Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 96 of 97
Found at i:38483627 original size:21 final size:23
Alignment explanation
Indices: 38483587--38483630 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
38483577 ATTAAATATA
*
38483587 AAAATATTAATAATTTTTAATTT
1 AAAATATTAATAATCTTTAATTT
38483610 AAAAT-TTAA-AATCTTTAATTT
1 AAAATATTAATAATCTTTAATTT
38483631 TATACTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 4 0.20
23 5 0.25
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
AAAATATTAATAATCTTTAATTT
Found at i:38487584 original size:2 final size:2
Alignment explanation
Indices: 38487572--38487671 Score: 146
Period size: 2 Copynumber: 49.0 Consensus size: 2
38487562 CTAATGTAAC
*
38487572 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* *
38487615 AT AT AT GCT NT 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
*
38487658 AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT
38487672 GCTGTCCAGA
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
2 86 0.97
3 3 0.03
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38491400 original size:2 final size:2
Alignment explanation
Indices: 38491393--38491429 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
38491383 TTTTTGTTAT
*
38491393 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38491430 GTATGTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38491418 original size:18 final size:18
Alignment explanation
Indices: 38491395--38491438 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
38491385 TTTGTTATTA
38491395 TATATATATATATATATG
1 TATATATATATATATATG
38491413 TATATATATATATATATG
1 TATATATATATATATATG
*
38491431 TATGTATA
1 TATATATA
38491439 AAGAAGAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (18 bp):
TATATATATATATATATG
Found at i:38492439 original size:1 final size:1
Alignment explanation
Indices: 38492433--38492476 Score: 79
Period size: 1 Copynumber: 44.0 Consensus size: 1
38492423 CCCACCCACT
*
38492433 CCCCCCCCCCCCCCCNCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
38492477 AAAGAATCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.98, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:38516542 original size:6 final size:6
Alignment explanation
Indices: 38516527--38516567 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
38516517 TCCTCCGCCA
*
38516527 ACCC-C ACCCTC ACCCTC ACCCTC ACCCTC ACCCTC ATCCTC
1 ACCCTC ACCCTC ACCCTC ACCCTC ACCCTC ACCCTC ACCCTC
38516568 GATCCGTTGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 4 0.12
6 30 0.88
ACGTcount: A:0.17, C:0.66, G:0.00, T:0.17
Consensus pattern (6 bp):
ACCCTC
Found at i:38533815 original size:20 final size:20
Alignment explanation
Indices: 38533774--38533847 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
38533764 GTAGGTATTT
*
38533774 ATCTATTAATAGA-TAGTATA
1 ATCTATCAATAGATTA-TATA
*
38533794 ATCTATCAATAGATTATGTA
1 ATCTATCAATAGATTATATA
* * *
38533814 ATCTATCGATAGAATTTTCT-
1 ATCTATCAATAG-ATTATATA
38533834 ATCTATC-ATAGATT
1 ATCTATCAATAGATT
38533848 TGTCTTTGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
18 3 0.06
19 4 0.09
20 33 0.70
21 7 0.15
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (20 bp):
ATCTATCAATAGATTATATA
Found at i:38534037 original size:20 final size:20
Alignment explanation
Indices: 38534000--38534038 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38533990 TAATTGAAAG
* *
38534000 TTAAAAAGTCAAATTTTATA
1 TTAAAAAGTAAAAATTTATA
*
38534020 TTAAAAATTAAAAATTTAT
1 TTAAAAAGTAAAAATTTAT
38534039 TCAATTTATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (20 bp):
TTAAAAAGTAAAAATTTATA
Found at i:38535224 original size:2 final size:2
Alignment explanation
Indices: 38535219--38535268 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
38535209 TCTCTCTATC
38535219 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38535261 TA TA -A TA T
1 TA TA TA TA T
38535269 GCCTCAGTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38539268 original size:20 final size:20
Alignment explanation
Indices: 38539243--38539284 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
38539233 AACGAGTGTG
38539243 ATCATTCTAAATATATTAAT
1 ATCATTCTAAATATATTAAT
38539263 ATCATTCTAAATATATTAAT
1 ATCATTCTAAATATATTAAT
38539283 AT
1 AT
38539285 TTGTTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (20 bp):
ATCATTCTAAATATATTAAT
Found at i:38541897 original size:4 final size:4
Alignment explanation
Indices: 38541888--38541923 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
38541878 TCATCATATG
*
38541888 CATA CATA CATA CCTA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA
38541924 TATAATTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:38548012 original size:13 final size:13
Alignment explanation
Indices: 38547994--38548019 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38547984 CTTAATCATA
38547994 AAATTGTTGGCTT
1 AAATTGTTGGCTT
38548007 AAATTGTTGGCTT
1 AAATTGTTGGCTT
38548020 TCAAATGCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
AAATTGTTGGCTT
Found at i:38550153 original size:2 final size:2
Alignment explanation
Indices: 38550146--38550259 Score: 135
Period size: 2 Copynumber: 58.0 Consensus size: 2
38550136 CAGAAAGATG
*
38550146 AT AT AT AT AT AT AT AT AT AT -T AT AT AT -T AT AT AT AT AGT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* **
38550187 AT A- AT AT AT AT AG CN 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
* * *
38550228 AT AT AT AT AT AT AT AT AT GT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38550260 TTGATAAATA
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
1 3 0.03
2 91 0.96
3 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38551369 original size:7 final size:7
Alignment explanation
Indices: 38551357--38551383 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
38551347 ATAACATCAA
38551357 TGGCACT
1 TGGCACT
38551364 TGGCACT
1 TGGCACT
38551371 TGGCACT
1 TGGCACT
38551378 TGGCAC
1 TGGCAC
38551384 CAAAGGCGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.26
Consensus pattern (7 bp):
TGGCACT
Found at i:38558258 original size:16 final size:15
Alignment explanation
Indices: 38558233--38558262 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
38558223 AACCACCCTA
38558233 CCCCCCCCCCCCCCG
1 CCCCCCCCCCCCCCG
38558248 CCCCCCGCCCCCCCC
1 CCCCCC-CCCCCCCC
38558263 ACAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.93, G:0.07, T:0.00
Consensus pattern (15 bp):
CCCCCCCCCCCCCCG
Found at i:38568002 original size:19 final size:19
Alignment explanation
Indices: 38567980--38568031 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
38567970 AAATTTTTGA
38567980 AATAAAATAATATTTTATT
1 AATAAAATAATATTTTATT
38567999 AATAAAATAATATTTTATT
1 AATAAAATAATATTTTATT
38568018 AATAAAATAATATT
1 AATAAAATAATATT
38568032 AAAATATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATAAAATAATATTTTATT
Found at i:38568050 original size:19 final size:18
Alignment explanation
Indices: 38567986--38568050 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 18
38567976 TTGAAATAAA
*
38567986 ATAATATTTTATTAATAAA
1 ATAATATTTTATTAA-AAT
38568005 ATAATATTTTATT--AAT
1 ATAATATTTTATTAAAAT
**
38568021 A-AA-ATAATATTAAAAT
1 ATAATATTTTATTAAAAT
38568037 ATTAATATTTTATT
1 A-TAATATTTTATT
38568051 CAGTGTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 6 0.17
15 2 0.06
16 7 0.19
18 2 0.06
19 19 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAATATTTTATTAAAAT
Found at i:38569113 original size:49 final size:49
Alignment explanation
Indices: 38569054--38569221 Score: 230
Period size: 49 Copynumber: 3.4 Consensus size: 49
38569044 TAATCTTGTG
*
38569054 TGATGATGATGACCCGATTATGTGCGAGTAGAGAGTGCGCATAGACCGA
1 TGATGATGATGACCCGACTATGTGCGAGTAGAGAGTGCGCATAGACCGA
* *
38569103 TGATGATGATGACTCGACTATGTGCGAGTAG-GAAGTGCGCATAGGCCGA
1 TGATGATGATGACCCGACTATGTGCGAGTAGAG-AGTGCGCATAGACCGA
* * * *
38569152 TGATGATGATGACCCGACTATATGCGAATAGAGAGTGCGCATAAACGGA
1 TGATGATGATGACCCGACTATGTGCGAGTAGAGAGTGCGCATAGACCGA
* * *
38569201 TGATCATGATGATCCGGCTAT
1 TGATGATGATGACCCGACTAT
38569222 AATCATGAAT
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
48 1 0.01
49 103 0.98
50 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (49 bp):
TGATGATGATGACCCGACTATGTGCGAGTAGAGAGTGCGCATAGACCGA
Found at i:38574393 original size:49 final size:49
Alignment explanation
Indices: 38574340--38574457 Score: 148
Period size: 49 Copynumber: 2.4 Consensus size: 49
38574330 TAATCGTGTG
* ** * *
38574340 ATGATGATGAGCCGGTTATGTGTGAGTA-AGGAGTGCGCATAGACCGATA
1 ATGATGATGACCCGACTATGTGCGAGTAGA-GAGTGCGCATAAACCGATA
* *
38574389 ATGATGATGACCCGACTATGTGCGAGTAGAGAGTGCGCATAAACGGATG
1 ATGATGATGACCCGACTATGTGCGAGTAGAGAGTGCGCATAAACCGATA
*
38574438 ATGATGATGATCCGACTATG
1 ATGATGATGACCCGACTATG
38574458 ATGATGAATG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
49 59 0.98
50 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.32, T:0.24
Consensus pattern (49 bp):
ATGATGATGACCCGACTATGTGCGAGTAGAGAGTGCGCATAAACCGATA
Found at i:38580154 original size:102 final size:102
Alignment explanation
Indices: 38579978--38580181 Score: 390
Period size: 102 Copynumber: 2.0 Consensus size: 102
38579968 AGTTTACATT
*
38579978 GCTTTTAAAAAATGTGACAATGAAACCCCCATTGCAATTGCAAGTAAAGCAAACTAATTTTTCTG
1 GCTTTTAAAAAATGTGAAAATGAAACCCCCATTGCAATTGCAAGTAAAGCAAACTAATTTTTCTG
38580043 AATTTCCAACCAAGAGAAAAGTTATCTTTAGACCAAG
66 AATTTCCAACCAAGAGAAAAGTTATCTTTAGACCAAG
*
38580080 GCTTTTAAAAAATGTGAAAATGAAACCCCCGTTGCAATTGCAAGTAAAGCAAACTAATTTTTCTG
1 GCTTTTAAAAAATGTGAAAATGAAACCCCCATTGCAATTGCAAGTAAAGCAAACTAATTTTTCTG
38580145 AATTTCCAACCAAGAGAAAAGTTATCTTTAGACCAAG
66 AATTTCCAACCAAGAGAAAAGTTATCTTTAGACCAAG
38580182 CTGCCTTGCC
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.27
Consensus pattern (102 bp):
GCTTTTAAAAAATGTGAAAATGAAACCCCCATTGCAATTGCAAGTAAAGCAAACTAATTTTTCTG
AATTTCCAACCAAGAGAAAAGTTATCTTTAGACCAAG
Found at i:38584415 original size:17 final size:18
Alignment explanation
Indices: 38584387--38584421 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
38584377 GGCGTTGATT
38584387 AGAAAAACAAAAGAAAAA
1 AGAAAAACAAAAGAAAAA
38584405 AGAAAAA-AAAAGAAAAA
1 AGAAAAACAAAAGAAAAA
38584422 CACTAAAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (18 bp):
AGAAAAACAAAAGAAAAA
Found at i:38586226 original size:43 final size:43
Alignment explanation
Indices: 38586165--38586252 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
38586155 CATCACAAGC
38586165 AGCACTAATCATGTCAAGGCAACAGGGATAATAAATACAGCTT
1 AGCACTAATCATGTCAAGGCAACAGGGATAATAAATACAGCTT
*
38586208 AGCACTAATCATGTCAAGGCAACAGGGATAGTAAATACAGCTT
1 AGCACTAATCATGTCAAGGCAACAGGGATAATAAATACAGCTT
38586251 AG
1 AG
38586253 ATAAGAGATC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (43 bp):
AGCACTAATCATGTCAAGGCAACAGGGATAATAAATACAGCTT
Found at i:38586621 original size:43 final size:43
Alignment explanation
Indices: 38586560--38586649 Score: 171
Period size: 43 Copynumber: 2.1 Consensus size: 43
38586550 CAAATTGCAC
38586560 TACGGATTCTACTTCTTTACACCCAGACCAAAGAAACATTTCA
1 TACGGATTCTACTTCTTTACACCCAGACCAAAGAAACATTTCA
*
38586603 TACGGATTCTATTTCTTTACACCCAGACCAAAGAAACATTTCA
1 TACGGATTCTACTTCTTTACACCCAGACCAAAGAAACATTTCA
38586646 TACG
1 TACG
38586650 TTATACACCT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.29
Consensus pattern (43 bp):
TACGGATTCTACTTCTTTACACCCAGACCAAAGAAACATTTCA
Found at i:38589175 original size:2 final size:2
Alignment explanation
Indices: 38589168--38589196 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38589158 TGAAGAAACA
38589168 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
38589197 ATATGTACCT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38597716 original size:25 final size:25
Alignment explanation
Indices: 38597683--38597741 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
38597673 GAATGATGTC
38597683 TGATGAAATAATGCTCCACAGAGAA
1 TGATGAAATAATGCTCCACAGAGAA
38597708 TGATGAAATAATGCTCCACAGAGAA
1 TGATGAAATAATGCTCCACAGAGAA
38597733 TGATGAAAT
1 TGATGAAAT
38597742 GACTGGCTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.22
Consensus pattern (25 bp):
TGATGAAATAATGCTCCACAGAGAA
Found at i:38608376 original size:17 final size:17
Alignment explanation
Indices: 38608335--38608377 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
38608325 GTTCTTAAAA
* *
38608335 ATAATTTTAATATATTT
1 ATAATTTTAAAAAATTT
* *
38608352 TTATTTTTAAAAAATTT
1 ATAATTTTAAAAAATTT
38608369 ATAATTTTA
1 ATAATTTTA
38608378 TTTCTACAAT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATAATTTTAAAAAATTT
Found at i:38608396 original size:53 final size:51
Alignment explanation
Indices: 38608278--38608376 Score: 137
Period size: 52 Copynumber: 1.9 Consensus size: 51
38608268 CCTAATAATT
*
38608278 TTAAAAATTTTATAATTACTTTTATTTTTAAAAAAAATTATAATTTTGTTC
1 TTAAAAATTTTTTAATTACTTTTATTTTTAAAAAAAATTATAATTTTGTTC
* * *
38608329 TTAAAAATAATTTTAATATATTTTTATTTTT-AAAAAATTTATAATTTT
1 TTAAAAAT-TTTTTAAT-TACTTTTATTTTTAAAAAAAATTATAATTTT
38608377 ATTTCTACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
51 8 0.19
52 22 0.52
53 12 0.29
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (51 bp):
TTAAAAATTTTTTAATTACTTTTATTTTTAAAAAAAATTATAATTTTGTTC
Found at i:38608655 original size:19 final size:19
Alignment explanation
Indices: 38608631--38608706 Score: 57
Period size: 19 Copynumber: 3.9 Consensus size: 19
38608621 AATTTCATTC
38608631 TTTAAAAACTTAAAAAAAT
1 TTTAAAAACTTAAAAAAAT
38608650 TTT-AAAACTCATAATAAATAA-
1 TTTAAAAACT--TAA-AAA-AAT
* * *
38608671 TTAAAAAAATTAAAAATAT
1 TTTAAAAACTTAAAAAAAT
* *
38608690 GTTAAAAACATAAAAAA
1 TTTAAAAACTTAAAAAA
38608707 TCTTTCAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
18 7 0.16
19 18 0.42
20 6 0.14
21 5 0.12
22 7 0.16
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.29
Consensus pattern (19 bp):
TTTAAAAACTTAAAAAAAT
Found at i:38608809 original size:10 final size:10
Alignment explanation
Indices: 38608730--38608986 Score: 83
Period size: 10 Copynumber: 24.7 Consensus size: 10
38608720 TGAAAAATCT
*
38608730 CTTAAAAA-C
1 CTTAAAAATA
* *
38608739 CTTAAATATG
1 CTTAAAAATA
*
38608749 CTTAAAAGTA
1 CTTAAAAATA
* *
38608759 TCTTTAAAATG
1 -CTTAAAAATA
*
38608770 CTTAAAAATT
1 CTTAAAAATA
* *
38608780 CATAAAAAAGA
1 C-TTAAAAATA
*
38608791 GTTAAAAATA
1 CTTAAAAATA
38608801 CTTAAAAATA
1 CTTAAAAATA
*
38608811 CATACAAAAT-
1 CTTA-AAAATA
38608821 CTTTAAAAAATGA
1 C-TT-AAAAAT-A
38608834 CTTAAAAA-A
1 CTTAAAAATA
*
38608843 TCTTCAAAAT-
1 -CTTAAAAATA
* *
38608853 CTATAAAATTC
1 CT-TAAAAATA
* *
38608864 CTTGAAAACA
1 CTTAAAAATA
38608874 CCTTAAAAATA
1 -CTTAAAAATA
**
38608885 CTTTCAAATA
1 CTTAAAAATA
*
38608895 CATGAAAAA-A
1 C-TTAAAAATA
*
38608905 CCTTTAAAATA
1 -CTTAAAAATA
*
38608916 CTTAAAATTA
1 CTTAAAAATA
* *
38608926 CCTTAAACATT
1 -CTTAAAAATA
* *
38608937 CTTAATAAGA
1 CTTAAAAATA
*
38608947 GCCTAAAAATA
1 -CTTAAAAATA
*
38608958 CTATAAAAAAAA
1 CT-T-AAAAATA
* *
38608970 CTTTAAAATC
1 CTTAAAAATA
38608980 CTTAAAA
1 CTTAAAA
38608987 TTTGTAATAA
Statistics
Matches: 175, Mismatches: 53, Indels: 39
0.66 0.20 0.15
Matches are distributed among these distances:
9 10 0.06
10 92 0.53
11 61 0.35
12 11 0.06
13 1 0.01
ACGTcount: A:0.53, C:0.14, G:0.04, T:0.30
Consensus pattern (10 bp):
CTTAAAAATA
Found at i:38608827 original size:31 final size:31
Alignment explanation
Indices: 38608722--38608841 Score: 91
Period size: 31 Copynumber: 3.8 Consensus size: 31
38608712 CAAATTTTTG
* * * *
38608722 AAAAATCTCTTAAAAA-CCTTAAATATGCTTA
1 AAAAATCT-TTAAAAATACTTAAAAATACATA
* * *
38608753 AAAGTATCTTT-AAAATGCTTAAAAATTCATA
1 AAA-AATCTTTAAAAATACTTAAAAATACATA
***
38608784 AAAAAGAGTTAAAAATACTTAAAAATACATA
1 AAAAATCTTTAAAAATACTTAAAAATACATA
*
38608815 CAAAATCTTTAAAAAATGACTTAAAAA
1 AAAAATCTTT-AAAAAT-ACTTAAAAA
38608842 ATCTTCAAAA
Statistics
Matches: 69, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
30 7 0.10
31 43 0.62
32 10 0.14
33 9 0.13
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (31 bp):
AAAAATCTTTAAAAATACTTAAAAATACATA
Found at i:38608851 original size:21 final size:21
Alignment explanation
Indices: 38608733--38608852 Score: 77
Period size: 21 Copynumber: 5.7 Consensus size: 21
38608723 AAAATCTCTT
* *
38608733 AAAAACCTTAAATATG-CTTA
1 AAAAATCTTAAAAATGACTTA
* *
38608753 AAAGTATCTTTAAAATG-CTTA
1 AAA-AATCTTAAAAATGACTTA
* * * *
38608774 AAAATTCATAAAAAAGAGTT-
1 AAAAATCTTAAAAATGACTTA
*
38608794 AAAAATACTTAAAAAT-ACATA
1 AAAAAT-CTTAAAAATGACTTA
*
38608815 CAAAATCTTTAAAAAATGACTTA
1 AAAAATC-TT-AAAAATGACTTA
*
38608838 AAAAATCTTCAAAAT
1 AAAAATCTTAAAAAT
38608853 CTATAAAATT
Statistics
Matches: 74, Mismatches: 19, Indels: 13
0.70 0.18 0.12
Matches are distributed among these distances:
20 19 0.26
21 37 0.50
22 8 0.11
23 10 0.14
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (21 bp):
AAAAATCTTAAAAATGACTTA
Found at i:38608851 original size:32 final size:32
Alignment explanation
Indices: 38608794--38608860 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
38608784 AAAAAGAGTT
*
38608794 AAAAATACTTAAAAATACATACAAAATCTTTA
1 AAAAATACTTAAAAATACATACAAAATCTATA
*
38608826 AAAAATGACTTAAAAA-ATC-TTCAAAATCTATA
1 AAAAAT-ACTTAAAAATA-CATACAAAATCTATA
38608858 AAA
1 AAA
38608861 TTCCTTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 21 0.68
33 10 0.32
ACGTcount: A:0.60, C:0.12, G:0.01, T:0.27
Consensus pattern (32 bp):
AAAAATACTTAAAAATACATACAAAATCTATA
Found at i:38608928 original size:21 final size:21
Alignment explanation
Indices: 38608848--38608929 Score: 55
Period size: 21 Copynumber: 4.0 Consensus size: 21
38608838 AAAAATCTTC
*
38608848 AAAAT-CTATAAAATT-CCTTG
1 AAAATACT-TAAAATTACCTTT
* *
38608868 AAAACACCTTAAAAATA-CTTT
1 AAAATA-CTTAAAATTACCTTT
* * *
38608889 CAAATACATGAAAA-AACCTTT
1 AAAATAC-TTAAAATTACCTTT
38608910 AAAATACTTAAAATTACCTT
1 AAAATACTTAAAATTACCTT
38608930 AAACATTCTT
Statistics
Matches: 46, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
20 11 0.24
21 33 0.72
22 2 0.04
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAATACTTAAAATTACCTTT
Found at i:38609117 original size:11 final size:10
Alignment explanation
Indices: 38609092--38609267 Score: 52
Period size: 10 Copynumber: 16.8 Consensus size: 10
38609082 TTGAAAGGAT
38609092 CTTAAAAATA
1 CTTAAAAATA
*
38609102 CTTAAAAATT
1 CTTAAAAATA
*
38609112 CATTAAAAAAAA
1 C-TT-AAAAATA
*
38609124 CTTCAAAAATG
1 CTT-AAAAATA
* ** *
38609135 CTTCATTAGA
1 CTTAAAAATA
* *
38609145 CTACAAAAATT
1 CT-TAAAAATA
*
38609156 TTTAAAAAATA
1 CTT-AAAAATA
38609167 CTTAAAAA-A
1 CTTAAAAATA
* *
38609176 CTTTACAAACA
1 C-TTAAAAATA
* *
38609187 CTTAAAATTC
1 CTTAAAAATA
38609197 CTTGAAAACAT-
1 CTT-AAAA-ATA
* *
38609208 CTTAAATATC
1 CTTAAAAATA
*
38609218 CTTTAAAAT-
1 CTTAAAAATA
* *
38609227 CAATAAAAAAA
1 C-TTAAAAATA
38609238 TCTTAAAAATA
1 -CTTAAAAATA
38609249 CTTCAAAAATA
1 CTT-AAAAATA
*
38609260 TTTAAAAA
1 CTTAAAAA
38609268 ATGGCTTGAA
Statistics
Matches: 117, Mismatches: 36, Indels: 26
0.65 0.20 0.15
Matches are distributed among these distances:
9 5 0.04
10 56 0.48
11 48 0.41
12 8 0.07
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.31
Consensus pattern (10 bp):
CTTAAAAATA
Found at i:38609225 original size:21 final size:20
Alignment explanation
Indices: 38609176--38609225 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
38609166 ACTTAAAAAA
38609176 CTTTACAAACACTTAAAATTC
1 CTTTA-AAACACTTAAAATTC
*
38609197 CTTGAAAACATCTT-AAATATC
1 CTTTAAAACA-CTTAAAAT-TC
38609218 CTTTAAAA
1 CTTTAAAA
38609226 TCAATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.34
Consensus pattern (20 bp):
CTTTAAAACACTTAAAATTC
Found at i:38609298 original size:105 final size:104
Alignment explanation
Indices: 38609148--38609350 Score: 282
Period size: 105 Copynumber: 1.9 Consensus size: 104
38609138 CATTAGACTA
* * * * *
38609148 CAAAAATTTTTAAAAAATACTTAAAAAACTTTACAAACACTTAAAATTCCTTGAAAACATCTTAA
1 CAAAAATATTTAAAAAATACTTAAAAAACTTTAAAAACACATAAAATTCCTTGAAAACACCATAA
*
38609213 ATATCCTTTAAAATCAATAAAAAAATCTTAAAAATACTT
66 AAATCCTTTAAAATCAATAAAAAAATCTTAAAAATACTT
* * *
38609252 CAAAAATATTTAAAAAATGGCTTGAAAAACTTTAAAAATC-CATAAAATTCCTTGCAAACACCAT
1 CAAAAATATTTAAAAAAT-ACTTAAAAAACTTTAAAAA-CACATAAAATTCCTTGAAAACACCAT
* *
38609316 AAAAATCCTTTGAAATCCATAAAAAAATCTTAAAA
64 AAAAATCCTTTAAAATCAATAAAAAAATCTTAAAA
38609351 TTCGTAATAA
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
104 17 0.20
105 68 0.79
106 1 0.01
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.29
Consensus pattern (104 bp):
CAAAAATATTTAAAAAATACTTAAAAAACTTTAAAAACACATAAAATTCCTTGAAAACACCATAA
AAATCCTTTAAAATCAATAAAAAAATCTTAAAAATACTT
Found at i:38609341 original size:21 final size:20
Alignment explanation
Indices: 38609287--38609340 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
38609277 AAAACTTTAA
*
38609287 AAATCCATAAAATTCCTTGC
1 AAATCCATAAAAATCCTTGC
*
38609307 AAACACCATAAAAATCCTTTG-
1 AAA-TCCATAAAAATCC-TTGC
38609328 AAATCCATAAAAA
1 AAATCCATAAAAA
38609341 AATCTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.41
21 14 0.48
22 3 0.10
ACGTcount: A:0.50, C:0.22, G:0.04, T:0.24
Consensus pattern (20 bp):
AAATCCATAAAAATCCTTGC
Found at i:38609390 original size:11 final size:11
Alignment explanation
Indices: 38609374--38609578 Score: 57
Period size: 11 Copynumber: 19.7 Consensus size: 11
38609364 ATTAAAAATA
38609374 TAAAAATCTCT
1 TAAAAATCTCT
*
38609385 TAAAAA-C-AT
1 TAAAAATCTCT
38609394 TAAAAATCT-T
1 TAAAAATCTCT
* *
38609404 TCAAATTC-CT
1 TAAAAATCTCT
38609414 TAAAAATCTCT
1 TAAAAATCTCT
*
38609425 TTAAAA-C-CT
1 TAAAAATCTCT
* *
38609434 TAAATAT-GCT
1 TAAAAATCTCT
***
38609444 TAAAAGGATCT
1 TAAAAATCTCT
* *
38609455 TCAAAAT-ACT
1 TAAAAATCTCT
*
38609465 T-AAAATCTAT
1 TAAAAATCTCT
* **
38609475 GAAAAAAGTCT
1 TAAAAATCTCT
*
38609486 TAAAAAT-GCT
1 TAAAAATCTCT
*
38609496 TCAAAATACT-T
1 TAAAAAT-CTCT
* *
38609507 CAAAAATCTTT
1 TAAAAATCTCT
38609518 TAAAAATC-CTT
1 TAAAAATCTC-T
38609529 TAGAAAA-C-CT
1 TA-AAAATCTCT
38609539 TAAAAAATC-CT
1 T-AAAAATCTCT
* *
38609550 TCAAATTCT-T
1 TAAAAATCTCT
38609560 TAAAAATAC-CT
1 TAAAAAT-CTCT
38609571 TAAAAATC
1 TAAAAATC
38609579 CTTTGAAATA
Statistics
Matches: 140, Mismatches: 35, Indels: 39
0.65 0.16 0.18
Matches are distributed among these distances:
9 18 0.13
10 55 0.39
11 63 0.45
12 4 0.03
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.33
Consensus pattern (11 bp):
TAAAAATCTCT
Found at i:38609523 original size:22 final size:21
Alignment explanation
Indices: 38609498--38609578 Score: 67
Period size: 22 Copynumber: 3.8 Consensus size: 21
38609488 AAAATGCTTC
38609498 AAAATACTTCAAAAATCTTTTA
1 AAAATACTTCAAAAATC-TTTA
* * * *
38609520 AAAATCCTTTAGAAAACCTTAA
1 AAAATACTTCA-AAAATCTTTA
* *
38609542 AAAATCCTTC-AAATTCTTTA
1 AAAATACTTCAAAAATCTTTA
38609562 AAAATACCTT-AAAAATC
1 AAAATA-CTTCAAAAATC
38609579 CTTTGAAATA
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
20 12 0.26
21 8 0.17
22 21 0.46
23 5 0.11
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.32
Consensus pattern (21 bp):
AAAATACTTCAAAAATCTTTA
Found at i:38609576 original size:31 final size:31
Alignment explanation
Indices: 38609521--38609581 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
38609511 AATCTTTTAA
*
38609521 AAATCCTTTAGAAAACCTTAAAAAATCCTTC
1 AAATCCTTTAAAAAACCTTAAAAAATCCTTC
*
38609552 AAATTCTTTAAAAATACCTT-AAAAATCCTT
1 AAATCCTTTAAAAA-ACCTTAAAAAATCCTT
38609582 TGAAATACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.33
Consensus pattern (31 bp):
AAATCCTTTAAAAAACCTTAAAAAATCCTTC
Found at i:38609835 original size:21 final size:21
Alignment explanation
Indices: 38609811--38609858 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
38609801 AAATCCATAA
38609811 AAAAAACCTT-AAAAATGCTTC
1 AAAAAA-CTTCAAAAATGCTTC
* * *
38609832 AAAATACTTCAAAAATGTTTT
1 AAAAAACTTCAAAAATGCTTC
38609853 AAAAAA
1 AAAAAA
38609859 TACTTTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.27
Consensus pattern (21 bp):
AAAAAACTTCAAAAATGCTTC
Found at i:38609911 original size:31 final size:31
Alignment explanation
Indices: 38609865--38609951 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
38609855 AAAATACTTT
* * *
38609865 AAAAAACCCTAAAAATCTTTAAAATTCCCTG
1 AAAAAACCTTAAAAATCTTTAAAATTCCATA
* *
38609896 AAAACACCTTAAAAATCTTTTGAAA-TCCATA
1 AAAAAACCTTAAAAATC-TTTAAAATTCCATA
*
38609927 AAAAAACCTTAAAAATGTTTAAAAT
1 AAAAAACCTTAAAAATCTTTAAAAT
38609952 GATTAAATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
30 6 0.13
31 34 0.74
32 6 0.13
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (31 bp):
AAAAAACCTTAAAAATCTTTAAAATTCCATA
Found at i:38609991 original size:11 final size:10
Alignment explanation
Indices: 38609160--38610010 Score: 127
Period size: 10 Copynumber: 82.4 Consensus size: 10
38609150 AAAATTTTTA
*
38609160 AAAAATACTT
1 AAAAATCCTT
* *
38609170 AAAAAACTTT
1 AAAAATCCTT
*
38609180 ACAAA-CACTT
1 AAAAATC-CTT
*
38609190 AAAATTCCTT
1 AAAAATCCTT
38609200 GAAAACAT-CTT
1 -AAAA-ATCCTT
*
38609211 AAATATCCTT
1 AAAAATCCTT
* * *
38609221 TAAAATCAATAA
1 AAAAATC-CT-T
38609233 AAAAAT-CTT
1 AAAAATCCTT
*
38609242 AAAAATACTT
1 AAAAATCCTT
**
38609252 CAAAAATATTT
1 -AAAAATCCTT
*
38609263 AAAAAATGGCTT
1 -AAAAAT-CCTT
*
38609275 GAAAAA-CTTT
1 -AAAAATCCTT
*
38609285 AAAAATCCAT
1 AAAAATCCTT
*
38609295 AAAATTCCTT
1 AAAAATCCTT
* *
38609305 GCAAACA-CCAT
1 --AAAAATCCTT
38609316 AAAAATCCTT
1 AAAAATCCTT
** *
38609326 TGAAATCCATAA
1 AAAAATCC-T-T
38609338 AAAAAT-CTT
1 AAAAATCCTT
* *
38609347 -AAAATTCGT
1 AAAAATCCTT
**
38609356 AATAAATAATT
1 AA-AAATCCTT
*
38609367 AAAAAT--AT
1 AAAAATCCTT
38609375 AAAAATCTCTT
1 AAAAATC-CTT
*
38609386 AAAAA-CATT
1 AAAAATCCTT
*
38609395 AAAAATCTTT
1 AAAAATCCTT
* *
38609405 CAAATTCCTT
1 AAAAATCCTT
38609415 AAAAATCTCTT
1 AAAAATC-CTT
*
38609426 TAAAA-CCTT
1 AAAAATCCTT
* *
38609435 AAATATGCTT
1 AAAAATCCTT
38609445 AAAAGGAT-CTT
1 AAAA--ATCCTT
* *
38609456 CAAAATACTT
1 AAAAATCCTT
38609466 -AAAAT-CTAT
1 AAAAATCCT-T
38609475 GAAAAAAGT-CTT
1 --AAAAA-TCCTT
*
38609487 AAAAATGCTT
1 AAAAATCCTT
* *
38609497 CAAAATACTT
1 AAAAATCCTT
*
38609507 CAAAAATCTTTT
1 -AAAAATC-CTT
38609519 AAAAATCCTTT
1 AAAAATCC-TT
38609530 AGAAAA-CCTT
1 A-AAAATCCTT
38609540 AAAAAATCCTT
1 -AAAAATCCTT
* * *
38609551 CAAATTCTTT
1 AAAAATCCTT
38609561 AAAAATACCTT
1 AAAAAT-CCTT
38609572 AAAAATCCTT
1 AAAAATCCTT
** *
38609582 TGAAATACATAAT
1 AAAAAT-CCT--T
*
38609595 AAAAAACCTT
1 AAAAATCCTT
* *
38609605 TAAAATGCTT
1 AAAAATCCTT
38609615 -AAAATGACCTT
1 AAAAAT--CCTT
* *
38609626 CAACATCCTT
1 AAAAATCCTT
* **
38609636 AAAGAGA-GCAA
1 AAA-A-ATCCTT
*
38609647 AAAAATCTTT
1 AAAAATCCTT
**
38609657 GAAAAAAACTT
1 -AAAAATCCTT
38609668 AAAAATCCTT
1 AAAAATCCTT
* *
38609678 -AAAATTCAT
1 AAAAATCCTT
**
38609687 AATAAATAATT
1 AA-AAATCCTT
**
38609698 AAAAA-AATT
1 AAAAATCCTT
38609707 AAAAATTCCTT
1 AAAAA-TCCTT
* *
38609718 AAAAA-CATA
1 AAAAATCCTT
***
38609727 AAAAAAATTT
1 AAAAATCCTT
* *
38609737 CAAATTCCTT
1 AAAAATCCTT
*
38609747 GAAAAATATCTT
1 -AAAAAT-CCTT
*
38609759 CAAAA-CCTT
1 AAAAATCCTT
*
38609768 AAAAATGCTT
1 AAAAATCCTT
**
38609778 GAAAGGGT-CTT
1 -AAA-AATCCTT
*
38609789 AAAAATTCTT
1 AAAAATCCTT
*
38609799 AAAAATCCATAA
1 AAAAATCC-T-T
*
38609811 AAAAAACCTT
1 AAAAATCCTT
*
38609821 AAAAATGCTT
1 AAAAATCCTT
* *
38609831 CAAAATACTT
1 AAAAATCCTT
**
38609841 CAAAAATGTTTT
1 -AAAAAT-CCTT
*
38609853 AAAAAATACTTT
1 -AAAAAT-CCTT
* *
38609865 AAAAAACCCT
1 AAAAATCCTT
*
38609875 AAAAATCTTT
1 AAAAATCCTT
* *
38609885 AAAATTCCCTG
1 AAAAAT-CCTT
38609896 AAAACA-CCTT
1 AAAA-ATCCTT
*
38609906 AAAAATCTTT
1 AAAAATCCTT
** *
38609916 TGAAATCCATA
1 AAAAATCC-TT
*
38609927 AAAAAACCTT
1 AAAAATCCTT
*
38609937 AAAAAT-GTT
1 AAAAATCCTT
* **
38609946 TAAAATGATT
1 AAAAATCCTT
*
38609956 AAATATCCTT
1 AAAAATCCTT
*
38609966 AAAAAGAGCC-T
1 -AAAA-ATCCTT
38609977 AAAAATCCTT
1 AAAAATCCTT
*
38609987 GAAAAAACCTT
1 -AAAAATCCTT
38609998 -AAAATCCTT
1 AAAAATCCTT
38610007 AAAA
1 AAAA
38610011 TACGTAATAA
Statistics
Matches: 595, Mismatches: 170, Indels: 152
0.65 0.19 0.17
Matches are distributed among these distances:
8 14 0.02
9 98 0.16
10 244 0.41
11 167 0.28
12 65 0.11
13 7 0.01
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.29
Consensus pattern (10 bp):
AAAAATCCTT
Found at i:38610471 original size:22 final size:21
Alignment explanation
Indices: 38610446--38610501 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
38610436 AAAATTATTC
*
38610446 AAAATACTTCTAAAATCTTTAA
1 AAAATACTT-TAAAAACTTTAA
38610468 AAAATACTTTAAAAACTTTAA
1 AAAATACTTTAAAAACTTTAA
*
38610489 AAAAT-CCTTAAAA
1 AAAATACTTTAAAA
38610502 TTCCTTGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 7 0.22
21 16 0.50
22 9 0.28
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATACTTTAAAAACTTTAA
Found at i:38610481 original size:10 final size:10
Alignment explanation
Indices: 38610446--38610522 Score: 50
Period size: 11 Copynumber: 7.4 Consensus size: 10
38610436 AAAATTATTC
38610446 AAAATACTTCT
1 AAAATACTT-T
38610457 AAAAT-CTTT
1 AAAATACTTT
38610466 AAAAAATACTTT
1 --AAAATACTTT
38610478 AAAA-ACTTT
1 AAAATACTTT
* *
38610487 AAAAAATCCTT
1 AAAATA-CTTT
* *
38610498 AAAATTCCTTG
1 AAAA-TACTTT
*
38610509 AAAACACTTT
1 AAAATACTTT
38610519 AAAA
1 AAAA
38610523 ATCTTTTGAA
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
9 10 0.19
10 15 0.29
11 23 0.44
12 4 0.08
ACGTcount: A:0.52, C:0.14, G:0.01, T:0.32
Consensus pattern (10 bp):
AAAATACTTT
Found at i:38610528 original size:10 final size:10
Alignment explanation
Indices: 38610457--38610528 Score: 58
Period size: 10 Copynumber: 6.9 Consensus size: 10
38610447 AAATACTTCT
38610457 AAAATCTTTAA
1 AAAATCTTT-A
38610468 AAAATACTTTA
1 AAAAT-CTTTA
38610479 AAAA-CTTTAA
1 AAAATCTTT-A
*
38610489 AAAATCCTTA
1 AAAATCTTTA
* *
38610499 AAATTCCTTGA
1 AAAAT-CTTTA
38610510 AAACA-CTTTA
1 AAA-ATCTTTA
38610520 AAAATCTTT
1 AAAATCTTT
38610529 TGAAATCCAT
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
9 5 0.10
10 21 0.43
11 19 0.39
12 4 0.08
ACGTcount: A:0.50, C:0.14, G:0.01, T:0.35
Consensus pattern (10 bp):
AAAATCTTTA
Found at i:38610879 original size:21 final size:22
Alignment explanation
Indices: 38610846--38610904 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
38610836 ATAAAAAATA
*
38610846 TTAAAAATGCTTAAAATGA-CC
1 TTAAAAATCCTTAAAATGAGCC
* *
38610867 TTAAATATCCTTAAAAAGAGCC
1 TTAAAAATCCTTAAAATGAGCC
38610889 -TAAAAATCCTTAAAAT
1 TTAAAAATCCTTAAAAT
38610905 TTTAAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (22 bp):
TTAAAAATCCTTAAAATGAGCC
Found at i:38610933 original size:19 final size:19
Alignment explanation
Indices: 38610890--38610933 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
38610880 AAAAGAGCCT
*
38610890 AAAAATCCTTAAAATTTTA
1 AAAAATCCTTAAAATTGTA
38610909 AAAAAT-CTTAAAATTCGTA
1 AAAAATCCTTAAAATT-GTA
*
38610928 ATAAAT
1 AAAAAT
38610934 AATTAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAAATCCTTAAAATTGTA
Found at i:38611008 original size:21 final size:21
Alignment explanation
Indices: 38610968--38611008 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
38610958 AAAAAAATAA
* **
38610968 AAAAATCTTTTAAATTCCTTT
1 AAAAATCTCTTAAAAACCTTT
38610989 AAAAATCTCTTAAAAACCTT
1 AAAAATCTCTTAAAAACCTT
38611009 AAGTATGCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAATCTCTTAAAAACCTTT
Found at i:38611107 original size:21 final size:21
Alignment explanation
Indices: 38611013--38611117 Score: 56
Period size: 21 Copynumber: 5.0 Consensus size: 21
38611003 AACCTTAAGT
38611013 ATGCTTAAAAGGATC-TT-AAAA
1 ATGCTTAAAA--ATCTTTAAAAA
**
38611034 ATGCTTAAAAATCCATAAAAA
1 ATGCTTAAAAATCTTTAAAAA
** * *
38611055 AAACTTTAAAATGCTTGAAAAGA
1 ATGCTTAAAAAT-CTTTAAAA-A
*
38611078 AT--TCAAAAATCTTTAAAAA
1 ATGCTTAAAAATCTTTAAAAA
* *
38611097 ATGCTTTAAAAAACCTTAAAA
1 ATGC-TTAAAAATCTTTAAAA
38611118 TCCTTAAAAT
Statistics
Matches: 63, Mismatches: 14, Indels: 13
0.70 0.16 0.14
Matches are distributed among these distances:
19 6 0.10
20 8 0.13
21 29 0.46
22 18 0.29
23 2 0.03
ACGTcount: A:0.53, C:0.11, G:0.08, T:0.28
Consensus pattern (21 bp):
ATGCTTAAAAATCTTTAAAAA
Found at i:38611122 original size:9 final size:10
Alignment explanation
Indices: 38611082--38611253 Score: 57
Period size: 10 Copynumber: 16.5 Consensus size: 10
38611072 AAAAGAATTC
*
38611082 AAAAATCTTT
1 AAAAATCCTT
*
38611092 AAAAAATGCTTT
1 -AAAAAT-CCTT
*
38611104 AAAAAACCTT
1 AAAAATCCTT
38611114 -AAAATCCTT
1 AAAAATCCTT
*
38611123 AAAATTCCTT
1 AAAAATCCTT
* *
38611133 GAAAATACTTT
1 AAAAAT-CCTT
38611144 AAAAATCCTTT
1 AAAAATCC-TT
**
38611155 GCAAA--CTAT
1 AAAAATCCT-T
38611164 GAAAAAAAT-CTT
1 ---AAAAATCCTT
*
38611176 AAAAATGCTT
1 AAAAATCCTT
* **
38611186 TAAAAGACTT
1 AAAAATCCTT
*
38611196 CAAAAATCATT
1 -AAAAATCCTT
38611207 -AAAATCTACTTT
1 AAAAATC--C-TT
*
38611219 AAAAAACCTT
1 AAAAATCCTT
*
38611229 AAAAATCCAT
1 AAAAATCCTT
*
38611239 AAAACTCCTT
1 AAAAATCCTT
38611249 AAAAA
1 AAAAA
38611254 CACTTTAAAA
Statistics
Matches: 119, Mismatches: 27, Indels: 31
0.67 0.15 0.18
Matches are distributed among these distances:
8 1 0.01
9 22 0.18
10 48 0.40
11 31 0.26
12 10 0.08
13 7 0.06
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (10 bp):
AAAAATCCTT
Found at i:38611148 original size:11 final size:11
Alignment explanation
Indices: 38611082--38611299 Score: 52
Period size: 11 Copynumber: 20.8 Consensus size: 11
38611072 AAAAGAATTC
38611082 AAAAAT-CTTT
1 AAAAATACTTT
*
38611092 AAAAAATGCTTT
1 -AAAAATACTTT
*
38611104 AAAAA-ACCTT
1 AAAAATACTTT
*
38611114 -AAAAT-CCTT
1 AAAAATACTTT
* *
38611123 -AAAATTCCTT
1 AAAAATACTTT
*
38611133 GAAAATACTTT
1 AAAAATACTTT
*
38611144 AAAAATCCTTT
1 AAAAATACTTT
** *
38611155 -GCAA-ACTATG
1 AAAAATACT-TT
*
38611165 AAAAA-AATCTT
1 AAAAATACT-TT
*
38611176 AAAAATGCTTT
1 AAAAATACTTT
* *
38611187 -AAAAGACTTC
1 AAAAATACTTT
*
38611197 AAAAAT-CATT
1 AAAAATACTTT
*
38611207 AAAATCTACTTT
1 AAAA-ATACTTT
*
38611219 AAAAA-ACCTT
1 AAAAATACTTT
**
38611229 AAAAAT-CCAT
1 AAAAATACTTT
* *
38611239 AAAACT-CCTT
1 AAAAATACTTT
*
38611249 AAAAACACTTT
1 AAAAATACTTT
38611260 AAAAATA-TTT
1 AAAAATACTTT
** *
38611270 TGAAATAC-AT
1 AAAAATACTTT
* *
38611280 AAAAAAACTTA
1 AAAAATACTTT
38611291 AAAAATACT
1 AAAAATACT
38611300 GAAAATGACC
Statistics
Matches: 150, Mismatches: 43, Indels: 28
0.68 0.19 0.13
Matches are distributed among these distances:
9 15 0.10
10 61 0.41
11 62 0.41
12 12 0.08
ACGTcount: A:0.52, C:0.15, G:0.03, T:0.30
Consensus pattern (11 bp):
AAAAATACTTT
Found at i:38611296 original size:115 final size:114
Alignment explanation
Indices: 38611028--38611294 Score: 322
Period size: 115 Copynumber: 2.3 Consensus size: 114
38611018 TAAAAGGATC
* ** * * *
38611028 TTAAAAATGCTTAAAAATCCATAAAAAAAACTTTAAAATGCTTGAAAAGAATTCAAAAATCTTTA
1 TTAAAAATACTTTGAAATACATAAAAAAAACTTAAAAATGCTTGAAAAGAATTCAAAAATCATTA
* * * * *
38611093 AAAAATGCTTTAAAAAACCTTAAAATCCTTAAAATTCCTTGAAAATACT
66 AAAAATACTTTAAAAAACCTTAAAATCCATAAAACTCCTTAAAAACACT
* * * * *
38611142 TTAAAAATCCTTTGCAA-ACTATGAAAAAAATCTTAAAAATGCTTTAAAAGACTTCAAAAATCAT
1 TTAAAAATACTTTGAAATAC-AT-AAAAAAAACTTAAAAATGCTTGAAAAGAATTCAAAAATCAT
**
38611206 TAAAATCTACTTTAAAAAACCTTAAAAATCCATAAAACTCCTTAAAAACACT
64 TAAAAAATACTTTAAAAAACCTT-AAAATCCATAAAACTCCTTAAAAACACT
*
38611258 TTAAAAATATTTTGAAATACAT-AAAAAAACTTAAAAA
1 TTAAAAATACTTTGAAATACATAAAAAAAACTTAAAAA
38611295 ATACTGAAAA
Statistics
Matches: 128, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
113 1 0.01
114 29 0.23
115 56 0.44
116 40 0.31
117 2 0.02
ACGTcount: A:0.53, C:0.14, G:0.04, T:0.29
Consensus pattern (114 bp):
TTAAAAATACTTTGAAATACATAAAAAAAACTTAAAAATGCTTGAAAAGAATTCAAAAATCATTA
AAAAATACTTTAAAAAACCTTAAAATCCATAAAACTCCTTAAAAACACT
Found at i:38611561 original size:21 final size:21
Alignment explanation
Indices: 38611537--38611605 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
38611527 CAAAAGTCTT
*
38611537 TTAAAAATACTTTAAAAAACC
1 TTAAAAATCCTTTAAAAAACC
* * *
38611558 TTAAAATTCCTTGAAAACACC
1 TTAAAAATCCTTTAAAAAACC
*
38611579 TTAAAAATCCTTT-AAAATCC
1 TTAAAAATCCTTTAAAAAACC
38611599 TTAAAAA
1 TTAAAAA
38611606 AAAACCTTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 12 0.30
21 28 0.70
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.30
Consensus pattern (21 bp):
TTAAAAATCCTTTAAAAAACC
Found at i:38611666 original size:10 final size:11
Alignment explanation
Indices: 38611642--38611677 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
38611632 AGATGAGCCT
* *
38611642 AAAAATATTTG
1 AAAAATCTTTA
38611653 AAAAATCTTTA
1 AAAAATCTTTA
38611664 AAAAATCTTTA
1 AAAAATCTTTA
38611675 AAA
1 AAA
38611678 TTAGTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (11 bp):
AAAAATCTTTA
Found at i:38611798 original size:11 final size:11
Alignment explanation
Indices: 38611782--38611864 Score: 64
Period size: 11 Copynumber: 7.7 Consensus size: 11
38611772 TCGAAGGATC
38611782 TTAAAAATACT
1 TTAAAAATACT
* *
38611793 TT-AAAATCCA
1 TTAAAAATACT
* *
38611803 TGAAAAAAACT
1 TTAAAAATACT
*
38611814 TTAAAAAT-TT
1 TTAAAAATACT
* *
38611824 TTCAAAAGACT
1 TTAAAAATACT
*
38611835 TCAAAAAT-CT
1 TTAAAAATACT
38611845 TTAAAAAATACT
1 TT-AAAAATACT
38611857 TTAAAAAT
1 TTAAAAAT
38611865 TTAAAAAAAA
Statistics
Matches: 52, Mismatches: 16, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
10 17 0.33
11 31 0.60
12 4 0.08
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (11 bp):
TTAAAAATACT
Found at i:38611871 original size:21 final size:20
Alignment explanation
Indices: 38611805--38611882 Score: 84
Period size: 21 Copynumber: 3.8 Consensus size: 20
38611795 AAAATCCATG
38611805 AAAAAAACTTTAAAAATTTTT
1 AAAAAAACTTTAAAAA-TTTT
* * *
38611826 CAAAAGACTTCAAAAATCTTT
1 AAAAAAACTTTAAAAAT-TTT
*
38611847 AAAAAATACTTTAAAAATTTA
1 AAAAAA-ACTTTAAAAATTTT
*
38611868 AAAAAAACCTTAAAA
1 AAAAAAACTTTAAAA
38611883 TTCCTTGAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
20 9 0.19
21 28 0.60
22 10 0.21
ACGTcount: A:0.59, C:0.10, G:0.01, T:0.29
Consensus pattern (20 bp):
AAAAAAACTTTAAAAATTTT
Found at i:38611893 original size:21 final size:22
Alignment explanation
Indices: 38611806--38611914 Score: 68
Period size: 21 Copynumber: 5.1 Consensus size: 22
38611796 AAATCCATGA
* * *
38611806 AAAAAACTTTAAAAAT-TTTTC
1 AAAAAACCTTAAAAATCCTTTG
* *
38611827 AAAAGA-CTTCAAAAAT-CTTTA
1 AAAAAACCTT-AAAAATCCTTTG
* **
38611848 AAAAATACTTTAAAAAT--TTAA
1 AAAAA-ACCTTAAAAATCCTTTG
*
38611869 AAAAAACCTTAAAATTCC-TTG
1 AAAAAACCTTAAAAATCCTTTG
*
38611890 AAAACACCTTAAAAATCCTTTG
1 AAAAAACCTTAAAAATCCTTTG
38611912 AAA
1 AAA
38611915 TTTATAAAAA
Statistics
Matches: 69, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
20 11 0.16
21 43 0.62
22 13 0.19
23 2 0.03
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.30
Consensus pattern (22 bp):
AAAAAACCTTAAAAATCCTTTG
Found at i:38612172 original size:11 final size:10
Alignment explanation
Indices: 38612145--38612303 Score: 54
Period size: 10 Copynumber: 15.0 Consensus size: 10
38612135 CATGAAAAGC
*
38612145 CTTAAAAATG
1 CTTAAAAATA
38612155 CTTAAAAATA
1 CTTAAAAATA
38612165 CTTCAAAAAT-
1 CTT-AAAAATA
*
38612175 CTTTTAAAAATCC
1 C--TTAAAAAT-A
**
38612188 CTTAAAAAGC
1 CTTAAAAATA
38612198 CTTTAAAAAATA
1 C-TT-AAAAATA
* * *
38612210 CTTTAAATTC
1 CTTAAAAATA
38612220 CTTGAAAACAT-
1 CTT-AAAA-ATA
*
38612231 CTTAAAAATC
1 CTTAAAAATA
* *
38612241 CTTGAAAATC
1 CTTAAAAATA
* *
38612251 CATAAAAAAAA
1 C-TTAAAAATA
*
38612262 CATTAAAAATG
1 C-TTAAAAATA
38612273 CTT-AAAATGA
1 CTTAAAAAT-A
* *
38612283 CTTTAAATATC
1 C-TTAAAAATA
38612294 CTTAAAAATA
1 CTTAAAAATA
38612304 GCCTATAAAT
Statistics
Matches: 113, Mismatches: 22, Indels: 28
0.69 0.13 0.17
Matches are distributed among these distances:
9 7 0.06
10 46 0.41
11 46 0.41
12 13 0.12
13 1 0.01
ACGTcount: A:0.50, C:0.15, G:0.04, T:0.31
Consensus pattern (10 bp):
CTTAAAAATA
Found at i:38612181 original size:22 final size:22
Alignment explanation
Indices: 38612156--38612212 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
38612146 TTAAAAATGC
*
38612156 TTAAAAATACTTCAAAAA-TCTT
1 TTAAAAATACTT-AAAAAGCCTT
*
38612178 TTAAAAATCCCTTAAAAAGCCTT
1 TTAAAAAT-ACTTAAAAAGCCTT
*
38612201 TAAAAAATACTT
1 TTAAAAATACTT
38612213 TAAATTCCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
TTAAAAATACTTAAAAAGCCTT
Found at i:38612215 original size:23 final size:22
Alignment explanation
Indices: 38612158--38612216 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
38612148 AAAAATGCTT
* * *
38612158 AAAAATACTTCAAAAATCTTTT
1 AAAAATACTTTAAAAACCTTTA
* *
38612180 AAAAATCCCTTAAAAAGCCTTTA
1 AAAAATACTTTAAAAA-CCTTTA
38612203 AAAAATACTTTAAA
1 AAAAATACTTTAAA
38612217 TTCCTTGAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 13 0.45
23 16 0.55
ACGTcount: A:0.53, C:0.15, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAAATACTTTAAAAACCTTTA
Found at i:38612381 original size:20 final size:20
Alignment explanation
Indices: 38612358--38612396 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38612348 TAATAAACAA
*
38612358 TTAAAAAAATTAAAAATCTC
1 TTAAAAAAATAAAAAATCTC
*
38612378 TTAAAAACATAAAAAATCT
1 TTAAAAAAATAAAAAATCT
38612397 TTCAAATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (20 bp):
TTAAAAAAATAAAAAATCTC
Found at i:38612383 original size:11 final size:10
Alignment explanation
Indices: 38612367--38612689 Score: 108
Period size: 11 Copynumber: 30.9 Consensus size: 10
38612357 ATTAAAAAAA
38612367 TTAAAAATCT
1 TTAAAAATCT
*
38612377 CTTAAAAA-CA
1 -TTAAAAATCT
*
38612387 TAAAAAATCT
1 TTAAAAATCT
* *
38612397 TTCAAATTCT
1 TTAAAAATCT
38612407 TTGAAAAATCT
1 TT-AAAAATCT
38612418 GTTAAAAATC-
1 -TTAAAAATCT
* *
38612428 ATAAATATGC-
1 TTAAAAAT-CT
38612438 TTAAAAGGATC-
1 TTAAAA--ATCT
*
38612449 TTAAACAAGC-
1 TTAAA-AATCT
38612459 TTAAAAATCAAT
1 TTAAAAATC--T
** *
38612471 GAAAAAAAACT
1 -TTAAAAATCT
38612482 TTAAAAATGCT
1 TTAAAAAT-CT
* ***
38612493 TCAAAAGGAT
1 TTAAAAATCT
*
38612503 TCAAAAATCT
1 TTAAAAATCT
38612513 TTAAAAAATGCT
1 TT-AAAAAT-CT
* *
38612525 TTAAAAAACC
1 TTAAAAATCT
38612535 TTAAAAATCCT
1 TTAAAAAT-CT
*
38612546 TT-AAATTCT
1 TTAAAAATCT
*
38612555 TTGAAAATACT
1 TTAAAAAT-CT
*
38612566 GTAAAAATCCT
1 TTAAAAAT-CT
*
38612577 TT-ACAATCT
1 TTAAAAATCT
*
38612586 ATAAAAAAT-T
1 -TTAAAAATCT
38612596 CTTAAAAATGCT
1 -TTAAAAAT-CT
*
38612608 TCAAAAGA-CT
1 TTAAAA-ATCT
38612618 TTAAAAATCAT
1 TTAAAAATC-T
*
38612629 TAAAAAATGCT
1 TTAAAAAT-CT
*
38612640 TTAAAAAACT
1 TTAAAAATCT
38612650 TT-AAAATCT
1 TTAAAAATCT
* *
38612659 CATAAAATTCT
1 -TTAAAAATCT
*
38612670 TTGAAAATACT
1 TTAAAAAT-CT
38612681 TTAAAAATC
1 TTAAAAATC
38612690 CTTTGAAATA
Statistics
Matches: 229, Mismatches: 55, Indels: 57
0.67 0.16 0.17
Matches are distributed among these distances:
9 28 0.12
10 85 0.37
11 98 0.43
12 12 0.05
13 6 0.03
ACGTcount: A:0.50, C:0.13, G:0.05, T:0.32
Consensus pattern (10 bp):
TTAAAAATCT
Found at i:38612487 original size:10 final size:10
Alignment explanation
Indices: 38612474--38612655 Score: 55
Period size: 10 Copynumber: 17.4 Consensus size: 10
38612464 AATCAATGAA
38612474 AAAAAACTTT
1 AAAAAACTTT
* *
38612484 AAAAATGCTTC
1 AAAAA-ACTTT
* *
38612495 AAAAGGA-TTC
1 AAAA-AACTTT
*
38612505 AAAAATCTTT
1 AAAAAACTTT
38612515 AAAAAATGCTTT
1 AAAAAA--CTTT
*
38612527 AAAAAACCTT
1 AAAAAACTTT
*
38612537 AAAAATCCTTT
1 AAAAA-ACTTT
**
38612548 -AAATTCTTT
1 AAAAAACTTT
* *
38612557 GAAAATACTGT
1 -AAAAAACTTT
*
38612568 AAAAATCCTTT
1 AAAAA-ACTTT
* * *
38612579 -ACAATCTAT
1 AAAAAACTTT
*
38612588 AAAAAATTCTT
1 AAAAAACT-TT
* *
38612599 AAAAATGCTTC
1 AAAAA-ACTTT
*
38612610 AAAAGACTTT
1 AAAAAACTTT
* *
38612620 AAAAATCATT
1 AAAAAACTTT
38612630 AAAAAATGCTTT
1 AAAAAA--CTTT
38612642 AAAAAACTTT
1 AAAAAACTTT
38612652 AAAA
1 AAAA
38612656 TCTCATAAAA
Statistics
Matches: 122, Mismatches: 36, Indels: 28
0.66 0.19 0.15
Matches are distributed among these distances:
9 7 0.06
10 64 0.52
11 31 0.25
12 20 0.16
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (10 bp):
AAAAAACTTT
Found at i:38612526 original size:12 final size:11
Alignment explanation
Indices: 38612505--38612655 Score: 67
Period size: 10 Copynumber: 14.3 Consensus size: 11
38612495 AAAAGGATTC
38612505 AAAAATCTTTA
1 AAAAATCTTTA
38612516 AAAAATGCTTTA
1 AAAAAT-CTTTA
*
38612528 AAAAA-CCTT-
1 AAAAATCTTTA
38612537 AAAAATCCTTT-
1 AAAAAT-CTTTA
*
38612548 -AAATTCTTT-
1 AAAAATCTTTA
* *
38612557 GAAAATACTGT-
1 AAAAAT-CTTTA
38612568 AAAAATCCTTT-
1 AAAAAT-CTTTA
* *
38612579 -ACAATCTATA
1 AAAAATCTTTA
38612589 AAAAAT-TCTT-
1 AAAAATCT-TTA
*
38612599 AAAAATGCTTCA
1 AAAAAT-CTTTA
*
38612611 AAAGA-CTTT-
1 AAAAATCTTTA
*
38612620 AAAAATCATTA
1 AAAAATCTTTA
38612631 AAAAATGCTTTA
1 AAAAAT-CTTTA
38612643 AAAAA-CTTTA
1 AAAAATCTTTA
38612653 AAA
1 AAA
38612656 TCTCATAAAA
Statistics
Matches: 108, Mismatches: 18, Indels: 29
0.70 0.12 0.19
Matches are distributed among these distances:
9 16 0.15
10 36 0.33
11 32 0.30
12 24 0.22
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (11 bp):
AAAAATCTTTA
Found at i:38612530 original size:21 final size:21
Alignment explanation
Indices: 38612505--38612693 Score: 97
Period size: 21 Copynumber: 9.0 Consensus size: 21
38612495 AAAAGGATTC
*
38612505 AAAAATCTTTAAAAAATGCTTT
1 AAAAATCTTT-AAAAATCCTTT
* *
38612527 AAAAAACCTTAAAAATCCTTT
1 AAAAATCTTTAAAAATCCTTT
* * * *
38612548 -AAATTCTTTGAAAATACTGT
1 AAAAATCTTTAAAAATCCTTT
* *
38612568 AAAAATCCTTT-ACAAT-CTATA
1 AAAAAT-CTTTAAAAATCCT-TT
* *
38612589 AAAAAT-TCTTAAAAATGCTTC
1 AAAAATCT-TTAAAAATCCTTT
* *
38612610 AAAAGA-CTTTAAAAATCATTA
1 AAAA-ATCTTTAAAAATCCTTT
*
38612631 AAAAATGCTTTAAAAA-ACTTT
1 AAAAAT-CTTTAAAAATCCTTT
* *
38612652 -AAAATC-TCATAAAATTCTTT
1 AAAAATCTTTA-AAAATCCTTT
*
38612672 GAAAATACTTTAAAAATCCTTT
1 AAAAAT-CTTTAAAAATCCTTT
38612694 GAAATACATA
Statistics
Matches: 127, Mismatches: 25, Indels: 30
0.70 0.14 0.16
Matches are distributed among these distances:
18 2 0.02
19 6 0.05
20 28 0.22
21 54 0.43
22 35 0.28
23 2 0.02
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (21 bp):
AAAAATCTTTAAAAATCCTTT
Found at i:38612623 original size:32 final size:33
Alignment explanation
Indices: 38612587--38612655 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 33
38612577 TTACAATCTA
*
38612587 TAAAAAATTC-TT-AAAAATGCTTCAAAAGACTT
1 TAAAAAA-TCATTAAAAAATGCTTCAAAAAACTT
*
38612619 T-AAAAATCATTAAAAAATGCTTTAAAAAACTT
1 TAAAAAATCATTAAAAAATGCTTCAAAAAACTT
38612651 TAAAA
1 TAAAA
38612656 TCTCATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 2 0.06
31 7 0.22
32 20 0.62
33 3 0.09
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.30
Consensus pattern (33 bp):
TAAAAAATCATTAAAAAATGCTTCAAAAAACTT
Found at i:38612624 original size:115 final size:117
Alignment explanation
Indices: 38612472--38612765 Score: 347
Period size: 115 Copynumber: 2.6 Consensus size: 117
38612462 AAAATCAATG
*
38612472 AAAAAAAA-CTTTAAAAATGCTTCAAAAGGA-TTCAAAAATCTTTAAAAAATGCTTTAAAAAACC
1 AAAAAAAATC-TTAAAAATGCTTCAAAAGGACTTTAAAAATCTTTAAAAAATGCTTTAAAAAA-C
* *
38612535 TTAAAAATC-CTTTAAATTCTTTGAAAATACTGTAAAAATCCTTT-ACAAT-C-T
64 TTAAAAATCTCATAAAATTCTTTGAAAATACTGTAAAAATCCTTTGA-AATACAT
* *
38612586 ATAAAAAATTCTTAAAAATGCTTCAAAA-GACTTTAAAAATCATTAAAAAATGCTTTAAAAAACT
1 A-AAAAAAATCTTAAAAATGCTTCAAAAGGACTTTAAAAATCTTTAAAAAATGCTTTAAAAAACT
* *
38612650 TTAAAATCTCATAAAATTCTTTGAAAATACTTTAAAAATCCTTTGAAATACAT
65 TAAAAATCTCATAAAATTCTTTGAAAATACTGTAAAAATCCTTTGAAATACAT
* * * * ** *
38612703 AAAAAAAACCTT-AAAATGCTT-AAAATGACCTTAAACAT-TTTTTAAAATAGCTTTAAAATACT
1 AAAAAAAATCTTAAAAATGCTTCAAAAGGACTTTAAAAATCTTTAAAAAAT-GCTTTAAAAAACT
38612765 T
65 T
38612766 GAATAAAAAC
Statistics
Matches: 156, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
114 23 0.15
115 119 0.76
116 12 0.08
117 2 0.01
ACGTcount: A:0.50, C:0.13, G:0.05, T:0.33
Consensus pattern (117 bp):
AAAAAAAATCTTAAAAATGCTTCAAAAGGACTTTAAAAATCTTTAAAAAATGCTTTAAAAAACTT
AAAAATCTCATAAAATTCTTTGAAAATACTGTAAAAATCCTTTGAAATACAT
Found at i:38612665 original size:32 final size:31
Alignment explanation
Indices: 38612505--38612689 Score: 105
Period size: 31 Copynumber: 5.9 Consensus size: 31
38612495 AAAAGGATTC
* *
38612505 AAAAAT-CTTTAAAAAATGCTTTAAAAAACCTT
1 AAAAATGCTTTAAAAAA--CTTTAAAAATCATT
* ** *
38612537 AAAAATCCTTT-AAATTCTTTGAAAAT-ACTGT
1 AAAAATGCTTTAAAAAACTTTAAAAATCA-T-T
* * * *
38612568 AAAAATCCTTT-ACAATCTATAAAAAATTC-TT
1 AAAAATGCTTTAAAAAACT-TTAAAAA-TCATT
* *
38612599 AAAAATGCTTCAAAAGACTTTAAAAATCATT
1 AAAAATGCTTTAAAAAACTTTAAAAATCATT
*
38612630 AAAAAATGCTTTAAAAAACTTT-AAAATC-TC
1 -AAAAATGCTTTAAAAAACTTTAAAAATCATT
* *
38612660 ATAAAATTCTTTGAAAATACTTTAAAAATC
1 A-AAAATGCTTT-AAAAAACTTTAAAAATC
38612690 CTTTGAAATA
Statistics
Matches: 121, Mismatches: 20, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
29 1 0.01
30 21 0.17
31 50 0.41
32 44 0.36
33 5 0.04
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.34
Consensus pattern (31 bp):
AAAAATGCTTTAAAAAACTTTAAAAATCATT
Found at i:38612707 original size:21 final size:22
Alignment explanation
Indices: 38612662--38612708 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
38612652 AAAATCTCAT
* * *
38612662 AAAATTCTTTGAAAATACTTTA
1 AAAATCCTTTGAAAATACATAA
38612684 AAAATCCTTTG-AAATACATAA
1 AAAATCCTTTGAAAATACATAA
38612705 AAAA
1 AAAA
38612709 AACCTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (22 bp):
AAAATCCTTTGAAAATACATAA
Found at i:38612947 original size:20 final size:21
Alignment explanation
Indices: 38612924--38612962 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38612914 CGTAAAAAAA
*
38612924 ACCTTAAA-ATTCTTAAAATG
1 ACCTTAAACATCCTTAAAATG
38612944 ACCTTAAACATCCTTAAAA
1 ACCTTAAACATCCTTAAAA
38612963 AGAGCCAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.31
Consensus pattern (21 bp):
ACCTTAAACATCCTTAAAATG
Found at i:38616095 original size:21 final size:21
Alignment explanation
Indices: 38616040--38616087 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
38616030 TGAAAAATCT
*
38616040 CTTAAAAA-A-CTTAAATATG
1 CTTAAAAAGATCTTAAAAATG
38616059 CTTAAAAAGATCTTAAAAATG
1 CTTAAAAAGATCTTAAAAATG
38616080 CTTAAAAA
1 CTTAAAAA
38616088 TCCATTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 8 0.31
20 1 0.04
21 17 0.65
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.29
Consensus pattern (21 bp):
CTTAAAAAGATCTTAAAAATG
Found at i:38616172 original size:10 final size:10
Alignment explanation
Indices: 38616154--38616179 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
38616144 TTTTAAAAAA
38616154 CTTTAAAATT
1 CTTTAAAATT
38616164 CTTTAAAATT
1 CTTTAAAATT
38616174 CTTTAA
1 CTTTAA
38616180 GAACTTCGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (10 bp):
CTTTAAAATT
Found at i:38616233 original size:11 final size:11
Alignment explanation
Indices: 38616219--38616267 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
38616209 AAAAAAAAGC
38616219 TTAAAAATGCT
1 TTAAAAATGCT
*
38616230 TT-AAAATACT
1 TTAAAAATGCT
*
38616240 TTAAAAGT-CT
1 TTAAAAATGCT
38616250 TTAAAAAATGCT
1 TT-AAAAATGCT
38616262 TTAAAA
1 TTAAAA
38616268 TTCGTTAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 13 0.41
11 15 0.47
12 4 0.12
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (11 bp):
TTAAAAATGCT
Found at i:38616236 original size:10 final size:10
Alignment explanation
Indices: 38616212--38616268 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
38616202 AATATAGAAA
* *
38616212 AAAAAGCTTA
1 AAAATGCTTT
38616222 AAAATGCTTT
1 AAAATGCTTT
*
38616232 AAAATACTTT
1 AAAATGCTTT
38616242 AAAA-GTCTTT
1 AAAATG-CTTT
38616252 AAAAAATGCTTT
1 --AAAATGCTTT
38616264 AAAAT
1 AAAAT
38616269 TCGTTAAGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 30 0.77
12 8 0.21
13 1 0.03
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (10 bp):
AAAATGCTTT
Found at i:38616275 original size:22 final size:22
Alignment explanation
Indices: 38616232--38616275 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
38616222 AAAATGCTTT
*
38616232 AAAATACTTTAAAAGTCTTTAA
1 AAAATACTTTAAAAGTCGTTAA
* *
38616254 AAAATGCTTTAAAATTCGTTAA
1 AAAATACTTTAAAAGTCGTTAA
38616276 GATTTCTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (22 bp):
AAAATACTTTAAAAGTCGTTAA
Found at i:38616492 original size:9 final size:10
Alignment explanation
Indices: 38616470--38616536 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 10
38616460 AAATATCATG
38616470 AAAAATCTCTT
1 AAAAA-CTCTT
38616481 AAAAAC-CTT
1 AAAAACTCTT
*
38616490 AAATACTCTT
1 AAAAACTCTT
38616500 AAAAGGA-TCTT
1 AAAA--ACTCTT
38616511 AAAAA-TGCTT
1 AAAAACT-CTT
*
38616521 AAAAATCTATT
1 AAAAA-CTCTT
38616532 AAAAA
1 AAAAA
38616537 AATTAAAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
9 10 0.21
10 15 0.32
11 20 0.43
12 2 0.04
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.30
Consensus pattern (10 bp):
AAAAACTCTT
Found at i:38616525 original size:11 final size:11
Alignment explanation
Indices: 38616511--38616600 Score: 57
Period size: 11 Copynumber: 8.4 Consensus size: 11
38616501 AAAGGATCTT
38616511 AAAAATGCTT-
1 AAAAATGCTTA
38616521 AAAAAT-CTATTA
1 AAAAATGC--TTA
*
38616533 AAAAA--ATTA
1 AAAAATGCTTA
38616542 AAAAATGCTT-
1 AAAAATGCTTA
*
38616552 CAAAA-GACTTA
1 AAAAATG-CTTA
*
38616563 AAAAATCCTTA
1 AAAAATGCTTA
38616574 AAAAATGCTTGA
1 AAAAATGCTT-A
**
38616586 AAAAAACCTTA
1 AAAAATGCTTA
38616597 AAAA
1 AAAA
38616601 TCTTTAAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
9 10 0.16
10 13 0.21
11 26 0.41
12 14 0.22
ACGTcount: A:0.59, C:0.11, G:0.06, T:0.24
Consensus pattern (11 bp):
AAAAATGCTTA
Found at i:38616545 original size:21 final size:20
Alignment explanation
Indices: 38616521--38616578 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
38616511 AAAAATGCTT
38616521 AAAAATCTATTAAAAAAATTA
1 AAAAATCT-TTAAAAAAATTA
* * *
38616542 AAAAATGCTTCAAAAGACTTA
1 AAAAAT-CTTTAAAAAAATTA
*
38616563 AAAAATCCTTAAAAAA
1 AAAAATCTTTAAAAAA
38616579 TGCTTGAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 7 0.23
21 21 0.70
22 2 0.07
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.24
Consensus pattern (20 bp):
AAAAATCTTTAAAAAAATTA
Found at i:38616600 original size:12 final size:11
Alignment explanation
Indices: 38616559--38616609 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
38616549 CTTCAAAAGA
38616559 CTTAAAAAATC
1 CTTAAAAAATC
*
38616570 CTTAAAAAATG
1 CTTAAAAAATC
*
38616581 CTTGAAAAAAAC
1 CTT-AAAAAATC
38616593 CTT-AAAAATC
1 CTTAAAAAATC
*
38616603 TTTAAAA
1 CTTAAAA
38616610 TTCCTTTGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
10 8 0.24
11 16 0.48
12 9 0.27
ACGTcount: A:0.55, C:0.14, G:0.04, T:0.27
Consensus pattern (11 bp):
CTTAAAAAATC
Found at i:38616607 original size:10 final size:10
Alignment explanation
Indices: 38616470--38616726 Score: 60
Period size: 10 Copynumber: 24.4 Consensus size: 10
38616460 AAATATCATG
38616470 AAAAATCTCTT
1 AAAAATCT-TT
*
38616481 AAAAA-CCTT
1 AAAAATCTTT
*
38616490 AAATA-CTCTT
1 AAAAATCT-TT
38616500 AAAAGGATC-TT
1 AAAA--ATCTTT
38616511 AAAAATGC-TT
1 AAAAAT-CTTT
38616521 AAAAATCTATT
1 AAAAATCT-TT
** *
38616532 AAAAAAATTA
1 AAAAATCTTT
*
38616542 AAAAATGCTTC
1 AAAAAT-CTTT
*
38616553 AAAAGA-CTTA
1 AAAA-ATCTTT
*
38616563 AAAAATCCTTA
1 AAAAAT-CTTT
*
38616574 AAAAATGCTTGA
1 AAAAAT-CTT-T
* *
38616586 AAAAAACCTT
1 AAAAATCTTT
38616596 AAAAATCTTT
1 AAAAATCTTT
*
38616606 AAAATTCCTTT
1 AAAAAT-CTTT
*
38616617 -GAAATCTGCTT
1 AAAAATCT--TT
38616628 AAAAATCCTTT
1 AAAAAT-CTTT
* * * *
38616639 GAAATTCATG
1 AAAAATCTTT
* *
38616649 AAAGGAAACCTT
1 AAA--AATCTTT
*
38616661 AAAAATGCTTC
1 AAAAAT-CTTT
*
38616672 AAAAAACTTT
1 AAAAATCTTT
*
38616682 AAAAA-CTCTA
1 AAAAATCT-TT
38616692 AAAAATGCTTT
1 AAAAAT-CTTT
* *
38616703 AAAAAACCTT
1 AAAAATCTTT
*
38616713 AAAAAACTTT
1 AAAAATCTTT
38616723 AAAA
1 AAAA
38616727 TTCCGAAAAA
Statistics
Matches: 183, Mismatches: 40, Indels: 47
0.68 0.15 0.17
Matches are distributed among these distances:
9 15 0.08
10 80 0.44
11 65 0.36
12 20 0.11
13 3 0.02
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (10 bp):
AAAAATCTTT
Found at i:38616683 original size:21 final size:19
Alignment explanation
Indices: 38616654--38616726 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 19
38616644 TCATGAAAGG
*
38616654 AAACCTTAAAAATGCTTCAAA
1 AAACTTTAAAAA--CTTCAAA
38616675 AAACTTTAAAAAC-TCTAAA
1 AAACTTTAAAAACTTC-AAA
38616694 AAATGCTTTAAAAAACCTT-AAA
1 AAA--CTTT-AAAAA-CTTCAAA
38616716 AAACTTTAAAA
1 AAACTTTAAAA
38616727 TTCCGAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
18 2 0.04
19 11 0.24
20 4 0.09
21 15 0.33
22 11 0.24
23 1 0.02
24 1 0.02
ACGTcount: A:0.56, C:0.15, G:0.03, T:0.26
Consensus pattern (19 bp):
AAACTTTAAAAACTTCAAA
Found at i:38616699 original size:31 final size:32
Alignment explanation
Indices: 38616661--38616726 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
38616651 AGGAAACCTT
*
38616661 AAAAATGCTTCAAAAAA-CTTTAAAAACTCTA
1 AAAAATGCTTCAAAAAACCTTAAAAAACTCTA
* *
38616692 AAAAATGCTTTAAAAAACCTTAAAAAACTTTA
1 AAAAATGCTTCAAAAAACCTTAAAAAACTCTA
38616724 AAA
1 AAA
38616727 TTCCGAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 16 0.52
32 15 0.48
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.26
Consensus pattern (32 bp):
AAAAATGCTTCAAAAAACCTTAAAAAACTCTA
Found at i:38616822 original size:20 final size:20
Alignment explanation
Indices: 38616799--38616841 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
38616789 AAAAAGTTAC
* *
38616799 AAAAATCTTAAAAAATACTT
1 AAAAATCGTAAAAAATAATT
* *
38616819 AAAATTCGTAATAAATAATT
1 AAAAATCGTAAAAAATAATT
38616839 AAA
1 AAA
38616842 GAAATTTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAAATCGTAAAAAATAATT
Found at i:38616964 original size:43 final size:41
Alignment explanation
Indices: 38616916--38617028 Score: 111
Period size: 43 Copynumber: 2.6 Consensus size: 41
38616906 CTTAAATATG
38616916 CTTTAAAGGATCTTAAAAATGCTTAAAAATCTATAAAAAAAAC
1 CTTTAAA--ATCTTAAAAATGCTTAAAAATCTATAAAAAAAAC
* * *
38616959 CTTTAAAATGCTTTAAAA-GACTTCAAAAATCTGTAAAAAATAC
1 CTTTAAAAT-CTTAAAAATG-CTT-AAAAATCTATAAAAAAAAC
* * *
38617002 TTTTGAAAACCTTAAAAATCCTTAAAA
1 CTTT-AAAATCTTAAAAATGCTTAAAA
38617029 TTACTTGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
41 3 0.05
42 14 0.24
43 37 0.64
44 4 0.07
ACGTcount: A:0.50, C:0.13, G:0.06, T:0.30
Consensus pattern (41 bp):
CTTTAAAATCTTAAAAATGCTTAAAAATCTATAAAAAAAAC
Found at i:38617026 original size:10 final size:10
Alignment explanation
Indices: 38617007--38617055 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
38616997 AATACTTTTG
38617007 AAAA-CCTTA
1 AAAATCCTTA
38617016 AAAATCCTTA
1 AAAATCCTTA
* * *
38617026 AAATTACTTG
1 AAAATCCTTA
38617036 AAAATGCCTTA
1 AAAAT-CCTTA
38617047 AAAATCCTT
1 AAAATCCTT
38617056 TGAAATTGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
9 4 0.12
10 20 0.62
11 8 0.25
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (10 bp):
AAAATCCTTA
Found at i:38617430 original size:32 final size:32
Alignment explanation
Indices: 38617385--38617462 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 32
38617375 AAAATCCATC
* *
38617385 AAAAAAGCC-TAAAAAATGCTCCAAAATACTT
1 AAAAAATCCTTAAAAAATGCTCCAAAAAACTT
* * *
38617416 AAAAAATCTTTAAAAATTGCTTCAAAAAACTT
1 AAAAAATCCTTAAAAAATGCTCCAAAAAACTT
*
38617448 TAAAAATCCTTAAAA
1 AAAAAATCCTTAAAA
38617463 TTCCTTGAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 7 0.18
32 32 0.82
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.26
Consensus pattern (32 bp):
AAAAAATCCTTAAAAAATGCTCCAAAAAACTT
Found at i:38617431 original size:21 final size:20
Alignment explanation
Indices: 38617407--38617489 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 20
38617397 AAAATGCTCC
38617407 AAAATACTTAAAAAATCTTTA
1 AAAAT-CTTAAAAAATCTTTA
38617428 AAAATTGCTTCAAAAAA-CTTTA
1 AAAA-T-CTT-AAAAAATCTTTA
* *
38617450 AAAATCCTT-AAAATTCCTTGA
1 AAAAT-CTTAAAAAAT-CTTTA
*
38617471 AAAATCTTTAAAAATCTTT
1 AAAATCTTAAAAAATCTTT
38617490 TGAAATCAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
19 4 0.08
20 6 0.12
21 22 0.43
22 13 0.25
23 6 0.12
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAATCTTAAAAAATCTTTA
Found at i:38617485 original size:116 final size:117
Alignment explanation
Indices: 38617331--38617586 Score: 267
Period size: 116 Copynumber: 2.2 Consensus size: 117
38617321 TGAAAAATCA
* * *
38617331 CTTAAAAA-CCTT-AAATATGCTTAAAAAGATCTTAAAAATGC-CTAAAAATCCATC-AAAAAAG
1 CTTAAAAATCCTTAAAATATCCTTAAAAAGATCTTAAAAAT-CTCTAAAAAT-CAACGAAAAAAA
* * *
38617392 CCTAAAAAATG-CTCCAAAATACTTAAAAAATCTTTAAAAATTGCTTCAAAAAAC
64 CCTAAAAAATGCCTCC-AAAGACTTAAAAAATATTTAAAAAATGCTTCAAAAAAC
* * * **
38617446 TTTAAAAATCCTTAAAAT-TCCTTGAAAA-ATCTTTAAAAATCTTTTGAAATCAACGAAAAAAAC
1 CTTAAAAATCCTTAAAATATCCTTAAAAAGATC-TTAAAAATCTCTAAAAATCAACGAAAAAAAC
* * *
38617509 CTAAAAAATGCCTTCAAAGACTTCAAAAATATTTAAAAAATGCTTTAAAAAAC
65 CTAAAAAATGCCTCCAAAGACTTAAAAAATATTTAAAAAATGCTTCAAAAAAC
* *
38617562 CTTAATATTCCTTAAAA-ACTCCTTA
1 CTTAAAAATCCTTAAAATA-TCCTTA
38617587 GAAATCCTTT
Statistics
Matches: 115, Mismatches: 18, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
115 14 0.12
116 89 0.77
117 12 0.10
ACGTcount: A:0.50, C:0.17, G:0.05, T:0.29
Consensus pattern (117 bp):
CTTAAAAATCCTTAAAATATCCTTAAAAAGATCTTAAAAATCTCTAAAAATCAACGAAAAAAACC
TAAAAAATGCCTCCAAAGACTTAAAAAATATTTAAAAAATGCTTCAAAAAAC
Found at i:38617496 original size:10 final size:10
Alignment explanation
Indices: 38617407--38617489 Score: 76
Period size: 10 Copynumber: 7.9 Consensus size: 10
38617397 AAAATGCTCC
*
38617407 AAAATACTTAA
1 AAAAT-CTTTA
38617418 AAAATCTTTA
1 AAAATCTTTA
*
38617428 AAAATTGCTTCA
1 AAAA-T-CTTTA
*
38617440 AAAAACTTTA
1 AAAATCTTTA
*
38617450 AAAATCCTTA
1 AAAATCTTTA
* *
38617460 AAATTCCTTGA
1 AAAAT-CTTTA
38617471 AAAATCTTTA
1 AAAATCTTTA
38617481 AAAATCTTT
1 AAAATCTTT
38617490 TGAAATCAAC
Statistics
Matches: 58, Mismatches: 11, Indels: 7
0.76 0.14 0.09
Matches are distributed among these distances:
10 37 0.64
11 13 0.22
12 8 0.14
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.35
Consensus pattern (10 bp):
AAAATCTTTA
Found at i:38617586 original size:11 final size:10
Alignment explanation
Indices: 38617553--38617653 Score: 67
Period size: 10 Copynumber: 9.7 Consensus size: 10
38617543 AAAAAATGCT
*
38617553 TTAAAAAACC
1 TTAAAAATCC
* *
38617563 TTAATATTCC
1 TTAAAAATCC
38617573 TTAAAAACTCC
1 TTAAAAA-TCC
*
38617584 TTAGAAATCC
1 TTAAAAATCC
**
38617594 TTTGAAATCC
1 TTAAAAATCC
* *
38617604 ATAAAAAAAACC
1 -T-TAAAAATCC
*
38617616 TTAAAAATGC
1 TTAAAAATCC
*
38617626 TTAAAATAACC
1 TTAAAA-ATCC
*
38617637 TTAAACATCC
1 TTAAAAATCC
38617647 TTAAAAA
1 TTAAAAA
38617654 GTGCAAAAAA
Statistics
Matches: 68, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
10 45 0.66
11 18 0.26
12 5 0.07
ACGTcount: A:0.50, C:0.19, G:0.03, T:0.29
Consensus pattern (10 bp):
TTAAAAATCC
Found at i:38617636 original size:21 final size:21
Alignment explanation
Indices: 38617571--38617653 Score: 69
Period size: 21 Copynumber: 3.9 Consensus size: 21
38617561 CCTTAATATT
* *
38617571 CCTTAAAAACTCCTT-AGAAAT
1 CCTTAAAAA-TCCTTAAAAAAA
** *
38617592 CCTTTGAAATCCATAAAAAAAA
1 CCTTAAAAATCC-TTAAAAAAA
* *
38617614 CCTTAAAAATGCTTAAAATAA
1 CCTTAAAAATCCTTAAAAAAA
*
38617635 CCTTAAACATCCTTAAAAA
1 CCTTAAAAATCCTTAAAAA
38617654 GTGCAAAAAA
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 3 0.06
21 31 0.66
22 13 0.28
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (21 bp):
CCTTAAAAATCCTTAAAAAAA
Found at i:38617651 original size:106 final size:106
Alignment explanation
Indices: 38617413--38617653 Score: 249
Period size: 106 Copynumber: 2.3 Consensus size: 106
38617403 CTCCAAAATA
* * *
38617413 CTTAAAAAATCTTTAAAAATTGCTTCAAAAAA--CTTTAAAAATCCTTAAAATTCCTTGAAAAAT
1 CTTAAAAAA-CTTCAAAAA-TACTT-AAAAAATGCTTTAAAAAACCTTAAAATTCCTTGAAAAAT
* * *
38617476 CTTTAAAAATCTTTTGAAATCAACGAAAAAAACCTAAAAAATGC
63 CCTTAAAAATCCTTTGAAATCAACAAAAAAAACCTAAAAAATGC
* * * *
38617520 CTTCAAAGACTTCAAAAATATTTAAAAAATGCTTTAAAAAACCTTAATATTCCTT-AAAAACTCC
1 CTTAAAAAACTTCAAAAATACTTAAAAAATGCTTTAAAAAACCTTAAAATTCCTTGAAAAA-TCC
* * * *
38617584 TTAGAAATCCTTTGAAATCCATAAAAAAAACCTTAAAAATG-
65 TTAAAAATCCTTTGAAATCAACAAAAAAAACCTAAAAAATGC
* *
38617625 CTTAAAATAACCTT-AAACATCCTTAAAAA
1 CTTAAAA-AA-CTTCAAAAATACTTAAAAA
38617654 GTGCAAAAAA
Statistics
Matches: 110, Mismatches: 19, Indels: 11
0.79 0.14 0.08
Matches are distributed among these distances:
104 6 0.05
105 14 0.13
106 80 0.73
107 10 0.09
ACGTcount: A:0.50, C:0.17, G:0.04, T:0.29
Consensus pattern (106 bp):
CTTAAAAAACTTCAAAAATACTTAAAAAATGCTTTAAAAAACCTTAAAATTCCTTGAAAAATCCT
TAAAAATCCTTTGAAATCAACAAAAAAAACCTAAAAAATGC
Found at i:38617911 original size:10 final size:10
Alignment explanation
Indices: 38617873--38618033 Score: 74
Period size: 10 Copynumber: 15.2 Consensus size: 10
38617863 TCAAGAAGCT
*
38617873 TTAACAATCC
1 TTAAAAATCC
* *
38617883 TTAAAATTTC
1 TTAAAAATCC
38617893 TTGAAAAATCC
1 TT-AAAAATCC
*
38617904 TTAAAAATCT
1 TTAAAAATCC
** *
38617914 TTTGAAATCAA
1 TTAAAAATC-C
* *
38617925 TCAAGAAAACC
1 TTAA-AAATCC
*
38617936 TTAAAAATGC
1 TTAAAAATCC
*
38617946 TTCAAAAA-AC
1 TT-AAAAATCC
*
38617956 TTCAAAAATCT
1 TT-AAAAATCC
38617967 TTAAAACATCC
1 TTAAAA-ATCC
38617978 TT-AAAATGACC
1 TTAAAAAT--CC
*
38617989 TTAAACATCC
1 TTAAAAATCC
*
38617999 TTCAAAAAAACC
1 TT--AAAAATCC
*
38618011 TTAAAATTCC
1 TTAAAAATCC
38618021 TTAAAAACTCC
1 TTAAAAA-TCC
38618032 TT
1 TT
38618034 TGAAATCCAA
Statistics
Matches: 112, Mismatches: 27, Indels: 23
0.69 0.17 0.14
Matches are distributed among these distances:
9 2 0.02
10 61 0.54
11 33 0.29
12 16 0.14
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (10 bp):
TTAAAAATCC
Found at i:38617962 original size:21 final size:20
Alignment explanation
Indices: 38617925--38617983 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
38617915 TTGAAATCAA
38617925 TCAAGAAAACCTTAAAAATGCT
1 TCAA-AAAACCTTAAAAAT-CT
38617947 TCAAAAAA-CTTCAAAAATCT
1 TCAAAAAACCTT-AAAAATCT
* *
38617967 TTAAAACATCCTTAAAA
1 TCAAAA-AACCTTAAAA
38617984 TGACCTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 10 0.31
21 15 0.47
22 7 0.22
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.25
Consensus pattern (20 bp):
TCAAAAAACCTTAAAAATCT
Found at i:38617994 original size:21 final size:21
Alignment explanation
Indices: 38617970--38618093 Score: 81
Period size: 21 Copynumber: 5.8 Consensus size: 21
38617960 AAAATCTTTA
**
38617970 AAACATCCTTAAAATGACCTT
1 AAACATCCTTAAAAAAACCTT
38617991 AAACATCCTTCAAAAAAACCTT
1 AAACATCCTT-AAAAAAACCTT
**
38618013 AAA-ATTCCTTAAAAACTCCTTT
1 AAACA-TCCTTAAAAAAACC-TT
* **
38618035 GAA-ATCCAACAAAAAAACCTT
1 AAACATCC-TTAAAAAAACCTT
* ** ** *
38618056 AAAAATAGTTAAAATGACCTC
1 AAACATCCTTAAAAAAACCTT
38618077 AAACATCCTTAAAAAAA
1 AAACATCCTTAAAAAAA
38618094 GCAAAAAAAA
Statistics
Matches: 76, Mismatches: 22, Indels: 10
0.70 0.20 0.09
Matches are distributed among these distances:
21 45 0.59
22 31 0.41
ACGTcount: A:0.51, C:0.22, G:0.03, T:0.24
Consensus pattern (21 bp):
AAACATCCTTAAAAAAACCTT
Found at i:38618022 original size:43 final size:43
Alignment explanation
Indices: 38617967--38618093 Score: 132
Period size: 43 Copynumber: 3.0 Consensus size: 43
38617957 TCAAAAATCT
38617967 TTAAAACATCCTTAAAATGACCTTAAACATCCTTCAAAAAAACC
1 TTAAAA-ATCCTTAAAATGACCTTAAACATCCTTCAAAAAAACC
* *** * **
38618011 TTAAAATTCCTTAAAAACTCCTTTGAA-ATCCAACAAAAAAACC
1 TTAAAAATCCTTAAAATGACC-TTAAACATCCTTCAAAAAAACC
** *
38618054 TTAAAAATAGTTAAAATGACCTCAAACATCCTT-AAAAAAA
1 TTAAAAATCCTTAAAATGACCTTAAACATCCTTCAAAAAAA
38618094 GCAAAAAAAA
Statistics
Matches: 64, Mismatches: 17, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
42 10 0.16
43 44 0.69
44 10 0.16
ACGTcount: A:0.50, C:0.21, G:0.03, T:0.25
Consensus pattern (43 bp):
TTAAAAATCCTTAAAATGACCTTAAACATCCTTCAAAAAAACC
Found at i:38618185 original size:39 final size:40
Alignment explanation
Indices: 38618109--38618185 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 40
38618099 AAAAAACTTG
* ** * *
38618109 AAAAAAATCTTTAAAATGCTTTAAATTCGTAACAAATAATT
1 AAAAAAA-CTTTAAAATCCTTTAAAAACATAAAAAATAATT
38618150 AAAAAAA-TTTAAAATCCTTTAAAAACATAAAAAATA
1 AAAAAAACTTTAAAATCCTTTAAAAACATAAAAAATA
38618186 TTCCAAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 24 0.77
41 7 0.23
ACGTcount: A:0.58, C:0.09, G:0.03, T:0.30
Consensus pattern (40 bp):
AAAAAAACTTTAAAATCCTTTAAAAACATAAAAAATAATT
Found at i:38618286 original size:20 final size:20
Alignment explanation
Indices: 38618263--38618326 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
38618253 AAATAAATGA
*
38618263 AAAAGCCTT-AAAAATGCTTT
1 AAAAGACTTCAAAAAT-CTTT
*
38618283 AAAATACTTCAAAAATCTTT
1 AAAAGACTTCAAAAATCTTT
* *
38618303 AAAAAATGCTTCAAAAAACTTT
1 AAAAGA--CTTCAAAAATCTTT
38618325 AA
1 AA
38618327 TAATCCTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 16 0.43
21 6 0.16
22 15 0.41
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.30
Consensus pattern (20 bp):
AAAAGACTTCAAAAATCTTT
Found at i:38618297 original size:22 final size:21
Alignment explanation
Indices: 38618272--38618349 Score: 70
Period size: 22 Copynumber: 3.7 Consensus size: 21
38618262 AAAAAGCCTT
38618272 AAAAATGCTTT-AAAATACTTC
1 AAAAAT-CTTTAAAAATACTTC
*
38618293 AAAAATCTTTAAAAAATGCTTC
1 AAAAATCTTT-AAAAATACTTC
* * *
38618315 AAAAAACTTTAATAATCCTT-
1 AAAAATCTTTAAAAATACTTC
* *
38618335 AAAATTCTTCAAAAA
1 AAAAATCTTTAAAAA
38618350 AATCCTTAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
20 15 0.32
21 14 0.30
22 18 0.38
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (21 bp):
AAAAATCTTTAAAAATACTTC
Found at i:38618307 original size:10 final size:10
Alignment explanation
Indices: 38618270--38618425 Score: 57
Period size: 10 Copynumber: 14.7 Consensus size: 10
38618260 TGAAAAAGCC
38618270 TTAAAAATGCT
1 TTAAAAAT-CT
38618281 TT-AAAATACT
1 TTAAAAAT-CT
*
38618291 TCAAAAATCT
1 TTAAAAATCT
38618301 TTAAAAAATGCT
1 TT-AAAAAT-CT
* *
38618313 TCAAAAAACT
1 TTAAAAATCT
* *
38618323 TTAATAATCC
1 TTAAAAATCT
*
38618333 TTAAAATTCT
1 TTAAAAATCT
* *
38618343 TCAAAAAAATCC
1 T--TAAAAATCT
38618355 TTAAAAATCCT
1 TTAAAAAT-CT
*
38618366 TT-CAAATCAAT
1 TTAAAAATC--T
**
38618377 GAAGAAAATCT
1 TTA-AAAATCT
*
38618388 TCAAAAATGCT
1 TTAAAAAT-CT
*
38618399 TCAAAAGA-CT
1 TTAAAA-ATCT
*
38618409 TCAAAAATCT
1 TTAAAAATCT
38618419 TTAAAAA
1 TTAAAAA
38618426 ATGCTTCAAT
Statistics
Matches: 108, Mismatches: 24, Indels: 27
0.68 0.15 0.17
Matches are distributed among these distances:
9 2 0.02
10 58 0.54
11 32 0.30
12 11 0.10
13 5 0.05
ACGTcount: A:0.50, C:0.15, G:0.04, T:0.31
Consensus pattern (10 bp):
TTAAAAATCT
Found at i:38618308 original size:32 final size:32
Alignment explanation
Indices: 38618262--38618350 Score: 94
Period size: 32 Copynumber: 2.9 Consensus size: 32
38618252 AAAATAAATG
* * *
38618262 AAAAAGCCTT-AAAAATGCTTTAAAATACTTC
1 AAAAATCCTTAAAAAATGCTTCAAAAAACTTC
* *
38618293 AAAAATCTTTAAAAAATGCTTCAAAAAACTTT
1 AAAAATCCTTAAAAAATGCTTCAAAAAACTTC
* *
38618325 AATAATCCTT--AAAATTCTTCAAAAAA
1 AAAAATCCTTAAAAAATGCTTCAAAAAA
38618351 ATCCTTAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
30 15 0.31
31 8 0.16
32 26 0.53
ACGTcount: A:0.52, C:0.15, G:0.03, T:0.30
Consensus pattern (32 bp):
AAAAATCCTTAAAAAATGCTTCAAAAAACTTC
Found at i:38618410 original size:21 final size:20
Alignment explanation
Indices: 38618386--38618424 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
38618376 TGAAGAAAAT
38618386 CTTCAAAAATGCTTCAAAAGA
1 CTTCAAAAAT-CTTCAAAAGA
*
38618407 CTTCAAAAATCTTTAAAA
1 CTTCAAAAATCTTCAAAA
38618425 AATGCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.18, G:0.05, T:0.28
Consensus pattern (20 bp):
CTTCAAAAATCTTCAAAAGA
Found at i:38618509 original size:21 final size:21
Alignment explanation
Indices: 38618485--38618531 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
38618475 GAAATCCATG
38618485 AAAAAAACCTTAAAAATGCTT
1 AAAAAAACCTTAAAAATGCTT
** *
38618506 AAAATGACCTTAAACATGCTT
1 AAAAAAACCTTAAAAATGCTT
38618527 AAAAA
1 AAAAA
38618532 GAGCCAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.23
Consensus pattern (21 bp):
AAAAAAACCTTAAAAATGCTT
Found at i:38618691 original size:10 final size:10
Alignment explanation
Indices: 38618678--38618843 Score: 70
Period size: 10 Copynumber: 15.8 Consensus size: 10
38618668 TTAAAAGGAT
38618678 CTTAAAAATG
1 CTTAAAAATG
*
38618688 CTTAAAAATC
1 CTTAAAAATG
** *
38618698 CAAAAAAAAAG
1 C-TTAAAAATG
38618709 TCTTAAAAATG
1 -CTTAAAAATG
* *
38618720 CTTCAAAATA
1 CTTAAAAATG
38618730 CTTCAAAAAT-
1 CTT-AAAAATG
38618740 CTTTAAAAAATG
1 C-TT-AAAAATG
* *
38618752 TTTCAAAAA-A
1 CTT-AAAAATG
*
38618762 CTTTAAAAATC
1 C-TTAAAAATG
* *
38618773 CTTCAAAATT
1 CTTAAAAATG
*
38618783 CATGAAAAA-G
1 C-TTAAAAATG
38618793 CCTTAAAAATG
1 -CTTAAAAATG
* *
38618804 CTTCAAAATA
1 CTTAAAAATG
38618814 CTTTAAAAAT-
1 C-TTAAAAATG
38618824 CTTTAAAAATG
1 C-TTAAAAATG
38618835 CTTCAAAAA
1 CTT-AAAAA
38618844 ACTTTAAAAA
Statistics
Matches: 117, Mismatches: 26, Indels: 25
0.70 0.15 0.15
Matches are distributed among these distances:
10 62 0.53
11 54 0.46
12 1 0.01
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (10 bp):
CTTAAAAATG
Found at i:38618738 original size:32 final size:31
Alignment explanation
Indices: 38618676--38618770 Score: 84
Period size: 32 Copynumber: 3.0 Consensus size: 31
38618666 GATTAAAAGG
* * **
38618676 ATCTTAAAAATGCTTAAAAATCCAAAAAAAA
1 ATCTTAAAAATGCTTCAAAATACTTAAAAAA
*
38618707 AGTCTTAAAAATGCTTCAAAATACTT-CAAAA
1 A-TCTTAAAAATGCTTCAAAATACTTAAAAAA
* * *
38618738 ATCTTTAAAAAATGTTTCAAAAAACTTTAAAAA
1 ATC-TT-AAAAATGCTTCAAAATACTTAAAAAA
38618771 TCCTTCAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
30 2 0.04
31 8 0.15
32 38 0.73
33 4 0.08
ACGTcount: A:0.55, C:0.13, G:0.04, T:0.28
Consensus pattern (31 bp):
ATCTTAAAAATGCTTCAAAATACTTAAAAAA
Found at i:38618791 original size:31 final size:31
Alignment explanation
Indices: 38618756--38618842 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 31
38618746 AAAATGTTTC
* *
38618756 AAAAAACTTTAAAAATCCTTCAAAATTCATG
1 AAAAAACTTTAAAAATGCTTCAAAATACATG
* * * *
38618787 AAAAAGCCTTAAAAATGCTTCAAAATACTTT
1 AAAAAACTTTAAAAATGCTTCAAAATACATG
*
38618818 AAAAATCTTTAAAAATGCTTCAAAA
1 AAAAAACTTTAAAAATGCTTCAAAA
38618843 AACTTTAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.52, C:0.15, G:0.05, T:0.29
Consensus pattern (31 bp):
AAAAAACTTTAAAAATGCTTCAAAATACATG
Found at i:38618833 original size:21 final size:21
Alignment explanation
Indices: 38618711--38618854 Score: 89
Period size: 21 Copynumber: 6.9 Consensus size: 21
38618701 AAAAAAAGTC
*
38618711 TTAAAAATGC-TTCAAAATACT
1 TTAAAAAT-CTTTAAAAATACT
* *
38618732 TCAAAAATCTTTAAAAA-ATGT
1 TTAAAAATCTTTAAAAATA-CT
* *
38618753 TTCAAAAAACTTTAAAAATCCT
1 TT-AAAAATCTTTAAAAATACT
* * * * * *
38618775 TCAAAATTCATGAAAAA-GCC
1 TTAAAAATCTTTAAAAATACT
*
38618795 TTAAAAATGC-TTCAAAATACT
1 TTAAAAAT-CTTTAAAAATACT
*
38618816 TTAAAAATCTTTAAAAATGCT
1 TTAAAAATCTTTAAAAATACT
* *
38618837 TCAAAAAACTTTAAAAAT
1 TTAAAAATCTTTAAAAAT
38618855 CCTTGAAATT
Statistics
Matches: 92, Mismatches: 24, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
20 15 0.16
21 61 0.66
22 16 0.17
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (21 bp):
TTAAAAATCTTTAAAAATACT
Found at i:38618855 original size:31 final size:32
Alignment explanation
Indices: 38618762--38618854 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 32
38618752 TTTCAAAAAA
* ** * *
38618762 CTTTAAAAATCCTTCAAAATTCATGAAAAA-G
1 CTTTAAAAATACTTCAAAAAACTTTAAAAATG
* * *
38618793 CCTTAAAAATGCTTCAAAATACTTTAAAAAT-
1 CTTTAAAAATACTTCAAAAAACTTTAAAAATG
*
38618824 CTTTAAAAATGCTTCAAAAAACTTTAAAAAT
1 CTTTAAAAATACTTCAAAAAACTTTAAAAAT
38618855 CCTTGAAATT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.31
Consensus pattern (32 bp):
CTTTAAAAATACTTCAAAAAACTTTAAAAATG
Found at i:38618917 original size:32 final size:31
Alignment explanation
Indices: 38618839--38618917 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
38618829 AAAATGCTTC
* * *
38618839 AAAAAACTTTAAAAATCCTTGAAATTTATTG
1 AAAAAACCTTAAAAATCCTTGAAATTCAATG
* *
38618870 AAAAATCCTTCAAAATCCTTTGAAA-TCAATG
1 AAAAAACCTTAAAAATCC-TTGAAATTCAATG
38618901 AAGAAAACCTTAAAAAT
1 AA-AAAACCTTAAAAAT
38618918 ACATCAAAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
31 21 0.54
32 18 0.46
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (31 bp):
AAAAAACCTTAAAAATCCTTGAAATTCAATG
Found at i:38619208 original size:21 final size:21
Alignment explanation
Indices: 38619182--38619233 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
38619172 AACCTTACAT
38619182 ATGCTTAAAA-GGATCTAAAAA
1 ATGCTTAAAATGGAT-TAAAAA
*
38619203 ATGCTTAAAAATGTATTAAAAA
1 ATGCTT-AAAATGGATTAAAAA
38619225 AT-CTTAAAA
1 ATGCTTAAAA
38619234 ATGCTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.14
21 9 0.32
22 12 0.43
23 3 0.11
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.29
Consensus pattern (21 bp):
ATGCTTAAAATGGATTAAAAA
Found at i:38619234 original size:21 final size:21
Alignment explanation
Indices: 38619197--38619320 Score: 96
Period size: 22 Copynumber: 5.9 Consensus size: 21
38619187 TAAAAGGATC
* *
38619197 TAAAAAATGCTTAAAAATGTAT
1 TAAAAAATACTTAAAAATCT-T
38619219 TAAAAAAT-CTTAAAAATGC-T
1 TAAAAAATACTTAAAAAT-CTT
38619239 T-AAAAATACTTCAAAAATCTT
1 TAAAAAATACTT-AAAAATCTT
* *
38619260 TAAAAAGTACTTCAAAAAACTT
1 TAAAAAATACTT-AAAAATCTT
* *
38619282 T-AAAAAT-CTTTAAAATTTCT
1 TAAAAAATACTTAAAAATCT-T
* *
38619302 TGAAAAATCCTTAAAAATC
1 TAAAAAATACTTAAAAATC
38619321 CTTTGAAATC
Statistics
Matches: 85, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
19 11 0.13
20 11 0.13
21 28 0.33
22 35 0.41
ACGTcount: A:0.52, C:0.11, G:0.04, T:0.32
Consensus pattern (21 bp):
TAAAAAATACTTAAAAATCTT
Found at i:38619255 original size:31 final size:29
Alignment explanation
Indices: 38619159--38619320 Score: 105
Period size: 31 Copynumber: 5.2 Consensus size: 29
38619149 AAATTTCATG
* * * *
38619159 AAAAATACTTAAAAA-CCTTACATATGCTT
1 AAAAAT-CTTAAAAATGCTTAAAAATACTT
*
38619188 AAAAGGATCTAAAAAATGCTTAAAAATGTA-TT
1 AAAA--ATCTTAAAAATGCTTAAAAA--TACTT
38619220 AAAAAATCTTAAAAATGCTTAAAAATACTT
1 -AAAAATCTTAAAAATGCTTAAAAATACTT
*
38619250 CAAAAATCTTTAAAAAGTACTTCAAAAA-ACTTT
1 -AAAAATC-TTAAAAA-TGCTT-AAAAATAC-TT
* * *
38619283 AAAAATCTTTAAAATTTCTTGAAAAATCCTT
1 AAAAATC-TTAAAAATGCTT-AAAAATACTT
38619314 AAAAATC
1 AAAAATC
38619321 CTTTGAAATC
Statistics
Matches: 109, Mismatches: 12, Indels: 22
0.76 0.08 0.15
Matches are distributed among these distances:
29 6 0.06
30 16 0.15
31 52 0.48
32 23 0.21
33 12 0.11
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (29 bp):
AAAAATCTTAAAAATGCTTAAAAATACTT
Found at i:38619270 original size:22 final size:21
Alignment explanation
Indices: 38619199--38619320 Score: 94
Period size: 21 Copynumber: 5.9 Consensus size: 21
38619189 AAAGGATCTA
* *
38619199 AAAAATGCTT-AAAAATGTATT
1 AAAAATACTTCAAAAATCT-TT
38619220 AAAAA-ATCTT-AAAAATGC-TT
1 AAAAATA-CTTCAAAAAT-CTTT
38619240 AAAAATACTTCAAAAATCTTT
1 AAAAATACTTCAAAAATCTTT
*
38619261 AAAAAGTACTTCAAAAAACTTT
1 AAAAA-TACTTCAAAAATCTTT
* * *
38619283 AAAAAT-CTTTAAAATTTCTTG
1 AAAAATACTTCAAAA-ATCTTT
*
38619304 AAAAATCCTT-AAAAATC
1 AAAAATACTTCAAAAATC
38619321 CTTTGAAATC
Statistics
Matches: 85, Mismatches: 8, Indels: 17
0.77 0.07 0.15
Matches are distributed among these distances:
20 20 0.24
21 42 0.49
22 23 0.27
ACGTcount: A:0.52, C:0.11, G:0.04, T:0.32
Consensus pattern (21 bp):
AAAAATACTTCAAAAATCTTT
Found at i:38619289 original size:32 final size:31
Alignment explanation
Indices: 38619228--38619320 Score: 100
Period size: 32 Copynumber: 3.0 Consensus size: 31
38619218 TTAAAAAATC
*
38619228 TTAAAAATGCTTAAAAATACTTCAAAAATCT
1 TTAAAAATACTTAAAAATACTTCAAAAATCT
*
38619259 TTAAAAAGTACTTCAAAAA-ACTTTAAAAATCT
1 TTAAAAA-TACTT-AAAAATACTTCAAAAATCT
* * *
38619291 TTAAAATTTCTTGAAAAATCCTT-AAAAATC
1 TTAAAAATACTT-AAAAATACTTCAAAAATC
38619321 CTTTGAAATC
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
31 23 0.43
32 25 0.47
33 5 0.09
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (31 bp):
TTAAAAATACTTAAAAATACTTCAAAAATCT
Found at i:38619321 original size:10 final size:10
Alignment explanation
Indices: 38619159--38619764 Score: 104
Period size: 10 Copynumber: 57.9 Consensus size: 10
38619149 AAATTTCATG
*
38619159 AAAAATACTT
1 AAAAATCCTT
38619169 AAAAA-CCTT
1 AAAAATCCTT
* * *
38619178 ACATATGCTT
1 AAAAATCCTT
*
38619188 AAAAGGAT-CTA
1 AAAA--ATCCTT
*
38619199 AAAAATGCTT
1 AAAAATCCTT
**
38619209 AAAAATGTATT
1 AAAAAT-CCTT
38619220 AAAAAAT-CTT
1 -AAAAATCCTT
*
38619230 AAAAATGCTT
1 AAAAATCCTT
*
38619240 AAAAATACTT
1 AAAAATCCTT
*
38619250 CAAAAATCTTT
1 -AAAAATCCTT
*
38619261 AAAAAGTACTT
1 AAAAA-TCCTT
* *
38619272 CAAAAAACTTT
1 -AAAAATCCTT
*
38619283 AAAAATCTTT
1 AAAAATCCTT
* *
38619293 AAAATTTCTT
1 AAAAATCCTT
38619303 GAAAAATCCTT
1 -AAAAATCCTT
38619314 AAAAATCCTT
1 AAAAATCCTT
** *
38619324 TGAAATCCATG
1 AAAAATCC-TT
*
38619335 AACAAAACCTT
1 AA-AAATCCTT
**
38619346 AAAAATGTTT
1 AAAAATCCTT
* **
38619356 CAAAAGACTT
1 AAAAATCCTT
* *
38619366 CAAGAATCTTT
1 -AAAAATCCTT
*
38619377 ATAAAATGCTTT
1 A-AAAAT-CCTT
38619389 AGAAAA-CC-T
1 A-AAAATCCTT
*
38619398 AAAATTCCTT
1 AAAAATCCTT
* *
38619408 CAAAATCCTC
1 AAAAATCCTT
*
38619418 AAAAATCGTT
1 AAAAATCCTT
** *
38619428 TGAAATCCATGAG
1 AAAAATCC-T--T
*
38619441 AAAAAT-CTA
1 AAAAATCCTT
* *
38619450 AAAAATACGTA
1 AAAAAT-CCTT
38619461 AAAAGAT-CTT
1 AAAA-ATCCTT
*
38619471 AAAAATGCTT
1 AAAAATCCTT
*
38619481 AAAAATACATT
1 AAAAAT-CCTT
* *
38619492 AAAAAGCCTG
1 AAAAATCCTT
*
38619502 AAAAATGCTTT
1 AAAAAT-CCTT
38619513 AAAAA--CTT
1 AAAAATCCTT
*
38619521 CAAAAATCTTT
1 -AAAAATCCTT
*
38619532 AAAAAAATGCTTT
1 --AAAAAT-CCTT
38619545 AAAAAAT-CTT
1 -AAAAATCCTT
*
38619555 AACAATCCTT
1 AAAAATCCTT
* * *
38619565 AAAATTCAATG
1 AAAAATC-CTT
* *
38619576 ACAATTCCTT
1 AAAAATCCTT
38619586 AAAAATCCTT
1 AAAAATCCTT
** *
38619596 TGAAATCCATGAA
1 AAAAATCC-T--T
*
38619609 AAAAAACCTT
1 AAAAATCCTT
*
38619619 AAAAATGCTT
1 AAAAATCCTT
** *
38619629 CAAAAGGCTTT
1 -AAAAATCCTT
**
38619640 AGCAAT-CTT
1 AAAAATCCTT
*
38619649 AAAAAAATACTTTT
1 --AAAAAT-C-CTT
38619663 AAAAA-CCTT
1 AAAAATCCTT
*
38619672 AAAATTCCTT
1 AAAAATCCTT
38619682 AAAAAGTCCTTT
1 AAAAA-TCC-TT
* *
38619694 AAAACTCTTT
1 AAAAATCCTT
38619704 AAAAATCCTT
1 AAAAATCCTT
** *
38619714 TGAAATCCAATA
1 AAAAATCC--TT
*
38619726 AAAAAACCTT
1 AAAAATCCTT
*
38619736 -AAAATGCTT
1 AAAAATCCTT
*
38619745 AAAATAACCTT
1 AAAA-ATCCTT
*
38619756 AAACATCCT
1 AAAAATCCT
38619765 CGAAAAGGGC
Statistics
Matches: 419, Mismatches: 127, Indels: 100
0.65 0.20 0.15
Matches are distributed among these distances:
8 5 0.01
9 51 0.12
10 191 0.46
11 96 0.23
12 61 0.15
13 13 0.03
14 2 0.00
ACGTcount: A:0.49, C:0.16, G:0.06, T:0.29
Consensus pattern (10 bp):
AAAAATCCTT
Found at i:38619351 original size:32 final size:31
Alignment explanation
Indices: 38619273--38619360 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
38619263 AAAGTACTTC
* * *
38619273 AAAAAACTTTAAAAATCTTTAAAATTTCTTG
1 AAAAAACCTTAAAAATCTTTAAAATTCCATG
* *
38619304 AAAAATCCTTAAAAATCCTTTGAAA-TCCATG
1 AAAAAACCTTAAAAAT-CTTTAAAATTCCATG
*
38619335 AACAAAACCTTAAAAATGTTTCAAAA
1 AA-AAAACCTTAAAAATCTTT-AAAA
38619361 GACTTCAAGA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
31 23 0.50
32 23 0.50
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.31
Consensus pattern (31 bp):
AAAAAACCTTAAAAATCTTTAAAATTCCATG
Found at i:38619483 original size:21 final size:21
Alignment explanation
Indices: 38619441--38619568 Score: 72
Period size: 21 Copynumber: 6.1 Consensus size: 21
38619431 AATCCATGAG
* * *
38619441 AAAAATC-TAAAAAATACGTA
1 AAAAATCTTTAAAAATGCTTA
38619461 AAAAGATC-TTAAAAATGCTT-
1 AAAA-ATCTTTAAAAATGCTTA
* * *
38619481 AAAAATACATTAAAAA-GCCTG
1 AAAAAT-CTTTAAAAATGCTTA
*
38619502 AAAAATGCTTTAAAAA--CTTC
1 AAAAAT-CTTTAAAAATGCTTA
38619522 AAAAATCTTTAAAAAAATGCTTTA
1 AAAAATCTTT--AAAAATGC-TTA
* *
38619546 AAAAATC-TTAACAATCCTTA
1 AAAAATCTTTAAAAATGCTTA
38619566 AAA
1 AAA
38619569 TTCAATGACA
Statistics
Matches: 88, Mismatches: 11, Indels: 18
0.75 0.09 0.15
Matches are distributed among these distances:
19 6 0.07
20 26 0.30
21 44 0.50
23 3 0.03
24 9 0.10
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.27
Consensus pattern (21 bp):
AAAAATCTTTAAAAATGCTTA
Found at i:38619487 original size:31 final size:31
Alignment explanation
Indices: 38619440--38619517 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
38619430 AAATCCATGA
* *
38619440 GAAAAAT-CTAAAAAATAC-GTAAAAAGATCT
1 GAAAAATGCTTAAAAATACAGTAAAAAG-CCT
* *
38619470 TAAAAATGCTTAAAAATACATTAAAAAGCCT
1 GAAAAATGCTTAAAAATACAGTAAAAAGCCT
38619501 GAAAAATGCTTTAAAAA
1 GAAAAATGC-TTAAAAA
38619518 CTTCAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 6 0.15
31 20 0.50
32 14 0.35
ACGTcount: A:0.58, C:0.10, G:0.09, T:0.23
Consensus pattern (31 bp):
GAAAAATGCTTAAAAATACAGTAAAAAGCCT
Found at i:38619544 original size:13 final size:12
Alignment explanation
Indices: 38619522--38619554 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
38619512 TAAAAACTTC
38619522 AAAAATCTTTAA
1 AAAAATCTTTAA
38619534 AAAAATGCTTT-A
1 AAAAAT-CTTTAA
38619546 AAAAATCTT
1 AAAAATCTT
38619555 AACAATCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.15
12 13 0.65
13 4 0.20
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (12 bp):
AAAAATCTTTAA
Done.