Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 201 of 206
Found at i:60799348 original size:10 final size:10
Alignment explanation
Indices: 60799329--60799357 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
60799319 TCCTACATAG
60799329 TAAA-TAAAA
1 TAAATTAAAA
60799338 TAAATTAAAA
1 TAAATTAAAA
60799348 TAAATTAAAA
1 TAAATTAAAA
60799358 ATTCAGGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAATTAAAA
Found at i:60800055 original size:31 final size:31
Alignment explanation
Indices: 60800017--60800081 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
60800007 ATTATTTTTT
60800017 TAATTTTAAAATACTTTTTTTAA-TTTTAAAA
1 TAATTTTAAAATAC-TTTTTTAATTTTTAAAA
60800048 TAATTTTAAAATACTTTTTTAATTTTTAAAA
1 TAATTTTAAAATACTTTTTTAATTTTTAAAA
60800079 TAA
1 TAA
60800082 AAATTTGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 8 0.24
31 25 0.76
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (31 bp):
TAATTTTAAAATACTTTTTTAATTTTTAAAA
Found at i:60800073 original size:19 final size:20
Alignment explanation
Indices: 60800010--60800054 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
60800000 TAAATATATT
60800010 ATTTTTTTAATTTTAAAATA
1 ATTTTTTTAATTTTAAAATA
*
60800030 CTTTTTTTAATTTTAAAATA
1 ATTTTTTTAATTTTAAAATA
60800050 ATTTT
1 ATTTT
60800055 AAAATACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTTTTAATTTTAAAATA
Found at i:60801837 original size:21 final size:21
Alignment explanation
Indices: 60801785--60801837 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
60801775 AAAAAAACCT
* *
60801785 ATAAATATTTTAAATATTTTT
1 ATAAATATTATAAATATTTTA
* *
60801806 ATTAATTTTATAAAT-TTTTAA
1 ATAAATATTATAAATATTTT-A
60801827 ATAAATATTAT
1 ATAAATATTAT
60801838 TGTGAACCGA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATAAATATTATAAATATTTTA
Found at i:60803715 original size:3 final size:3
Alignment explanation
Indices: 60803707--60803772 Score: 89
Period size: 3 Copynumber: 22.0 Consensus size: 3
60803697 TAGAAGAGTC
* * *
60803707 TGA TGA TGA AGA TGA TGA TGA TGA TGA TGA TGA -GTC TGA TGG TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG-A TGA TGA TGA
60803752 TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA
60803773 AACAATGGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 1 0.02
3 53 0.96
4 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.35, T:0.32
Consensus pattern (3 bp):
TGA
Found at i:60808604 original size:5 final size:5
Alignment explanation
Indices: 60808594--60808619 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
60808584 TATTGATGCT
60808594 AATTA AATTA AATTA AATTA AATTA A
1 AATTA AATTA AATTA AATTA AATTA A
60808620 TATTTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATTA
Found at i:60815195 original size:2 final size:2
Alignment explanation
Indices: 60815188--60815239 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
60815178 ATTCTACAAA
60815188 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60815230 AT AT AT AT AT
1 AT AT AT AT AT
60815240 TCAGAATGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60815445 original size:2 final size:2
Alignment explanation
Indices: 60815438--60815483 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
60815428 ATTCTATAAA
60815438 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60815480 AT AT
1 AT AT
60815484 CATAACTACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60824979 original size:15 final size:15
Alignment explanation
Indices: 60824959--60824988 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
60824949 GATCTCCTGT
60824959 GGTTCAGGATGGGGC
1 GGTTCAGGATGGGGC
60824974 GGTTCAGGATGGGGC
1 GGTTCAGGATGGGGC
60824989 CATTGTAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.53, T:0.20
Consensus pattern (15 bp):
GGTTCAGGATGGGGC
Found at i:60827045 original size:27 final size:29
Alignment explanation
Indices: 60826992--60827052 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
60826982 ATAAAAATTA
*
60826992 TTTAAATTTTGTAAAAATAATTGTTATTT
1 TTTAAATTTTGTAAAAATAATTATTATTT
60827021 TTTAAA-TTT-TAAAAA-AATTAATTATTT
1 TTTAAATTTTGTAAAAATAATT-ATTATTT
*
60827048 GTTAA
1 TTTAA
60827053 TGTGACATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 4 0.14
27 16 0.55
28 3 0.10
29 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (29 bp):
TTTAAATTTTGTAAAAATAATTATTATTT
Found at i:60828786 original size:20 final size:19
Alignment explanation
Indices: 60828726--60828796 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 19
60828716 AAAACTATAA
60828726 ATTTTAGAATTTTTATAAA-T
1 ATTTT-GAATTTTTA-AAATT
60828746 ATTTTGAA-TTTTAAAATTT
1 ATTTTGAATTTTTAAAA-TT
60828765 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTT-AAAATT
60828785 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
60828797 TTTTGTAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.06
18 5 0.11
19 18 0.38
20 17 0.36
21 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAATT
Found at i:60832370 original size:31 final size:31
Alignment explanation
Indices: 60832325--60832396 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
60832315 TTTTTTATCT
*
60832325 AATTAGATACCTGAACTTGG-TTTCTTAGTTCA
1 AATTAG-TACCTGAACTTGGCTTT-TTAGTCCA
*
60832357 AATTGGTACCTGAACTTGGCTTTTTAGTCCA
1 AATTAGTACCTGAACTTGGCTTTTTAGTCCA
60832388 AATTAGTAC
1 AATTAGTAC
60832397 TTACAGTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 28 0.78
32 8 0.22
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (31 bp):
AATTAGTACCTGAACTTGGCTTTTTAGTCCA
Found at i:60837182 original size:111 final size:111
Alignment explanation
Indices: 60836959--60837174 Score: 315
Period size: 111 Copynumber: 1.9 Consensus size: 111
60836949 ATCTAAGATA
* * *
60836959 ACTCAAGACACATCATAACACTATTCTACTTAAGCTTATGACACCAAATCACTTGTCATTTATCT
1 ACTCAAGACACATCATAACACCATTCTACTTAAGCCTATGACACCAAATCACTTGTCATTTATCC
*
60837024 CTAATCTACCAATAGTAAATCAACACGTGACACCTCGAGACGAGAG
66 CTAATCTACCAATAGCAAATCAACACGTGACACCTCGAGACGAGAG
* * * *
60837070 ACTCAAGGCACGTCATAGCACCATTCTACTTAAGCCTATGACACCAGATCACTTGTCATTTATCC
1 ACTCAAGACACATCATAACACCATTCTACTTAAGCCTATGACACCAAATCACTTGTCATTTATCC
* * * * *
60837135 CTAGTTTACTAATAGCGAATCGACACGTGACACCTCGAGA
66 CTAATCTACCAATAGCAAATCAACACGTGACACCTCGAGA
60837175 TGGGAGACAA
Statistics
Matches: 92, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
111 92 1.00
ACGTcount: A:0.34, C:0.27, G:0.13, T:0.26
Consensus pattern (111 bp):
ACTCAAGACACATCATAACACCATTCTACTTAAGCCTATGACACCAAATCACTTGTCATTTATCC
CTAATCTACCAATAGCAAATCAACACGTGACACCTCGAGACGAGAG
Found at i:60840488 original size:26 final size:25
Alignment explanation
Indices: 60840432--60840505 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 25
60840422 TTTCTCACCC
60840432 CAATTTTACCCCAGTAAAATTTTGA
1 CAATTTTACCCCAGTAAAATTTTGA
*
60840457 CAATTTTACCCTC-GATAAGATTTTGA
1 CAATTTTACCC-CAG-TAAAATTTTGA
* *
60840483 CGATTTTACCCCCAATAAAATTT
1 CAATTTTA-CCCCAGTAAAATTT
60840506 CGAGAAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
25 12 0.29
26 26 0.63
27 3 0.07
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (25 bp):
CAATTTTACCCCAGTAAAATTTTGA
Found at i:60840662 original size:6 final size:6
Alignment explanation
Indices: 60840648--60840680 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
60840638 GGATTGCAAG
*
60840648 TTTCTA TTTCCA TTTCCA TTTCCA TTTCCA TTT
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTT
60840681 TTGGAAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.15, C:0.27, G:0.00, T:0.58
Consensus pattern (6 bp):
TTTCCA
Found at i:60842314 original size:21 final size:21
Alignment explanation
Indices: 60842290--60842333 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
60842280 ACAAATACAT
**
60842290 AATGAACAGGTTAAGTGCTAA
1 AATGAACAAATTAAGTGCTAA
60842311 AATGAACAAATTAAGTGCTAA
1 AATGAACAAATTAAGTGCTAA
60842332 AA
1 AA
60842334 CTCTCATATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.50, C:0.09, G:0.18, T:0.23
Consensus pattern (21 bp):
AATGAACAAATTAAGTGCTAA
Found at i:60843193 original size:134 final size:134
Alignment explanation
Indices: 60842953--60843221 Score: 520
Period size: 134 Copynumber: 2.0 Consensus size: 134
60842943 ATGCAAGATG
*
60842953 TCACATTATGTTGCCGAAGTAACTCGAATGTCTTTCGTTCATTAATTGGACTAAGAAATTAAATT
1 TCACATTATGTTGCCAAAGTAACTCGAATGTCTTTCGTTCATTAATTGGACTAAGAAATTAAATT
60843018 TAAAAACATTTGTACAAAATTATGGAAAATAAATAAAATAAACTATAGGACTTTAAAATCATTTT
66 TAAAAACATTTGTACAAAATTATGGAAAATAAATAAAATAAACTATAGGACTTTAAAATCATTTT
60843083 AAAA
131 AAAA
60843087 TCACATTATGTTGCCAAAGTAACTCGAATGTCTTTCGTTCATTAATTGGACTAAGAAATTAAATT
1 TCACATTATGTTGCCAAAGTAACTCGAATGTCTTTCGTTCATTAATTGGACTAAGAAATTAAATT
*
60843152 TAAAAACATTTGTACAAAATTATGGAAAATAAATAAAATAAATTATAGGACTTTAAAATCATTTT
66 TAAAAACATTTGTACAAAATTATGGAAAATAAATAAAATAAACTATAGGACTTTAAAATCATTTT
60843217 AAAA
131 AAAA
60843221 T
1 T
60843222 ACTTTAGAAT
Statistics
Matches: 133, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 133 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (134 bp):
TCACATTATGTTGCCAAAGTAACTCGAATGTCTTTCGTTCATTAATTGGACTAAGAAATTAAATT
TAAAAACATTTGTACAAAATTATGGAAAATAAATAAAATAAACTATAGGACTTTAAAATCATTTT
AAAA
Found at i:60847695 original size:50 final size:50
Alignment explanation
Indices: 60847620--60847720 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
60847610 TGCCCAGGCC
60847620 TGGCCTGGGAAAAATATCATAAGCCCGAGCCCGGCCCGGCCCGGCTCATT
1 TGGCCTGGGAAAAATATCATAAGCCCGAGCCCGGCCCGGCCCGGCTCATT
60847670 TGGCCTGGGAAAAATATCATAAGCCCGAGCCCGGCCCGGCCCGGCTCATT
1 TGGCCTGGGAAAAATATCATAAGCCCGAGCCCGGCCCGGCCCGGCTCATT
60847720 T
1 T
60847721 TTAAAATAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.22, C:0.34, G:0.28, T:0.17
Consensus pattern (50 bp):
TGGCCTGGGAAAAATATCATAAGCCCGAGCCCGGCCCGGCCCGGCTCATT
Found at i:60847751 original size:25 final size:25
Alignment explanation
Indices: 60847717--60847780 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 25
60847707 GGCCCGGCTC
* * *
60847717 ATTTTTAAAATAAACATTAAAAAAT
1 ATTTTAAAAATAAAAATAAAAAAAT
60847742 ATTTTAAAAATAAAAAAATAAAAAAAT
1 ATTTTAAAAAT--AAAAATAAAAAAAT
60847769 ATTTTAAAAATA
1 ATTTTAAAAATA
60847781 TTTTAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.32
27 23 0.68
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
ATTTTAAAAATAAAAATAAAAAAAT
Found at i:60847789 original size:10 final size:11
Alignment explanation
Indices: 60847763--60847788 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
60847753 AAAAAAATAA
60847763 AAAAATATTTT
1 AAAAATATTTT
60847774 AAAAATATTTT
1 AAAAATATTTT
60847785 AAAA
1 AAAA
60847789 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:60852059 original size:2 final size:2
Alignment explanation
Indices: 60852052--60852089 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
60852042 TCTTCGAACA
60852052 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60852090 TTACATGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60855282 original size:30 final size:31
Alignment explanation
Indices: 60855248--60855315 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 31
60855238 TGTGGCGATG
*
60855248 AGTAAATT-TACAATTTGATCACTCAATATT
1 AGTAAATTGTACAAGTTGATCACTCAATATT
* * * *
60855278 AGT-AATTGTACAAGTTGGTCATTGATTATT
1 AGTAAATTGTACAAGTTGATCACTCAATATT
60855308 AGTAAATT
1 AGTAAATT
60855316 CGTAAGTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 4 0.13
30 23 0.74
31 4 0.13
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (31 bp):
AGTAAATTGTACAAGTTGATCACTCAATATT
Found at i:60870028 original size:21 final size:20
Alignment explanation
Indices: 60869992--60870033 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 20
60869982 CTATTCATAC
60869992 ATTATAAAATATTAAA-AAA
1 ATTATAAAATATTAAATAAA
60870011 ATTATAATAATAATTAAATAAA
1 ATTATAA-AAT-ATTAAATAAA
60870033 A
1 A
60870034 ATATTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 3 0.15
21 6 0.30
22 4 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTATAAAATATTAAATAAA
Found at i:60878016 original size:16 final size:18
Alignment explanation
Indices: 60877986--60878020 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
60877976 GTTCAATTAA
60877986 ATAAATTATTAAAAAAAT
1 ATAAATTATTAAAAAAAT
60878004 ATAAA-TATTAAAAAAAT
1 ATAAATTATTAAAAAAAT
60878021 TAATAAGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAATTATTAAAAAAAT
Found at i:60881443 original size:31 final size:31
Alignment explanation
Indices: 60881408--60881477 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
60881398 ATTATAAAAT
*
60881408 AGTCATTAAAATATT-TAAAATTTTTTATTTA
1 AGTCATTAAAATATTCGAAAA-TTTTTATTTA
*
60881439 AGTCATTAAATTATTCGAAAATTTTTATTTA
1 AGTCATTAAAATATTCGAAAATTTTTATTTA
*
60881470 AGTTATTA
1 AGTCATTA
60881478 GGCAGTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (31 bp):
AGTCATTAAAATATTCGAAAATTTTTATTTA
Found at i:60882349 original size:14 final size:14
Alignment explanation
Indices: 60882328--60882361 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
60882318 TGGTATGAGT
60882328 TTAT-GGGTTTTAG
1 TTATAGGGTTTTAG
*
60882341 TTATAGGGTTTTGG
1 TTATAGGGTTTTAG
60882355 TTATAGG
1 TTATAGG
60882362 CAAATGATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTAG
Found at i:60891666 original size:2 final size:2
Alignment explanation
Indices: 60891659--60891688 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
60891649 GAGTCCTTCC
60891659 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
60891689 TAAAAAAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60895478 original size:19 final size:19
Alignment explanation
Indices: 60895433--60895479 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
60895423 AAATTATAAT
* *
60895433 TATTTTTAAATTTATAAAA
1 TATTTTTATATATATAAAA
*
60895452 -AGTATTTATATATATAAAA
1 TA-TTTTTATATATATAAAA
60895471 TATTTTTAT
1 TATTTTTAT
60895480 TTAATTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
18 1 0.05
19 20 0.91
20 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TATTTTTATATATATAAAA
Found at i:60896917 original size:33 final size:33
Alignment explanation
Indices: 60896847--60896920 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
60896837 TTAAAAGTTT
* * *
60896847 ATATAAAAACCAAATAATCCTATGTTTAAATCT
1 ATATAAAAACCAAATAACCCTATGTCTAAATCG
* *
60896880 ATATAAAAACCAAATAACCCTATGTCTGATTCG
1 ATATAAAAACCAAATAACCCTATGTCTAAATCG
60896913 ATATAAAA
1 ATATAAAA
60896921 TCAAACCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (33 bp):
ATATAAAAACCAAATAACCCTATGTCTAAATCG
Found at i:60899164 original size:21 final size:21
Alignment explanation
Indices: 60899138--60899177 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
60899128 AATCGAATCG
* *
60899138 AGTCGAGTGAAATGAAATTCA
1 AGTCGAGTCAAATCAAATTCA
60899159 AGTCGAGTCAAATCAAATT
1 AGTCGAGTCAAATCAAATT
60899178 GAGTGAAATT
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:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (21 bp):
AGTCGAGTCAAATCAAATTCA
Found at i:60899501 original size:19 final size:19
Alignment explanation
Indices: 60899435--60899502 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
60899425 TTTTATATAT
60899435 TTTTTAAAAATATGAATTTTGAA
1 TTTTTAAAAAT-T--ATTTTG-A
*
60899458 TTTTTTATAAA-TATTTTGA
1 -TTTTTAAAAATTATTTTGA
**
60899477 AATTTAAAAATTATTTTGA
1 TTTTTAAAAATTATTTTGA
60899496 TTTTTAA
1 TTTTTAA
60899503 TTTGTAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
18 7 0.19
19 14 0.38
20 6 0.16
22 1 0.03
24 9 0.24
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (19 bp):
TTTTTAAAAATTATTTTGA
Found at i:60912564 original size:64 final size:65
Alignment explanation
Indices: 60912479--60912611 Score: 223
Period size: 64 Copynumber: 2.1 Consensus size: 65
60912469 ATTTGTTTCT
*
60912479 TGAAGTACTCTTGTGTCTCACACTTGTATCCGTAGTATATCCTGATCCCAAAGACCCCAAATACA
1 TGAAGTACTCTTGCGTCTCACACTTGTATCCGTAGTATATCCTGATCCCAAAGACCCCAAATACA
* * *
60912544 TGAAGTCCTC-TGCGTCTCACACTTGTATCCGTAGTATATCCTGATTCCAAAGACTCCAAATACA
1 TGAAGTACTCTTGCGTCTCACACTTGTATCCGTAGTATATCCTGATCCCAAAGACCCCAAATACA
60912608 TGAA
1 TGAA
60912612 AAATCATATG
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
64 55 0.86
65 9 0.14
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.29
Consensus pattern (65 bp):
TGAAGTACTCTTGCGTCTCACACTTGTATCCGTAGTATATCCTGATCCCAAAGACCCCAAATACA
Found at i:60914055 original size:3 final size:3
Alignment explanation
Indices: 60914049--60914082 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
60914039 AAGAGTCTCG
60914049 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
60914083 ATAGCATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:60922635 original size:5 final size:5
Alignment explanation
Indices: 60922618--60922667 Score: 59
Period size: 5 Copynumber: 10.2 Consensus size: 5
60922608 CCCTGCATTG
* *
60922618 AGAAA AGGAAA AGAAA AG-AA A-AAA AGGAA AGCAA AGAAA AGAAA AGAAA
1 AGAAA A-GAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
60922667 A
1 A
60922668 CGAGAGTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
4 6 0.15
5 28 0.72
6 5 0.13
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:60922648 original size:18 final size:19
Alignment explanation
Indices: 60922620--60922667 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
60922610 CTGCATTGAG
60922620 AAAAGGAAAAGAAAAGAAA
1 AAAAGGAAAAGAAAAGAAA
*
60922639 AAAAGG-AAAGCAAAGAAA
1 AAAAGGAAAAGAAAAGAAA
*
60922657 AGAAAAGAAAA
1 A-AAAGGAAAA
60922668 CGAGAGTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 12 0.48
19 10 0.40
20 3 0.12
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (19 bp):
AAAAGGAAAAGAAAAGAAA
Found at i:60923510 original size:15 final size:15
Alignment explanation
Indices: 60923490--60923523 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
60923480 ACAAAAAATC
60923490 TATTGTGAATAGTCG
1 TATTGTGAATAGTCG
60923505 TATTGTGAATAGTCG
1 TATTGTGAATAGTCG
60923520 TATT
1 TATT
60923524 TTGTTACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.24, T:0.44
Consensus pattern (15 bp):
TATTGTGAATAGTCG
Found at i:60925100 original size:21 final size:22
Alignment explanation
Indices: 60925055--60925111 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
60925045 AATTATTGCT
*
60925055 TTTTGTTGTTGTTT-TTACTGC
1 TTTTGTTGTTGTTTGTCACTGC
*
60925076 TTTTGTTGTTGTTTGTCATTG-
1 TTTTGTTGTTGTTTGTCACTGC
* *
60925097 TTTTGGTGCTGTTTG
1 TTTTGTTGTTGTTTG
60925112 GCTATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.04, C:0.07, G:0.25, T:0.65
Consensus pattern (22 bp):
TTTTGTTGTTGTTTGTCACTGC
Found at i:60925207 original size:23 final size:23
Alignment explanation
Indices: 60925177--60925222 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
60925167 TTTATTGTTA
*
60925177 TTACTATTATTTTAGAGTTATTT
1 TTACTATTATTTTAGAGGTATTT
60925200 TTACTATTATTTTAGAGGTATTT
1 TTACTATTATTTTAGAGGTATTT
60925223 GCTTGATAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.59
Consensus pattern (23 bp):
TTACTATTATTTTAGAGGTATTT
Found at i:60929245 original size:22 final size:22
Alignment explanation
Indices: 60929164--60929238 Score: 132
Period size: 22 Copynumber: 3.4 Consensus size: 22
60929154 ATGGCAGAGT
*
60929164 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
60929186 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
60929208 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
*
60929230 ACGAACTAA
1 ACGTACTAA
60929239 ACCCTCAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:60932648 original size:29 final size:30
Alignment explanation
Indices: 60932595--60932653 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
60932585 GAATTGGATC
* *
60932595 AAATCAAAATTTTATGTATAAAATTGCACA
1 AAATCAAAATTTCATGTATAAAATTACACA
**
60932625 AAATCAAAA-TTCATGTATTCAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
60932654 TTAAACCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTACACA
Found at i:60932707 original size:6 final size:6
Alignment explanation
Indices: 60932696--60932723 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
60932686 TATCCCTAAA
60932696 TATAAT TATAAT TATAAT TATAAT TATA
1 TATAAT TATAAT TATAAT TATAAT TATA
60932724 TTCCAAACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATAAT
Found at i:60932889 original size:29 final size:29
Alignment explanation
Indices: 60932856--60932911 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
60932846 TTTGATCTCT
60932856 ATATTGTTATAATGTTATTAATTAGTTTA
1 ATATTGTTATAATGTTATTAATTAGTTTA
*
60932885 ATATTTTTATAATGTTATTAATTAGTT
1 ATATTGTTATAATGTTATTAATTAGTT
60932912 CAAATAGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (29 bp):
ATATTGTTATAATGTTATTAATTAGTTTA
Found at i:60942474 original size:5 final size:5
Alignment explanation
Indices: 60942464--60942488 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
60942454 TGGGACTTTC
60942464 AACGG AACGG AACGG AACGG AACGG
1 AACGG AACGG AACGG AACGG AACGG
60942489 CAAATGGCAA
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:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (5 bp):
AACGG
Found at i:60947028 original size:11 final size:11
Alignment explanation
Indices: 60947008--60947112 Score: 61
Period size: 11 Copynumber: 10.4 Consensus size: 11
60946998 CAAAAATTAA
60947008 AAAAAGTATTTT
1 AAAAA-TATTTT
60947020 AAAAATATTTT
1 AAAAATATTTT
60947031 --AAA-A--TT
1 AAAAATATTTT
* *
60947037 AAAAA-AATTA
1 AAAAATATTTT
60947047 AAAAAGTATTTT
1 AAAAA-TATTTT
**
60947059 AAAAA-AAATT
1 AAAAATATTTT
60947069 --AAA-ATTTT
1 AAAAATATTTT
*
60947077 AAAAAT-TTTA
1 AAAAATATTTT
60947087 AAAAATATTTT
1 AAAAATATTTT
*
60947098 AAAAGTATTTT
1 AAAAATATTTT
60947109 AAAA
1 AAAA
60947113 TAAAAAAATA
Statistics
Matches: 73, Mismatches: 10, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
6 2 0.03
8 11 0.15
9 3 0.04
10 21 0.29
11 23 0.32
12 13 0.18
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:60947053 original size:39 final size:39
Alignment explanation
Indices: 60946981--60947126 Score: 156
Period size: 40 Copynumber: 3.7 Consensus size: 39
60946971 ATCAAAAATT
60946981 TATTTTAAAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT--AA-AAAAATT-AAAAAAGTATTTTAAAAA
60947025 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
** ** *
60947064 -AAATTAAAATTTTAAAAATTTTAAAAAA-TATTTTAAAAG
1 TATTTTAAAA--TTAAAAAAATTAAAAAAGTATTTTAAAAA
60947103 TATTTTAAAA-TAAAAAAA-TAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAA
60947127 TATTTATTAT
Statistics
Matches: 90, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
36 6 0.07
37 6 0.07
38 7 0.08
39 28 0.31
40 29 0.32
41 2 0.02
43 6 0.07
44 6 0.07
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (39 bp):
TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
Found at i:60947114 original size:21 final size:20
Alignment explanation
Indices: 60947015--60947112 Score: 55
Period size: 21 Copynumber: 5.0 Consensus size: 20
60947005 TAAAAAAAGT
60947015 ATTTTAAAAATATTTT-AAA
1 ATTTTAAAAATATTTTAAAA
* **
60947034 A--TTAAAAAAATTAAAAAA
1 ATTTTAAAAATATTTTAAAA
**
60947052 GTATTTTAAAAA-AAATT-AAA
1 --ATTTTAAAAATATTTTAAAA
*
60947072 ATTTTAAAAAT-TTTAAAAAA
1 ATTTTAAAAATATTT-TAAAA
*
60947092 TATTTTAAAAGTATTTTAAAA
1 -ATTTTAAAAATATTTTAAAA
60947113 TAAAAAAATA
Statistics
Matches: 57, Mismatches: 12, Indels: 18
0.66 0.14 0.21
Matches are distributed among these distances:
17 10 0.18
18 14 0.25
19 1 0.02
20 7 0.12
21 15 0.26
22 10 0.18
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
ATTTTAAAAATATTTTAAAA
Found at i:60947742 original size:3 final size:3
Alignment explanation
Indices: 60947736--60947773 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
60947726 GCAACTAAGG
60947736 GAA GAA GAA GAA GAA GAA GAA GAA G-A GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
60947774 TATTGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:60947924 original size:3 final size:3
Alignment explanation
Indices: 60947916--60947951 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
60947906 TTACAGTCTA
*
60947916 TTC TTC TTC TTC TTC TT- TTC CTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
60947952 GTTATTAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:60949454 original size:30 final size:30
Alignment explanation
Indices: 60949420--60949482 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
60949410 ACTTATTTTA
*
60949420 TTGTTAATTTTGTTATTATTTTA-ATGGCAT
1 TTGTTAATTTTGCTATTATTTTAGA-GGCAT
60949450 TTGTTAATTTTGCTATTATTTTAGAGGCAT
1 TTGTTAATTTTGCTATTATTTTAGAGGCAT
60949480 TTG
1 TTG
60949483 CTTGTTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.22, C:0.05, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGCTATTATTTTAGAGGCAT
Found at i:60952963 original size:23 final size:23
Alignment explanation
Indices: 60952937--60952981 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
60952927 GATCCTTGCA
* *
60952937 ATTACTTTAAAATTTTTTTTGTC
1 ATTACTTGAAAATTTTATTTGTC
* *
60952960 ATTAGTTGAATATTTTATTTGT
1 ATTACTTGAAAATTTTATTTGT
60952982 AAAATATCCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.04, G:0.09, T:0.60
Consensus pattern (23 bp):
ATTACTTGAAAATTTTATTTGTC
Found at i:60962083 original size:23 final size:23
Alignment explanation
Indices: 60962047--60962090 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
60962037 GAAAAATATT
60962047 AAATATATA-TTTTTTATTTTTA
1 AAATATATATTTTTTTATTTTTA
60962069 AAATATAATATTTTTTTATTTT
1 AAATAT-ATATTTTTTTATTTT
60962091 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
AAATATATATTTTTTTATTTTTA
Found at i:60962220 original size:59 final size:57
Alignment explanation
Indices: 60962157--60962280 Score: 212
Period size: 59 Copynumber: 2.1 Consensus size: 57
60962147 TCAAATTTGT
*
60962157 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATT-A-ACAATTAATAATTTGATAAA
*
60962216 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAACAATTAATAATTTGATAAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAACAATTAATAATTTGATAAA
60962273 TTTACTAA
1 TTTACTAA
60962281 CAATTAATTT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
57 27 0.43
58 1 0.02
59 35 0.56
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.42
Consensus pattern (57 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAACAATTAATAATTTGATAAA
Found at i:60962290 original size:16 final size:16
Alignment explanation
Indices: 60962269--60962310 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
60962259 AATAATTTGA
*
60962269 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
60962285 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
60962301 TAGTTTTAAT
1 TAATTTTAAT
60962311 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:60962294 original size:22 final size:23
Alignment explanation
Indices: 60962284--60962339 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
60962274 TTACTAACAA
* * *
60962284 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
60962306 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
60962329 TTAATTTTAAT
1 TTAATTTTAAT
60962340 TTTAGTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:60966404 original size:30 final size:30
Alignment explanation
Indices: 60966368--60966434 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
60966358 TAGTGATTTG
*
60966368 TGAAAATTGAATC-AAATCAAAATTTTATGTA
1 TGAAAATCGAA-CAAAATCAAAA-TTTATGTA
* *
60966399 T-AAAATCGCACAAAATCAATATTTATGTA
1 TGAAAATCGAACAAAATCAAAATTTATGTA
60966428 TGAAAAT
1 TGAAAAT
60966435 AGATATTAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 10 0.32
30 20 0.65
31 1 0.03
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (30 bp):
TGAAAATCGAACAAAATCAAAATTTATGTA
Found at i:60967702 original size:21 final size:20
Alignment explanation
Indices: 60967645--60967703 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
60967635 ATAAAACAAC
* *
60967645 TAAAAAACGATTGAATCGCT
1 TAAAAAACCATTGAATCGAT
* * *
60967665 AAAAAAATCAATCGAATCGAT
1 TAAAAAA-CCATTGAATCGAT
60967686 TAAAAAACCAGTTGAATC
1 TAAAAAACCA-TTGAATC
60967704 AAATTAAAAG
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 8 0.27
21 22 0.73
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.22
Consensus pattern (20 bp):
TAAAAAACCATTGAATCGAT
Found at i:60968837 original size:2 final size:2
Alignment explanation
Indices: 60968832--60968863 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
60968822 AAAATGACAA
60968832 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
60968864 CTTACCGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60969270 original size:12 final size:12
Alignment explanation
Indices: 60969253--60969279 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
60969243 ATTAAGGGGC
60969253 TGTATTTATATA
1 TGTATTTATATA
60969265 TGTATTTATATA
1 TGTATTTATATA
60969277 TGT
1 TGT
60969280 TGGAGGTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (12 bp):
TGTATTTATATA
Found at i:60970483 original size:27 final size:28
Alignment explanation
Indices: 60970453--60970516 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
60970443 TATTAATATA
* *
60970453 AATTTAAATATGATAATTAGAATA-TTT
1 AATTTAAATATGAAAATTACAATACTTT
* *
60970480 AATTTAAAAATGAAAATTTCAATACTTT
1 AATTTAAATATGAAAATTACAATACTTT
*
60970508 AATTAAAAT
1 AATTTAAAT
60970517 TACATCATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 20 0.67
28 10 0.33
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.41
Consensus pattern (28 bp):
AATTTAAATATGAAAATTACAATACTTT
Found at i:60976183 original size:3 final size:3
Alignment explanation
Indices: 60976175--60976200 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
60976165 AATAAGTGTT
60976175 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
60976201 CAATCATCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:60976460 original size:26 final size:28
Alignment explanation
Indices: 60976429--60976494 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 28
60976419 TGATTAAGAT
*
60976429 ATAATATTATT-ATATTTTATTATTT-TA
1 ATAATATTATTCATA-GTTATTATTTATA
*
60976456 A-AATATTTTTCATAGTTATTATTTACTA
1 ATAATATTATTCATAGTTATTATTTA-TA
60976484 ATAATATTATT
1 ATAATATTATT
60976495 TTAAATCATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 17 0.53
27 4 0.12
28 3 0.09
29 8 0.25
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (28 bp):
ATAATATTATTCATAGTTATTATTTATA
Found at i:60977233 original size:34 final size:35
Alignment explanation
Indices: 60977189--60977255 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
60977179 CAGTAAAATG
60977189 TTTTCCGTAAAATGATTT-CTGAAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
* *
60977223 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
60977256 CTGGTATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:60977358 original size:20 final size:20
Alignment explanation
Indices: 60977333--60977384 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
60977323 GGAAAAGTTG
60977333 TTTTTACATATATT-AATAAA
1 TTTTTACATATATTAAAT-AA
* *
60977353 TTTTT--ATATTTTAAATTA
1 TTTTTACATATATTAAATAA
60977371 TTTTTACATATATT
1 TTTTTACATATATT
60977385 GCAATGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 12 0.46
19 3 0.12
20 11 0.42
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTACATATATTAAATAA
Found at i:60978099 original size:22 final size:22
Alignment explanation
Indices: 60978074--60978118 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
60978064 TTGAATTTGG
60978074 ATCTTCAAAGTTTGGAACCTCA
1 ATCTTCAAAGTTTGGAACCTCA
60978096 ATCTTCAAAGTTTGGAACCTCA
1 ATCTTCAAAGTTTGGAACCTCA
60978118 A
1 A
60978119 CCTTTGCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.31
Consensus pattern (22 bp):
ATCTTCAAAGTTTGGAACCTCA
Found at i:60979075 original size:12 final size:13
Alignment explanation
Indices: 60979053--60979081 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
60979043 GAAGTAGAAG
60979053 AGAATGAAAAAAA
1 AGAATGAAAAAAA
60979066 AGAA-GAAAAAAA
1 AGAATGAAAAAAA
60979078 AGAA
1 AGAA
60979082 AAGTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (13 bp):
AGAATGAAAAAAA
Found at i:60984646 original size:31 final size:31
Alignment explanation
Indices: 60984608--60984718 Score: 88
Period size: 31 Copynumber: 3.7 Consensus size: 31
60984598 TTGGCCAAAA
*
60984608 AAAAGTTTAAGCCCCAATGTGGAAACAATTG
1 AAAAGTTCAAGCCCCAATGTGGAAACAATTG
* * * *
60984639 AAAAGTTTAAGGCCTAATTTGGAAA-AA---
1 AAAAGTTCAAGCCCCAATGTGGAAACAATTG
* *
60984666 AAAAGTTCAGGCCCCAATATAGG-AACAATTG
1 AAAAGTTCAAGCCCCAATGT-GGAAACAATTG
** *
60984697 CCAAGTTCAGGCCCCAATGTGG
1 AAAAGTTCAAGCCCCAATGTGG
60984719 GTATAGTTGT
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
27 17 0.27
28 4 0.06
30 4 0.06
31 39 0.61
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.22
Consensus pattern (31 bp):
AAAAGTTCAAGCCCCAATGTGGAAACAATTG
Found at i:60990403 original size:14 final size:14
Alignment explanation
Indices: 60990384--60990413 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
60990374 ACACCAACGT
60990384 TCACTTAATTTTAA
1 TCACTTAATTTTAA
60990398 TCACTTAATTTTAA
1 TCACTTAATTTTAA
60990412 TC
1 TC
60990414 TCTACAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (14 bp):
TCACTTAATTTTAA
Found at i:60990916 original size:16 final size:16
Alignment explanation
Indices: 60990897--60990951 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
60990887 TAATTAAAGG
*
60990897 TTTAAATTATTTTAAA
1 TTTAAATTAATTTAAA
* * *
60990913 TTTAGATTAATATAAT
1 TTTAAATTAATTTAAA
* *
60990929 TTTTAATCAATTTAAA
1 TTTAAATTAATTTAAA
60990945 TTTAAAT
1 TTTAAAT
60990952 CGTAATTTTT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (16 bp):
TTTAAATTAATTTAAA
Found at i:60992523 original size:3 final size:3
Alignment explanation
Indices: 60992515--60992547 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
60992505 ATTACTCTTC
*
60992515 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
60992548 CTGTCTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:60995310 original size:18 final size:22
Alignment explanation
Indices: 60995267--60995312 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
60995257 CCTGCTTTTT
60995267 TCAAGTTCGGATCTTTTTGAGC
1 TCAAGTTCGGATCTTTTTGAGC
60995289 TCAAGTTC-GAT-TTTTTG-G-
1 TCAAGTTCGGATCTTTTTGAGC
60995307 TCAAGT
1 TCAAGT
60995313 CAAGTTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.25
19 1 0.04
20 6 0.25
21 3 0.12
22 8 0.33
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (22 bp):
TCAAGTTCGGATCTTTTTGAGC
Found at i:60998126 original size:16 final size:16
Alignment explanation
Indices: 60998102--60998151 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
60998092 AATTTTACCA
*
60998102 TTATTAATTTAAAATT
1 TTATAAATTTAAAATT
60998118 TTATAAATTATAAAA-T
1 TTATAAATT-TAAAATT
* *
60998134 ATCTAAA-TTAAAATT
1 TTATAAATTTAAAATT
60998149 TTA
1 TTA
60998152 CCATTTTAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 5 0.19
15 3 0.11
16 14 0.52
17 5 0.19
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATAAATTTAAAATT
Found at i:61000241 original size:90 final size:91
Alignment explanation
Indices: 61000037--61000242 Score: 213
Period size: 90 Copynumber: 2.3 Consensus size: 91
61000027 AACTTGTAAC
* ** * *
61000037 TATTCTCATATTGGGATTTAAA-TTTTTTTTAGTTCAAGTTAGGCTCTAAACTTGTCAATTGTTT
1 TATTCTCACATTGGGGCTTAAACTTTTTTTTAGTCCAAGTTAGGCTCTAAACTTGGCAATTGTTT
* *
61000101 CCGTATTAGGGCCTGAACTGAACAAT
66 CCATATTAGGGCCTGAACTGAACAAA
* * ** * * * *
61000127 TATTCCCACACTGACGCTTGAACTTTTTTTT-GTCCAAGTTAGTCTTTGAACTTGGCAATTG-TT
1 TATTCTCACATTGGGGCTTAAACTTTTTTTTAGTCCAAGTTAGGCTCTAAACTTGGCAATTGTTT
* *
61000190 CCTATATTTGGGCCTGAACTTG-GCAAA
66 CC-ATATTAGGGCCTGAAC-TGAACAAA
61000217 TATTCTCACATTGGGGCTTAAACTTT
1 TATTCTCACATTGGGGCTTAAACTTT
61000243 AAGGTTTTCA
Statistics
Matches: 91, Mismatches: 22, Indels: 6
0.76 0.18 0.05
Matches are distributed among these distances:
89 4 0.04
90 77 0.85
91 10 0.11
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (91 bp):
TATTCTCACATTGGGGCTTAAACTTTTTTTTAGTCCAAGTTAGGCTCTAAACTTGGCAATTGTTT
CCATATTAGGGCCTGAACTGAACAAA
Found at i:61006989 original size:15 final size:15
Alignment explanation
Indices: 61006971--61007000 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
61006961 AATATTAATG
61006971 ATTAAAATATAATAA
1 ATTAAAATATAATAA
*
61006986 ATTAAAATTTAATAA
1 ATTAAAATATAATAA
61007001 CCAAAATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATTAAAATATAATAA
Found at i:61012607 original size:16 final size:17
Alignment explanation
Indices: 61012576--61012607 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
61012566 AATTTGCTCA
61012576 ATTCAAACCTAAAAACG
1 ATTCAAACCTAAAAACG
61012593 ATTCAAACC-AAAAAC
1 ATTCAAACCTAAAAAC
61012608 AACTCGAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.16
Consensus pattern (17 bp):
ATTCAAACCTAAAAACG
Found at i:61015599 original size:24 final size:24
Alignment explanation
Indices: 61015572--61015618 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
61015562 TGAATATTAC
61015572 AAGATATAGAAAAGTAAT-TAAATT
1 AAGAT-TAGAAAAGTAATATAAATT
**
61015596 AAGATTTTAAAAGTAATATAAAT
1 AAGATTAGAAAAGTAATATAAAT
61015619 AGATTGATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (24 bp):
AAGATTAGAAAAGTAATATAAATT
Found at i:61018634 original size:16 final size:16
Alignment explanation
Indices: 61018613--61018646 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61018603 GACACTTTAA
* *
61018613 TTTTTGAGGACACATT
1 TTTTTGAAGAAACATT
61018629 TTTTTGAAGAAACATT
1 TTTTTGAAGAAACATT
61018645 TT
1 TT
61018647 GATTCCAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (16 bp):
TTTTTGAAGAAACATT
Found at i:61020680 original size:50 final size:47
Alignment explanation
Indices: 61020612--61020713 Score: 132
Period size: 50 Copynumber: 2.1 Consensus size: 47
61020602 ACAAATAATA
*
61020612 TAAACAAATATTTATATTTATGTAAAACACCATATCTAAACAAAACAAAT
1 TAAATAAATATTTATATTTATGTAAAACACCATATCT-AA-AAAAC-AAT
* * * *
61020662 TAAATAAATATTTATATTTTTTTAAAACATCATATCTGAAAAACAAT
1 TAAATAAATATTTATATTTATGTAAAACACCATATCTAAAAAACAAT
61020709 TAAAT
1 TAAAT
61020714 CGATGCTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
47 8 0.17
48 5 0.11
49 1 0.02
50 33 0.70
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.35
Consensus pattern (47 bp):
TAAATAAATATTTATATTTATGTAAAACACCATATCTAAAAAACAAT
Found at i:61021940 original size:19 final size:19
Alignment explanation
Indices: 61021893--61021952 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 19
61021883 TACAACACCA
*
61021893 AAAAAGTATATATTTAATAT
1 AAAAAGTATATATTTGAT-T
* *
61021913 ATATA-TATATATTTGATT
1 AAAAAGTATATATTTGATT
61021931 AAAAAG--TATATTTGATT
1 AAAAAGTATATATTTGATT
61021948 AAAAA
1 AAAAA
61021953 TAAATATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
17 16 0.47
18 4 0.12
19 11 0.32
20 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.42
Consensus pattern (19 bp):
AAAAAGTATATATTTGATT
Found at i:61021959 original size:18 final size:17
Alignment explanation
Indices: 61021920--61021952 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
61021910 TATATATATA
61021920 TATATTTGATTAAAAAG
1 TATATTTGATTAAAAAG
61021937 TATATTTGATTAAAAA
1 TATATTTGATTAAAAA
61021953 TAAATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATTTGATTAAAAAG
Found at i:61027268 original size:21 final size:20
Alignment explanation
Indices: 61027231--61027269 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
61027221 TATTTAACCA
* *
61027231 TTTTATAATTTTTATAATAT
1 TTTTAAAATTTTAATAATAT
61027251 TTTTAAAACTTTTAATAAT
1 TTTTAAAA-TTTTAATAAT
61027270 TTATTTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAAAATTTTAATAATAT
Found at i:61032426 original size:51 final size:51
Alignment explanation
Indices: 61032362--61032474 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 51
61032352 ATTGGTATAA
* * *
61032362 TAATAAATTTAG-CCTTCAAAATTTACACATTTTGTCAATTTGGTCATGATT
1 TAATAAATTTAGCCCGT-AAAATTTACACATTCTGTCAATTTAGTCATGATT
* * * *
61032413 TAATAAATTTAGCCCGTAATATTTATATATTCTGTCAATTTAGTCTTGATT
1 TAATAAATTTAGCCCGTAAAATTTACACATTCTGTCAATTTAGTCATGATT
*
61032464 TAACAAATTTA
1 TAATAAATTTA
61032475 TCTCACAACA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 50 0.94
52 3 0.06
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (51 bp):
TAATAAATTTAGCCCGTAAAATTTACACATTCTGTCAATTTAGTCATGATT
Found at i:61034162 original size:15 final size:14
Alignment explanation
Indices: 61034120--61034174 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
61034110 TCTTTGAAAA
*
61034120 TTTAAAATTTAA-T
1 TTTAAATTTTAATT
* *
61034133 TTTATATTTTTATT
1 TTTAAATTTTAATT
61034147 TTTAAAATTTTAATT
1 TTT-AAATTTTAATT
61034162 TTGTAAATTTTAA
1 TT-TAAATTTTAA
61034175 AATTTAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
13 9 0.26
14 4 0.12
15 20 0.59
16 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TTTAAATTTTAATT
Found at i:61043333 original size:18 final size:17
Alignment explanation
Indices: 61043310--61043343 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
61043300 AATAAATTAT
61043310 TAAAAAAATTCATAAAAA
1 TAAAAAAATT-ATAAAAA
61043328 TAAAAAAATTATAAAA
1 TAAAAAAATTATAAAA
61043344 TTAGGTTCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAAAAAATTATAAAAA
Found at i:61047410 original size:27 final size:28
Alignment explanation
Indices: 61047371--61047428 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
61047361 TCTGATCAGG
61047371 CAAATTAAATTGGCT-GCACCAAAGGTGC
1 CAAATTAAATTGG-TGGCACCAAAGGTGC
*
61047399 CAAA-TAAATTGGTGGCACCAATGGTGC
1 CAAATTAAATTGGTGGCACCAAAGGTGC
61047426 CAA
1 CAA
61047429 TGTGATTGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 1 0.04
27 23 0.82
28 4 0.14
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (28 bp):
CAAATTAAATTGGTGGCACCAAAGGTGC
Found at i:61047871 original size:37 final size:37
Alignment explanation
Indices: 61047824--61047894 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
61047814 AGTATTACTT
*
61047824 AATATTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
61047861 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
61047895 AAAAAAATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:61047899 original size:19 final size:19
Alignment explanation
Indices: 61047830--61047898 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
61047820 ACTTAATATT
61047830 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
61047849 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
61047867 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
61047886 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
61047899 AAATGAGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 20 0.47
19 23 0.53
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:61048031 original size:27 final size:27
Alignment explanation
Indices: 61047975--61048059 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
61047965 TTTTTTTCCT
* *
61047975 TTGGCACCA-TGGTGCCGCCAA-TCACA
1 TTGGCACCATTGGTGCCACCAATTTA-A
* *
61048001 TTGGCACCATTGGTGCCACCGATTTAT
1 TTGGCACCATTGGTGCCACCAATTTAA
* *
61048028 TTGGCACCTTTGGTGCCGCCAATTTAA
1 TTGGCACCATTGGTGCCACCAATTTAA
61048055 TTGGC
1 TTGGC
61048060 CTGATTAGGT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
26 9 0.18
27 38 0.78
28 2 0.04
ACGTcount: A:0.19, C:0.28, G:0.24, T:0.29
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCACCAATTTAA
Found at i:61053564 original size:83 final size:81
Alignment explanation
Indices: 61053361--61053650 Score: 243
Period size: 83 Copynumber: 3.5 Consensus size: 81
61053351 GCCAAAAGGT
*
61053361 TTAAACTTTATTCATACAAACCCTCCCAATTTCCCTAACAAATT-AAATAACAAATAAAAAC-TT
1 TTAAAC-TT-TTCATACAAA--C-CCCAATTTCCCTAAC-AATTCAAATAACAAATCAAAACTTT
** *
61053424 GATCTTAATCAAGACCCAAAGG
60 GATCTTAATCAAGACAAAAAGC
* *
61053446 TTAAACTTTTCATACAAACCCCAAATTTCCCTAACAATTCAAATAACAAATCAGAACTTTGGTCT
1 TTAAACTTTTCATACAAACCCC-AATTTCCCTAACAATTCAAATAACAAATCAAAACTTTGATCT
*
61053511 TAATCAAGGCTAAAAAGC
65 TAATCAAGAC-AAAAAGC
* * * * *
61053529 TTACA-TTGTTCATTCAAACCCACAATTTCCATAACAATTCGAATAA-ACAATCAAAAC-TTGGT
1 TTAAACTT-TTCATACAAACCC-CAATTTCCCTAACAATTCAAATAACA-AATCAAAACTTTGAT
* * * *
61053591 TTTATTCAA-AGC-CAAAGT
63 CTTAATCAAGA-CAAAAAGC
61053609 TTAAACTTTTTTCATACAAACCCCACAATTTCCCTAACAATT
1 TTAAAC--TTTTCATACAAA-CCC-CAATTTCCCTAACAATT
61053651 AAGACCAAAA
Statistics
Matches: 173, Mismatches: 20, Indels: 26
0.79 0.09 0.12
Matches are distributed among these distances:
80 15 0.09
81 28 0.16
82 40 0.23
83 81 0.47
84 3 0.02
85 6 0.03
ACGTcount: A:0.41, C:0.23, G:0.06, T:0.30
Consensus pattern (81 bp):
TTAAACTTTTCATACAAACCCCAATTTCCCTAACAATTCAAATAACAAATCAAAACTTTGATCTT
AATCAAGACAAAAAGC
Found at i:61053809 original size:84 final size:81
Alignment explanation
Indices: 61053646--61053938 Score: 278
Period size: 79 Copynumber: 3.6 Consensus size: 81
61053636 ATTTCCCTAA
* * ** * * *
61053646 CAATTAAGACCAAAAGG-TTAAACATTTCATACAAACCCCCCAATTTCCCTAACAATTCC-AAT-
1 CAATCAAGGCCAAAAGGTTTAAATTTTTCATACAAA--CCCCAATTTCCTTCACGA-TCCAAATA
* *
61053708 AACAAATCAGAACTTGGTCT
63 AAC-AATCAGAATTTGGTTT
61053728 CAATCAAGGCCAAAAGGTTTAAAATTTTTTCATACAAACCCTCAATTTCCTTCACGATCCAAATA
1 CAATCAAGGCCAAAAGGTTT-AAA-TTTTTCATACAAACCC-CAATTTCCTTCACGATCCAAATA
*
61053793 AACAATCAAAATTTGGTTT
63 AACAATCAGAATTTGGTTT
* * * * * *
61053812 CAATCAAAGCC-AAA-GTTTGAACTTCTAATAC-AACCCACAATTTCCTTCACGATTCAAATAAA
1 CAATCAAGGCCAAAAGGTTTAAATTTTTCATACAAACCC-CAATTTCCTTCACGATCCAAATAAA
*
61053874 CAATCAGGACTTT-GTTT
65 CAATCA-GAATTTGGTTT
61053891 CAATCAAGGCCAAAAGG-TTAAACTTTTTCATACAAACCCCTAATTTCC
1 CAATCAAGGCCAAAAGGTTTAAA-TTTTTCATACAAACCCC-AATTTCC
61053939 CTAACAATTC
Statistics
Matches: 175, Mismatches: 24, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
79 49 0.28
80 18 0.10
81 11 0.06
82 31 0.18
83 11 0.06
84 41 0.23
85 14 0.08
ACGTcount: A:0.39, C:0.25, G:0.08, T:0.28
Consensus pattern (81 bp):
CAATCAAGGCCAAAAGGTTTAAATTTTTCATACAAACCCCAATTTCCTTCACGATCCAAATAAAC
AATCAGAATTTGGTTT
Found at i:61053821 original size:219 final size:217
Alignment explanation
Indices: 61053434--61053835 Score: 581
Period size: 219 Copynumber: 1.8 Consensus size: 217
61053424 GATCTTAATC
* *
61053434 AAGACCCAAAGGTTAAACTTTTCATACAAACCCCAAATTTCCCTAACAATTCAAATAACAAATCA
1 AAGACCAAAAGGTTAAACATTTCATACAAACCCCAAATTTCCCTAACAATTCAAATAACAAATCA
* * * *
61053499 GAACTTTGGTCTTAATCAAGGCTAAAAAGCTTACATTGTTCATTCAAACCCACAATTTCCATAAC
66 GAACTTTGGTCTCAATCAAGGCCAAAAAGCTTAAATTGTTCATACAAACCCACAATTTCCATAAC
* * * *
61053564 AATTCGAATAAACAATCAAAACTTGGTTTTATTCAAAGCCAAAGTTTAAACTTTTTTCATACAAA
131 AATCCAAATAAACAATCAAAACTTGGTTTCAATCAAAGCCAAAGTTTAAACTTTTTTCATACAAA
61053629 CCCCACAATTTCCCTAACAATT
196 CCCCACAATTTCCCTAACAATT
* *
61053651 AAGACCAAAAGGTTAAACATTTCATACAAACCCCCCAATTTCCCTAACAATTCCAATAACAAATC
1 AAGACCAAAAGGTTAAACATTTCATACAAA-CCCCAAATTTCCCTAACAATTCAAATAACAAATC
* * * * *
61053716 AGAAC-TTGGTCTCAATCAAGGCCAAAAGGTTTAAAATTTTTTCATACAAACCCTCAATTTCCTT
65 AGAACTTTGGTCTCAATCAAGGCCAAAAAGCTT-AAA-TTGTTCATACAAACCCACAATTTCCAT
* * * *
61053780 CACGATCCAAATAAACAATCAAAATTTGGTTTCAATCAAAGCCAAAGTTTGAACTT
128 AACAATCCAAATAAACAATCAAAACTTGGTTTCAATCAAAGCCAAAGTTTAAACTT
61053836 CTAATACAAC
Statistics
Matches: 161, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
217 51 0.32
218 39 0.24
219 71 0.44
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.28
Consensus pattern (217 bp):
AAGACCAAAAGGTTAAACATTTCATACAAACCCCAAATTTCCCTAACAATTCAAATAACAAATCA
GAACTTTGGTCTCAATCAAGGCCAAAAAGCTTAAATTGTTCATACAAACCCACAATTTCCATAAC
AATCCAAATAAACAATCAAAACTTGGTTTCAATCAAAGCCAAAGTTTAAACTTTTTTCATACAAA
CCCCACAATTTCCCTAACAATT
Found at i:61057753 original size:12 final size:11
Alignment explanation
Indices: 61057726--61057768 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
61057716 GATAAATGTT
*
61057726 ATTTAATTAAG
1 ATTTTATTAAG
61057737 ATTTTATTAAG
1 ATTTTATTAAG
* *
61057748 ATTTTTAGTAAT
1 A-TTTTATTAAG
61057760 ATTTTATTA
1 ATTTTATTA
61057769 TTAAATGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (11 bp):
ATTTTATTAAG
Found at i:61062680 original size:2 final size:2
Alignment explanation
Indices: 61062673--61062697 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61062663 ACTATCTTCA
61062673 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
61062698 AAACTATAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61063306 original size:4 final size:4
Alignment explanation
Indices: 61063291--61063327 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
61063281 CTGGTATGCA
* *
61063291 TATG TGTG TATG TATG TATG TATT TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
61063328 TTTTTAATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.54
Consensus pattern (4 bp):
TATG
Found at i:61069595 original size:14 final size:14
Alignment explanation
Indices: 61069575--61069617 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
61069565 AAATTAAATG
61069575 AATTAAATTTCTAAA
1 AATTAAATTT-TAAA
* * *
61069590 AATAAAAGTATAAA
1 AATTAAATTTTAAA
61069604 AATTAAATTTTAAA
1 AATTAAATTTTAAA
61069618 TCCTCAAAGA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (14 bp):
AATTAAATTTTAAA
Found at i:61074650 original size:3 final size:3
Alignment explanation
Indices: 61074642--61074681 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
61074632 GCCATCAGAA
61074642 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
61074682 CAGAAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:61090846 original size:31 final size:31
Alignment explanation
Indices: 61090779--61090838 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
61090769 TTTAGTATCT
** *
61090779 AAGTTTAGCTTCAATGTTCAATTTGGTACTC
1 AAGTTTAGCTTCAACATTCAATTCGGTACTC
*
61090810 AAGTTTGGCTTCAACATTCAATTCGGTAC
1 AAGTTTAGCTTCAACATTCAATTCGGTAC
61090839 CTGAGTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (31 bp):
AAGTTTAGCTTCAACATTCAATTCGGTACTC
Found at i:61095949 original size:13 final size:13
Alignment explanation
Indices: 61095931--61095965 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
61095921 TTTGATATAG
61095931 AAATGATATGATT
1 AAATGATATGATT
61095944 AAATGATATGATT
1 AAATGATATGATT
61095957 AAATGATAT
1 AAATGATAT
61095966 TTTTTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (13 bp):
AAATGATATGATT
Found at i:61097481 original size:16 final size:15
Alignment explanation
Indices: 61097455--61097485 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
61097445 AGGTGCTCAT
61097455 GGGTTGGGCCGGGCC
1 GGGTTGGGCCGGGCC
61097470 GGGTTCGGGCCGGGCC
1 GGGTT-GGGCCGGGCC
61097486 ATAAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.00, C:0.29, G:0.58, T:0.13
Consensus pattern (15 bp):
GGGTTGGGCCGGGCC
Found at i:61097635 original size:21 final size:20
Alignment explanation
Indices: 61097609--61097740 Score: 106
Period size: 20 Copynumber: 6.3 Consensus size: 20
61097599 AATAAATACC
*
61097609 AAAAAATTATTTTAAAAATT
1 AAAAAAATATTTTAAAAATT
61097629 AAAAAAAGTATTTTAAAAATATT
1 AAAAAAA-TATTTT-AAAA-ATT
**
61097652 TTAAAAATATTTT-AAAATT
1 AAAAAAATATTTTAAAAATT
*
61097671 AAATTAAAAAATTTTAAAAAGTATT
1 AAA--AAAATATTTT-AAAA--ATT
**
61097696 TTAAAAATATTTT-AAAATT
1 AAAAAAATATTTTAAAAATT
* *
61097715 AAAAAAGTATTTTAAAATTT
1 AAAAAAATATTTTAAAAATT
61097735 AAAAAA
1 AAAAAA
61097741 TAAATATATT
Statistics
Matches: 89, Mismatches: 13, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
19 17 0.19
20 20 0.22
21 18 0.20
22 10 0.11
23 20 0.22
25 4 0.04
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
AAAAAAATATTTTAAAAATT
Found at i:61097643 original size:44 final size:42
Alignment explanation
Indices: 61097610--61097731 Score: 176
Period size: 44 Copynumber: 2.8 Consensus size: 42
61097600 ATAAATACCA
61097610 AAAAATTATTTTAAAAATTAAAAAAAGTATTTTAAAAATATTTT
1 AAAAA-TATTTT-AAAATTAAAAAAAGTATTTTAAAAATATTTT
*
61097654 AAAAATATTTTAAAATTAAATTAAAA-AATTTTAAAAAGTATTTT
1 AAAAATATTTTAAAATTAAA--AAAAGTATTTTAAAAA-TATTTT
61097698 AAAAATATTTTAAAATT-AAAAAAGTATTTTAAAA
1 AAAAATATTTTAAAATTAAAAAAAGTATTTTAAAA
61097732 TTTAAAAAAT
Statistics
Matches: 72, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
41 4 0.06
42 18 0.25
43 18 0.25
44 32 0.44
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.39
Consensus pattern (42 bp):
AAAAATATTTTAAAATTAAAAAAAGTATTTTAAAAATATTTT
Found at i:61097731 original size:11 final size:11
Alignment explanation
Indices: 61097610--61097712 Score: 113
Period size: 11 Copynumber: 9.4 Consensus size: 11
61097600 ATAAATACCA
61097610 AAAAATTATTTT
1 AAAAA-TATTTT
**
61097622 -AAAA-ATTAA
1 AAAAATATTTT
61097631 AAAAAGTATTTT
1 AAAAA-TATTTT
61097643 AAAAATATTTT
1 AAAAATATTTT
61097654 AAAAATATTTT
1 AAAAATATTTT
* **
61097665 AAAATTAAATT
1 AAAAATATTTT
61097676 AAAAA-ATTTT
1 AAAAATATTTT
61097686 AAAAAGTATTTT
1 AAAAA-TATTTT
61097698 AAAAATATTTT
1 AAAAATATTTT
61097709 AAAA
1 AAAA
61097713 TTAAAAAAGT
Statistics
Matches: 76, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
9 3 0.04
10 12 0.16
11 43 0.57
12 18 0.24
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:61097738 original size:18 final size:18
Alignment explanation
Indices: 61097610--61097739 Score: 73
Period size: 22 Copynumber: 6.3 Consensus size: 18
61097600 ATAAATACCA
*
61097610 AAAAATTATTTTAAAAATTAA
1 AAAAA-TATTTT-AAAATT-T
61097631 AAAAAGTATTTTAAAAATATTTT
1 AAAAA-TATTTT--AAA-A-TTT
61097654 AAAAATATTTTAAAATTAAATT
1 AAAAATATTTTAAAA-T---TT
61097676 AAAAA-ATTTTAAAAAGTATTTT
1 AAAAATATTTT--AAA--A-TTT
*
61097698 AAAAATATTTTAAAATTA
1 AAAAATATTTTAAAATTT
61097716 AAAAAGTATTTTAAAATTT
1 AAAAA-TATTTTAAAATTT
61097735 AAAAA
1 AAAAA
61097740 ATAAATATAT
Statistics
Matches: 93, Mismatches: 4, Indels: 26
0.76 0.03 0.21
Matches are distributed among these distances:
18 7 0.08
19 21 0.23
20 3 0.03
21 19 0.20
22 24 0.26
23 14 0.15
24 2 0.02
25 3 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
AAAAATATTTTAAAATTT
Found at i:61106535 original size:17 final size:17
Alignment explanation
Indices: 61106513--61106548 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
61106503 ATTTAGTGCA
*
61106513 CACCTTATTTTTTTTTT
1 CACCTTATTTTTTCTTT
61106530 CACCTTATTTTTTCTTT
1 CACCTTATTTTTTCTTT
61106547 CA
1 CA
61106549 TGATCTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.64
Consensus pattern (17 bp):
CACCTTATTTTTTCTTT
Found at i:61108920 original size:22 final size:23
Alignment explanation
Indices: 61108895--61108941 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
61108885 ACTTCTTGAG
61108895 AATTTAGA-TTGTTATTTTCTAA
1 AATTTAGACTTGTTATTTTCTAA
* * *
61108917 AATTTCGACTTGTTTTTTTGTAA
1 AATTTAGACTTGTTATTTTCTAA
61108940 AA
1 AA
61108942 GTAAATTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.53
Consensus pattern (23 bp):
AATTTAGACTTGTTATTTTCTAA
Found at i:61109828 original size:2 final size:2
Alignment explanation
Indices: 61109821--61109854 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
61109811 TACACCACCA
61109821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61109855 GTATTCGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61110046 original size:16 final size:16
Alignment explanation
Indices: 61110016--61110056 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
61110006 TAACCAAATG
*
61110016 AATATACATATATATCA
1 AATATAAATATAT-TCA
61110033 AATTATAAATATATTCA
1 AA-TATAAATATATTCA
61110050 AATATAA
1 AATATAA
61110057 TCACATTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 7 0.32
18 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (16 bp):
AATATAAATATATTCA
Found at i:61110272 original size:21 final size:20
Alignment explanation
Indices: 61110248--61110295 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
61110238 TGCTCATCAA
61110248 ACTTATTTATCAAATATATAT
1 ACTTATTT-TCAAATATATAT
*
61110269 ACTTGATCTTCAAATATATAT
1 ACTT-ATTTTCAAATATATAT
61110290 A-TTATT
1 ACTTATT
61110296 GACATATCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.08
20 2 0.08
21 17 0.71
22 3 0.12
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (20 bp):
ACTTATTTTCAAATATATAT
Found at i:61111291 original size:14 final size:14
Alignment explanation
Indices: 61111272--61111299 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
61111262 AAGGTTAGGC
61111272 CGAATCTTCATTAT
1 CGAATCTTCATTAT
61111286 CGAATCTTCATTAT
1 CGAATCTTCATTAT
61111300 ACTCATACAA
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:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (14 bp):
CGAATCTTCATTAT
Found at i:61112919 original size:29 final size:29
Alignment explanation
Indices: 61112856--61112921 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
61112846 ACTTACACGC
*
61112856 CCGTGTGGCTCACACAATAGAGCACACAG
1 CCGTGTGGCTCACACAACAGAGCACACAG
* * *
61112885 CTGTGTGGCTCACACAGCAGAGCATAC-G
1 CCGTGTGGCTCACACAACAGAGCACACAG
61112913 ACCGTGTGG
1 -CCGTGTGG
61112922 TGTCGTGTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.17
Consensus pattern (29 bp):
CCGTGTGGCTCACACAACAGAGCACACAG
Found at i:61122359 original size:3 final size:3
Alignment explanation
Indices: 61122351--61122472 Score: 140
Period size: 3 Copynumber: 40.7 Consensus size: 3
61122341 CCTTTTTAGC
* * * * *
61122351 ATT ATT ATT ATT ATA ATT ATT ATT -TT CCTC ATT ATT -TT AAT GTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT
*
61122395 ATT ATCT TTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
**
61122441 ATT ATT ATT ATT ATT ATT ACC ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
61122473 AATTGCTCTT
Statistics
Matches: 100, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
2 4 0.04
3 93 0.93
4 3 0.03
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:61122520 original size:23 final size:24
Alignment explanation
Indices: 61122493--61122541 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
61122483 ATATATATTT
*
61122493 TATATACATA-TACATATTTTTTA
1 TATATACATACTACATACTTTTTA
*
61122516 TATATACTTACGTACATACTTTTTA
1 TATATACATAC-TACATACTTTTTA
61122541 T
1 T
61122542 TTATTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
25 13 0.59
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (24 bp):
TATATACATACTACATACTTTTTA
Found at i:61123455 original size:107 final size:107
Alignment explanation
Indices: 61123235--61123453 Score: 321
Period size: 108 Copynumber: 2.0 Consensus size: 107
61123225 AAAGGAAATT
* *
61123235 TTTTTAAAATAAGGCAATGTTTTGCATTTGGTAATTCGAGAAACGTGCCCTAAGGTGCTGGGTGT
1 TTTTTAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGT
* ** *
61123300 CGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAA
66 CGATTTTTCTCGTTCAACCAAATAGCGAAATATCCTCTTAAA
* **
61123342 TTTTTAAAATGAGGCAATGTTTTGTGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
1 TTTTTAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAG-AAACATGCCCTAAGGTGCTGGGTG
* * *
61123407 TCGATTTTTCTCGTTTAACTAAATAGCGAAATATCCTCTTGAA
65 TCGATTTTTCTCGTTCAACCAAATAGCGAAATATCCTCTTAAA
61123450 TTTT
1 TTTT
61123454 AATCCATGTC
Statistics
Matches: 99, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
107 36 0.36
108 63 0.64
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (107 bp):
TTTTTAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGT
CGATTTTTCTCGTTCAACCAAATAGCGAAATATCCTCTTAAA
Found at i:61126093 original size:14 final size:14
Alignment explanation
Indices: 61126071--61126101 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
61126061 GTTTCTGAAA
61126071 ATAAACTATAATTT
1 ATAAACTATAATTT
*
61126085 ATAATCTATAATTT
1 ATAAACTATAATTT
61126099 ATA
1 ATA
61126102 TAACATCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (14 bp):
ATAAACTATAATTT
Found at i:61127227 original size:3 final size:3
Alignment explanation
Indices: 61127219--61127267 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
61127209 AAGATTAATA
* * * *
61127219 AAG AAG AAG AAG GAG AAG AAG GAG AAG GAG AAG GAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
61127267 A
1 A
61127268 GTCGAGCATA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:61127901 original size:15 final size:16
Alignment explanation
Indices: 61127881--61127914 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
61127871 TGGGCGTATC
61127881 TTTGGCTTTTTTT-TT
1 TTTGGCTTTTTTTATT
61127896 TTTGGCTTTTTTTATT
1 TTTGGCTTTTTTTATT
61127912 TTT
1 TTT
61127915 AAGGCTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.03, C:0.06, G:0.12, T:0.79
Consensus pattern (16 bp):
TTTGGCTTTTTTTATT
Found at i:61130172 original size:6 final size:6
Alignment explanation
Indices: 61130158--61130187 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
61130148 CCCCGCAACA
*
61130158 AATAAT AATAGT AATAGT AATAGT AATAGT
1 AATAGT AATAGT AATAGT AATAGT AATAGT
61130188 CGAGCGTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (6 bp):
AATAGT
Found at i:61131277 original size:133 final size:133
Alignment explanation
Indices: 61131100--61131494 Score: 386
Period size: 133 Copynumber: 2.9 Consensus size: 133
61131090 AAAAATTAGA
* * * * * * *
61131100 ATATAGCGGCATTTTCTGAGAAATGCCGGTAATGATAACGAATTTGAGGAAAAAATCTGAGCAAA
1 ATATAGCGGCGTTTTC-GGGAAACGCCGGTAAAGATATCTAATTTGAGGAAAAAATTTGAGCAAA
*
61131165 ACAATACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCGCATTTTAAAAAACGCTGGAAAAGA
65 ACGATACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCGCATTTTAAAAAACGC-GGAAAAGA
61131230 AT-GC
129 ATGGC
61131234 AT-TAGCGGCGTTTTCAGGGAAACGCCGGTAAAGATATCTAATTTGAGGAAAAAATTTG-GACAA
1 ATATAGCGGCGTTTTC-GGGAAACGCCGGTAAAGATATCTAATTTGAGGAAAAAATTTGAG-CAA
* * * * * * * * * * *
61131297 AACGCTACAGTTTTATTGCTTCATTTTATTTCCTTAGTGGCGCACTGTAAAATACGCCGCAAATA
64 AACGATACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCGCATTTTAAAAAACGCGGAAAAGA
* *
61131362 TTGGG
129 ATGGC
* * **
61131367 ATATAGTGGCGTTATT-GGAGAAACGCCGATAAAGATATCTAATTTGAGGAAAATTTTTGAGCAA
1 ATATAGCGGCGTT-TTCGG-GAAACGCCGGTAAAGATATCTAATTTGAGGAAAAAATTTGAGCAA
* * * * * * *
61131431 AACGGTACCATTTTGTTGTTTCCTTTT-TATGCTTTAGTGGTGAAATGTTAAAAAACGCCGGAAA
64 AACGATACCGTTTTGTTGTTTCATTTTAT-TTCTTTAGTGGCG-CATTTTAAAAAACG-CGGAAA
61131495 CGGTTTGGAT
Statistics
Matches: 210, Mismatches: 42, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
132 7 0.03
133 105 0.50
134 82 0.39
135 12 0.06
136 4 0.02
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (133 bp):
ATATAGCGGCGTTTTCGGGAAACGCCGGTAAAGATATCTAATTTGAGGAAAAAATTTGAGCAAAA
CGATACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCGCATTTTAAAAAACGCGGAAAAGAAT
GGC
Found at i:61131864 original size:20 final size:21
Alignment explanation
Indices: 61131839--61131879 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
61131829 TTTGTGATCT
*
61131839 GGGCTTAGAG-TTTAGGTTTA
1 GGGCTTAGAGATTGAGGTTTA
*
61131859 GGGCTTGGAGATTGAGGTTTA
1 GGGCTTAGAGATTGAGGTTTA
61131880 AGGTTTAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.20, C:0.05, G:0.39, T:0.37
Consensus pattern (21 bp):
GGGCTTAGAGATTGAGGTTTA
Found at i:61135402 original size:30 final size:29
Alignment explanation
Indices: 61135308--61135414 Score: 101
Period size: 29 Copynumber: 3.7 Consensus size: 29
61135298 CAAAAATAAA
* *
61135308 AAAATTACATTTTGACCCCTAAAATTTTT
1 AAAATTACACTTTAACCCCTAAAATTTTT
* * *
61135337 GAAACTT-CACTTTAACCCCTCAACTTTTT
1 -AAAATTACACTTTAACCCCTAAAATTTTT
* * *
61135366 AAAATTACATTTTGA-CCCTAAATTTTTCT
1 AAAATTACACTTTAACCCCTAAAATTTT-T
61135395 CAAAATTACACTTTAACCCC
1 -AAAATTACACTTTAACCCC
61135415 ATAAGTTTTG
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
28 15 0.25
29 25 0.41
30 18 0.30
31 3 0.05
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAATTACACTTTAACCCCTAAAATTTTT
Found at i:61135763 original size:22 final size:22
Alignment explanation
Indices: 61135738--61135802 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
61135728 AGCAAAGATA
*
61135738 CAAA-AAAGTAAAAAAAAAATAG
1 CAAACAAAG-AAAAAAAAAAGAG
*
61135760 CAAACAAAGAAGAAAAAAAGAG
1 CAAACAAAGAAAAAAAAAAGAG
* *
61135782 CAAAGAAAGAAAAGAAAAAGA
1 CAAACAAAGAAAAAAAAAAGA
61135803 AGAAAATAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 33 0.89
23 4 0.11
ACGTcount: A:0.75, C:0.06, G:0.15, T:0.03
Consensus pattern (22 bp):
CAAACAAAGAAAAAAAAAAGAG
Done.