Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 337 of 362
Found at i:112173190 original size:25 final size:25
Alignment explanation
Indices: 112173116--112173191 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
112173106 GTCTTACACA
* *
112173116 TTTCATATCAGGTTGCCATGGTATC
1 TTTCATATCATGTTGCTATGGTATC
* * *
112173141 TTTCA-ACCATGGT-CT-T-GCA-C
1 TTTCATATCATGTTGCTATGGTATC
112173161 GTTTCATATCATGTTGCTATGGTATC
1 -TTTCATATCATGTTGCTATGGTATC
112173187 TTTCA
1 TTTCA
112173192 ACCATGGTCT
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
20 1 0.03
21 7 0.19
22 7 0.19
23 3 0.08
24 6 0.16
25 12 0.32
26 1 0.03
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (25 bp):
TTTCATATCATGTTGCTATGGTATC
Found at i:112175413 original size:11 final size:11
Alignment explanation
Indices: 112175397--112175435 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
112175387 ACTAAATAAT
112175397 TAATAATAAAA
1 TAATAATAAAA
*
112175408 TAATAATGAAA
1 TAATAATAAAA
112175419 TAATAATAAAA
1 TAATAATAAAA
*
112175430 AAATAA
1 TAATAA
112175436 AATATTTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:112178784 original size:22 final size:22
Alignment explanation
Indices: 112178756--112178800 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
112178746 AATGGATGAA
112178756 TGAATAAATGACAAATGAATGT
1 TGAATAAATGACAAATGAATGT
*
112178778 TGAATAAATGACGAATGAATGT
1 TGAATAAATGACAAATGAATGT
112178800 T
1 T
112178801 AGTCATGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.04, G:0.20, T:0.29
Consensus pattern (22 bp):
TGAATAAATGACAAATGAATGT
Found at i:112182670 original size:22 final size:23
Alignment explanation
Indices: 112182645--112182693 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
112182635 AAGAAACCAG
112182645 AAATTT-GGTGTGAGGGAAATGA
1 AAATTTCGGTGTGAGGGAAATGA
* *
112182667 AAATTTCTGTGTGAGGGAGATGA
1 AAATTTCGGTGTGAGGGAAATGA
112182690 AAAT
1 AAAT
112182694 AAAATTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.37, C:0.02, G:0.33, T:0.29
Consensus pattern (23 bp):
AAATTTCGGTGTGAGGGAAATGA
Found at i:112183214 original size:20 final size:21
Alignment explanation
Indices: 112183175--112183214 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
112183165 AAATTTTAAA
*
112183175 AACCACAATATTGAAAAATAC
1 AACCACAATATTCAAAAATAC
*
112183196 AACCACAA-ATTCCAAAATA
1 AACCACAATATTCAAAAATA
112183215 GTTAATTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.57, C:0.23, G:0.03, T:0.17
Consensus pattern (21 bp):
AACCACAATATTCAAAAATAC
Found at i:112186989 original size:22 final size:23
Alignment explanation
Indices: 112186945--112186986 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
112186935 TTAACTTAAC
112186945 AACTAACTTAACTCAAAATAATT
1 AACTAACTTAACTCAAAATAATT
*
112186968 AACTAA-TTAA-TCATAATAA
1 AACTAACTTAACTCAAAATAA
112186987 ATTTTTAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 4 0.22
23 6 0.33
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (23 bp):
AACTAACTTAACTCAAAATAATT
Found at i:112187979 original size:17 final size:16
Alignment explanation
Indices: 112187953--112187998 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
112187943 ATATTAAAAA
* *
112187953 ATTTATATATGTTTTTT
1 ATTTAAATAT-TTATTT
112187970 ATTTAAATATTTATTT
1 ATTTAAATATTTATTT
112187986 ATTTATAATATTT
1 ATTTA-AATATTT
112187999 TACTATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
ATTTAAATATTTATTT
Found at i:112190731 original size:6 final size:6
Alignment explanation
Indices: 112190720--112190754 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
112190710 TTCATATATA
* *
112190720 TGCGTG TGCGTG TGTGTG TGCGTG TGCGTG CGCGT
1 TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG TGCGT
112190755 ATATATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.17, G:0.49, T:0.34
Consensus pattern (6 bp):
TGCGTG
Found at i:112200185 original size:35 final size:35
Alignment explanation
Indices: 112200139--112200208 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
112200129 ACATACATAG
* *
112200139 TTTTTATTCCTCATTTCTGTTGGGTTTTTCACACA
1 TTTTTATTCCTCATTCCTGTTGGATTTTTCACACA
112200174 TTTTTATTCCTCATTCCTGTTGGATTTTTCACACA
1 TTTTTATTCCTCATTCCTGTTGGATTTTTCACACA
112200209 GGAAGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.16, C:0.21, G:0.10, T:0.53
Consensus pattern (35 bp):
TTTTTATTCCTCATTCCTGTTGGATTTTTCACACA
Found at i:112201191 original size:31 final size:31
Alignment explanation
Indices: 112201153--112201216 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
112201143 CCCTTTCATA
*
112201153 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTAGGCCGAAGCCT
**
112201184 TTTCATATTTCATATTACTAGGCCGAAGCCT
1 TTTCATATTTCATAACACTAGGCCGAAGCCT
112201215 TT
1 TT
112201217 ACTGTAACCG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTAGGCCGAAGCCT
Found at i:112201472 original size:23 final size:23
Alignment explanation
Indices: 112201422--112201500 Score: 124
Period size: 22 Copynumber: 3.4 Consensus size: 23
112201412 CTGGAGGCCT
*
112201422 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACT-GGGCATA
112201447 AGCCCTTTTAATAACTGGGCATA
1 AGCCCTTTTAATAACTGGGCATA
112201470 AGCCC-TTTAATAACTGGGCATA
1 AGCCCTTTTAATAACTGGGCATA
112201492 AGCCCTTTT
1 AGCCCTTTT
112201501 GCACTTCCTC
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
22 22 0.42
23 14 0.27
24 12 0.23
25 4 0.08
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (23 bp):
AGCCCTTTTAATAACTGGGCATA
Found at i:112201575 original size:20 final size:20
Alignment explanation
Indices: 112201550--112201616 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
112201540 TTATGAATAC
112201550 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
112201570 ATCATGTGCATAGCATACAT
1 ATCATGTGCATATCATACAT
*
112201590 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
112201610 ACCATGT
1 ATCATGT
112201617 TTACTAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:112204675 original size:41 final size:41
Alignment explanation
Indices: 112204559--112204664 Score: 203
Period size: 41 Copynumber: 2.6 Consensus size: 41
112204549 AGTGAAATTA
112204559 TTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGACACAT
1 TTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGACACAT
112204600 TTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGACACAT
1 TTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGACACAT
*
112204641 TTCGGACTATAAGTCTAGCAGGCT
1 TTCAGACTATAAGTCTAGCAGGCT
112204665 AAGAGCCGGT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (41 bp):
TTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGACACAT
Found at i:112204933 original size:33 final size:33
Alignment explanation
Indices: 112204877--112204974 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
112204867 ATAGATATGT
*
112204877 ATATATATATATGT-TGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
*
112204909 ATATATTTATGTGTATGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
* * *
112204942 AAATAAGTGTATGTATCTATGCATTCGGCATAG
1 ATAT-A-TATATG--TGTATGCATTCGGCATAG
112204975 ATGGGTATAG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 21 0.38
34 1 0.02
35 5 0.09
37 17 0.30
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (33 bp):
ATATATATATGTGTATGCATTCGGCATAGGTGA
Found at i:112212310 original size:41 final size:41
Alignment explanation
Indices: 112212194--112212299 Score: 203
Period size: 41 Copynumber: 2.6 Consensus size: 41
112212184 GTGAAAATTA
112212194 TTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGACACAT
1 TTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGACACAT
112212235 TTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGACACAT
1 TTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGACACAT
*
112212276 TTCGGACTATAAGTCTAGCAGGCT
1 TTCAGACTATAAGTCTAGCAGGCT
112212300 AAGAGCCGGT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (41 bp):
TTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGACACAT
Found at i:112212570 original size:33 final size:33
Alignment explanation
Indices: 112212514--112212611 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
112212504 ATAGATATGT
*
112212514 ATATATATATATGT-TGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
*
112212546 ATATATTTATGTGTATGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
* * *
112212579 AAATAAGTGTATGTATCTATGCATTCGGCATAG
1 ATAT-A-TATATG--TGTATGCATTCGGCATAG
112212612 ATGGGTATAG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 21 0.38
34 1 0.02
35 5 0.09
37 17 0.30
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (33 bp):
ATATATATATGTGTATGCATTCGGCATAGGTGA
Found at i:112220322 original size:23 final size:23
Alignment explanation
Indices: 112220292--112220340 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
112220282 CCTAGCCTCA
112220292 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
112220315 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
112220338 TTT
1 TTT
112220341 TGCCCTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:112220416 original size:20 final size:20
Alignment explanation
Indices: 112220391--112220457 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
112220381 TTATGAATAC
112220391 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
112220411 ATCATGTGCATAGCAAACAT
1 ATCATGTGCATATCATACAT
* *
112220431 GTCATGTACATATCATACAT
1 ATCATGTGCATATCATACAT
*
112220451 ACCATGT
1 ATCATGT
112220458 TTACTAAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:112231026 original size:16 final size:17
Alignment explanation
Indices: 112231005--112231036 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
112230995 CTTCATCGAA
112231005 AAAAAAAAGAA-AAAAT
1 AAAAAAAAGAACAAAAT
112231021 AAAAAAAAGAACAAAA
1 AAAAAAAAGAACAAAA
112231037 CAAGACAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.88, C:0.03, G:0.06, T:0.03
Consensus pattern (17 bp):
AAAAAAAAGAACAAAAT
Found at i:112234382 original size:77 final size:77
Alignment explanation
Indices: 112234287--112234447 Score: 250
Period size: 77 Copynumber: 2.1 Consensus size: 77
112234277 TTTCAAATAT
* * *
112234287 TTATAGTGTTCCAATAACTATAAATGAATGAATGCAATTAATCAAAAGATTATACTACTTGATTT
1 TTATAATGTTCCAATAACTAAAAATCAATGAATGCAATTAATCAAAAGATTATACTACTTGATTT
112234352 TTTGAAAAAGAA
66 TTTGAAAAAGAA
* ** * *
112234364 TTATAATGTTCCACTAACTAAAAATCAATGGGTGTACTTAATCAAAAGATTATACTACTTGATTT
1 TTATAATGTTCCAATAACTAAAAATCAATGAATGCAATTAATCAAAAGATTATACTACTTGATTT
112234429 TTTGAAAAAGAA
66 TTTGAAAAAGAA
112234441 TTATAAT
1 TTATAAT
112234448 TTTTTGATCA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (77 bp):
TTATAATGTTCCAATAACTAAAAATCAATGAATGCAATTAATCAAAAGATTATACTACTTGATTT
TTTGAAAAAGAA
Found at i:112238842 original size:12 final size:12
Alignment explanation
Indices: 112238825--112238890 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 12
112238815 TTTCGTTTTT
112238825 TTATTATTGTTA
1 TTATTATTGTTA
**
112238837 TTATTATTCCTA
1 TTATTATTGTTA
* * **
112238849 ATATTAGTAATA
1 TTATTATTGTTA
*
112238861 ATATTATT-TCTA
1 TTATTATTGT-TA
112238873 TTATTATTGTTA
1 TTATTATTGTTA
112238885 TTATTA
1 TTATTA
112238891 ATATTCTGGT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
12 42 0.98
13 1 0.02
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (12 bp):
TTATTATTGTTA
Found at i:112239675 original size:17 final size:17
Alignment explanation
Indices: 112239655--112239688 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
112239645 TACTATTATA
112239655 TATATATATATATTTTT
1 TATATATATATATTTTT
* *
112239672 TATATCTGTATATTTTT
1 TATATATATATATTTTT
112239689 ATACCATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (17 bp):
TATATATATATATTTTT
Found at i:112242060 original size:22 final size:22
Alignment explanation
Indices: 112242035--112242076 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
112242025 ATAATTTAAA
*
112242035 ATATAATTTTATTAATATATAT
1 ATATAAATTTATTAATATATAT
112242057 ATATAAATTTATTAATATAT
1 ATATAAATTTATTAATATAT
112242077 GTAAAAACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATAAATTTATTAATATATAT
Found at i:112242184 original size:19 final size:20
Alignment explanation
Indices: 112242160--112242204 Score: 83
Period size: 19 Copynumber: 2.3 Consensus size: 20
112242150 ATTCAAACGT
112242160 CAGAAAAGTAAATCA-TTTC
1 CAGAAAAGTAAATCATTTTC
112242179 CAGAAAAGTAAATCATTTTC
1 CAGAAAAGTAAATCATTTTC
112242199 CAGAAA
1 CAGAAA
112242205 TCATTTTTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (20 bp):
CAGAAAAGTAAATCATTTTC
Found at i:112242927 original size:27 final size:25
Alignment explanation
Indices: 112242887--112242940 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 25
112242877 TGGTGATTTA
*
112242887 GAGTATGACACGAATATTGTTAAGTTT
1 GAGTATGACACGAA-ATT-CTAAGTTT
* *
112242914 GAGTTTGACTCGAAATTCTAAGTTT
1 GAGTATGACACGAAATTCTAAGTTT
112242939 GA
1 GA
112242941 TACTCTAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 9 0.38
26 3 0.12
27 12 0.50
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.37
Consensus pattern (25 bp):
GAGTATGACACGAAATTCTAAGTTT
Found at i:112246333 original size:24 final size:24
Alignment explanation
Indices: 112246303--112246354 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
112246293 AAAATAAAAC
* * *
112246303 AAGATAATAGAGTTCAGTTGGGAA
1 AAGATAACAAAGTTCAATTGGGAA
*
112246327 AAGATAACAAAGTTTAATTGGGAA
1 AAGATAACAAAGTTCAATTGGGAA
112246351 AAGA
1 AAGA
112246355 AACTCGATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.04, G:0.25, T:0.23
Consensus pattern (24 bp):
AAGATAACAAAGTTCAATTGGGAA
Found at i:112247871 original size:26 final size:26
Alignment explanation
Indices: 112247822--112247872 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
112247812 GACACACTGC
* *
112247822 AGCTCTTCATGAGCTTCTTGATTAAA
1 AGCTCTTCATGAGCTTCCTAATTAAA
**
112247848 AGCTCTTTGTGAGCTTCCTAATTAA
1 AGCTCTTCATGAGCTTCCTAATTAA
112247873 TGGTTCTCTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (26 bp):
AGCTCTTCATGAGCTTCCTAATTAAA
Found at i:112249250 original size:15 final size:16
Alignment explanation
Indices: 112249230--112249263 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
112249220 ATTTTTTTAA
112249230 AAATTATAAAAAT-AT
1 AAATTATAAAAATGAT
*
112249245 AAATTATTAAAATGAT
1 AAATTATAAAAATGAT
112249261 AAA
1 AAA
112249264 ATTAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATGAT
Found at i:112252347 original size:17 final size:17
Alignment explanation
Indices: 112252325--112252365 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
112252315 ATAATTCATT
* * *
112252325 TTATTTTTCAAATATAA
1 TTATTTTTAAAAAAAAA
112252342 TTATTTTTAAAAAAAAA
1 TTATTTTTAAAAAAAAA
112252359 TTATTTT
1 TTATTTT
112252366 CACCCCAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATTTTTAAAAAAAAA
Found at i:112252433 original size:5 final size:5
Alignment explanation
Indices: 112252423--112252447 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
112252413 AAATGTTTTG
112252423 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
112252448 GGTATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:112255642 original size:46 final size:46
Alignment explanation
Indices: 112255592--112255719 Score: 222
Period size: 46 Copynumber: 2.8 Consensus size: 46
112255582 TGGTTGAGCA
*
112255592 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
112255638 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
112255684 CCCG-AGTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
112255720 GCGGGTTACA
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
45 31 0.39
46 48 0.61
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:112259023 original size:54 final size:54
Alignment explanation
Indices: 112258941--112259049 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
112258931 AGGTAAAAAT
*
112258941 TAAATCCTTCTTGTTAAGAGTGAGTAGGCTCCTTTGGGAGAAGTCTTTGAAGTG
1 TAAATCCTTCTTGTTAAGAGTGAGTAGGCTCCTTTGAGAGAAGTCTTTGAAGTG
112258995 TAAATCCTTCTTGTTAAGAGTGAGTAGGCTCCTTTGAGAGAAGTCTTTGAAGTG
1 TAAATCCTTCTTGTTAAGAGTGAGTAGGCTCCTTTGAGAGAAGTCTTTGAAGTG
112259049 T
1 T
112259050 CGTTTGCTGG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.36
Consensus pattern (54 bp):
TAAATCCTTCTTGTTAAGAGTGAGTAGGCTCCTTTGAGAGAAGTCTTTGAAGTG
Found at i:112281516 original size:23 final size:23
Alignment explanation
Indices: 112281490--112281533 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
112281480 ATTAACGAAT
* *
112281490 CAAATATTAAAATATAAATTTGC
1 CAAACATTAAAACATAAATTTGC
*
112281513 CAAACATTAAAGCATAAATTT
1 CAAACATTAAAACATAAATTT
112281534 TGTTGTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (23 bp):
CAAACATTAAAACATAAATTTGC
Found at i:112285516 original size:30 final size:32
Alignment explanation
Indices: 112285464--112285544 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 32
112285454 AGACTATACC
*
112285464 TTTATGATTTTTAAAAAATTAAA-T-TAATTT
1 TTTATTATTTTTAAAAAATTAAAGTATAATTT
* * *
112285494 TTTATTATTTTTAGAGAGTTAAAGTATAATTT
1 TTTATTATTTTTAAAAAATTAAAGTATAATTT
112285526 TATTATTATTAATTTAAAA
1 T-TTATTATT--TTTAAAA
112285545 TTTTATAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
30 19 0.47
31 1 0.03
32 7 0.17
33 8 0.20
35 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (32 bp):
TTTATTATTTTTAAAAAATTAAAGTATAATTT
Found at i:112286661 original size:23 final size:23
Alignment explanation
Indices: 112286634--112286677 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
112286624 TTCTAAAATT
112286634 TTAAAATCTGAAAAATAAAAGAA
1 TTAAAATCTGAAAAATAAAAGAA
* *
112286657 TTAAATTCTTAAAAATAAAAG
1 TTAAAATCTGAAAAATAAAAG
112286678 TACAAGGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (23 bp):
TTAAAATCTGAAAAATAAAAGAA
Found at i:112289599 original size:16 final size:16
Alignment explanation
Indices: 112289580--112289624 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
112289570 TAAAATTTTC
*
112289580 TTTTTTTAAAATAAAA
1 TTTTTATAAAATAAAA
*
112289596 TTTTTATAAAATTAAA
1 TTTTTATAAAATAAAA
112289612 -TTTTATAAAATAA
1 TTTTTATAAAATAA
112289625 TACTAGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTTTATAAAATAAAA
Found at i:112290187 original size:16 final size:16
Alignment explanation
Indices: 112290148--112290188 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
112290138 TATTTAAAAA
112290148 TATAATTTTATCATTT
1 TATAATTTTATCATTT
112290164 TA-ATATTTTAT-ATCTT
1 TATA-ATTTTATCAT-TT
112290180 TATAATTTT
1 TATAATTTT
112290189 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.14
16 18 0.82
17 1 0.05
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (16 bp):
TATAATTTTATCATTT
Found at i:112292080 original size:29 final size:28
Alignment explanation
Indices: 112292047--112292120 Score: 93
Period size: 26 Copynumber: 2.8 Consensus size: 28
112292037 CAGGCGCGAC
112292047 TTTTTTTATATTAAAATATATATTTTTT
1 TTTTTTTATATTAAAATATATATTTTTT
*
112292075 GTTTTTTTA-AATAAAATAT-TATTTTTT
1 -TTTTTTTATATTAAAATATATATTTTTT
*
112292102 TTATTTT-TATTAAAA-ATAT
1 TTTTTTTATATTAAAATATAT
112292121 TTAAATTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
25 2 0.05
26 13 0.32
27 8 0.20
28 9 0.22
29 8 0.20
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (28 bp):
TTTTTTTATATTAAAATATATATTTTTT
Found at i:112292117 original size:27 final size:27
Alignment explanation
Indices: 112292047--112292121 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 27
112292037 CAGGCGCGAC
*
112292047 TTTTTTTATATTAAAATATATATTTTTTG
1 TTTTTTTAT-TAAAAATAT-TATTTTTTG
*
112292076 TTTTTTTA-AATAAAATATTATTTTTT-
1 TTTTTTTATTA-AAAATATTATTTTTTG
112292102 TTATTTTTATTAAAAATATT
1 TT-TTTTTATTAAAAATATT
112292122 TAAATTTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
26 2 0.05
27 22 0.55
28 8 0.20
29 8 0.20
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (27 bp):
TTTTTTTATTAAAAATATTATTTTTTG
Found at i:112292736 original size:21 final size:22
Alignment explanation
Indices: 112292698--112292738 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
112292688 TTGACAAATG
* *
112292698 TTTTTATTAAAATTATTTAAAA
1 TTTTAATTAAAATAATTTAAAA
112292720 TTTTAATTAAAA-AATTTAA
1 TTTTAATTAAAATAATTTAA
112292739 CACCCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAATTAAAATAATTTAAAA
Found at i:112292985 original size:26 final size:27
Alignment explanation
Indices: 112292955--112293020 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 27
112292945 CCCACCATTT
*
112292955 GCGCCTCTGAGATAGGCAC-ATTAGTC
1 GCGCCTCTGAGATAGGCACAACTAGTC
* * *
112292981 GCGCCTATTAGA-AGGCTCAACTAGTC
1 GCGCCTCTGAGATAGGCACAACTAGTC
112293007 GCGCCTCTGAGATA
1 GCGCCTCTGAGATA
112293021 AGCGCAACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
25 5 0.16
26 26 0.81
27 1 0.03
ACGTcount: A:0.24, C:0.27, G:0.26, T:0.23
Consensus pattern (27 bp):
GCGCCTCTGAGATAGGCACAACTAGTC
Found at i:112293112 original size:27 final size:29
Alignment explanation
Indices: 112293070--112293123 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
112293060 ATCTGAAAAT
*
112293070 AAAAAAATAATATTTT-ATTTAAAAAACA
1 AAAAAAATAATATTTTAATGTAAAAAACA
*
112293098 AAAAAAAT-ATTTTTTAATGTAAAAAA
1 AAAAAAATAATATTTTAATGTAAAAAA
112293124 AAGAGTCGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAAAAATAATATTTTAATGTAAAAAACA
Found at i:112293317 original size:21 final size:21
Alignment explanation
Indices: 112293293--112293332 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
112293283 TTTATTAGGT
112293293 AAATAATAAACAACATTTTAC
1 AAATAATAAACAACATTTTAC
* *
112293314 AAATAATAAATATCATTTT
1 AAATAATAAACAACATTTT
112293333 GAGAGTGTTT
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:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATAATAAACAACATTTTAC
Found at i:112295964 original size:160 final size:160
Alignment explanation
Indices: 112295700--112296021 Score: 626
Period size: 160 Copynumber: 2.0 Consensus size: 160
112295690 ATATGATGGA
112295700 TTTGAAATTCATGTGTTTGAAAAAAATTGAAAGTTCATAAAATTCAAAAGAAAATAGCATGTAGT
1 TTTGAAATTCATGTGTTTGAAAAAAATTGAAAGTTCATAAAATTCAAAAGAAAATAGCATGTAGT
112295765 ATACGTGAATTGTCATGCGAGATATCATGCTTAAAAATTTGTTTTTTTAGTCAATATTTCTATTA
66 ATACGTGAATTGTCATGCGAGATATCATGCTTAAAAATTTGTTTTTTTAGTCAATATTTCTATTA
*
112295830 AAAAATAATAATTCGGCTCTTTTTGAAAGG
131 AAAAACAATAATTCGGCTCTTTTTGAAAGG
112295860 TTTGAAATTCATGTGTTTGAAAAAAATTGAAAGTTCATAAAATTCAAAAGAAAATAGCATGTAGT
1 TTTGAAATTCATGTGTTTGAAAAAAATTGAAAGTTCATAAAATTCAAAAGAAAATAGCATGTAGT
*
112295925 ATACGTGAATTGTCATGCGAGATATCATGCTTAAAAATTTGTTTTTTTGGTCAATATTTCTATTA
66 ATACGTGAATTGTCATGCGAGATATCATGCTTAAAAATTTGTTTTTTTAGTCAATATTTCTATTA
112295990 AAAAACAATAATTCGGCTCTTTTTGAAAGG
131 AAAAACAATAATTCGGCTCTTTTTGAAAGG
112296020 TT
1 TT
112296022 GATAGTCAAA
Statistics
Matches: 160, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 160 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (160 bp):
TTTGAAATTCATGTGTTTGAAAAAAATTGAAAGTTCATAAAATTCAAAAGAAAATAGCATGTAGT
ATACGTGAATTGTCATGCGAGATATCATGCTTAAAAATTTGTTTTTTTAGTCAATATTTCTATTA
AAAAACAATAATTCGGCTCTTTTTGAAAGG
Found at i:112296207 original size:31 final size:31
Alignment explanation
Indices: 112296172--112296269 Score: 115
Period size: 31 Copynumber: 3.2 Consensus size: 31
112296162 CGTCATTAGC
* * **
112296172 CACTAAACTATGGGTAAGTTTTCATTTTGGT
1 CACTAAACTATGCGAAAGTTTTCATTTAAGT
*
112296203 CACTAAACTATTCGAAAGTTTTCATTTAAGT
1 CACTAAACTATGCGAAAGTTTTCATTTAAGT
* * * *
112296234 CACTAAAATATTCAAAAGCTTTCATTTAAGT
1 CACTAAACTATGCGAAAGTTTTCATTTAAGT
112296265 CACTA
1 CACTA
112296270 GGTTGTTAAG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (31 bp):
CACTAAACTATGCGAAAGTTTTCATTTAAGT
Found at i:112306789 original size:17 final size:18
Alignment explanation
Indices: 112306748--112306792 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
112306738 AAATCTGACT
112306748 ATTCAATCAAACTAATCA
1 ATTCAATCAAACTAATCA
** *
112306766 AACCAAT-AACCTAATCA
1 ATTCAATCAAACTAATCA
112306783 ATTCAATCAA
1 ATTCAATCAA
112306793 TAAATTTATT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (18 bp):
ATTCAATCAAACTAATCA
Found at i:112308374 original size:29 final size:29
Alignment explanation
Indices: 112308310--112308376 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
112308300 ATTTGGCCTT
* * * *
112308310 ATTTGATTCTTTTTAATATTACATAGATTA
1 ATTTGA-TCTATTTAATAATACAGAGACTA
* *
112308340 AATTGATCTATTTAATAATAGAGAGACTA
1 ATTTGATCTATTTAATAATACAGAGACTA
112308369 ATTTGATC
1 ATTTGATC
112308377 AGATCCTTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.45
Consensus pattern (29 bp):
ATTTGATCTATTTAATAATACAGAGACTA
Found at i:112312606 original size:109 final size:108
Alignment explanation
Indices: 112312415--112312634 Score: 314
Period size: 109 Copynumber: 2.0 Consensus size: 108
112312405 AAAACCTCTT
* * **
112312415 GAAGGATCCATGAACGGGAGTGAAGATCTCAAGAGCAGCATATCAATGAGAATTGGAGATCGGTT
1 GAAGGATCCATGAACGGGAGTGAAGAGCTCAAGAGCAGCAGATCAATGAGAACCGGAGATCGGTT
* * * * *
112312480 CAAAGCATCGAAGCAGCTTCACTGATCGATACGATGAGTGAGA
66 CAAAGCATCGAAACAGCTTCACGGATCGATACAAAGAGTAAGA
* * * *
112312523 GAAGGATCCATTAACGGGATTGAAGAGCTCGAGAGCAGCAGATCGATTGAGAACCGGAGATCGGT
1 GAAGGATCCATGAACGGGAGTGAAGAGCTCAAGAGCAGCAGATC-AATGAGAACCGGAGATCGGT
112312588 TCAAAGCATCGAAACAGCTTCACGGATCGATACAAAGAGTAAGA
65 TCAAAGCATCGAAACAGCTTCACGGATCGATACAAAGAGTAAGA
112312632 GAA
1 GAA
112312635 CCATGAATAC
Statistics
Matches: 98, Mismatches: 13, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
108 39 0.40
109 59 0.60
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.18
Consensus pattern (108 bp):
GAAGGATCCATGAACGGGAGTGAAGAGCTCAAGAGCAGCAGATCAATGAGAACCGGAGATCGGTT
CAAAGCATCGAAACAGCTTCACGGATCGATACAAAGAGTAAGA
Found at i:112313198 original size:17 final size:17
Alignment explanation
Indices: 112313165--112313212 Score: 78
Period size: 17 Copynumber: 2.7 Consensus size: 17
112313155 TTAGAGTACA
112313165 TTTAATACACTGATTAAAT
1 TTTAA-ACAC-GATTAAAT
112313184 TTTAAACACGATTAAAT
1 TTTAAACACGATTAAAT
112313201 TTTAAACACGAT
1 TTTAAACACGAT
112313213 CTATATCCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 20 0.69
18 4 0.14
19 5 0.17
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (17 bp):
TTTAAACACGATTAAAT
Found at i:112314710 original size:28 final size:28
Alignment explanation
Indices: 112314678--112314734 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
112314668 TCTCCTGTTA
112314678 AAAATTTCAT-CAATTTCTACGGTCAGAC
1 AAAATTTCATAC-ATTTCTACGGTCAGAC
*
112314706 AAAATTTCATACATTTCTACTGTCAGAC
1 AAAATTTCATACATTTCTACGGTCAGAC
112314734 A
1 A
112314735 CTGATCCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (28 bp):
AAAATTTCATACATTTCTACGGTCAGAC
Found at i:112319592 original size:17 final size:16
Alignment explanation
Indices: 112319544--112319601 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
112319534 GTGTAGGTTC
112319544 TTAATTTAAAGGTTTAAT
1 TTAA-TTAAA-GTTTAAT
* * *
112319562 TTGATTGAATTTTAGAT
1 TTAATTAAAGTTTA-AT
112319579 TTAATTAAAGTTTAAT
1 TTAATTAAAGTTTAAT
*
112319595 ATAATTA
1 TTAATTA
112319602 TTAAATACGG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
16 12 0.38
17 17 0.53
18 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (16 bp):
TTAATTAAAGTTTAAT
Found at i:112319739 original size:19 final size:19
Alignment explanation
Indices: 112319704--112319741 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
112319694 TAAAAATAAA
**
112319704 ATATTGAATCTTGTTGACC
1 ATATTGAATCTAATTGACC
112319723 ATATTGAATCTAATTGACC
1 ATATTGAATCTAATTGACC
112319742 GTAATAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (19 bp):
ATATTGAATCTAATTGACC
Found at i:112320592 original size:19 final size:19
Alignment explanation
Indices: 112320568--112320604 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
112320558 AGCCCAAGAG
112320568 AAATAACCCCTTAATTTTA
1 AAATAACCCCTTAATTTTA
*
112320587 AAATAATCCCTTAATTTT
1 AAATAACCCCTTAATTTT
112320605 TTCTCTCGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATAACCCCTTAATTTTA
Found at i:112320995 original size:14 final size:15
Alignment explanation
Indices: 112320976--112321005 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
112320966 TTTTTTCTTA
112320976 TTTATTTATT-TTAT
1 TTTATTTATTATTAT
112320990 TTTATTTATTATTAT
1 TTTATTTATTATTAT
112321005 T
1 T
112321006 AACTTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATTTATTATTAT
Found at i:112321072 original size:22 final size:22
Alignment explanation
Indices: 112321013--112321084 Score: 92
Period size: 22 Copynumber: 3.1 Consensus size: 22
112321003 ATTAACTTTA
112321013 AAAATTTTGAAATATATA-TTTG
1 AAAATTTT-AAATATATATTTTG
*
112321035 AAATATTTTATTAATATATATTTTT
1 AAA-ATTTTA--AATATATATTTTG
112321060 AAAATTTTAAATATATATTTTG
1 AAAATTTTAAATATATATTTTG
112321082 AAA
1 AAA
112321085 TTACTTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
22 19 0.43
23 5 0.11
24 14 0.32
25 6 0.14
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
AAAATTTTAAATATATATTTTG
Found at i:112321620 original size:22 final size:23
Alignment explanation
Indices: 112321580--112321638 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
112321570 GAAAGTTTAA
112321580 AATATTT-AAATATTT-AAAAAT
1 AATATTTAAAATATTTAAAAAAT
*
112321601 AATATTTAAAAT-TTTAAAAAGT
1 AATATTTAAAATATTTAAAAAAT
*
112321623 AAT-TTCAAAATATTTA
1 AATATTTAAAATATTTA
112321639 TTTAAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
AATATTTAAAATATTTAAAAAAT
Found at i:112321668 original size:24 final size:22
Alignment explanation
Indices: 112321623--112321691 Score: 61
Period size: 24 Copynumber: 3.1 Consensus size: 22
112321613 TTTAAAAAGT
* *
112321623 AATTTCAAAATATTTATT-TAA
1 AATTTAAAAATATATATTATAA
112321644 AATTTAAAAAATATATATTAATAA
1 AATTT-AAAAATATATATT-ATAA
**
112321668 AATATTTTAAATATATATT-TAA
1 AAT-TTAAAAATATATATTATAA
112321690 AA
1 AA
112321692 ATTTTTAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 5 0.12
22 16 0.40
24 17 0.43
25 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTTAAAAATATATATTATAA
Found at i:112321677 original size:13 final size:13
Alignment explanation
Indices: 112321645--112321692 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
112321635 TTTATTTAAA
112321645 ATTTAAAAAATAT
1 ATTTAAAAAATAT
112321658 ATATTAATAAAATAT
1 AT-TTAA-AAAATAT
*
112321673 -TTT-AAATATAT
1 ATTTAAAAAATAT
112321684 ATTTAAAAA
1 ATTTAAAAA
112321693 TTTTTAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATTTAAAAAATAT
Found at i:112321690 original size:22 final size:22
Alignment explanation
Indices: 112321630--112321696 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 22
112321620 AGTAATTTCA
* **
112321630 AAATATTTATTTAAAAT-TTAAA
1 AAATATATATTTAAAATATT-TT
112321652 AAATATATATTAATAAAATATTTT
1 AAATATATATT--TAAAATATTTT
112321676 AAATATATATTTAAAA-ATTTT
1 AAATATATATTTAAAATATTTT
112321697 TAAAGTTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 5 0.13
22 15 0.38
24 17 0.44
25 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATATATATTTAAAATATTTT
Found at i:112321697 original size:22 final size:22
Alignment explanation
Indices: 112321630--112321700 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
112321620 AGTAATTTCA
* **
112321630 AAATATTTATTT-AAAATTTAAA
1 AAATATATATTTAAAAATTT-TT
*
112321652 AAATATATATTAATAAAATATTTT
1 AAATATATATTTA-AAAAT-TTTT
112321676 AAATATATATTTAAAAATTTTT
1 AAATATATATTTAAAAATTTTT
112321698 AAA
1 AAA
112321701 GTTAATAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
22 17 0.41
23 5 0.12
24 17 0.41
25 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATATATATTTAAAAATTTTT
Found at i:112321745 original size:25 final size:24
Alignment explanation
Indices: 112321717--112321767 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
112321707 AATAATACAT
112321717 AAAAGAAAAG-AAAAGAAAAAAAGAC
1 AAAAGAAAAGTAAAA-AAAAAAA-AC
112321742 AAAAGAAAAGTAAAAAAAAAAAAC
1 AAAAGAAAAGTAAAAAAAAAAAAC
112321766 AA
1 AA
112321768 GGACTGACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 4 0.16
25 17 0.68
26 4 0.16
ACGTcount: A:0.82, C:0.04, G:0.12, T:0.02
Consensus pattern (24 bp):
AAAAGAAAAGTAAAAAAAAAAAAC
Found at i:112325495 original size:26 final size:24
Alignment explanation
Indices: 112325459--112325540 Score: 85
Period size: 26 Copynumber: 3.2 Consensus size: 24
112325449 TTTTTCAACC
*
112325459 TAAATTGTTTTGTATATTAATTATTT
1 TAAATTGTTTT-TATAAT-ATTATTT
* *
112325485 TAAATTG-TTTTATACTATTCACTT
1 TAAATTGTTTTTATAATATT-ATTT
112325509 TAAATTGCTTTTTATAATATCTATTT
1 TAAATTG-TTTTTATAATAT-TATTT
112325535 TAAATT
1 TAAATT
112325541 TATTTTTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
23 3 0.06
24 15 0.31
25 3 0.06
26 26 0.54
27 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.05, T:0.57
Consensus pattern (24 bp):
TAAATTGTTTTTATAATATTATTT
Found at i:112325919 original size:12 final size:12
Alignment explanation
Indices: 112325896--112325930 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
112325886 CCCGACCCAA
*
112325896 TTTTAATATTAT
1 TTTTAATTTTAT
*
112325908 TTTTTATTTTAT
1 TTTTAATTTTAT
112325920 TTTTAATTTTA
1 TTTTAATTTTA
112325931 GTAACTTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTAATTTTAT
Found at i:112327472 original size:14 final size:16
Alignment explanation
Indices: 112327420--112327474 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 16
112327410 ACCAAATTGT
*
112327420 ATTTTTTATTTAATTA
1 ATTTTTTATATAATTA
*
112327436 GATGATTTTTATATAATTT
1 -AT--TTTTTATATAATTA
112327455 ATTTTTTAT-TAA-TA
1 ATTTTTTATATAATTA
112327469 ATTTTT
1 ATTTTT
112327475 ATTTTAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 7 0.21
15 3 0.09
16 7 0.21
17 2 0.06
18 2 0.06
19 12 0.36
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (16 bp):
ATTTTTTATATAATTA
Found at i:112331648 original size:15 final size:15
Alignment explanation
Indices: 112331628--112331656 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
112331618 ATGTATAAGT
112331628 GTAACTTTAGTCATG
1 GTAACTTTAGTCATG
112331643 GTAACTTTAGTCAT
1 GTAACTTTAGTCAT
112331657 TACTTGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (15 bp):
GTAACTTTAGTCATG
Found at i:112333204 original size:27 final size:27
Alignment explanation
Indices: 112333174--112333246 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 27
112333164 TGTCTTGATT
112333174 TTGTTAGATATTGATTATGTTTCAAGC
1 TTGTTAGATATTGATTATGTTTCAAGC
*
112333201 TTGTTAGATATTGAGTTTATTATGTTTTAAGC
1 TTGTTAGATATT--G---ATTATGTTTCAAGC
*
112333233 TTGTTGGATATTGA
1 TTGTTAGATATTGA
112333247 AATGATTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 13 0.33
29 1 0.03
30 1 0.03
32 24 0.62
ACGTcount: A:0.25, C:0.04, G:0.21, T:0.51
Consensus pattern (27 bp):
TTGTTAGATATTGATTATGTTTCAAGC
Found at i:112334296 original size:22 final size:22
Alignment explanation
Indices: 112334198--112334283 Score: 77
Period size: 22 Copynumber: 3.8 Consensus size: 22
112334188 ACTTTTAATG
*
112334198 TGGTGTAATATTAGTTATGCACT-
1 TGGTATAATATTAGTTAT-CA-TA
* *
112334221 TGG-ATAATATTGTTGTTATCATG
1 TGGTATAATA-T-TAGTTATCATA
*
112334244 TGGTGTAATATTAGTTATCATA
1 TGGTATAATATTAGTTATCATA
*
112334266 TGGTGTAATATTAGTTAT
1 TGGTATAATATTAGTTAT
112334284 GCACTTGGAT
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
22 33 0.61
23 10 0.19
24 11 0.20
ACGTcount: A:0.28, C:0.05, G:0.21, T:0.47
Consensus pattern (22 bp):
TGGTATAATATTAGTTATCATA
Found at i:112334343 original size:68 final size:68
Alignment explanation
Indices: 112334198--112334346 Score: 219
Period size: 68 Copynumber: 2.2 Consensus size: 68
112334188 ACTTTTAATG
* * *
112334198 TGGTGTAATATTAGTTATGCACTTGGATAATATTGTTGTTATCATGTGGTGTAATATTAGTTATC
1 TGGTATAATATTAGTTATGCACTTGGATAATATTGTTGTTATCATGTGGTGTAATACTAATTATC
112334263 ATA
66 ATA
* *
112334266 TGGTGTAATATTAGTTATGCACTTGGATAATGTTGTTGTTATCATGTGGTGTAATACTAATTATG
1 TGGTATAATATTAGTTATGCACTTGGATAATATTGTTGTTATCATGTGGTGTAATACTAATTAT-
* *
112334331 TATT
65 CATA
112334335 TGG-ATAATATTA
1 TGGTATAATATTA
112334347 TTAATTTCTA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
68 69 0.93
69 5 0.07
ACGTcount: A:0.28, C:0.05, G:0.21, T:0.46
Consensus pattern (68 bp):
TGGTATAATATTAGTTATGCACTTGGATAATATTGTTGTTATCATGTGGTGTAATACTAATTATC
ATA
Found at i:112334761 original size:14 final size:14
Alignment explanation
Indices: 112334742--112334800 Score: 75
Period size: 14 Copynumber: 4.2 Consensus size: 14
112334732 ACAGAAAAGT
112334742 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
112334756 AAATCATTTTTCAAG
1 AAATCA-TTTTCCAG
* *
112334771 AAATTATTTTTCAG
1 AAATCATTTTCCAG
112334785 AAATCATTTTCC-G
1 AAATCATTTTCCAG
112334798 AAA
1 AAA
112334801 AACATTTTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
13 4 0.11
14 22 0.58
15 12 0.32
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:112334772 original size:15 final size:14
Alignment explanation
Indices: 112334742--112334794 Score: 79
Period size: 14 Copynumber: 3.7 Consensus size: 14
112334732 ACAGAAAAGT
*
112334742 AAATCATTTTCCAG
1 AAATCATTTTTCAG
112334756 AAATCATTTTTCAAG
1 AAATCATTTTTC-AG
*
112334771 AAATTATTTTTCAG
1 AAATCATTTTTCAG
112334785 AAATCATTTT
1 AAATCATTTT
112334795 CCGAAAAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
14 22 0.63
15 13 0.37
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (14 bp):
AAATCATTTTTCAG
Found at i:112335742 original size:19 final size:19
Alignment explanation
Indices: 112335718--112335760 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
112335708 AGTACGTCAA
112335718 TTTTAAAACAAAATGAGGG
1 TTTTAAAACAAAATGAGGG
112335737 TTTTAAAACAAAATGAGGG
1 TTTTAAAACAAAATGAGGG
112335756 TTTTA
1 TTTTA
112335761 GGTAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.33
Consensus pattern (19 bp):
TTTTAAAACAAAATGAGGG
Found at i:112335980 original size:13 final size:13
Alignment explanation
Indices: 112335948--112335981 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
112335938 AACATTTTTT
112335948 TAATTTTAATTAA
1 TAATTTTAATTAA
**
112335961 TGTTTTTAATTAA
1 TAATTTTAATTAA
112335974 TAATTTTA
1 TAATTTTA
112335982 TTTTTGTAAG
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TAATTTTAATTAA
Found at i:112336344 original size:14 final size:14
Alignment explanation
Indices: 112336325--112336352 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
112336315 ATATAAATAT
112336325 TATATATCAAAAAA
1 TATATATCAAAAAA
112336339 TATATATCAAAAAA
1 TATATATCAAAAAA
112336353 GTTAATTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (14 bp):
TATATATCAAAAAA
Found at i:112336595 original size:13 final size:13
Alignment explanation
Indices: 112336577--112336604 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
112336567 AAAATATATT
112336577 TATTAATTAAAAA
1 TATTAATTAAAAA
112336590 TATTAATTAAAAA
1 TATTAATTAAAAA
112336603 TA
1 TA
112336605 AAAAAGAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TATTAATTAAAAA
Found at i:112345093 original size:17 final size:17
Alignment explanation
Indices: 112345071--112345104 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
112345061 ATCCACTAAT
*
112345071 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
112345088 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
112345105 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:112349722 original size:17 final size:17
Alignment explanation
Indices: 112349700--112349733 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
112349690 ATCCACTAAT
*
112349700 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
112349717 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
112349734 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:112351803 original size:17 final size:17
Alignment explanation
Indices: 112351783--112351840 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
112351773 AAACGAGAAT
112351783 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
* **
112351800 TTTTGAAAACACGAATGTT
1 TTTTTAAAACACGAA--AA
112351819 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
*
112351836 ATTTT
1 TTTTT
112351841 GGAAACGCGA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
17 18 0.56
19 14 0.44
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:112351829 original size:36 final size:37
Alignment explanation
Indices: 112351782--112351851 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
112351772 AAAACGAGAA
112351782 TTTTTTAAAACACG-AAAATTTTGAAAACACGAATGT
1 TTTTTTAAAACACGAAAAATTTTGAAAACACGAATGT
* *
112351818 TTTTTTAAAACACGAAAAATTTTGGAAACGCGAA
1 TTTTTTAAAACACGAAAAATTTTGAAAACACGAA
112351852 AAGTTTACAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 14 0.45
37 17 0.55
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (37 bp):
TTTTTTAAAACACGAAAAATTTTGAAAACACGAATGT
Found at i:112352424 original size:18 final size:17
Alignment explanation
Indices: 112352398--112352451 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
112352388 AATAAGCATA
112352398 ATAATAAATATAATGATAT
1 ATAA-AAATATAAT-ATAT
*
112352417 ATAAAAATAATACTATAT
1 ATAAAAAT-ATAATATAT
*
112352435 ATAAAAGTAT-ATATAT
1 ATAAAAATATAATATAT
112352451 A
1 A
112352452 CGTACAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
18 15 0.48
19 8 0.26
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (17 bp):
ATAAAAATATAATATAT
Found at i:112352540 original size:3 final size:3
Alignment explanation
Indices: 112352532--112352562 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
112352522 AGATAGTGAA
*
112352532 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
112352563 TGTGAAGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:112352653 original size:26 final size:26
Alignment explanation
Indices: 112352624--112352691 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
112352614 ATAAAGGGAT
*
112352624 ATAAATAAATGGTAAAACAAAGTAA-A-
1 ATAAATAAAT-GTAAAA-AAAGAAACAG
**
112352650 ATAAATGTATGTAAAAAAAGAAACAG
1 ATAAATAAATGTAAAAAAAGAAACAG
*
112352676 ATAAATAAATATAAAA
1 ATAAATAAATGTAAAA
112352692 GAAATATAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
24 6 0.18
25 7 0.21
26 21 0.62
ACGTcount: A:0.66, C:0.03, G:0.10, T:0.21
Consensus pattern (26 bp):
ATAAATAAATGTAAAAAAAGAAACAG
Found at i:112352887 original size:29 final size:30
Alignment explanation
Indices: 112352855--112352911 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
112352845 ATTAGCAGCG
* *
112352855 TGAAAATGATAA-AATAACAAATATTTAAA
1 TGAAAATAATAAGAACAACAAATATTTAAA
* *
112352884 TGAAGATAATAAGAACAGCAAATATTTA
1 TGAAAATAATAAGAACAACAAATATTTA
112352912 GAAAGTAAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 10 0.43
30 13 0.57
ACGTcount: A:0.58, C:0.05, G:0.11, T:0.26
Consensus pattern (30 bp):
TGAAAATAATAAGAACAACAAATATTTAAA
Found at i:112353242 original size:13 final size:14
Alignment explanation
Indices: 112353224--112353253 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
112353214 TTCATCTTTG
112353224 TTATTTTTTATT-T
1 TTATTTTTTATTCT
112353237 TTATTTTTTATTCT
1 TTATTTTTTATTCT
112353251 TTA
1 TTA
112353254 CTTCATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (14 bp):
TTATTTTTTATTCT
Found at i:112360682 original size:21 final size:22
Alignment explanation
Indices: 112360634--112360683 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
112360624 AAATATTTCA
*
112360634 ATTTTCCTTAATTTTCCCTTCT
1 ATTTTCCTCAATTTTCCCTTCT
* *
112360656 -TCTTCCTCAATTTTCTCTT-T
1 ATTTTCCTCAATTTTCCCTTCT
112360676 ATTTTCCT
1 ATTTTCCT
112360684 TGTCATTTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTTCCTCAATTTTCCCTTCT
Found at i:112368781 original size:14 final size:15
Alignment explanation
Indices: 112368749--112368787 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
112368739 TATGATAAGT
*
112368749 ATAATAAATAATAGT
1 ATAATAAATAATAGC
112368764 ATAATAAA-AATAGC
1 ATAATAAATAATAGC
112368778 ATAATAAATA
1 ATAATAAATA
112368788 GTAGGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (15 bp):
ATAATAAATAATAGC
Found at i:112370159 original size:45 final size:45
Alignment explanation
Indices: 112370091--112370203 Score: 131
Period size: 44 Copynumber: 2.5 Consensus size: 45
112370081 TACGATCTGT
* * * * *
112370091 TCCACTCTTGCTCA-TCGATGATAAAATCTGGTATGTTTAGCCTGC
1 TCCACTCCTGCTCAGT-GAAGATAAAAGCTGATATGTTTAACCTGC
*
112370136 TCCACTCCTGCTCAGTGAAGAT-AAGGCTGATATGTTTAACCTGC
1 TCCACTCCTGCTCAGTGAAGATAAAAGCTGATATGTTTAACCTGC
* *
112370180 TTCACTCCTGCTCAGTAAAGATAA
1 TCCACTCCTGCTCAGTGAAGATAA
112370204 GGTCGATGGT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 38 0.66
45 19 0.33
46 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (45 bp):
TCCACTCCTGCTCAGTGAAGATAAAAGCTGATATGTTTAACCTGC
Found at i:112370186 original size:44 final size:44
Alignment explanation
Indices: 112370122--112370390 Score: 163
Period size: 44 Copynumber: 6.0 Consensus size: 44
112370112 TAAAATCTGG
*
112370122 TATGTTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGA
1 TATGTTTAACCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGA
* *
112370166 TATGTTTAACCTGCTTCACTCCTGCTCAGTAAAGATAAGG-TCGA
1 TATGTTTAACCTGCTCCACTCCTGCTCAGTGAAGATAAGGCT-GA
* * * * * * * * *
112370210 T-GGTTGGAATCTGCTCCATTGCAGATACA-TGGAGATAAGATTCGTTGAA
1 TATGTT-TAACCTGCTCCACTCCTGCT-CAGTGAAGATAAG----GCTG-A
* * * * * * * *
112370259 AACG--TGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCT-A
1 TATGTTTAACCTGCTCCACTCCTGCTCAGTGAAGATAAG-GCTGA
* * * *
112370301 CTATGCTTAGCCTGCTCCACCCCTGCTCAGTGAAGATAAGGCTAA
1 -TATGTTTAACCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGA
* * *
112370346 TATGTTTAACCTGTTTCACTCCTGCTCAGTGAAGATAAGGTTGA
1 TATGTTTAACCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGA
112370390 T
1 T
112370391 GGTTGGAATC
Statistics
Matches: 165, Mismatches: 45, Indels: 30
0.69 0.19 0.12
Matches are distributed among these distances:
42 1 0.01
43 6 0.04
44 102 0.62
45 29 0.18
46 2 0.01
47 20 0.12
48 2 0.01
49 2 0.01
50 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.30
Consensus pattern (44 bp):
TATGTTTAACCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGA
Found at i:112370429 original size:180 final size:180
Alignment explanation
Indices: 112370099--112370521 Score: 634
Period size: 180 Copynumber: 2.4 Consensus size: 180
112370089 GTTCCACTCT
* * * *
112370099 TGCTCATCGATGATAAAATCTGGTATGTTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCT
1 TGCTCAGCGAAGATAAGATCTGCTATGTTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCT
*
112370164 GATATGTTTAACCTGCTTCACTCCTGCTCAGTAAAGATAAGGTCGATGGTTGGAATCTGCTCCAT
66 AATATGTTTAACCTGCTTCACTCCTGCTCAGTAAAGATAAGGTCGATGGTTGGAATCTGCTCCAT
*
112370229 TGCAGATACATGGAGATAAGATTCGTTGAAAACGTGATCTGCT-T-CGCTCC
131 TGCAGATACATGGAGATAAGATTCGTCGAAAACGTGATCTGCTCTGC-CT-C
* * *
112370279 TGCTCAGCGAAGATAAGATCTACTATGCTTAGCCTGCTCCACCCCTGCTCAGTGAAGATAAGGCT
1 TGCTCAGCGAAGATAAGATCTGCTATGTTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCT
* * *
112370344 AATATGTTTAACCTGTTTCACTCCTGCTCAGTGAAGATAAGGTTGATGGTTGGAATCTGCTCCAT
66 AATATGTTTAACCTGCTTCACTCCTGCTCAGTAAAGATAAGGTCGATGGTTGGAATCTGCTCCAT
* * *
112370409 TGCCGATACATGGAGATAAGATTCGTCGAAAATGTGATTTGCTCTGCCTC
131 TGCAGATACATGGAGATAAGATTCGTCGAAAACGTGATCTGCTCTGCCTC
* * ** *
112370459 TGCTCAGCGAAGATAAGATCTGCTGTGTTTAACCTGCTTTACTCCTACTCAGTGAAGATAAGG
1 TGCTCAGCGAAGATAAGATCTGCTATGTTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGG
112370522 TTGATGGTTG
Statistics
Matches: 218, Mismatches: 23, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
180 214 0.98
181 3 0.01
182 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (180 bp):
TGCTCAGCGAAGATAAGATCTGCTATGTTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCT
AATATGTTTAACCTGCTTCACTCCTGCTCAGTAAAGATAAGGTCGATGGTTGGAATCTGCTCCAT
TGCAGATACATGGAGATAAGATTCGTCGAAAACGTGATCTGCTCTGCCTC
Found at i:112370471 original size:135 final size:135
Alignment explanation
Indices: 112370320--112370661 Score: 528
Period size: 135 Copynumber: 2.5 Consensus size: 135
112370310 GCCTGCTCCA
* ** *
112370320 CCCCTGCTCAGTGAAGATAAG-GCTAATATGTTTAACCTGTTTCACTCCTGCTCAGTGAAGATAA
1 CCCCTGCTCAGTGAAGATAAGATCTGCTGTGTTTAACCTGTTTCACTCCTGCTCAGTGAAGATAA
*
112370384 GGTTGATGGTTGGAATCTGCTCCATTGCCGATACATGGAGATAAGATTCG-TCGAAAATGTGATT
66 GGTTGATGGTTGGAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCT-G-AAATGTGATC
*
112370448 TGCTCTG
129 TACTCTG
* * *
112370455 CCTCTGCTCAGCGAAGATAAGATCTGCTGTGTTTAACCTGCTTT-ACTCCTACTCAGTGAAGATA
1 CCCCTGCTCAGTGAAGATAAGATCTGCTGTGTTTAACCTG-TTTCACTCCTGCTCAGTGAAGATA
*
112370519 AGGTTGATGGTTGGAATCTGCTCCATTGTCGATACATGGAGATAAGATTCGCTGAAATGTGATCT
65 AGGTTGATGGTTGGAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCTGAAATGTGATCT
112370584 ACTCTG
130 ACTCTG
*
112370590 CCCCTGCTCAGTGAAGATAAGATCTGCTGTGTTTAACCTGCTTCACTCCTGCTCAGTGAAGATAA
1 CCCCTGCTCAGTGAAGATAAGATCTGCTGTGTTTAACCTGTTTCACTCCTGCTCAGTGAAGATAA
*
112370655 GGATGAT
66 GGTTGAT
112370662 AAACTCTGTA
Statistics
Matches: 188, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
134 2 0.01
135 98 0.52
136 84 0.45
137 4 0.02
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (135 bp):
CCCCTGCTCAGTGAAGATAAGATCTGCTGTGTTTAACCTGTTTCACTCCTGCTCAGTGAAGATAA
GGTTGATGGTTGGAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCTGAAATGTGATCTA
CTCTG
Found at i:112378682 original size:5 final size:5
Alignment explanation
Indices: 112378672--112378702 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
112378662 ATATGATGTT
112378672 ATGCA ATGCA ATGCA ATGCA ATGCAA ATGCA
1 ATGCA ATGCA ATGCA ATGCA ATGC-A ATGCA
112378703 TGATATGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATGCA
Found at i:112382924 original size:13 final size:15
Alignment explanation
Indices: 112382916--112382957 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
112382906 ATAATATATA
112382916 AGTATAATAAATAAT
1 AGTATAATAAATAAT
112382931 AGTATAATAAA-AAT
1 AGTATAATAAATAAT
*
112382945 AGCATAATAAATA
1 AGTATAATAAATA
112382958 GTAGGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (15 bp):
AGTATAATAAATAAT
Found at i:112386778 original size:3 final size:3
Alignment explanation
Indices: 112386770--112386935 Score: 73
Period size: 3 Copynumber: 57.7 Consensus size: 3
112386760 AAAACGATAG
* * * * * *
112386770 TAA TAA TAA TAG TAG TAA AAA TAA AAA TAA T-A TAG TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
112386817 -AA AAA T-A TAA TAA TAA TAA TAG TAA TAA T-A CAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
112386862 TAA AAA GGT-A TAA TAA T-A TAT TAGA TAG TAA AAA TAA -AA -AA TAA
1 TAA TAA --TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
* * * *
112386906 AAA TAA AAA TAG TAA TAA -AA -AA TGA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
112386936 GTGATATTAG
Statistics
Matches: 119, Mismatches: 33, Indels: 22
0.68 0.19 0.13
Matches are distributed among these distances:
2 18 0.15
3 98 0.82
4 3 0.03
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:112386823 original size:22 final size:23
Alignment explanation
Indices: 112386772--112386879 Score: 56
Period size: 23 Copynumber: 4.4 Consensus size: 23
112386762 AACGATAGTA
* * *
112386772 ATAATAATAGTAGTAAAAATAAAA
1 ATAATAATAATAATAAAAAT-AAT
* *
112386796 ATAATATAGTAATAGTAATAAAAAAAT
1 ATAATA-A-TAATAAT-A-AAAATAAT
**
112386823 ATAATAATAATAATAGTAATAAT
1 ATAATAATAATAATAAAAATAAT
* *
112386846 ACAATAGTAATAATAATAAA-AAGGT
1 ATAATAATAATAATAA-AAATAA--T
112386871 ATAATAATA
1 ATAATAATA
112386880 TATTAGATAG
Statistics
Matches: 64, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
23 20 0.31
24 9 0.14
25 15 0.23
26 7 0.11
27 9 0.14
28 4 0.06
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.29
Consensus pattern (23 bp):
ATAATAATAATAATAAAAATAAT
Found at i:112386856 original size:48 final size:51
Alignment explanation
Indices: 112386791--112386897 Score: 141
Period size: 48 Copynumber: 2.2 Consensus size: 51
112386781 GTAGTAAAAA
*
112386791 TAAAAATA-ATATAGTAATAGTAATAAAAAAATATAATAATA-A-TA-ATAG
1 TAAAAATACA-ATAGTAATAATAATAAAAAAATATAATAATATATTAGATAG
* **
112386839 TAATAATACAATAGTAATAATAATAAAAAGGTATAATAATATATTAGATAG
1 TAAAAATACAATAGTAATAATAATAAAAAAATATAATAATATATTAGATAG
112386890 TAAAAATA
1 TAAAAATA
112386898 AAAAATAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
48 35 0.70
49 2 0.04
50 2 0.04
51 11 0.22
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.30
Consensus pattern (51 bp):
TAAAAATACAATAGTAATAATAATAAAAAAATATAATAATATATTAGATAG
Found at i:112386859 original size:14 final size:14
Alignment explanation
Indices: 112386766--112386861 Score: 92
Period size: 14 Copynumber: 6.9 Consensus size: 14
112386756 AACGAAAACG
112386766 ATAGTAATAATAATA
1 ATAGTAATAATAA-A
* *
112386781 GTAGTAAAAATAAA
1 ATAGTAATAATAAA
*
112386795 A-A-TAAT-ATAGTA
1 ATAGTAATAATA-AA
*
112386807 ATAGTAATAAAAAA
1 ATAGTAATAATAAA
112386821 ATA-TAATAATAATA
1 ATAGTAATAATAA-A
*
112386835 ATAGTAATAATACA
1 ATAGTAATAATAAA
112386849 ATAGTAATAATAA
1 ATAGTAATAATAA
112386862 TAAAAAGGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
11 3 0.05
12 5 0.08
13 10 0.15
14 26 0.40
15 21 0.32
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.29
Consensus pattern (14 bp):
ATAGTAATAATAAA
Found at i:112386908 original size:13 final size:13
Alignment explanation
Indices: 112386890--112386928 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
112386880 TATTAGATAG
112386890 TAAAAATAAAAAA
1 TAAAAATAAAAAA
112386903 TAAAAAT-AAAAA
1 TAAAAATAAAAAA
**
112386915 TAGTAATAAAAAA
1 TAAAAATAAAAAA
112386928 T
1 T
112386929 GATAATAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:112387156 original size:3 final size:3
Alignment explanation
Indices: 112387145--112387222 Score: 54
Period size: 3 Copynumber: 26.7 Consensus size: 3
112387135 AAAATGGTGG
* * * *
112387145 TAA TGA TAA TAA TAA TAA TAA TAA TAA TGA TGA -AA TAA T-T TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
112387191 TAG TAA TAA TGA CAA TAG TAGA -AA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA
112387223 GTATTTGAAT
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
2 3 0.05
3 54 0.95
ACGTcount: A:0.58, C:0.01, G:0.09, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:112387223 original size:15 final size:15
Alignment explanation
Indices: 112387144--112387225 Score: 67
Period size: 15 Copynumber: 5.2 Consensus size: 15
112387134 AAAAATGGTG
*
112387144 GTAATGATAATAATA
1 GTAATAATAATAATA
*
112387159 ATAATAATAATAATGA
1 GTAATAATAATAAT-A
*
112387175 TGAAATAATTTAATAATA
1 -GTAATAA--TAATAATA
* *
112387193 GTAATAATGACAATA
1 GTAATAATAATAATA
112387208 GTAGA-AATAATAATA
1 GTA-ATAATAATAATA
112387223 GTA
1 GTA
112387226 TTTGAATAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
15 32 0.60
16 2 0.04
17 11 0.21
18 1 0.02
19 7 0.13
ACGTcount: A:0.56, C:0.01, G:0.11, T:0.32
Consensus pattern (15 bp):
GTAATAATAATAATA
Found at i:112389119 original size:19 final size:19
Alignment explanation
Indices: 112389076--112389119 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
112389066 CAAATAAAAA
**
112389076 ATTTTAAAATTTATGATTC
1 ATTTTAAAATTTAAAATTC
* *
112389095 AATTTAAAATTTAAAATTG
1 ATTTTAAAATTTAAAATTC
112389114 ATTTTA
1 ATTTTA
112389120 GAAAAAAAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (19 bp):
ATTTTAAAATTTAAAATTC
Found at i:112389669 original size:35 final size:35
Alignment explanation
Indices: 112389629--112389699 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
112389619 TCTAGGATCA
*
112389629 CATATCTTTGAAAATCCCCTTT-CATATTTGCCAAG
1 CATATCTTTGAAAAT-CACTTTCCATATTTGCCAAG
* *
112389664 CATATCTTTGAAGATTACTTTCCATATTTGCCAAG
1 CATATCTTTGAAAATCACTTTCCATATTTGCCAAG
112389699 C
1 C
112389700 TCCGAAGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 4 0.12
35 28 0.88
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (35 bp):
CATATCTTTGAAAATCACTTTCCATATTTGCCAAG
Found at i:112394803 original size:35 final size:35
Alignment explanation
Indices: 112394764--112394834 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
112394754 TCTAAGATCA
*
112394764 CATATCTTTAAAGATCCCCTTCCATATTTGCCAAG
1 CATATCTTTAAAGATCACCTTCCATATTTGCCAAG
* * *
112394799 CATATCTTTGAAGATTACTTTCCATATTTGCCAAG
1 CATATCTTTAAAGATCACCTTCCATATTTGCCAAG
112394834 C
1 C
112394835 TCCAGAGATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.37
Consensus pattern (35 bp):
CATATCTTTAAAGATCACCTTCCATATTTGCCAAG
Found at i:112398261 original size:12 final size:12
Alignment explanation
Indices: 112398244--112398268 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
112398234 TGATTATAAC
112398244 AAAAAAAGAAAA
1 AAAAAAAGAAAA
112398256 AAAAAAAGAAAA
1 AAAAAAAGAAAA
112398268 A
1 A
112398269 TTGTCAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:112401864 original size:19 final size:19
Alignment explanation
Indices: 112401840--112402002 Score: 76
Period size: 19 Copynumber: 8.7 Consensus size: 19
112401830 TATTTTGCTA
*
112401840 ATAAAAATTATTAAAAGTC
1 ATAAAAATTATTAAAAATC
112401859 ATAAAAGATTA-TAAAAATC
1 ATAAAA-ATTATTAAAAATC
** *
112401878 ATAAAAATTATCGAATAT-
1 ATAAAAATTATTAAAAATC
*
112401896 -TTAAAA-TATTAAAATAT-
1 ATAAAAATTATTAAAA-ATC
* * * *
112401913 ATGAAAATTAATATAAACTT
1 ATAAAAATTATTA-AAAATC
*
112401933 ATAAAAAATTATTATAAATATT
1 AT-AAAAATTATTA-AAA-ATC
*
112401955 ATAAAAATT-TTATAAA--
1 ATAAAAATTATTAAAAATC
* *
112401971 A-AAACA-TATTAAAATTC
1 ATAAAAATTATTAAAAATC
112401988 TATAAAAATTATTAA
1 -ATAAAAATTATTAA
112402003 TAGTATAAAA
Statistics
Matches: 110, Mismatches: 19, Indels: 29
0.70 0.12 0.18
Matches are distributed among these distances:
14 1 0.01
15 9 0.08
16 6 0.05
17 7 0.06
18 11 0.10
19 34 0.31
20 18 0.16
21 20 0.18
22 4 0.04
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
ATAAAAATTATTAAAAATC
Found at i:112401940 original size:21 final size:22
Alignment explanation
Indices: 112401916--112401961 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
112401906 AAAATATATG
*
112401916 AAAATTAATATAAA-CTTATAA
1 AAAATTAATATAAATATTATAA
*
112401937 AAAATTATTATAAATATTATAA
1 AAAATTAATATAAATATTATAA
112401959 AAA
1 AAA
112401962 TTTTATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAATTAATATAAATATTATAA
Found at i:112402039 original size:9 final size:9
Alignment explanation
Indices: 112401840--112402042 Score: 79
Period size: 10 Copynumber: 20.8 Consensus size: 9
112401830 TATTTTGCTA
112401840 ATAAAAATT
1 ATAAAAATT
* *
112401849 ATTAAAAGTC
1 A-TAAAAATT
112401859 ATAAAAGATT
1 ATAAAA-ATT
*
112401869 ATAAAAATC
1 ATAAAAATT
112401878 ATAAAAATT
1 ATAAAAATT
* *
112401887 ATCGAATATT
1 AT-AAAAATT
112401897 -T-AAAA-T
1 ATAAAAATT
*
112401903 ATTAAAATAT
1 ATAAAAAT-T
*
112401913 ATGAAAATT
1 ATAAAAATT
*
112401922 AATATAAACTT
1 -ATA-AAAATT
112401933 ATAAAAAATT
1 AT-AAAAATT
112401943 ATTATAAATATT
1 A-TA-AAA-ATT
112401955 ATAAAAATTTT
1 ATAAAAA--TT
*
112401966 ATAAAAAAACAT
1 AT--AAAAA-TT
*
112401978 ATTAAAATTCT
1 A-TAAAAAT-T
112401989 ATAAAAATT
1 ATAAAAATT
* * *
112401998 ATTAATAGT
1 ATAAAAATT
*
112402007 ATAAAAAATG
1 AT-AAAAATT
*
112402017 ATATAAACTT
1 ATA-AAAATT
112402027 ATAAAAATT
1 ATAAAAATT
112402036 ATAAAAA
1 ATAAAAA
112402043 AAAATCATAA
Statistics
Matches: 145, Mismatches: 28, Indels: 42
0.67 0.13 0.20
Matches are distributed among these distances:
6 1 0.01
7 4 0.03
8 4 0.03
9 43 0.30
10 59 0.41
11 22 0.15
12 6 0.04
13 6 0.04
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:112402557 original size:13 final size:12
Alignment explanation
Indices: 112402536--112402578 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
112402526 TTAAGAATTC
112402536 TAATTTTTTAAA
1 TAATTTTTTAAA
*
112402548 TAAGTTTTTTAATT
1 TAA-TTTTTTAA-A
112402562 TAATTTTTTAAA
1 TAATTTTTTAAA
*
112402574 AAATT
1 TAATT
112402579 ATTAGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 7 0.27
13 16 0.62
14 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
TAATTTTTTAAA
Found at i:112418695 original size:76 final size:76
Alignment explanation
Indices: 112418608--112418756 Score: 201
Period size: 76 Copynumber: 2.0 Consensus size: 76
112418598 AATATGCCCT
* * * *
112418608 CGGACTTGTACTCCTCAGGCTTTTACAATTTAATCCCTCTAGTTTT-TATTTAAAAAACTTAATC
1 CGGACCTGTACTCCTCAAGCTTGTACAATTTAATCCCTCTACTTTTGT-TTTAAAAAACTTAATC
112418672 CTTTACTTTGAA
65 CTTTACTTTGAA
* * * *
112418684 CGGACCTGTACTCTTTAAGCTTGTACAATTTAATTCCTCTACTTTTGTTTTTAAAAACTTAATCC
1 CGGACCTGTACTCCTCAAGCTTGTACAATTTAATCCCTCTACTTTTGTTTTAAAAAACTTAATCC
*
112418749 TTTGCTTT
66 TTTACTTT
112418757 AATTGTTAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 62 0.98
77 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (76 bp):
CGGACCTGTACTCCTCAAGCTTGTACAATTTAATCCCTCTACTTTTGTTTTAAAAAACTTAATCC
TTTACTTTGAA
Found at i:112425082 original size:19 final size:19
Alignment explanation
Indices: 112425060--112425102 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
112425050 TTTTATATTA
*
112425060 TTAAAATATATTATTATCC
1 TTAAAATATATTATTAACC
*
112425079 TTAATATATATTATTAACC
1 TTAAAATATATTATTAACC
112425098 TTAAA
1 TTAAA
112425103 CTTAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAAATATATTATTAACC
Found at i:112432324 original size:31 final size:31
Alignment explanation
Indices: 112432249--112432324 Score: 75
Period size: 31 Copynumber: 2.4 Consensus size: 31
112432239 ACTATACTTC
* *
112432249 AATTTGAAGAATTTTAATTTTATACTTTTCCA
1 AATTTTAA-AATTTTAATTTTATACTTTTCAA
* *
112432281 AATTGGT-CAATTTTAATTATTATACTTTT-AA
1 AATT-TTAAAATTTTAATT-TTATACTTTTCAA
112432312 AATTTTAAAATTT
1 AATTTTAAAATTT
112432325 CAATCTTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
30 1 0.03
31 20 0.57
32 14 0.40
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (31 bp):
AATTTTAAAATTTTAATTTTATACTTTTCAA
Found at i:112441193 original size:45 final size:44
Alignment explanation
Indices: 112441142--112441281 Score: 221
Period size: 45 Copynumber: 3.2 Consensus size: 44
112441132 ACTCGTCATT
*
112441142 CTATTAAAAATTACTTTCATTTCTACTATTAAAAACTACTAACTA
1 CTATTAAAAA-GACTTTCATTTCTACTATTAAAAACTACTAACTA
112441187 CTATT--AAAGACTTTCATTTCTACTATTAAAAACTACTAACTA
1 CTATTAAAAAGACTTTCATTTCTACTATTAAAAACTACTAACTA
* *
112441229 CTACTATTAAAGACTTTCATTTCTACTATTAAAAACTACTAACTA
1 CTATTA-AAAAGACTTTCATTTCTACTATTAAAAACTACTAACTA
112441274 CTATTAAA
1 CTATTAAA
112441282 GACTAGATAT
Statistics
Matches: 88, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
42 37 0.42
43 3 0.03
44 1 0.01
45 47 0.53
ACGTcount: A:0.41, C:0.19, G:0.01, T:0.39
Consensus pattern (44 bp):
CTATTAAAAAGACTTTCATTTCTACTATTAAAAACTACTAACTA
Found at i:112441203 original size:42 final size:42
Alignment explanation
Indices: 112441154--112441285 Score: 237
Period size: 42 Copynumber: 3.1 Consensus size: 42
112441144 ATTAAAAATT
112441154 ACTTTCATTTCTACTATTAAAAACTACTAACTACTATTAAAG
1 ACTTTCATTTCTACTATTAAAAACTACTAACTACTATTAAAG
112441196 ACTTTCATTTCTACTATTAAAAACTACTAACTACTACTATTAAAG
1 ACTTTCATTTCTACTATTAAAAACTACT-A--ACTACTATTAAAG
112441241 ACTTTCATTTCTACTATTAAAAACTACTAACTACTATTAAAG
1 ACTTTCATTTCTACTATTAAAAACTACTAACTACTATTAAAG
112441283 ACT
1 ACT
112441286 AGATATACGT
Statistics
Matches: 87, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
42 44 0.51
43 1 0.01
44 1 0.01
45 41 0.47
ACGTcount: A:0.40, C:0.20, G:0.02, T:0.38
Consensus pattern (42 bp):
ACTTTCATTTCTACTATTAAAAACTACTAACTACTATTAAAG
Found at i:112441358 original size:16 final size:16
Alignment explanation
Indices: 112441337--112441368 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
112441327 TTAGCTATAT
112441337 CGGTTTTTAACCATCA
1 CGGTTTTTAACCATCA
112441353 CGGTTTTTAACCATCA
1 CGGTTTTTAACCATCA
112441369 ATTTGACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (16 bp):
CGGTTTTTAACCATCA
Found at i:112444757 original size:22 final size:22
Alignment explanation
Indices: 112444729--112444807 Score: 68
Period size: 22 Copynumber: 3.3 Consensus size: 22
112444719 TCAAACTAAA
112444729 TTAAAATCATTTAAATAATAAT
1 TTAAAATCATTTAAATAATAAT
* * * *
112444751 TTAAAATATATTTTTTGCACTAACTAAA
1 TTAAAAT-CA---TTT-AAATAA-TAAT
112444779 TTAAAATCATTTAAATAATAAT
1 TTAAAATCATTTAAATAATAAT
112444801 TTAAAAT
1 TTAAAAT
112444808 ATAGTTTTTG
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
22 17 0.40
23 5 0.12
24 3 0.07
26 3 0.07
27 5 0.12
28 10 0.23
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (22 bp):
TTAAAATCATTTAAATAATAAT
Found at i:112444782 original size:50 final size:50
Alignment explanation
Indices: 112444722--112444823 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
112444712 AATCTTATCA
*
112444722 AACTAAATTAAAATCATTTAAATAATAATTTAAAATATATTTTTTGCACT
1 AACTAAATTAAAATCATTTAAATAATAATTTAAAATATAGTTTTTGCACT
112444772 AACTAAATTAAAATCATTTAAATAATAATTTAAAATATAGTTTTTGCACT
1 AACTAAATTAAAATCATTTAAATAATAATTTAAAATATAGTTTTTGCACT
112444822 AA
1 AA
112444824 TTTTATCATG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (50 bp):
AACTAAATTAAAATCATTTAAATAATAATTTAAAATATAGTTTTTGCACT
Found at i:112444824 original size:27 final size:26
Alignment explanation
Indices: 112444744--112444824 Score: 71
Period size: 22 Copynumber: 3.2 Consensus size: 26
112444734 ATCATTTAAA
112444744 TAATAATTTAAAATATATTTTTTGCAC
1 TAATAATTTAAAATATA-TTTTTGCAC
* * * *
112444771 TAACTAAATTAAAAT-CA--TTT-AAA
1 TAA-TAATTTAAAATATATTTTTGCAC
112444794 TAATAATTTAAAATATAGTTTTTGCAC
1 TAATAATTTAAAATATA-TTTTTGCAC
112444821 TAAT
1 TAAT
112444825 TTTATCATGA
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
22 10 0.25
23 5 0.12
24 3 0.08
26 3 0.08
27 9 0.22
28 10 0.25
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (26 bp):
TAATAATTTAAAATATATTTTTGCAC
Found at i:112444868 original size:22 final size:22
Alignment explanation
Indices: 112444840--112444888 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
112444830 CATGAATTCT
*
112444840 GTTTTGAGCATTTTTATCATAA
1 GTTTTGAGCATATTTATCATAA
*
112444862 GTTTTGATCATATTTATCATAA
1 GTTTTGAGCATATTTATCATAA
*
112444884 CTTTT
1 GTTTT
112444889 ATAATACGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.53
Consensus pattern (22 bp):
GTTTTGAGCATATTTATCATAA
Found at i:112445902 original size:22 final size:21
Alignment explanation
Indices: 112445853--112445916 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
112445843 GTATAACAGT
* *
112445853 AAAAATATAATTTTATTTTTT
1 AAAAATTTAATTTTATTTTTA
*
112445874 AATAATTTATATTTTATTTTTA
1 AAAAATTTA-ATTTTATTTTTA
* **
112445896 AAAAATTAAATTAAATTTTTA
1 AAAAATTTAATTTTATTTTTA
112445917 GTTCAAATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AAAAATTTAATTTTATTTTTA
Found at i:112446908 original size:14 final size:14
Alignment explanation
Indices: 112446871--112446912 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
112446861 AAATAAAAAC
*
112446871 ATACAAAAATTAAA
1 ATACAAAAATTATA
*
112446885 ATGAC-TAAATTATA
1 AT-ACAAAAATTATA
112446899 ATACAAAAATTATA
1 ATACAAAAATTATA
112446913 TCTACAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 2 0.09
14 19 0.83
15 2 0.09
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (14 bp):
ATACAAAAATTATA
Found at i:112453051 original size:11 final size:11
Alignment explanation
Indices: 112453035--112453071 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
112453025 AGGTCAAGGT
112453035 AAAATTCTAAA
1 AAAATTCTAAA
*
112453046 AAAATT-T-AG
1 AAAATTCTAAA
112453055 AAAATTCTAAA
1 AAAATTCTAAA
112453066 AAAATT
1 AAAATT
112453072 TAGACAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 7 0.32
10 2 0.09
11 13 0.59
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (11 bp):
AAAATTCTAAA
Found at i:112453060 original size:20 final size:20
Alignment explanation
Indices: 112453035--112453075 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
112453025 AGGTCAAGGT
112453035 AAAATTCTAAAAAAATTTAG
1 AAAATTCTAAAAAAATTTAG
112453055 AAAATTCTAAAAAAATTTAG
1 AAAATTCTAAAAAAATTTAG
112453075 A
1 A
112453076 CAAACAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAATTCTAAAAAAATTTAG
Done.