Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008798.1 Hibiscus syriacus cultivar Beakdansim tig00111947_pilon, whole genome shotgun sequence
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: 1825372
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:892493 original size:62 final size:62
Alignment explanation
Indices: 892415--892539 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
892405 AATTTAAATT
892415 TTTCCAGAATTCTATTTGTTTATCAAGTCTTACAATAACTATGTATTTAATATATATATATA
1 TTTCCAGAATTCTATTTGTTTATCAAGTCTTACAATAACTATGTATTTAATATATATATATA
892477 TTTCCAGAATTCTATTTGTTTATCAAGTCTTACAATAACTATGTATTTAATATATATATATA
1 TTTCCAGAATTCTATTTGTTTATCAAGTCTTACAATAACTATGTATTTAATATATATATATA
892539 T
1 T
892540 ATATATATAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.47
Consensus pattern (62 bp):
TTTCCAGAATTCTATTTGTTTATCAAGTCTTACAATAACTATGTATTTAATATATATATATA
Found at i:892533 original size:2 final size:2
Alignment explanation
Indices: 892526--892551 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
892516 TATGTATTTA
892526 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
892552 TCACATTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:920358 original size:2 final size:2
Alignment explanation
Indices: 920351--920389 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
920341 TCAAATCATA
920351 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
920390 GTTAATAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:928804 original size:29 final size:28
Alignment explanation
Indices: 928772--928829 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
928762 TAATTTAGTT
*
928772 TTATAAAAACTAATATCGTAAAAACATTA
1 TTATAAAAACTAATATCATAAAAA-ATTA
* *
928801 TTATAAAGATTAATATCATAAAAAATTA
1 TTATAAAAACTAATATCATAAAAAATTA
928829 T
1 T
928830 GTAAAATTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.34
Consensus pattern (28 bp):
TTATAAAAACTAATATCATAAAAAATTA
Found at i:932611 original size:2 final size:2
Alignment explanation
Indices: 932604--932629 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
932594 ATGAATTGAG
932604 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
932630 GAGGTTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:938296 original size:32 final size:32
Alignment explanation
Indices: 938243--938336 Score: 100
Period size: 32 Copynumber: 2.9 Consensus size: 32
938233 GCTGGGCATG
* * *
938243 GGAGGCGCGTTCCATACGACGCGCCATTCAACA
1 GGAGGCACGTTCCATAGGACGCACCATTCAA-A
* * *
938276 GG-GGTACGTTCCATAGGACGCAACATTCAAG
1 GGAGGCACGTTCCATAGGACGCACCATTCAAA
* *
938307 GGAGGCATGTTCCATAGGAAGCACCATTCA
1 GGAGGCACGTTCCATAGGACGCACCATTCA
938337 TAAAACCCAT
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
31 2 0.04
32 46 0.92
33 2 0.04
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.18
Consensus pattern (32 bp):
GGAGGCACGTTCCATAGGACGCACCATTCAAA
Found at i:938697 original size:20 final size:20
Alignment explanation
Indices: 938674--938740 Score: 134
Period size: 20 Copynumber: 3.4 Consensus size: 20
938664 AATTTTATAT
938674 TTTTAAGAAAAAATTAGAAA
1 TTTTAAGAAAAAATTAGAAA
938694 TTTTAAGAAAAAATTAGAAA
1 TTTTAAGAAAAAATTAGAAA
938714 TTTTAAGAAAAAATTAGAAA
1 TTTTAAGAAAAAATTAGAAA
938734 TTTTAAG
1 TTTTAAG
938741 TTAGACAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (20 bp):
TTTTAAGAAAAAATTAGAAA
Found at i:944283 original size:26 final size:26
Alignment explanation
Indices: 944232--944283 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
944222 TGAATAAAAA
**
944232 ATATTTTTTTATTAAAAGTCACCACT
1 ATATTTTTTTATTAAAACACACCACT
* *
944258 ATATTTTTTTATTCAAACACATCACT
1 ATATTTTTTTATTAAAACACACCACT
944284 GTTTGAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.17, G:0.02, T:0.46
Consensus pattern (26 bp):
ATATTTTTTTATTAAAACACACCACT
Found at i:946017 original size:273 final size:274
Alignment explanation
Indices: 945477--946155 Score: 904
Period size: 273 Copynumber: 2.5 Consensus size: 274
945467 TAGTGAAATT
* * *
945477 TTGCTTGAATTCTACATTGAATGAGCTCTAAAAAAGTCAACTGGTGCATTATTGTT-ACAATAAA
1 TTGCTTGAATTCTACATTGAATGAGCTCTGAAAAAGTAAAATGGTGCATTATTGTTGA-AATAAA
* * * * * *** *
945541 TGACTTCTGAAATGTAGTTGAAACGGTGCATTGATTGAGGACAAAAAAGTAACCGAAAT-AGTGA
65 TGACTTCTGAAAAGTAGTTGAAACGATGCATTAATTGAGCACCAAAAAGTAGTTG-AATCATTGA
*
945605 A-AATTTTGGCTTTGTTAAAATACACGTTTTTTTATGATTTGAAGTGATAATTCAACACTGAAAA
129 ATAATTTTGGCTTTGTTAAAATACACG-TTTTTTATGATTTGAACTGATAATTCAACACTGAAAA
* * * * **
945669 ACTTTCTGATTTGAGTTGATATGTCGCTAAAAAGTTGTAGAAGATGATAATACACCACATTTTTC
193 ACTTTCTAATTTAAGTTGATATATCACTAAAAAGTTACAGAAGATGATAATACACCACATTTTTC
*
945734 ACCCATTTTCTGAAAAG
258 ACCAATTTTCTGAAAAG
* *
945751 TTGCTTGAGTTCTGCATTGAATGAGCTCTGAAAAAGATAAAATGGTGCATTATTGTTGAAATAAA
1 TTGCTTGAATTCTACATTGAATGAGCTCTGAAAAAG-TAAAATGGTGCATTATTGTTGAAATAAA
*
945816 TGACCTCTGAAAAGTAGTTGAAACGATGCATTAATTGAGCACCAAAAAGTAGTTGAATCATTGAA
65 TGACTTCTGAAAAGTAGTTGAAACGATGCATTAATTGAGCACCAAAAAGTAGTTGAATCATTGAA
*
945881 TAA-TTTGG-TTTGGTTAAAATACACG-TTTTTATGATTTGAACTGATAATTCAACACTGAAAAG
130 TAATTTTGGCTTT-GTTAAAATACACGTTTTTTATGATTTGAACTGATAATTCAACACTGAAAAA
* * * *
945943 CTTTTTAATTTAAGTTGATATATCACTGAAAAGTTACAGAATATGATAATGCACCAC-TATTTTC
194 CTTTCTAATTTAAGTTGATATATCACTAAAAAGTTACAGAAGATGATAATACACCACAT-TTTTC
946007 ACCAATTTTCTGAAAAG
258 ACCAATTTTCTGAAAAG
* * * *
946024 TTGATTGATTTCTACATTGAATGAGCTCTGAAAAAGCTAAAATAGTGCATTATTGTTGCAATAAA
1 TTGCTTGAATTCTACATTGAATGAGCTCTGAAAAAG-TAAAATGGTGCATTATTGTTGAAATAAA
* ** * * *
946089 TGATTTCAAAAAAGTAGCTGAAACGATGCACTAATTGAGCACCAAACAGTAGTTGAATCATTGAA
65 TGACTTCTGAAAAGTAGTTGAAACGATGCATTAATTGAGCACCAAAAAGTAGTTGAATCATTGAA
946154 TA
130 TA
946156 CTGAGATGAC
Statistics
Matches: 358, Mismatches: 41, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
272 1 0.00
273 222 0.62
274 39 0.11
275 93 0.26
276 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (274 bp):
TTGCTTGAATTCTACATTGAATGAGCTCTGAAAAAGTAAAATGGTGCATTATTGTTGAAATAAAT
GACTTCTGAAAAGTAGTTGAAACGATGCATTAATTGAGCACCAAAAAGTAGTTGAATCATTGAAT
AATTTTGGCTTTGTTAAAATACACGTTTTTTATGATTTGAACTGATAATTCAACACTGAAAAACT
TTCTAATTTAAGTTGATATATCACTAAAAAGTTACAGAAGATGATAATACACCACATTTTTCACC
AATTTTCTGAAAAG
Found at i:949618 original size:22 final size:22
Alignment explanation
Indices: 949575--949618 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
949565 GTTGACCCTT
*
949575 TTTATTTATATTTTTAATATTA
1 TTTATTTATATTTATAATATTA
*
949597 TTTATTTTTATTTAATAA-ATTA
1 TTTATTTATATTT-ATAATATTA
949619 ATTTTATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTATTTATATTTATAATATTA
Found at i:951407 original size:15 final size:18
Alignment explanation
Indices: 951387--951423 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
951377 TGAGTAAAGG
951387 TATGTAT-AAA-T-GATA
1 TATGTATGAAATTAGATA
951402 TATGTATGAAATTAGATA
1 TATGTATGAAATTAGATA
951420 TATG
1 TATG
951424 AGAATAGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 3 0.16
17 1 0.05
18 8 0.42
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (18 bp):
TATGTATGAAATTAGATA
Found at i:951762 original size:22 final size:22
Alignment explanation
Indices: 951734--951794 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
951724 GGGTCTACGC
*
951734 GGTCATTCGGGACATATACAGT-
1 GGTCATTCGGGACAAATACA-TA
*
951756 GGTCATTCGAGACAAATACATA
1 GGTCATTCGGGACAAATACATA
*
951778 GGTCATTCGGGAAAAAT
1 GGTCATTCGGGACAAAT
951795 TTCATATGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 1 0.03
22 33 0.97
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (22 bp):
GGTCATTCGGGACAAATACATA
Found at i:952714 original size:19 final size:21
Alignment explanation
Indices: 952670--952718 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
952660 CTGTTTACAT
952670 CTGTTCATACGGTATTGTTCA
1 CTGTTCATACGGTATTGTTCA
**
952691 CTGTTCATATTGTATT-TT-A
1 CTGTTCATACGGTATTGTTCA
952710 CTGTTCATA
1 CTGTTCATA
952719 AAACATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 10 0.38
20 2 0.08
21 14 0.54
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.49
Consensus pattern (21 bp):
CTGTTCATACGGTATTGTTCA
Found at i:953072 original size:3 final size:3
Alignment explanation
Indices: 953064--953104 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
953054 GAAAATGCAA
953064 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
953105 CTTCTTAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:954188 original size:27 final size:26
Alignment explanation
Indices: 954149--954223 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 26
954139 ATAAATTCAT
954149 AATATTTTATATAGTATTAACTTTAATA
1 AATATTTT-T-TAGTATTAACTTTAATA
* *
954177 AATA-TTTTTA-TATTAAC-TTATTG
1 AATATTTTTTAGTATTAACTTTAATA
*
954200 AATATATTTTAGTATTAA-TTTAAT
1 AATATTTTTTAGTATTAACTTTAAT
954224 TTAAAAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
23 8 0.20
24 12 0.30
25 12 0.30
26 1 0.03
27 3 0.08
28 4 0.10
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (26 bp):
AATATTTTTTAGTATTAACTTTAATA
Found at i:954190 original size:24 final size:26
Alignment explanation
Indices: 954160--954223 Score: 82
Period size: 24 Copynumber: 2.6 Consensus size: 26
954150 ATATTTTATA
954160 TAGTATTAACTTTAATAAATAT-TTT
1 TAGTATTAACTTTAATAAATATATTT
* *
954185 TA-TATTAAC-TTATTGAATATATTT
1 TAGTATTAACTTTAATAAATATATTT
954209 TAGTATTAA-TTTAAT
1 TAGTATTAACTTTAAT
954224 TTAAAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 9 0.27
24 12 0.36
25 12 0.36
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (26 bp):
TAGTATTAACTTTAATAAATATATTT
Found at i:954244 original size:27 final size:27
Alignment explanation
Indices: 954214--954284 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
954204 TATTTTAGTA
954214 TTAATTTAATTTAAAAATAATTTATTG
1 TTAATTTAATTTAAAAATAATTTATTG
* * *
954241 TTAACTTAATTTAAAAATATTTTATTT
1 TTAATTTAATTTAAAAATAATTTATTG
* *
954268 TTATTTTTATTTAAAAA
1 TTAATTTAATTTAAAAA
954285 ATATAGTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (27 bp):
TTAATTTAATTTAAAAATAATTTATTG
Found at i:954522 original size:24 final size:26
Alignment explanation
Indices: 954484--954550 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 26
954474 TTTTAAAAAT
* *
954484 ATATTTTATCATTATTTTAACTTA-AA
1 ATATATTAT-ATTATTTCAACTTACAA
*
954510 ATATA-TATTTTATTTCAACTTACTAA
1 ATATATTATATTATTTCAACTTAC-AA
954536 ATATATTATATTATT
1 ATATATTATATTATT
954551 ACTTTAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
24 12 0.35
25 3 0.09
26 11 0.32
27 8 0.24
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (26 bp):
ATATATTATATTATTTCAACTTACAA
Found at i:954654 original size:27 final size:28
Alignment explanation
Indices: 954611--954665 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
954601 CATAAGATAT
954611 ATATTTTTAAACGAAA-TAAAAATAAAA
1 ATATTTTTAAACGAAATTAAAAATAAAA
** *
954638 ATATTTTTAAATTAAATTAATAATAAAA
1 ATATTTTTAAACGAAATTAAAAATAAAA
954666 TACATTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (28 bp):
ATATTTTTAAACGAAATTAAAAATAAAA
Found at i:961963 original size:20 final size:21
Alignment explanation
Indices: 961907--961965 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
961897 AGAACCCCAG
*
961907 GGGGGTATCGATTCCC-CTGT
1 GGGGGTATCGATTCCCTCTAT
* *
961927 GGGGGAATCGGTTCCCTC-AT
1 GGGGGTATCGATTCCCTCTAT
961947 GGGGGTATCGATTCCCTCT
1 GGGGGTATCGATTCCCTCT
961966 GCACCAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.12, C:0.25, G:0.34, T:0.29
Consensus pattern (21 bp):
GGGGGTATCGATTCCCTCTAT
Found at i:972964 original size:18 final size:18
Alignment explanation
Indices: 972937--972971 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
972927 TTTGAAAATT
972937 AATTAAAAAATAGTTCTA
1 AATTAAAAAATAGTTCTA
* *
972955 AATTACAAAATATTTCT
1 AATTAAAAAATAGTTCT
972972 TTAAGTGTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (18 bp):
AATTAAAAAATAGTTCTA
Found at i:974018 original size:6 final size:6
Alignment explanation
Indices: 973975--973999 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
973965 TTCAATATTT
973975 AAACCG AAACCG AAACCG AAACCG A
1 AAACCG AAACCG AAACCG AAACCG A
974000 CTAGTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (6 bp):
AAACCG
Found at i:974073 original size:5 final size:5
Alignment explanation
Indices: 974063--974089 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
974053 GTTCGGGTTT
974063 TTCGG TTCGG TTCGG TTCGG TTCGG TT
1 TTCGG TTCGG TTCGG TTCGG TTCGG TT
974090 TTTCGGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.37, T:0.44
Consensus pattern (5 bp):
TTCGG
Found at i:975118 original size:14 final size:14
Alignment explanation
Indices: 975099--975154 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
975089 CGTTAGTGAA
975099 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
975113 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
975127 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
975137 CATTCGGTTATGTT
1 CGTTCGGTTATGTT
975151 CGTT
1 CGTT
975155 TATGTTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 8 0.22
11 1 0.03
13 1 0.03
14 26 0.72
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:975127 original size:24 final size:24
Alignment explanation
Indices: 975100--975174 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
975090 GTTAGTGAAC
* *
975100 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCATTCGGTTAT
975124 GTTCGTTTATGTTCATTCGGTTAT
1 GTTCGTTTATGTTCATTCGGTTAT
**
975148 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCATTCGGTTAT
975172 GTT
1 GTT
975175 TAACCCAATC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (24 bp):
GTTCGTTTATGTTCATTCGGTTAT
Found at i:976254 original size:16 final size:16
Alignment explanation
Indices: 976231--976307 Score: 127
Period size: 16 Copynumber: 4.8 Consensus size: 16
976221 GGATCTCCAA
976231 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
976247 CATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
976263 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
**
976279 CGTTTATGTTCGTGCG
1 CGTTTATGTTCGTGTT
976295 CGTTTATGTTCGT
1 CGTTTATGTTCGT
976308 TTATTTATTA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 57 1.00
ACGTcount: A:0.08, C:0.14, G:0.25, T:0.53
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:981162 original size:9 final size:9
Alignment explanation
Indices: 981150--981233 Score: 68
Period size: 9 Copynumber: 9.1 Consensus size: 9
981140 TCTATTTTAA
981150 TTATTATAT
1 TTATTATAT
981159 TTA-TATAT
1 TTATTATAT
*
981167 TT-TAATTAT
1 TTATTA-TAT
981176 TTATTATAT
1 TTATTATAT
981185 TTATT-TAT
1 TTATTATAT
*
981193 TAATATTATTAA
1 T--TATTA-TAT
981205 TTATTATTAT
1 TTATTA-TAT
981215 TATATT-TAT
1 T-TATTATAT
981224 TTATTATAT
1 TTATTATAT
981233 T
1 T
981234 CATTTAATTT
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
8 16 0.26
9 24 0.39
10 15 0.24
11 4 0.06
12 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTATTATAT
Found at i:981167 original size:13 final size:13
Alignment explanation
Indices: 981145--981239 Score: 92
Period size: 13 Copynumber: 7.6 Consensus size: 13
981135 AAATATCTAT
*
981145 TTTAATTATTATA
1 TTTATTTATTATA
* *
981158 TTTATATATTTTA
1 TTTATTTATTATA
*
981171 ATTATTTATTATA
1 TTTATTTATTATA
981184 TTTATTTATTA-A
1 TTTATTTATTATA
*
981196 TATTA-TTAAT-TA
1 T-TTATTTATTATA
981208 -TTA-TTATTATA
1 TTTATTTATTATA
981219 TTTATTTATTATA
1 TTTATTTATTATA
*
981232 TTCATTTA
1 TTTATTTA
981240 ATTTCTACGT
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
10 7 0.10
11 2 0.03
12 10 0.15
13 48 0.72
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTATTTATTATA
Found at i:981167 original size:22 final size:22
Alignment explanation
Indices: 981142--981228 Score: 73
Period size: 22 Copynumber: 4.2 Consensus size: 22
981132 ATGAAATATC
981142 TATTTTAATTATTATATTTATA
1 TATTTTAATTATTATATTTATA
981164 TATTTTAATTATT-TA--T-TA
1 TATTTTAATTATTATATTTATA
*
981182 TA-TTTATTTATTA-ATATTAT-
1 TATTTTAATTATTATAT-TTATA
*
981202 TAATTATT-ATTATTATATTTATT
1 T-ATT-TTAATTATTATATTTATA
981225 TATT
1 TATT
981229 ATATTCATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 20
0.71 0.03 0.27
Matches are distributed among these distances:
17 10 0.19
18 4 0.08
19 1 0.02
20 2 0.04
21 4 0.08
22 27 0.51
23 5 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTTTAATTATTATATTTATA
Found at i:981210 original size:16 final size:16
Alignment explanation
Indices: 981163--981217 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
981153 TTATATTTAT
*
981163 ATATT-TTAATTATTT
1 ATATTATTAATTATTA
*
981178 AT-TATATTTATTTATTA
1 ATAT-TA-TTAATTATTA
981195 ATATTATTAATTATTA
1 ATATTATTAATTATTA
*
981211 TTATTAT
1 ATATTAT
981218 ATTTATTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
14 1 0.03
15 3 0.09
16 15 0.47
17 12 0.38
18 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATATTATTAATTATTA
Found at i:981869 original size:20 final size:21
Alignment explanation
Indices: 981828--981865 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
981818 ATTTTAAAAA
*
981828 ACTTGAAAATTTATAAAGATT
1 ACTTGAAAATTTATAAAAATT
981849 ACTT-AAAATTT-TAAAAA
1 ACTTGAAAATTTATAAAAA
981866 ATTAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 7 0.44
21 4 0.25
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (21 bp):
ACTTGAAAATTTATAAAAATT
Found at i:981883 original size:15 final size:16
Alignment explanation
Indices: 981818--981875 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 16
981808 TATTGTATAC
981818 ATTTTAAAAAACTTGAAA
1 ATTTTAAAAAA-TT-AAA
*
981836 ATTTATAAAGATTACTTAAA
1 ATTT-TAAA-A--AATTAAA
981856 ATTTTAAAAAATTAAA
1 ATTTTAAAAAATTAAA
981872 ATTT
1 ATTT
981876 AAGAAATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
16 10 0.29
18 5 0.15
19 8 0.24
20 8 0.24
21 2 0.06
22 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (16 bp):
ATTTTAAAAAATTAAA
Found at i:982939 original size:229 final size:227
Alignment explanation
Indices: 982534--982982 Score: 799
Period size: 229 Copynumber: 2.0 Consensus size: 227
982524 GTAAATTATC
* * *
982534 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
982599 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
982664 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
982729 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
982762 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
982827 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
982892 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
982957 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
982983 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
228 40 0.19
229 171 0.81
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:983238 original size:20 final size:19
Alignment explanation
Indices: 983215--983261 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
983205 CGATATAACA
983215 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
983235 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
983255 GGTAAAA
1 GGTAAAA
983262 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:983263 original size:17 final size:19
Alignment explanation
Indices: 983224--983266 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
983214 AGGTAAAAAT
983224 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
983244 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
983261 ATGATA
1 ATGATA
983267 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:985543 original size:21 final size:21
Alignment explanation
Indices: 985496--985560 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
985486 AAGACAATCA
* *
985496 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
985518 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
985538 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
985559 AG
1 AG
985561 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:985641 original size:33 final size:33
Alignment explanation
Indices: 985594--985659 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
985584 AAATAGATGG
* *
985594 AGTGGTGAATGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
985627 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
985660 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.48, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:987499 original size:18 final size:19
Alignment explanation
Indices: 987455--987502 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
987445 AATGTAGGGT
987455 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
987474 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
987493 T-ATTTTGTAT
1 TAATTTTGTAT
987503 GTGAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:987955 original size:199 final size:198
Alignment explanation
Indices: 987621--988988 Score: 2594
Period size: 199 Copynumber: 6.9 Consensus size: 198
987611 CAATATGGCC
987621 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAAC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
987686 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
987751 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAAT
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAAT
**
987816 GGCC
195 GGAA
987820 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAAC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
987885 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
987950 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTT-TTTTCCAGAATGAA
988015 TGGAA
194 TGGAA
988020 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
***
988085 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACTTATTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
988150 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
988215 GAA
196 GAA
988218 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
988282 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
988347 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
988412 GAA
196 GAA
988415 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
988480 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
988545 AATATGTCTAAATAATGTATCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
988610 GGAA
195 GGAA
*
988614 AACAGGGTGCACCCATAAGGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
988679 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
988744 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTT-TTTTCCAGAATGAAT
988809 GGAA
195 GGAA
988813 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
988878 CAAAAGTATAATGTAATATGTAATTTTCCAATCTAACCGGTACAATTATACCGGTTTTATTAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
988943 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
988989 CTAATTTAAA
Statistics
Matches: 1149, Mismatches: 16, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
197 193 0.17
198 195 0.17
199 709 0.62
200 52 0.05
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (198 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
GAA
Found at i:990469 original size:12 final size:12
Alignment explanation
Indices: 990452--990504 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
990442 GGTCGCAGAA
*
990452 GATGAAGCTGAC
1 GATGAAGATGAC
990464 GATGAAGATGAC
1 GATGAAGATGAC
*
990476 GATGATGATGAC
1 GATGAAGATGAC
* *
990488 GATGATGATGAT
1 GATGAAGATGAC
990500 GATGA
1 GATGA
990505 TGAAGATGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.36, C:0.08, G:0.34, T:0.23
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:990484 original size:3 final size:3
Alignment explanation
Indices: 990464--990517 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
990454 TGAAGCTGAC
* * * *
990464 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
990512 GAT GAT
1 GAT GAT
990518 CCAAACAAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:990485 original size:18 final size:18
Alignment explanation
Indices: 990449--990517 Score: 72
Period size: 18 Copynumber: 4.0 Consensus size: 18
990439 AGCGGTCGCA
* *
990449 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
990467 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
*
990485 GACGAT---GATGATGAT
1 GAAGATGAAGATGATGAT
*
990500 GATGATGAAGATGATGAT
1 GAAGATGAAGATGATGAT
990518 CCAAACAAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
15 14 0.33
18 29 0.67
ACGTcount: A:0.38, C:0.06, G:0.33, T:0.23
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:990505 original size:12 final size:12
Alignment explanation
Indices: 990460--990517 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
990450 AAGATGAAGC
*
990460 TGACGATGAAGA
1 TGACGATGATGA
990472 TGACGATGATGA
1 TGACGATGATGA
990484 TGACGATGATGA
1 TGACGATGATGA
*
990496 TGATGATGATGA
1 TGACGATGATGA
* *
990508 AGATGATGAT
1 TGACGATGAT
990518 CCAAACAAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.36, C:0.05, G:0.33, T:0.26
Consensus pattern (12 bp):
TGACGATGATGA
Found at i:992249 original size:183 final size:183
Alignment explanation
Indices: 991941--992832 Score: 1595
Period size: 183 Copynumber: 4.9 Consensus size: 183
991931 CTTTCAACAT
** * * *
991941 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
992006 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
992071 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
992124 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
992189 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
992254 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* * *
992307 ATTATAATCTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATACGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
* *
992372 GGTCTATAACCTATATCGACACTTTTTAATATTATGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
992437 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* *
992490 ATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATACGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
992555 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
992620 AATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* *
992673 TTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCAAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
* * *
992738 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTAGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
992803 AATGTGTCGATACCATTTAAAAAAGTGTCG
131 AATGTGTCGATACGATTTAAAAAAGTGTCG
992833 GTAATTTTAA
Statistics
Matches: 684, Mismatches: 25, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 684 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:993102 original size:20 final size:22
Alignment explanation
Indices: 993077--993152 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 22
993067 ACTTTCAATA
*
993077 TAATAGGTA-AAC-ATATGATG
1 TAATAGGTAGAACTATATAATG
*
993097 TAATAGGTAGACCTTATATAATG
1 TAATAGGTAGAAC-TATATAATG
**
993120 TAATAGGTATCG-TTTATATAATG
1 TAATAGGTA--GAACTATATAATG
993143 TAATAGGTAG
1 TAATAGGTAG
993153 TGGTTATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
20 9 0.19
21 3 0.06
23 34 0.72
25 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (22 bp):
TAATAGGTAGAACTATATAATG
Found at i:993120 original size:23 final size:24
Alignment explanation
Indices: 993089--993152 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 24
993079 ATAGGTAAAC
*
993089 ATATGATGTAATAGGTAGAC-CTT
1 ATATAATGTAATAGGTAGACGCTT
* *
993112 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGACGCTT
993135 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
993153 TGGTTATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.03
23 35 0.97
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (24 bp):
ATATAATGTAATAGGTAGACGCTT
Found at i:993159 original size:23 final size:23
Alignment explanation
Indices: 993089--993161 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
993079 ATAGGTAAAC
* **
993089 ATATGATGTAATAGGTAGACCTT
1 ATATAATGTAATAGGTAGTGCTT
*
993112 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
993135 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
993158 ATAT
1 ATAT
993162 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:993382 original size:25 final size:25
Alignment explanation
Indices: 993348--993398 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
993338 ACAACAAATC
*
993348 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
993373 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
993398 A
1 A
993399 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:993808 original size:18 final size:18
Alignment explanation
Indices: 993787--993823 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
993777 GTAATTGGAG
993787 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
993805 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
993823 T
1 T
993824 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:993831 original size:24 final size:24
Alignment explanation
Indices: 993779--993825 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
993769 TTTCATATGT
* *
993779 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
993803 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
993826 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:994125 original size:39 final size:39
Alignment explanation
Indices: 994082--994168 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
994072 TCCGATGCTC
*
994082 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
994121 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
994160 ATCAAAATC
1 ATCAAAATC
994169 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:994605 original size:23 final size:23
Alignment explanation
Indices: 994574--994646 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
994564 ATAGGTAAAC
*
994574 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
994597 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
994620 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
994643 ATAT
1 ATAT
994647 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:996126 original size:18 final size:19
Alignment explanation
Indices: 996101--996184 Score: 68
Period size: 19 Copynumber: 4.5 Consensus size: 19
996091 AAATTTAGTT
996101 TTTATATTAATTATAATT-
1 TTTATATTAATTATAATTC
* *
996119 TGTATATTATAAATT-TGATT-
1 T-T-TA-TATTAATTATAATTC
**
996139 TTTATATTAATTCCAATTC
1 TTTATATTAATTATAATTC
*
996158 TTTATATTATTTATAATTC
1 TTTATATTAATTATAATTC
996177 -TTATATTA
1 TTTATATTA
996185 TAAATTTTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
17 7 0.13
18 14 0.26
19 18 0.34
20 7 0.13
21 7 0.13
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTATATTAATTATAATTC
Found at i:996198 original size:13 final size:14
Alignment explanation
Indices: 996164--996200 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
996154 ATTCTTTATA
996164 TTATTTAT-AATTC
1 TTATTTATAAATTC
996177 TTATATTATAAATT-
1 TTAT-TTATAAATTC
996191 TTATTTATAA
1 TTATTTATAA
996201 TCACTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTATAAATTC
Found at i:996807 original size:23 final size:22
Alignment explanation
Indices: 996777--996853 Score: 102
Period size: 23 Copynumber: 3.4 Consensus size: 22
996767 CAACAACCGA
996777 CAAGCATCAATTTAC-CAATTCAG
1 CAAGCATC-A-TTACACAATTCAG
996800 CAAGCATCATTACATCAATTCAG
1 CAAGCATCATTACA-CAATTCAG
996823 CAAGCATCATTACATCAATTCAG
1 CAAGCATCATTACA-CAATTCAG
*
996846 CAAACATC
1 CAAGCATC
996854 CTGTATTAAG
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
21 4 0.08
22 1 0.02
23 46 0.90
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (22 bp):
CAAGCATCATTACACAATTCAG
Found at i:997909 original size:74 final size:75
Alignment explanation
Indices: 997788--997938 Score: 277
Period size: 74 Copynumber: 2.0 Consensus size: 75
997778 TTCAAGTTTC
997788 TTAGTAGGATCCAAGACATACAACATTTCTGCAACTGCCACTCTATGCATCAAAGAATC-CAGAA
1 TTAGTAGGATCCAAGACATACAACATTTCTGCAACTGCCACTCTATGCATCAAAGAATCGCAGAA
997852 CACAGAAGTA
66 CACAGAAGTA
997862 TTAGTAGGATCCAAGACATACAACATTTCTGCAACTGCCACTCTATGCATCAAAGAATCTGCAGA
1 TTAGTAGGATCCAAGACATACAACATTTCTGCAACTGCCACTCTATGCATCAAAGAATC-GCAGA
*
997927 ACACGGAAGTA
65 ACACAGAAGTA
997938 T
1 T
997939 ATATTGAACG
Statistics
Matches: 74, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
74 59 0.80
76 15 0.20
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.23
Consensus pattern (75 bp):
TTAGTAGGATCCAAGACATACAACATTTCTGCAACTGCCACTCTATGCATCAAAGAATCGCAGAA
CACAGAAGTA
Found at i:999213 original size:31 final size:30
Alignment explanation
Indices: 999141--999356 Score: 116
Period size: 31 Copynumber: 6.8 Consensus size: 30
999131 TATATATTAT
* *
999141 AATTAATATTAATATAATATA-ATTTATAA
1 AATTAATATTAATATAAAATATAGTTATAA
**
999170 TTTGTAATTATTAATATAAAATATAGTCTATAA
1 AAT-TAA-TATTAATATAAAATATAGT-TATAA
*
999203 AATTAATATTAATATAAACTATATGTTATAA
1 AATTAATATTAATATAAAATATA-GTTATAA
* * * * *
999234 ATTTTATAGTATAGTTTATAAACTATAGTTAATAT
1 AATTAATA-T-TA--ATATAAAATATAGTT-ATAA
*
999269 AATTAATATTAATAT--AGTATAGTTTATAA
1 AATTAATATTAATATAAAATATAG-TTATAA
* *
999298 ACTATATATTATATTAATATAAATTATATTTA-AGA
1 A--AT-TA--ATATTAATATAAAATATAGTTATA-A
* *
999333 TAATTAACATTAATATAAACTATA
1 -AATTAATATTAATATAAAATATA
999357 TATTATATTA
Statistics
Matches: 147, Mismatches: 20, Indels: 38
0.72 0.10 0.19
Matches are distributed among these distances:
29 11 0.07
30 5 0.03
31 62 0.42
32 10 0.07
33 12 0.08
34 17 0.12
35 24 0.16
36 6 0.04
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (30 bp):
AATTAATATTAATATAAAATATAGTTATAA
Found at i:999224 original size:24 final size:25
Alignment explanation
Indices: 999179--999225 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
999169 ATTTGTAATT
**
999179 ATTAATATAAAATATAGTCTATAAA
1 ATTAATATAAAATATAAACTATAAA
*
999204 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
999226 TGTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAA
Found at i:999260 original size:14 final size:14
Alignment explanation
Indices: 999243--999303 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
999233 AATTTTATAG
*
999243 TATAGTTTATAAAC
1 TATAGTTAATAAAC
*
999257 TATAGTTAATATAAT
1 TATAGTTAATA-AAC
* *
999272 TAATA-TTAATATAG
1 T-ATAGTTAATAAAC
*
999286 TATAGTTTATAAAC
1 TATAGTTAATAAAC
999300 TATA
1 TATA
999304 TATTATATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
13 3 0.08
14 22 0.59
15 9 0.24
16 3 0.08
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (14 bp):
TATAGTTAATAAAC
Found at i:999282 original size:15 final size:15
Alignment explanation
Indices: 999262--999350 Score: 56
Period size: 15 Copynumber: 5.6 Consensus size: 15
999252 TAAACTATAG
999262 TTAATATAATTAATA
1 TTAATATAATTAATA
* *
999277 TTAATATAGTATAGTTTA
1 TTAATATAAT-TA--ATA
*
999295 TAAACTATATATT-ATA
1 TTAA-TATA-ATTAATA
999311 TTAATATAAATT-ATA
1 TTAATAT-AATTAATA
* *
999326 TTTAAGATAATTAACA
1 -TTAATATAATTAATA
999342 TTAATATAA
1 TTAATATAA
999351 ACTATATATT
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
15 30 0.53
16 16 0.28
18 5 0.09
19 5 0.09
20 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.45
Consensus pattern (15 bp):
TTAATATAATTAATA
Found at i:999397 original size:21 final size:21
Alignment explanation
Indices: 999215--999420 Score: 77
Period size: 21 Copynumber: 9.5 Consensus size: 21
999205 TTAATATTAA
*
999215 TATAAACTATA-TGTTATAAAT
1 TATATACTATAGT-TTATAAAT
* * *
999236 TTTATAGTATAGTTTATAAAC
1 TATATACTATAGTTTATAAAT
* * *
999257 TATAGTTAATATA-ATTA-ATAT
1 TATA--TACTATAGTTTATAAAT
* *
999278 TAATATAGTATAGTTTATAAAC
1 T-ATATACTATAGTTTATAAAT
*
999300 TATATATTATA-TTAATATAAAT
1 TATATACTATAGTT--TATAAAT
* * *
999322 TATAT-TTA-AGATAATTAACAT
1 TATATACTATAGTTTA-TAA-AT
999343 TAATATAAACTATA-TATTATATTAA-
1 T-ATAT--ACTATAGT-TTATA--AAT
*
999368 TATAAACTATAGTTTATAAAT
1 TATATACTATAGTTTATAAAT
* *
999389 TATATACTATAGGTTATAAAG
1 TATATACTATAGTTTATAAAT
*
999410 TATAAACTATA
1 TATATACTATA
999421 TACACTACAA
Statistics
Matches: 139, Mismatches: 25, Indels: 42
0.67 0.12 0.20
Matches are distributed among these distances:
19 1 0.01
20 14 0.10
21 68 0.49
22 36 0.26
23 7 0.05
24 3 0.02
25 5 0.04
26 4 0.03
27 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (21 bp):
TATATACTATAGTTTATAAAT
Found at i:999595 original size:41 final size:42
Alignment explanation
Indices: 999546--999987 Score: 376
Period size: 41 Copynumber: 10.8 Consensus size: 42
999536 TTAGCGGCGA
* *
999546 TAGTGGCGTTTTTTTAACAAACGCCGCAAAAGAGTAGTAC-T
1 TAGTGGCGTTTTTATAACAAACGCCGCAATAGAGTAGTACTT
* *
999587 TAGCGGCGTTTTTAT-ACAAACGCCGTAATAGAGTAGTACTT
1 TAGTGGCGTTTTTATAACAAACGCCGCAATAGAGTAGTACTT
* * *
999628 TAGGGGCGTTTTTAT-ACAAACGCTGCAAAAGAGTAGTACTT
1 TAGTGGCGTTTTTATAACAAACGCCGCAATAGAGTAGTACTT
* ** * *
999669 TAGCGGTATTTTTAT-ACAAACGCCGCAATAGAGTATTATTT
1 TAGTGGCGTTTTTATAACAAACGCCGCAATAGAGTAGTACTT
* * * * *
999710 TAGTGGTGTTTTTAT-ACAAATGCCGTAATAGGGT--TCATCTG
1 TAGTGGCGTTTTTATAACAAACGCCGCAATAGAGTAGT-A-CTT
* *
999751 TAGTGGCATTTTT-CAACAAACGCCGCAATAGAGTAGTACTT
1 TAGTGGCGTTTTTATAACAAACGCCGCAATAGAGTAGTACTT
* * * *
999792 TAGTGGCGTTTTTATAA-AAATGCCACAATAGGGT-TTATCTT
1 TAGTGGCGTTTTTATAACAAACGCCGCAATAGAGTAGTA-CTT
* * * *
999833 TAGTGGTGTTTTT-CAAGAAACACCGCAATAGAGTAGTACTT
1 TAGTGGCGTTTTTATAACAAACGCCGCAATAGAGTAGTACTT
** * * * * *
999874 TAGCAGTGTTTTTAT-ATAAATGCCGCAATAGGGT--TCATCTG
1 TAGTGGCGTTTTTATAACAAACGCCGCAATAGAGTAGT-A-CTT
* *
999915 TAGTGGCATTTTT-TCAACAAACGCCGCAATAAAGTAGTACTT
1 TAGTGGCGTTTTTAT-AACAAACGCCGCAATAGAGTAGTACTT
* *
999957 TAGCGGCGTTTTTAT-ACAAAAGCCGCAATAG
1 TAGTGGCGTTTTTATAACAAACGCCGCAATAG
999988 TTTGGTATGT
Statistics
Matches: 320, Mismatches: 63, Indels: 36
0.76 0.15 0.09
Matches are distributed among these distances:
39 2 0.01
40 29 0.09
41 252 0.79
42 33 0.10
43 3 0.01
44 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (42 bp):
TAGTGGCGTTTTTATAACAAACGCCGCAATAGAGTAGTACTT
Found at i:999690 original size:82 final size:81
Alignment explanation
Indices: 999586--999987 Score: 434
Period size: 82 Copynumber: 4.9 Consensus size: 81
999576 AGAGTAGTAC
* * * * *
999586 TTAGCGGCGTTTTTATACAAACGCCGTAATAGAGTAGTACTTTAGGGGCGTTTTTATACAAACGC
1 TTAGTGGCATTTTTATACAAACGCCGCAATAGAGTAGTACTTTAGCGGCGTTTTTATACAAATGC
* * *
999651 TGCAAAAGAG-TAGTACT
66 CGCAATAGGGTTA-T-CT
* * * * * *
999668 TTAGCGGTATTTTTATACAAACGCCGCAATAGAGTATTATTTTAGTGGTGTTTTTATACAAATGC
1 TTAGTGGCATTTTTATACAAACGCCGCAATAGAGTAGTACTTTAGCGGCGTTTTTATACAAATGC
*
999733 CGTAATAGGGTTCATCT
66 CGCAATAGGGTT-ATCT
* * *
999750 GTAGTGGCATTTTTCA-ACAAACGCCGCAATAGAGTAGTACTTTAGTGGCGTTTTTATAAAAATG
1 TTAGTGGCATTTTT-ATACAAACGCCGCAATAGAGTAGTACTTTAGCGGCGTTTTTATACAAATG
*
999814 CCACAATAGGGTTTATCT
65 CCGCAATAGGG-TTATCT
** * * * * *
999832 TTAGTGGTGTTTTTCA-AGAAACACCGCAATAGAGTAGTACTTTAGCAGTGTTTTTATATAAATG
1 TTAGTGGCATTTTT-ATACAAACGCCGCAATAGAGTAGTACTTTAGCGGCGTTTTTATACAAATG
999896 CCGCAATAGGGTTCATCT
65 CCGCAATAGGGTT-ATCT
* * *
999914 GTAGTGGCATTTTT-TCAACAAACGCCGCAATAAAGTAGTACTTTAGCGGCGTTTTTATACAAAA
1 TTAGTGGCATTTTTAT--ACAAACGCCGCAATAGAGTAGTACTTTAGCGGCGTTTTTATACAAAT
999978 GCCGCAATAG
64 GCCGCAATAG
999988 TTTGGTATGT
Statistics
Matches: 271, Mismatches: 41, Indels: 15
0.83 0.13 0.05
Matches are distributed among these distances:
81 2 0.01
82 213 0.79
83 55 0.20
84 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (81 bp):
TTAGTGGCATTTTTATACAAACGCCGCAATAGAGTAGTACTTTAGCGGCGTTTTTATACAAATGC
CGCAATAGGGTTATCT
Found at i:999793 original size:164 final size:165
Alignment explanation
Indices: 999602--999976 Score: 522
Period size: 164 Copynumber: 2.3 Consensus size: 165
999592 GCGTTTTTAT
* * **
999602 ACAAACGCCGTAATAGAGTAGTACTTTAGGGGCGTTTTTATACAAACGCTGCAAAAGAGTAGTA-
1 ACAAACGCCGCAATAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGCCACAAAAGAGT-GTAT
* * * **
999666 CTTTAGCGGTATTTTT-ATACAAACGCCGCAATAGAGTATTATTTTAGTGGTGTTTTTATACAAA
65 CTTTAGCGGTATTTTTCA-ACAAACACCGCAATAGAGTAGTACTTTAGCAGTGTTTTTATACAAA
*
999730 TGCCGTAATAGGGTTCATCTGTAGTGGCA-TTTTTCA
129 TGCCGCAATAGGGTTCATCTGTAGTGGCATTTTTTCA
* * * * * *
999766 ACAAACGCCGCAATAGAGTAGTACTTTAGTGGCGTTTTTATAAAAATGCCACAATAGGGTTTATC
1 ACAAACGCCGCAATAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGCCACAAAAGAGTGTATC
* * * *
999831 TTTAGTGGTGTTTTTCAAGAAACACCGCAATAGAGTAGTACTTTAGCAGTGTTTTTATATAAATG
66 TTTAGCGGTATTTTTCAACAAACACCGCAATAGAGTAGTACTTTAGCAGTGTTTTTATACAAATG
999896 CCGCAATAGGGTTCATCTGTAGTGGCATTTTTTCA
131 CCGCAATAGGGTTCATCTGTAGTGGCATTTTTTCA
*
999931 ACAAACGCCGCAATAAAGTAGTACTTTAGCGGCGTTTTTATACAAA
1 ACAAACGCCGCAATAGAGTAGTACTTTAGCGGCGTTTTTATACAAA
999977 AGCCGCAATA
Statistics
Matches: 186, Mismatches: 22, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
163 2 0.01
164 133 0.72
165 51 0.27
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (165 bp):
ACAAACGCCGCAATAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGCCACAAAAGAGTGTATC
TTTAGCGGTATTTTTCAACAAACACCGCAATAGAGTAGTACTTTAGCAGTGTTTTTATACAAATG
CCGCAATAGGGTTCATCTGTAGTGGCATTTTTTCA
Found at i:1002189 original size:22 final size:21
Alignment explanation
Indices: 1002130--1002189 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1002120 TGATTTATTA
*
1002130 TTATGGATTTCAATTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* * *
1002151 TTATGGATTTTATGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
1002172 TTTATGGATGTCAAGTTT
1 -TTATGGATTTCAAGTTT
1002190 ATTGGAAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.18, C:0.05, G:0.20, T:0.57
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:1002462 original size:86 final size:87
Alignment explanation
Indices: 1002317--1002516 Score: 293
Period size: 86 Copynumber: 2.3 Consensus size: 87
1002307 TTTGTATCTT
* *
1002317 AAAACGCCGCTATAGATAT-GACA-TT-TTGCGGCGTTTGTTCTAAAAAATGCCGCTAAATCTCA
1 AAAACGCCGCTA-A-ATATCAACACTTATTGCGGCGTTTGTTCTAAAAAACGCCGCTAAATCTCA
*
1002379 AGACCTATTACGGCGTTTGTGGGA
64 AGACCTATTACGGCGTTTATGGGA
*
1002403 AAAACGCCGCTAAATATCAACACTTATTGCGGCGTTTG-T-TAGACAAACGCCGCTAAATCTCAA
1 AAAACGCCGCTAAATATCAACACTTATTGCGGCGTTTGTTCTA-AAAAACGCCGCTAAATCTCAA
1002466 GACCTATTACGGCGTTTATGGGA
65 GACCTATTACGGCGTTTATGGGA
*
1002489 AAAACGCCGCTAAATATCAACACCTATT
1 AAAACGCCGCTAAATATCAACACTTATT
1002517 ACAACGTTTT
Statistics
Matches: 105, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
84 4 0.04
85 6 0.06
86 83 0.79
87 12 0.11
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (87 bp):
AAAACGCCGCTAAATATCAACACTTATTGCGGCGTTTGTTCTAAAAAACGCCGCTAAATCTCAAG
ACCTATTACGGCGTTTATGGGA
Found at i:1002525 original size:43 final size:43
Alignment explanation
Indices: 1002359--1002518 Score: 221
Period size: 43 Copynumber: 3.7 Consensus size: 43
1002349 GTTTGTTCTA
* * *
1002359 AAAAATGCCGCTAAATCTCAAGACCTATTACGGCGTTTGTGGG
1 AAAAACGCCGCTAAATATCAACACCTATTACGGCGTTTGTGGG
* * **
1002402 AAAAACGCCGCTAAATATCAACACTTATTGCGGCGTTTGTTAG
1 AAAAACGCCGCTAAATATCAACACCTATTACGGCGTTTGTGGG
* * * *
1002445 ACAAACGCCGCTAAATCTCAAGACCTATTACGGCGTTTATGGG
1 AAAAACGCCGCTAAATATCAACACCTATTACGGCGTTTGTGGG
1002488 AAAAACGCCGCTAAATATCAACACCTATTAC
1 AAAAACGCCGCTAAATATCAACACCTATTAC
1002519 AACGTTTTTT
Statistics
Matches: 99, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 99 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (43 bp):
AAAAACGCCGCTAAATATCAACACCTATTACGGCGTTTGTGGG
Found at i:1002704 original size:14 final size:14
Alignment explanation
Indices: 1002674--1002718 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1002664 AGTACACTAA
*
1002674 TATAAACTATTGTT
1 TATAAACTATAGTT
*
1002688 TATAAACTATAGGT
1 TATAAACTATAGTT
*
1002702 TATATA-TATAGTT
1 TATAAACTATAGTT
1002715 TATA
1 TATA
1002719 TAACATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (14 bp):
TATAAACTATAGTT
Found at i:1002726 original size:20 final size:21
Alignment explanation
Indices: 1002703--1002766 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
1002693 ACTATAGGTT
1002703 ATATATATAGTTTATATA-AC
1 ATATATATAGTTTATATATAC
*
1002723 ATATAAATAGATTGTATATATAC
1 ATATATATAG-TT-TATATATAC
* *
1002746 ATACACTATAGGTTATATATA
1 ATATA-TATAGTTTATATATA
1002767 TAGTTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 9 0.25
21 2 0.06
22 14 0.39
23 7 0.19
24 4 0.11
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (21 bp):
ATATATATAGTTTATATATAC
Found at i:1002800 original size:20 final size:20
Alignment explanation
Indices: 1002761--1002800 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1002751 CTATAGGTTA
* * *
1002761 TATATATAGTTTATATATAC
1 TATACATAGTTTACACATAC
1002781 TATACATAGTTTACACATAC
1 TATACATAGTTTACACATAC
1002801 ATGTACTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (20 bp):
TATACATAGTTTACACATAC
Found at i:1002820 original size:57 final size:57
Alignment explanation
Indices: 1002693--1002828 Score: 188
Period size: 57 Copynumber: 2.4 Consensus size: 57
1002683 TTGTTTATAA
* *
1002693 ACTATAGGTTATATATATAGTTTATATAACATATAAATAGATTGTATATATACATAC
1 ACTATAGGTTATATATATAGTTTATATAACATATAAATAGATTGTACACATACATAC
* **
1002750 ACTATAGGTTATATATATAGTTTATATATAC-TATACATAG-TT-TACACATACATGT
1 ACTATAGGTTATATATATAGTTTATATA-ACATATAAATAGATTGTACACATACATAC
*
1002805 ACTATAAGTTATATATATAGTTTA
1 ACTATAGGTTATATATATAGTTTA
1002829 CACGTATACA
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
55 32 0.44
56 2 0.03
57 36 0.50
58 2 0.03
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (57 bp):
ACTATAGGTTATATATATAGTTTATATAACATATAAATAGATTGTACACATACATAC
Found at i:1002845 original size:37 final size:35
Alignment explanation
Indices: 1002781--1002859 Score: 104
Period size: 37 Copynumber: 2.2 Consensus size: 35
1002771 TTATATATAC
* *
1002781 TATACATAGTTTACACATACATGTACTATAAGTTA
1 TATATATAGTTTACACATACATATACTATAAGTTA
*
1002816 TATATATAGTTTACACGTATACATATACTATAGGTTA
1 TATATATAGTTTACAC--ATACATATACTATAAGTTA
*
1002853 CATATAT
1 TATATAT
1002860 TAACTATTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 15 0.39
37 23 0.61
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (35 bp):
TATATATAGTTTACACATACATATACTATAAGTTA
Found at i:1002858 original size:35 final size:35
Alignment explanation
Indices: 1002786--1002858 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
1002776 TATACTATAC
* * *
1002786 ATAGTTTACACATACATGTACTATAAGTTATATAT
1 ATAGTTTACACATACATATACTATAAGGTATACAT
1002821 ATAGTTTACACGTATACATATACTAT-AGGT-TACAT
1 ATAGTTTACAC--ATACATATACTATAAGGTATACAT
1002856 ATA
1 ATA
1002859 TTAACTATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 18 0.55
36 3 0.09
37 12 0.36
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (35 bp):
ATAGTTTACACATACATATACTATAAGGTATACAT
Found at i:1004132 original size:72 final size:69
Alignment explanation
Indices: 1004056--1004418 Score: 331
Period size: 75 Copynumber: 5.0 Consensus size: 69
1004046 CAAAAAATAT
* *
1004056 TTTTTAACTATATATTATATAATTTCAAAAATATTTTTTAAAACTATATATCATATAATTTCTTA
1 TTTTTAACTATATATTATATAATTTCAAAAAT-TTTTTAAAAACTATATATCATATAAGTT-TT-
1004121 AAAAATG
63 AAAAATG
* *
1004128 TTTTTTAAAACTATATATTATATAATTTCAAAAATGTTTTT-AAAACTATATATTATATAATTTT
1 -TTTTT--AACTATATATTATATAATTTCAAAAAT-TTTTTAAAAACTATATATCATATAA-GTT
1004192 TTAAAAATG
61 TTAAAAATG
*
1004201 TTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTAAAAACTATATATC--ATAAGTTT
1 TTTTT--AACTATATATTATATAA--TTTCAAAAATTTTTTAAAAACTATATATCATATAAGTTT
*
1004264 TCAAAATCG
62 TAAAAAT-G
* * *
1004273 TTTTAAAAACTATATAATATATAAATTTTC-AAAATTGTTTTAAAAACTATATAACATATAAACG
1 TTTT--TAACTATATATTATAT-AA-TTTCAAAAATT-TTTTAAAAACTATATATCATAT-AA-G
*
1004337 TTTTCAAAATG
59 TTTTAAAAATG
* * * *
1004348 TTTTCAAAACTATATATTATATATATTTTAAAAATGTTTTCAAAAACTATATAAT-ATATAAATT
1 TTTT--TAACTATATATTATATA-ATTTCAAAAAT-TTTTTAAAAACTATAT-ATCATATAAGTT
*
1004412 TTCAAAA
61 TTAAAAA
1004419 GTCGTTTTCT
Statistics
Matches: 255, Mismatches: 16, Indels: 38
0.83 0.05 0.12
Matches are distributed among these distances:
71 14 0.05
72 69 0.27
73 27 0.11
74 50 0.20
75 82 0.32
76 13 0.05
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (69 bp):
TTTTTAACTATATATTATATAATTTCAAAAATTTTTTAAAAACTATATATCATATAAGTTTTAAA
AATG
Found at i:1004161 original size:37 final size:35
Alignment explanation
Indices: 1004036--1004446 Score: 380
Period size: 37 Copynumber: 11.1 Consensus size: 35
1004026 ATACTATAAA
* *
1004036 ATATATATTTCAAAAAATATTTTT-TAACTATATATT
1 ATATA-ATTTC-AAAAATGTTTTTAAAACTATATATT
* *
1004072 ATATAATTTCAAAAATATTTTTTAAAACTATATATC
1 ATATAATTTCAAAAAT-GTTTTTAAAACTATATATT
1004108 ATATAATTTCTTAAAAAATGTTTTTTAAAACTATATATT
1 ATATAATTTC---AAAAATG-TTTTTAAAACTATATATT
1004147 ATATAATTTCAAAAATGTTTTTAAAACTATATATT
1 ATATAATTTCAAAAATGTTTTTAAAACTATATATT
*
1004182 ATATAATTTTTTAAAAATGTTTTTAAAACTATATATT
1 ATATAA--TTTCAAAAATGTTTTTAAAACTATATATT
* *
1004219 ATATAATTTTTCAAAAATGTTTTAAAAACTATATATC
1 ATATAA--TTTCAAAAATGTTTTTAAAACTATATATT
* * *
1004256 ATA-AGTTTTC-AAAATCGTTTTAAAAACTATATAAT
1 ATATA-ATTTCAAAAAT-GTTTTTAAAACTATATATT
* * **
1004291 ATATAAATTTTCAAAATTGTTTTAAAAACTATATAAC
1 ATAT-AA-TTTCAAAAATGTTTTTAAAACTATATATT
*
1004328 ATATAAACGTTTTC-AAAATGTTTTCAAAACTATATATT
1 ATAT-AA---TTTCAAAAATGTTTTTAAAACTATATATT
* * *
1004366 ATATATATTTTAAAAATGTTTTCAAAAACTATATAAT
1 ATATA-ATTTCAAAAATGTTTT-TAAAACTATATATT
* *
1004403 ATATAAATTTTCAAAAGTCGTTTTCTGAAAATTATATATT
1 ATAT-AA-TTTCAAAAAT-GTTTT-T-AAAACTATATATT
1004443 ATAT
1 ATAT
1004447 TTCGTCAAAA
Statistics
Matches: 325, Mismatches: 27, Indels: 42
0.82 0.07 0.11
Matches are distributed among these distances:
34 11 0.03
35 61 0.19
36 43 0.13
37 113 0.35
38 38 0.12
39 44 0.14
40 15 0.05
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (35 bp):
ATATAATTTCAAAAATGTTTTTAAAACTATATATT
Found at i:1004179 original size:74 final size:71
Alignment explanation
Indices: 1004048--1004446 Score: 428
Period size: 74 Copynumber: 5.4 Consensus size: 71
1004038 ATATATTTCA
* * * *
1004048 AAAAATATTTTT-TAACTATATATTATATAATTTCAAAAATATTTTTTAAAACTATATATCATAT
1 AAAAATGTTTTTAAAACTATATATTATATAATTTCAAAAAT-GTTTTAAAAACTATATATCATAT
*
1004112 AATTTCTT
65 AAGTT-TT
* *
1004120 AAAAAATGTTTTTTAAAACTATATATTATATAATTTCAAAAATGTTTTTAAAACTATATATTATA
1 -AAAAATG-TTTTTAAAACTATATATTATATAATTTCAAAAATGTTTTAAAAACTATATATCATA
*
1004185 TAATTTTTT
64 TAA-GTTTT
1004194 AAAAATGTTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTAAAAACTATATATC--A
1 AAAAATGTTTTTAAAACTATATATTATATAA--TTTCAAAAATGTTTTAAAAACTATATATCATA
1004257 TAAGTTTT
64 TAAGTTTT
* * * * *
1004265 CAAAATCGTTTTAAAAACTATATAATATATAAATTTTCAAAATTGTTTTAAAAACTATATAACAT
1 AAAAAT-GTTTTTAAAACTATATATTATAT-AA-TTTCAAAAATGTTTTAAAAACTATATATCAT
1004330 ATAAACGTTTT
63 AT-AA-GTTTT
* * *
1004341 CAAAATGTTTTCAAAACTATATATTATATATATTTTAAAAATGTTTTCAAAAACTATATAAT-AT
1 AAAAATGTTTTTAAAACTATATATTATATA-ATTTCAAAAATGTTTT-AAAAACTATAT-ATCAT
*
1004405 ATAAATTTT
63 ATAAGTTTT
* *
1004414 CAAAAGTCGTTTTCTGAAAATTATATATTATAT
1 -AAAAAT-GTTTT-T-AAAACTATATATTATAT
1004447 TTCGTCAAAA
Statistics
Matches: 286, Mismatches: 22, Indels: 32
0.84 0.06 0.09
Matches are distributed among these distances:
71 9 0.03
72 77 0.27
73 19 0.07
74 79 0.28
75 74 0.26
76 12 0.04
77 16 0.06
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (71 bp):
AAAAATGTTTTTAAAACTATATATTATATAATTTCAAAAATGTTTTAAAAACTATATATCATATA
AGTTTT
Found at i:1005427 original size:84 final size:84
Alignment explanation
Indices: 1005077--1005420 Score: 385
Period size: 84 Copynumber: 4.1 Consensus size: 84
1005067 ATTTTATCGA
* * * *
1005077 CAGATAGCCCTTCTTGCCTTG-GCCTATGCTGTAAATAATGTGCCTTGGAGCTGAACGTAGTCGA
1 CAGATAGCCCTTCTAGCCTTGAG-CTATACTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
1005141 ACTCGAAGGTC--T--TTGG
65 ACTCGAAGGTCTTTGGTTGG
* * * * *
1005157 CAGATAGCCCTTCTAGCCTTGAGCTATACCGCAAATGACGCGCCTTGGAGCTGAGCGTAGTCAAA
1 CAGATAGCCCTTCTAGCCTTGAGCTATACTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
1005222 CTCGAAGGTCTTTGCTTGG
66 CTCGAAGGTCTTTGGTTGG
* * * * * * * *
1005241 CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGCATAGTCGAA
1 CAGATAGCCCTTCTAGCCTTGAGCTATACTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
1005306 CTCGAAGGTCTTTGG-TGA
66 CTCGAAGGTCTTTGGTTGG
* * * * * *
1005324 CAGATAACCCTTATAGCCTTGAGTTATACTGTAAATGATGTGCCCTTGAAGCTGAGCGGAATCGA
1 CAGATAGCCCTTCTAGCCTTGAGCTATACTGTAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
* *
1005389 ACTTGAAGGTATTTGGTTGG
65 ACTCGAAGGTCTTTGGTTGG
1005409 CAGATAGCCCTT
1 CAGATAGCCCTT
1005421 GTGCCTTTGA
Statistics
Matches: 219, Mismatches: 38, Indels: 9
0.82 0.14 0.03
Matches are distributed among these distances:
80 64 0.29
81 1 0.00
82 1 0.00
83 38 0.17
84 102 0.47
85 13 0.06
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (84 bp):
CAGATAGCCCTTCTAGCCTTGAGCTATACTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTGGTTGG
Found at i:1005664 original size:84 final size:83
Alignment explanation
Indices: 1005422--1005833 Score: 452
Period size: 84 Copynumber: 5.0 Consensus size: 83
1005412 ATAGCCCTTG
* * * * * *
1005422 TGCCTTTGAACTGAGTGTAGTCGCACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGA
1 TGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAA
* *
1005487 GTCATGCTGCAAATGATG
66 GTTATGCTGCAAATGATA
* ** * *
1005505 TGCCATGGAGCTGAACGTAGTCGAACTCGAAGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAA
1 TGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAA
* * *
1005567 GCTATGCTACAAATGATG
66 GTTATGCTGCAAATGATA
* * *
1005585 CGCCTTTGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTA
1 TGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTAGACTTA
*
1005650 AGTTGTGCTGCAAATGATA
65 AGTTATGCTGCAAATGATA
* ** * * * *
1005669 TGCCTTGGAGCTAAACGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGA
1 TGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAA
* *
1005734 GTTATACTGTAAATGATA
66 GTTATGCTGCAAATGATA
* * * * * *
1005752 TGCCTTCGAAGCTAAGTGTAATCGAACTCGAAGGTCTTTTGTTAGCAGATAACCCTTATTGACTT
1 TGCCTT-GGAGCTGAGTGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTAGACTT
*
1005817 AAGTTATACTGCAAATG
64 AAGTTATGCTGCAAATG
1005834 TTGTCTTAAA
Statistics
Matches: 272, Mismatches: 51, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
80 65 0.24
81 1 0.00
83 77 0.28
84 92 0.34
85 37 0.14
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (83 bp):
TGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAA
GTTATGCTGCAAATGATA
Found at i:1005693 original size:164 final size:167
Alignment explanation
Indices: 1005423--1005833 Score: 533
Period size: 164 Copynumber: 2.5 Consensus size: 167
1005413 TAGCCCTTGT
* * * * *
1005423 GCCTTTGAACTGAGTGTAGTCGCACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTAGCCTTGA
1 GCCTTTGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAA
* * *
1005487 GTCATGCTGCAAATGATGTGCCATGGAGCTGAACGTAGTCGAACTCGAAGGTCTTT-G-G-CAGA
66 GTTATGCTGCAAATGATATGCCATGGAGCTAAACGTAGTCGAACTCGAAGGTCTTTGGTGACAGA
* * * *
1005549 TAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGC
131 TAACCCTTCTAGACTTAAGCTATACTACAAATGATAC
*
1005586 GCCTTTGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAA
1 GCCTTTGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAA
* *
1005651 GTTGTGCTGCAAATGATATGCCTTGGAGCTAAACGTAGTCGAACTCGAAGGTCTTTGGTGACAGA
66 GTTATGCTGCAAATGATATGCCATGGAGCTAAACGTAGTCGAACTCGAAGGTCTTTGGTGACAGA
* * * ** *
1005716 TAACCCTTCTAGCCTTGAGTTATACTGTAAATGATAT
131 TAACCCTTCTAGACTTAAGCTATACTACAAATGATAC
* * * * * *
1005753 GCCTTCGAAGCTAAGTGTAATCGAACTCGAAGGTCTTTTGTTAGCAGATAACCCTTATTGACTTA
1 GCCTTTG-AGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTA
*
1005818 AGTTATACTGCAAATG
65 AGTTATGCTGCAAATG
1005834 TTGTCTTAAA
Statistics
Matches: 213, Mismatches: 30, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
163 31 0.15
164 78 0.37
165 1 0.00
166 1 0.00
167 37 0.17
168 65 0.31
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (167 bp):
GCCTTTGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAA
GTTATGCTGCAAATGATATGCCATGGAGCTAAACGTAGTCGAACTCGAAGGTCTTTGGTGACAGA
TAACCCTTCTAGACTTAAGCTATACTACAAATGATAC
Found at i:1005802 original size:388 final size:388
Alignment explanation
Indices: 1005077--1005808 Score: 1119
Period size: 388 Copynumber: 1.9 Consensus size: 388
1005067 ATTTTATCGA
* * * *
1005077 CAGATAGCCCTTCTTGCCTTGGCCTATGCTGTAAATAATGTGCCTTGGAGCTGAACGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGGCCTATGCTGCAAATAATGTGCCATGGAGCTGAACGTAGTCGAA
* * *
1005142 CTCGAAGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGCTATACCGCAAATGACGCGCCTTGGAG
66 CTCGAAGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATACCACAAATGACGCGCCTTGGAG
* *
1005207 CTGAGCGTAGTCAAACTCGAAGGTCTTTGCTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTG
131 CTGAGCGTAGTCAAACTCAAAGGTCTTTGCTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTG
* * *
1005272 TAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTA
196 CAAATGATATGCCTTGGAGCTAAACATAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTA
* * *
1005337 TAGCCTTGAGTTATACTGTAAATGATGTGCCCTTGAAGCTGAGCGGAATCGAACTTGAAGGTATT
261 TAGCCTTGAGTTATACTGTAAATGATATGCCCTTGAAGCTAAGCGGAATCGAACTCGAAGGTATT
* *
1005402 TGGTTGGCAGATAGCCCTTGTGCCTTTGAACTGAGTGTAGTCGCACTCGAAGGTCTTTGGTGG
326 TGGTTAGCAGATAACCCTTGTGCCTTTGAACTGAGTGTAGTCGCACTCGAAGGTCTTTGGTGG
* *
1005465 CAGATAACCCTTCTAGCCTTGAGTC-ATGCTGCAAATGATGTGCCATGGAGCTGAACGTAGTCGA
1 CAGATAACCCTTCTAGCCTTG-GCCTATGCTGCAAATAATGTGCCATGGAGCTGAACGTAGTCGA
* * * * *
1005529 ACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGCGCCTTTGA
65 ACTCGAAGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATACCACAAATGACGCGCCTTGGA
* * *
1005594 GCTGAGTGTAGTCGAACTCAAAGGTCTTTTG-TTGGCAGATAACCCTTCTAGACTTAAGTTGTGC
130 GCTGAGCGTAGTCAAACTCAAAGGTC-TTTGCTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
*
1005658 TGCAAATGATATGCCTTGGAGCTAAACGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCT
194 TGCAAATGATATGCCTTGGAGCTAAACATAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCT
* * *
1005723 TCTAGCCTTGAGTTATACTGTAAATGATATG-CCTTCGAAGCTAAGTGTAATCGAACTCGAAGGT
259 TATAGCCTTGAGTTATACTGTAAATGATATGCCCTT-GAAGCTAAGCGGAATCGAACTCGAAGGT
* *
1005787 CTTTTGTTAGCAGATAACCCTT
323 ATTTGGTTAGCAGATAACCCTT
1005809 ATTGACTTAA
Statistics
Matches: 308, Mismatches: 33, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
387 4 0.01
388 298 0.97
389 6 0.02
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (388 bp):
CAGATAACCCTTCTAGCCTTGGCCTATGCTGCAAATAATGTGCCATGGAGCTGAACGTAGTCGAA
CTCGAAGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATACCACAAATGACGCGCCTTGGAG
CTGAGCGTAGTCAAACTCAAAGGTCTTTGCTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTG
CAAATGATATGCCTTGGAGCTAAACATAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTA
TAGCCTTGAGTTATACTGTAAATGATATGCCCTTGAAGCTAAGCGGAATCGAACTCGAAGGTATT
TGGTTAGCAGATAACCCTTGTGCCTTTGAACTGAGTGTAGTCGCACTCGAAGGTCTTTGGTGG
Found at i:1010874 original size:12 final size:13
Alignment explanation
Indices: 1010857--1010885 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1010847 CTTAGTTGAG
1010857 AAAATTAAAA-TT
1 AAAATTAAAATTT
1010869 AAAATTAAAATTT
1 AAAATTAAAATTT
1010882 AAAA
1 AAAA
1010886 CATCGATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:1011734 original size:34 final size:35
Alignment explanation
Indices: 1011695--1011769 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
1011685 AGTAAACAGG
1011695 AAAAAATAATAATAATACTATAAAATATAT-ATTTC
1 AAAAAATAATAATAA-ACTATAAAATATATAATTTC
* ** * *
1011730 AAAAAATATTTTTAAACTATATATTATATAATTTC
1 AAAAAATAATAATAAACTATAAAATATATAATTTC
1011765 AAAAA
1 AAAAA
1011770 TGTTTTTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 12 0.35
35 22 0.65
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.37
Consensus pattern (35 bp):
AAAAAATAATAATAAACTATAAAATATATAATTTC
Found at i:1011844 original size:37 final size:35
Alignment explanation
Indices: 1011719--1012008 Score: 298
Period size: 37 Copynumber: 7.9 Consensus size: 35
1011709 ATACTATAAA
*
1011719 ATATATATTTCAAAAAATATTTTT-AAACTATATATT
1 ATATA-ATTTC-AAAAATGTTTTTAAAACTATATATT
*
1011755 ATATAATTTCAAAAATGTTTTTTAAAACTATATATC
1 ATATAATTTCAAAAATG-TTTTTAAAACTATATATT
1011791 ATATAATTTCTTAAAAAATGTTTTTTAAAACTATATATT
1 ATATAATTTC---AAAAATG-TTTTTAAAACTATATATT
*
1011830 ATATAATTTCAAAAATGTTTTTAAAATTATATATT
1 ATATAATTTCAAAAATGTTTTTAAAACTATATATT
** * *
1011865 ATATAAATTT-TTAATTTTTTTTAAAACTATATATT
1 ATAT-AATTTCAAAAATGTTTTTAAAACTATATATT
* *
1011900 ATATAATTTTTCAAAAATGTTTTAAAAACTATATATC
1 ATATAA--TTTCAAAAATGTTTTTAAAACTATATATT
* * *
1011937 ATATAAGTTTTC-AAAATCATTTTAAAAACTATATAAT
1 ATATAA--TTTCAAAAAT-GTTTTTAAAACTATATATT
* *
1011974 ATATAAATTTTCAAAATTGTTTTAAAAACTATATA
1 ATAT-AA-TTTCAAAAATGTTTTTAAAACTATATA
1012009 ACATATAAAT
Statistics
Matches: 221, Mismatches: 21, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
34 8 0.04
35 55 0.25
36 46 0.21
37 71 0.32
38 6 0.03
39 35 0.16
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.47
Consensus pattern (35 bp):
ATATAATTTCAAAAATGTTTTTAAAACTATATATT
Found at i:1011861 original size:74 final size:72
Alignment explanation
Indices: 1011731--1012016 Score: 348
Period size: 74 Copynumber: 3.9 Consensus size: 72
1011721 ATATATTTCA
*
1011731 AAAAATATTTTT-AAACTATATATTATATAA-TTTCAAAAATGTTTTTTAAAACTATATATCATA
1 AAAAATATTTTTAAAACTATATATTATATAATTTTCAAAAATG-TTTTAAAAACTATATATCATA
1011794 TAATTTCTT
65 TAATTT-TT
* * * *
1011803 AAAAAATGTTTTTTAAAACTATATATTATATAA-TTTCAAAAATGTTTTTAAAATTATATATTAT
1 -AAAAAT-ATTTTTAAAACTATATATTATATAATTTTCAAAAATGTTTTAAAAACTATATATCAT
1011867 ATAAATTTTT
64 AT-AATTTTT
* *
1011877 --AATTTTTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTAAAAACTATATATCATA
1 AAAAATATTTTTAAAACTATATATTATATAA-TTTTCAAAAATGTTTTAAAAACTATATATCATA
*
1011940 TAAGTTTT
65 TAATTTTT
* * * * *
1011948 CAAAATCATTTTAAAAACTATATAATATATAAATTTTCAAAATTGTTTTAAAAACTATATAACAT
1 AAAAAT-ATTTTTAAAACTATATATTATAT-AATTTTCAAAAATGTTTTAAAAACTATATATCAT
1012013 ATAA
64 ATAA
1012017 ATGTTTTCAA
Statistics
Matches: 190, Mismatches: 14, Indels: 17
0.86 0.06 0.08
Matches are distributed among these distances:
70 25 0.13
71 9 0.05
72 30 0.16
73 9 0.05
74 81 0.43
75 36 0.19
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (72 bp):
AAAAATATTTTTAAAACTATATATTATATAATTTTCAAAAATGTTTTAAAAACTATATATCATAT
AATTTTT
Found at i:1011885 original size:109 final size:107
Alignment explanation
Indices: 1011719--1012016 Score: 350
Period size: 109 Copynumber: 2.7 Consensus size: 107
1011709 ATACTATAAA
* *
1011719 ATATATATTTCAAAAAATATTTTT-AAACTATATATTATAT-AATTTCAAAAATGTTTTTTAAAA
1 ATATA-ATTTC-AAAAATATTTTTAAAACTATATATTATATAAATTT--TAAATTTTTTTTAAAA
* *
1011782 CTATATATCATATAATTTCTTAAAAAATGTTTTTTAAAACTATATATT
62 CTATATATCATATAATTT-TTAAAAAATG-TTTTAAAAACTATATATC
* * *
1011830 ATATAATTTCAAAAATGTTTTTAAAATTATATATTATATAAATTTTTAATTTTTTTTAAAACTAT
1 ATATAATTTCAAAAATATTTTTAAAACTATATATTATATAAATTTTAAATTTTTTTTAAAACTAT
* *
1011895 ATATTATATAATTTTTCAAAAATGTTTTAAAAACTATATATC
66 ATATCATATAATTTTTAAAAAATGTTTTAAAAACTATATATC
* * * *
1011937 ATATAAGTTTTC-AAAATCATTTTAAAAACTATATAATATATAAATTTTCAAAATTGTTTTAAAA
1 ATATAA--TTTCAAAAAT-ATTTTTAAAACTATATATTATATAAATTTT--AAATTTTTTTTAAA
*
1012001 ACTATATAACATATAA
61 ACTATATATCATATAA
1012017 ATGTTTTCAA
Statistics
Matches: 162, Mismatches: 18, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
107 22 0.14
108 14 0.09
109 71 0.44
110 20 0.12
111 35 0.22
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (107 bp):
ATATAATTTCAAAAATATTTTTAAAACTATATATTATATAAATTTTAAATTTTTTTTAAAACTAT
ATATCATATAATTTTTAAAAAATGTTTTAAAAACTATATATC
Found at i:1012041 original size:64 final size:64
Alignment explanation
Indices: 1011956--1012082 Score: 184
Period size: 64 Copynumber: 2.0 Consensus size: 64
1011946 TTCAAAATCA
*
1011956 TTTTAAAAACTATATAATATATAAATTTTCAAAATTGTTTT-AAAAACTATATAACATATAAATG
1 TTTTAAAAACTATATAATATATAAATTTT-AAAAATGTTTTCAAAAACTATATAACATATAAATG
* * * * *
1012020 TTTTCAAAACTATATATTATATATATTTTAAAAATGTTTTCAAAAACTGTATAATATATAAAT
1 TTTTAAAAACTATATAATATATAAATTTTAAAAATGTTTTCAAAAACTATATAACATATAAAT
1012083 TTTCGAAAGT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 10 0.18
64 46 0.82
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (64 bp):
TTTTAAAAACTATATAATATATAAATTTTAAAAATGTTTTCAAAAACTATATAACATATAAATG
Found at i:1012048 original size:25 final size:27
Alignment explanation
Indices: 1011993--1012053 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
1011983 TTCAAAATTG
*
1011993 TTTTAAAAACTATATAACATATAAATG
1 TTTTAAAAACTATATAACATATAAATA
* * *
1012020 TTTTCAAAACTATAT-A-TTATATATA
1 TTTTAAAAACTATATAACATATAAATA
1012045 TTTTAAAAA
1 TTTTAAAAA
1012054 TGTTTTCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 14 0.48
26 1 0.03
27 14 0.48
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.43
Consensus pattern (27 bp):
TTTTAAAAACTATATAACATATAAATA
Found at i:1012078 original size:37 final size:36
Alignment explanation
Indices: 1012015--1012085 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
1012005 TATAACATAT
* *
1012015 AAATGTTTTCAAAACTATATATTATATATATTTTAA
1 AAATGTTTTCAAAACTATATAATATATAAATTTTAA
*
1012051 AAATGTTTTCAAAAACTGTATAATATATAAATTTT
1 AAATGTTTTC-AAAACTATATAATATATAAATTTT
1012086 CGAAAGTCGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 10 0.32
37 21 0.68
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
AAATGTTTTCAAAACTATATAATATATAAATTTTAA
Found at i:1012130 original size:101 final size:102
Alignment explanation
Indices: 1011914--1012098 Score: 243
Period size: 101 Copynumber: 1.8 Consensus size: 102
1011904 AATTTTTCAA
* *
1011914 AAATGTT-TTAAAAACTATATATCATATAAGTTTTCAAAATCATTTTAAAAACTATATAATATAT
1 AAATGTTGTCAAAAACTATATATCATATAAGTTTTAAAAATCATTTTAAAAACTATATAATATAT
*
1011978 AAATTTTCAAAATTGTTTTAAAAACTATATAACATAT
66 AAATTTTCAAAATCGTTTTAAAAACTATATAACATAT
* * * *
1012015 AAATGTTTTC-AAAACTATATATTATATATA-TTTTAAAAAT-GTTTTCAAAAACTGTATAATAT
1 AAATGTTGTCAAAAACTATATATCATATA-AGTTTTAAAAATCATTTT-AAAAACTATATAATAT
*
1012077 ATAAATTTTCGAAAGTCGTTTT
64 ATAAATTTTC-AAAATCGTTTT
1012099 CTGAAAATTA
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
100 4 0.05
101 58 0.79
102 11 0.15
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (102 bp):
AAATGTTGTCAAAAACTATATATCATATAAGTTTTAAAAATCATTTTAAAAACTATATAATATAT
AAATTTTCAAAATCGTTTTAAAAACTATATAACATAT
Found at i:1012243 original size:2 final size:2
Alignment explanation
Indices: 1012236--1012564 Score: 127
Period size: 2 Copynumber: 165.0 Consensus size: 2
1012226 TTCTATAAAC
1012236 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
* * * *
1012278 CTA TA GTA -A TA TA AA T- TA TA -A TT TA TA AA CTA TA TA T- TT
1 -TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * *
1012317 TA TA TA GTT TA TA TA TA TA TA GTT TA TA TG TA TA TA CTA TA T-
1 TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA
* * * * * *
1012359 TA -A TA TA AA T- TA TA T- TT TA TA AA CTA TA TA CTT TT TA TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA -TA
* * * *
1012401 TA TA CA TA TA TA GTT TA TA TA CA TA GTT TA TA TA TA TA GT- TCA
1 TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA -TA T-A
* * * **
1012444 TA TA AA CA TA -A TT TA TA TA TA TA GC T- TA TA -A TA -A T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1012481 TA TA GTT TT TA -A TA TA AA TA TA GTT 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
* *
1012524 TA TA TA CTT TA TA TA TA AA CT- TA TA T- TA TA TA TA TA T- TA TA
1 TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
1012565 GTTTTTTTTC
Statistics
Matches: 244, Mismatches: 48, Indels: 70
0.67 0.13 0.19
Matches are distributed among these distances:
1 18 0.07
2 207 0.85
3 19 0.08
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1012363 original size:75 final size:75
Alignment explanation
Indices: 1012229--1012421 Score: 286
Period size: 75 Copynumber: 2.6 Consensus size: 75
1012219 ATAGTGTTTC
* * *
1012229 TATAAACTATATA-TATATATA-TATATATATATATA-TATATATATATATACTATAGTAATATA
1 TATAAACTATATATTTTATATAGTTTATATATATATAGTTTATATATATATACTATAGTAATATA
1012291 AATTATAATT
66 AATTATAATT
* *
1012301 TATAAACTATATATTTTATATAGTTTATATATATATAGTTTATATGTATATACTATATTAATATA
1 TATAAACTATATATTTTATATAGTTTATATATATATAGTTTATATATATATACTATAGTAATATA
*
1012366 AATTATATTT
66 AATTATAATT
*
1012376 TATAAACTATATACTTTT-TATAGTTTATACATATATAGTTTATATA
1 TATAAACTATATA-TTTTATATAGTTTATATATATATAGTTTATATA
1012422 CATAGTTTAT
Statistics
Matches: 109, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
72 13 0.12
73 7 0.06
74 13 0.12
75 72 0.66
76 4 0.04
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (75 bp):
TATAAACTATATATTTTATATAGTTTATATATATATAGTTTATATATATATACTATAGTAATATA
AATTATAATT
Found at i:1012414 original size:15 final size:13
Alignment explanation
Indices: 1012394--1012568 Score: 99
Period size: 13 Copynumber: 12.6 Consensus size: 13
1012384 ATATACTTTT
1012394 TATAGTTTATACATA
1 TATAGTTTAT--ATA
1012409 TATAGTTTATATA
1 TATAGTTTATATA
*
1012422 CATAGTTTATATA
1 TATAGTTTATATA
*
1012435 TATAGTTCATATAAA
1 TATAGTT--TATATA
* *
1012450 CATAATTTATATA
1 TATAGTTTATATA
1012463 TATAGCTTATAATAATTA
1 TATAG-TT-T-AT-A-TA
1012481 TATAGTTTTTAATATAAA
1 TATAG--TTT-ATAT--A
1012499 TATAGTTTATATA
1 TATAGTTTATATA
1012512 TATA-TATATATATA
1 TATAGT-T-TATATA
*
1012526 TATACTTTATATA
1 TATAGTTTATATA
**
1012539 TA-AACTTATAT-
1 TATAGTTTATATA
*
1012550 TATA-TATATAT-
1 TATAGTTTATATA
1012561 TATAGTTT
1 TATAGTTT
1012569 TTTTTCAATT
Statistics
Matches: 131, Mismatches: 14, Indels: 33
0.74 0.08 0.19
Matches are distributed among these distances:
11 11 0.08
12 11 0.08
13 43 0.33
14 13 0.10
15 26 0.20
16 6 0.05
17 2 0.02
18 17 0.13
19 2 0.02
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:1012692 original size:15 final size:16
Alignment explanation
Indices: 1012658--1012707 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1012648 CTTTTGTGTT
1012658 TTTTAATTTATTTCAA
1 TTTTAATTTATTTCAA
* *
1012674 TTTTAA-TTCTTTCAC
1 TTTTAATTTATTTCAA
*
1012689 TTTTATATGTA-TTCAA
1 TTTTA-ATTTATTTCAA
1012705 TTT
1 TTT
1012708 AGTCCTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 12 0.44
16 14 0.52
17 1 0.04
ACGTcount: A:0.26, C:0.10, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTTAATTTATTTCAA
Found at i:1021585 original size:22 final size:22
Alignment explanation
Indices: 1021560--1021651 Score: 129
Period size: 22 Copynumber: 4.4 Consensus size: 22
1021550 ATATTAGACA
*
1021560 TTCGGGACGTATCCAGTGGTTC
1 TTCGGGACGTATCCAGTGGTCC
1021582 TTCGGGACGTATCCAGTGGTCC
1 TTCGGGACGTATCCAGTGGTCC
*
1021604 TTCAGGAC--A--CAGTGGTCC
1 TTCGGGACGTATCCAGTGGTCC
*
1021622 TTCAGGACGTATCCAGTGGTCC
1 TTCGGGACGTATCCAGTGGTCC
1021644 TTCGGGAC
1 TTCGGGAC
1021652 AAATACTGAA
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
18 17 0.27
20 2 0.03
22 44 0.70
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.27
Consensus pattern (22 bp):
TTCGGGACGTATCCAGTGGTCC
Found at i:1021618 original size:18 final size:19
Alignment explanation
Indices: 1021594--1021652 Score: 75
Period size: 18 Copynumber: 3.0 Consensus size: 19
1021584 CGGGACGTAT
1021594 CCAGTGGTCCTTCAGGACA
1 CCAGTGGTCCTTCAGGACA
1021613 -CAGTGGTCCTTCAGGACGTA
1 CCAGTGGTCCTTCAGGAC--A
*
1021633 TCCAGTGGTCCTTCGGGACA
1 -CCAGTGGTCCTTCAGGACA
1021653 AATACTGAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
18 17 0.49
20 2 0.06
22 16 0.46
ACGTcount: A:0.19, C:0.29, G:0.29, T:0.24
Consensus pattern (19 bp):
CCAGTGGTCCTTCAGGACA
Found at i:1021630 original size:40 final size:40
Alignment explanation
Indices: 1021573--1021652 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
1021563 GGGACGTATC
* *
1021573 CAGTGGTTCTTCGGGACGTATCCAGTGGTCCTTCAGGACA
1 CAGTGGTCCTTCAGGACGTATCCAGTGGTCCTTCAGGACA
*
1021613 CAGTGGTCCTTCAGGACGTATCCAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCAGGACGTATCCAGTGGTCCTTCAGGACA
1021653 AATACTGAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.17, C:0.26, G:0.30, T:0.26
Consensus pattern (40 bp):
CAGTGGTCCTTCAGGACGTATCCAGTGGTCCTTCAGGACA
Found at i:1028331 original size:22 final size:21
Alignment explanation
Indices: 1028303--1028455 Score: 155
Period size: 22 Copynumber: 7.6 Consensus size: 21
1028293 GGGTATATTA
1028303 GTCCTTCGGGACTTATCCAGTG
1 GTCCTTCGGGAC-TATCCAGTG
* *
1028325 GTCCTTCAGGACATATCCTGTG
1 GTCCTTCGGGAC-TATCCAGTG
1028347 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGAC-TATCCAGTG
1028369 GTCCTTCGGGAC-AT--AGTG
1 GTCCTTCGGGACTATCCAGTG
* *
1028387 GTCCTTCAGGATGTATCCAGTG
1 GTCCTTCGGGA-CTATCCAGTG
*
1028409 GTCCTTCAGGA--AT--AGTG
1 GTCCTTCGGGACTATCCAGTG
1028426 GTCCTTCGGGAC-AT--AGTG
1 GTCCTTCGGGACTATCCAGTG
1028444 GTCCTTCGGGAC
1 GTCCTTCGGGAC
1028456 AAATACTGAA
Statistics
Matches: 117, Mismatches: 9, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
17 14 0.12
18 32 0.27
19 2 0.02
20 4 0.03
22 65 0.56
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.29
Consensus pattern (21 bp):
GTCCTTCGGGACTATCCAGTG
Found at i:1028366 original size:44 final size:40
Alignment explanation
Indices: 1028303--1028456 Score: 192
Period size: 44 Copynumber: 3.9 Consensus size: 40
1028293 GGGTATATTA
*
1028303 GTCCTTCGGGACTTATCCAGTGGTCCTTCAGGACATATCCTGTG
1 GTCCTTCGGGACGTATCCAGTGGTCCTTCAGGACATA----GTG
*
1028347 GTCCTTCGGGACGTATCCAGTGGTCCTTCGGGACATAGTG
1 GTCCTTCGGGACGTATCCAGTGGTCCTTCAGGACATAGTG
* *
1028387 GTCCTTCAGGATGTATCCAGTGGTCCTTCAGGA-ATAGTG
1 GTCCTTCGGGACGTATCCAGTGGTCCTTCAGGACATAGTG
*
1028426 GTCCTTCGGGAC--AT--AGTGGTCCTTCGGGACA
1 GTCCTTCGGGACGTATCCAGTGGTCCTTCAGGACA
1028457 AATACTGAAC
Statistics
Matches: 101, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
35 14 0.14
36 1 0.01
37 2 0.02
39 16 0.16
40 33 0.33
44 35 0.35
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (40 bp):
GTCCTTCGGGACGTATCCAGTGGTCCTTCAGGACATAGTG
Found at i:1028404 original size:62 final size:57
Alignment explanation
Indices: 1028303--1028456 Score: 182
Period size: 62 Copynumber: 2.5 Consensus size: 57
1028293 GGGTATATTA
* *
1028303 GTCCTTCGGGACTTATCCAGTGGTCCTTCAGGACATATCCTGTGGTCCTTCGGGACGTATCCAGT
1 GTCCTTCGGGAC--AT--AGTGGTCCTTCAGGACATATCCAGTGGTCCTTCAGGA---AT--AGT
1028368 G
57 G
**
1028369 GTCCTTCGGGACATAGTGGTCCTTCAGGATGTATCCAGTGGTCCTTCAGGAATAGTG
1 GTCCTTCGGGACATAGTGGTCCTTCAGGACATATCCAGTGGTCCTTCAGGAATAGTG
*
1028426 GTCCTTCGGGACATAGTGGTCCTTCGGGACA
1 GTCCTTCGGGACATAGTGGTCCTTCAGGACA
1028457 AATACTGAAC
Statistics
Matches: 81, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
57 32 0.40
59 2 0.02
62 33 0.41
64 2 0.02
66 12 0.15
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (57 bp):
GTCCTTCGGGACATAGTGGTCCTTCAGGACATATCCAGTGGTCCTTCAGGAATAGTG
Found at i:1042659 original size:13 final size:13
Alignment explanation
Indices: 1042641--1042667 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1042631 CACATTTAAA
1042641 CAGTCTTCATATG
1 CAGTCTTCATATG
1042654 CAGTCTTCATATG
1 CAGTCTTCATATG
1042667 C
1 C
1042668 GCGTTTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:1043986 original size:23 final size:23
Alignment explanation
Indices: 1043960--1044009 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1043950 TGTCCTTATG
*
1043960 ACACGGATTTCTATGCTATCATA
1 ACACGCATTTCTATGCTATCATA
* *
1043983 ACACGCTTTTCTATGCTTTCATA
1 ACACGCATTTCTATGCTATCATA
1044006 ACAC
1 ACAC
1044010 ATTTTTTCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.36
Consensus pattern (23 bp):
ACACGCATTTCTATGCTATCATA
Found at i:1044015 original size:23 final size:23
Alignment explanation
Indices: 1043967--1044015 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1043957 ATGACACGGA
*
1043967 TTTCTATGCTATCATAACACGCT
1 TTTCTATGCTATCATAACACACT
* *
1043990 TTTCTATGCTTTCATAACACATT
1 TTTCTATGCTATCATAACACACT
1044013 TTT
1 TTT
1044016 TCTCAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.47
Consensus pattern (23 bp):
TTTCTATGCTATCATAACACACT
Found at i:1045049 original size:20 final size:20
Alignment explanation
Indices: 1045005--1045195 Score: 193
Period size: 20 Copynumber: 9.4 Consensus size: 20
1044995 GATTCTGACT
*
1045005 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
1045026 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
1045046 ATCGTAACGAGAATACGTAAA
1 ATCGCAACGCGTATCCGT-AA
*
1045067 AACGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * **
1045087 ATCGCAACGAGAATAAGTAA
1 ATCGCAACGCGTATCCGTAA
*
1045107 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
1045127 ATCACAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
1045147 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
1045167 ATCGCAATGCGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
1045187 ATCGCAACG
1 ATCGCAACG
1045196 AGATTCTGAC
Statistics
Matches: 137, Mismatches: 32, Indels: 3
0.80 0.19 0.02
Matches are distributed among these distances:
20 105 0.77
21 32 0.23
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:1045127 original size:40 final size:40
Alignment explanation
Indices: 1045005--1045195 Score: 274
Period size: 40 Copynumber: 4.7 Consensus size: 40
1044995 GATTCTGACT
* *
1045005 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTAA
* *
1045046 ATCGTAACGAGAATACGTAAAAACGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTAA
* *
1045087 ATCGCAACGAGAATAAGTAAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
* *
1045127 ATCACAACGAGAATACGTAAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
* *
1045167 ATCGCAATGCGAATACGTAAATCGCAACG
1 ATCGCAACGAGAATACGTAAATCGCAACG
1045196 AGATTCTGAC
Statistics
Matches: 134, Mismatches: 16, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
40 81 0.60
41 53 0.40
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (40 bp):
ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
Found at i:1046056 original size:24 final size:24
Alignment explanation
Indices: 1046029--1046082 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1046019 GTATTCGAAA
1046029 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1046053 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1046077 TTTGAT
1 TTTGAT
1046083 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1048506 original size:20 final size:20
Alignment explanation
Indices: 1048481--1048535 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
1048471 AGACATTCAT
* *
1048481 TTGACTATCACAATGCGGGA
1 TTGACTATCACAACGCGGAA
*
1048501 TTGACTATCGCAACGCGGAA
1 TTGACTATCACAACGCGGAA
* *
1048521 ATGACTATCGCAACG
1 TTGACTATCACAACG
1048536 AGAGAATCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (20 bp):
TTGACTATCACAACGCGGAA
Found at i:1048567 original size:19 final size:19
Alignment explanation
Indices: 1048540--1048698 Score: 194
Period size: 19 Copynumber: 8.8 Consensus size: 19
1048530 GCAACGAGAG
*
1048540 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1048559 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1048578 AATCGCAA--CG-ACTG--
1 AATCGCAATGCGAAATGAA
1048592 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
1048612 AATCGCAACGCG--A-G--
1 AATCGCAATGCGAAATGAA
*
1048626 AATTGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1048645 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1048664 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1048683 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
1048699 TAGTTTCGCG
Statistics
Matches: 121, Mismatches: 8, Indels: 22
0.80 0.05 0.15
Matches are distributed among these distances:
14 18 0.15
16 7 0.06
17 4 0.03
18 3 0.02
19 78 0.64
20 11 0.09
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1048596 original size:33 final size:33
Alignment explanation
Indices: 1048559--1048692 Score: 171
Period size: 34 Copynumber: 3.9 Consensus size: 33
1048549 GCGAAATGAA
1048559 AATCGCAATGCGAAATGAAAATCGCAACGACTG
1 AATCGCAATGCGAAATGAAAATCGCAACGACTG
*
1048592 AATCGCAATGCGAAAATGAAAATCGCAACG-CGAG
1 AATCGCAATGCG-AAATGAAAATCGCAACGAC-TG
* *
1048626 AATTGCAATGCGAAATGAAAATCGCAATGCGAAATG
1 AATCGCAATGCGAAATGAAAATCGCAA--CG-ACTG
1048662 AAAATCGCAATGCGAAATGAAAATCGCAACG
1 --AATCGCAATGCGAAATGAAAATCGCAACG
1048693 CGAAATTAGT
Statistics
Matches: 88, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
33 28 0.32
34 29 0.33
35 2 0.02
36 3 0.03
38 26 0.30
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGACTG
Found at i:1048652 original size:86 final size:86
Alignment explanation
Indices: 1048507--1048671 Score: 267
Period size: 86 Copynumber: 1.9 Consensus size: 86
1048497 GGGATTGACT
* **
1048507 ATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAATGCGA
1 ATCGCAACGCGAAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAATGCGA
1048572 AATGAAAATCGCAACGACTGA
66 AATGAAAATCGCAACGACTGA
* * **
1048593 ATCGCAATGCGAAAATGAAAATCGCAACGCGAGAATTGCAATGCGAAATGAAAATCGCAATGCGA
1 ATCGCAACGCGAAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAATGCGA
1048658 AATGAAAATCGCAA
66 AATGAAAATCGCAA
1048672 TGCGAAATGA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 72 1.00
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (86 bp):
ATCGCAACGCGAAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAATGCGA
AATGAAAATCGCAACGACTGA
Found at i:1048727 original size:20 final size:19
Alignment explanation
Indices: 1048702--1048788 Score: 94
Period size: 20 Copynumber: 4.7 Consensus size: 19
1048692 GCGAAATTAG
*
1048702 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
1048721 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
1048739 ---CTCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
1048755 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
1048774 TTTCCGCGTTGCGAT
1 TTT-CGCATTGCGAT
1048789 ATTCTGTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
14 9 0.16
16 4 0.07
18 4 0.07
19 18 0.32
20 22 0.39
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:1050339 original size:21 final size:21
Alignment explanation
Indices: 1050273--1050339 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1050263 ATGAATCGGG
*
1050273 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1050293 CCTCTTTAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1050315 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1050336 CTCT
1 CTCT
1050340 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1052460 original size:19 final size:19
Alignment explanation
Indices: 1052438--1052490 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
1052428 AGAATCGCAA
*
1052438 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
1052457 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
1052476 TGCGATTTTCATTTC
1 TGCGATTTTGATTTC
1052491 TCTCGTTGCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.09, C:0.17, G:0.23, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:1052502 original size:40 final size:41
Alignment explanation
Indices: 1052454--1052545 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 41
1052444 TTTGGTTTCG
*
1052454 CGTTGCGATTTTTA-TTTCGCGTTGCGATTTTCATTTCTC-T
1 CGTTGCGATTTTCATTTTCGCGTTGCGATTTTCATTT-TCAT
** * *
1052494 CGTTGCGATAGTCATTTTTGTGTTGCGATTTTCATTTTCAT
1 CGTTGCGATTTTCATTTTCGCGTTGCGATTTTCATTTTCAT
1052535 -GTTGCGATTTT
1 CGTTGCGATTTT
1052546 AAGTTTAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
40 22 0.51
41 21 0.49
ACGTcount: A:0.12, C:0.16, G:0.20, T:0.52
Consensus pattern (41 bp):
CGTTGCGATTTTCATTTTCGCGTTGCGATTTTCATTTTCAT
Found at i:1052543 original size:20 final size:20
Alignment explanation
Indices: 1052449--1052545 Score: 99
Period size: 20 Copynumber: 4.8 Consensus size: 20
1052439 GCGATTTTGG
* *
1052449 TTTCGCGTTGCGATTTTTA-
1 TTTCGTGTTGCGATTTTCAT
*
1052468 TTTCGCGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
**
1052488 TTCTC-TCGTTGCGATAGTCAT
1 TT-TCGT-GTTGCGATTTTCAT
*
1052509 TTTTGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
*
1052529 TTTCATGTTGCGATTTT
1 TTTCGTGTTGCGATTTT
1052546 AAGTTTAGAA
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
19 18 0.28
20 30 0.46
21 17 0.26
ACGTcount: A:0.11, C:0.16, G:0.20, T:0.53
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTCAT
Found at i:1053133 original size:20 final size:20
Alignment explanation
Indices: 1053108--1053300 Score: 192
Period size: 20 Copynumber: 9.5 Consensus size: 20
1053098 TTTAAAAATT
1053108 GCGTTGCGATTTACGGATAC
1 GCGTTGCGATTTACGGATAC
* *
1053128 GCGTTGCGATTTTACGTAT-T
1 GCGTTGCGA-TTTACGGATAC
1053148 GTCGTTGCGATTTACGGATAC
1 G-CGTTGCGATTTACGGATAC
** * *
1053169 GTATTGCGATTTACGTATTC
1 GCGTTGCGATTTACGGATAC
* * *
1053189 TCGTTGCGATTTACGTATTC
1 GCGTTGCGATTTACGGATAC
* **
1053209 TCGTTATGATTTACGGATAC
1 GCGTTGCGATTTACGGATAC
*
1053229 GCGTTGCGATTTTACGTATTA-
1 GCGTTGCGA-TTTACGGA-TAC
*
1053250 TCGTTGCGATTTACGGATAC
1 GCGTTGCGATTTACGGATAC
1053270 GCGTTGCGATTTTACGGATAC
1 GCGTTGCGA-TTTACGGATAC
*
1053291 TCGTTGCGAT
1 GCGTTGCGAT
1053301 AGTCAGAATC
Statistics
Matches: 143, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.01
20 88 0.62
21 51 0.36
22 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (20 bp):
GCGTTGCGATTTACGGATAC
Found at i:1053166 original size:41 final size:39
Alignment explanation
Indices: 1053105--1053300 Score: 189
Period size: 41 Copynumber: 4.8 Consensus size: 39
1053095 CGCTTTAAAA
* *
1053105 ATTGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGT
1 ATTGCGTTGCGATTTACGGATACTCGTTGCGA-TTTACGG
* *
1053145 ATTGTCGTTGCGATTTACGGATACGT-ATTGCGATTTACGT
1 ATTG-CGTTGCGATTTACGGATAC-TCGTTGCGATTTACGG
* * * **
1053185 ATTCTCGTTGCGATTTACGTATTCTCGTTATGATTTACGG
1 ATT-GCGTTGCGATTTACGGATACTCGTTGCGATTTACGG
* *
1053225 ATACGCGTTGCGATTTTACGTATTA-TCGTTGCGATTTACGG
1 AT-TGCGTTGCGA-TTTACGGA-TACTCGTTGCGATTTACGG
*
1053266 ATACGCGTTGCGATTTTACGGATACTCGTTGCGAT
1 AT-TGCGTTGCGA-TTTACGGATACTCGTTGCGAT
1053301 AGTCAGAATC
Statistics
Matches: 133, Mismatches: 15, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
39 1 0.01
40 53 0.40
41 78 0.59
42 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.39
Consensus pattern (39 bp):
ATTGCGTTGCGATTTACGGATACTCGTTGCGATTTACGG
Found at i:1053442 original size:19 final size:19
Alignment explanation
Indices: 1053420--1053463 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1053410 ATCGCGTTGT
*
1053420 GATTTTTATTTCGCATTGC
1 GATTTTTATTTCGCATTAC
1053439 GATTTTTATTTCGCATTAC
1 GATTTTTATTTCGCATTAC
1053458 GATTTT
1 GATTTT
1053464 GTTGGTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.55
Consensus pattern (19 bp):
GATTTTTATTTCGCATTAC
Found at i:1057931 original size:120 final size:119
Alignment explanation
Indices: 1057711--1057936 Score: 267
Period size: 120 Copynumber: 1.9 Consensus size: 119
1057701 AATTTACTAA
* ** * ** * * **
1057711 AATGAAACAGAAACTAAACTTTAGGTATGGTTTTGAAAATTTTAAAAGTTTAGGTACTAAAATGG
1 AATGAAACAAAAACTAAACTTTAGGTATGACTTTAAAAAAATGAAAAGTTTAGATACTAAAACAG
* *
1057776 ACCAAAACTAATAGTTTAGGTACTAAATGAATAATTTACCCAATTTTTAATGGTG
66 ACCAAAAATAATAGTTTAGATACTAAATG-ATAATTTACCCAATTTTTAATGGTG
*
1057831 AATGAAACAAAAACTAAA-TGTTAGGTATGACTTTAAAAAAATGGAAAGTTTAGATACTAAAACA
1 AATGAAACAAAAACTAAACT-TTAGGTATGACTTTAAAAAAATGAAAAGTTTAGATACTAAAACA
**
1057895 GATTAAAAATAATAGTTTAGATACTAAGCATG-TAATTTACCC
65 GACCAAAAATAATAGTTTAGATACTAA--ATGATAATTTACCC
1057937 TATAAATAAC
Statistics
Matches: 88, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
119 1 0.01
120 84 0.95
122 3 0.03
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (119 bp):
AATGAAACAAAAACTAAACTTTAGGTATGACTTTAAAAAAATGAAAAGTTTAGATACTAAAACAG
ACCAAAAATAATAGTTTAGATACTAAATGATAATTTACCCAATTTTTAATGGTG
Found at i:1060564 original size:14 final size:15
Alignment explanation
Indices: 1060545--1060573 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1060535 TTCTTTTTAT
1060545 TAAATT-AATAATAA
1 TAAATTAAATAATAA
1060559 TAAATTAAATAATAA
1 TAAATTAAATAATAA
1060574 CATGTAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAATTAAATAATAA
Found at i:1061642 original size:75 final size:75
Alignment explanation
Indices: 1061548--1061731 Score: 242
Period size: 75 Copynumber: 2.5 Consensus size: 75
1061538 TATAAATAAA
* * * *
1061548 GTCAAATATCAAGACTCAAACCACAATATTAAGTTTAAAACGATAAAATCCATAAACAAATCACA
1 GTCAAATCTCAAGACTCAAACCACAATATTAAGTCTAAAACAATAAAATCCATAAACAAACCACA
1061613 ATATTAAAAT
66 ATATTAAAAT
* * * * * *
1061623 GTCAAATCTCAAGATTCAAACCACAATATTAACTCTATAATAATAAAATCCATAATCAAACCATA
1 GTCAAATCTCAAGACTCAAACCACAATATTAAGTCTAAAACAATAAAATCCATAAACAAACCACA
1061688 ATATTAAAAT
66 ATATTAAAAT
* * * *
1061698 GCCAAATCTTAAGACTGAAACCATAATATTAAGT
1 GTCAAATCTCAAGACTCAAACCACAATATTAAGT
1061732 ATAGAAAAAT
Statistics
Matches: 93, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 93 1.00
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.26
Consensus pattern (75 bp):
GTCAAATCTCAAGACTCAAACCACAATATTAAGTCTAAAACAATAAAATCCATAAACAAACCACA
ATATTAAAAT
Done.