
1213228 CGTCTCCGTT
Statistics
Matches: 131, Mismatches: 18, Indels: 12
0.81 0.11 0.07
Matches are distributed among these distances:
120 27 0.21
121 3 0.02
132 101 0.77
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (122 bp):
GATTCCCCGAATTGCCAAACATCGAACATTGCCTTCGTCTTTAGAAAACACGAACGAAATTCCAA
AGAGACATTCGATTATTTTGCGCAAACGAGAAATTGCAACCCAACACGATAGGACAC
Found at i:1213223 original size:132 final size:133
Alignment explanation
Indices: 1212984--1213250 Score: 394
Period size: 132 Copynumber: 2.0 Consensus size: 133
1212974 ATTGCCTCGC
* * * *
1212984 TTTAGAAAACACGAATGAAATTCCAAAGGGATATTCGATTATTTTGCGCAAACGAGAAGTTGCAA
1 TTTAGAAAACACGAACGAAATTCCAAAGAGACATTCGATTATTTTGCGCAAACGAGAAATTGCAA
* *
1213049 CCCAACACGATAGGACACGATTCCCCGAATTGCCAAACATCGAACAT-TTCCTTCGTTTTAAA-A
66 CCCAACACGATAGGACACGATTCCCCGAATTGCCAAACATCGAACATCGT-CTCCGTTTTAAAGA
1213112 ATTT
130 ATTT
* * *
1213116 TTTAGAAAACATGAACGAAATTCTAAAGAGACATTCGATTATTTTGGGCAAACGAGAAATTGCAA
1 TTTAGAAAACACGAACGAAATTCCAAAGAGACATTCGATTATTTTGCGCAAACGAGAAATTGCAA
* * * *
1213181 CCCAGCACGATAGGGCACGATTCCCCGAATTGCTAAATATCGAACATCGTCTCCGTTTTAAAGAA
66 CCCAACACGATAGGACACGATTCCCCGAATTGCCAAACATCGAACATCGTCTCCGTTTTAAAGAA
1213246 TTT
131 TTT
1213249 TT
1 TT
1213251 AAACAAATAA
Statistics
Matches: 120, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
132 112 0.93
133 8 0.07
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (133 bp):
TTTAGAAAACACGAACGAAATTCCAAAGAGACATTCGATTATTTTGCGCAAACGAGAAATTGCAA
CCCAACACGATAGGACACGATTCCCCGAATTGCCAAACATCGAACATCGTCTCCGTTTTAAAGAA
TTT
Found at i:1214082 original size:2 final size:2
Alignment explanation
Indices: 1214075--1214128 Score: 53
Period size: 2 Copynumber: 29.0 Consensus size: 2
1214065 CATGTACACA
* *
1214075 AT AT AT AT A- AT AT AT AT A- AA AT AT AT AT AT AT A- AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1214114 AT A- AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1214129 GGTATAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
1 4 0.09
2 40 0.91
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1214091 original size:11 final size:11
Alignment explanation
Indices: 1214075--1214127 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
1214065 CATGTACACA
1214075 ATATATATAAT
1 ATATATATAAT
*
1214086 ATATATAAAAT
1 ATATATATAAT
1214097 ATATATAT-AT
1 ATATATATAAT
* *
1214107 AATATTTATAAA
1 -ATATATATAAT
1214119 ATATATATA
1 ATATATATA
1214128 TGGTATAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 2 0.06
11 32 0.91
12 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
ATATATATAAT
Found at i:1214107 original size:24 final size:24
Alignment explanation
Indices: 1214075--1214128 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
1214065 CATGTACACA
1214075 ATATATATAATATATATAAAATAT
1 ATATATATAATATATATAAAATAT
*
1214099 ATATATATAATATTTATAAAATAT
1 ATATATATAATATATATAAAATAT
1214123 ATATAT
1 ATATAT
1214129 GGTATAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATATATATAATATATATAAAATAT
Found at i:1214116 original size:15 final size:15
Alignment explanation
Indices: 1214079--1214108 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1214069 TACACAATAT
1214079 ATATAATATATATAAA
1 ATAT-ATATATATAAA
1214095 ATATATATATATAA
1 ATATATATATATAA
1214109 TATTTATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATATATATATAAA
Found at i:1219374 original size:2 final size:2
Alignment explanation
Indices: 1219367--1219419 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
1219357 CATGTACACA
*
1219367 AT AT AT AT A- AT AT A- AT AT AT AT AT AT AT AT A- AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1219406 AA AA AT AT AT AT AT
1 AT AT AT AT AT AT AT
1219420 GGTATAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1221743 original size:2 final size:2
Alignment explanation
Indices: 1221736--1221781 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1221726 TAGGTCACCC
1221736 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1221777 TA TA T
1 TA TA T
1221782 TATCTTCTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1224068 original size:30 final size:30
Alignment explanation
Indices: 1224033--1224135 Score: 107
Period size: 31 Copynumber: 3.4 Consensus size: 30
1224023 TAACTAGGTC
*
1224033 CCTTCAAAATTTTAAAAAATTCTAAATAAA
1 CCTTCAAAATTTTAAAAAATTCTAATTAAA
* *
1224063 CCTTCAAATAGTTTAAAAAATTTTAATTAAA
1 CCTTCAAA-ATTTTAAAAAATTCTAATTAAA
* * ** * *
1224094 CCCTCAAATTTTTTGAAAATTCTCATTAAT
1 CCTTCAAAATTTTAAAAAATTCTAATTAAA
1224124 CCTCTCAAAATT
1 CCT-TCAAAATT
1224136 GTAACATTTT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
30 25 0.43
31 33 0.57
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.38
Consensus pattern (30 bp):
CCTTCAAAATTTTAAAAAATTCTAATTAAA
Found at i:1225025 original size:22 final size:22
Alignment explanation
Indices: 1224997--1225039 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1224987 GGGTTGAATG
1224997 TATATATATATACACAGCATAA
1 TATATATATATACACAGCATAA
1225019 TATATATATATACACAGCATA
1 TATATATATATACACAGCATA
1225040 TTGAGTAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.33
Consensus pattern (22 bp):
TATATATATATACACAGCATAA
Found at i:1225596 original size:4 final size:4
Alignment explanation
Indices: 1225587--1225628 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
1225577 TCATACTCTA
* * *
1225587 ATAT ATAT ATAT ATAT ATAT ATAT ATGT ATGT ATAT GTAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT
1225629 GTAATTTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:1225602 original size:10 final size:10
Alignment explanation
Indices: 1225587--1225628 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
1225577 TCATACTCTA
1225587 ATATATATAT
1 ATATATATAT
1225597 ATATATATAT
1 ATATATATAT
*
1225607 ATATATGTAT
1 ATATATATAT
* *
1225617 GTATATGTAT
1 ATATATATAT
1225627 AT
1 AT
1225629 GTAATTTAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (10 bp):
ATATATATAT
Found at i:1225631 original size:6 final size:6
Alignment explanation
Indices: 1225587--1225628 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
1225577 TCATACTCTA
* * *
1225587 ATATAT ATATAT ATATAT ATATAT ATGTAT GTATAT GTATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
1225629 GTAATTTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (6 bp):
ATATAT
Found at i:1230405 original size:127 final size:126
Alignment explanation
Indices: 1230098--1230406 Score: 372
Period size: 126 Copynumber: 2.4 Consensus size: 126
1230088 TCTTTAAAAT
* ** *
1230098 GAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATCGTATTGGGTTGCAATTTCC
1 GAAGGCAATGTTCGATGTTTGGCAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTACAATTTCC
* * * * *
1230163 CGTTTGTTCAAAATAATCAAATATTCCTTTGGAATTTCACTCGTGTCTTTAAAAATTCAAC
66 CATTTGTTCAAAATAATCAAACATCCCTTTGGAATTTCACTCATATCTTTAAAAATTCAAC
* * * *
1230224 GAAGGAAATGTTTGATGCTTGGCAATTC-ATGGAATCGTGCCCTATCGTGCTGGGTTACAATTTT
1 GAAGGCAATGTTCGATGTTTGGCAATTCGA-GGAATCGTGCCCTATCGTGCTGGGTTACAATTTC
* * **
1230288 CCATTTGTTCAAAATAATCGAACATCCCTTTTGAATTTCACTCATAT-TTTCTAAATTCTAAAAC
65 CCATTTGTTCAAAATAATCAAACATCCCTTTGGAATTTCACTCATATCTTTAAAAATTC---AAC
* * * *
1230352 -AAGGCAATGTTCAATGTTTGGAAATTCGAGCAATCGTGCCCTACCGTGCTGGGTT
1 GAAGGCAATGTTCGATGTTTGGCAATTCGAGGAATCGTGCCCTATCGTGCTGGGTT
1230407 TTGACTTTAC
Statistics
Matches: 154, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
125 9 0.06
126 95 0.62
127 46 0.30
128 4 0.03
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (126 bp):
GAAGGCAATGTTCGATGTTTGGCAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTACAATTTCC
CATTTGTTCAAAATAATCAAACATCCCTTTGGAATTTCACTCATATCTTTAAAAATTCAAC
Found at i:1231813 original size:6 final size:6
Alignment explanation
Indices: 1231804--1231837 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
1231794 GATTTTCTCC
1231804 AAATGA AAATGA AAATGA AAATGGA GAAATGA AA
1 AAATGA AAATGA AAATGA AAAT-GA -AAATGA AA
1231838 TCATTTGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 18 0.69
7 4 0.15
8 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.15
Consensus pattern (6 bp):
AAATGA
Found at i:1233653 original size:18 final size:18
Alignment explanation
Indices: 1233632--1233667 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1233622 ACCTACCCAA
*
1233632 TTATTTATTAAAAATTTT
1 TTATGTATTAAAAATTTT
1233650 TTATGTATTAAAAATTTT
1 TTATGTATTAAAAATTTT
1233668 ATATATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TTATGTATTAAAAATTTT
Found at i:1236144 original size:30 final size:30
Alignment explanation
Indices: 1236108--1236164 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
1236098 CAATTGGCTA
1236108 CCACACGGCCTGGCCACACGCTCGTGTGGT
1 CCACACGGCCTGGCCACACGCTCGTGTGGT
1236138 CCACACGGCCTGGCCACACGCTCGTGT
1 CCACACGGCCTGGCCACACGCTCGTGT
1236165 TGTGTACCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.14, C:0.42, G:0.28, T:0.16
Consensus pattern (30 bp):
CCACACGGCCTGGCCACACGCTCGTGTGGT
Found at i:1236980 original size:46 final size:46
Alignment explanation
Indices: 1236920--1237135 Score: 308
Period size: 46 Copynumber: 4.7 Consensus size: 46
1236910 TTTGACATGA
* * * * * *
1236920 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** **
1236966 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1237012 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
1237058 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1237104 TGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACAC
1237136 TCAGGTTGCC
Statistics
Matches: 155, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 4 0.03
46 151 0.97
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:1237077 original size:92 final size:92
Alignment explanation
Indices: 1236920--1237184 Score: 341
Period size: 92 Copynumber: 3.0 Consensus size: 92
1236910 TTTGACATGA
* * * * * *
1236920 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTATCAGGTTGCCATGGTATCTTTCAAC
***
1236985 CATGGTCTTGTTCATTTCATATCACAT
66 CATGGTCTTACACATTTCATATCACAT
1237012 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTC-TATCAGGTTGCCATGGTATCTTTCAA
* **
1237076 CCATGGTCTTACACATTTTATATCAGGT
65 CCATGGTCTTACACATTTCATATCACAT
*
1237104 TGCCATGGTATCTTTCAACCATGGTCTT--ACA----C--TCAGGTTGCCATAGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTATCAGGTTGCCATGGTATCTTTCAAC
1237161 CATGGTCTTACACATTTCATATCA
66 CATGGTCTTACACATTTCATATCA
1237185 GAGAGCACAC
Statistics
Matches: 158, Mismatches: 14, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
84 47 0.30
87 1 0.01
90 3 0.02
91 4 0.03
92 103 0.65
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTATCAGGTTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCATATCACAT
Found at i:1237153 original size:38 final size:38
Alignment explanation
Indices: 1237098--1237173 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
1237088 ACATTTTATA
*
1237098 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATAGTATCTTTCAACCATGGTCTTACAC
1237136 TCAGGTTGCCATAGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATAGTATCTTTCAACCATGGTCTTACAC
1237174 ATTTCATATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.34
Consensus pattern (38 bp):
TCAGGTTGCCATAGTATCTTTCAACCATGGTCTTACAC
Found at i:1239338 original size:11 final size:11
Alignment explanation
Indices: 1239322--1239373 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
1239312 TATACTAAAT
1239322 AAATAATAATA
1 AAATAATAATA
*
1239333 AAATAAT-ATT
1 AAATAATAATA
* *
1239343 AAATATCTCATA
1 AAATA-ATAATA
*
1239355 AAATATTAATA
1 AAATAATAATA
1239366 AAATAATA
1 AAATAATA
1239374 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:1244469 original size:12 final size:12
Alignment explanation
Indices: 1244452--1244476 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1244442 ATATATATGG
1244452 CTTGATGGCAGA
1 CTTGATGGCAGA
1244464 CTTGATGGCAGA
1 CTTGATGGCAGA
1244476 C
1 C
1244477 AAAAATGAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (12 bp):
CTTGATGGCAGA
Found at i:1245418 original size:2 final size:2
Alignment explanation
Indices: 1245411--1245445 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1245401 GGTTGTCTTT
1245411 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1245446 GTACATGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1245901 original size:61 final size:60
Alignment explanation
Indices: 1245788--1245901 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 60
1245778 TTGACATTTT
*
1245788 TTTCTTAATTTGATACTTAAGTTTTTTTGGATCCAATTTGGTACTTGAACTTAGCACTTC
1 TTTCTTAATTTGATACTTAAGTTTTTTTGGATCCAATTTGGTACTTAAACTTAGCACTTC
* *
1245848 TTTC-TAATTTGGTACTTAAGTTTTATTTTAGG-TTCAATTTGGTACTTAAACTTA
1 TTTCTTAATTTGATACTTAAG-TTT-TTTT-GGATCCAATTTGGTACTTAAACTTA
1245902 TCAAATGTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
59 15 0.31
60 7 0.15
61 24 0.50
62 2 0.04
ACGTcount: A:0.25, C:0.12, G:0.13, T:0.50
Consensus pattern (60 bp):
TTTCTTAATTTGATACTTAAGTTTTTTTGGATCCAATTTGGTACTTAAACTTAGCACTTC
Found at i:1246600 original size:30 final size:31
Alignment explanation
Indices: 1246565--1246646 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 31
1246555 CAAAAAGATT
* * **
1246565 AAGTACCAAATTAGGAATAAGTGTCAAGTTC
1 AAGTACCAAATTAAGAAAAAGCATCAAGTTC
*
1246596 -AGTACCGAATTAAGAAAAAGCATCAAGTTC
1 AAGTACCAAATTAAGAAAAAGCATCAAGTTC
*
1246626 AAGTACCAAATTGAACAAAAA
1 AAGTACCAAATT-AAGAAAAA
1246647 AGTCTAGGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 25 0.60
31 10 0.24
32 7 0.17
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.21
Consensus pattern (31 bp):
AAGTACCAAATTAAGAAAAAGCATCAAGTTC
Found at i:1249339 original size:19 final size:18
Alignment explanation
Indices: 1249309--1249344 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1249299 GGGATCATTC
*
1249309 TTTTTTTAGTTATTTTAA
1 TTTTTTTAGTTAATTTAA
1249327 TTTTTTTATGTTAATTTA
1 TTTTTTTA-GTTAATTTA
1249345 GTCATTAACG
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:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (18 bp):
TTTTTTTAGTTAATTTAA
Found at i:1251596 original size:26 final size:24
Alignment explanation
Indices: 1251556--1251615 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
1251546 TTATTTCATT
* * *
1251556 AAATAAAAAAATTTAAAAATATAA
1 AAATAAATATATTTAAAAACATAA
1251580 TAAATCAAATATATTTAAAAACATAA
1 -AAAT-AAATATATTTAAAAACATAA
1251606 AAATAAATAT
1 AAATAAATAT
1251616 TAAAACAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (24 bp):
AAATAAATATATTTAAAAACATAA
Found at i:1251627 original size:22 final size:22
Alignment explanation
Indices: 1251586--1251644 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
1251576 ATAATAAATC
* *
1251586 AAATATAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
1251606 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
1251628 AAAT-AATACTAAAACAA
1 AAATAAATATTAAAACAA
1251645 TTCTTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 18 0.53
22 9 0.26
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:1251721 original size:15 final size:16
Alignment explanation
Indices: 1251691--1251723 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1251681 AAATAGTTAT
1251691 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
1251708 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
1251723 A
1 A
1251724 AAATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:1252088 original size:22 final size:22
Alignment explanation
Indices: 1252063--1252104 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1252053 GATTCTACGA
1252063 ATTTTTTTAAATTAAAAAATAG
1 ATTTTTTTAAATTAAAAAATAG
1252085 ATTTTTTTAAATTAAAAAAT
1 ATTTTTTTAAATTAAAAAAT
1252105 GATAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTTTTTAAATTAAAAAATAG
Found at i:1264753 original size:23 final size:23
Alignment explanation
Indices: 1264723--1264772 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
1264713 ACCAAGCAAT
1264723 AAAAACAATAGCTTAATAATAAG
1 AAAAACAATAGCTTAATAATAAG
1264746 AAAAACAATAGCTTAATAATAAG
1 AAAAACAATAGCTTAATAATAAG
1264769 AAAA
1 AAAA
1264773 CATTTCTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.20
Consensus pattern (23 bp):
AAAAACAATAGCTTAATAATAAG
Found at i:1265987 original size:57 final size:55
Alignment explanation
Indices: 1265926--1266425 Score: 245
Period size: 63 Copynumber: 9.1 Consensus size: 55
1265916 AGCTTAGTGG
*
1265926 TAGTGAAGGTGAAGAAAGTGGTGAAGATGCATATGTTGATGATTGGAGGTCTAAGC-
1 TAGTGAAGGTG--GAAAGTGGTGAAGATGCATATGCTGATGATTGGAGGTCTAAGCT
* * *
1265982 T--T--A-GT-G---GTGGTCAAGAGGCATATGCTGATGATTGGAGCTCTAAGCTTAGT
1 TAGTGAAGGTGGAAAGTGGTGAAGATGCATATGCTGATGATTGGAGGTCTAAGC----T
* *
1266032 GGTAGTGAAGGTGAAGAAAGTGGTGAAGATGCATATGCTGATGATTGGAAGTCCAAGC-
1 --TAGTGAAGGTG--GAAAGTGGTGAAGATGCATATGCTGATGATTGGAGGTCTAAGCT
* * * *
1266090 T--T--A-GT-G---GTGGTCAAGAGGCTTATGCTGATGATTGGAGCTCTAAGCTTAGT
1 TAGTGAAGGTGGAAAGTGGTGAAGATGCATATGCTGATGATTGGAGGTCTAAGC----T
1266140 GGTAGTGAAGGTGAAGAAAGTGGTGAAGATGCATATGCTGATGATTGGAGGTCTAAGC-
1 --TAGTGAAGGTG--GAAAGTGGTGAAGATGCATATGCTGATGATTGGAGGTCTAAGCT
* * * *
1266198 T--T--A-GT-G---GTGGTCAAGAGGCATATGCTGACGATTGGAGCTCTAAGCTTAGT
1 TAGTGAAGGTGGAAAGTGGTGAAGATGCATATGCTGATGATTGGAGGTCTAAGC----T
* *
1266248 GGTAGTGAAGGTGAAGAAAGTGGTGAAGATGCATATGTTGATGATTGGAGCTCTAAGCT
1 --TAGTGAAGGTG--GAAAGTGGTGAAGATGCATATGCTGATGATTGGAGGTCTAAGCT
** ** *
1266307 TAGTCGCAACCATGGAAA-TGGTGAAGATGCATATTTTGATAATTGGAGGTCTAAGCT
1 TAGT-G-AA-GGTGGAAAGTGGTGAAGATGCATATGCTGATGATTGGAGGTCTAAGCT
* ** ** *
1266364 TAGAGGCAACCATGGAAA-TGGTGAAGATGCATATTTTGATGATTGGAGGTCTAAACT
1 TAG-TG-AA-GGTGGAAAGTGGTGAAGATGCATATGCTGATGATTGGAGGTCTAAGCT
1266421 TAGTG
1 TAGTG
1266426 GCAGCCAGGG
Statistics
Matches: 350, Mismatches: 36, Indels: 116
0.70 0.07 0.23
Matches are distributed among these distances:
45 103 0.29
48 3 0.01
51 6 0.02
52 6 0.02
54 6 0.02
56 7 0.02
57 102 0.29
58 5 0.01
59 3 0.01
60 5 0.01
63 104 0.30
ACGTcount: A:0.29, C:0.10, G:0.33, T:0.28
Consensus pattern (55 bp):
TAGTGAAGGTGGAAAGTGGTGAAGATGCATATGCTGATGATTGGAGGTCTAAGCT
Found at i:1266003 original size:45 final size:45
Alignment explanation
Indices: 1265943--1266034 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
1265933 GGTGAAGAAA
* * * *
1265943 GTGGTGAAGATGCATATGTTGATGATTGGAGGTCTAAGCTTAGTG
1 GTGGTCAAGAGGCATATGCTGATGATTGGAGCTCTAAGCTTAGTG
1265988 GTGGTCAAGAGGCATATGCTGATGATTGGAGCTCTAAGCTTAGTG
1 GTGGTCAAGAGGCATATGCTGATGATTGGAGCTCTAAGCTTAGTG
1266033 GT
1 GT
1266035 AGTGAAGGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.24, C:0.10, G:0.35, T:0.32
Consensus pattern (45 bp):
GTGGTCAAGAGGCATATGCTGATGATTGGAGCTCTAAGCTTAGTG
Found at i:1266064 original size:108 final size:108
Alignment explanation
Indices: 1265912--1266310 Score: 735
Period size: 108 Copynumber: 3.7 Consensus size: 108
1265902 TTTATGGGGG
*
1265912 TCTAAGCTTAGTGGTAGTGAAGGTGAAGAAAGTGGTGAAGATGCATATGTTGATGATTGGAGGTC
1 TCTAAGCTTAGTGGTAGTGAAGGTGAAGAAAGTGGTGAAGATGCATATGCTGATGATTGGAGGTC
1265977 TAAGCTTAGTGGTGGTCAAGAGGCATATGCTGATGATTGGAGC
66 TAAGCTTAGTGGTGGTCAAGAGGCATATGCTGATGATTGGAGC
*
1266020 TCTAAGCTTAGTGGTAGTGAAGGTGAAGAAAGTGGTGAAGATGCATATGCTGATGATTGGAAGTC
1 TCTAAGCTTAGTGGTAGTGAAGGTGAAGAAAGTGGTGAAGATGCATATGCTGATGATTGGAGGTC
* *
1266085 CAAGCTTAGTGGTGGTCAAGAGGCTTATGCTGATGATTGGAGC
66 TAAGCTTAGTGGTGGTCAAGAGGCATATGCTGATGATTGGAGC
1266128 TCTAAGCTTAGTGGTAGTGAAGGTGAAGAAAGTGGTGAAGATGCATATGCTGATGATTGGAGGTC
1 TCTAAGCTTAGTGGTAGTGAAGGTGAAGAAAGTGGTGAAGATGCATATGCTGATGATTGGAGGTC
*
1266193 TAAGCTTAGTGGTGGTCAAGAGGCATATGCTGACGATTGGAGC
66 TAAGCTTAGTGGTGGTCAAGAGGCATATGCTGATGATTGGAGC
* *
1266236 TCTAAGCTTAGTGGTAGTGAAGGTGAAGAAAGTGGTGAAGATGCATATGTTGATGATTGGAGCTC
1 TCTAAGCTTAGTGGTAGTGAAGGTGAAGAAAGTGGTGAAGATGCATATGCTGATGATTGGAGGTC
1266301 TAAGCTTAGT
66 TAAGCTTAGT
1266311 CGCAACCATG
Statistics
Matches: 281, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 281 1.00
ACGTcount: A:0.28, C:0.09, G:0.34, T:0.28
Consensus pattern (108 bp):
TCTAAGCTTAGTGGTAGTGAAGGTGAAGAAAGTGGTGAAGATGCATATGCTGATGATTGGAGGTC
TAAGCTTAGTGGTGGTCAAGAGGCATATGCTGATGATTGGAGC
Found at i:1266114 original size:45 final size:45
Alignment explanation
Indices: 1266051--1266142 Score: 132
Period size: 45 Copynumber: 2.0 Consensus size: 45
1266041 GGTGAAGAAA
* *
1266051 GTGGTGAAGATGCATATGCTGATGATTGGAAG-TCCAAGCTTAGTG
1 GTGGTCAAGAGGCATATGCTGATGATTGG-AGCTCCAAGCTTAGTG
* *
1266096 GTGGTCAAGAGGCTTATGCTGATGATTGGAGCTCTAAGCTTAGTG
1 GTGGTCAAGAGGCATATGCTGATGATTGGAGCTCCAAGCTTAGTG
1266141 GT
1 GT
1266143 AGTGAAGGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 2 0.05
45 40 0.95
ACGTcount: A:0.24, C:0.12, G:0.34, T:0.30
Consensus pattern (45 bp):
GTGGTCAAGAGGCATATGCTGATGATTGGAGCTCCAAGCTTAGTG
Found at i:1266219 original size:45 final size:45
Alignment explanation
Indices: 1266159--1266250 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
1266149 GGTGAAGAAA
* * * *
1266159 GTGGTGAAGATGCATATGCTGATGATTGGAGGTCTAAGCTTAGTG
1 GTGGTCAAGAGGCATATGCTGACGATTGGAGCTCTAAGCTTAGTG
1266204 GTGGTCAAGAGGCATATGCTGACGATTGGAGCTCTAAGCTTAGTG
1 GTGGTCAAGAGGCATATGCTGACGATTGGAGCTCTAAGCTTAGTG
1266249 GT
1 GT
1266251 AGTGAAGGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.24, C:0.12, G:0.35, T:0.29
Consensus pattern (45 bp):
GTGGTCAAGAGGCATATGCTGACGATTGGAGCTCTAAGCTTAGTG
Found at i:1266438 original size:57 final size:57
Alignment explanation
Indices: 1266263--1266476 Score: 304
Period size: 57 Copynumber: 3.7 Consensus size: 57
1266253 TGAAGGTGAA
* * *
1266263 GAAAGTGGTGAAGATGCATATGTTGATGATTGGAGCTCTAAGCTTAGTCGCAACCATG
1 GAAA-TGGTGAAGATGCATATTTTGATGATTGGAGGTCTAAGCTTAGTGGCAACCATG
* *
1266321 GAAATGGTGAAGATGCATATTTTGATAATTGGAGGTCTAAGCTTAGAGGCAACCATG
1 GAAATGGTGAAGATGCATATTTTGATGATTGGAGGTCTAAGCTTAGTGGCAACCATG
* * *
1266378 GAAATGGTGAAGATGCATATTTTGATGATTGGAGGTCTAAACTTAGTGGCAGCCAGG
1 GAAATGGTGAAGATGCATATTTTGATGATTGGAGGTCTAAGCTTAGTGGCAACCATG
* * *
1266435 GAAATAGTGAAGATGAATATTTTGAT-ACTTGGAGATCTAAGC
1 GAAATGGTGAAGATGCATATTTTGATGA-TTGGAGGTCTAAGC
1266477 CCAGTTCCAA
Statistics
Matches: 141, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
56 1 0.01
57 136 0.96
58 4 0.03
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.29
Consensus pattern (57 bp):
GAAATGGTGAAGATGCATATTTTGATGATTGGAGGTCTAAGCTTAGTGGCAACCATG
Found at i:1269859 original size:2 final size:2
Alignment explanation
Indices: 1269852--1269885 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1269842 TCTATCTATC
1269852 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1269886 CATGATTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1272461 original size:13 final size:13
Alignment explanation
Indices: 1272443--1272473 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1272433 CTTGGGTGTA
1272443 CGCGAGCTGGGAC
1 CGCGAGCTGGGAC
1272456 CGCGAGCTGGGAC
1 CGCGAGCTGGGAC
1272469 CGCGA
1 CGCGA
1272474 ACTCTTTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.32, G:0.45, T:0.06
Consensus pattern (13 bp):
CGCGAGCTGGGAC
Found at i:1274000 original size:284 final size:287
Alignment explanation
Indices: 1273420--1274059 Score: 699
Period size: 284 Copynumber: 2.2 Consensus size: 287
1273410 GGAAATAGTA
* * * * * * *
1273420 ATAAGTATATAATTGACGACACTCTTAAAAGTGAGTCCATTCTAGCACAAAAAATAATATATCGA
1 ATAAGTATGTAACTGATGACACTTTTAAAGGTGAGTCTATTCTCGCACAAAAAATAATATATCGA
* *
1273485 TATAAAAAATGTAAGTTTAATCATTTGTGATATTTTAATGACTTTATATTTACATTTGTTATTTT
66 TATAAAAAATGTAAGTTCAATCATTTATGATATTTTAATGACTTTATATTTACA-TTGTTATTTT
** *
1273550 TTTCTTCTTAGAAAAAGTAAGGTATTTAAGTGTTTAACCTAGAGTTTAGACCGTTTTAAAACATT
130 TTTCTTCTTAGAAAAAAAAAGGTATTTAAGTGCTTAACCTAGAG--TAGA-C--TTTAAAACA-T
*** * * *
1273615 TTTAATTAGTTGATGTTATAAATTATATTGGGATATTTTCAGATCCATCTAAAGACTTCAATGGT
189 AGAAATTAGTTGATGTTATAAATTATAATGGGAAATTTTCAGATCCATATAAAGACTTCAATGGT
* * *
1273680 CCAACTAATTCACGAGGAACTCCTGTAAATAATG
254 CCAACAAATTCACAAGGAACTCCTGTAAAAAATG
* ** * *
1273714 ATAAGTATGTTACTGATGACGTTTTTAAAGGTGAGTCTATTCTCGCACACAAAAATAATTTATCT
1 ATAAGTATGTAACTGATGACACTTTTAAAGGTGAGTCTATTCTCGCACA-AAAAATAATATATCG
* * * *
1273779 ATGTGAAAAA-GATAAGTTCAATCATTTATGTTATTTTAATGATTTTATATTTACA-T-TTA-TT
65 ATATAAAAAATG-TAAGTTCAATCATTTATGATATTTTAATGACTTTATATTTACATTGTTATTT
*
1273840 TTTT-TTCTTA-AAAAGAAAAAGGTATTTAAGTGCTTAACCTAGAG-AGA-TTTAAATTCA-AGA
129 TTTTCTTCTTAGAAAA-AAAAAGGTATTTAAGTGCTTAACCTAGAGTAGACTTTAAA-ACATAGA
* * * * *
1273900 AATTGGATTTGATGTTGTAAATTATAATGGGAAATATTT-AGATCCATATGAAGATTTCAATTGT
192 AATT--AGTTGATGTTATAAATTATAATGGGAAAT-TTTCAGATCCATATAAAGACTTCAATGGT
* *
1273964 CTAACAAATTCACAAGGAACTCTTGTAAAAAATG
254 CCAACAAATTCACAAGGAACTCCTGTAAAAAATG
* * *
1273998 ATAAGTATGTAATTGATGACACTTTTAAAGGTGAGT-TCATTCTCGTACAAAAATTAATATAT
1 ATAAGTATGTAACTGATGACACTTTTAAAGGTGAGTCT-ATTCTCGCACAAAAAATAATATAT
1274060 TTATAGTAGA
Statistics
Matches: 293, Mismatches: 45, Indels: 27
0.80 0.12 0.07
Matches are distributed among these distances:
282 4 0.01
283 18 0.06
284 119 0.41
285 3 0.01
287 3 0.01
289 4 0.01
290 32 0.11
291 6 0.02
292 3 0.01
293 1 0.00
294 40 0.14
295 60 0.20
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.38
Consensus pattern (287 bp):
ATAAGTATGTAACTGATGACACTTTTAAAGGTGAGTCTATTCTCGCACAAAAAATAATATATCGA
TATAAAAAATGTAAGTTCAATCATTTATGATATTTTAATGACTTTATATTTACATTGTTATTTTT
TTCTTCTTAGAAAAAAAAAGGTATTTAAGTGCTTAACCTAGAGTAGACTTTAAAACATAGAAATT
AGTTGATGTTATAAATTATAATGGGAAATTTTCAGATCCATATAAAGACTTCAATGGTCCAACAA
ATTCACAAGGAACTCCTGTAAAAAATG
Found at i:1274690 original size:6 final size:6
Alignment explanation
Indices: 1274675--1274709 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1274665 GTATAGACAT
*
1274675 AAAA-A AAAAGA AAAAGA AAAAGA AAAAGA AGAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
1274710 TAGATTCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:1275010 original size:57 final size:57
Alignment explanation
Indices: 1274922--1275095 Score: 303
Period size: 57 Copynumber: 3.1 Consensus size: 57
1274912 AAGGTGAAGA
* * *
1274922 AAATGGTGAAGATGCATATGTTAATGATTGGAGGTCTACGCTTAGTAGCAACCATGG
1 AAATGGTGAAGATGCATATTTTGATGATTGGAGGTCTAAGCTTAGTAGCAACCATGG
*
1274979 AAATGGTGAAGATGCATATTTTGATGATTGGAGGTCTAAGCTTAGTGGCAACCATGG
1 AAATGGTGAAGATGCATATTTTGATGATTGGAGGTCTAAGCTTAGTAGCAACCATGG
*
1275036 AAATGGTGAAGATGCATATTTGGATGATTGGAGGTCTAAGCTTAGTAGCAACCATGG
1 AAATGGTGAAGATGCATATTTTGATGATTGGAGGTCTAAGCTTAGTAGCAACCATGG
1275093 AAA
1 AAA
1275096 GGAGGAATTT
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 111 1.00
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.28
Consensus pattern (57 bp):
AAATGGTGAAGATGCATATTTTGATGATTGGAGGTCTAAGCTTAGTAGCAACCATGG
Found at i:1275180 original size:105 final size:105
Alignment explanation
Indices: 1275020--1275235 Score: 265
Period size: 105 Copynumber: 2.1 Consensus size: 105
1275010 AGGTCTAAGC
* * * * ** *
1275020 TTAGTGGCAACCATGGAAATGGTGAAGATGCATATTTGGATGATTGGAGGTCTAAGCTTAGTAGC
1 TTAGTGGCAACCAGGGAAATAGTGAAGATGAATATTTGGATGATTGGAGATCTAAGCCCAGTACC
* * * * *
1275085 AACCATGGAAAGGAGGAATTTGATGAT-TGGAGCCATGATT
66 AACAATGGAAACGAAGAATTTGACGATCGGGA-CCATGATT
* * *
1275125 TTAGTGGCAGCCAGGGAAATAGTGAAGATGAATATTTTGAT-ACTTGGAGATCTAAGCCCAGTTC
1 TTAGTGGCAACCAGGGAAATAGTGAAGATGAATATTTGGATGA-TTGGAGATCTAAGCCCAGTAC
1275189 CAACAATGGAAACGAAGAATTTGACGATCGGGACCATGATT
65 CAACAATGGAAACGAAGAATTTGACGATCGGGACCATGATT
1275230 TTAGTG
1 TTAGTG
1275236 CCCGTCATGG
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
104 1 0.01
105 90 0.96
106 3 0.03
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.27
Consensus pattern (105 bp):
TTAGTGGCAACCAGGGAAATAGTGAAGATGAATATTTGGATGATTGGAGATCTAAGCCCAGTACC
AACAATGGAAACGAAGAATTTGACGATCGGGACCATGATT
Found at i:1276608 original size:23 final size:22
Alignment explanation
Indices: 1276565--1276636 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
1276555 TTTTTTTTGT
* *
1276565 TTTTAATATTATTTT-CTTATTT
1 TTTTACTATTATTTTGC-TATTA
* *
1276587 TTTTTCTCTCTATTTTGCTATTA
1 TTTTACTAT-TATTTTGCTATTA
*
1276610 TTTTACTATTATGTTGCTATTA
1 TTTTACTATTATTTTGCTATTA
1276632 TTTTA
1 TTTTA
1276637 TTGTTATTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
22 23 0.56
23 17 0.41
24 1 0.02
ACGTcount: A:0.19, C:0.10, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTTACTATTATTTTGCTATTA
Found at i:1276611 original size:11 final size:11
Alignment explanation
Indices: 1276597--1276635 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
1276587 TTTTTCTCTC
1276597 TATTTTGCTAT
1 TATTTTGCTAT
*
1276608 TATTTTACTAT
1 TATTTTGCTAT
*
1276619 TATGTTGCTAT
1 TATTTTGCTAT
1276630 TATTTT
1 TATTTT
1276636 ATTGTTATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.64
Consensus pattern (11 bp):
TATTTTGCTAT
Found at i:1279918 original size:21 final size:21
Alignment explanation
Indices: 1279892--1279977 Score: 100
Period size: 21 Copynumber: 4.1 Consensus size: 21
1279882 GGCTTTATCG
* *
1279892 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
*
1279913 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
*
1279934 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
* * * *
1279955 TTTAGGCACTTTATGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
1279976 AT
1 AT
1279978 ACTGATCAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (21 bp):
ATCAGGCACCTCATGTGTCGT
Found at i:1281283 original size:15 final size:15
Alignment explanation
Indices: 1281263--1281292 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1281253 ATTATTTATT
1281263 CTCAAAAGTCAACTA
1 CTCAAAAGTCAACTA
1281278 CTCAAAAGTCAACTA
1 CTCAAAAGTCAACTA
1281293 TAAAATCGAC
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:0.47, C:0.27, G:0.07, T:0.20
Consensus pattern (15 bp):
CTCAAAAGTCAACTA
Found at i:1282497 original size:26 final size:25
Alignment explanation
Indices: 1282460--1282508 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
1282450 AACTTATCAA
*
1282460 TTTTTTCGAA-TTAAATATCTAAATT
1 TTTTTTCCAATTTAAA-ATCTAAATT
1282485 TTTTTATCCAATTTAAAATCTAAA
1 TTTTT-TCCAATTTAAAATCTAAA
1282509 CATATCGACC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 11 0.52
27 5 0.24
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (25 bp):
TTTTTTCCAATTTAAAATCTAAATT
Found at i:1284062 original size:2 final size:2
Alignment explanation
Indices: 1284055--1284082 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1284045 TTTTGGCAGC
1284055 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1284083 GTGCTCCATT
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):
TA
Found at i:1285398 original size:227 final size:227
Alignment explanation
Indices: 1284993--1286190 Score: 1528
Period size: 227 Copynumber: 5.2 Consensus size: 227
1284983 CCAATGCTAG
* * * * *
1284993 CTACCATGCAGGAAGTTATAGAAATGAACAATCAATCCAAGGTAAATCATTTTATTTCCATTATA
1 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTTCATTATA
* * * * * *
1285058 TGTACATATGTTAATGTTTAGGTTTTCGAGAACAGAACTCGACTATTTAAGCCAAATTAACTAAG
66 TGTATATATGTTAATGTTTAGGTTTTTGAGAATAAAACTCAACTGTTTAAGCCAAATTAACTAAG
* * * *
1285123 CTTTAACATTTAAAATTTGAGTTTAAATGTTTTTAGATTATTCAGGTAATAGTACTGGACCATCT
131 CTTTAACATTTAAAATTTGGGTTTAAATGTTTTCAGACTATTCAGGTAATAATACTGGACCATCT
1285188 AAGGAATTTAGTGCTCCAAGCTCTCTAGGAGC
196 AAGGAATTTAGTGCTCCAAGCTCTCTAGGAGC
* *
1285220 CTACCAGGCTGGAAGTTATAGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTTCATTAAA
1 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTTCATTATA
* * *
1285285 TGTATGTATGTTAATATTTAGGTTTTTGAGAATAAAACTCAATTGTTTAAGCCAAATTAACTAAG
66 TGTATATATGTTAATGTTTAGGTTTTTGAGAATAAAACTCAACTGTTTAAGCCAAATTAACTAAG
* * ** * *
1285350 CTTTAACATTTAAAATTTAGGTTTAAATGTTTTCAGACTGTTCAGGTAATGGTACTGGATCATAT
131 CTTTAACATTTAAAATTTGGGTTTAAATGTTTTCAGACTATTCAGGTAATAATACTGGACCATCT
* *
1285415 GAGGAATTTAGTGCTCCAAGCTTTCTAGGAGC
196 AAGGAATTTAGTGCTCCAAGCTCTCTAGGAGC
* *
1285447 CTACCAGGCTGGAAGTTATGGAAATAAACAATCAATCCAAGGTAAATCATTTGATATATCTATTA
1 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGAT-TTTC-ATTA
* * *
1285512 TATATATATAT-TTAATGTTTACGTTTTCGAGAATAAAACTCAACTGTTTAAGCCAAATTAACTA
64 TATGTATATATGTTAATGTTTAGGTTTTTGAGAATAAAACTCAACTGTTTAAGCCAAATTAACTA
* * * * *
1285576 AGCTTTAACATTCAAAATTTGGGTTTAAA----TTCAGATTATTCAAGCAATAATACTGGACTAT
129 AGCTTTAACATTTAAAATTTGGGTTTAAATGTTTTCAGACTATTCAGGTAATAATACTGGACCAT
* * *
1285637 CTAAGAAATTTAGTGCTCCAAGCTCTCTGGGAGT
194 CTAAGGAATTTAGTGCTCCAAGCTCTCTAGGAGC
* * *
1285671 CGACCAGGCTGGAGGTTATGAAAATGAACAATCAATCCAAGGTAAATCATTTGA-TTTCTATTAT
1 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTTC-ATTAT
*
1285735 ATGTATATATGTTAATGTTTAGGTTTAGGTTTAGGTTTTCGAGAATAAAACTCAACTGTTCAAGC
65 ATGTATATATGTTAA----T--GTTTAGG--T---TTTT-GAGAATAAAACTCAACTGTTTAAGC
* * * * *
1285800 TAAATTAACAAAGTTTTAACATTTAAAATTTGGGTTCTAAATGTCTTCAGACTATTCAGGCAATA
118 CAAATTAACTAAGCTTTAACATTTAAAATTTGGGTT-TAAATGTTTTCAGACTATTCAGGTAATA
* * * *
1285865 ATACTGGACTATTTAAGGAATTTAGTGCTCCAAGCTCTCTAAGTGC
182 ATACTGGACCATCTAAGGAATTTAGTGCTCCAAGCTCTCTAGGAGC
* *
1285911 CTACCAGACTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTTCATTACA
1 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTTCATTATA
* * * *
1285976 TGTATATATATGTTAATGTTTACGTTTTTGAAAATAAAACTCAACTATTTAAGCTAAATTAACTA
66 TG--TATATATGTTAATGTTTAGGTTTTTGAGAATAAAACTCAACTGTTTAAGCCAAATTAACTA
* * **
1286041 AGCTTTAACATTTAAAATTTGGGTCTAAATATTTTCAGACTATTCAGGTAATAATACTACACCAT
129 AGCTTTAACATTTAAAATTTGGGTTTAAATGTTTTCAGACTATTCAGGTAATAATACTGGACCAT
**
1286106 CTAAAAAATTTAGTGCTCCAAGCTCTCTAGGTA-C
194 CTAAGGAATTTAGTGCTCCAAGCTCTCTAGG-AGC
* ** * * *
1286140 CTACCATGCCAGAAGTTATGGAAATAAACAATCAATTCAAGGTAAAGCATT
1 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATT
1286191 ATGCCTACAT
Statistics
Matches: 846, Mismatches: 101, Indels: 46
0.85 0.10 0.05
Matches are distributed among these distances:
222 18 0.02
223 4 0.00
224 102 0.12
227 257 0.30
228 79 0.09
229 124 0.15
230 55 0.07
231 5 0.01
234 4 0.00
235 56 0.07
236 10 0.01
238 1 0.00
240 115 0.14
241 4 0.00
242 12 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (227 bp):
CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTTCATTATA
TGTATATATGTTAATGTTTAGGTTTTTGAGAATAAAACTCAACTGTTTAAGCCAAATTAACTAAG
CTTTAACATTTAAAATTTGGGTTTAAATGTTTTCAGACTATTCAGGTAATAATACTGGACCATCT
AAGGAATTTAGTGCTCCAAGCTCTCTAGGAGC
Found at i:1287518 original size:11 final size:11
Alignment explanation
Indices: 1287502--1287558 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
1287492 AAAGCAATTG
*
1287502 TTTTGTTGTTA
1 TTTTGTTATTA
*
1287513 TTTTGTTATCA
1 TTTTGTTATTA
** *
1287524 TTTTACTGTTA
1 TTTTGTTATTA
*
1287535 TATTGTTATTA
1 TTTTGTTATTA
*
1287546 TTTTATTATTA
1 TTTTGTTATTA
1287557 TT
1 TT
1287559 GTTACGTTGT
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.19, C:0.04, G:0.09, T:0.68
Consensus pattern (11 bp):
TTTTGTTATTA
Found at i:1287533 original size:22 final size:22
Alignment explanation
Indices: 1287508--1287550 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1287498 ATTGTTTTGT
*
1287508 TGTTATTTTGTTATCATTTTAC
1 TGTTATATTGTTATCATTTTAC
*
1287530 TGTTATATTGTTATTATTTTA
1 TGTTATATTGTTATCATTTTA
1287551 TTATTATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.09, T:0.65
Consensus pattern (22 bp):
TGTTATATTGTTATCATTTTAC
Found at i:1287557 original size:22 final size:22
Alignment explanation
Indices: 1287510--1287557 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1287500 TGTTTTGTTG
* *
1287510 TTATTTTGTTATCATTTTACTG
1 TTATATTGTTATCATTTTACTA
* *
1287532 TTATATTGTTATTATTTTATTA
1 TTATATTGTTATCATTTTACTA
1287554 TTAT
1 TTAT
1287558 TGTTACGTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.67
Consensus pattern (22 bp):
TTATATTGTTATCATTTTACTA
Found at i:1299344 original size:36 final size:36
Alignment explanation
Indices: 1299297--1299370 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
1299287 TTATTTCTTT
1299297 AACCCCAAAAATAAAAAGAAGAAGAAGAAAAAGAAG
1 AACCCCAAAAATAAAAAGAAGAAGAAGAAAAAGAAG
*
1299333 AACCCCAAAAATGAAAAGAAGAAGAAGAAAAAGAAG
1 AACCCCAAAAATAAAAAGAAGAAGAAGAAAAAGAAG
1299369 AA
1 AA
1299371 GGTTCTTTGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.69, C:0.11, G:0.18, T:0.03
Consensus pattern (36 bp):
AACCCCAAAAATAAAAAGAAGAAGAAGAAAAAGAAG
Found at i:1299847 original size:142 final size:139
Alignment explanation
Indices: 1299561--1299912 Score: 540
Period size: 140 Copynumber: 2.6 Consensus size: 139
1299551 ACCTTAGTAC
* *
1299561 ATCTAAGTATGATGATGTTCTGTCATTTTTTCGTCATTTCTAAGAAGCCTACAAGAAGGAATATT
1 ATCTAAGTACGAT-ATGTTCTGTCATTTTTT-GTCATTTCTAAGAAGCCTACAAGAAGCAATATT
*
1299626 ----G--GAAGAAGAAGGTTAAACCTACTTCAAAATGAATTCCTTCCTTTTTTTCCACAAGACTA
64 GGAAGAAGAAGAAGAAGGTTAAACCCACTTCAAAATGAATTCCTTCCTTTTTTTCCACAAGACTA
1299685 CGGGGGAGAAT
129 CGGGGGAGAAT
* *
1299696 ATCTAAGTACGATATGTTCTGTCATTTTTTATCATTTCTAAGAAGCCTACAAGACGCAATATTGG
1 ATCTAAGTACGATATGTTCTGTCATTTTTTGTCATTTCTAAGAAGCCTACAAGAAGCAATATTGG
1299761 AAGAAGAAGAAGAAGGTTAAACCCACTTCAAAATGAATTCCTTCCTTTTTTTTTTCCACAAGACT
66 AAGAAGAAGAAGAAGGTTAAACCCACTTCAAAATGAATTCCTTCC---TTTTTTTCCACAAGACT
1299826 ACGGGGGAGAAT
128 ACGGGGGAGAAT
* *
1299838 ATCTAAGTACG--ATGTTCTGTCATTTTTTGTCATTTCTAAGAAGCCTACAAGAGGTAATATTGG
1 ATCTAAGTACGATATGTTCTGTCATTTTTTGTCATTTCTAAGAAGCCTACAAGAAGCAATATTGG
1299901 AAGAAGAAGAAG
66 AAGAAGAAGAAG
1299913 GAGGAGGAGG
Statistics
Matches: 200, Mismatches: 8, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
133 30 0.15
134 17 0.09
135 12 0.06
137 1 0.00
139 39 0.19
140 61 0.31
142 40 0.20
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (139 bp):
ATCTAAGTACGATATGTTCTGTCATTTTTTGTCATTTCTAAGAAGCCTACAAGAAGCAATATTGG
AAGAAGAAGAAGAAGGTTAAACCCACTTCAAAATGAATTCCTTCCTTTTTTTCCACAAGACTACG
GGGGAGAAT
Found at i:1299917 original size:3 final size:3
Alignment explanation
Indices: 1299911--1299939 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1299901 AAGAAGAAGA
1299911 AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
1299940 AGTTAAATTC
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:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:1303358 original size:24 final size:23
Alignment explanation
Indices: 1303315--1303362 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
1303305 TGAAGTAGGA
1303315 TCTTCAAAGTTTCTTCTTTTATTT
1 TCTTCAAAGTTTCTTCTTTT-TTT
*
1303339 TCTTCAAAG-TTCATTTTTTTTTT
1 TCTTCAAAGTTTC-TTCTTTTTTT
1303362 T
1 T
1303363 AGTGAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.17, C:0.15, G:0.04, T:0.65
Consensus pattern (23 bp):
TCTTCAAAGTTTCTTCTTTTTTT
Found at i:1303485 original size:2 final size:2
Alignment explanation
Indices: 1303478--1303507 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1303468 ATTTTAATTA
1303478 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1303508 TACACAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1307704 original size:10 final size:9
Alignment explanation
Indices: 1307688--1307712 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1307678 TTAATCAATT
1307688 TAAAAAAAA
1 TAAAAAAAA
1307697 TAAAAAAAA
1 TAAAAAAAA
1307706 TAAAAAA
1 TAAAAAA
1307713 CCAAAGTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:1310566 original size:75 final size:75
Alignment explanation
Indices: 1310475--1310706 Score: 322
Period size: 75 Copynumber: 3.1 Consensus size: 75
1310465 TAGTAACCGG
* * * * * *
1310475 ATTGGGTGCTACAACAGGGGACATAGCTGGAGCCAGCGAAGAAACCGAATCCTCACTGGTTTTTA
1 ATTGGTTGCTAAAACAGGGGACATTGCCGGAGCCGGCGAAGAAACCGAATCCTCACCGGTTTTTA
*
1310540 CAACAGAATC
66 CAACGGAATC
*
1310550 ATTGGTTGCTAAAACAGGGGACATTGCCGGAACCGGCGAAGAAACCGAATCCTCACCGGTTTTTA
1 ATTGGTTGCTAAAACAGGGGACATTGCCGGAGCCGGCGAAGAAACCGAATCCTCACCGGTTTTTA
1310615 CAACGGAATC
66 CAACGGAATC
** * *
1310625 ATTGGTTGCTAATGCAGGGGGA-ATTGCCGGAGCCGGCGAAGAAACCAAATCCTCACCGGTTTTA
1 ATTGGTTGCTAAAACA-GGGGACATTGCCGGAGCCGGCGAAGAAACCGAATCCTCACCGGTTTTT
*
1310689 ACAATGGAATC
65 ACAACGGAATC
*
1310700 ATCGGTT
1 ATTGGTT
1310707 TCAGTAATGG
Statistics
Matches: 141, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
75 136 0.96
76 5 0.04
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.21
Consensus pattern (75 bp):
ATTGGTTGCTAAAACAGGGGACATTGCCGGAGCCGGCGAAGAAACCGAATCCTCACCGGTTTTTA
CAACGGAATC
Found at i:1314621 original size:18 final size:18
Alignment explanation
Indices: 1314600--1314638 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1314590 TATATTAGGA
*
1314600 TAATTACGGTACTTACAG
1 TAATTACGGTAATTACAG
* *
1314618 TAATTATGGTAATTATAG
1 TAATTACGGTAATTACAG
1314636 TAA
1 TAA
1314639 AGGTTATATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (18 bp):
TAATTACGGTAATTACAG
Found at i:1315140 original size:1 final size:1
Alignment explanation
Indices: 1315136--1315161 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1315126 ATGAAAAATG
1315136 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
1315162 ACATTACCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1317852 original size:53 final size:53
Alignment explanation
Indices: 1317772--1317877 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
1317762 GATCCCTCTC
1317772 AAGAAAAAATTGGAGCAATTTAATCTCTGTCAATTTCAAAAGTGAGCAAATAA
1 AAGAAAAAATTGGAGCAATTTAATCTCTGTCAATTTCAAAAGTGAGCAAATAA
1317825 AAGAAAAAATTGGAGCAATTTAATCTCTGTCAATTTCAAAAGTGAGCAAATAA
1 AAGAAAAAATTGGAGCAATTTAATCTCTGTCAATTTCAAAAGTGAGCAAATAA
1317878 GGATAATTAA
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:0.47, C:0.11, G:0.15, T:0.26
Consensus pattern (53 bp):
AAGAAAAAATTGGAGCAATTTAATCTCTGTCAATTTCAAAAGTGAGCAAATAA
Found at i:1319250 original size:2 final size:2
Alignment explanation
Indices: 1319237--1319269 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1319227 TCACATATGC
*
1319237 AT AT AG 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 A
1319270 CTTTATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1322066 original size:15 final size:17
Alignment explanation
Indices: 1322033--1322074 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
1322023 GCAATTAGGG
1322033 TTAGGGTTTTGAGAATT
1 TTAGGGTTTTGAGAATT
*
1322050 TT-GGGTTTTTA-AATT
1 TTAGGGTTTTGAGAATT
1322065 TTAGGGTTTT
1 TTAGGGTTTT
1322075 AAAGAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 6 0.26
16 15 0.65
17 2 0.09
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (17 bp):
TTAGGGTTTTGAGAATT
Found at i:1322075 original size:15 final size:15
Alignment explanation
Indices: 1322033--1322077 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
1322023 GCAATTAGGG
1322033 TTAGGGTTTTGAGAATT
1 TTAGGGTTTT-A-AATT
1322050 TT-GGGTTTTTAAATT
1 TTAGGG-TTTTAAATT
1322065 TTAGGGTTTTAAA
1 TTAGGGTTTTAAA
1322078 GAAAAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 13 0.50
16 7 0.27
17 6 0.23
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (15 bp):
TTAGGGTTTTAAATT
Found at i:1322180 original size:96 final size:95
Alignment explanation
Indices: 1322064--1322236 Score: 229
Period size: 96 Copynumber: 1.8 Consensus size: 95
1322054 GTTTTTAAAT
* * ** *
1322064 TTTAGGGTTTTAAAGAAAAAAATTAAATAAATTAAGGTTTAGTGTTTGTTAATTAAATTAATTAC
1 TTTAGGGTTTTAAAGAAAAAAATCAAATAAATTAAGGTTTAGGGTTACTTAAGTAAATTAATTA-
*
1322129 TAATTTTAAAAAATTAGATTATGGTTTAGTG
65 TAAATTTAAAAAATTAGATTATGGTTTAGTG
* * * * * *
1322160 TTTATGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTTGGGTTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTAAAGAAAAAAATCAAATAAATTAAGGTTTAGGGTTACTTAAGTAAATTAATTAT
1322225 AAATTTAAAAAA
66 AAATTTAAAAAA
1322237 AAATTAGATT
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
95 12 0.18
96 53 0.82
ACGTcount: A:0.42, C:0.02, G:0.15, T:0.41
Consensus pattern (95 bp):
TTTAGGGTTTTAAAGAAAAAAATCAAATAAATTAAGGTTTAGGGTTACTTAAGTAAATTAATTAT
AAATTTAAAAAATTAGATTATGGTTTAGTG
Done.