Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold66
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: 4623749
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 850 characters in sequence are not A, C, G, or T
File 5 of 26
Found at i:872211 original size:13 final size:13
Alignment explanation
Indices: 872193--872226 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
872183 AGGCTCCCTC
872193 TCCCTCTCATGTA
1 TCCCTCTCATGTA
*
872206 TCCCTCTTATGTA
1 TCCCTCTCATGTA
*
872219 TCCTTCTC
1 TCCCTCTC
872227 CAATTCATTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.12, C:0.38, G:0.06, T:0.44
Consensus pattern (13 bp):
TCCCTCTCATGTA
Found at i:872771 original size:3 final size:3
Alignment explanation
Indices: 872763--872802 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
872753 AATATATCAA
872763 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
872803 GTTGTCAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:879405 original size:93 final size:93
Alignment explanation
Indices: 879287--879471 Score: 223
Period size: 93 Copynumber: 2.0 Consensus size: 93
879277 AATATAAATC
* ** * * * *
879287 TATACTATATTAAAATTGTTGATTAAATTGGTATCACGAATTAATCGGATATTAAGTT-AATTAG
1 TATACTATATTAAAATTGTTAATTAAATTAATATAACGAATTAATCGAATATCAA-TTCAATTAA
*
879351 TAAAATTATTTAAAAA-TTTTTAAACTATT
65 TAAAATTA-TTAAAAAGTTTTAAAACTATT
* * *
879380 TATATTATATTAAAA-TGATTAATTAAATTAATATAATGAGTTAATCGAATATCAATTCAATTAA
1 TATACTATATTAAAATTG-TTAATTAAATTAATATAACGAATTAATCGAATATCAATTCAATTAA
879444 TAAAATTATTAAAAAGTTTTAAAACTAT
65 TAAAATTATTAAAAAGTTTTAAAACTAT
879472 ATCAATAATG
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
92 11 0.14
93 67 0.86
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.42
Consensus pattern (93 bp):
TATACTATATTAAAATTGTTAATTAAATTAATATAACGAATTAATCGAATATCAATTCAATTAAT
AAAATTATTAAAAAGTTTTAAAACTATT
Found at i:880155 original size:24 final size:25
Alignment explanation
Indices: 880107--880155 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
880097 TGTATTTTAG
* * *
880107 TAATTTATAAATATTATTTATAATT
1 TAATTTATAAAAATTATATAAAATT
880132 TAATTT-TAAAAATTATATAAAATT
1 TAATTTATAAAAATTATATAAAATT
880156 AAAAAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TAATTTATAAAAATTATATAAAATT
Found at i:881337 original size:15 final size:16
Alignment explanation
Indices: 881305--881342 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
881295 AACAAAATGT
881305 AAAAAATTAAAGTGAATA
1 AAAAAATTAAA--GAATA
881323 AAAAAATTAAA-AATA
1 AAAAAATTAAAGAATA
881338 AAAAA
1 AAAAA
881343 GGGAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 9 0.45
18 11 0.55
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (16 bp):
AAAAAATTAAAGAATA
Found at i:881784 original size:29 final size:30
Alignment explanation
Indices: 881722--881786 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
881712 AAATTAATCC
* ** *
881722 AAAATTTTTTCAAGATACCTATTTACAATA
1 AAAAATTTTTCAAGATACCTATACACAAAA
*
881752 AAAAATTTTTCAAGATACCTA-ACCCAAAA
1 AAAAATTTTTCAAGATACCTATACACAAAA
881781 AAAAAT
1 AAAAAT
881787 ATAAGTCAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.31
Consensus pattern (30 bp):
AAAAATTTTTCAAGATACCTATACACAAAA
Found at i:882909 original size:33 final size:33
Alignment explanation
Indices: 882872--882944 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
882862 ATAACTAATT
882872 TCCAAGACAAAAAAAATAGATGGATAAACATCC
1 TCCAAGACAAAAAAAATAGATGGATAAACATCC
*** * * *
882905 TCCAAGACGGCACACATGGATGGATAAACATCC
1 TCCAAGACAAAAAAAATAGATGGATAAACATCC
882938 TCCAAGA
1 TCCAAGA
882945 ACTAGCAGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.45, C:0.23, G:0.16, T:0.15
Consensus pattern (33 bp):
TCCAAGACAAAAAAAATAGATGGATAAACATCC
Found at i:884201 original size:18 final size:17
Alignment explanation
Indices: 884162--884213 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
884152 GTTAAGAGTT
884162 TAAATTTTA-AT-AATA
1 TAAATTTTATATAAATA
884177 TCAAATTTTATATAAATA
1 T-AAATTTTATATAAATA
884195 TATAA-TTTAT-TAAATA
1 TA-AATTTTATATAAATA
884211 TAA
1 TAA
884214 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
15 2 0.06
16 16 0.48
17 8 0.24
18 7 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATTTTATATAAATA
Found at i:884229 original size:18 final size:20
Alignment explanation
Indices: 884206--884243 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
884196 ATAATTTATT
884206 AAATA-TAAT-TAAAATAAA
1 AAATATTAATATAAAATAAA
*
884224 AAATATTAATATAACATAAA
1 AAATATTAATATAAAATAAA
884244 TATAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 8 0.47
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATATTAATATAAAATAAA
Found at i:884243 original size:25 final size:26
Alignment explanation
Indices: 884188--884250 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
884178 CAAATTTTAT
* **
884188 ATAAATATATAATTTATTAAATATAA
1 ATAAATATAAAAAATATTAAATATAA
*
884214 TTAAA-ATAAAAAATATT-AATATAA
1 ATAAATATAAAAAATATTAAATATAA
884238 CATAAATATAAAA
1 -ATAAATATAAAA
884251 TTATCAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
24 7 0.23
25 13 0.43
26 10 0.33
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
ATAAATATAAAAAATATTAAATATAA
Found at i:885553 original size:14 final size:14
Alignment explanation
Indices: 885512--885555 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
885502 ATAAAATAAT
* *
885512 TATATTTAAATATG
1 TATATTTATATATA
*
885526 TATATATATATATA
1 TATATTTATATATA
*
885540 TATATTTATGTATA
1 TATATTTATATATA
885554 TA
1 TA
885556 CACCGTCTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (14 bp):
TATATTTATATATA
Found at i:885726 original size:2 final size:2
Alignment explanation
Indices: 885719--885748 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
885709 TTGGCATTAA
885719 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
885749 GTTTTGGTTG
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:887430 original size:1 final size:1
Alignment explanation
Indices: 887424--887451 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
887414 ATTAGAAGGG
887424 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
887452 CAGTTCTTCC
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:890056 original size:11 final size:11
Alignment explanation
Indices: 890042--890070 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
890032 ATTAATATAA
890042 AAATAATATTT
1 AAATAATATTT
890053 AAAT-ATATTT
1 AAATAATATTT
890063 AAATAATA
1 AAATAATA
890071 AATTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AAATAATATTT
Found at i:890060 original size:21 final size:22
Alignment explanation
Indices: 890039--890086 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
890029 AGTATTAATA
890039 TAAA-AATAATATTTAAATATATT
1 TAAATAATAA-ATTTAAATATA-T
*
890062 TAAATAATAAATTTAAA-ATTT
1 TAAATAATAAATTTAAATATAT
890083 TAAA
1 TAAA
890087 ATCAGACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 5 0.22
22 2 0.09
23 11 0.48
24 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATAATAAATTTAAATATAT
Found at i:890375 original size:21 final size:21
Alignment explanation
Indices: 890343--890382 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
890333 TTATTATATT
* *
890343 TAATAAATAATTTAAAATTTG
1 TAATAAAAAATTAAAAATTTG
890364 TAATAAAAAATTAAAAATT
1 TAATAAAAAATTAAAAATT
890383 AAAACTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
TAATAAAAAATTAAAAATTTG
Found at i:890409 original size:17 final size:17
Alignment explanation
Indices: 890368--890410 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
890358 AATTTGTAAT
* *
890368 AAAAAATTAAAAATTAA
1 AAAAAATAAAAAATGAA
**
890385 AACTAATAAAAAATGAA
1 AAAAAATAAAAAATGAA
890402 AAAAAATAA
1 AAAAAATAA
890411 GCTAAAAATT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (17 bp):
AAAAAATAAAAAATGAA
Found at i:893507 original size:2 final size:2
Alignment explanation
Indices: 893502--893526 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
893492 TCTCTCTCTT
893502 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
893527 GGAGGATTTA
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:894299 original size:13 final size:12
Alignment explanation
Indices: 894240--894296 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
894230 TGGAAATTCA
894240 AAAAAG-AAAAG
1 AAAAAGCAAAAG
*
894251 AAAAAACAAAAG
1 AAAAAGCAAAAG
* *
894263 GAAAAGGAAAAG
1 AAAAAGCAAAAG
* *
894275 GAAAAGAAAGAAG
1 AAAAAGCAA-AAG
894288 AAAAAGCAA
1 AAAAAGCAA
894297 GAAAACATGG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
11 5 0.14
12 22 0.59
13 10 0.27
ACGTcount: A:0.75, C:0.04, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAAGCAAAAG
Found at i:895606 original size:24 final size:24
Alignment explanation
Indices: 895563--895608 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
895553 CTAGTAATGT
*
895563 TTATAAAGGTGAAGATTATAAAAA
1 TTATAAAGGTGAAGAATATAAAAA
895587 TTATAAAGGTGAA-ACATATAAA
1 TTATAAAGGTGAAGA-ATATAAA
895609 TTTTAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.28
Consensus pattern (24 bp):
TTATAAAGGTGAAGAATATAAAAA
Found at i:895615 original size:22 final size:24
Alignment explanation
Indices: 895563--895615 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
895553 CTAGTAATGT
*
895563 TTATAAAGGTGAAGATTATAAAAA
1 TTATAAAGGTGAAGATCATAAAAA
*
895587 TTATAAAGGTGAA-A-CATATAAA
1 TTATAAAGGTGAAGATCATAAAAA
*
895609 TTTTAAA
1 TTATAAA
895616 TTTATTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 12 0.46
23 1 0.04
24 13 0.50
ACGTcount: A:0.53, C:0.02, G:0.13, T:0.32
Consensus pattern (24 bp):
TTATAAAGGTGAAGATCATAAAAA
Found at i:902150 original size:19 final size:19
Alignment explanation
Indices: 902126--902163 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
902116 CTAAACATCA
902126 GCATTTTTATATATTCGAG
1 GCATTTTTATATATTCGAG
902145 GCATTTTTATATATTCGAG
1 GCATTTTTATATATTCGAG
902164 TGGGACTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (19 bp):
GCATTTTTATATATTCGAG
Found at i:910392 original size:22 final size:22
Alignment explanation
Indices: 910365--910408 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
910355 ATTCAAAATG
910365 CTTAAAATTCTCTTTAAAGGTA
1 CTTAAAATTCTCTTTAAAGGTA
910387 CTTAAAATTCTCTTTAAAGGTA
1 CTTAAAATTCTCTTTAAAGGTA
910409 ATCAGATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (22 bp):
CTTAAAATTCTCTTTAAAGGTA
Found at i:914091 original size:2 final size:2
Alignment explanation
Indices: 914084--914156 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
914074 CTGATCCAAA
914084 CT CT CT CT CT CT CT CT CT 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 CT CT CT
914126 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
914157 CGTCGTCAAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:916079 original size:2 final size:2
Alignment explanation
Indices: 916072--916098 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
916062 CGAAAAGTAC
916072 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
916099 GTTTAATTAT
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:917214 original size:2 final size:2
Alignment explanation
Indices: 917207--917239 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
917197 GGGCAAAGAC
917207 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 A
917240 AACTTAGACT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:920758 original size:2 final size:2
Alignment explanation
Indices: 920751--920776 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
920741 AATTTCTCAC
920751 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
920777 TTAATTACAC
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:921347 original size:15 final size:17
Alignment explanation
Indices: 921316--921350 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
921306 TAAGTGACAA
921316 ATTGAAATGAGAATATG
1 ATTGAAATGAGAATATG
921333 ATTGAAA-GA-AATATG
1 ATTGAAATGAGAATATG
921348 ATT
1 ATT
921351 TGAATCATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 2 0.11
17 7 0.39
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (17 bp):
ATTGAAATGAGAATATG
Found at i:921863 original size:31 final size:31
Alignment explanation
Indices: 921825--921891 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
921815 TAACAACTAC
921825 TAATTGATGAAATTTAGTTACTAAGAATGAG
1 TAATTGATGAAATTTAGTTACTAAGAATGAG
*
921856 TAATTGATGAAATTTAGTTACTAAGGATGAG
1 TAATTGATGAAATTTAGTTACTAAGAATGAG
921887 TAATT
1 TAATT
921892 TTTGACCTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.37
Consensus pattern (31 bp):
TAATTGATGAAATTTAGTTACTAAGAATGAG
Found at i:925173 original size:75 final size:76
Alignment explanation
Indices: 925086--925227 Score: 205
Period size: 75 Copynumber: 1.9 Consensus size: 76
925076 TAACCTACTC
* * * * *
925086 GAATTATTAAAAATTTTATCTAAAATTCGATTTATACGAGCAAAACCTACAAATAACTTA-ATTC
1 GAATTATCAAAAATTTTATCTAAAACTCGATTTATACGAACAAAACCGACAAATAACTCAGATTC
925150 TTAAGTGGCTT
66 TTAAGTGGCTT
* * *
925161 GAATTATCAAAAATTTTATCTAAAACTCGATTTGTACGAACAAAGCCGATAAATAACTCAGATTC
1 GAATTATCAAAAATTTTATCTAAAACTCGATTTATACGAACAAAACCGACAAATAACTCAGATTC
925226 TT
66 TT
925228 GGACGGCCTA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
75 52 0.90
76 6 0.10
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.34
Consensus pattern (76 bp):
GAATTATCAAAAATTTTATCTAAAACTCGATTTATACGAACAAAACCGACAAATAACTCAGATTC
TTAAGTGGCTT
Found at i:928497 original size:2 final size:2
Alignment explanation
Indices: 928490--928514 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
928480 CTTCTTTTTC
928490 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
928515 AAAACAGCTT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:928889 original size:32 final size:33
Alignment explanation
Indices: 928853--928924 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 33
928843 TATTTATATT
928853 TATTTTAAATTT-ATTA-TAAATAATAATTATAA
1 TATTTTAAATTTAATTATTAAATAA-AATTATAA
** *
928885 TA-TTTAAATTTAATTATTATTTAAATTTATAA
1 TATTTTAAATTTAATTATTAAATAAAATTATAA
928917 TATTTTAA
1 TATTTTAA
928925 CCCATAAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 9 0.26
32 15 0.44
33 10 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TATTTTAAATTTAATTATTAAATAAAATTATAA
Found at i:928917 original size:19 final size:19
Alignment explanation
Indices: 928864--928917 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
928854 ATTTTAAATT
*
928864 TATTATAAATAATAATTATAA
1 TATT-TAAATTATAATTAT-A
928885 TATTTAAATT-TAATTAT-
1 TATTTAAATTATAATTATA
928902 TATTTAAATTTATAAT
1 TATTTAAA-TTATAAT
928918 ATTTTAACCC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 8 0.27
18 2 0.07
19 11 0.37
20 5 0.17
21 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TATTTAAATTATAATTATA
Found at i:936017 original size:23 final size:21
Alignment explanation
Indices: 935968--936018 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
935958 TATTTTTAAT
935968 TTAATAAAAAAATTAAAAATA
1 TTAATAAAAAAATTAAAAATA
935989 TT-ATAAAAATAATTTTAAAAA-A
1 TTAATAAAAA-AA--TTAAAAATA
936011 TTAATAAA
1 TTAATAAA
936019 TTAAATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 7 0.27
21 4 0.15
22 3 0.12
23 12 0.46
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TTAATAAAAAAATTAAAAATA
Found at i:936031 original size:14 final size:14
Alignment explanation
Indices: 936008--936040 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
935998 TAATTTTAAA
936008 AAATTAATAAA-TT
1 AAATTAATAAATTT
936021 AAATTATATAAATTT
1 AAATTA-ATAAATTT
936036 AAATT
1 AAATT
936041 TAAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 5 0.28
15 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATTAATAAATTT
Found at i:936039 original size:15 final size:13
Alignment explanation
Indices: 936008--936054 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
935998 TAATTTTAAA
936008 AAATTAATAAATT
1 AAATTAATAAATT
936021 AAATTATATAAATTT
1 AAATTA-ATAAA-TT
936036 AAATT--TAAATT
1 AAATTAATAAATT
*
936047 AATTTAAT
1 AAATTAAT
936055 TTTTTAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
11 6 0.21
12 4 0.14
13 7 0.24
14 5 0.17
15 7 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AAATTAATAAATT
Found at i:937354 original size:19 final size:19
Alignment explanation
Indices: 937326--937378 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
937316 TAGTTTTTAG
**
937326 ATTTTAAAATATTAAA-TT
1 ATTTTAAAATAAAAAATTT
937344 ATTTATAAAATAAAAAATTT
1 ATTT-TAAAATAAAAAATTT
937364 ATTTTTAAAATAAAA
1 A-TTTTAAAATAAAA
937379 TAAGATATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 4 0.13
19 10 0.33
20 13 0.43
21 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTTTAAAATAAAAAATTT
Found at i:943043 original size:22 final size:21
Alignment explanation
Indices: 943018--943062 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
943008 AAATGATTCG
*
943018 AATTCGATAAATTTAAATATTA
1 AATTCAATAAATTTAAA-ATTA
* *
943040 AATTTAATTAATTTAAAATTA
1 AATTCAATAAATTTAAAATTA
943061 AA
1 AA
943063 ATAATTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
AATTCAATAAATTTAAAATTA
Found at i:943067 original size:16 final size:16
Alignment explanation
Indices: 943048--943120 Score: 110
Period size: 16 Copynumber: 4.6 Consensus size: 16
943038 TAAATTTAAT
943048 TAATTTAAAATTAAAA
1 TAATTTAAAATTAAAA
943064 TAATTTAAAATTAAAA
1 TAATTTAAAATTAAAA
* *
943080 TGATTTAAATTTAAAA
1 TAATTTAAAATTAAAA
* *
943096 TAATGTAAAATTATAA
1 TAATTTAAAATTAAAA
943112 TAATTTAAA
1 TAATTTAAA
943121 TGATCTAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
TAATTTAAAATTAAAA
Found at i:943086 original size:32 final size:32
Alignment explanation
Indices: 943039--943120 Score: 110
Period size: 32 Copynumber: 2.6 Consensus size: 32
943029 TTTAAATATT
* * *
943039 AAATTTAATTAATTTAAAATTAAAATAATTTA
1 AAATTAAAATAATTTAAAATTAAAATAATGTA
* *
943071 AAATTAAAATGATTTAAATTTAAAATAATGTA
1 AAATTAAAATAATTTAAAATTAAAATAATGTA
*
943103 AAATTATAATAATTTAAA
1 AAATTAAAATAATTTAAA
943121 TGATCTAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (32 bp):
AAATTAAAATAATTTAAAATTAAAATAATGTA
Found at i:943749 original size:5 final size:5
Alignment explanation
Indices: 943734--943844 Score: 74
Period size: 5 Copynumber: 23.0 Consensus size: 5
943724 AGAGTGAATA
*
943734 TATATT TATAT TATAT TATAT TATAT TATAAT TATAT T-TA- AAGTAT
1 TATA-T TATAT TATAT TATAT TATAT TAT-AT TATAT TATAT TA-TAT
* * * * * *
943780 TATAT TAT-T TAT-T TATAA TATTT TTTAT TATA- TAAAT TTTAA TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
*
943827 TA-AT AAT-T TATAT TATAT
1 TATAT TATAT TATAT TATAT
943845 AAATTTTAAA
Statistics
Matches: 81, Mismatches: 16, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
4 19 0.23
5 52 0.64
6 10 0.12
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:943755 original size:16 final size:16
Alignment explanation
Indices: 943734--943844 Score: 83
Period size: 15 Copynumber: 7.0 Consensus size: 16
943724 AGAGTGAATA
943734 TATATTTATATTATAT
1 TATATTTATATTATAT
943750 TATA-TTATATTATAAT
1 TATATTTATATTAT-AT
943766 TATATTTAAAGTATTATA-
1 TATATTT--A-TATTATAT
*
943784 T-TATTTAT-TTATAA
1 TATATTTATATTATAT
*
943798 TAT-TTTTTATTATA-
1 TATATTTATATTATAT
* *
943812 TAAATTT-TAATATAT
1 TATATTTATATTATAT
943827 TAATAATTTATATTATAT
1 T-AT-ATTTATATTATAT
943845 AAATTTTAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 24
0.73 0.05 0.23
Matches are distributed among these distances:
13 5 0.06
14 14 0.18
15 20 0.26
16 11 0.14
17 11 0.14
18 8 0.10
19 2 0.03
20 6 0.08
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.59
Consensus pattern (16 bp):
TATATTTATATTATAT
Found at i:943773 original size:32 final size:32
Alignment explanation
Indices: 943734--943844 Score: 99
Period size: 32 Copynumber: 3.5 Consensus size: 32
943724 AGAGTGAATA
943734 TATATTTATATTATATTATATTATATTATAAT
1 TATATTTATATTATATTATATTATATTATAAT
943766 TATATTTAAAGTATTATATTAT-TTAT-TTATAA-
1 TATATTT--A-TATTATATTATATTATATTATAAT
* * * *
943798 TAT-TTTTTATTATA-TAAATTTTAATAT-AT
1 TATATTTATATTATATTATATTATATTATAAT
943827 TAATAATTTATATTATAT
1 T-AT-ATTTATATTATAT
943845 AAATTTTAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 19
0.73 0.06 0.22
Matches are distributed among these distances:
27 2 0.03
28 11 0.17
29 4 0.06
30 2 0.03
31 3 0.05
32 20 0.31
33 6 0.09
34 5 0.08
35 11 0.17
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.59
Consensus pattern (32 bp):
TATATTTATATTATATTATATTATATTATAAT
Found at i:943825 original size:14 final size:14
Alignment explanation
Indices: 943802--943858 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 14
943792 TTATAATATT
*
943802 TTTTATTATATAAA
1 TTTTAATATATAAA
943816 TTTTAATATATTAATAA
1 TTTTAATATA-T-A-AA
*
943833 TTTATATTATATAAA
1 TTT-TAATATATAAA
*
943848 TTTTAAAATAT
1 TTTTAATATAT
943859 TCATATATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 15 0.43
15 6 0.17
16 2 0.06
17 6 0.17
18 6 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTTAATATATAAA
Found at i:943845 original size:32 final size:32
Alignment explanation
Indices: 943795--943875 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
943785 TATTTATTTA
* * *
943795 TAATATTTTTTATTATATAAATTTTAATATAT
1 TAATAATTTATATTATATAAATTTTAAAATAT
943827 TAATAATTTATATTATATAAATTTTAAAATAT
1 TAATAATTTATATTATATAAATTTTAAAATAT
*
943859 TCATATATTTATATTAT
1 TAATA-ATTTATATTAT
943876 TTTTTTATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 33 0.75
33 11 0.25
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (32 bp):
TAATAATTTATATTATATAAATTTTAAAATAT
Found at i:943996 original size:18 final size:19
Alignment explanation
Indices: 943962--944015 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
943952 ATGATACAAA
*
943962 AAAATAATTAAAATATAATTT
1 AAAATAA-T-AAATATAATAT
943983 AAAATAAT-AATATAATAT
1 AAAATAATAAATATAATAT
*
944001 AAAATTATAAATATA
1 AAAATAATAAATATA
944016 TAAATATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 16 0.53
19 6 0.20
20 1 0.03
21 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATAATAAATATAATAT
Found at i:944527 original size:3 final size:3
Alignment explanation
Indices: 944519--944546 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
944509 CATGCTCAAT
944519 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
944547 AGTATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:944979 original size:13 final size:13
Alignment explanation
Indices: 944963--944992 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
944953 AATTAATTAT
944963 AATAAATATTAAC
1 AATAAATATTAAC
*
944976 AATAAATATTAAT
1 AATAAATATTAAC
944989 AATA
1 AATA
944993 TAAAAAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAAATATTAAC
Found at i:944988 original size:23 final size:23
Alignment explanation
Indices: 944936--944990 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
944926 AATTATAAAT
* * *
944936 ATATTAAT-AATATTCATAATTA
1 ATATTAATAAATATTAACAATAA
944958 AT-TATAATAAATATTAACAATAA
1 ATAT-TAATAAATATTAACAATAA
944981 ATATTAATAA
1 ATATTAATAA
944991 TATAAAAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 1 0.04
22 6 0.22
23 19 0.70
24 1 0.04
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (23 bp):
ATATTAATAAATATTAACAATAA
Found at i:946159 original size:13 final size:14
Alignment explanation
Indices: 946124--946160 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
946114 AAATATGATA
946124 TTTTTATTATGTATT
1 TTTTTATTA-GTATT
946139 TTTTTATTA-TATT
1 TTTTTATTAGTATT
946152 TTTTTATTA
1 TTTTTATTA
946161 ATAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
15 9 0.41
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTTTATTAGTATT
Found at i:946242 original size:18 final size:18
Alignment explanation
Indices: 946219--946255 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
946209 TTTTAATATC
946219 AAATTAAAAATCAAATCA
1 AAATTAAAAATCAAATCA
* *
946237 AAATTATAAATTAAATCA
1 AAATTAAAAATCAAATCA
946255 A
1 A
946256 TATTTAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (18 bp):
AAATTAAAAATCAAATCA
Found at i:946722 original size:14 final size:15
Alignment explanation
Indices: 946680--946722 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
946670 TGAACTAGCA
946680 TTCTTTTTTTCTT-T
1 TTCTTTTTTTCTTAT
*
946694 TTCTTTTTTT-GTAT
1 TTCTTTTTTTCTTAT
946708 TT-TTTTTTTCTTAT
1 TTCTTTTTTTCTTAT
946722 T
1 T
946723 GAACTTCTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.05, C:0.09, G:0.02, T:0.84
Consensus pattern (15 bp):
TTCTTTTTTTCTTAT
Found at i:948384 original size:47 final size:47
Alignment explanation
Indices: 948329--948464 Score: 236
Period size: 47 Copynumber: 2.9 Consensus size: 47
948319 GCACTTACAT
**
948329 GATATCTCCCATCATGCTGATAAGACTCCAATACTGATATTTGGTAA
1 GATATCTCCCATCATGCTGATAAGACTTGAATACTGATATTTGGTAA
*
948376 GGTATCTCCCATCATGCTGATAAGACTTGAATACTGATATTTGGTAA
1 GATATCTCCCATCATGCTGATAAGACTTGAATACTGATATTTGGTAA
*
948423 GATATCTCCCATCATGCTGATAAGACTTGAATGCTGATATTT
1 GATATCTCCCATCATGCTGATAAGACTTGAATACTGATATTT
948465 TCTACATATT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 84 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (47 bp):
GATATCTCCCATCATGCTGATAAGACTTGAATACTGATATTTGGTAA
Found at i:950163 original size:25 final size:25
Alignment explanation
Indices: 950124--950171 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
950114 AAAATTTTAA
*
950124 AATAAATATAAATTATTTTATTTTT
1 AATAAATATAAATTATTTAATTTTT
950149 AATAAA-ATAATATTATTTAATTT
1 AATAAATATAA-ATTATTTAATTT
950172 ATTGATACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
AATAAATATAAATTATTTAATTTTT
Found at i:950967 original size:19 final size:19
Alignment explanation
Indices: 950945--951015 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
950935 TATAAATATT
950945 AATTATTTAAAAATTTTTA
1 AATTATTTAAAAATTTTTA
* * *
950964 AATTTTTTATAAATATTTA
1 AATTATTTAAAAATTTTTA
*
950983 TAATTAAATTAAAATTATTTTT-
1 -AATT-ATTTAAAA--ATTTTTA
*
951005 TATTATTTAAA
1 AATTATTTAAA
951016 TTAATTTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
19 16 0.41
20 10 0.26
21 8 0.21
23 5 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATTATTTAAAAATTTTTA
Found at i:951029 original size:15 final size:16
Alignment explanation
Indices: 951009--951040 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
950999 ATTTTTTATT
951009 ATTTAAATT-AATTTA
1 ATTTAAATTAAATTTA
951024 ATTTAAATTAAATTTA
1 ATTTAAATTAAATTTA
951040 A
1 A
951041 AAAAATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTAAATTAAATTTA
Found at i:953429 original size:19 final size:20
Alignment explanation
Indices: 953381--953429 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
953371 TTGAATAAGA
953381 ATTTTATAAATTCGAATTAGT
1 ATTTTAT-AATTCGAATTAGT
*
953402 -TAATT-TAATTCGAATTA-T
1 AT-TTTATAATTCGAATTAGT
953420 ATTTTATAAT
1 ATTTTATAAT
953430 AATAATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 8
0.70 0.06 0.24
Matches are distributed among these distances:
18 3 0.13
19 16 0.70
20 2 0.09
21 2 0.09
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (20 bp):
ATTTTATAATTCGAATTAGT
Found at i:958392 original size:3 final size:3
Alignment explanation
Indices: 958384--958408 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
958374 TGAAGGTGAA
958384 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
958409 GAGATAGTGG
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:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:959668 original size:2 final size:2
Alignment explanation
Indices: 959663--959687 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
959653 TTTTTTTTTA
959663 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 A
959688 AAAGAAGAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:960897 original size:16 final size:17
Alignment explanation
Indices: 960857--960899 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
960847 CTTATTCTTT
960857 TTAAGATTAAAATTTAAA
1 TTAA-ATTAAAATTTAAA
960875 TTAAATTAAAATTT-AA
1 TTAAATTAAAATTTAAA
*
960891 TTCAATTAA
1 TTAAATTAA
960900 TTTATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 10 0.42
17 10 0.42
18 4 0.17
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TTAAATTAAAATTTAAA
Found at i:960922 original size:16 final size:16
Alignment explanation
Indices: 960903--960949 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
960893 CAATTAATTT
960903 ATATAATAATTTTATA
1 ATATAATAATTTTATA
*
960919 ATATAAT-ATTTAATAA
1 ATATAATAATTTTAT-A
*
960935 ATTTAA-AATTTTATA
1 ATATAATAATTTTATA
960950 TGAACTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 7 0.27
16 19 0.73
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATAATAATTTTATA
Found at i:961035 original size:2 final size:2
Alignment explanation
Indices: 961028--961058 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
961018 TCCTCTTGTT
961028 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 T
961059 GTATTCTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:963707 original size:19 final size:20
Alignment explanation
Indices: 963661--963707 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
963651 TATTTTATTA
* *
963661 ATTAAATCTATTTATTAAAT
1 ATTAAATTTATTTAATAAAT
* *
963681 TTTTAATTTA-TTAATAAAT
1 ATTAAATTTATTTAATAAAT
963700 ATTAAATT
1 ATTAAATT
963708 AAATAAACTA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTAAATTTATTTAATAAAT
Found at i:964737 original size:12 final size:12
Alignment explanation
Indices: 964720--964745 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
964710 TTGACTACTA
964720 ATTTACACTTTT
1 ATTTACACTTTT
964732 ATTTACACTTTT
1 ATTTACACTTTT
964744 AT
1 AT
964746 CCGGTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTTACACTTTT
Found at i:966816 original size:13 final size:13
Alignment explanation
Indices: 966795--966824 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
966785 TTTTAAATAT
*
966795 ATATTAAATATAA
1 ATATCAAATATAA
966808 ATATCAAATATAA
1 ATATCAAATATAA
966821 ATAT
1 ATAT
966825 TTAAGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATCAAATATAA
Found at i:966981 original size:2 final size:2
Alignment explanation
Indices: 966974--967002 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
966964 ACGTTGCCTT
966974 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
967003 TATCCCCACA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:967844 original size:31 final size:32
Alignment explanation
Indices: 967798--967873 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
967788 TCATACATTC
*
967798 ATTAAT-TTAAAGTAAT-AAAAAAATGAACTA
1 ATTAATGTTATAGTAATAAAAAAAATGAACTA
967828 ATTAATGTTATAGTAATAAAAAAAATGAACTA
1 ATTAATGTTATAGTAATAAAAAAAATGAACTA
967860 ATTAATGTTATAGT
1 ATTAATGTTATAGT
967874 GGCAGTTGCT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
30 6 0.14
31 9 0.21
32 28 0.65
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (32 bp):
ATTAATGTTATAGTAATAAAAAAAATGAACTA
Found at i:969553 original size:2 final size:2
Alignment explanation
Indices: 969546--969577 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
969536 CAGAGCATAC
969546 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
969578 GCATACACAC
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:973851 original size:24 final size:23
Alignment explanation
Indices: 973796--973852 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
973786 TTAATTTTTT
* *
973796 TAAATT-AATTTTTATATTTTAT
1 TAAATTAAATTTATATATTTTAA
*
973818 TAGATATAAATTTATATATTATTAA
1 TAAAT-TAAATTTATATATT-TTAA
973843 TAAATTAAAT
1 TAAATTAAAT
973853 AATATTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 4 0.14
23 1 0.04
24 16 0.57
25 7 0.25
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TAAATTAAATTTATATATTTTAA
Found at i:973860 original size:18 final size:19
Alignment explanation
Indices: 973823--973860 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
973813 TTTATTAGAT
* *
973823 ATAAATTTATATATTATTA
1 ATAAATTTAAATAATATTA
973842 ATAAA-TTAAATAATATTA
1 ATAAATTTAAATAATATTA
973860 A
1 A
973861 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAAATTTAAATAATATTA
Found at i:974583 original size:18 final size:18
Alignment explanation
Indices: 974548--974605 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
974538 AAGTTATATT
*
974548 ATTTTAAA-T-TTTTAAA
1 ATTTTAAATTATTTTTAA
974564 ATTTTAAATTATTTTTAA
1 ATTTTAAATTATTTTTAA
* *
974582 ATTTAAAATCATTTTT-A
1 ATTTTAAATTATTTTTAA
974599 ATTTTAA
1 ATTTTAA
974606 TCATTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
16 8 0.22
17 8 0.22
18 20 0.56
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTAAATTATTTTTAA
Found at i:974588 original size:17 final size:17
Alignment explanation
Indices: 974555--974611 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
974545 ATTATTTTAA
*
974555 ATTTTTAAAATTTTAAATT
1 ATTTTT-AAA-TTTAAATC
974574 ATTTTTAAATTTAAAATC
1 ATTTTTAAATTT-AAATC
*
974592 ATTTTT-AATTTTAATC
1 ATTTTTAAATTTAAATC
974608 ATTT
1 ATTT
974612 CAATTCCTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 8 0.23
17 8 0.23
18 13 0.37
19 6 0.17
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTTAAATTTAAATC
Found at i:976204 original size:2 final size:2
Alignment explanation
Indices: 976191--976236 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
976181 CATTACTGCC
*
976191 AT AT AG 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
976233 AT AT
1 AT AT
976237 TACTTGGTCG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:977920 original size:5 final size:5
Alignment explanation
Indices: 977908--977973 Score: 50
Period size: 5 Copynumber: 13.8 Consensus size: 5
977898 AGGAGTATAA
* * * *
977908 AATA- AATAT AATAT AATAT AATAT AA-AT ATTTT AAAATT TATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATA-T AATAT AATAT
*
977957 AAT-T TAT-T AATAT AATA
1 AATAT AATAT AATAT AATA
977974 AAATTTATAT
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
4 13 0.27
5 32 0.67
6 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
AATAT
Found at i:977927 original size:21 final size:24
Alignment explanation
Indices: 977885--977937 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 24
977875 TTAAAAATAT
977885 TAAATATAATTATAGGAGTATAAAA
1 TAAATATAATTATA-GAGTATAAAA
*
977910 TAAATATAA-TATA-A-TATAATA
1 TAAATATAATTATAGAGTATAAAA
977931 TAAATAT
1 TAAATAT
977938 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 13 0.48
22 1 0.04
24 4 0.15
25 9 0.33
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (24 bp):
TAAATATAATTATAGAGTATAAAA
Found at i:977969 original size:13 final size:14
Alignment explanation
Indices: 977943--977972 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
977933 AATATTTTAA
977943 AATTTATATAATAT
1 AATTTATATAATAT
977957 AATTTAT-TAATAT
1 AATTTATATAATAT
977970 AAT
1 AAT
977973 AAAATTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTATATAATAT
Found at i:977976 original size:32 final size:30
Alignment explanation
Indices: 977918--977999 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 30
977908 AATAAATATA
**
977918 ATATAATATAATATAAATATTTTAAAATTT
1 ATATAATATAATATAAATATAATAAAATTT
*
977948 ATATAATATAATTTATTAATATAATAAAATTT
1 ATATAATATAA--TATAAATATAATAAAATTT
977980 ATATTAATATACAATATAAA
1 ATA-TAATAT--AATATAAA
978000 AATGGTCAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
30 11 0.26
32 19 0.44
33 11 0.26
35 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (30 bp):
ATATAATATAATATAAATATAATAAAATTT
Found at i:978852 original size:2 final size:2
Alignment explanation
Indices: 978845--978876 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
978835 CAAATGAAAT
978845 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
978877 AAGATCAAAC
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):
TA
Found at i:978941 original size:3 final size:3
Alignment explanation
Indices: 978935--978960 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
978925 GAGGAAGAAA
978935 GCG GCG GCG GCG GCG GCG GCG GCG GC
1 GCG GCG GCG GCG GCG GCG GCG GCG GC
978961 AGCAAATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.65, T:0.00
Consensus pattern (3 bp):
GCG
Found at i:981280 original size:12 final size:12
Alignment explanation
Indices: 981259--981307 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
981249 TATTTAAAAA
* *
981259 TTATAATAATTT
1 TTATATTAATAT
981271 TTATATTAATAT
1 TTATATTAATAT
981283 TTATA-T-ATAT
1 TTATATTAATAT
981293 TTATTATTAA-AT
1 TTA-TATTAATAT
981305 TTA
1 TTA
981308 AATAAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 7 0.22
11 3 0.09
12 21 0.66
13 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTATATTAATAT
Found at i:981319 original size:22 final size:23
Alignment explanation
Indices: 981274--981325 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
981264 ATAATTTTTA
* * *
981274 TATTAATATTTATATATATTTAT
1 TATTAATATTTAAATAAATATAT
981297 TATTAA-ATTTAAATAAATATAT
1 TATTAATATTTAAATAAATATAT
*
981319 TTTTAAT
1 TATTAAT
981326 CCAAATCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTAATATTTAAATAAATATAT
Found at i:991677 original size:4 final size:4
Alignment explanation
Indices: 991668--991696 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
991658 AGTTAGGTGC
991668 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
991697 CCTTTTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:994621 original size:28 final size:29
Alignment explanation
Indices: 994589--994661 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 29
994579 ACGCTTTCAA
* *
994589 AATATTAATATGATGT-AAAAATAATTAT-
1 AATATTAATATAATATAAAAAATAA-TATG
994617 AATA-TAATATAATATAAAAAATAATATG
1 AATATTAATATAATATAAAAAATAATATG
994645 AAT-TTAATATAAATATA
1 AATATTAATAT-AATATA
994662 TAAATATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 12 0.31
28 21 0.54
29 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (29 bp):
AATATTAATATAATATAAAAAATAATATG
Found at i:994655 original size:23 final size:22
Alignment explanation
Indices: 994615--994657 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
994605 AAAAATAATT
994615 ATAATATAATATAATATAAAAA
1 ATAATATAATATAATATAAAAA
*
994637 ATAATATGAATTTAATATAAA
1 ATAATAT-AATATAATATAAA
994658 TATATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
ATAATATAATATAATATAAAAA
Found at i:994674 original size:17 final size:17
Alignment explanation
Indices: 994654--994735 Score: 53
Period size: 17 Copynumber: 4.5 Consensus size: 17
994644 GAATTTAATA
994654 TAAATATATAAATATTT
1 TAAATATATAAATATTT
994671 TAAATTTATATAATATAAATTAT
1 TAAA--TATATAA-AT--ATT-T
*
994694 T-AATAAATTAAA-ATTT
1 TAAATATA-TAAATATTT
994710 ATATAA-ATATAAATATTT
1 -TA-AATATATAAATATTT
994728 TAAATATA
1 TAAATATA
994736 ATTATTATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 24
0.66 0.03 0.31
Matches are distributed among these distances:
16 3 0.06
17 17 0.33
18 6 0.12
19 9 0.18
20 6 0.12
21 3 0.06
22 5 0.10
23 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATATATAAATATTT
Found at i:994688 original size:5 final size:5
Alignment explanation
Indices: 994609--994664 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
994599 TGATGTAAAA
*
994609 ATAATT ATAAT ATAAT ATAAT ATAA- A-AA- ATAAT ATGAAT TTAAT ATAA-
1 ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT ATAAT
994657 AT-AT ATAA
1 ATAAT ATAA
994665 ATATTTTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
3 4 0.09
4 7 0.16
5 24 0.56
6 8 0.19
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:994690 original size:32 final size:31
Alignment explanation
Indices: 994649--994762 Score: 110
Period size: 32 Copynumber: 3.6 Consensus size: 31
994639 AATATGAATT
994649 TAATATAAATATATAAATATTTTAAATTTATA
1 TAATATAAATATATAAATA-TTTAAATTTATA
* *
994681 TAATATAAAT-TATTAATAAATTAAAATTTATA
1 TAATATAAATATA-TAA-ATATTTAAATTTATA
* *
994713 TAAATATAAATATTTTAAATA--TAATTATTATA
1 T-AATATAAATA-TATAAATATTTAAAT-TTATA
994745 TAATA-AAATATATAAATA
1 TAATATAAATATATAAATA
994763 CGTCTAAAAC
Statistics
Matches: 69, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
29 7 0.10
30 5 0.07
31 9 0.13
32 31 0.45
33 13 0.19
34 3 0.04
35 1 0.01
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TAATATAAATATATAAATATTTAAATTTATA
Found at i:997457 original size:71 final size:72
Alignment explanation
Indices: 997341--997493 Score: 265
Period size: 71 Copynumber: 2.1 Consensus size: 72
997331 TCATTATTAT
997341 GTATGATTTGATTCAATATTGTTCCTTTTTTTTTGGGTGTAC-ATATATATATATGTATATATAT
1 GTATGATTTGATTCAATATTGTTCCTTTTTTTTTGGGTGTACAATATATATATATGTATATATAT
997405 TTGGGAA
66 TTGGGAA
997412 GTATGATTTGATTCAATATTGTTCCTTTTTTTTTGGGTGTACATATATATATATATATGTATATA
1 GTATGATTTGATTCAATATTGTTCCTTTTTTTTTGGGTGTAC--A-ATATATATATATGTATATA
997477 TATTTGGGAA
63 TATTTGGGAA
997487 GTA-GATT
1 GTATGATT
997494 ACATTTGTCT
Statistics
Matches: 78, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
71 42 0.54
74 4 0.05
75 32 0.41
ACGTcount: A:0.27, C:0.05, G:0.17, T:0.50
Consensus pattern (72 bp):
GTATGATTTGATTCAATATTGTTCCTTTTTTTTTGGGTGTACAATATATATATATGTATATATAT
TTGGGAA
Found at i:1002034 original size:11 final size:11
Alignment explanation
Indices: 1002020--1002080 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
1002010 ATTAATAAAA
1002020 ATATAATTATT
1 ATATAATTATT
* *
1002031 ATATAATAAACT
1 ATATAAT-TATT
*
1002043 ATATAAATATT
1 ATATAATTATT
*
1002054 ATATAAATA-T
1 ATATAATTATT
1002064 ATA-AATTATT
1 ATATAATTATT
1002074 AATATAA
1 -ATATAA
1002081 AATTTAGTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
9 4 0.10
10 5 0.12
11 21 0.52
12 10 0.25
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
ATATAATTATT
Found at i:1002053 original size:23 final size:22
Alignment explanation
Indices: 1002012--1002059 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
1002002 ATTTTAAAAT
*
1002012 TAATAAAAATATAATTATTATA
1 TAATAAAAATATAAATATTATA
*
1002034 TAATAAACTATATAAATATTATA
1 TAATAAA-AATATAAATATTATA
1002057 TAA
1 TAA
1002060 ATATATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TAATAAAAATATAAATATTATA
Found at i:1002078 original size:21 final size:21
Alignment explanation
Indices: 1002010--1002081 Score: 82
Period size: 21 Copynumber: 3.5 Consensus size: 21
1002000 ATATTTTAAA
1002010 ATTAATA-AAA-ATAT-AATT
1 ATTAATATAAATATATAAATT
1002028 ATTATATAATAAACTATATAAA-T
1 ATTA-AT-ATAAA-TATATAAATT
1002051 ATT-ATATAAATATATAAATT
1 ATTAATATAAATATATAAATT
1002071 ATTAATATAAA
1 ATTAATATAAA
1002082 ATTTAGTCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
18 4 0.09
19 10 0.22
20 10 0.22
21 12 0.26
23 8 0.17
24 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTAATATAAATATATAAATT
Found at i:1004311 original size:14 final size:15
Alignment explanation
Indices: 1004292--1004320 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1004282 TATAAATTAA
1004292 AATTAAA-AATTTTT
1 AATTAAATAATTTTT
1004306 AATTAAATAATTTTT
1 AATTAAATAATTTTT
1004321 TACTGATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTAAATAATTTTT
Found at i:1005084 original size:34 final size:34
Alignment explanation
Indices: 1005020--1005202 Score: 253
Period size: 34 Copynumber: 5.4 Consensus size: 34
1005010 GTGAACATAC
*
1005020 TGTTGATTAAAT--GATGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGA-GATTTGGTAGCTTACCAT
* *
1005053 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1005087 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
1005121 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1005155 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1005189 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1005203 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 11 0.08
34 119 0.90
35 2 0.02
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1005641 original size:34 final size:34
Alignment explanation
Indices: 1005575--1005759 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
1005565 AAGTGGGAGA
*
1005575 ATTGTTGATTAAAT--GATGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGA-GATTTGGTAGCTTACC
* *
1005608 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1005642 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
1005676 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1005710 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1005744 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1005760 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 13 0.10
34 119 0.89
35 2 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1010121 original size:18 final size:18
Alignment explanation
Indices: 1010089--1010153 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
1010079 TATTAAATCA
*
1010089 AATTTAAATAAAAATTTT
1 AATTTAAATATAAATTTT
*
1010107 AATTTAATTATAAATATTT
1 AATTTAAATATAAAT-TTT
* **
1010126 -ATATAAATATATTTTTT
1 AATTTAAATATAAATTTT
*
1010143 AATTTATATAT
1 AATTTAAATAT
1010154 TTTTTTAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
17 3 0.08
18 31 0.84
19 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AATTTAAATATAAATTTT
Found at i:1010718 original size:2 final size:2
Alignment explanation
Indices: 1010711--1010736 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1010701 GATTGCGAGC
1010711 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
1010737 TGGCAGTAGA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1017800 original size:14 final size:15
Alignment explanation
Indices: 1017742--1017809 Score: 66
Period size: 16 Copynumber: 4.3 Consensus size: 15
1017732 AGGATATGAA
1017742 AAATATAATATAAAT
1 AAATATAATATAAAT
*
1017757 ATAATATATTTTATAAAT
1 A-AATATA--ATATAAAT
*
1017775 ACGAAAATAATAT-AAT
1 A--AATATAATATAAAT
1017791 AAATATAATATAAAT
1 AAATATAATATAAAT
1017806 AAAT
1 AAAT
1017810 TATATTTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
14 9 0.21
15 8 0.19
16 10 0.23
17 3 0.07
18 8 0.19
19 5 0.12
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (15 bp):
AAATATAATATAAAT
Found at i:1019095 original size:199 final size:195
Alignment explanation
Indices: 1018725--1019112 Score: 668
Period size: 199 Copynumber: 2.0 Consensus size: 195
1018715 AAATAAATAT
1018725 GTATTCAATATTAGTATATTTAATTATTTTTTTTCAAAATTTTTATATAATTTAAAAGTTTTAAA
1 GTATTCAATATTAGTATATTTAATTATTTTTTTTCAAAATTTTTATATAATTTAAAAGTTTTAAA
1018790 AAAATTATATCTTTATATTTATCTACGTGTGTCAGACAATAGAATAAAGGAGTTAGAGCTACGTT
66 AAAATTATATCTTTATATTTATCTACGTGTGTCAGACAATAGAATAAAGGAGTTAGAGCTACGTT
*
1018855 GAAACTGGTTTTCACTGTGAAAAATCAAGTACCTGGCAGATCAACATTTGAACTCCACCTTCTTA
131 GAAACTGGTTTTCACTGTAAAAAATCAAGTACCTGGCAGATCAACATTTGAACTCCACCTTCTTA
** * *
1018920 GTATTCAATATTAGTATATTTAATTATTTTTTTTTTAAATTTTTATATAATTTAAGAGTTTTAGA
1 GTATTCAATATTAGTATATTTAATTATTTTTTTTCAAAATTTTTATATAATTTAAAAGTTTTAAA
* * *
1018985 AAGATTATATTTTTATATTTATCTCTATATGTGTGTCAGACAATAGAATAAAGGAGTTAGAGCTA
66 AAAATTATATCTTTATATTTA--TC--TACGTGTGTCAGACAATAGAATAAAGGAGTTAGAGCTA
1019050 CGTTGAAACTGGTTTTCACTGTAAAAAATCAAGTACCTGGCAGATCAACATTTGAACTCCACC
127 CGTTGAAACTGGTTTTCACTGTAAAAAATCAAGTACCTGGCAGATCAACATTTGAACTCCACC
1019113 CTCTAGGAAA
Statistics
Matches: 181, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
195 80 0.44
197 2 0.01
199 99 0.55
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (195 bp):
GTATTCAATATTAGTATATTTAATTATTTTTTTTCAAAATTTTTATATAATTTAAAAGTTTTAAA
AAAATTATATCTTTATATTTATCTACGTGTGTCAGACAATAGAATAAAGGAGTTAGAGCTACGTT
GAAACTGGTTTTCACTGTAAAAAATCAAGTACCTGGCAGATCAACATTTGAACTCCACCTTCTTA
Found at i:1022504 original size:26 final size:25
Alignment explanation
Indices: 1022463--1022519 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
1022453 TTGCTTTTTT
*
1022463 TTTTACTTTAAATTAAAA-AATATTA
1 TTTTAATTTAAATTAAAATAAT-TTA
1022488 TTTTAATTTAAATTTAAAATAATTTA
1 TTTTAATTTAAA-TTAAAATAATTTA
*
1022514 ATTTAA
1 TTTTAA
1022520 GATCAAGTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 11 0.39
26 14 0.50
27 3 0.11
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTTAATTTAAATTAAAATAATTTA
Found at i:1024191 original size:20 final size:21
Alignment explanation
Indices: 1024163--1024201 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1024153 TAAAATAAAA
1024163 ATAATAAAATTTAAATTTTTG
1 ATAATAAAATTTAAATTTTTG
1024184 ATAA-AAAATTTAAATTTT
1 ATAATAAAATTTAAATTTT
1024202 AAAATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (21 bp):
ATAATAAAATTTAAATTTTTG
Found at i:1025355 original size:30 final size:30
Alignment explanation
Indices: 1025321--1025386 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 30
1025311 TTTTATTTAT
*
1025321 TTAATTTTAAATATATAA-AAATAAAAAT-TA
1 TTAATTTT-AATA-ATAATAAACAAAAATATA
1025351 TTAA-TTTAATAATAATAAACAAAAATATA
1 TTAATTTTAATAATAATAAACAAAAATATA
*
1025380 TTTATTT
1 TTAATTT
1025387 ATGATAGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 4 0.13
28 13 0.42
29 8 0.26
30 6 0.19
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (30 bp):
TTAATTTTAATAATAATAAACAAAAATATA
Found at i:1025804 original size:2 final size:2
Alignment explanation
Indices: 1025793--1025824 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1025783 AATTTTATTA
1025793 AT AT -T 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
1025825 AATGCCTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1026055 original size:4 final size:4
Alignment explanation
Indices: 1026037--1026070 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
1026027 CACGATATCA
1026037 TAAT T-AT TAAAT TAAT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT T-AAT TAAT TAAT TAAT TAAT TAAT TA
1026071 TCTTTGTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.11
4 22 0.79
5 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:1031445 original size:16 final size:17
Alignment explanation
Indices: 1031419--1031456 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1031409 AATTAAAATT
1031419 TTTATATTTAAATTTAA
1 TTTATATTTAAATTTAA
*
1031436 TTTA-ATTTAAATTTGA
1 TTTATATTTAAATTTAA
1031452 TTTAT
1 TTTAT
1031457 TAACTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TTTATATTTAAATTTAA
Found at i:1031924 original size:2 final size:2
Alignment explanation
Indices: 1031917--1031941 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1031907 ACCAGAAATT
1031917 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
1031942 GAAAAATGTG
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:1032794 original size:20 final size:20
Alignment explanation
Indices: 1032757--1032794 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1032747 TTATTAAATA
**
1032757 ATTTAAATTAAATTAAATTG
1 ATTTAAATTAAAAAAAATTG
1032777 ATTTAAATTAAAAAAAAT
1 ATTTAAATTAAAAAAAAT
1032795 CTTTATCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
ATTTAAATTAAAAAAAATTG
Found at i:1041340 original size:22 final size:21
Alignment explanation
Indices: 1041296--1041336 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1041286 ATAATTCATT
*
1041296 TTTTTATAATTTTGTAATTTA
1 TTTTTATAATTTTCTAATTTA
1041317 TTTTT-TAATTTTACTAATTT
1 TTTTTATAATTTT-CTAATTT
1041337 TATTGATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTTATAATTTTCTAATTTA
Found at i:1042073 original size:19 final size:19
Alignment explanation
Indices: 1042046--1042094 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
1042036 TTTATTTTAA
* *
1042046 TTAATATTAAAATTTTTATT
1 TTAA-ATTAAAATTTTAAGT
1042066 TTAAATT-AAATTTTAAGT
1 TTAAATTAAAATTTTAAGT
1042084 TTAAATATAAA
1 TTAAAT-TAAA
1042095 TAATTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 15 0.60
19 4 0.16
20 6 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TTAAATTAAAATTTTAAGT
Found at i:1042106 original size:20 final size:18
Alignment explanation
Indices: 1042065--1042113 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
1042055 AAATTTTTAT
* *
1042065 TTTAAATTAAATTTTAAG
1 TTTAAATTAAATATTAAA
1042083 TTTAAATATAAATAATTAAA
1 TTTAAAT-TAAAT-ATTAAA
1042103 TTTAAAATTAA
1 TTT-AAATTAA
1042114 TTAAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 7 0.27
19 5 0.19
20 10 0.38
21 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TTTAAATTAAATATTAAA
Found at i:1042195 original size:18 final size:18
Alignment explanation
Indices: 1042172--1042220 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1042162 AATCTCTAAT
1042172 AATTTAATTTTTATTTTA
1 AATTTAATTTTTATTTTA
**
1042190 AATTTAATTTAAATTTTA
1 AATTTAATTTTTATTTTA
* *
1042208 AAATTAAATTTTA
1 AATTTAATTTTTA
1042221 ATTAAGCTCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTTAATTTTTATTTTA
Found at i:1042217 original size:19 final size:18
Alignment explanation
Indices: 1042184--1042223 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1042174 TTTAATTTTT
*
1042184 ATTTTAAATTTAATTTAA
1 ATTTTAAATTAAATTTAA
*
1042202 ATTTTAAAATTAAATTTTA
1 ATTTT-AAATTAAATTTAA
1042221 ATT
1 ATT
1042224 AAGCTCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTAAATTAAATTTAA
Found at i:1042250 original size:13 final size:12
Alignment explanation
Indices: 1042171--1042255 Score: 68
Period size: 12 Copynumber: 7.1 Consensus size: 12
1042161 TAATCTCTAA
*
1042171 TAATTTAATTTT
1 TAATTTAAATTT
*
1042183 TATTTTAAA-TT
1 TAATTTAAATTT
1042194 TAATTTAAATTT
1 TAATTTAAATTT
*
1042206 TAAAATTAAATTT
1 T-AATTTAAATTT
**
1042219 TAA-TT-AAGCT
1 TAATTTAAATTT
*
1042229 CAATTTAAATTT
1 TAATTTAAATTT
1042241 TAAGTTTAAACTTT
1 TAA-TTTAAA-TTT
1042255 T
1 T
1042256 TATAACTTGA
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
10 5 0.09
11 14 0.25
12 17 0.30
13 17 0.30
14 4 0.07
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (12 bp):
TAATTTAAATTT
Found at i:1043288 original size:35 final size:35
Alignment explanation
Indices: 1043249--1043322 Score: 80
Period size: 35 Copynumber: 2.1 Consensus size: 35
1043239 AAATCATCTG
*
1043249 ATTTAAAAGTTTAAT-TTAAAATGAATTAAATTTA
1 ATTTAAAAGTTTAATATTAAAATAAATTAAATTTA
* * * *
1043283 TATTT-ATATTTTAATATTTAAATAAATTTAATTTA
1 -ATTTAAAAGTTTAATATTAAAATAAATTAAATTTA
1043318 ATTTA
1 ATTTA
1043323 TTATTTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
34 12 0.38
35 20 0.62
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (35 bp):
ATTTAAAAGTTTAATATTAAAATAAATTAAATTTA
Found at i:1043328 original size:35 final size:34
Alignment explanation
Indices: 1043258--1043328 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 34
1043248 GATTTAAAAG
*
1043258 TTTAATTTAAAATGAATTAAATTTATATTTATAT
1 TTTAATTTAAAATAAATTAAATTTATATTTATAT
* *
1043292 TTTAATATTTAAATAAATTTAATTTA-ATTTATTAT
1 TTTAAT-TTAAAATAAATTAAATTTATATTTA-TAT
1043327 TT
1 TT
1043329 ATTTAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 11 0.34
35 21 0.66
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (34 bp):
TTTAATTTAAAATAAATTAAATTTATATTTATAT
Found at i:1050022 original size:37 final size:38
Alignment explanation
Indices: 1049970--1050060 Score: 96
Period size: 38 Copynumber: 2.4 Consensus size: 38
1049960 TAATTTAAAA
* *
1049970 TTTTATTTTATTATTTA-AAATAAAATTAAAAAATATT
1 TTTTATATTAATATTTATAAATAAAATTAAAAAATATT
* * **
1050007 TTTTATATTAATATTTATAATTAAATTTAATTAATATT
1 TTTTATATTAATATTTATAAATAAAATTAAAAAATATT
1050045 TTATTA-ATTAAATATT
1 TT-TTATATT-AATATT
1050061 AATATGAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
37 15 0.33
38 21 0.47
39 9 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (38 bp):
TTTTATATTAATATTTATAAATAAAATTAAAAAATATT
Found at i:1051573 original size:16 final size:16
Alignment explanation
Indices: 1051552--1051582 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1051542 ATGTCTGAGT
1051552 TTAACTCTGATTTCTC
1 TTAACTCTGATTTCTC
*
1051568 TTAACTTTGATTTCT
1 TTAACTCTGATTTCT
1051583 TTCCAGAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.55
Consensus pattern (16 bp):
TTAACTCTGATTTCTC
Found at i:1054400 original size:3 final size:3
Alignment explanation
Indices: 1054392--1054425 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1054382 CCTTTGTTCT
1054392 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1054426 GGTTTTCAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1060831 original size:20 final size:21
Alignment explanation
Indices: 1060798--1060842 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
1060788 AATCCATAAC
1060798 AAATGAAAAATATTTAAATTT
1 AAATGAAAAATATTTAAATTT
* **
1060819 AAAT-AAAATTATTTTTATTT
1 AAATGAAAAATATTTAAATTT
1060839 AAAT
1 AAAT
1060843 TAATTTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AAATGAAAAATATTTAAATTT
Found at i:1061001 original size:17 final size:17
Alignment explanation
Indices: 1060979--1061013 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1060969 TTTAAACTTT
1060979 AAAAA-TATAAATTTAAA
1 AAAAATTAT-AATTTAAA
1060996 AAAAATTATAATTTAAA
1 AAAAATTATAATTTAAA
1061013 A
1 A
1061014 TAATTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAATTATAATTTAAA
Found at i:1061013 original size:16 final size:18
Alignment explanation
Indices: 1060979--1061025 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
1060969 TTTAAACTTT
1060979 AAAAA-TATAAATTTAAA
1 AAAAATTATAAATTTAAA
1060996 AAAAATTAT-AATTT-AA
1 AAAAATTATAAATTTAAA
*
1061012 AATAATT-TAAATTT
1 AAAAATTATAAATTT
1061026 TAAATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 1 0.04
16 13 0.48
17 10 0.37
18 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAATTATAAATTTAAA
Done.