Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 4 of 207
Found at i:1141668 original size:19 final size:18
Alignment explanation
Indices: 1141641--1141676 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1141631 AAAAATTAAA
1141641 AATTAAAAATTAAAAATT
1 AATTAAAAATTAAAAATT
*
1141659 AATTATAAAATTATAAAT
1 AATTA-AAAATTAAAAAT
1141677 ATAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTAAAAATTAAAAATT
Found at i:1147291 original size:11 final size:12
Alignment explanation
Indices: 1147277--1147311 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
1147267 AGAAAAAAAA
1147277 AAGAGAG-AGGG
1 AAGAGAGAAGGG
1147288 AAGAGAGAAGGG
1 AAGAGAGAAGGG
1147300 -AGAGAGAAGGG
1 AAGAGAGAAGGG
1147311 A
1 A
1147312 GGGGAATCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (12 bp):
AAGAGAGAAGGG
Found at i:1147949 original size:11 final size:12
Alignment explanation
Indices: 1147933--1147967 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
1147923 GAAAAAAAAA
1147933 AAGAGAG-AGGG
1 AAGAGAGAAGGG
1147944 AAGAGAGAAGGG
1 AAGAGAGAAGGG
1147956 -AGAGAGAAGGG
1 AAGAGAGAAGGG
1147967 A
1 A
1147968 GGGGAATCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (12 bp):
AAGAGAGAAGGG
Found at i:1148064 original size:655 final size:655
Alignment explanation
Indices: 1147119--1148431 Score: 2601
Period size: 655 Copynumber: 2.0 Consensus size: 655
1147109 GAAAACACGC
1147119 GGATCCTCTAGCGGGTCGGGTCGGATGGGTCGGGCATGGCCAAAACGACGTCGTTTTGGGGCTTA
1 GGATCCTCTAGCGGGTCGGGTCGGATGGGTCGGGCATGGCCAAAACGACGTCGTTTTGGGGCTTA
1147184 AGTGTAGCCCCCAAAACGACGTCGTTTTGGAGGGCTATATAAGGCCTAAACTAACCAAAAAAAAA
66 AGTGTAGCCCCCAAAACGACGTCGTTTTGGAGGGCTATATAAGGCCTAAACTAACCAAAAAAAAA
1147249 TCATTTGGGGAGAGGGAAAGAAAAAAAAAAGAGAGAGGGAAGAGAGAAGGGAGAGAGAAGGGAGG
131 TCATTTGGGGAGAGGGAAAGAAAAAAAAAAGAGAGAGGGAAGAGAGAAGGGAGAGAGAAGGGAGG
1147314 GGAATCCGGCCAGGGGCCGGTCACCGGACGGCCACCGGAGGCTTGCCGGCGCCGGCGCCGGCCAC
196 GGAATCCGGCCAGGGGCCGGTCACCGGACGGCCACCGGAGGCTTGCCGGCGCCGGCGCCGGCCAC
*
1147379 CGCACGAGGTGGCCGGAAAAGGTAAAAAAAATTTTTTTTTGTTTTTTTTTTATTTGTTGTATATT
261 CGCACGAGGTGGCCGGAAAAGGTAAAAAAAAATTTTTTTTGTTTTTTTTTTATTTGTTGTATATT
1147444 TTTATGTTAAATAGATAGAAAATAAAGAAATATATGTATATGTATATAAAAATCGAAAGGAAAAA
326 TTTATGTTAAATAGATAGAAAATAAAGAAATATATGTATATGTATATAAAAATCGAAAGGAAAAA
1147509 AGAAAAAAATACAACCTTTTGTTTTTTCTTTTTGTTTTTAACAATCACTGCTATCTGTTTATTGA
391 AGAAAAAAATACAACCTTTTGTTTTTTCTTTTTGTTTTTAACAATCACTGCTATCTGTTTATTGA
1147574 AGACTGTAAATTTCTCTTTAGTGTTTACAAAGTAGAAAAGAAGAAGAAAGAAAAAAAAAAGCCCC
456 AGACTGTAAATTTCTCTTTAGTGTTTACAAAGTAGAAAAGAAGAAGAAAGAAAAAAAAAAGCCCC
1147639 CCGTACAATTTTTGATTCGTGTTTTTATAACCCATTTTCATCTAATTTCCTATTGTTTCTGTTTT
521 CCGTACAATTTTTGATTCGTGTTTTTATAACCCATTTTCATCTAATTTCCTATTGTTTCTGTTTT
1147704 GTCTCTTTGCATGGGATGGGCACGATGGAGGTGACAGAGGCATGGGGTGCAGACGGTGATGGGCA
586 GTCTCTTTGCATGGGATGGGCACGATGGAGGTGACAGAGGCATGGGGTGCAGACGGTGATGGGCA
1147769 TGCGT
651 TGCGT
1147774 GGATCCTCTAGCGGGTCGGGTCGGATGGGTCGGGCATGGCCAAAACGACGTCGTTTTGGGGCTTA
1 GGATCCTCTAGCGGGTCGGGTCGGATGGGTCGGGCATGGCCAAAACGACGTCGTTTTGGGGCTTA
1147839 AGTGTAGCCCCCAAAACGACGTCGTTTTGGAGGGCTATATAAGGCCTAAACTAACCAAAAAAAAA
66 AGTGTAGCCCCCAAAACGACGTCGTTTTGGAGGGCTATATAAGGCCTAAACTAACCAAAAAAAAA
1147904 TCATTTGGGGAGAGGGAAAGAAAAAAAAAAAGAGAGAGGGAAGAGAGAAGGGAGAGAGAAGGGAG
131 TCATTTGGGGAGAGGGAAAG-AAAAAAAAAAGAGAGAGGGAAGAGAGAAGGGAGAGAGAAGGGAG
1147969 GGGAATCCGGCCAGGGGCCGGTCACCGGACGGCCACCGGAGGCTTGCCGGCGCCGGCGCCGGCCA
195 GGGAATCCGGCCAGGGGCCGGTCACCGGACGGCCACCGGAGGCTTGCCGGCGCCGGCGCCGGCCA
1148034 CCGCACGAGGTGGCCGGAAAAGGT-AAAAAAAATTTTTTTTGTTTTTTTTTTATTTGTTGTATAT
260 CCGCACGAGGTGGCCGGAAAAGGTAAAAAAAAATTTTTTTTGTTTTTTTTTTATTTGTTGTATAT
1148098 TTTTATGTTAAATAGATAGAAAATAAAGAAATATATGTATATGTATATAAAAATCGAAAGGAAAA
325 TTTTATGTTAAATAGATAGAAAATAAAGAAATATATGTATATGTATATAAAAATCGAAAGGAAAA
1148163 AAGAAAAAAATACAACCTTTTGTTTTTTCTTTTTGTTTTTAACAATCACTGCTATCTGTTTATTG
390 AAGAAAAAAATACAACCTTTTGTTTTTTCTTTTTGTTTTTAACAATCACTGCTATCTGTTTATTG
1148228 AAGACTGTAAATTTCTCTTTAGTGTTTACAAAGTAGAAAAGAAGAAGAAAGAAAAAAAAAAGCCC
455 AAGACTGTAAATTTCTCTTTAGTGTTTACAAAGTAGAAAAGAAGAAGAAAGAAAAAAAAAAGCCC
1148293 CCCGTACAATTTTTGATTCGTGTTTTTATAACCCATTTTCATCTAATTTCCTATTGTTTCTGTTT
520 CCCGTACAATTTTTGATTCGTGTTTTTATAACCCATTTTCATCTAATTTCCTATTGTTTCTGTTT
1148358 TGTCTCTTTGCATGGGATGGGCACGATGGAGGTGACAGAGGCATGGGGTGCAGACGGTGATGGGC
585 TGTCTCTTTGCATGGGATGGGCACGATGGAGGTGACAGAGGCATGGGGTGCAGACGGTGATGGGC
1148423 ATGCGT
650 ATGCGT
1148429 GGA
1 GGA
1148432 GGCTGGCGCG
Statistics
Matches: 656, Mismatches: 1, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
655 523 0.80
656 133 0.20
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.27
Consensus pattern (655 bp):
GGATCCTCTAGCGGGTCGGGTCGGATGGGTCGGGCATGGCCAAAACGACGTCGTTTTGGGGCTTA
AGTGTAGCCCCCAAAACGACGTCGTTTTGGAGGGCTATATAAGGCCTAAACTAACCAAAAAAAAA
TCATTTGGGGAGAGGGAAAGAAAAAAAAAAGAGAGAGGGAAGAGAGAAGGGAGAGAGAAGGGAGG
GGAATCCGGCCAGGGGCCGGTCACCGGACGGCCACCGGAGGCTTGCCGGCGCCGGCGCCGGCCAC
CGCACGAGGTGGCCGGAAAAGGTAAAAAAAAATTTTTTTTGTTTTTTTTTTATTTGTTGTATATT
TTTATGTTAAATAGATAGAAAATAAAGAAATATATGTATATGTATATAAAAATCGAAAGGAAAAA
AGAAAAAAATACAACCTTTTGTTTTTTCTTTTTGTTTTTAACAATCACTGCTATCTGTTTATTGA
AGACTGTAAATTTCTCTTTAGTGTTTACAAAGTAGAAAAGAAGAAGAAAGAAAAAAAAAAGCCCC
CCGTACAATTTTTGATTCGTGTTTTTATAACCCATTTTCATCTAATTTCCTATTGTTTCTGTTTT
GTCTCTTTGCATGGGATGGGCACGATGGAGGTGACAGAGGCATGGGGTGCAGACGGTGATGGGCA
TGCGT
Found at i:1149904 original size:18 final size:19
Alignment explanation
Indices: 1149867--1149905 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1149857 ATATAAAAAT
*
1149867 AATTAAAAATAATTTTTAA
1 AATTAAAAATAATTTATAA
*
1149886 AATTCAAAAT-ATTTATAA
1 AATTAAAAATAATTTATAA
1149904 AA
1 AA
1149906 ATGTTAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTAAAAATAATTTATAA
Found at i:1155189 original size:19 final size:19
Alignment explanation
Indices: 1155165--1155205 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1155155 GAAATCCCCA
1155165 TTTGAAATTACTAATA-AAT
1 TTTGAAATT-CTAATATAAT
*
1155184 TTTGAAATTCTATTATAAT
1 TTTGAAATTCTAATATAAT
1155203 TTT
1 TTT
1155206 ACCCAAACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (19 bp):
TTTGAAATTCTAATATAAT
Found at i:1156971 original size:39 final size:39
Alignment explanation
Indices: 1156904--1156983 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 39
1156894 TGCAATTATA
* * * * *
1156904 AAGCGTAGAATTAAACTATTATAGCACAAATGGATTAAG
1 AAGCGTAGAATCAAACAATTACAACACAAATAGATTAAG
*
1156943 AAGCGTAGCATCAAACAATTACAACACAAATAGATTAAG
1 AAGCGTAGAATCAAACAATTACAACACAAATAGATTAAG
1156982 AA
1 AA
1156984 TCAAAATAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.50, C:0.14, G:0.15, T:0.21
Consensus pattern (39 bp):
AAGCGTAGAATCAAACAATTACAACACAAATAGATTAAG
Found at i:1160071 original size:29 final size:29
Alignment explanation
Indices: 1160013--1160073 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
1160003 ATAAATTAAT
*
1160013 AAATGATTAAATTATTTTTAGTCCTCTTA
1 AAATGATTAAATTATTTTTAATCCTCTTA
*
1160042 AAATGA-TAAATTTTTAATTTAATCCT-TTA
1 AAATGATTAAATTATT--TTTAATCCTCTTA
1160071 AAA
1 AAA
1160074 ATTATAAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 8 0.29
29 12 0.43
30 8 0.29
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (29 bp):
AAATGATTAAATTATTTTTAATCCTCTTA
Found at i:1165166 original size:11 final size:12
Alignment explanation
Indices: 1165150--1165178 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1165140 ATTTTCCTTA
1165150 TTTTATTTT-AT
1 TTTTATTTTAAT
1165161 TTTTATTTTAAT
1 TTTTATTTTAAT
1165173 TTTTAT
1 TTTTAT
1165179 CATTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTTAAT
Found at i:1167154 original size:22 final size:22
Alignment explanation
Indices: 1167129--1167171 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1167119 TATTCAAATA
1167129 ATAACAATAAAAT-AGTAGTAAC
1 ATAACAATAAAATGA-TAGTAAC
*
1167151 ATAACAATGAAATGATAGTAA
1 ATAACAATAAAATGATAGTAA
1167172 AACAGTGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.58, C:0.07, G:0.12, T:0.23
Consensus pattern (22 bp):
ATAACAATAAAATGATAGTAAC
Found at i:1167206 original size:22 final size:22
Alignment explanation
Indices: 1167181--1167225 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1167171 AAACAGTGAG
1167181 AAAACAACAAAAAAAATAGCAAA
1 AAAACAA-AAAAAAAATAGCAAA
* *
1167204 AAAACAAAAAGAAAATATCAAA
1 AAAACAAAAAAAAAATAGCAAA
1167226 TTTTTTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.78, C:0.11, G:0.04, T:0.07
Consensus pattern (22 bp):
AAAACAAAAAAAAAATAGCAAA
Found at i:1171129 original size:18 final size:18
Alignment explanation
Indices: 1171102--1171194 Score: 159
Period size: 18 Copynumber: 5.2 Consensus size: 18
1171092 TACGACCGTT
1171102 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
1171120 TACGGCACTATTCACATA
1 TACGGTACTATTCACGTA
1171138 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
1171156 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
1171174 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
1171192 TAC
1 TAC
1171195 AGTAGTTGGG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 70 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:1177417 original size:17 final size:20
Alignment explanation
Indices: 1177376--1177418 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1177366 TTGCTACTAC
1177376 TTTGTTGTTATTGTATAACT
1 TTTGTTGTTATTGTATAACT
*
1177396 CTTGTT-TTATTGT-TAA-T
1 TTTGTTGTTATTGTATAACT
1177413 TTTGTT
1 TTTGTT
1177419 ACTACTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 6 0.29
18 3 0.14
19 7 0.33
20 5 0.24
ACGTcount: A:0.16, C:0.05, G:0.14, T:0.65
Consensus pattern (20 bp):
TTTGTTGTTATTGTATAACT
Found at i:1181421 original size:22 final size:24
Alignment explanation
Indices: 1181386--1181443 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
1181376 AATTGTGTAT
* *
1181386 TTTTATTATATTAA-AG-ATATAA
1 TTTTATAATTTTAATAGTATATAA
* *
1181408 TTTTATAATTTTAATAGTTTATAT
1 TTTTATAATTTTAATAGTATATAA
1181432 TTTTATAATTTT
1 TTTTATAATTTT
1181444 TAAATTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 12 0.40
23 2 0.07
24 16 0.53
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (24 bp):
TTTTATAATTTTAATAGTATATAA
Found at i:1181467 original size:30 final size:31
Alignment explanation
Indices: 1181431--1181498 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
1181421 ATAGTTTATA
** *
1181431 TTTTTATAATTTTTAAATTTTTAAAT-TAAT
1 TTTTTATAATTTTTAAAGGTTAAAATATAAT
* *
1181461 TTTTTATTATTTTTAGAGGTTAAAATATAAT
1 TTTTTATAATTTTTAAAGGTTAAAATATAAT
1181492 TTTTTAT
1 TTTTTAT
1181499 TAAAAATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 21 0.66
31 11 0.34
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (31 bp):
TTTTTATAATTTTTAAAGGTTAAAATATAAT
Found at i:1182796 original size:20 final size:19
Alignment explanation
Indices: 1182780--1182819 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1182770 ACCAAAAATT
1182780 TATTTTAAAAATTAAAAAAA
1 TATTTT-AAAATTAAAAAAA
1182800 TATTTTAAAATTAAAAAAA
1 TATTTTAAAATTAAAAAAA
1182819 T
1 T
1182820 TTAAAAAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TATTTTAAAATTAAAAAAA
Found at i:1196316 original size:20 final size:19
Alignment explanation
Indices: 1196258--1196316 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
1196248 AGATATGTTG
1196258 AAAATCATAGAAAATTA-TT
1 AAAATCATA-AAAATTATTT
**
1196277 AGAAATCATATTAATTATTT
1 A-AAATCATAAAAATTATTT
1196297 AAAACTCATAAAAATTATTT
1 AAAA-TCATAAAAATTATTT
1196317 TTTTTGGCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 9 0.27
20 24 0.73
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (19 bp):
AAAATCATAAAAATTATTT
Found at i:1196602 original size:93 final size:93
Alignment explanation
Indices: 1196491--1196675 Score: 370
Period size: 93 Copynumber: 2.0 Consensus size: 93
1196481 ATTATTTAAA
1196491 AGATATTTTTTGTGTCATATATAGAGATTGTGAACCGATGACATGCTGGTTAACATTTGGGGTCA
1 AGATATTTTTTGTGTCATATATAGAGATTGTGAACCGATGACATGCTGGTTAACATTTGGGGTCA
1196556 ACATGCCACAACATTAGTTCACAATCTT
66 ACATGCCACAACATTAGTTCACAATCTT
1196584 AGATATTTTTTGTGTCATATATAGAGATTGTGAACCGATGACATGCTGGTTAACATTTGGGGTCA
1 AGATATTTTTTGTGTCATATATAGAGATTGTGAACCGATGACATGCTGGTTAACATTTGGGGTCA
1196649 ACATGCCACAACATTAGTTCACAATCT
66 ACATGCCACAACATTAGTTCACAATCT
1196676 CTTTATAATT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (93 bp):
AGATATTTTTTGTGTCATATATAGAGATTGTGAACCGATGACATGCTGGTTAACATTTGGGGTCA
ACATGCCACAACATTAGTTCACAATCTT
Found at i:1204070 original size:19 final size:20
Alignment explanation
Indices: 1204046--1204086 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1204036 AAATTTTTTT
1204046 TTTAAG-TTTT-TCAATTAAA
1 TTTAAGATTTTGT-AATTAAA
1204065 TTTAAGATTTTGTAATTAAA
1 TTTAAGATTTTGTAATTAAA
1204085 TT
1 TT
1204087 CAGGATTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 13 0.65
21 1 0.05
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (20 bp):
TTTAAGATTTTGTAATTAAA
Found at i:1208366 original size:41 final size:41
Alignment explanation
Indices: 1208284--1208389 Score: 131
Period size: 41 Copynumber: 2.6 Consensus size: 41
1208274 CATCGGCACG
***
1208284 AAGCCTGCTAGGCATAAAGCCTGATCTGATACACCAACATA
1 AAGCCTGCTAGGCATAAAGCCTGATAAAATACACCAACATA
** **
1208325 AAGCCTGCTAGGCATAAAGCCTGATAAAATTTACCGGCATA
1 AAGCCTGCTAGGCATAAAGCCTGATAAAATACACCAACATA
* *
1208366 AAGCCTGCTAGGCACAGAGCCTGA
1 AAGCCTGCTAGGCATAAAGCCTGA
1208390 ATATCACTGA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (41 bp):
AAGCCTGCTAGGCATAAAGCCTGATAAAATACACCAACATA
Found at i:1218544 original size:18 final size:18
Alignment explanation
Indices: 1218521--1218556 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1218511 TGAATTTTAG
*
1218521 ACCTTCATACATATCAAT
1 ACCTTCACACATATCAAT
*
1218539 ACCTTCACATATATCAAT
1 ACCTTCACACATATCAAT
1218557 TACTTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (18 bp):
ACCTTCACACATATCAAT
Found at i:1221538 original size:21 final size:21
Alignment explanation
Indices: 1221512--1221552 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1221502 AGACGAGCAA
* *
1221512 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1221533 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1221553 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1223486 original size:16 final size:16
Alignment explanation
Indices: 1223453--1223486 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1223443 GGAGATTGTT
* *
1223453 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
1223469 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
1223485 AA
1 AA
1223487 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:1229612 original size:16 final size:17
Alignment explanation
Indices: 1229591--1229622 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1229581 TTATAAACAA
1229591 AAGAAAGAAA-AGAAAT
1 AAGAAAGAAACAGAAAT
1229607 AAGAAAGAAACAGAAA
1 AAGAAAGAAACAGAAA
1229623 GCTTAAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (17 bp):
AAGAAAGAAACAGAAAT
Found at i:1233951 original size:29 final size:29
Alignment explanation
Indices: 1233918--1234002 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 29
1233908 TCAACAATGA
1233918 ATTAATAGCATTTCCAACTTCTGTATGTT
1 ATTAATAGCATTTCCAACTTCTGTATGTT
* * * *
1233947 ATTAATGGCA-AT-CAA---C--AATG-A
1 ATTAATAGCATTTCCAACTTCTGTATGTT
1233968 ATTAATAGCATTTCCAACTTCTGTATGTT
1 ATTAATAGCATTTCCAACTTCTGTATGTT
1233997 ATTAAT
1 ATTAAT
1234003 GGAAATCAAC
Statistics
Matches: 40, Mismatches: 8, Indels: 16
0.62 0.12 0.25
Matches are distributed among these distances:
21 9 0.22
22 4 0.10
23 3 0.08
24 1 0.03
26 1 0.03
27 3 0.08
28 4 0.10
29 15 0.38
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (29 bp):
ATTAATAGCATTTCCAACTTCTGTATGTT
Found at i:1233982 original size:50 final size:50
Alignment explanation
Indices: 1233907--1234060 Score: 299
Period size: 50 Copynumber: 3.1 Consensus size: 50
1233897 CCATAAAAAG
1233907 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGCA
1 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGCA
*
1233957 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGAA
1 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGCA
1234007 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGCA
1 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGCA
1234057 ATCA
1 ATCA
1234061 GTTTGGTTAA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 102 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (50 bp):
ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGCA
Found at i:1235796 original size:162 final size:162
Alignment explanation
Indices: 1235509--1235834 Score: 503
Period size: 162 Copynumber: 2.0 Consensus size: 162
1235499 GTAAACCACA
* * * *
1235509 CAGTTGGTCACTCAACTTTTATATGTATTCATTTTGGGCACCAAATTTAAAAGTTTACAATTTAG
1 CAGTTGGCCACTCAACTTTTATAAGTATTCATTTTGGACACCAAATTTAAAAGTTCACAATTTAG
* * *
1235574 GTACTGTCGTTATATACTTTTATCATTTTAGTCACTATCGTTACATACCTTTTTTATCATTTTAG
66 GTACTGTCATTATATACTTTTATCATTTTAGCCACTATCGTTACATACCTTTTATATCATTTTAG
* *
1235639 TCACCCA-TAGTTAATTTGCCATTAAATGTACT
131 TCACCCACCA-TTAATTTGCCATTAAATATACT
*
1235671 CAGTTGGCCACTCAACTTTTATAAGTATTCATTTTGGACACCAAAATTTAAAAGTTCGCAATTTA
1 CAGTTGGCCACTCAACTTTTATAAGTATTCATTTTGGACACC-AAATTTAAAAGTTCACAATTTA
*
1235736 GGTACTGTTATTATATACTTTTATCATTTTAGCCACTATCGTTACATA-CTTTTATATCATTTTA
65 GGTACTGTCATTATATACTTTTATCATTTTAGCCACTATCGTTACATACCTTTTATATCATTTTA
* *
1235800 GTCGCCCACCATTAATTTTCCATTAAATATACT
130 GTCACCCACCATTAATTTGCCATTAAATATACT
1235833 CA
1 CA
1235835 TTTTTAATCA
Statistics
Matches: 149, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
162 83 0.56
163 66 0.44
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.42
Consensus pattern (162 bp):
CAGTTGGCCACTCAACTTTTATAAGTATTCATTTTGGACACCAAATTTAAAAGTTCACAATTTAG
GTACTGTCATTATATACTTTTATCATTTTAGCCACTATCGTTACATACCTTTTATATCATTTTAG
TCACCCACCATTAATTTGCCATTAAATATACT
Found at i:1235972 original size:23 final size:23
Alignment explanation
Indices: 1235937--1235991 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
1235927 AAAAAGAAAA
* *
1235937 ATAAAAAGATAAATTAGTTTTTC-
1 ATAAAAA-CTAAAGTAGTTTTTCT
*
1235960 AGTAAAAACTAAAGTATTTTTTCT
1 A-TAAAAACTAAAGTAGTTTTTCT
1235984 ATAAAAAC
1 ATAAAAAC
1235992 CTAGGTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.36
Consensus pattern (23 bp):
ATAAAAACTAAAGTAGTTTTTCT
Found at i:1236208 original size:26 final size:24
Alignment explanation
Indices: 1236179--1236234 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 24
1236169 TAAAAGAAAT
1236179 TAAAAAGATAAAATGAGTGACCAAAA
1 TAAAAA-AT-AAATGAGTGACCAAAA
* *
1236205 TAAAAACTTAATGAGTGACCAAAA
1 TAAAAAATAAATGAGTGACCAAAA
1236229 TAAAAA
1 TAAAAA
1236235 CTTTCTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 21 0.75
25 1 0.04
26 6 0.21
ACGTcount: A:0.61, C:0.09, G:0.12, T:0.18
Consensus pattern (24 bp):
TAAAAAATAAATGAGTGACCAAAA
Found at i:1236221 original size:24 final size:24
Alignment explanation
Indices: 1236190--1236237 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1236180 AAAAAGATAA
1236190 AATGAGTGACCAAAATAAAAACTT
1 AATGAGTGACCAAAATAAAAACTT
1236214 AATGAGTGACCAAAATAAAAACTT
1 AATGAGTGACCAAAATAAAAACTT
1236238 TCTAAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.21
Consensus pattern (24 bp):
AATGAGTGACCAAAATAAAAACTT
Found at i:1236352 original size:31 final size:31
Alignment explanation
Indices: 1236293--1236358 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
1236283 AGGCGAGTTG
**
1236293 CTAAAATGATAAAAGGATATAATGATAGTGA
1 CTAAAATGATAAAAGGATATAACAATAGTGA
** * *
1236324 CTAAAATGATAAAATTATGTAACAATAGTGC
1 CTAAAATGATAAAAGGATATAACAATAGTGA
1236355 CTAA
1 CTAA
1236359 GTTGCAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (31 bp):
CTAAAATGATAAAAGGATATAACAATAGTGA
Found at i:1239568 original size:19 final size:19
Alignment explanation
Indices: 1239544--1239582 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1239534 TCACATATAG
*
1239544 TTATATGTCTCATCAATAA
1 TTATATGTCACATCAATAA
1239563 TTATATGTCACATCAATAA
1 TTATATGTCACATCAATAA
1239582 T
1 T
1239583 ACAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.41
Consensus pattern (19 bp):
TTATATGTCACATCAATAA
Found at i:1254138 original size:18 final size:18
Alignment explanation
Indices: 1254115--1254207 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
1254105 CCCAACTACT
* *
1254115 GTATACGTGAACAGTATC
1 GTATACGTGAATAGTACC
*
1254133 GTATACGTGAATAGTTCC
1 GTATACGTGAATAGTACC
*
1254151 GTATATGTGAATAGTACC
1 GTATACGTGAATAGTACC
* *
1254169 GTATACGTAAATAGTGCC
1 GTATACGTGAATAGTACC
1254187 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
1254205 GTA
1 GTA
1254208 AGCGGTCGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:1258576 original size:18 final size:17
Alignment explanation
Indices: 1258553--1258601 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 17
1258543 TATTATTTTC
1258553 AAAATTTATTATTAAAAT
1 AAAATTTATTATT-AAAT
*
1258571 AAAATTAATTTATTAAAT
1 AAAATTTA-TTATTAAAT
1258589 AATAATTTATTAT
1 AA-AATTTATTAT
1258602 ATGATTAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 17 0.63
19 10 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAATTTATTATTAAAT
Found at i:1258885 original size:19 final size:19
Alignment explanation
Indices: 1258861--1258898 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1258851 CTTATAAGTC
1258861 ATTTTCCATTG-ATCAAACT
1 ATTTTCCA-TGAATCAAACT
1258880 ATTTTCCATGAATCAAACT
1 ATTTTCCATGAATCAAACT
1258899 TTGAATACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.39
Consensus pattern (19 bp):
ATTTTCCATGAATCAAACT
Found at i:1260761 original size:50 final size:49
Alignment explanation
Indices: 1260687--1260796 Score: 188
Period size: 50 Copynumber: 2.3 Consensus size: 49
1260677 ACTGACGTTG
*
1260687 TTAATGGCAAT--CAATGAATTAATAGCATTTCCAACTTCTGTATGTTA
1 TTAATGGCAATCACAATGAATTAATAGCATTTCCAACTTCTGTATGATA
1260734 TTAATGGCAATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGATA
1 TTAATGGCAATC-ACAATGAATTAATAGCATTTCCAACTTCTGTATGATA
1260784 TTAATGGCAATCA
1 TTAATGGCAATCA
1260797 GTTTGGTTAA
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
47 11 0.19
49 1 0.02
50 47 0.80
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (49 bp):
TTAATGGCAATCACAATGAATTAATAGCATTTCCAACTTCTGTATGATA
Found at i:1262376 original size:31 final size:32
Alignment explanation
Indices: 1262334--1262396 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 32
1262324 TTAAGTACTG
*
1262334 TCGTTATATAC-TTTTATCATTTTAGTCACTA
1 TCGTTACATACTTTTTATCATTTTAGTCACTA
1262365 TCGTTACATACTTTTTTTATCATTTTAGTCAC
1 TCGTTACATAC--TTTTTATCATTTTAGTCAC
1262397 CCACTGTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 10 0.36
34 18 0.64
ACGTcount: A:0.24, C:0.17, G:0.06, T:0.52
Consensus pattern (32 bp):
TCGTTACATACTTTTTATCATTTTAGTCACTA
Found at i:1263174 original size:21 final size:22
Alignment explanation
Indices: 1263132--1263181 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1263122 CACATGCGTG
*
1263132 GGATTTTTCTTGAAATTATCTT
1 GGATTTTTCTGGAAATTATCTT
* *
1263154 GGATTTTTC-GGATATTTTCTT
1 GGATTTTTCTGGAAATTATCTT
1263175 GG-TTTTT
1 GGATTTTT
1263182 ATTGAGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.20
21 11 0.44
22 9 0.36
ACGTcount: A:0.16, C:0.08, G:0.18, T:0.58
Consensus pattern (22 bp):
GGATTTTTCTGGAAATTATCTT
Found at i:1263763 original size:19 final size:19
Alignment explanation
Indices: 1263739--1263777 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1263729 TCACAGATAG
*
1263739 TTATATTTCTCATCAATAA
1 TTATATGTCTCATCAATAA
1263758 TTATATGTCTCATCAATAA
1 TTATATGTCTCATCAATAA
1263777 T
1 T
1263778 ACAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.46
Consensus pattern (19 bp):
TTATATGTCTCATCAATAA
Found at i:1265060 original size:46 final size:45
Alignment explanation
Indices: 1264990--1265128 Score: 170
Period size: 46 Copynumber: 3.0 Consensus size: 45
1264980 ACAATGCTAT
* * *
1264990 AACTCAGTATGGCTTTCTTCACTGAAATACCATACCTACTTTTCTC
1 AACTCAGTATGG-TTTCTTAACTGAAATACCATACCTACATTTCAC
* *
1265036 GACTCAGTACGGTTATCTTAACTGAAATACCATACCTACATTTCAC
1 AACTCAGTATGGTT-TCTTAACTGAAATACCATACCTACATTTCAC
* * * *
1265082 AACTCAATATGGTTTACTTTACTGAAATACCACACCTACATTCCAC
1 AACTCAGTATGGTTT-CTTAACTGAAATACCATACCTACATTTCAC
1265128 A
1 A
1265129 CTTTTCCATG
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
45 3 0.04
46 77 0.96
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.32
Consensus pattern (45 bp):
AACTCAGTATGGTTTCTTAACTGAAATACCATACCTACATTTCAC
Found at i:1267736 original size:40 final size:40
Alignment explanation
Indices: 1267686--1267802 Score: 198
Period size: 40 Copynumber: 2.9 Consensus size: 40
1267676 CGTTTGGAGC
* * **
1267686 AAAAGCGCCGCTAAAGAGTGAGCAATAGCGGCGTTTAATT
1 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
1267726 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
1 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
1267766 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTA
1 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTA
1267803 TAGATAACGC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (40 bp):
AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
Found at i:1267945 original size:111 final size:112
Alignment explanation
Indices: 1267750--1268335 Score: 957
Period size: 111 Copynumber: 5.3 Consensus size: 112
1267740 AGAGTGAGCA
** *
1267750 TTAGTGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1267815 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
*
1267862 TTAGTGGCGTTTATTGTAAAGCGCCGCT-AAGAGTGAGCATTAGTGGCGTTTATAGATTACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1267926 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTT-GGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
* * *
1267972 TTAGTGGCATTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGCGGCGTTTATAAATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1268037 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTT-GGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
**
1268083 TTAGTGGCGTTTATTGCGAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1268148 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
* ** * * * * *
1268195 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGCTTATAAAAAATGTCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
* *
1268260 CAAATAATACTCCCAGACGGTGCCGTTTTGTGTCCTTTGGGGGGG-C
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
1268306 ATTAGTGGCGTTT-TTGTAAAGCGCCGCTAA
1 -TTAGTGGCGTTTATTGTAAAGCGCCGCTAA
1268336 TCTAGGTGTT
Statistics
Matches: 446, Mismatches: 25, Indels: 7
0.93 0.05 0.01
Matches are distributed among these distances:
110 35 0.08
111 268 0.60
112 143 0.32
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (112 bp):
TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
Found at i:1268939 original size:12 final size:12
Alignment explanation
Indices: 1268922--1268947 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1268912 ATATATAACT
1268922 GTAAAAGAGGTC
1 GTAAAAGAGGTC
1268934 GTAAAAGAGGTC
1 GTAAAAGAGGTC
1268946 GT
1 GT
1268948 GCTATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.35, T:0.19
Consensus pattern (12 bp):
GTAAAAGAGGTC
Found at i:1269420 original size:84 final size:83
Alignment explanation
Indices: 1269331--1269531 Score: 330
Period size: 84 Copynumber: 2.4 Consensus size: 83
1269321 TAGTTAAACT
* *
1269331 TTTAGTGGCGTTTTTAAGAAAATGCCACAAATAATGCAATTCCAGACCACGAAAACGGTGTCGTT
1 TTTAGTGGCGTTTTTAA-AAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTT
1269396 TCTGTTCACAGCTGTAATA
65 TCTGTTCACAGCTGTAATA
* *
1269415 TTTAGTGGCGTTTTTCTAAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTTGTT
1 TTTAGTGGCGTTTTT-AAAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTT
1269480 TCTGTTCACAGCTGTAATA
65 TCTGTTCACAGCTGTAATA
1269499 TTTAGTGGCGTTTTTACCAAAAACGCCACAAAA
1 TTTAGTGGCGTTTTTA--AAAAACGCCACAAAA
1269532 CGGTGTTAAT
Statistics
Matches: 109, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
84 93 0.85
85 16 0.15
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (83 bp):
TTTAGTGGCGTTTTTAAAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTTT
CTGTTCACAGCTGTAATA
Found at i:1270552 original size:11 final size:11
Alignment explanation
Indices: 1270515--1270554 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
1270505 GAATATCTCA
1270515 AACT-ATGGGT
1 AACTAATGGGT
*
1270525 AACTAGTGGGT
1 AACTAATGGGT
1270536 AACTAATGGGT
1 AACTAATGGGT
1270547 AACTAATG
1 AACTAATG
1270555 TATTATCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 4 0.15
11 23 0.85
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.28
Consensus pattern (11 bp):
AACTAATGGGT
Found at i:1273544 original size:21 final size:21
Alignment explanation
Indices: 1273518--1273588 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
1273508 CTACAACTTA
* *
1273518 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
1273539 AAGCAGCGACTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* * *
1273560 AAGCGGAGGCTGCAGCAAGAG
1 AAGCAGAGGCTGCAGCGAGGG
1273581 AAGCAGAG
1 AAGCAGAG
1273589 TAGAGCAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.34, C:0.18, G:0.45, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:1274024 original size:42 final size:41
Alignment explanation
Indices: 1273914--1274203 Score: 314
Period size: 42 Copynumber: 6.9 Consensus size: 41
1273904 TTTTGTATAA
* ******
1273914 AAGCGCCACTAAAGAACATGTTCTTTAGCGGCGATTAGAAAAA
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCG-TT-TTCTTT
* * *
1273957 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCCTT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTT-CTTT
1273999 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTT-TTCCT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTCTT--T
* * *
1274041 AAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTT-TTT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTCTTT
* *
1274081 ACAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCT
1 --AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTCTT-T
* *
1274125 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTCTT-T
* *
1274167 AAGCGCCGCTAAAGAACATGGTCTTTAACGGCGTTTT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTT
1274204 TGTTTGTAAA
Statistics
Matches: 217, Mismatches: 23, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
40 2 0.01
42 182 0.84
43 32 0.15
44 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (41 bp):
AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTCTTT
Found at i:1274090 original size:84 final size:83
Alignment explanation
Indices: 1273914--1274204 Score: 377
Period size: 84 Copynumber: 3.5 Consensus size: 83
1273904 TTTTGTATAA
* ******* *
1273914 AAGCGCCACTAAAGAACATGTTCTTTAGCGGCGATTAGAAAAAAAACGCCGCTAAAGAACATGAT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTTTCCTAAGCGCCGCTAAAGAACATGAT
*
1273979 CTTTAGCGGCGTTTTCCCTT-
65 CTTTAGCGGCGTTTT--TTTC
*
1273999 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGGTC
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGATC
* *
1274064 TTTAGTGGCATTTTTTTAC
66 TTTAGCGGCGTTTTTTT-C
* *
1274083 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGATC
1274148 TTTAGCGGCGTTTTTTTC
66 TTTAGCGGCGTTTTTTTC
* *
1274166 TAAGCGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTT
1 -AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT
1274205 GTTTGTAAAC
Statistics
Matches: 182, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
82 2 0.01
83 1 0.01
84 147 0.81
85 32 0.18
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (83 bp):
AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGATC
TTTAGCGGCGTTTTTTTC
Found at i:1274128 original size:126 final size:126
Alignment explanation
Indices: 1273957--1274193 Score: 413
Period size: 126 Copynumber: 1.9 Consensus size: 126
1273947 ATTAGAAAAA
*
1273957 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCCTTAAGCGCCGCTAAAGAACATGTTC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCCTTAAGCGCCGCTAAAGAACATGATC
1274022 TTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTTAC
66 TTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTTAC
* **
1274083 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTT-TTTCTAAGCGCCGCTAAAGAACATGAT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCCT-TAAGCGCCGCTAAAGAACATGAT
*
1274147 CTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTA
65 CTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGGTCTTTA
1274194 ACGGCGTTTT
Statistics
Matches: 105, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
125 1 0.01
126 104 0.99
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (126 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCCTTAAGCGCCGCTAAAGAACATGATC
TTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTTAC
Found at i:1274204 original size:42 final size:42
Alignment explanation
Indices: 1273960--1274204 Score: 359
Period size: 42 Copynumber: 5.8 Consensus size: 42
1273950 AGAAAAAAAA
**
1273960 CGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTCCCTTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC-TAAG
* *
1274002 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* * * *
1274044 CGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTTAC-AAA
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT-CTAAG
*
1274086 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
1274128 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* *
1274170 CGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
1274205 GTTTGTAAAC
Statistics
Matches: 186, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
41 1 0.01
42 178 0.96
43 7 0.04
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
Found at i:1282416 original size:17 final size:17
Alignment explanation
Indices: 1282394--1282427 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1282384 TACATCAATG
1282394 ATCAATCCATTTCCATT
1 ATCAATCCATTTCCATT
* *
1282411 ATCAATTCTTTTCCATT
1 ATCAATCCATTTCCATT
1282428 TTTCTTGTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.47
Consensus pattern (17 bp):
ATCAATCCATTTCCATT
Found at i:1288069 original size:17 final size:17
Alignment explanation
Indices: 1288036--1288093 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
1288026 TATTTTCTTG
*
1288036 AAAA-TGATTTTCAAAA
1 AAAATTGATTTTTAAAA
1288052 AAAATTGATTTTTGAAAA
1 AAAATTGATTTTT-AAAA
** *
1288070 ATGATTTATTTTTTAAAA
1 AAAATTGA-TTTTTAAAA
1288088 AAAATT
1 AAAATT
1288094 AAATTTTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 4 0.12
17 7 0.21
18 17 0.52
19 5 0.15
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (17 bp):
AAAATTGATTTTTAAAA
Found at i:1288069 original size:18 final size:18
Alignment explanation
Indices: 1288043--1288093 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
1288033 TTGAAAATGA
1288043 TTTTCAAAAAAAATTGAT
1 TTTTCAAAAAAAATTGAT
* ** *
1288061 TTTTGAAAAATGATTTAT
1 TTTTCAAAAAAAATTGAT
*
1288079 TTTTTAAAAAAAATT
1 TTTTCAAAAAAAATT
1288094 AAATTTTTAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (18 bp):
TTTTCAAAAAAAATTGAT
Found at i:1288100 original size:18 final size:17
Alignment explanation
Indices: 1288042--1288102 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
1288032 CTTGAAAATG
* *
1288042 ATTTTCAAAAAAAATTG
1 ATTTTTAAAAAAAATTA
* *
1288059 ATTTTTGAAAAATGATTTA
1 ATTTTT-AAAAA-AAATTA
*
1288078 TTTTTTAAAAAAAATTAA
1 ATTTTTAAAAAAAATT-A
1288096 ATTTTTA
1 ATTTTTA
1288103 TGGTGTTTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
17 8 0.24
18 17 0.52
19 8 0.24
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.46
Consensus pattern (17 bp):
ATTTTTAAAAAAAATTA
Found at i:1293062 original size:16 final size:17
Alignment explanation
Indices: 1293041--1293072 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1293031 TTATAAACAA
1293041 AAGAAAGAAA-AGAAAT
1 AAGAAAGAAACAGAAAT
1293057 AAGAAAGAAACAGAAA
1 AAGAAAGAAACAGAAA
1293073 GCTTAAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (17 bp):
AAGAAAGAAACAGAAAT
Found at i:1297403 original size:29 final size:29
Alignment explanation
Indices: 1297370--1297454 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 29
1297360 TCAACAATGA
1297370 ATTAATAGCATTTCCAACTTCTGTATGTT
1 ATTAATAGCATTTCCAACTTCTGTATGTT
* * * *
1297399 ATTAATGGCA-AT-CAA---C--AATG-A
1 ATTAATAGCATTTCCAACTTCTGTATGTT
1297420 ATTAATAGCATTTCCAACTTCTGTATGTT
1 ATTAATAGCATTTCCAACTTCTGTATGTT
1297449 ATTAAT
1 ATTAAT
1297455 GGAAATCAAC
Statistics
Matches: 40, Mismatches: 8, Indels: 16
0.62 0.12 0.25
Matches are distributed among these distances:
21 9 0.22
22 4 0.10
23 3 0.08
24 1 0.03
26 1 0.03
27 3 0.08
28 4 0.10
29 15 0.38
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (29 bp):
ATTAATAGCATTTCCAACTTCTGTATGTT
Found at i:1297434 original size:50 final size:50
Alignment explanation
Indices: 1297359--1297512 Score: 299
Period size: 50 Copynumber: 3.1 Consensus size: 50
1297349 CCATAAAAAG
1297359 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGCA
1 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGCA
*
1297409 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGAA
1 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGCA
1297459 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGCA
1 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGCA
1297509 ATCA
1 ATCA
1297513 GTTTGGTTAA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 102 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (50 bp):
ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGCA
Found at i:1299071 original size:31 final size:33
Alignment explanation
Indices: 1299036--1299107 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 33
1299026 TTAGGTACTG
* *
1299036 TCGTTATATAC-TTTTATCATTTTAGTCA-CTA
1 TCGTTACATACTTTTTATCATTTTAGTCACCCA
1299067 TCGTTACATACTTTTTTTATCATTTTAGTCACCCA
1 TCGTTACATAC--TTTTTATCATTTTAGTCACCCA
1299102 TCGTTA
1 TCGTTA
1299108 ATTTGCCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 10 0.29
34 17 0.49
35 8 0.23
ACGTcount: A:0.24, C:0.19, G:0.07, T:0.50
Consensus pattern (33 bp):
TCGTTACATACTTTTTATCATTTTAGTCACCCA
Found at i:1299252 original size:162 final size:162
Alignment explanation
Indices: 1298965--1299290 Score: 510
Period size: 162 Copynumber: 2.0 Consensus size: 162
1298955 GTAAACCACA
* * * *
1298965 CAGTTGGTCACTCAACTTTTATATGTATTCATTTTGGGCACCAAATTTAAAAGTTTACAATTTAG
1 CAGTTGGCCACTCAACTTTTATAAGTATTCATTTTGGACACCAAATTTAAAAGTTCACAATTTAG
* * *
1299030 GTACTGTCGTTATATACTTTTATCATTTTAGTCACTATCGTTACATACTTTTTTTATCATTTTAG
66 GTACTGTCATTATATACTTTTATCATTTTAGCCACTATCGTTACATACTTTTTATATCATTTTAG
* * *
1299095 TCACCCATCGTTAATTTGCCATTAAATGTACT
131 TCACCCACCATTAATTTGCCATTAAATATACT
*
1299127 CAGTTGGCCACTCAACTTTTATAAGTATTCATTTTGGACACCAAAATTTAAAAGTTCGCAATTTA
1 CAGTTGGCCACTCAACTTTTATAAGTATTCATTTTGGACACC-AAATTTAAAAGTTCACAATTTA
*
1299192 GGTACTGTTATTATATACTTTTATCATTTTAGCCACTATCGTTACATAC-TTTTATATCATTTTA
65 GGTACTGTCATTATATACTTTTATCATTTTAGCCACTATCGTTACATACTTTTTATATCATTTTA
* *
1299256 GTCGCCCACCATTAATTTTCCATTAAATATACT
130 GTCACCCACCATTAATTTGCCATTAAATATACT
1299289 CA
1 CA
1299291 TTTTTAATCA
Statistics
Matches: 149, Mismatches: 14, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
162 83 0.56
163 66 0.44
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.43
Consensus pattern (162 bp):
CAGTTGGCCACTCAACTTTTATAAGTATTCATTTTGGACACCAAATTTAAAAGTTCACAATTTAG
GTACTGTCATTATATACTTTTATCATTTTAGCCACTATCGTTACATACTTTTTATATCATTTTAG
TCACCCACCATTAATTTGCCATTAAATATACT
Found at i:1299427 original size:23 final size:23
Alignment explanation
Indices: 1299392--1299446 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
1299382 AAAAAGAAAA
* *
1299392 ATAAAAAGATAAATTAGTTTTTC-
1 ATAAAAA-CTAAAGTAGTTTTTCT
*
1299415 AGTAAAAACTAAAGTATTTTTTCT
1 A-TAAAAACTAAAGTAGTTTTTCT
1299439 ATAAAAAC
1 ATAAAAAC
1299447 CTAGGTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.36
Consensus pattern (23 bp):
ATAAAAACTAAAGTAGTTTTTCT
Found at i:1299806 original size:31 final size:31
Alignment explanation
Indices: 1299747--1299812 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
1299737 AGGCGAGTTG
**
1299747 CTAAAATGATAAAAGGATATAATGATAGTGA
1 CTAAAATGATAAAAGGATATAACAATAGTGA
** * *
1299778 CTAAAATGATAAAATTATGTAACAATAGTGC
1 CTAAAATGATAAAAGGATATAACAATAGTGA
1299809 CTAA
1 CTAA
1299813 GTTGCAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (31 bp):
CTAAAATGATAAAAGGATATAACAATAGTGA
Found at i:1300962 original size:23 final size:23
Alignment explanation
Indices: 1300932--1300975 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1300922 AAATGTGACC
1300932 TTTTATTTTTTATTT-TGTTTTCG
1 TTTTATTTTTT-TTTATGTTTTCG
1300955 TTTTATTTTTTTTTATGTTTT
1 TTTTATTTTTTTTTATGTTTT
1300976 TTATTATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.09, C:0.02, G:0.07, T:0.82
Consensus pattern (23 bp):
TTTTATTTTTTTTTATGTTTTCG
Found at i:1300974 original size:17 final size:17
Alignment explanation
Indices: 1300932--1300975 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1300922 AAATGTGACC
*
1300932 TTTTATTTTTTATTTTG
1 TTTTATGTTTTATTTTG
* *
1300949 TTTT-CGTTTTATTTTT
1 TTTTATGTTTTATTTTG
1300965 TTTTATGTTTT
1 TTTTATGTTTT
1300976 TTATTATTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.09, C:0.02, G:0.07, T:0.82
Consensus pattern (17 bp):
TTTTATGTTTTATTTTG
Found at i:1302528 original size:14 final size:14
Alignment explanation
Indices: 1302509--1302535 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1302499 TGTGTGGACT
1302509 ATATTTTAAGAATA
1 ATATTTTAAGAATA
1302523 ATATTTTAAGAAT
1 ATATTTTAAGAAT
1302536 CAATTTTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
ATATTTTAAGAATA
Found at i:1315041 original size:51 final size:50
Alignment explanation
Indices: 1314924--1315077 Score: 258
Period size: 51 Copynumber: 3.1 Consensus size: 50
1314914 CCATAAAAAG
1314924 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTA-T-ATGGCA
1 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGCA
* *
1314972 ATCAACAATGAATCAATAGCATTTCCAACTTCTCGTATGTTATTAATGGAA
1 ATCAACAATGAATTAATAGCATTTCCAACTTCT-GTATGTTATTAATGGCA
1315023 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATTGGCA
1 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAA-TGGCA
1315074 ATCA
1 ATCA
1315078 GTTTGGTTAA
Statistics
Matches: 98, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
48 32 0.33
49 8 0.08
50 13 0.13
51 45 0.46
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (50 bp):
ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGCA
Found at i:1317646 original size:17 final size:17
Alignment explanation
Indices: 1317624--1317657 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1317614 TACATCAATG
1317624 ATCAATCCATTTCCATT
1 ATCAATCCATTTCCATT
* *
1317641 ATCAATTCTTTTCCATT
1 ATCAATCCATTTCCATT
1317658 TTTCTTGTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.47
Consensus pattern (17 bp):
ATCAATCCATTTCCATT
Found at i:1323284 original size:18 final size:17
Alignment explanation
Indices: 1323251--1323307 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
1323241 TATTTTCTTG
*
1323251 AAAA-TGATTTTCAAAA
1 AAAATTGATTTTTAAAA
1323267 AAAATTGATTTTTGAAAA
1 AAAATTGATTTTT-AAAA
** *
1323285 ATGATTTATTTTTAAAA
1 AAAATTGATTTTTAAAA
1323302 AAAATT
1 AAAATT
1323308 AAATTTTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 4 0.12
17 15 0.45
18 14 0.42
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (17 bp):
AAAATTGATTTTTAAAA
Found at i:1323313 original size:18 final size:17
Alignment explanation
Indices: 1323257--1323316 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
1323247 CTTGAAAATG
* *
1323257 ATTTTCAAAAAAAATTG
1 ATTTTTAAAAAAAATTA
** *
1323274 ATTTTTGAAAAATGATTT
1 ATTTTT-AAAAAAAATTA
1323292 ATTTTTAAAAAAAATTAA
1 ATTTTTAAAAAAAATT-A
1323310 ATTTTTA
1 ATTTTTA
1323317 TGGTGTTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
17 13 0.38
18 21 0.62
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (17 bp):
ATTTTTAAAAAAAATTA
Found at i:1327164 original size:15 final size:16
Alignment explanation
Indices: 1327138--1327171 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1327128 AAAATGTATA
1327138 TAAATAAATAATAAAT
1 TAAATAAATAATAAAT
*
1327154 TAAAT-AATAATATAT
1 TAAATAAATAATAAAT
1327169 TAA
1 TAA
1327172 CATTTTCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAATAAATAATAAAT
Found at i:1332503 original size:2 final size:2
Alignment explanation
Indices: 1332496--1332541 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
1332486 ATGTATATCA
* * * *
1332496 AG AG AG AG GG AG AG AG GG AG AG AG GG GG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1332538 AG AG
1 AG AG
1332542 CTATTTTCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1332510 original size:8 final size:8
Alignment explanation
Indices: 1332497--1332541 Score: 63
Period size: 8 Copynumber: 5.6 Consensus size: 8
1332487 TGTATATCAA
1332497 GAGAGAGG
1 GAGAGAGG
1332505 GAGAGAGG
1 GAGAGAGG
1332513 GAGAGAGG
1 GAGAGAGG
* *
1332521 GGGAGAGA
1 GAGAGAGG
*
1332529 GAGAGAGA
1 GAGAGAGG
1332537 GAGAG
1 GAGAG
1332542 CTATTTTCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (8 bp):
GAGAGAGG
Found at i:1338167 original size:16 final size:18
Alignment explanation
Indices: 1338132--1338169 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1338122 ATCCTTATTT
1338132 AAATAAAATACAATAGTA
1 AAATAAAATACAATAGTA
1338150 AAATAAAATA-AA-AGTA
1 AAATAAAATACAATAGTA
1338166 AAAT
1 AAAT
1338170 CCATATAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAATACAATAGTA
Found at i:1344290 original size:16 final size:16
Alignment explanation
Indices: 1344256--1344290 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1344246 ACTGAAAAAG
*
1344256 AAATTGAAAAGATGAA
1 AAATTGAAAAGATAAA
1344272 AAATTGAAAAGATAAA
1 AAATTGAAAAGATAAA
1344288 AAA
1 AAA
1344291 AAATAGAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (16 bp):
AAATTGAAAAGATAAA
Found at i:1353524 original size:17 final size:19
Alignment explanation
Indices: 1353497--1353534 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
1353487 AGTTTTAATT
1353497 TTTTTTAATC-ATTTCAAG
1 TTTTTTAATCAATTTCAAG
1353515 TTTTTT-ATCAATTTCAAG
1 TTTTTTAATCAATTTCAAG
1353533 TT
1 TT
1353535 CGAATCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTTTTAATCAATTTCAAG
Found at i:1364364 original size:42 final size:41
Alignment explanation
Indices: 1364286--1364364 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 41
1364276 CAATTATGTA
* * *
1364286 ATATTAGATAGATTATATTAAGTTTTATGTTTGATTTTAGT
1 ATATTAGATAGATTATATTAAGTGTTAAGTTCGATTTTAGT
*
1364327 ATATTAGTTTAGATTATATTGAA-TGTTAAGTTCGATTT
1 ATATTAG-ATAGATTATATT-AAGTGTTAAGTTCGATTT
1364365 ATTATAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 7 0.22
42 23 0.72
43 2 0.06
ACGTcount: A:0.32, C:0.01, G:0.15, T:0.52
Consensus pattern (41 bp):
ATATTAGATAGATTATATTAAGTGTTAAGTTCGATTTTAGT
Found at i:1366679 original size:58 final size:58
Alignment explanation
Indices: 1366614--1366737 Score: 248
Period size: 58 Copynumber: 2.1 Consensus size: 58
1366604 GTCATCTTAC
1366614 TTGAAAATAATGTGAATCTTTGAAATTTGGTCTTACTAGTAGATGAATGAACTTATAT
1 TTGAAAATAATGTGAATCTTTGAAATTTGGTCTTACTAGTAGATGAATGAACTTATAT
1366672 TTGAAAATAATGTGAATCTTTGAAATTTGGTCTTACTAGTAGATGAATGAACTTATAT
1 TTGAAAATAATGTGAATCTTTGAAATTTGGTCTTACTAGTAGATGAATGAACTTATAT
1366730 TTGAAAAT
1 TTGAAAAT
1366738 GTGGCAATGA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 66 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (58 bp):
TTGAAAATAATGTGAATCTTTGAAATTTGGTCTTACTAGTAGATGAATGAACTTATAT
Found at i:1376352 original size:7 final size:7
Alignment explanation
Indices: 1376330--1376363 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
1376320 TTATTTATGA
1376330 ATAT-TT
1 ATATATT
1376336 ATAT-TT
1 ATATATT
1376342 ATATATT
1 ATATATT
1376349 ATATATT
1 ATATATT
1376356 ATATATT
1 ATATATT
1376363 A
1 A
1376364 AAGTTAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 10 0.37
7 17 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATATATT
Found at i:1381916 original size:20 final size:20
Alignment explanation
Indices: 1381893--1381934 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1381883 GCTCTTAACG
*
1381893 TTTA-TATTTTTTTTTGTTAA
1 TTTAGTATTTATTTTT-TTAA
*
1381913 TTTAGTCTTTATTTTTTTAA
1 TTTAGTATTTATTTTTTTAA
1381933 TT
1 TT
1381935 AAATTTGACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTAGTATTTATTTTTTTAA
Found at i:1395394 original size:17 final size:18
Alignment explanation
Indices: 1395374--1395409 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1395364 TATAAATTCT
1395374 TTAAAAATATA-TATTAA
1 TTAAAAATATATTATTAA
*
1395391 TTAAAATTATATTATTAA
1 TTAAAAATATATTATTAA
1395409 T
1 T
1395410 ATGTTTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAAAATATATTATTAA
Found at i:1399549 original size:29 final size:30
Alignment explanation
Indices: 1399490--1399547 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1399480 TCCGAGCCTT
*
1399490 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
1399520 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
1399548 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:1399776 original size:13 final size:13
Alignment explanation
Indices: 1399758--1399789 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1399748 TTTCCAGCAA
1399758 TTATGAATTTATT
1 TTATGAATTTATT
1399771 TTATGAATTTATT
1 TTATGAATTTATT
*
1399784 TGATGA
1 TTATGA
1399790 TGATCTAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:1399958 original size:50 final size:50
Alignment explanation
Indices: 1399883--1400075 Score: 296
Period size: 50 Copynumber: 3.8 Consensus size: 50
1399873 ATTTGGGTAA
1399883 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
1399933 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
1399983 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
1400033 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
1400076 TGTTATTATT
Statistics
Matches: 129, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 95 0.74
51 34 0.26
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:1404702 original size:3 final size:3
Alignment explanation
Indices: 1404694--1404725 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1404684 TCGTCTTCGT
*
1404694 CGC CGC CGC CGC CGC CGC CGC CGC CGA CGC CG
1 CGC CGC CGC CGC CGC CGC CGC CGC CGC CGC CG
1404726 AAACGCCGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.62, G:0.34, T:0.00
Consensus pattern (3 bp):
CGC
Found at i:1409038 original size:4 final size:4
Alignment explanation
Indices: 1409029--1409062 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
1409019 AAGTTTTATT
*
1409029 TTTA TTTA TTTA TTTA TTTA TTTA CTTA GTTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA T
1409063 GTAATGGCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 24 0.89
5 3 0.11
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:1418591 original size:83 final size:84
Alignment explanation
Indices: 1418492--1418648 Score: 237
Period size: 84 Copynumber: 1.9 Consensus size: 84
1418482 AGGGTGGCTA
* * *
1418492 AAGTGCAATTTTACTATATGTTAGTTTATAATTTCT-T-TATTTAAAAGAGGACTGAATTGAAAA
1 AAGTGCAATTTCACTATATATTAATTTATAATTT-TATCTATTTAAAAGAGGACTGAATTGAAAA
1418555 TTTTTCATTTGGGGGGGTCG
65 TTTTTCATTTGGGGGGGTCG
* * *
1418575 AAGTGCAATTTCACTATATATTAATTTATAGTTTTATCTATTTATAAGAGGACTGAATTGAAATT
1 AAGTGCAATTTCACTATATATTAATTTATAATTTTATCTATTTAAAAGAGGACTGAATTGAAAAT
1418640 TTTTCATTT
66 TTTTCATTT
1418649 TCCCCTGCCT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
82 1 0.02
83 31 0.47
84 34 0.52
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.45
Consensus pattern (84 bp):
AAGTGCAATTTCACTATATATTAATTTATAATTTTATCTATTTAAAAGAGGACTGAATTGAAAAT
TTTTCATTTGGGGGGGTCG
Found at i:1442828 original size:31 final size:31
Alignment explanation
Indices: 1442768--1442830 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 31
1442758 TAACAAAATG
*
1442768 GTCATTGAACTACTTGAAAATTTTCATTTAA
1 GTCATTGAACTACTTGAAAATCTTCATTTAA
1442799 GTCATTGAACTA-TTCGAAATATCTT-ATTTAA
1 GTCATTGAACTACTT-GAAA-ATCTTCATTTAA
1442830 G
1 G
1442831 GCACTAGGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 2 0.07
31 23 0.79
32 4 0.14
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (31 bp):
GTCATTGAACTACTTGAAAATCTTCATTTAA
Found at i:1446731 original size:14 final size:15
Alignment explanation
Indices: 1446707--1446736 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1446697 GTATCTGAAT
1446707 AATTAATTAATATTA
1 AATTAATTAATATTA
1446722 AATT-ATTAATATTA
1 AATTAATTAATATTA
1446736 A
1 A
1446737 TTAGTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTAATTAATATTA
Found at i:1446946 original size:18 final size:17
Alignment explanation
Indices: 1446923--1446960 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
1446913 AATTATAACG
1446923 AATATAATAAAATATTTA
1 AATATAATAAAATA-TTA
*
1446941 AATATAATTAAATATTA
1 AATATAATAAAATATTA
1446958 AAT
1 AAT
1446961 TTGTAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATATAATAAAATATTA
Found at i:1449259 original size:78 final size:78
Alignment explanation
Indices: 1449130--1449286 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
1449120 AGGTATTCTG
1449130 TAATAATTTTCTTATTTTGTGAACAATTCTAAATATGAAATATAGGCTTTCATGATACTTACATA
1 TAATAATTTTCTTATTTTGTGAACAATTCTAAATATGAAATATAGGCTTTCATGATACTTACATA
1449195 AATATTTTGGAGT
66 AATATTTTGGAGT
1449208 TAATAATTTTCTTATTTTGTGAACAATTCTAAATATGAAATATAGGCTTTCATGATACTTACATA
1 TAATAATTTTCTTATTTTGTGAACAATTCTAAATATGAAATATAGGCTTTCATGATACTTACATA
1449273 AATATTTTGGAGT
66 AATATTTTGGAGT
1449286 T
1 T
1449287 TTCATGAATG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (78 bp):
TAATAATTTTCTTATTTTGTGAACAATTCTAAATATGAAATATAGGCTTTCATGATACTTACATA
AATATTTTGGAGT
Found at i:1468189 original size:137 final size:131
Alignment explanation
Indices: 1467933--1468189 Score: 397
Period size: 131 Copynumber: 1.9 Consensus size: 131
1467923 GAAGATTGAC
*
1467933 TAAGACGAAGGCGAAGGAGATCCGATCATGGAAGGAGAGAAAGAGATCAGCCGTGAAGTGTGGTC
1 TAAGACGAAGGCGAAGGAGATCCGATCATGGAAGGAGAGAAAGAGATCAGCCGTGAAGTGTGGAC
* *
1467998 TTGCCGCCGAGAAGAACACGGCGGAGGAAGAGGAGAAAGTAGCGCCATTGAAATGTATAGATCGA
66 TTACCGCAGAGAAGAACACGGCGGAGGAAGAGGAGAAAGTAGCGCCATTGAAATGTATAGATCGA
1468063 A
131 A
* * * *
1468064 TAAGACGAGGGCGAAGGAGATCCTATCATGGAAGGAGAGAAAGAGATCGGCCGTGAAGTGTGGAG
1 TAAGACGAAGGCGAAGGAGATCCGATCATGGAAGGAGAGAAAGAGATCAGCCGTGAAGTGTGGAC
1468129 TTACCGTCGAGGAGAAGAAGAACACGGCGGAGGAAGAGGAGAAAGTAGCGCCATTGAAATG
66 TTACCG-C----AG-AGAAGAACACGGCGGAGGAAGAGGAGAAAGTAGCGCCATTGAAATG
1468190 CGATTGGCGC
Statistics
Matches: 113, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
131 65 0.58
132 1 0.01
136 1 0.01
137 46 0.41
ACGTcount: A:0.36, C:0.14, G:0.37, T:0.13
Consensus pattern (131 bp):
TAAGACGAAGGCGAAGGAGATCCGATCATGGAAGGAGAGAAAGAGATCAGCCGTGAAGTGTGGAC
TTACCGCAGAGAAGAACACGGCGGAGGAAGAGGAGAAAGTAGCGCCATTGAAATGTATAGATCGA
A
Found at i:1470035 original size:39 final size:41
Alignment explanation
Indices: 1469973--1470061 Score: 130
Period size: 39 Copynumber: 2.2 Consensus size: 41
1469963 TGAAAAGTAT
*
1469973 TTATATT-AAAAACACTACCATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACTACAATAAATATAATAAATATTTTA
*
1470013 TTATATTAAAAAACAC-A-AATAAATATAATAATTATTTTA
1 TTATATTAAAAAACACTACAATAAATATAATAAATATTTTA
*
1470052 TTACATTAAA
1 TTATATTAAA
1470062 TATAATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
39 29 0.64
40 8 0.18
41 8 0.18
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (41 bp):
TTATATTAAAAAACACTACAATAAATATAATAAATATTTTA
Found at i:1471271 original size:52 final size:52
Alignment explanation
Indices: 1471215--1471313 Score: 126
Period size: 52 Copynumber: 1.9 Consensus size: 52
1471205 AAAATAAAAA
* *
1471215 ACTCAAGCCTTAAACCTACCCTGACCCCAATTGACTCGATCCAAAAAGGAAT
1 ACTCAAGCCTTAAACCTACCCTGACCCCAATTAACCCGATCCAAAAAGGAAT
* * * * * *
1471267 ACTCAAGCGTTAGACCTGCCCTGATCTCAATTAACCCGATTCAAAAA
1 ACTCAAGCCTTAAACCTACCCTGACCCCAATTAACCCGATCCAAAAA
1471314 ATAAAAATTG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 39 1.00
ACGTcount: A:0.35, C:0.31, G:0.12, T:0.21
Consensus pattern (52 bp):
ACTCAAGCCTTAAACCTACCCTGACCCCAATTAACCCGATCCAAAAAGGAAT
Found at i:1474469 original size:19 final size:19
Alignment explanation
Indices: 1474436--1474472 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1474426 CATACTTTGA
**
1474436 TTTTTTTTATTTTCATAAT
1 TTTTTTTTACATTCATAAT
1474455 TTTTTTTTACATTCATAA
1 TTTTTTTTACATTCATAA
1474473 ATATATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTTTTACATTCATAAT
Found at i:1478879 original size:29 final size:30
Alignment explanation
Indices: 1478812--1478879 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
1478802 ATTTGCAATT
* * *
1478812 ATTTGATTCTTTTTAATAGTATAGAGACTAC
1 ATTTGA-TCTATTTAATAATAAAGAGACTAC
*
1478843 A-TTAATCTATTTAATAATAAAGAGACTA-
1 ATTTGATCTATTTAATAATAAAGAGACTAC
1478871 ATTTGATCT
1 ATTTGATCT
1478880 GGTCCCTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 1 0.03
29 26 0.84
30 3 0.10
31 1 0.03
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (30 bp):
ATTTGATCTATTTAATAATAAAGAGACTAC
Found at i:1492902 original size:14 final size:14
Alignment explanation
Indices: 1492883--1492911 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1492873 AATTCATTGT
1492883 ATTCAAATAAACTA
1 ATTCAAATAAACTA
1492897 ATTCAAATAAACTA
1 ATTCAAATAAACTA
1492911 A
1 A
1492912 GGGTGAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (14 bp):
ATTCAAATAAACTA
Found at i:1494519 original size:15 final size:15
Alignment explanation
Indices: 1494499--1494528 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1494489 TTAAAATTAA
1494499 AATATACCTTACCAT
1 AATATACCTTACCAT
1494514 AATATACCTTACCAT
1 AATATACCTTACCAT
1494529 TTCACTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (15 bp):
AATATACCTTACCAT
Found at i:1495538 original size:22 final size:22
Alignment explanation
Indices: 1495513--1495564 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 22
1495503 AAATTATGTG
1495513 AAAATAATTTTAATTTTA-ATA
1 AAAATAATTTTAATTTTACATA
*
1495534 TAAAAT-A-TTTATTTTTACATA
1 -AAAATAATTTTAATTTTACATA
1495555 AGAAATAATT
1 A-AAATAATT
1495565 AAATTAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 10 0.40
21 8 0.32
22 6 0.24
23 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
AAAATAATTTTAATTTTACATA
Found at i:1508478 original size:6 final size:6
Alignment explanation
Indices: 1508467--1508532 Score: 123
Period size: 6 Copynumber: 11.0 Consensus size: 6
1508457 TCAGGTTCCC
*
1508467 ACATAT ACATAT ACATAT ACATAT ACATTT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1508515 ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT
1508533 GTGTATGGTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (6 bp):
ACATAT
Found at i:1513455 original size:27 final size:27
Alignment explanation
Indices: 1513423--1513476 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1513413 AGAAATTTTA
*
1513423 AATTTAACCAAGTTCAAGTTATTAATT
1 AATTTAACCAAGTTCAAGTTATCAATT
** *
1513450 AATTTAATGAAGTTGAAGTTATCAATT
1 AATTTAACCAAGTTCAAGTTATCAATT
1513477 TTTAATAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (27 bp):
AATTTAACCAAGTTCAAGTTATCAATT
Found at i:1516377 original size:2 final size:2
Alignment explanation
Indices: 1516370--1516401 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1516360 AAATGGATGC
*
1516370 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1516402 TGGATTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1521023 original size:27 final size:27
Alignment explanation
Indices: 1520969--1521031 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
1520959 TAAATTTCAA
*
1520969 AATTATATATAAACTTTAATTTAATGT
1 AATTATACATAAACTTTAATTTAATGT
**
1520996 ACA-TATACATAAACTTTAATTTGGTGT
1 A-ATTATACATAAACTTTAATTTAATGT
1521023 AATTATACA
1 AATTATACA
1521032 CGTAAAACCC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 1 0.03
27 29 0.94
28 1 0.03
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (27 bp):
AATTATACATAAACTTTAATTTAATGT
Found at i:1529417 original size:13 final size:13
Alignment explanation
Indices: 1529378--1529421 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
1529368 CTGAAAATTT
1529378 TTTTATGGGAAAA
1 TTTTATGGGAAAA
1529391 TTTTGCAT-GGAAAA
1 TTTT--ATGGGAAAA
1529405 TTTTATGGGAAAA
1 TTTTATGGGAAAA
1529418 TTTT
1 TTTT
1529422 TCTCCAGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.07
13 14 0.50
14 10 0.36
15 2 0.07
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.43
Consensus pattern (13 bp):
TTTTATGGGAAAA
Found at i:1529422 original size:14 final size:14
Alignment explanation
Indices: 1529377--1529422 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1529367 TCTGAAAATT
1529377 TTTTTATGGGAAAA
1 TTTTTATGGGAAAA
*
1529391 TTTTGCAT-GGAAAA
1 TTTT-TATGGGAAAA
1529405 -TTTTATGGGAAAA
1 TTTTTATGGGAAAA
1529418 TTTTT
1 TTTTT
1529423 CTCCAGCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 2 0.07
13 9 0.33
14 14 0.52
15 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.46
Consensus pattern (14 bp):
TTTTTATGGGAAAA
Found at i:1534450 original size:177 final size:178
Alignment explanation
Indices: 1534119--1534455 Score: 489
Period size: 177 Copynumber: 1.9 Consensus size: 178
1534109 TTTAGTATGC
* * *
1534119 AATCCCTAATAAACCTCGAAACAGTCTTTTGTATGGTATTGACGCAATGTATAGTTTACAGTTCT
1 AATCCCGAATAAACCTCGAAACAGTCTTTTGAATGGTATTGACACAATGTATAGTTTACAGTTCT
* * * *
1534184 TTGACTCGATCATACGATGAGGCCATCTAACTTCACCGAGAATATTGTAAAAGTAACCACCTTGG
66 TTGACTCGAACAAACAATGAGGCCATCTAACTTCACCGAGAATATTGTAAAAGAAACCACCTTGG
* * *
1534249 ATGACAGAAGTTGTATTGAAAAAGT-TCAACTCGACCGGCAGTATCCA
131 ACGACAGAAGTCGTATTCAAAAAGTCTCAACTCGACCGGCAGTATCCA
** * * *
1534296 AATCCCGAATAAACCTCGAGGCGGTCTTTTGAATGGTATTGACACAATGTATGGTTTACAGTTTT
1 AATCCCGAATAAACCTCGAAACAGTCTTTTGAATGGTATTGACACAATGTATAGTTTACAGTTCT
* **
1534361 TTGACTCGAAGAAACAATGAGGCTGTCTAACTTCACCGAGAATATTGTAAAAGAAACCACCTTGG
66 TTGACTCGAACAAACAATGAGGCCATCTAACTTCACCGAGAATATTGTAAAAGAAACCACCTTGG
1534426 ACGACAGAAAGTCGTA-TCAAAAAGTCTCAA
131 ACGACAG-AAGTCGTATTCAAAAAGTCTCAA
1534456 AACTGCCAGT
Statistics
Matches: 140, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
177 129 0.92
178 11 0.08
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (178 bp):
AATCCCGAATAAACCTCGAAACAGTCTTTTGAATGGTATTGACACAATGTATAGTTTACAGTTCT
TTGACTCGAACAAACAATGAGGCCATCTAACTTCACCGAGAATATTGTAAAAGAAACCACCTTGG
ACGACAGAAGTCGTATTCAAAAAGTCTCAACTCGACCGGCAGTATCCA
Found at i:1535721 original size:19 final size:20
Alignment explanation
Indices: 1535697--1535752 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
1535687 TTCGTTTTAA
1535697 GTATTTTCCGTCAAAATC-C
1 GTATTTTCCGTCAAAATCAC
*
1535716 GTATTTTCCATCAAAATTCAC
1 GTATTTTCCGTCAAAA-TCAC
*
1535737 -CATTTTCCGTCAAAAT
1 GTATTTTCCGTCAAAAT
1535753 TCGCCATCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 16 0.50
20 15 0.47
21 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (20 bp):
GTATTTTCCGTCAAAATCAC
Found at i:1535743 original size:20 final size:20
Alignment explanation
Indices: 1535718--1535759 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1535708 CAAAATCCGT
1535718 ATTTTCCATCAAAATTCACC
1 ATTTTCCATCAAAATTCACC
* *
1535738 ATTTTCCGTCAAAATTCGCC
1 ATTTTCCATCAAAATTCACC
1535758 AT
1 AT
1535760 CAATATGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.36
Consensus pattern (20 bp):
ATTTTCCATCAAAATTCACC
Found at i:1536521 original size:57 final size:56
Alignment explanation
Indices: 1536439--1536548 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 56
1536429 CTGGTCAAAC
* * *
1536439 TTTATAATTAGTATCTTTATTTTACTCAACTTATAAATTTAGTCCCTTATTTTAAAT
1 TTTATAATTAGTACCTGTATCTTACTCAACTTATAAATTTAGTCCCTT-TTTTAAAT
*
1536496 TTTATAATTAGTCCCTGTATCTTACTCAACTTATAAATTTAGTCCCTTTTTTA
1 TTTATAATTAGTACCTGTATCTTACTCAACTTATAAATTTAGTCCCTTTTTTA
1536549 TTAGTTTACC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
56 5 0.10
57 44 0.90
ACGTcount: A:0.29, C:0.15, G:0.05, T:0.51
Consensus pattern (56 bp):
TTTATAATTAGTACCTGTATCTTACTCAACTTATAAATTTAGTCCCTTTTTTAAAT
Found at i:1536539 original size:31 final size:29
Alignment explanation
Indices: 1536459--1536548 Score: 98
Period size: 26 Copynumber: 3.1 Consensus size: 29
1536449 GTATCTTTAT
1536459 TTTACTCAACTTATAAATTTAGTCCCTTA
1 TTTACTCAACTTATAAATTTAGTCCCTTA
* *
1536488 TTT--T-AAATTTTATAA-TTAGTCCCTGTA
1 TTTACTCAACTTATA-AATTTAGTCCCT-TA
*
1536515 TCTTACTCAACTTATAAATTTAGTCCCTTT
1 T-TTACTCAACTTATAAATTTAGTCCCTTA
1536545 TTTA
1 TTTA
1536549 TTAGTTTACC
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
26 15 0.31
27 6 0.12
28 2 0.04
29 6 0.12
30 5 0.10
31 15 0.31
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (29 bp):
TTTACTCAACTTATAAATTTAGTCCCTTA
Found at i:1539472 original size:22 final size:22
Alignment explanation
Indices: 1539444--1539485 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1539434 CAACATATAG
1539444 AGCAATACAAGCTTCCATTTAA
1 AGCAATACAAGCTTCCATTTAA
1539466 AGCAATACAAGCTTCCATTT
1 AGCAATACAAGCTTCCATTT
1539486 CTGTCAACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.29
Consensus pattern (22 bp):
AGCAATACAAGCTTCCATTTAA
Found at i:1540763 original size:33 final size:33
Alignment explanation
Indices: 1540721--1540818 Score: 196
Period size: 33 Copynumber: 3.0 Consensus size: 33
1540711 AAACAGCGCG
1540721 ACTTTAATATAACACCACAAGAAACCTAATACA
1 ACTTTAATATAACACCACAAGAAACCTAATACA
1540754 ACTTTAATATAACACCACAAGAAACCTAATACA
1 ACTTTAATATAACACCACAAGAAACCTAATACA
1540787 ACTTTAATATAACACCACAAGAAACCTAATAC
1 ACTTTAATATAACACCACAAGAAACCTAATAC
1540819 TTACCAAATG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 65 1.00
ACGTcount: A:0.51, C:0.24, G:0.03, T:0.21
Consensus pattern (33 bp):
ACTTTAATATAACACCACAAGAAACCTAATACA
Found at i:1541797 original size:16 final size:16
Alignment explanation
Indices: 1541762--1541806 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
1541752 ATCTTTATTT
*
1541762 GAATAAATGTAGAGCGAA
1 GAATAAA-G-AGAACGAA
1541780 GAATAAAGAGAACGAA
1 GAATAAAGAGAACGAA
*
1541796 GAACAAAGAGA
1 GAATAAAGAGA
1541807 GCAATAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 17 0.68
17 1 0.04
18 7 0.28
ACGTcount: A:0.58, C:0.07, G:0.27, T:0.09
Consensus pattern (16 bp):
GAATAAAGAGAACGAA
Found at i:1543382 original size:41 final size:41
Alignment explanation
Indices: 1543325--1543409 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
1543315 TAATCTTCAC
1543325 TAAGAAAAAAGTTAACCCATTAATATAATAATTCAATAAAA
1 TAAGAAAAAAGTTAACCCATTAATATAATAATTCAATAAAA
1543366 TAAGAAAAAAGTTAACCCATTAATATAATAATTCAATAAAA
1 TAAGAAAAAAGTTAACCCATTAATATAATAATTCAATAAAA
1543407 TAA
1 TAA
1543410 TTCAATCCTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.27
Consensus pattern (41 bp):
TAAGAAAAAAGTTAACCCATTAATATAATAATTCAATAAAA
Found at i:1544002 original size:15 final size:17
Alignment explanation
Indices: 1543982--1544013 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1543972 CAATTTTTTT
1543982 AAAAAAT-T-TATAATA
1 AAAAAATATATATAATA
1543997 AAAAAATATATATAATA
1 AAAAAATATATATAATA
1544014 CTTCAAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAAATATATATAATA
Found at i:1545864 original size:19 final size:19
Alignment explanation
Indices: 1545806--1545864 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 19
1545796 GTTCAACCAA
1545806 AAAAAATATTAAAAATTGTAAT
1 AAAAAATA--AAAAATTG-AAT
* *
1545828 AATAACTAATAAAA-TGAAT
1 AAAAAATAA-AAAATTGAAT
1545847 AAAAAATAAAAAATTGAA
1 AAAAAATAAAAAATTGAA
1545865 ATTTTTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
18 4 0.13
19 14 0.45
20 3 0.10
21 4 0.13
22 6 0.19
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (19 bp):
AAAAAATAAAAAATTGAAT
Found at i:1568762 original size:23 final size:23
Alignment explanation
Indices: 1568708--1568762 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
1568698 TAAATTAAAT
*
1568708 ATTAATATTCGTTATTTTAAAAA
1 ATTAATATTCGTTATTTGAAAAA
* ** *
1568731 AATGTTATTCGTTGTTTGAAAAA
1 ATTAATATTCGTTATTTGAAAAA
*
1568754 GTTAATATT
1 ATTAATATT
1568763 TTTTTAAAAA
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (23 bp):
ATTAATATTCGTTATTTGAAAAA
Found at i:1607190 original size:26 final size:26
Alignment explanation
Indices: 1607168--1607227 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
1607158 GTCTCGATAT
1607168 ATGGCTCTTTGTGAGCTTTTCGATTA
1 ATGGCTCTTTGTGAGCTTTTCGATTA
*
1607194 AAGGCTCTTTGTGAGC-TTTCTGATTA
1 ATGGCTCTTTGTGAGCTTTTC-GATTA
1607220 ATGGCTCT
1 ATGGCTCT
1607228 CCGGAGCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 4 0.13
26 27 0.87
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (26 bp):
ATGGCTCTTTGTGAGCTTTTCGATTA
Found at i:1607234 original size:25 final size:26
Alignment explanation
Indices: 1607178--1607242 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
1607168 ATGGCTCTTT
**
1607178 GTGAGCTTTTCGATTAAAGGCTCTTT
1 GTGAGCTTTTCGATTAAAGGCTCTCC
*
1607204 GTGAGC-TTTCTGATTAATGGCTCTCC
1 GTGAGCTTTTC-GATTAAAGGCTCTCC
*
1607230 G-GAGCTTCTCGAT
1 GTGAGCTTTTCGAT
1607243 ATAGCTTGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
25 11 0.33
26 22 0.67
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (26 bp):
GTGAGCTTTTCGATTAAAGGCTCTCC
Found at i:1607296 original size:25 final size:24
Alignment explanation
Indices: 1607268--1607338 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
1607258 TTCTCGATAT
1607268 ATGGCTATCCAGAGCTTCCTGATTA
1 ATGGCT-TCCAGAGCTTCCTGATTA
* *
1607293 ATGGCTCTTCAGAGCTACCT-ATTA
1 ATGGCT-TCCAGAGCTTCCTGATTA
*
1607317 TTGGC-TCACATGAGCTTCCTGA
1 ATGGCTTC-CA-GAGCTTCCTGA
1607339 ATATGACTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
22 1 0.03
23 2 0.05
24 16 0.43
25 18 0.49
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (24 bp):
ATGGCTTCCAGAGCTTCCTGATTA
Found at i:1607321 original size:24 final size:25
Alignment explanation
Indices: 1607268--1607323 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
1607258 TTCTCGATAT
* * *
1607268 ATGGCTATCCAGAGCTTCCTGATTA
1 ATGGCTCTTCAGAGCTACCTGATTA
1607293 ATGGCTCTTCAGAGCTACCT-ATTA
1 ATGGCTCTTCAGAGCTACCTGATTA
*
1607317 TTGGCTC
1 ATGGCTC
1607324 ACATGAGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 10 0.37
25 17 0.63
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (25 bp):
ATGGCTCTTCAGAGCTACCTGATTA
Found at i:1609583 original size:24 final size:24
Alignment explanation
Indices: 1609534--1609583 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1609524 TAATCTGATT
* *
1609534 ATAATAATAAAATAAATAAGGTAA
1 ATAAAAATAAAATAAATAAGGAAA
*
1609558 ATAAAAATAAAAATAAA-ATGGAAA
1 ATAAAAAT-AAAATAAATAAGGAAA
1609582 AT
1 AT
1609584 GCATGATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (24 bp):
ATAAAAATAAAATAAATAAGGAAA
Done.