Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold253
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: 2064896
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 9 of 13
Found at i:1122687 original size:12 final size:12
Alignment explanation
Indices: 1122645--1122696 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
1122635 TATAAACTAT
1122645 TAATATAA-AAA
1 TAATATAATAAA
1122656 TAATAATAATATTTAA
1 TAAT-ATAATA---AA
1122672 TAATATAATAAA
1 TAATATAATAAA
*
1122684 TAATAAAATAAA
1 TAATATAATAAA
1122696 T
1 T
1122697 TTTTGTATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
11 4 0.11
12 18 0.51
13 1 0.03
15 6 0.17
16 6 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TAATATAATAAA
Found at i:1122687 original size:15 final size:15
Alignment explanation
Indices: 1122645--1122694 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1122635 TATAAACTAT
1122645 TAATATAA-AAATAA
1 TAATATAATAAATAA
**
1122659 T-A-ATAATATTTAA
1 TAATATAATAAATAA
1122672 TAATATAATAAATAA
1 TAATATAATAAATAA
*
1122687 TAAAATAA
1 TAATATAA
1122695 ATTTTTGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
12 4 0.14
13 6 0.21
14 2 0.07
15 16 0.57
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAATATAATAAATAA
Found at i:1123160 original size:2 final size:2
Alignment explanation
Indices: 1123153--1123177 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1123143 ATTACACCAT
1123153 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
1123178 GTATCAATGC
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:1123442 original size:19 final size:19
Alignment explanation
Indices: 1123418--1123470 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
1123408 ATAAAAAAAC
*
1123418 TTATTAAAAAATATATTTA
1 TTATTAAAAAATAAATTTA
*
1123437 TTATTAAAAATTAAATTTA
1 TTATTAAAAAATAAATTTA
1123456 -TATCTAAAAAATAAA
1 TTAT-TAAAAAATAAA
1123471 AATATATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 3 0.10
19 27 0.90
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
TTATTAAAAAATAAATTTA
Found at i:1124060 original size:17 final size:15
Alignment explanation
Indices: 1124016--1124057 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1124006 ATCTTGATAT
* *
1124016 ATAACAAAATATTAG
1 ATAAAAAAATATTAA
1124031 ATAAAAAAATATTAA
1 ATAAAAAAATATTAA
*
1124046 ATGAAAAAATAT
1 ATAAAAAAATAT
1124058 ATTTATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (15 bp):
ATAAAAAAATATTAA
Found at i:1124423 original size:15 final size:14
Alignment explanation
Indices: 1124369--1124427 Score: 64
Period size: 14 Copynumber: 4.0 Consensus size: 14
1124359 ATATAATTAA
1124369 TTAATATTTAATATAT
1 TTAATATTTAA-AT-T
*
1124385 TTAAAATTTAAATT
1 TTAATATTTAAATT
1124399 TTAATATTTATAATT
1 TTAATATTTA-AATT
* *
1124414 TTTATCTTTAAATT
1 TTAATATTTAAATT
1124428 ATGATTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
14 14 0.37
15 14 0.37
16 10 0.26
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (14 bp):
TTAATATTTAAATT
Found at i:1124711 original size:28 final size:29
Alignment explanation
Indices: 1124641--1124713 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
1124631 AAAAATATTA
* *
1124641 ATTTAATTTATTATTTAATTAATAAAAAT
1 ATTTAAATTATAATTTAATTAATAAAAAT
**
1124670 -TTTATGTT-TAAATTTAATT-ATAAAAAT
1 ATTTAAATTAT-AATTTAATTAATAAAAAT
1124697 ATTTAAATTATAATTTA
1 ATTTAAATTATAATTTA
1124714 GTTCCATTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
27 9 0.25
28 26 0.72
29 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (29 bp):
ATTTAAATTATAATTTAATTAATAAAAAT
Found at i:1124982 original size:16 final size:17
Alignment explanation
Indices: 1124928--1125068 Score: 95
Period size: 17 Copynumber: 8.5 Consensus size: 17
1124918 TATTATGATG
1124928 ATATAAAAATTAA-AT-
1 ATATAAAAATTAATATA
* *
1124943 GTA-AAATATTAATATA
1 ATATAAAAATTAATATA
*
1124959 ATATAAAAATTAATTTA
1 ATATAAAAATTAATATA
*
1124976 A-ATAAAAAATAATATA
1 ATATAAAAATTAATATA
1124992 AT-TAAATAATATAA-ATA
1 ATATAAA-AAT-TAATATA
* *
1125009 TATATTAAAATTTATATA
1 -ATATAAAAATTAATATA
*
1125027 ATATAAATTATTAATAT-
1 ATATAAA-AATTAATATA
1125044 AT-T-AAAATT-ATATCA
1 ATATAAAAATTAATAT-A
1125059 ATATGAAAAA
1 ATAT-AAAAA
1125069 ATTGAACATG
Statistics
Matches: 97, Mismatches: 14, Indels: 27
0.70 0.10 0.20
Matches are distributed among these distances:
13 4 0.04
14 11 0.11
15 8 0.08
16 22 0.23
17 27 0.28
18 22 0.23
19 3 0.03
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (17 bp):
ATATAAAAATTAATATA
Found at i:1124998 original size:20 final size:20
Alignment explanation
Indices: 1124973--1125017 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
1124963 AAAAATTAAT
1124973 TTAAATAA-A-AAATAATATAA
1 TTAAATAATATAAAT-ATAT-A
1124993 TTAAATAATATAAATATATA
1 TTAAATAATATAAATATATA
1125013 TTAAA
1 TTAAA
1125018 ATTTATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 14 0.61
21 5 0.22
22 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TTAAATAATATAAATATATA
Found at i:1125000 original size:13 final size:13
Alignment explanation
Indices: 1124982--1125049 Score: 50
Period size: 13 Copynumber: 5.2 Consensus size: 13
1124972 TTTAAATAAA
1124982 AAATAATATAATT
1 AAATAATATAATT
*
1124995 AAATAATATAAAT
1 AAATAATATAATT
* * *
1125008 ATATATTAAAATTT
1 AAATAATATAA-TT
*
1125022 ATATAATATAAATT
1 AAATAATAT-AATT
*
1125036 -ATTAATAT-ATT
1 AAATAATATAATT
1125047 AAA
1 AAA
1125050 ATTATATCAA
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
11 3 0.07
12 1 0.02
13 26 0.62
14 10 0.24
15 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATAATATAATT
Found at i:1125019 original size:21 final size:21
Alignment explanation
Indices: 1124948--1125036 Score: 62
Period size: 21 Copynumber: 4.3 Consensus size: 21
1124938 TAAATGTAAA
* *
1124948 ATATTAATATAATATAAAAAT
1 ATATTAAAATAATATAAATAT
*
1124969 -TAATTTAAATAA-A-AAATAAT
1 AT-ATTAAAATAATATAAAT-AT
1124989 ATAATT-AAATAATATAAATAT
1 AT-ATTAAAATAATATAAATAT
*
1125010 ATATTAAAAT-TTATATAATAT
1 ATATTAAAATAATATA-AATAT
*
1125031 AAATTA
1 ATATTA
1125037 TTAATATATT
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
19 3 0.05
20 17 0.30
21 32 0.57
22 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATATTAAAATAATATAAATAT
Found at i:1125197 original size:19 final size:20
Alignment explanation
Indices: 1125173--1125219 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1125163 TATTTATATA
1125173 TAAATAATA-C-ATAATATTT
1 TAAATAATATCAATAA-ATTT
1125192 TAAAT-ATATCAATAAATTT
1 TAAATAATATCAATAAATTT
1125211 TAAA-AATAT
1 TAAATAATAT
1125220 ATTTATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.12
19 18 0.72
20 4 0.16
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATAATATCAATAAATTT
Found at i:1127271 original size:17 final size:17
Alignment explanation
Indices: 1127249--1127298 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
1127239 TTTAAAAAAT
1127249 TAAATATATTTATATTA
1 TAAATATATTTATATTA
* *
1127266 TAAATATACTTATATCA
1 TAAATATATTTATATTA
*
1127283 -AATACATATTTATATT
1 TAA-ATATATTTATATT
1127299 TAATATTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 2 0.07
17 25 0.93
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAATATATTTATATTA
Found at i:1127678 original size:79 final size:81
Alignment explanation
Indices: 1127542--1127697 Score: 208
Period size: 79 Copynumber: 2.0 Consensus size: 81
1127532 ATACTTATTT
* * * * * *
1127542 GTCAAAATAAGAAAGTTTGAATCTATCACCGTTTTGTCACGTTAGATCATTACATATAAAATATT
1 GTCAAAATAAGAAAATTTAAATCTATCACCATTTTATCACATTAAATCATTACATATAAAATATT
*
1127607 TATTG-ATTCATGCAA
66 TAATGAATTCATGCAA
* * *
1127622 GTCAAAATAA-AAAATTTAAATTTATCATCATTTTATCATATTAAATCATTACATATAAAATATT
1 GTCAAAATAAGAAAATTTAAATCTATCACCATTTTATCACATTAAATCATTACATATAAAATATT
1127686 TAATGAATTCAT
66 TAATGAATTCAT
1127698 AGTCATTCAG
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
79 49 0.75
80 16 0.25
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (81 bp):
GTCAAAATAAGAAAATTTAAATCTATCACCATTTTATCACATTAAATCATTACATATAAAATATT
TAATGAATTCATGCAA
Found at i:1127959 original size:18 final size:19
Alignment explanation
Indices: 1127925--1127964 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1127915 ATATATACAA
1127925 TTAATATTAATATAACATT
1 TTAATATTAATATAACATT
1127944 TTAATA-TAAT-TAAACATT
1 TTAATATTAATAT-AACATT
1127962 TTA
1 TTA
1127965 GAGGACATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 1 0.05
18 13 0.65
19 6 0.30
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATATTAATATAACATT
Found at i:1128230 original size:13 final size:13
Alignment explanation
Indices: 1128212--1128250 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1128202 AAACACATAT
1128212 ATATTTATATTTA
1 ATATTTATATTTA
*
1128225 ATATTTATTTTTA
1 ATATTTATATTTA
*
1128238 A-ATTTAAATTTA
1 ATATTTATATTTA
1128250 A
1 A
1128251 AATATAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATTTATATTTA
Found at i:1128707 original size:2 final size:2
Alignment explanation
Indices: 1128690--1128725 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1128680 ATTTAAATTC
* *
1128690 CT CT CT TT CT CA CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1128726 TTTTTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1135907 original size:13 final size:13
Alignment explanation
Indices: 1135888--1135918 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1135878 TTTTTTAAAA
1135888 AATATTTATATTT
1 AATATTTATATTT
*
1135901 TATATTTATATTT
1 AATATTTATATTT
1135914 AATAT
1 AATAT
1135919 ATATTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:1137441 original size:17 final size:17
Alignment explanation
Indices: 1137416--1137450 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1137406 TAAAAATAAG
* *
1137416 TGTTGGATATAATTATA
1 TGTTAGATATAAGTATA
1137433 TGTTAGATATAAGTATA
1 TGTTAGATATAAGTATA
1137450 T
1 T
1137451 TAATTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (17 bp):
TGTTAGATATAAGTATA
Found at i:1138785 original size:12 final size:12
Alignment explanation
Indices: 1138768--1138804 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1138758 ATTAATATAT
1138768 TTTTAAAAAATA
1 TTTTAAAAAATA
1138780 TTTTAAATAAATA
1 TTTTAAA-AAATA
*
1138793 TCTTAAAAAATA
1 TTTTAAAAAATA
1138805 AAAATTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (12 bp):
TTTTAAAAAATA
Found at i:1144026 original size:2 final size:2
Alignment explanation
Indices: 1144019--1144045 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1144009 TAGAATATTA
1144019 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 A
1144046 CTTTTTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1146799 original size:13 final size:13
Alignment explanation
Indices: 1146783--1146807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1146773 TTTTTTTTAA
1146783 ATATTTATATTCG
1 ATATTTATATTCG
1146796 ATATTTATATTC
1 ATATTTATATTC
1146808 ATCATATATT
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:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
ATATTTATATTCG
Found at i:1147026 original size:50 final size:50
Alignment explanation
Indices: 1146925--1147032 Score: 137
Period size: 50 Copynumber: 2.2 Consensus size: 50
1146915 ACCCGAATCA
* * * *
1146925 GTTATAAAAAGACATACACATATTTAACACTTATCTCGAATCAATATCAG
1 GTTATAAAAAGACATACACATATTTAACACTTATCCCAAATCAAGAACAG
* *
1146975 GTTATAAAAAGACATACACATATTTAGCACTTA-CCCAAATCGAGGAACAG
1 GTTATAAAAAGACATACACATATTTAACACTTATCCCAAATC-AAGAACAG
*
1147025 GTTGTAAA
1 GTTATAAA
1147033 GAGGAGAAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
49 6 0.12
50 44 0.88
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.27
Consensus pattern (50 bp):
GTTATAAAAAGACATACACATATTTAACACTTATCCCAAATCAAGAACAG
Found at i:1150391 original size:413 final size:413
Alignment explanation
Indices: 1149545--1151529 Score: 3808
Period size: 413 Copynumber: 4.8 Consensus size: 413
1149535 TGAACAAGAA
* *
1149545 AGTAAAAGAAAAATATCTGAGATGACACGTGGGAAAAGGATAGGATTTCAAGGGTTTAAAATTGG
1 AGTAAAAGAAAAATATCTGAGATGACACGTGGGGAAAGGATAGGATTTGAAGGGTTTAAAATTGG
*
1149610 TAAGATATCCCTTGGCAGATTTGATTGGCTTCTTTGCAGGTTGAGTTAATCTCATTTCAGAGGTT
66 TAAGATATCCCTTGGCAGATTTGATTGGCTTCTTTGCAGGTTGAGTTTATCTCATTTCAGAGGTT
1149675 TTCCATGCAAATTGGCAAAAAGTCTGCAATTTGTTGGCAAATCACTCTTATGAACCCCACTTTCT
131 TTCCATGCAAATTGGCAAAAAGTCTGCAATTTGTTGGCAAATCACTC---T--------CTTTCT
*
1149740 CAGTTATGTTTTTGTCAACATGCCAGTGAGGGTTTATTTTGAAGAACTTTTTGTTAAATCTTATG
185 CAGTTATGTCTTTGTCAACATGCCAGTGAGGGTTTATTTTGAAGAACTTTTTGTT-AATCTTATG
*
1149805 TCCCCAAAAGCTCCATTTTTGGTAATTTTTTTGTCACTTTGTTACAATAAGAGCTTTTCTGGTTG
249 TCCCCAAAAGCTCCACTTTTGGTAATTTTTTTGTCACTTTGTTACAATAAGAGCTTTTCTGGTTG
1149870 ATTCTAATATCATGGAGTTTTTATGGAAAGGCATATATATATACCTATATATTTGTTAATAGCTT
314 ATTCTAATATCATGGAGTTTTTATGGAAAGGCATATATATATACCTATATATTTGTTAATAGCTT
1149935 AGTAGCATGATTTAGCAAGTGGCCCTACTGCCTCT
379 AGTAGCATGATTTAGCAAGTGGCCCTACTGCCTCT
1149970 AGTAAAAGAAAAATATCTGAGATGACACGTGGGGAAAGGATAGGATTTGAAGGGTTTAAAATTGG
1 AGTAAAAGAAAAATATCTGAGATGACACGTGGGGAAAGGATAGGATTTGAAGGGTTTAAAATTGG
1150035 TAAGATATCCCTTGGCAGATTTGATTGGCTTCTTTGCAGGTTGAGTTTATCTCATTTCAGAGGTT
66 TAAGATATCCCTTGGCAGATTTGATTGGCTTCTTTGCAGGTTGAGTTTATCTCATTTCAGAGGTT
1150100 TTCCATGCAAATTGGCAAAAAGTCTGCAATTTGTTGGCAAATCACTCTCTTTCTCAGTTATGTCT
131 TTCCATGCAAATTGGCAAAAAGTCTGCAATTTGTTGGCAAATCACTCTCTTTCTCAGTTATGTCT
1150165 TTGTCAACATGCCAGTGAGGGTTTATTTTGAAGAACTTTTTGTTAATCTTATGTCCCCAAAAGCT
196 TTGTCAACATGCCAGTGAGGGTTTATTTTGAAGAACTTTTTGTTAATCTTATGTCCCCAAAAGCT
1150230 CCACTTTTGGTAATTTTTTTGTCACTTTGTTACAATAAGAGCTTTTCTGGTTGATTCTAATATCA
261 CCACTTTTGGTAATTTTTTTGTCACTTTGTTACAATAAGAGCTTTTCTGGTTGATTCTAATATCA
1150295 TGGAGTTTTTATGGAAAGGCATATATATATACCTATATATTTGTTAATAGCTTAGTAGCATGATT
326 TGGAGTTTTTATGGAAAGGCATATATATATACCTATATATTTGTTAATAGCTTAGTAGCATGATT
1150360 TAGCAAGTGGCCCTACTGCCTCT
391 TAGCAAGTGGCCCTACTGCCTCT
1150383 AGTAAAAGAAAAATATCTGAGATGACACGTGGGGAAAGGATAGGATTTGAAGGGTTTAAAATTGG
1 AGTAAAAGAAAAATATCTGAGATGACACGTGGGGAAAGGATAGGATTTGAAGGGTTTAAAATTGG
1150448 TAAGATATCCCTTGGCAGATTTGATTGGCTTCTTTGCAGGTTGAGTTTATCTCATTTCAGAGGTT
66 TAAGATATCCCTTGGCAGATTTGATTGGCTTCTTTGCAGGTTGAGTTTATCTCATTTCAGAGGTT
1150513 TTCCATGCAAATTGGCAAAAAGTCTGCAATTTGTTGGCAAATCACTCTCTTTCTCAGTTATGTCT
131 TTCCATGCAAATTGGCAAAAAGTCTGCAATTTGTTGGCAAATCACTCTCTTTCTCAGTTATGTCT
1150578 TTGTCAACATGCCAGTGAGGGTTTATTTTGAAGAACTTTTTGTTAATCTTATGTCCCCAAAAGCT
196 TTGTCAACATGCCAGTGAGGGTTTATTTTGAAGAACTTTTTGTTAATCTTATGTCCCCAAAAGCT
1150643 CCACTTTTGGTAATTTTTTTGTCACTTTGTTACAATAAGAGCTTTTCTGGTTGATTCTAATATCA
261 CCACTTTTGGTAATTTTTTTGTCACTTTGTTACAATAAGAGCTTTTCTGGTTGATTCTAATATCA
1150708 TGGAGTTTTTATGGAAAGGCATATATATATACCTATATATTTGTTAATAGCTTAGTAGCATGATT
326 TGGAGTTTTTATGGAAAGGCATATATATATACCTATATATTTGTTAATAGCTTAGTAGCATGATT
1150773 TAGCAAGTGGCCCTACTGCCTCT
391 TAGCAAGTGGCCCTACTGCCTCT
1150796 AGTAAAAGAAAAATATCTGAGATGACACGTGGGGAAAGGATAGGATTTGAAGGGTTTAAAATTGG
1 AGTAAAAGAAAAATATCTGAGATGACACGTGGGGAAAGGATAGGATTTGAAGGGTTTAAAATTGG
1150861 TAAGATATCCCTTGGCAGATTTGATTGGCTTCTTTGCAGGTTGAGTTTATCTCATTTCAGAGGTT
66 TAAGATATCCCTTGGCAGATTTGATTGGCTTCTTTGCAGGTTGAGTTTATCTCATTTCAGAGGTT
1150926 TTCCATGCAAATTGGCAAAAAGTCTGCAATTTGTTGGCAAATCACTCTCTTTCTCAGTTATGTCT
131 TTCCATGCAAATTGGCAAAAAGTCTGCAATTTGTTGGCAAATCACTCTCTTTCTCAGTTATGTCT
1150991 TTGTCAACATGCCAGTGAGGGTTTATTTTGAAGAACTTTTTGTTAATCTTATGTCCCCAAAAGCT
196 TTGTCAACATGCCAGTGAGGGTTTATTTTGAAGAACTTTTTGTTAATCTTATGTCCCCAAAAGCT
1151056 CCACTTTTGGTAATTTTTTTGTCACTTTGTTACAATAAGAGCTTTTCTGGTTGATTCTAATATCA
261 CCACTTTTGGTAATTTTTTTGTCACTTTGTTACAATAAGAGCTTTTCTGGTTGATTCTAATATCA
1151121 TGGAGTTTTTATGGAAAGGCATATATATATACCTATATATTTGTTAATAGCTTAGTAGCATGATT
326 TGGAGTTTTTATGGAAAGGCATATATATATACCTATATATTTGTTAATAGCTTAGTAGCATGATT
1151186 TAGCAAGTGGCCCTACTGCCTCT
391 TAGCAAGTGGCCCTACTGCCTCT
1151209 AGTAAAAGAAAAATATCTGAGATGACACGTGGGGAAAGGATAGGATTTGAAGGGTTTAAAATTGG
1 AGTAAAAGAAAAATATCTGAGATGACACGTGGGGAAAGGATAGGATTTGAAGGGTTTAAAATTGG
*
1151274 TAAGATATCCCTTGGCAGATTTGATTGGCTTCTTTGCAGGTTGAGTTTATCTCATTTCAAAGGTT
66 TAAGATATCCCTTGGCAGATTTGATTGGCTTCTTTGCAGGTTGAGTTTATCTCATTTCAGAGGTT
1151339 TTCCATGCAAATTGGCAAAAAGTCTGCAATTTGTTGGCAAATCACTCTCTTTCTCAGTTATGTCT
131 TTCCATGCAAATTGGCAAAAAGTCTGCAATTTGTTGGCAAATCACTCTCTTTCTCAGTTATGTCT
1151404 TTGTCAACATGCCAGTGAGGGTTTATTTTGAAGAACTTTTTGTTAATCTTATGTCCCCAAAAGCT
196 TTGTCAACATGCCAGTGAGGGTTTATTTTGAAGAACTTTTTGTTAATCTTATGTCCCCAAAAGCT
1151469 CCACTTTTGGTAATTTTTTTGTCACTTTGTTACAATAAGAGCTTTTCTGGTTGATTCTAAT
261 CCACTTTTGGTAATTTTTTTGTCACTTTGTTACAATAAGAGCTTTTCTGGTTGATTCTAAT
1151530 TTGTAATCTT
Statistics
Matches: 1554, Mismatches: 6, Indels: 12
0.99 0.00 0.01
Matches are distributed among these distances:
413 1319 0.85
414 60 0.04
422 1 0.00
425 174 0.11
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (413 bp):
AGTAAAAGAAAAATATCTGAGATGACACGTGGGGAAAGGATAGGATTTGAAGGGTTTAAAATTGG
TAAGATATCCCTTGGCAGATTTGATTGGCTTCTTTGCAGGTTGAGTTTATCTCATTTCAGAGGTT
TTCCATGCAAATTGGCAAAAAGTCTGCAATTTGTTGGCAAATCACTCTCTTTCTCAGTTATGTCT
TTGTCAACATGCCAGTGAGGGTTTATTTTGAAGAACTTTTTGTTAATCTTATGTCCCCAAAAGCT
CCACTTTTGGTAATTTTTTTGTCACTTTGTTACAATAAGAGCTTTTCTGGTTGATTCTAATATCA
TGGAGTTTTTATGGAAAGGCATATATATATACCTATATATTTGTTAATAGCTTAGTAGCATGATT
TAGCAAGTGGCCCTACTGCCTCT
Found at i:1151998 original size:18 final size:18
Alignment explanation
Indices: 1151972--1152006 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1151962 AAAAAATTAT
*
1151972 AATTTAATATATGAAAAA
1 AATTAAATATATGAAAAA
*
1151990 AATTAAATATATTAAAA
1 AATTAAATATATGAAAA
1152007 TTTAAATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
AATTAAATATATGAAAAA
Found at i:1153083 original size:2 final size:2
Alignment explanation
Indices: 1153070--1153099 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1153060 TAAAATGTAA
*
1153070 AT AT AC 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
1153100 CAAAGCAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1153142 original size:9 final size:9
Alignment explanation
Indices: 1153110--1153148 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
1153100 CAAAGCAAAT
1153110 AATATTAAA
1 AATATTAAA
*
1153119 AATTAATTTAA
1 AA-T-ATTAAA
1153130 AATATTAAA
1 AATATTAAA
1153139 AATATTAAA
1 AATATTAAA
1153148 A
1 A
1153149 TTTTATACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 17 0.65
10 2 0.08
11 7 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AATATTAAA
Found at i:1156508 original size:28 final size:27
Alignment explanation
Indices: 1156427--1156512 Score: 66
Period size: 33 Copynumber: 2.9 Consensus size: 27
1156417 TAATTTTTTA
*
1156427 TAAATTTTAAGATTAAAATATTAAATTTAT
1 TAAATTTTAA-ATTAAAA-ATT-AATTAAT
*
1156457 TAAATATTAATTAATTATATAAATTAATTAAAT
1 TAAAT-TT--TAAATTA-A-AAATTAATT-AAT
1156490 TAAATTTTAAATTAAAAA-TAATT
1 TAAATTTTAAATTAAAAATTAATT
1156513 TTTTTATGGT
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
27 5 0.11
28 3 0.06
29 1 0.02
30 11 0.23
31 2 0.04
32 10 0.21
33 13 0.28
34 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (27 bp):
TAAATTTTAAATTAAAAATTAATTAAT
Found at i:1159077 original size:37 final size:39
Alignment explanation
Indices: 1159024--1159096 Score: 98
Period size: 37 Copynumber: 1.9 Consensus size: 39
1159014 AGATAAAAAT
*
1159024 ATTTTTATTTAAATTT-AATTATAA-AAATATTTTTAAA
1 ATTTTTATTTAAATTTAAATAATAATAAATATTTTTAAA
*
1159061 ATTTTTA-TTAATATTTAAATAATAATTAATATTTTT
1 ATTTTTATTTAA-ATTTAAATAATAATAAATATTTTT
1159097 GAATTGGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 4 0.13
37 11 0.35
38 7 0.23
39 9 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (39 bp):
ATTTTTATTTAAATTTAAATAATAATAAATATTTTTAAA
Found at i:1159499 original size:14 final size:15
Alignment explanation
Indices: 1159474--1159624 Score: 57
Period size: 14 Copynumber: 10.1 Consensus size: 15
1159464 GTAATTTATA
1159474 TATTTATATTATATT
1 TATTTATATTATATT
1159489 TATTT-TATTATATT
1 TATTTATATTATATT
* **
1159503 ATAATTATATT-TAAAA
1 -TATTTATATTAT-ATT
*
1159519 TATTTTATATTATATA
1 TA-TTTATATTATATT
* *
1159535 AATTT-TAATATATT
1 TATTTATATTATATT
1159549 AATAATTTATATTATA--
1 --T-ATTTATATTATATT
** *
1159565 TATTT-TAAAATATG
1 TATTTATATTATATT
*
1159579 TATTTATATTACATCAT
1 TATTTATATTATAT--T
*
1159596 AATTT-TATTAT-TT
1 TATTTATATTATATT
**
1159609 TATACATATTATATT
1 TATTTATATTATATT
1159624 T
1 T
1159625 TTATAATTGT
Statistics
Matches: 99, Mismatches: 21, Indels: 32
0.65 0.14 0.21
Matches are distributed among these distances:
12 5 0.05
13 7 0.07
14 28 0.28
15 24 0.24
16 20 0.20
17 9 0.09
18 6 0.06
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.58
Consensus pattern (15 bp):
TATTTATATTATATT
Found at i:1159522 original size:25 final size:27
Alignment explanation
Indices: 1159472--1159587 Score: 75
Period size: 25 Copynumber: 4.4 Consensus size: 27
1159462 TAGTAATTTA
***
1159472 TATATT-TATATTATATTTATTTTA-T
1 TATATTATATATTATATTTAAAATATT
1159497 TATATTATA-ATTATATTTAAAATATTT
1 TATATTATATATTATATTTAAAATA-TT
* *
1159524 TATATTATATA-AAT-TTTAATATATT
1 TATATTATATATTATATTTAAAATATT
* *
1159549 AATAATT-TATATTATATATTTTAAAATATG
1 TAT-ATTATATA-T-TATA-TTTAAAATATT
1159579 TAT-TTATAT
1 TATATTATAT
1159588 TACATCATAA
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
25 26 0.37
26 13 0.19
27 12 0.17
28 5 0.07
29 3 0.04
30 11 0.16
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (27 bp):
TATATTATATATTATATTTAAAATATT
Found at i:1159531 original size:46 final size:49
Alignment explanation
Indices: 1159471--1159561 Score: 134
Period size: 46 Copynumber: 1.9 Consensus size: 49
1159461 ATAGTAATTT
** *
1159471 ATATATTTATATTATATTTATTTTATTATATT-ATAA-TTATATTTAAA
1 ATATATTTATATTATATAAATTTTAATATATTAATAATTTATATTTAAA
1159518 ATAT-TTTATATTATATAAATTTTAATATATTAATAATTTATATT
1 ATATATTTATATTATATAAATTTTAATATATTAATAATTTATATT
1159562 ATATATTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
46 24 0.62
47 8 0.21
48 7 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (49 bp):
ATATATTTATATTATATAAATTTTAATATATTAATAATTTATATTTAAA
Found at i:1159568 original size:46 final size:45
Alignment explanation
Indices: 1159467--1159571 Score: 133
Period size: 46 Copynumber: 2.3 Consensus size: 45
1159457 TAACATAGTA
** *
1159467 ATTTATATA-TTTATATTATATTTATTTTATTATATTATAATTAT
1 ATTTATATATTTTATATTATATAAATTTTAATATATTATAATTAT
*
1159511 ATTTAAAATATTTTATATTATATAAATTTTAATATATTAATAATT-T
1 ATTT-ATATATTTTATATTATATAAATTTTAATATATT-ATAATTAT
1159557 ATATTATATATTTTA
1 AT-TTATATATTTTA
1159572 AAATATGTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
44 4 0.08
45 4 0.08
46 36 0.69
47 8 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (45 bp):
ATTTATATATTTTATATTATATAAATTTTAATATATTATAATTAT
Found at i:1159572 original size:30 final size:30
Alignment explanation
Indices: 1159478--1159577 Score: 87
Period size: 32 Copynumber: 3.2 Consensus size: 30
1159468 TTTATATATT
* *
1159478 TATATT-AT-ATTTATTTTATTATATTATAA
1 TATATTAATAATTTATATTA-TATATTTTAA
*
1159507 TTATATTTAAAATATTTTATATTATATAAATTTTAA
1 -TATA-TT--AATAATTTATATTATAT--ATTTTAA
1159543 TATATTAATAATTTATATTATATATTTTAA
1 TATATTAATAATTTATATTATATATTTTAA
*
1159573 AATAT
1 TATAT
1159578 GTATTTATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
30 15 0.26
31 2 0.03
32 16 0.28
34 7 0.12
35 12 0.21
36 6 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TATATTAATAATTTATATTATATATTTTAA
Found at i:1159577 original size:32 final size:31
Alignment explanation
Indices: 1159517--1159577 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
1159507 TTATATTTAA
*
1159517 AATATTTTATATTATATAAATTTTAATATATT
1 AATAATTTATATTATAT-AATTTTAATATATT
*
1159549 AATAATTTATATTATAT-ATTTTAAAATAT
1 AATAATTTATATTATATAATTTTAATATAT
1159578 GTATTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 11 0.41
32 16 0.59
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
AATAATTTATATTATATAATTTTAATATATT
Found at i:1159583 original size:27 final size:26
Alignment explanation
Indices: 1159496--1159589 Score: 75
Period size: 27 Copynumber: 3.3 Consensus size: 26
1159486 ATTTATTTTA
1159496 TTATATTATAATTATATTTAAAATA-T-T
1 TTATATTAT-A-TAT-TTTAAAATATTAT
*
1159523 TTATATTATATAAATTTTAATATATTAATAAT
1 TTATATTATAT--ATTTTAA-A-A-T-ATTAT
1159555 TTATATTATATATTTTAAAATATGTAT
1 TTATATTATATATTTTAAAATAT-TAT
1159582 TTATATTA
1 TTATATTA
1159590 CATCATAATT
Statistics
Matches: 56, Mismatches: 2, Indels: 18
0.74 0.03 0.24
Matches are distributed among these distances:
25 1 0.02
26 8 0.14
27 23 0.41
28 2 0.04
29 2 0.04
30 8 0.14
32 12 0.21
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (26 bp):
TTATATTATATATTTTAAAATATTAT
Found at i:1160714 original size:2 final size:2
Alignment explanation
Indices: 1160709--1160745 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1160699 GAAATATTAC
1160709 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1160746 CACGAATTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1162126 original size:13 final size:14
Alignment explanation
Indices: 1162108--1162137 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1162098 ACACTTGGTA
1162108 TTTTT-CTTCTTTT
1 TTTTTCCTTCTTTT
1162121 TTTTTCCTTCTTTT
1 TTTTTCCTTCTTTT
1162135 TTT
1 TTT
1162138 CAACACTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTCCTTCTTTT
Found at i:1162472 original size:19 final size:19
Alignment explanation
Indices: 1162445--1162483 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1162435 CACTTAAATA
*
1162445 TTGGCTCATGACAAAACAT
1 TTGGCTCATGAAAAAACAT
* *
1162464 TTGGTTCATTAAAAAACAT
1 TTGGCTCATGAAAAAACAT
1162483 T
1 T
1162484 CTTCAACAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (19 bp):
TTGGCTCATGAAAAAACAT
Found at i:1163798 original size:21 final size:22
Alignment explanation
Indices: 1163750--1163791 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1163740 ATTTGTAGCA
*
1163750 AAATTTCAATTTTATTAATTTC
1 AAATTTCAATTTAATTAATTTC
*
1163772 AAATTTTAATTTAATTAATT
1 AAATTTCAATTTAATTAATT
1163792 CATATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (22 bp):
AAATTTCAATTTAATTAATTTC
Found at i:1166176 original size:3 final size:3
Alignment explanation
Indices: 1166168--1166198 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1166158 CTACAAAATG
1166168 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1166199 GAAGAAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1166479 original size:11 final size:11
Alignment explanation
Indices: 1166460--1166502 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
1166450 ACAAGAGCGG
*
1166460 TATATATAATA
1 TATAAATAATA
1166471 TATAAATAATA
1 TATAAATAATA
*
1166482 TATAATATTATAA
1 TATAA-ATAAT-A
1166495 TATAAATA
1 TATAAATA
1166503 TTAAAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 15 0.56
12 6 0.22
13 6 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TATAAATAATA
Found at i:1166484 original size:18 final size:20
Alignment explanation
Indices: 1166461--1166503 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
1166451 CAAGAGCGGT
1166461 ATATATAATA-TATAA-ATA
1 ATATATAATATTATAATATA
1166479 ATATATAATATTATAATATA
1 ATATATAATATTATAATATA
1166499 A-ATAT
1 ATATAT
1166504 TAAAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.43
19 9 0.39
20 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATATAATATTATAATATA
Found at i:1166511 original size:33 final size:32
Alignment explanation
Indices: 1166461--1166550 Score: 78
Period size: 33 Copynumber: 2.7 Consensus size: 32
1166451 CAAGAGCGGT
*
1166461 ATATATAATATATAAATAATATATAA-TA-TTATA
1 ATATA-AATATAAAAATAA-AT-TAATTATTTATA
1166494 ATATAAATATTAAAAATAAATTAATTATTTATA
1 ATATAAATA-TAAAAATAAATTAATTATTTATA
* *
1166527 TTATAAAATTTAATAAA-AAATTAA
1 ATAT-AAATATAA-AAATAAATTAA
1166551 ATTAAAAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
31 3 0.06
32 8 0.16
33 31 0.63
34 7 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
ATATAAATATAAAAATAAATTAATTATTTATA
Found at i:1166554 original size:25 final size:26
Alignment explanation
Indices: 1166526--1166620 Score: 75
Period size: 25 Copynumber: 3.5 Consensus size: 26
1166516 AATTATTTAT
*
1166526 ATTATAAAATTTAATAAAAAAT-TAA
1 ATTATAAAATTTAATAAAAAATAAAA
* * *
1166551 ATTAAAAAATATATTAAAAAATAAAA
1 ATTATAAAATTTAATAAAAAATAAAA
* * *
1166577 AATATAACAATTTAAAAATATAAATAAAT
1 ATTATAA-AATTTAATAA-A-AAATAAAA
*
1166606 TTTAATAAAATTTAA
1 ATT-ATAAAATTTAA
1166621 AATTTATATT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
25 19 0.36
26 7 0.13
27 7 0.13
28 1 0.02
29 15 0.28
30 4 0.08
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (26 bp):
ATTATAAAATTTAATAAAAAATAAAA
Found at i:1166573 original size:12 final size:12
Alignment explanation
Indices: 1166523--1166573 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
1166513 ATTAATTATT
*
1166523 TATATTATAAAA
1 TATATTAAAAAA
* *
1166535 TTTAATAAAAAA
1 TATATTAAAAAA
*
1166547 TTAAATTAAAAAA
1 -TATATTAAAAAA
1166560 TATATTAAAAAA
1 TATATTAAAAAA
1166572 TA
1 TA
1166574 AAAAATATAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
12 22 0.71
13 9 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TATATTAAAAAA
Found at i:1166804 original size:18 final size:16
Alignment explanation
Indices: 1166757--1166806 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 16
1166747 GTAGCGTCTG
1166757 TTAATAATTTTTATA-T
1 TTAA-AATTTTTATATT
1166773 TTAAAATATTTTATATT
1 TTAAAAT-TTTTATATT
1166790 TATATAAATTTTTATAT
1 T-TA-AAATTTTTATAT
1166807 GTATTATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.10
16 11 0.37
17 2 0.07
18 10 0.33
19 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTAAAATTTTTATATT
Found at i:1166814 original size:19 final size:19
Alignment explanation
Indices: 1166765--1166810 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1166755 TGTTAATAAT
1166765 TTTTATAT-T-TA-AAATA
1 TTTTATATGTATATAAATA
*
1166781 TTTTATATTTATATAAAT-
1 TTTTATATGTATATAAATA
1166799 TTTTATATGTAT
1 TTTTATATGTAT
1166811 TATATTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 8 0.31
17 1 0.04
18 13 0.50
19 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTATATGTATATAAATA
Found at i:1166839 original size:27 final size:27
Alignment explanation
Indices: 1166778--1166835 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
1166768 TATATTTAAA
*
1166778 ATATTTTATATTTATATAAATTTTTAT
1 ATATATTATATTTATATAAATTTTTAT
* *
1166805 ATGTATTATA-TTATA-AAATTTTTAC
1 ATATATTATATTTATATAAATTTTTAT
1166830 ATATAT
1 ATATAT
1166836 ATTAATGTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 14 0.52
26 5 0.19
27 8 0.30
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (27 bp):
ATATATTATATTTATATAAATTTTTAT
Found at i:1170997 original size:228 final size:225
Alignment explanation
Indices: 1170619--1171917 Score: 1101
Period size: 228 Copynumber: 5.7 Consensus size: 225
1170609 TAGAGTTCGA
* * * * *
1170619 CCATCTTCTAA-CTGCTTCCCAGCAAAGATCAACCTCTGCTGGTCTGGAGGAATCCCCTCCTTGT
1 CCATCTTC-AAGCTGTTTCCCAGCAAAAATCAACCTCTGCTGGTCAGGAGGGATACCCTCCTTGT
* * * * * * * * *
1170683 CCTGAATCTTTGCTTTCACATTGTCAATTGTGTCTGAGCTCTCAACCTCCAGGGTAATGGTTTTC
65 CCTGGATCTTGGCCTTAACATTATCAATTGTATCAGAGCTCTCCACCTCCAAGGTAATGGTTTT-
* * * * * * * * *
1170748 CCAGTTAAGGTCTTGACAAATATCTGCATCCCTCCTCTAAGGCGCAAAACCAAATGAAGGGTTGA
129 CCAG-TAAAGTTTTCACAAATATCTGCATCCCACCACTAAGACG-AACACCAAGTGGAGGGTTGA
* *
1170813 CTCCTTTTGGATGCTATAGTCTGCAAGCGTCCTC
192 CTCCTTTTGGATGTTATAGTCTGCAAGGGTCCTC
* * * * *
1170847 CCATCCTCGAGCTGCTTT-CCGGCAAAAATCAACCTCTGCTGGTCAGGGGGGATACCCTCCTTAT
1 CCATCTTCAAGCTG-TTTCCCAGCAAAAATCAACCTCTGCTGGTCAGGAGGGATACCCTCCTTGT
* * *
1170911 CTTGGATCTTGGCCTTAACATTATCAATTGTGTCAGAGCTCTCCACCTCCAAAGTAATGGTTTTA
65 CCTGGATCTTGGCCTTAACATTATCAATTGTATCAGAGCTCTCCACCTCCAAGGTAATGGTTTT-
* * *
1170976 CCAGTCAAAGTTTTCACAAATATCTGCATTCCACCACGAAGACGCAGCACCAAGTGGAGGGTTGA
129 CCAGT-AAAGTTTTCACAAATATCTGCATCCCACCACTAAGACG-AACACCAAGTGGAGGGTTGA
* * *
1171041 CT-CTTTCTGGATATTATAATCTGCAAGTGTCCTC
192 CTCCTTT-TGGATGTTATAGTCTGCAAGGGTCCTC
* * * * * * * *
1171075 CCATCTTCTAGCTGTTTGCCAGCAAAAATCAACCTTTGTTGATCAGGTGGAATACCTTCCTTGTC
1 CCATCTTCAAGCTGTTTCCCAGCAAAAATCAACCTCTGCTGGTCAGGAGGGATACCCTCCTTGTC
* * * * * * * *
1171140 CTGGATCTTGGCTTTTACGTTGTCAATTGTATCAGAACTCTCAACTTCCAAGGTAATAGTCTTTC
66 CTGGATCTTGGCCTTAACATTATCAATTGTATCAGAGCTCTCCACCTCCAAGGTAATGGT-TTTC
* * * * * * *
1171205 CTGTGAGAGTCTTCACAAAAATTTGCATACCACCACGT-AGACGTAACACCAAATGGAGGGTTGA
130 CAGT-AAAGTTTTCACAAATATCTGCATCCCACCAC-TAAGACG-AACACCAAGTGGAGGGTTGA
* * * *
1171269 CTCCTTCTGAATGTTATAGTCTGCAAGGGTTCTA
192 CTCCTTTTGGATGTTATAGTCTGCAAGGGTCCTC
* * *
1171303 CCATCTTCAAGCTGTTTCCCAGCAAAAATTAACCTCTGCTGGTCTGGTGGGATACCCTCCTTGTC
1 CCATCTTCAAGCTGTTTCCCAGCAAAAATCAACCTCTGCTGGTCAGGAGGGATACCCTCCTTGTC
* * * * * * * * *
1171368 CTGAATTTTGGACTTAATATTATCGATCGTATCAGAACTCTCCACCTCCAAAGTGATGGTTTTTC
66 CTGGATCTTGGCCTTAACATTATCAATTGTATCAGAGCTCTCCACCTCCAAGGTAATGG-TTTTC
** * * * * * * *
1171433 CAGTGAGGGTTTTAACAAAGATCTGCATGCCACCCCTCAGACGAAGGA-CAAGGTGGAGGGTAGA
130 CAGT-AAAGTTTTCACAAATATCTGCATCCCACCACTAAGACGAA-CACCAA-GTGGAGGGTTGA
* * * * **
1171497 CT-CTTTCTGGATGTTGTAATCAGCAAGGGTGCGG
192 CTCCTTT-TGGATGTTATAGTCTGCAAGGGTCCTC
* * * * *
1171531 CCATCTTCGAGTTGTTTACCAGCAAAGAT-AAGCCTCTGCTGGTCTGGAGGGAT-CCCTTCCTTG
1 CCATCTTCAAGCTGTTTCCCAGCAAAAATCAA-CCTCTGCTGGTCAGGAGGGATACCC-TCCTTG
* * * * * *
1171594 TCTTGGATCTTGGCCTTGACATTATCAATTGTGTCGGAGCTTTCCACCT-CAAGGGTTATGGTCT
64 TCCTGGATCTTGGCCTTAACATTATCAATTGTATCAGAGCTCTCCACCTCCAA-GGTAATGGT-T
* * * * * * * *
1171658 TTCCAGTAAGGGTTTTCACAAATATCTGCATGCCACCCCTGAGACGAAGGACTAGGTGGAGGGTG
127 TTCCAGTAA-AGTTTTCACAAATATCTGCATCCCACCACTAAGACGAA-CACCAAGTGGAGGGTT
* * * * **
1171723 GACTCCTTTTGGATGTTGTAGTCAGCAAGTGTTCGG
190 GACTCCTTTTGGATGTTATAGTCTGCAAGGGTCCTC
* * * *
1171759 CCATCCTCAAGCTGTTTCCCAGCAAAGAT-AAGCCTCTGTTGGTCAGGAGGGAT-CCCTTCTTTG
1 CCATCTTCAAGCTGTTTCCCAGCAAAAATCAA-CCTCTGCTGGTCAGGAGGGATACCC-TCCTTG
* * *
1171822 TCTTGGATCTTGGCCTTCACATTATCAATTGTATCAGAGCTCTCCACCT-CAAGGGTAATAGTCT
64 TCCTGGATCTTGGCCTTAACATTATCAATTGTATCAGAGCTCTCCACCTCCAA-GGTAATGGT-T
* * *
1171886 TGCCAGTAAGAGTTTTGACAAAGATCTGCATC
127 TTCCAGTAA-AGTTTTCACAAATATCTGCATC
1171918 TGCTGTCAAC
Statistics
Matches: 885, Mismatches: 166, Indels: 40
0.81 0.15 0.04
Matches are distributed among these distances:
227 28 0.03
228 843 0.95
229 14 0.02
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (225 bp):
CCATCTTCAAGCTGTTTCCCAGCAAAAATCAACCTCTGCTGGTCAGGAGGGATACCCTCCTTGTC
CTGGATCTTGGCCTTAACATTATCAATTGTATCAGAGCTCTCCACCTCCAAGGTAATGGTTTTCC
AGTAAAGTTTTCACAAATATCTGCATCCCACCACTAAGACGAACACCAAGTGGAGGGTTGACTCC
TTTTGGATGTTATAGTCTGCAAGGGTCCTC
Found at i:1171417 original size:456 final size:453
Alignment explanation
Indices: 1170550--1171916 Score: 1395
Period size: 456 Copynumber: 3.0 Consensus size: 453
1170540 AAATTAGAAA
* * * * * * * * * * *
1170550 CCACCACGGAGGCGAAGGACAAGATGGAGAGTGGACTCCTTCTGGATATTGTAGTCAGCTAGAGT
1 CCACCACGAAGACGAAGCACAAGGTGGAGGGTAGACTCTTTCTGGATATTATAATCAGCAAGGGT
* * * * * *
1170615 TCGACCATCTTCTAACTGCTTCCCAGCAAAGATCAACCTCTGCTGGTCTGGAGGAATCCCCTCCT
66 CCGCCCATCTTCTAGCTGTTTACCAGCAAAGATCAACCTCTGCTGGTCTGGAGGAATCCCTTCCT
* * * *
1170680 TGTCCTGAATCTTTGCTTTCACATTGTCAATTGTGTCTGAGCTCTCAACCTCCAGGGTAATGGT-
131 TGTCCTGGATCTTGGCTTTCACATTGTCAATTGTGTCAGAGCTCTCAACCTCCAAGGTAATGGTC
* * * * *
1170744 TTTCCCAGTTAAG-GTCTTGACAAATATCTGCATCCCTCCTCTAAGGCGCAAAACCAAATGAAGG
196 TTT-CCAG-TAAGAGTCTTCACAAATATCTGCATACCACC-CTAAGACG-AAAACCAAATGGAGG
* * * * *
1170808 GTTGACTCCTTTTGGATGCTATAGTCTGCAAGCGTCCTCCCATCCTCGAGCTGCTTT-CCGGCAA
257 GTTGACTCCTTTTGGATGTTATAGTCTGCAAGCGTTCTACCATCCTCAAGCTG-TTTCCCAGCAA
* * *
1170872 AAATCAACCTCTGCTGGTCAGGGGGGATACCCTCCTTATCTTGGATCTTGGCCTTAACATTATCA
321 AAATTAACCTCTGCTGGTCAGGAGGGATACCCTCCTTGTCTTGGATCTTGGCCTTAACATTATCA
* * *
1170937 ATTGTGTCAGAGCTCTCCACCTCCAAAGTAATGGTTTTACCAGTCAAAGTTTTCACAAATATCTG
386 ATTGTATCAGAGCTCTCCACCTCCAAAGTAATGGTTTTACCAGT-AAAGTTTTAACAAAGATCTG
*
1171002 CATT
450 CATG
* * * *
1171006 CCACCACGAAGACGCAGCACCAA-GTGGAGGGTTGACTCTTTCTGGATATTATAATCTGCAAGTG
1 CCACCACGAAGACGAAGCA-CAAGGTGGAGGGTAGACTCTTTCTGGATATTATAATCAGCAAGGG
* * * * * * * * *
1171070 TCCTCCCATCTTCTAGCTGTTTGCCAGCAAAAATCAACCTTTGTTGATCAGGTGGAATACCTTCC
65 TCCGCCCATCTTCTAGCTGTTTACCAGCAAAGATCAACCTCTGCTGGTCTGGAGGAATCCCTTCC
* * * * * *
1171135 TTGTCCTGGATCTTGGCTTTTACGTTGTCAATTGTATCAGAACTCTCAACTTCCAAGGTAATAGT
130 TTGTCCTGGATCTTGGCTTTCACATTGTCAATTGTGTCAGAGCTCTCAACCTCCAAGGTAATGGT
* * * * *
1171200 CTTTCCTGTGAGAGTCTTCACAAAAATTTGCATACCACCACGT-AGACGTAACACCAAATGGAGG
195 CTTTCCAGTAAGAGTCTTCACAAATATCTGCATACCACC-C-TAAGACG-AAAACCAAATGGAGG
* * * *
1171264 GTTGACTCCTTCTGAATGTTATAGTCTGCAAGGGTTCTACCATCTTCAAGCTGTTTCCCAGCAAA
257 GTTGACTCCTTTTGGATGTTATAGTCTGCAAGCGTTCTACCATCCTCAAGCTGTTTCCCAGCAAA
* * * * * * * *
1171329 AATTAACCTCTGCTGGTCTGGTGGGATACCCTCCTTGTCCTGAATTTTGGACTTAATATTATCGA
322 AATTAACCTCTGCTGGTCAGGAGGGATACCCTCCTTGTCTTGGATCTTGGCCTTAACATTATCAA
* * * * **
1171394 TCGTATCAGAACTCTCCACCTCCAAAGTGATGGTTTTTCCAGTGAGGGTTTTAACAAAGATCTGC
387 TTGTATCAGAGCTCTCCACCTCCAAAGTAATGGTTTTACCAGT-AAAGTTTTAACAAAGATCTGC
1171459 ATG
451 ATG
* ** * * *
1171462 CCACCCCTCAGACGAAGGACAAGGTGGAGGGTAGACTCTTTCTGGATGTTGTAATCAGCAAGGGT
1 CCACCACGAAGACGAAGCACAAGGTGGAGGGTAGACTCTTTCTGGATATTATAATCAGCAAGGGT
* * * * *
1171527 GCGGCCATCTTCGAGTTGTTTACCAGCAAAGAT-AAGCCTCTGCTGGTCTGGAGGGATCCCTTCC
66 CCGCCCATCTTCTAGCTGTTTACCAGCAAAGATCAA-CCTCTGCTGGTCTGGAGGAATCCCTTCC
* * * * * * * *
1171591 TTGTCTTGGATCTTGGCCTTGACATTATCAATTGTGTCGGAGCTTTCCACCT-CAAGGGTTATGG
130 TTGTCCTGGATCTTGGCTTTCACATTGTCAATTGTGTCAGAGCTCTCAACCTCCAA-GGTAATGG
* * * * * * **
1171655 TCTTTCCAGTAAGGGTTTTCACAAATATCTGCATGCCACCCCTGAGACGAAGGACTAGGTGGAGG
194 TCTTTCCAGTAAGAGTCTTCACAAATATCTGCATACCA-CCCTAAGACGAA-AACCAAATGGAGG
* * * * **
1171720 GTGGACTCCTTTTGGATGTTGTAGTCAGCAAGTGTTCGGCCATCCTCAAGCTGTTTCCCAGCAAA
257 GTTGACTCCTTTTGGATGTTATAGTCTGCAAGCGTTCTACCATCCTCAAGCTGTTTCCCAGCAAA
* * * *
1171785 GA-TAAGCCTCTGTTGGTCAGGAGGGAT-CCCTTCTTTGTCTTGGATCTTGGCCTTCACATTATC
322 AATTAA-CCTCTGCTGGTCAGGAGGGATACCC-TCCTTGTCTTGGATCTTGGCCTTAACATTATC
* * * * *
1171848 AATTGTATCAGAGCTCTCCACCT-CAAGGGTAATAGTCTTGCCAGTAAGAGTTTTGACAAAGATC
385 AATTGTATCAGAGCTCTCCACCTCCAA-AGTAATGGTTTTACCAGTAA-AGTTTTAACAAAGATC
1171912 TGCAT
448 TGCAT
1171917 CTGCTGTCAA
Statistics
Matches: 738, Mismatches: 158, Indels: 30
0.80 0.17 0.03
Matches are distributed among these distances:
455 27 0.04
456 702 0.95
457 9 0.01
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (453 bp):
CCACCACGAAGACGAAGCACAAGGTGGAGGGTAGACTCTTTCTGGATATTATAATCAGCAAGGGT
CCGCCCATCTTCTAGCTGTTTACCAGCAAAGATCAACCTCTGCTGGTCTGGAGGAATCCCTTCCT
TGTCCTGGATCTTGGCTTTCACATTGTCAATTGTGTCAGAGCTCTCAACCTCCAAGGTAATGGTC
TTTCCAGTAAGAGTCTTCACAAATATCTGCATACCACCCTAAGACGAAAACCAAATGGAGGGTTG
ACTCCTTTTGGATGTTATAGTCTGCAAGCGTTCTACCATCCTCAAGCTGTTTCCCAGCAAAAATT
AACCTCTGCTGGTCAGGAGGGATACCCTCCTTGTCTTGGATCTTGGCCTTAACATTATCAATTGT
ATCAGAGCTCTCCACCTCCAAAGTAATGGTTTTACCAGTAAAGTTTTAACAAAGATCTGCATG
Found at i:1173006 original size:20 final size:21
Alignment explanation
Indices: 1172981--1173028 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1172971 ATTTTTAAAA
* *
1172981 ATTTATTT-ATCTGAAATAAT
1 ATTTATTTAATATAAAATAAT
*
1173001 ATTTATTTAATATAAAATATT
1 ATTTATTTAATATAAAATAAT
1173022 ATTTATT
1 ATTTATT
1173029 ATACCTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
ATTTATTTAATATAAAATAAT
Found at i:1173025 original size:17 final size:18
Alignment explanation
Indices: 1172998--1173031 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1172988 TATCTGAAAT
1172998 AATATTTATTTAATATAA
1 AATATTTATTTAATATAA
*
1173016 AATA-TTATTTATTATA
1 AATATTTATTTAATATA
1173032 CCTAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATATTTATTTAATATAA
Found at i:1174357 original size:30 final size:30
Alignment explanation
Indices: 1174323--1174380 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1174313 GCCTTAACCA
*
1174323 TAAAGTAGTACAAAGAAAGTTTTAAGAAAT
1 TAAAGTAGAACAAAGAAAGTTTTAAGAAAT
* *
1174353 TAAAGTAGAACTAAGGAAGTTTTAAGAA
1 TAAAGTAGAACAAAGAAAGTTTTAAGAA
1174381 GTTATTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.52, C:0.03, G:0.19, T:0.26
Consensus pattern (30 bp):
TAAAGTAGAACAAAGAAAGTTTTAAGAAAT
Found at i:1174867 original size:228 final size:227
Alignment explanation
Indices: 1174492--1175570 Score: 1142
Period size: 228 Copynumber: 4.7 Consensus size: 227
1174482 CAAAGTTGAT
* * * * ** * * *
1174492 TCCTTCTGAATGTTGTAGTCTGCCAGGGTCCTTCCATCTTCAAGTTGCTTCCCTGCAAAGATCAG
1 TCCTTTTGAATGTTGTAGTCAGCAAGGGTACGGCCATCCTCAAGTTGCTTACCAGCAAAGATCAG
* * * *
1174557 CCTCTGCTGGTCTGGGGGGATTCCTTCCTTATCCTGGATCTTGGCCTTAACATTGTCTATTGTGT
66 CCTCTGCTGGTCT-GGGGGATACCTTCCTTGTCCTGGATCTTGGCCTTAACATTGTCAATAGTGT
* * * * * * *
1174622 CCGAACTTTCAACTTCCAGGGTGATGGTCTTTCCTGTCAATGTCTTCACAAAAATTTGCATCCCA
130 CAGAACTCTCCACCTCCAGGGTGATGGTCTTTCCAGTCAAGGTCTTCACAAAAATTTGCATACCA
* * * *
1174687 CCACGAAGGCGAAGCACTAAGTGGAGGGTCGAC
195 CCACGAAGACGGAGCACCAAGTGGAGGGTGGAC
* * * ** * *
1174720 TCTTTTTGAATGTTGTAGTCTGCAAGGGTCCTCCCATCCTCAAGCTGCTTACCAGCAAAAATCAG
1 TCCTTTTGAATGTTGTAGTCAGCAAGGGTACGGCCATCCTCAAGTTGCTTACCAGCAAAGATCAG
* * * * *
1174785 CCTCTGCTGGTCTGGAGGGATACCTTCCTTGTCTTGAATTTTGGCCTTAACATTGTCGACAGTGT
66 CCTCTGCTGGTCTGG-GGGATACCTTCCTTGTCCTGGATCTTGGCCTTAACATTGTCAATAGTGT
* * * * * * *
1174850 CAGAGCTCTCGACTTCCAAGGTGATGGT-TTTGCCGGT-TAGCGTCTTCACAAAAATCTGCATAC
130 CAGAACTCTCCACCTCCAGGGTGATGGTCTTT-CCAGTCAAG-GTCTTCACAAAAATTTGCATAC
*
1174913 CACCACGAAGACGGAGCACCAAGTGGAGGGTAGAC
193 CACCACGAAGACGGAGCACCAAGTGGAGGGTGGAC
* * *
1174948 TCCTTTTGGATGTTGTAGTCAGCTAGGGTACGACCATCCTCAAGTTGCTTACCAGCAAAGATCAG
1 TCCTTTTGAATGTTGTAGTCAGCAAGGGTACGGCCATCCTCAAGTTGCTTACCAGCAAAGATCAG
* * * * * *
1175013 CCTCTGCTGGTCTGGGGGAATACCCTCCTTATCCTGGATCTTTGCCTTAACATTGTCTATGGTAT
66 CCTCTGCTGGTCTGGGGG-ATACCTTCCTTGTCCTGGATCTTGGCCTTAACATTGTCAATAGTGT
* * ** * * * * *
1175078 CCGAACTCTCTACCTCCAATGTAATGGTCTTTCCAGTCAAGGTCTTGACAAAGATTTGCATTCCT
130 CAGAACTCTCCACCTCCAGGGTGATGGTCTTTCCAGTCAAGGTCTTCACAAAAATTTGCATACCA
* * *
1175143 CCTCGAAGGCGGAGCACCAAGTGGAGTGTGGAC
195 CCACGAAGACGGAGCACCAAGTGGAGGGTGGAC
* * * *
1175176 TCCTTTTGGATGTTGTAGTCAGCTAGGGTACGGCCATCTTCAAGTTGCTTACCAGCAAAGATCAA
1 TCCTTTTGAATGTTGTAGTCAGCAAGGGTACGGCCATCCTCAAGTTGCTTACCAGCAAAGATCAG
* * * * * *
1175241 CCTCTGCTGGTCTGGGGGAATGCCTTCCTTGTCCTGAATCTTAGCCTTCACATTATCAATAGTAT
66 CCTCTGCTGGTCTGGGGG-ATACCTTCCTTGTCCTGGATCTTGGCCTTAACATTGTCAATAGTGT
* * * *
1175306 CGGAACTCTCCACCTCCAGTGTTATGGTCTTTCCAGT-AAGGGTCTTCACAAAGATTTGCATACC
130 CAGAACTCTCCACCTCCAGGGTGATGGTCTTTCCAGTCAA-GGTCTTCACAAAAATTTGCATACC
* * * *
1175370 ACCCCTCAA-ACGGAGGACCAAGTGGAGCGTGGAC
194 ACCAC-GAAGACGGAGCACCAAGTGGAGGGTGGAC
* * * * *
1175404 TCCTTCTGAATATTGTAGTCAGCAAGGGTACGGCCATCCTCCAGTTGTTTACCAGCAAAGATAAG
1 TCCTTTTGAATGTTGTAGTCAGCAAGGGTACGGCCATCCTCAAGTTGCTTACCAGCAAAGATCAG
* * * * * * * *
1175469 CCTCTGTTGGTCAGGCGGGATTCCTTCTTTGTCTTGGATCTTGGCCTTAACGTTATCAATGGTGT
66 CCTCTGCTGGTCTGG-GGGATACCTTCCTTGTCCTGGATCTTGGCCTTAACATTGTCAATAGTGT
* * *
1175534 CAGAGCTTTCCACCTCAAGGGTGATGGT-TTTGCCAGT
130 CAGAACTCTCCACCTCCAGGGTGATGGTCTTT-CCAGT
1175571 GAGAGTCTTA
Statistics
Matches: 724, Mismatches: 117, Indels: 20
0.84 0.14 0.02
Matches are distributed among these distances:
227 14 0.02
228 700 0.97
229 10 0.01
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (227 bp):
TCCTTTTGAATGTTGTAGTCAGCAAGGGTACGGCCATCCTCAAGTTGCTTACCAGCAAAGATCAG
CCTCTGCTGGTCTGGGGGATACCTTCCTTGTCCTGGATCTTGGCCTTAACATTGTCAATAGTGTC
AGAACTCTCCACCTCCAGGGTGATGGTCTTTCCAGTCAAGGTCTTCACAAAAATTTGCATACCAC
CACGAAGACGGAGCACCAAGTGGAGGGTGGAC
Found at i:1175590 original size:456 final size:455
Alignment explanation
Indices: 1174492--1175595 Score: 1286
Period size: 456 Copynumber: 2.4 Consensus size: 455
1174482 CAAAGTTGAT
* * * ** * * *
1174492 TCCTTCTGAATGTTGTAGTCTGCCAGGGTCCTTCCATCTTCAAGTTGCTTCCCTGCAAAGATCAG
1 TCCTTCTGAATGTTGTAGTCAGCAAGGGTACGACCATCCTCAAGTTGCTTACCAGCAAAGATCAG
*
1174557 CCTCTGCTGGTCTGGGGGGATTCCTTCCTTATCCTGGATCTTGGCCTTAACATTGTCTATTGTGT
66 CCTCTGCTGGTCT-GGGGGATTCCTTCCTTATCCTGGATCTTGGCCTTAACATTGTCTATGGTGT
* * * * * *
1174622 CCGAACTTTCAACTTCCAGGGTGATGGTCTTTCCTGTCAATGTCTTCACAAAAATTTGCATCCCA
130 CCGAACTTTCAACCTCAAGGGTGATGGTCTTTCCAGTCAAGGTCTTAACAAAGATTTGCATCCCA
* * * * *
1174687 CCACGAAGGCGAAGCACTAAGTGGAGGGTCGACTCTTTTTGAATGTTGTAGTCTGCAAGGGTCCT
195 CCACGAAGGCGAAGCACCAAGTGGAGGGTCGACTCCTTTTGAATGTTGTAGTCAGCAAGGGTACG
*
1174752 CCCATCCTCAAGCTGCTTACCAGCAAAAATCAGCCTCTGCTGGTCTGGAGGGATACCTTCCTTGT
260 CCCATCCTCAAGCTGCTTACCAGCAAAAATCAACCTCTGCTGGTCTGGAGGGATACCTTCCTTGT
* * * * * * * * *
1174817 CTTGAATTTTGGCCTTAACATTGTCGACAGTGTCAGAGCTCTCGACTTCCAAGGTGATGGTTTTG
325 CCTGAATCTTAGCCTTAACATTATCAACAGTATCAGAACTCTCCACCTCCAAGGTGATGGTTTTG
* * * *
1174882 CCGGTTAGCGTCTTCACAAAAATCTGCATACCACCACGAAGACGGAGCACCAAGTGGAGGGTAGA
390 CCAGTAAGCGTCTTCACAAAAATCTGCATACCACCACCAAGACGGAGCACCAAGTGGAGCGTAGA
1174947 C
455 C
* * *
1174948 TCCTTTTGGATGTTGTAGTCAGCTAGGGTACGACCATCCTCAAGTTGCTTACCAGCAAAGATCAG
1 TCCTTCTGAATGTTGTAGTCAGCAAGGGTACGACCATCCTCAAGTTGCTTACCAGCAAAGATCAG
* * * *
1175013 CCTCTGCTGGTCTGGGGGAATACCCTCCTTATCCTGGATCTTTGCCTTAACATTGTCTATGGTAT
66 CCTCTGCTGGTCTGGGGG-ATTCCTTCCTTATCCTGGATCTTGGCCTTAACATTGTCTATGGTGT
* * * * * *
1175078 CCGAACTCTCTACCTCCAA-TGTAATGGTCTTTCCAGTCAAGGTCTTGACAAAGATTTGCATTCC
130 CCGAACTTTCAACCT-CAAGGGTGATGGTCTTTCCAGTCAAGGTCTTAACAAAGATTTGCATCCC
* * * * * * *
1175142 TCCTCGAAGGCGGAGCACCAAGTGGAGTGTGGACTCCTTTTGGATGTTGTAGTCAGCTAGGGTAC
194 ACCACGAAGGCGAAGCACCAAGTGGAGGGTCGACTCCTTTTGAATGTTGTAGTCAGCAAGGGTAC
* * * * *
1175207 GGCCATCTTCAAGTTGCTTACCAGCAAAGATCAACCTCTGCTGGTCTGG-GGGAATGCCTTCCTT
259 GCCCATCCTCAAGCTGCTTACCAGCAAAAATCAACCTCTGCTGGTCTGGAGGG-ATACCTTCCTT
* * * *
1175271 GTCCTGAATCTTAGCCTTCACATTATCAATAGTATCGGAACTCTCCACCTCC-AGTGTTATGGTC
323 GTCCTGAATCTTAGCCTTAACATTATCAACAGTATCAGAACTCTCCACCTCCAAG-GTGATGGT-
* * * * *
1175335 TTT-CCAGTAAGGGTCTTCACAAAGATTTGCATACCACCCCTCAA-ACGGAGGACCAAGTGGAGC
386 TTTGCCAGTAAGCGTCTTCACAAAAATCTGCATACCACCAC-CAAGACGGAGCACCAAGTGGAGC
*
1175398 GTGGAC
450 GTAGAC
* * * * *
1175404 TCCTTCTGAATATTGTAGTCAGCAAGGGTACGGCCATCCTCCAGTTGTTTACCAGCAAAGATAAG
1 TCCTTCTGAATGTTGTAGTCAGCAAGGGTACGACCATCCTCAAGTTGCTTACCAGCAAAGATCAG
* * * * * * * *
1175469 CCTCTGTTGGTCAGGCGGGATTCCTTCTTTGTCTTGGATCTTGGCCTTAACGTTATCAATGGTGT
66 CCTCTGCTGGTCTGG-GGGATTCCTTCCTTATCCTGGATCTTGGCCTTAACATTGTCTATGGTGT
* * * * *
1175534 CAGAGCTTTCCACCTCAAGGGTGATGGT-TTTGCCAGT-GAGAGTCTTAACGAAGATTTGCATC
130 CCGAACTTTCAACCTCAAGGGTGATGGTCTTT-CCAGTCAAG-GTCTTAACAAAGATTTGCATC
1175596 TATTTTTGAA
Statistics
Matches: 541, Mismatches: 97, Indels: 20
0.82 0.15 0.03
Matches are distributed among these distances:
455 18 0.03
456 513 0.95
457 10 0.02
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (455 bp):
TCCTTCTGAATGTTGTAGTCAGCAAGGGTACGACCATCCTCAAGTTGCTTACCAGCAAAGATCAG
CCTCTGCTGGTCTGGGGGATTCCTTCCTTATCCTGGATCTTGGCCTTAACATTGTCTATGGTGTC
CGAACTTTCAACCTCAAGGGTGATGGTCTTTCCAGTCAAGGTCTTAACAAAGATTTGCATCCCAC
CACGAAGGCGAAGCACCAAGTGGAGGGTCGACTCCTTTTGAATGTTGTAGTCAGCAAGGGTACGC
CCATCCTCAAGCTGCTTACCAGCAAAAATCAACCTCTGCTGGTCTGGAGGGATACCTTCCTTGTC
CTGAATCTTAGCCTTAACATTATCAACAGTATCAGAACTCTCCACCTCCAAGGTGATGGTTTTGC
CAGTAAGCGTCTTCACAAAAATCTGCATACCACCACCAAGACGGAGCACCAAGTGGAGCGTAGAC
Found at i:1176675 original size:19 final size:20
Alignment explanation
Indices: 1176637--1176677 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1176627 TTAATATTTT
1176637 TATTTAAAAATATAAAATTA
1 TATTTAAAAATATAAAATTA
* *
1176657 TATTTAAATAT-TTAAATTA
1 TATTTAAAAATATAAAATTA
1176676 TA
1 TA
1176678 AAATTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATTTAAAAATATAAAATTA
Found at i:1176708 original size:24 final size:24
Alignment explanation
Indices: 1176637--1176702 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 24
1176627 TTAATATTTT
*
1176637 TATTTAAAAATATAAAATTATATTTAAA
1 TATTT-AAATTATAAAA-T-TA-TTAAA
1176665 TATTTAAATTATAAAATTATTAAA
1 TATTTAAATTATAAAATTATTAAA
1176689 -ATTTATAATTATAA
1 TATTTA-AATTATAA
1176703 TTTTATAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
23 5 0.14
24 13 0.36
25 2 0.06
26 1 0.03
27 10 0.28
28 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TATTTAAATTATAAAATTATTAAA
Found at i:1176923 original size:18 final size:18
Alignment explanation
Indices: 1176870--1176923 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
1176860 AATAAATATT
**
1176870 AAAATTTTAAAAATTATA
1 AAAATTTTAAATTTTATA
* *
1176888 AAAATATATATTATTTTATA
1 AAAAT-TTTA-AATTTTATA
1176908 AAAATTTTAAATTTTA
1 AAAATTTTAAATTTTA
1176924 CTAATAATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
18 11 0.39
19 6 0.21
20 11 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAATTTTAAATTTTATA
Found at i:1177169 original size:16 final size:17
Alignment explanation
Indices: 1177141--1177174 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1177131 ATATGATATT
1177141 AATTAATAAATTTAAAA
1 AATTAATAAATTTAAAA
1177158 AATTAA-AAATTTAAAA
1 AATTAATAAATTTAAAA
1177174 A
1 A
1177175 GATTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATTAATAAATTTAAAA
Found at i:1177183 original size:16 final size:16
Alignment explanation
Indices: 1177141--1177183 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1177131 ATATGATATT
1177141 AATTAATAAATTTAAAA
1 AATT-ATAAATTTAAAA
*
1177158 AATTAAAAATTTAAAA
1 AATTATAAATTTAAAA
1177174 AGATT-TAAAT
1 A-ATTATAAAT
1177184 ATATATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
AATTATAAATTTAAAA
Found at i:1177440 original size:18 final size:18
Alignment explanation
Indices: 1177419--1177462 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1177409 AATTAAAAGA
1177419 TTTTAAAAAAATAGTGAT
1 TTTTAAAAAAATAGTGAT
* * * *
1177437 TTTTTAATACATAGTTAT
1 TTTTAAAAAAATAGTGAT
1177455 TTTTAAAA
1 TTTTAAAA
1177463 TTTTTAAATA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (18 bp):
TTTTAAAAAAATAGTGAT
Found at i:1180358 original size:2 final size:2
Alignment explanation
Indices: 1180351--1180384 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1180341 GGCCTCCTTC
1180351 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
1180385 GTTTTATATT
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):
AT
Found at i:1199716 original size:42 final size:42
Alignment explanation
Indices: 1199657--1199737 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
1199647 TCGAACTCAG
*
1199657 TTGAAAACTAAGTTTAAATATTATATTTCAAATGTAAATAAA
1 TTGAAAACCAAGTTTAAATATTATATTTCAAATGTAAATAAA
*
1199699 TTGAAAACCAAGTTTAAATATTATATTTTAAATGTAAAT
1 TTGAAAACCAAGTTTAAATATTATATTTCAAATGTAAAT
1199738 TAAGAGTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (42 bp):
TTGAAAACCAAGTTTAAATATTATATTTCAAATGTAAATAAA
Found at i:1199930 original size:17 final size:16
Alignment explanation
Indices: 1199881--1199931 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
1199871 TATATAATAT
1199881 AAATTATT-AACGTATA
1 AAATTATTAAAC-TATA
* *
1199897 AAATTAATAAAAATATA
1 AAATT-ATTAAACTATA
1199914 AAATATATTAAACTATA
1 AAAT-TATTAAACTATA
1199931 A
1 A
1199932 TGATAATACA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
16 5 0.18
17 20 0.71
18 3 0.11
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (16 bp):
AAATTATTAAACTATA
Found at i:1204660 original size:2 final size:2
Alignment explanation
Indices: 1204653--1204679 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1204643 CAATAAAATC
1204653 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 A
1204680 AAACAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1206428 original size:31 final size:30
Alignment explanation
Indices: 1206393--1206460 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
1206383 AAAAAGTATG
1206393 ATTTAAT-AATAAAATGCATTTAATATAATAA
1 ATTTAATAAATAAAATGC-TTTAAT-TAATAA
* * * *
1206424 ATTTATTAAATAAAATTCTTTAATTATTTA
1 ATTTAATAAATAAAATGCTTTAATTAATAA
1206454 ATTTAAT
1 ATTTAAT
1206461 GATACAATCA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 10 0.32
31 12 0.39
32 9 0.29
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (30 bp):
ATTTAATAAATAAAATGCTTTAATTAATAA
Found at i:1207488 original size:18 final size:20
Alignment explanation
Indices: 1207454--1207491 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
1207444 ACTGCATTAG
1207454 ATAACTATTTATTAATTAAA
1 ATAACTATTTATTAATTAAA
1207474 ATAA-TATTT-TTAATTAAA
1 ATAACTATTTATTAATTAAA
1207492 TTTAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 5 0.28
20 4 0.22
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAACTATTTATTAATTAAA
Found at i:1208082 original size:16 final size:15
Alignment explanation
Indices: 1208061--1208108 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
1208051 TCTTCTTAAA
1208061 TAATATTTATATAATT
1 TAATATTTATAT-ATT
1208077 TAATATTTATATATT
1 TAATATTTATATATT
*
1208092 T-ATATTATATTTATT
1 TAATATT-TATATATT
1208107 TA
1 TA
1208109 TTTTGTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 5 0.17
15 12 0.41
16 12 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TAATATTTATATATT
Found at i:1208092 original size:8 final size:8
Alignment explanation
Indices: 1208063--1208109 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
1208053 TTCTTAAATA
1208063 ATATTTAT
1 ATATTTAT
1208071 ATAATTTA-
1 AT-ATTTAT
1208079 ATATTTAT
1 ATATTTAT
1208087 ATATTTAT
1 ATATTTAT
*
1208095 AT-TATAT
1 ATATTTAT
*
1208102 TTATTTAT
1 ATATTTAT
1208110 TTTGTTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 10 0.30
8 18 0.55
9 5 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATATTTAT
Found at i:1211409 original size:20 final size:19
Alignment explanation
Indices: 1211374--1211422 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1211364 AACTAATTGT
* *
1211374 ATATTTTATTAATTATTTA
1 ATATTTTAATACTTATTTA
*
1211393 TTATATTTAATACTTATTTA
1 ATAT-TTTAATACTTATTTA
1211413 ATATTTTAAT
1 ATATTTTAAT
1211423 TTTTTTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATTTTAATACTTATTTA
Found at i:1220472 original size:17 final size:17
Alignment explanation
Indices: 1220450--1220486 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1220440 TGTTAGACTA
1220450 TTTAATTGTCTTT-TTTT
1 TTTAATT-TCTTTGTTTT
1220467 TTTAATTTCTTTGTTTT
1 TTTAATTTCTTTGTTTT
1220484 TTT
1 TTT
1220487 TTAATTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.11, C:0.05, G:0.05, T:0.78
Consensus pattern (17 bp):
TTTAATTTCTTTGTTTT
Found at i:1220483 original size:16 final size:17
Alignment explanation
Indices: 1220450--1220485 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1220440 TGTTAGACTA
*
1220450 TTTAATTGTCTTTTTTT
1 TTTAATTGTCTTTGTTT
1220467 TTTAATT-TCTTTGTTT
1 TTTAATTGTCTTTGTTT
1220483 TTT
1 TTT
1220486 TTTAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.78
Consensus pattern (17 bp):
TTTAATTGTCTTTGTTT
Found at i:1220502 original size:19 final size:19
Alignment explanation
Indices: 1220461--1220508 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1220451 TTAATTGTCT
*** *
1220461 TTTTTTTTTAATTTCTTTG
1 TTTTTTTTTAATTTAAGTA
1220480 TTTTTTTTTAATTTAAGTA
1 TTTTTTTTTAATTTAAGTA
1220499 TTTTTATTTT
1 TTTTT-TTTT
1220509 GCTATTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (19 bp):
TTTTTTTTTAATTTAAGTA
Found at i:1222462 original size:24 final size:23
Alignment explanation
Indices: 1222435--1222487 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
1222425 TTTAAATTTA
**
1222435 AATAAAAATATTTTTTTATTTTTT
1 AATAAAAATATGATTTTA-TTTTT
**
1222459 AATACTAATATGATTTTATTTTT
1 AATAAAAATATGATTTTATTTTT
1222482 AATAAA
1 AATAAA
1222488 TTATTATAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
AATAAAAATATGATTTTATTTTT
Found at i:1222800 original size:40 final size:37
Alignment explanation
Indices: 1222728--1222802 Score: 89
Period size: 40 Copynumber: 1.9 Consensus size: 37
1222718 AAATTAATAA
*
1222728 TTTATATTATATAAATTTTGATATGCTCTCATATTCGT
1 TTTATATTATATAAATTTT-ATATGCACTCATATTCGT
1222766 TTTATATTTATATTAAATTTT-TATGTCACATCATATT
1 TTTATA-TTATA-TAAATTTTATATG-CAC-TCATATT
1222803 ATATATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
38 10 0.31
39 7 0.22
40 15 0.47
ACGTcount: A:0.31, C:0.09, G:0.05, T:0.55
Consensus pattern (37 bp):
TTTATATTATATAAATTTTATATGCACTCATATTCGT
Found at i:1223833 original size:2 final size:2
Alignment explanation
Indices: 1223808--1223858 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
1223798 TAATGGTTAC
* * *
1223808 AT AT AT AG AT AT AG AT AT AG 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
1223850 AT AT A- AT AT
1 AT AT AT AT AT
1223859 TTGAATTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1224053 original size:20 final size:19
Alignment explanation
Indices: 1224002--1224053 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
1223992 ATATTTTATT
1224002 TATA-TTTAATTATAAAAAA
1 TATATTTTAATT-TAAAAAA
* *
1224021 TATATATTGATTTAAAAATA
1 TATATTTTAATTTAAAAA-A
*
1224041 TATTTTTTAATTT
1 TATATTTTAATTT
1224054 TTTAAATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TATATTTTAATTTAAAAAA
Found at i:1224802 original size:3 final size:3
Alignment explanation
Indices: 1224796--1224828 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1224786 AACAACAGCA
*
1224796 ATT ATT ATT ATT ATT TTT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1224829 GCTTTCATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:1225012 original size:2 final size:2
Alignment explanation
Indices: 1225005--1225036 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1224995 AAAGAGCTAA
1225005 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
1225037 GATTTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1226860 original size:20 final size:18
Alignment explanation
Indices: 1226818--1226861 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
1226808 TAATAAATAA
1226818 ATAA-TAATAATATTTTT
1 ATAATTAATAATATTTTT
1226835 AT-ATTAATATATATCTTTT
1 ATAATTAATA-ATAT-TTTT
1226854 ATAATTAA
1 ATAATTAA
1226862 ATTTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 7 0.30
18 4 0.17
19 6 0.26
20 5 0.22
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
ATAATTAATAATATTTTT
Found at i:1227531 original size:2 final size:2
Alignment explanation
Indices: 1227524--1227549 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1227514 TATGGGAGTG
1227524 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
1227550 CATTTATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1228396 original size:3 final size:3
Alignment explanation
Indices: 1228388--1228430 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
1228378 GGTTCCAAGA
* *
1228388 TGG TGG TGG TGG TGG TGG TGG TGG CGG TGG CGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1228431 TCAACTTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.05, G:0.65, T:0.30
Consensus pattern (3 bp):
TGG
Found at i:1229011 original size:2 final size:2
Alignment explanation
Indices: 1229004--1229034 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1228994 AAGTATGCGC
1229004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1229035 AAAAAGTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1231164 original size:84 final size:84
Alignment explanation
Indices: 1231014--1231179 Score: 217
Period size: 84 Copynumber: 2.0 Consensus size: 84
1231004 AATGAAGTTA
* * * *
1231014 TTTAATTAGTTAATTTTAATTGAACCCCAATCTCAAATTGATTTTGTTTATGTTTAACATTCTTA
1 TTTAATTAGTTAATTTTAATTGAACCCCAATCTCAAATTGATTTAGTTCACGTTTAACATACTTA
1231079 TTAATATAATTTTTTAAGT
66 TTAATATAATTTTTTAAGT
* * ** * * *
1231098 TTTAATTAGTTCATTTTGATTGAACCTTAATCTCCAATTGATTTAGTTCACG-TTAGGCATAGTT
1 TTTAATTAGTTAATTTTAATTGAACCCCAATCTCAAATTGATTTAGTTCACGTTTA-ACATACTT
1231162 ATTAATATAATTTTTTAA
65 ATTAATATAATTTTTTAA
1231180 ATATTAATGA
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
83 3 0.04
84 67 0.96
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.49
Consensus pattern (84 bp):
TTTAATTAGTTAATTTTAATTGAACCCCAATCTCAAATTGATTTAGTTCACGTTTAACATACTTA
TTAATATAATTTTTTAAGT
Found at i:1231256 original size:16 final size:17
Alignment explanation
Indices: 1231232--1231271 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1231222 AATTAAATCG
1231232 ATTTATA-TTAAATATT
1 ATTTATATTTAAATATT
*
1231248 ATTTTTATTTAAATATT
1 ATTTATATTTAAATATT
*
1231265 AATTATA
1 ATTTATA
1231272 AAATATAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTATATTTAAATATT
Found at i:1231282 original size:20 final size:19
Alignment explanation
Indices: 1231257--1231295 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
1231247 TATTTTTATT
1231257 TAAATATTAATTATAAAATA
1 TAAATATTAA-TATAAAATA
1231277 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
1231296 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATATTAATATAAAATA
Found at i:1231323 original size:43 final size:41
Alignment explanation
Indices: 1231272--1231356 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 41
1231262 ATTAATTATA
* *
1231272 AAATATAAATATTAATA-TAAAATAATATTTTAATAATATAAT
1 AAATATAAAT-TTAA-ACTAAAATAAAATTTTAAAAATATAAT
*
1231314 AAATAATAAATTTAAACTTAAAATAAAATTTTAAAAATTTAAT
1 AAAT-ATAAATTTAAAC-TAAAATAAAATTTTAAAAATATAAT
1231357 TCCCGAGGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
41 1 0.03
42 8 0.22
43 28 0.76
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (41 bp):
AAATATAAATTTAAACTAAAATAAAATTTTAAAAATATAAT
Found at i:1231555 original size:25 final size:25
Alignment explanation
Indices: 1231521--1231606 Score: 84
Period size: 25 Copynumber: 3.3 Consensus size: 25
1231511 TGTTTTGTTG
1231521 CAATAATTTATTCCTTTATTAATTA
1 CAATAATTTATTCCTTTATTAATTA
* *
1231546 CAATAGTTTATT-CTAAATATTAAAGTTA
1 CAATAATTTATTCCT--TTATT-AA-TTA
**
1231574 CAATAATTTACCCCTTTATTAATTA
1 CAATAATTTATTCCTTTATTAATTA
*
1231599 CAACAATT
1 CAATAATT
1231607 AAGTAAATCT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
24 2 0.04
25 21 0.43
26 6 0.12
27 6 0.12
28 12 0.24
29 2 0.04
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.44
Consensus pattern (25 bp):
CAATAATTTATTCCTTTATTAATTA
Found at i:1231859 original size:26 final size:24
Alignment explanation
Indices: 1231830--1231890 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 24
1231820 TTTTATTTTG
1231830 AATATATATTTAGATATAAATATAAA
1 AATATATATTTA-A-ATAAATATAAA
* *
1231856 AATATAATTTTTTAAATATATATAAA
1 AATAT-A-TATTTAAATAAATATAAA
1231882 AATA-ATATT
1 AATATATATT
1231891 CATGTTGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
23 3 0.10
24 1 0.03
26 19 0.63
27 2 0.07
28 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AATATATATTTAAATAAATATAAA
Found at i:1232851 original size:23 final size:24
Alignment explanation
Indices: 1232812--1232857 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
1232802 TATTTTTAAA
1232812 AATAAAATTATATTTTAT-AAAAT
1 AATAAAATTATATTTTATCAAAAT
1232835 AATAAAA-TATATATTTATCAAAA
1 AATAAAATTATAT-TTTATCAAAA
1232858 ATTTTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 12 0.57
24 4 0.19
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
AATAAAATTATATTTTATCAAAAT
Found at i:1233220 original size:17 final size:19
Alignment explanation
Indices: 1233200--1233242 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1233190 TTATTACTTT
1233200 AAATTAT-TAAAAAA-ATA
1 AAATTATATAAAAAATATA
1233217 AAATTATATAAAAAATTATA
1 AAATTATATAAAAAA-TATA
1233237 AAATTA
1 AAATTA
1233243 CGTCATGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.30
18 7 0.30
20 9 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATTATATAAAAAATATA
Found at i:1233437 original size:30 final size:30
Alignment explanation
Indices: 1233382--1233438 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1233372 AAATAAATTT
*
1233382 ATTAAAAATAAAATTTATATTAAATATGTA
1 ATTAAAAATAAAATTTATATAAAATATGTA
1233412 ATTAAATAATAATAA-TTA-ATAAAATAT
1 ATTAAA-AATAA-AATTTATATAAAATAT
1233439 AAAATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 14 0.58
31 8 0.33
32 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
ATTAAAAATAAAATTTATATAAAATATGTA
Found at i:1233600 original size:15 final size:15
Alignment explanation
Indices: 1233580--1233610 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1233570 CAATAAATGT
*
1233580 AATTTAAATTAATAA
1 AATTTAAATAAATAA
1233595 AATTTAAATAAATAA
1 AATTTAAATAAATAA
1233610 A
1 A
1233611 CTAAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATTTAAATAAATAA
Found at i:1240081 original size:22 final size:22
Alignment explanation
Indices: 1240043--1240106 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
1240033 TTTTCGATTA
*
1240043 AAATAATATTTT-TTTTAAATTT
1 AAATAAT-TTTTAATTTAAATTT
* * *
1240065 TATTAATTTTTAATTTATATTT
1 AAATAATTTTTAATTTAAATTT
* *
1240087 AAATAATTTTTGATATAAAT
1 AAATAATTTTTAATTTAAAT
1240107 AAATTTTTTA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
AAATAATTTTTAATTTAAATTT
Found at i:1241364 original size:27 final size:27
Alignment explanation
Indices: 1241334--1241405 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
1241324 CCACTATTTA
*
1241334 TATTTGTAAAAAATGGT-AGTTCTTTTG
1 TATTTGTAAAAAATAGTGA-TTCTTTTG
* * *
1241361 TATTTGTTAAAACTAGTGATTCTTTTT
1 TATTTGTAAAAAATAGTGATTCTTTTG
*
1241388 TGTTTGTAAAAAATAGTG
1 TATTTGTAAAAAATAGTG
1241406 GCTTGTTGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
27 36 0.97
28 1 0.03
ACGTcount: A:0.31, C:0.04, G:0.17, T:0.49
Consensus pattern (27 bp):
TATTTGTAAAAAATAGTGATTCTTTTG
Found at i:1244892 original size:27 final size:25
Alignment explanation
Indices: 1244856--1244930 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 25
1244846 TAAAAACTAC
*
1244856 CTTTTTTGTTTGTCAAAAATGGTGA
1 CTTTTTTGTTTGTCAAAAATGATGA
*
1244881 TTCTTTTTTGTTTGTAAAAAATGATGA
1 --CTTTTTTGTTTGTCAAAAATGATGA
* *
1244908 C-TTGTTGTTTGTCAAAATTGATG
1 CTTTTTTGTTTGTCAAAAATGATG
1244931 GCTAATTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
24 19 0.44
25 1 0.02
27 23 0.53
ACGTcount: A:0.25, C:0.07, G:0.19, T:0.49
Consensus pattern (25 bp):
CTTTTTTGTTTGTCAAAAATGATGA
Found at i:1248241 original size:17 final size:19
Alignment explanation
Indices: 1248200--1248241 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
1248190 TTTAAACTTA
1248200 TTTATAAAATATAAATATT
1 TTTATAAAATATAAATATT
**
1248219 AATATAAAA-AT-AATATT
1 TTTATAAAATATAAATATT
1248236 TTTATA
1 TTTATA
1248242 GTTTTTTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
17 10 0.53
18 2 0.11
19 7 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTATAAAATATAAATATT
Found at i:1248835 original size:16 final size:17
Alignment explanation
Indices: 1248807--1248842 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
1248797 TAAATTAATT
1248807 AATTTATTTAAAATAAA
1 AATTTATTTAAAATAAA
1248824 AATTTA-TTAAAATAAA
1 AATTTATTTAAAATAAA
1248840 AAT
1 AAT
1248843 AAAAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTTATTTAAAATAAA
Found at i:1248844 original size:22 final size:21
Alignment explanation
Indices: 1248815--1248869 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 21
1248805 TTAATTTATT
1248815 TAAAATAAAAATTTATTAAAA
1 TAAAATAAAAATTTATTAAAA
* *
1248836 TAAAAATAAAAAATTATTTAAA
1 T-AAAATAAAAATTTATTAAAA
1248858 TAAAATAAAAAT
1 TAAAATAAAAAT
1248870 ATATGAAGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAAATAAAAATTTATTAAAA
Found at i:1248956 original size:2 final size:2
Alignment explanation
Indices: 1248949--1248977 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1248939 ACTTCAAGTT
1248949 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1248978 TATTACAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1253434 original size:15 final size:16
Alignment explanation
Indices: 1253408--1253438 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1253398 TATAAATTAA
1253408 AATATATTTTTATATT
1 AATATATTTTTATATT
1253424 AATAT-TTTTTATATT
1 AATATATTTTTATATT
1253439 TTTATAATTA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
AATATATTTTTATATT
Found at i:1253436 original size:23 final size:23
Alignment explanation
Indices: 1253410--1253453 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1253400 TAAATTAAAA
1253410 TATATTTTTAT-ATTAATATTTTT
1 TATATTTTTATAATTAA-ATTTTT
1253433 TATATTTTTATAATTAAATTT
1 TATATTTTTATAATTAAATTT
1253454 AAATAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TATATTTTTATAATTAAATTTTT
Found at i:1253840 original size:20 final size:20
Alignment explanation
Indices: 1253817--1253857 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1253807 ATTTAAATGT
* *
1253817 TTATAATAATATTTAAAAAA
1 TTATAAAAAAATTTAAAAAA
*
1253837 TTATAAAAAAATTTTAAAAA
1 TTATAAAAAAATTTAAAAAA
1253857 T
1 T
1253858 AAAAATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TTATAAAAAAATTTAAAAAA
Found at i:1253902 original size:20 final size:20
Alignment explanation
Indices: 1253861--1253899 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1253851 TAAAAATAAA
1253861 AATTAAATAATATAATATTT
1 AATTAAATAATATAATATTT
1253881 AATTAAAATAA-AT-ATATTT
1 AATT-AAATAATATAATATTT
1253900 TAAATTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 6 0.33
21 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTAAATAATATAATATTT
Found at i:1253905 original size:21 final size:21
Alignment explanation
Indices: 1253860--1253905 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
1253850 TTAAAAATAA
1253860 AAATTAAATAATATAATATTT
1 AAATTAAATAATATAATATTT
1253881 -AATTAAAATAA-AT-ATATTTT
1 AAATT-AAATAATATAATA-TTT
1253901 AAATT
1 AAATT
1253906 TGATTAACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATTAAATAATATAATATTT
Found at i:1254510 original size:16 final size:17
Alignment explanation
Indices: 1254489--1254527 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1254479 TTTAATTTTT
* *
1254489 TTATAATTTTAATAT-A
1 TTATAATATAAATATGA
1254505 TTATAATATAAATATGA
1 TTATAATATAAATATGA
1254522 TTATAA
1 TTATAA
1254528 GATACAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TTATAATATAAATATGA
Found at i:1255150 original size:31 final size:33
Alignment explanation
Indices: 1255097--1255159 Score: 94
Period size: 31 Copynumber: 1.9 Consensus size: 33
1255087 TATGATATAA
1255097 AAAATATTATAAATATGATAAAAATAAATAAAAT
1 AAAATATTATAAATAT-ATAAAAATAAATAAAAT
*
1255131 AAAATTTTA-AAATAT-TAAAAATAAATAAA
1 AAAATATTATAAATATATAAAAATAAATAAA
1255160 TAGGTAGCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 14 0.50
33 6 0.21
34 8 0.29
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (33 bp):
AAAATATTATAAATATATAAAAATAAATAAAAT
Found at i:1256161 original size:74 final size:74
Alignment explanation
Indices: 1256005--1256194 Score: 292
Period size: 74 Copynumber: 2.6 Consensus size: 74
1255995 AGTTACCCAT
* **
1256005 AAATACTCCATCAATTGCATTTGGTAAGTATTTCTC-TTTTTTTTTAAAAAAAATTTACCCAAAA
1 AAATACTCCATTAATTGCATTTGGTAAGTATTTCTCTTTTTTTTTTAAAAAAAAAGTACCCAAAA
1256069 AACCCTTTA
66 AACCCTTTA
* * * *
1256078 AAATCCTCCATTAATTGCATTTGGTAAGTATTTATCTTTTTTTTTTAAAAAAAAAGTATCCAAAT
1 AAATACTCCATTAATTGCATTTGGTAAGTATTTCTCTTTTTTTTTTAAAAAAAAAGTACCCAAAA
1256143 AACCCTTTA
66 AACCCTTTA
* *
1256152 AAATACTCCATTAATTGCATTTGATAACTATTTCTCTTTTTTT
1 AAATACTCCATTAATTGCATTTGGTAAGTATTTCTCTTTTTTT
1256195 CCTTTAAATT
Statistics
Matches: 105, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 33 0.31
74 72 0.69
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (74 bp):
AAATACTCCATTAATTGCATTTGGTAAGTATTTCTCTTTTTTTTTTAAAAAAAAAGTACCCAAAA
AACCCTTTA
Found at i:1256342 original size:6 final size:6
Alignment explanation
Indices: 1256322--1256355 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
1256312 GTTTTCAATA
1256322 AAAATAT AAATATT AAAATT AAAATT AAAATT AA
1 AAAAT-T AAA-ATT AAAATT AAAATT AAAATT AA
1256356 TGAAAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 17 0.65
7 7 0.27
8 2 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:1256515 original size:153 final size:153
Alignment explanation
Indices: 1256349--1256626 Score: 495
Period size: 153 Copynumber: 1.8 Consensus size: 153
1256339 ATTAAAATTA
*
1256349 AAATTAATGAAAAATTACTTTTTAAAA-ATATTTCATAAATGAATTAAATTAAACTAATTTTAGT
1 AAATTAATGAAAAATTACTTTTTAAAATAT-TTTCATAAATGAATTAAATTAAACTAAGTTTAGT
*
1256413 TTCAGTAAATATTTTTCATCTAAATTGATATCCGATAATCCTCAGAAGGAAAATGAAAAAATTAT
65 TTCAATAAATATTTTTCATCTAAATTGATATCCGATAATCCTCAGAAGGAAAATGAAAAAATTAT
1256478 AGATAAAAAATTTTAAACTTATTT
130 AGATAAAAAATTTTAAACTTATTT
*
1256502 AAATTAATTAAAAATTACTTTTTAAAATATTTTCATAAATGAATTAAATTAAACTAAGTTTAGTT
1 AAATTAATGAAAAATTACTTTTTAAAATATTTTCATAAATGAATTAAATTAAACTAAGTTTAGTT
* *
1256567 TCAATAAATATTTTTTATCTAAATTGATATCCGATAATCCTCAGAAGGGAAATGAAAAAA
66 TCAATAAATATTTTTCATCTAAATTGATATCCGATAATCCTCAGAAGGAAAATGAAAAAA
1256627 AAAGGGCCAA
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
153 117 0.98
154 2 0.02
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.38
Consensus pattern (153 bp):
AAATTAATGAAAAATTACTTTTTAAAATATTTTCATAAATGAATTAAATTAAACTAAGTTTAGTT
TCAATAAATATTTTTCATCTAAATTGATATCCGATAATCCTCAGAAGGAAAATGAAAAAATTATA
GATAAAAAATTTTAAACTTATTT
Found at i:1257442 original size:2 final size:2
Alignment explanation
Indices: 1257435--1257460 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1257425 GCCAAGTAAA
1257435 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
1257461 GTTGTTCTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1260736 original size:2 final size:2
Alignment explanation
Indices: 1260729--1260761 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1260719 TCTCTAAGCT
1260729 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1260762 TGCACTCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1260924 original size:24 final size:22
Alignment explanation
Indices: 1260881--1260932 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
1260871 TTAAAATTTT
*
1260881 AATATAT--TATAATATAAATA
1 AATATATGATATAATACAAATA
*
1260901 TAATTATATGATATAATACGAATA
1 -AA-TATATGATATAATACAAATA
1260925 AATATATG
1 AATATATG
1260933 TGTAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 2 0.08
22 11 0.42
23 2 0.08
24 11 0.42
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (22 bp):
AATATATGATATAATACAAATA
Found at i:1261744 original size:21 final size:21
Alignment explanation
Indices: 1261713--1261774 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
1261703 TAAAAAATTT
*
1261713 AAATAAAAATATTAAATTTTAA
1 AAAT-AAAATATAAAATTTTAA
* *
1261735 AAATAAAATAAAAAAATTTAA
1 AAATAAAATATAAAATTTTAA
* *
1261756 AAA-AATA-ATCAAATTTTAA
1 AAATAAAATATAAAATTTTAA
1261775 CTTTAACATT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
19 9 0.27
20 3 0.09
21 17 0.52
22 4 0.12
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATAAAATATAAAATTTTAA
Found at i:1261827 original size:21 final size:23
Alignment explanation
Indices: 1261798--1261854 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 23
1261788 AACTTAAATT
*
1261798 TTATCTAATTTA-TT-TTTTAAA
1 TTATATAATTTATTTCTTTTAAA
1261819 TTATATAATATATATTTCTTTTAAA
1 TTATATAAT-T-TATTTCTTTTAAA
*
1261844 AT-TATAATTTA
1 TTATATAATTTA
1261855 CATTCAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 8 0.27
22 3 0.10
23 3 0.10
24 8 0.27
25 8 0.27
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATATAATTTATTTCTTTTAAA
Found at i:1262678 original size:29 final size:29
Alignment explanation
Indices: 1262632--1262689 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1262622 TTTATTTATT
1262632 TTAATTTCAAAAATAAAAAAGTAAAAATAC
1 TTAATTTCAAAAATAAAAAA-TAAAAATAC
* *
1262662 TTAATTT-AATAATAAAAAATCAAAATAC
1 TTAATTTCAAAAATAAAAAATAAAAATAC
1262690 ATTTCTAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 8 0.31
29 11 0.42
30 7 0.27
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (29 bp):
TTAATTTCAAAAATAAAAAATAAAAATAC
Found at i:1264790 original size:27 final size:27
Alignment explanation
Indices: 1264741--1264826 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 27
1264731 TAACTGATTG
* ***
1264741 AAATAAAAAATTTTAACTTTATTATAA
1 AAATTAAAAATTTTAAAAATATTATAA
1264768 AAATTAAAAATTTTAAAAATATTATAA
1 AAATTAAAAATTTTAAAAATATTATAA
*
1264795 TTAAATTAAAAAAATTTAAAAATA--ATAA
1 --AAATT-AAAAATTTTAAAAATATTATAA
1264823 AAAT
1 AAAT
1264827 ATATTAACTT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
26 4 0.08
27 23 0.45
28 4 0.08
29 5 0.10
30 15 0.29
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (27 bp):
AAATTAAAAATTTTAAAAATATTATAA
Found at i:1264813 original size:30 final size:27
Alignment explanation
Indices: 1264760--1264826 Score: 84
Period size: 30 Copynumber: 2.4 Consensus size: 27
1264750 ATTTTAACTT
*
1264760 TATTATAAAAATTAAAAATTTTAAAAA
1 TATTATAAAAATTAAAAAATTTAAAAA
1264787 TATTATAATTAAATTAAAAAAATTTAAAAA
1 TATTATAA--AAATT-AAAAAATTTAAAAA
1264817 TA--ATAAAAAT
1 TATTATAAAAAT
1264827 ATATTAACTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
26 4 0.11
27 8 0.22
28 4 0.11
29 5 0.14
30 15 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
TATTATAAAAATTAAAAAATTTAAAAA
Found at i:1264833 original size:30 final size:30
Alignment explanation
Indices: 1264768--1264833 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
1264758 TTTATTATAA
* * * *
1264768 AAATT-AAAAATTTTAAAAATATTATAATT
1 AAATTAAAAAAATTTAAAAATAATAAAAAT
1264797 AAATTAAAAAAATTTAAAAATAATAAAAAT
1 AAATTAAAAAAATTTAAAAATAATAAAAAT
*
1264827 ATATTAA
1 AAATTAA
1264834 CTTCGATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (30 bp):
AAATTAAAAAAATTTAAAAATAATAAAAAT
Done.