Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 4 of 182
Found at i:1187979 original size:38 final size:37
Alignment explanation
Indices: 1187939--1188022 Score: 98
Period size: 37 Copynumber: 2.2 Consensus size: 37
1187929 CAACAAATTT
* *
1187939 AAAAAATATATAATATATCAAATACATTTAAAA-ACATTA
1 AAAAAATAT-TAA-AAAT-AAATAAATTTAAAATACATTA
*
1187978 AAACAAATATTAAAAATAATTAAATTTAAAATACATTA
1 AAA-AAATATTAAAAATAAATAAATTTAAAATACATTA
1188016 AAAAAAT
1 AAAAAAT
1188023 TTATATTAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
37 16 0.40
38 12 0.30
39 6 0.15
40 6 0.15
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (37 bp):
AAAAAATATTAAAAATAAATAAATTTAAAATACATTA
Found at i:1188239 original size:12 final size:12
Alignment explanation
Indices: 1188149--1188240 Score: 59
Period size: 12 Copynumber: 8.1 Consensus size: 12
1188139 ATAACATCCA
*
1188149 AACAACAAAAAT
1 AACAACAAAAAC
1188161 AACAACAAAAAC
1 AACAACAAAAAC
**
1188173 AAC-AGTAAAAC
1 AACAACAAAAAC
**
1188184 AAC-A-TTAAA-
1 AACAACAAAAAC
* *
1188193 AATAACAAAAAT
1 AACAACAAAAAC
*
1188205 AGCAACAAAAAC
1 AACAACAAAAAC
*
1188217 AAC-ACGAAAAC
1 AACAACAAAAAC
*
1188228 AACAACCAAAAC
1 AACAACAAAAAC
1188240 A
1 A
1188241 GTAAAAAAGT
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
9 2 0.03
10 5 0.08
11 23 0.37
12 33 0.52
ACGTcount: A:0.70, C:0.21, G:0.03, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:1188247 original size:44 final size:44
Alignment explanation
Indices: 1188148--1188240 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
1188138 AATAACATCC
**
1188148 AAACAACAAAAATAACAACAAAAACAACAGTAAAACAACATTAA
1 AAACAACAAAAATAACAACAAAAACAACAGTAAAACAACAACAA
* * *
1188192 AAATAACAAAAATAGCAACAAAAACAACACG-AAAACAACAACCA
1 AAACAACAAAAATAACAACAAAAACAACA-GTAAAACAACAACAA
1188236 AAACA
1 AAACA
1188241 GTAAAAAAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 41 0.98
45 1 0.02
ACGTcount: A:0.70, C:0.20, G:0.03, T:0.06
Consensus pattern (44 bp):
AAACAACAAAAATAACAACAAAAACAACAGTAAAACAACAACAA
Found at i:1188285 original size:31 final size:30
Alignment explanation
Indices: 1188235--1188298 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 30
1188225 AACAACAACC
1188235 AAAACAGTAAAAAAGTACCAAAACAGTAAA
1 AAAACAGTAAAAAAGTACCAAAACAGTAAA
1188265 AAAACA-TAAAAATAGCTACCAAAACAGTAAA
1 AAAACAGTAAAAA-AG-TACCAAAACAGTAAA
1188296 AAA
1 AAA
1188299 TAGCACCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 6 0.19
30 8 0.25
31 18 0.56
ACGTcount: A:0.67, C:0.14, G:0.08, T:0.11
Consensus pattern (30 bp):
AAAACAGTAAAAAAGTACCAAAACAGTAAA
Found at i:1188288 original size:21 final size:22
Alignment explanation
Indices: 1188264--1188309 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1188254 AAAACAGTAA
1188264 AAAAACA-T-AAAAATAGCTACC
1 AAAAACAGTAAAAAATAGC-ACC
1188285 -AAAACAGTAAAAAATAGCACC
1 AAAAACAGTAAAAAATAGCACC
1188306 AAAA
1 AAAA
1188310 CAACAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
20 6 0.27
21 4 0.18
22 12 0.55
ACGTcount: A:0.65, C:0.17, G:0.07, T:0.11
Consensus pattern (22 bp):
AAAAACAGTAAAAAATAGCACC
Found at i:1188288 original size:22 final size:23
Alignment explanation
Indices: 1188263--1188314 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
1188253 CAAAACAGTA
1188263 AAAAAACA-T-AAAAATAGCTACC
1 AAAAAACAGTAAAAAATAGC-ACC
1188285 --AAAACAGTAAAAAATAGCACC
1 AAAAAACAGTAAAAAATAGCACC
1188306 AAAACAACA
1 AAAA-AACA
1188315 ATATAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
20 6 0.24
21 4 0.16
22 9 0.36
23 2 0.08
24 4 0.16
ACGTcount: A:0.65, C:0.19, G:0.06, T:0.10
Consensus pattern (23 bp):
AAAAAACAGTAAAAAATAGCACC
Found at i:1188310 original size:21 final size:20
Alignment explanation
Indices: 1188265--1188311 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
1188255 AAACAGTAAA
1188265 AAAACATAAAAATAGCTACC
1 AAAACATAAAAATAGCTACC
1188285 AAAACAGTAAAAAATAGC-ACC
1 AAAACA-T-AAAAATAGCTACC
1188306 AAAACA
1 AAAACA
1188312 ACAATATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 6 0.24
21 10 0.40
22 9 0.36
ACGTcount: A:0.64, C:0.19, G:0.06, T:0.11
Consensus pattern (20 bp):
AAAACATAAAAATAGCTACC
Found at i:1196735 original size:19 final size:18
Alignment explanation
Indices: 1196699--1196741 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
1196689 ATATTTTCCG
1196699 TTTTCTCATGTTTTTAATAA
1 TTTT-TCATGTTTTTAAT-A
1196719 TTTTTCAT-TTTTATAATA
1 TTTTTCATGTTTT-TAATA
1196737 TTTTT
1 TTTTT
1196742 AATAGTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 10 0.45
19 8 0.36
20 4 0.18
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTTCATGTTTTTAATA
Found at i:1203537 original size:24 final size:25
Alignment explanation
Indices: 1203490--1203539 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
1203480 TCATCTTTTC
1203490 GAGCCTTAAAAGAAGGGGAAAAAAA
1 GAGCCTTAAAAGAAGGGGAAAAAAA
1203515 GAGCCTTAAAAGAA-GGGAAAAAAA
1 GAGCCTTAAAAGAAGGGGAAAAAAA
1203539 G
1 G
1203540 TCAAATTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.56, C:0.08, G:0.28, T:0.08
Consensus pattern (25 bp):
GAGCCTTAAAAGAAGGGGAAAAAAA
Found at i:1209086 original size:63 final size:63
Alignment explanation
Indices: 1208983--1209116 Score: 187
Period size: 63 Copynumber: 2.1 Consensus size: 63
1208973 ATTCGTATGG
* * *
1208983 TAGAAAACAACCACCGGAAACACCACCTAATTTCAATGAATCAGGTGTAGACAAAACGAGTCA
1 TAGAAAACAACCACCGGAAACAACACCTAACTCCAATGAATCAGGTGTAGACAAAACGAGTCA
* * * * *
1209046 TAGAAAACAGCCACTGGAAGCAACACCTAACTCCATTGAATCAGGTGTAGACAAAATGAGTCA
1 TAGAAAACAACCACCGGAAACAACACCTAACTCCAATGAATCAGGTGTAGACAAAACGAGTCA
*
1209109 TCGAAAAC
1 TAGAAAAC
1209117 TTGAGAGAGC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.16
Consensus pattern (63 bp):
TAGAAAACAACCACCGGAAACAACACCTAACTCCAATGAATCAGGTGTAGACAAAACGAGTCA
Found at i:1218299 original size:7 final size:7
Alignment explanation
Indices: 1218287--1218334 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
1218277 TTTTGAAATT
1218287 TAAAAAA
1 TAAAAAA
1218294 TAAAAAA
1 TAAAAAA
**
1218301 TAAAATT
1 TAAAAAA
1218308 TATAAAAA
1 TA-AAAAA
1218316 TAAAAATA
1 TAAAAA-A
*
1218324 TAAAAAC
1 TAAAAAA
1218331 TAAA
1 TAAA
1218335 TCTTAAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
7 22 0.65
8 12 0.35
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAAAAA
Found at i:1218306 original size:21 final size:23
Alignment explanation
Indices: 1218282--1218328 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
1218272 CTAAATTTTG
1218282 AAATTTA-AAAAATAAAAA-ATA
1 AAATTTATAAAAATAAAAATATA
1218303 AAATTTATAAAAATAAAAATATA
1 AAATTTATAAAAATAAAAATATA
1218326 AAA
1 AAA
1218329 ACTAAATCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.29
22 11 0.46
23 6 0.25
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (23 bp):
AAATTTATAAAAATAAAAATATA
Found at i:1218316 original size:15 final size:14
Alignment explanation
Indices: 1218289--1218334 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
1218279 TTGAAATTTA
1218289 AAAAATA-AAAAAT
1 AAAAATATAAAAAT
*
1218302 AAAATTTATAAAAAT
1 AAAA-ATATAAAAAT
1218317 AAAAATATAAAAACT
1 AAAAATATAAAAA-T
1218332 AAA
1 AAA
1218335 TCTTAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 4 0.14
14 10 0.36
15 14 0.50
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAAATATAAAAAT
Found at i:1218629 original size:10 final size:10
Alignment explanation
Indices: 1218614--1218639 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1218604 TTTTAAAATA
1218614 TTAATTGAGT
1 TTAATTGAGT
1218624 TTAATTGAGT
1 TTAATTGAGT
1218634 TTAATT
1 TTAATT
1218640 TGTTTAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (10 bp):
TTAATTGAGT
Found at i:1219371 original size:2 final size:2
Alignment explanation
Indices: 1219364--1219394 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1219354 CAACCTTTCC
1219364 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1219395 TCAACGAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1223052 original size:15 final size:15
Alignment explanation
Indices: 1223032--1223085 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
1223022 AAATAAGTCC
1223032 ACGACGAAGACGAAG
1 ACGACGAAGACGAAG
1223047 ACGACGAAGACGAAG
1 ACGACGAAGACGAAG
* *
1223062 ACGACGAAGAAGATG
1 ACGACGAAGACGAAG
*
1223077 ACGATGAAG
1 ACGACGAAG
1223086 GCGAGTTCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.46, C:0.17, G:0.33, T:0.04
Consensus pattern (15 bp):
ACGACGAAGACGAAG
Found at i:1226502 original size:22 final size:22
Alignment explanation
Indices: 1226477--1226518 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1226467 CAATAACACC
*
1226477 AAAATAATAGCAACATAATAGT
1 AAAATAATAGCAAAATAATAGT
**
1226499 AAAATGGTAGCAAAATAATA
1 AAAATAATAGCAAAATAATA
1226519 AGAAAACAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.07, G:0.12, T:0.21
Consensus pattern (22 bp):
AAAATAATAGCAAAATAATAGT
Found at i:1228846 original size:19 final size:19
Alignment explanation
Indices: 1228822--1228858 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1228812 CCCTTTTTTG
* *
1228822 ATATATGCATACATATATT
1 ATATATACATACAAATATT
1228841 ATATATACATACAAATAT
1 ATATATACATACAAATAT
1228859 ATAAAATATG
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:0.49, C:0.11, G:0.03, T:0.38
Consensus pattern (19 bp):
ATATATACATACAAATATT
Found at i:1230699 original size:190 final size:189
Alignment explanation
Indices: 1230357--1230843 Score: 719
Period size: 190 Copynumber: 2.6 Consensus size: 189
1230347 AAAAAAAAAA
* * * * *
1230357 AATACAACCTTGACTAAAAATATTTGACAGCTGTGAGATTTGAACCCAGGCCCTTCCGGACCAGA
1 AATACAACCTTGAATAAAAATATATGACAGCTGTGGGATTTGAACCCACGCCCTTTCGGACCAGA
** * ** *
1230422 GCCTAAATCTGGCGCCTTAGACCACTCGGCCAAACTGTCTTGTTTGCCCAATTACCAGCCCTACC
66 GCCTAAATCTGGCGCCTTAGACCACTCGGCCAAACTGTCTTGCCTGCACAAAAACCAACCCTACC
* * * *
1230487 TTATAAGGCCATTTTCTAATTTTAAAGACGGAAAAAAAAAACCAAACTGGGCTTGCCCG
131 TTATAAGGCAATTGTCTAATTTTAAAGACAGAAAAAAAAAACCAAACTAGGCTTGCCCG
* * * *
1230546 AATACAACCTTGAATAAAAAATACATGACAGCCGTGGGACTTGAACCCACGCCCTTTCAGACCAG
1 AATACAACCTTGAAT-AAAAATATATGACAGCTGTGGGATTTGAACCCACGCCCTTTCGGACCAG
*
1230611 AGCCTAAATCTGGCGCCTTAGACCACTCGGCCAAACTGTCTTGCCTGCACAAAAACCAACCCTAA
65 AGCCTAAATCTGGCGCCTTAGACCACTCGGCCAAACTGTCTTGCCTGCACAAAAACCAACCCTAC
1230676 CTT-TAAAGGTCAATTGT-TAATTTTAAAGACAGAAAAAAAAAACCAAACTAGGCTTGCCCG
130 CTTAT-AAGG-CAATTGTCTAATTTTAAAGACAGAAAAAAAAAACCAAACTAGGCTTGCCCG
* *
1230736 AATACAATCTT-ATTAAAAATAATATGACAGCTGTGGGATTTGAACCCACGCCCTTTCGGACCAG
1 AATACAACCTTGAATAAAAAT-ATATGACAGCTGTGGGATTTGAACCCACGCCCTTTCGGACCAG
1230800 AGCCTAAATCTGGCGCCTTAGACCACTCGGCCAAACTGTCTTGC
65 AGCCTAAATCTGGCGCCTTAGACCACTCGGCCAAACTGTCTTGC
1230844 TGTTCCAAAC
Statistics
Matches: 268, Mismatches: 26, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
188 6 0.02
189 100 0.37
190 157 0.59
191 5 0.02
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (189 bp):
AATACAACCTTGAATAAAAATATATGACAGCTGTGGGATTTGAACCCACGCCCTTTCGGACCAGA
GCCTAAATCTGGCGCCTTAGACCACTCGGCCAAACTGTCTTGCCTGCACAAAAACCAACCCTACC
TTATAAGGCAATTGTCTAATTTTAAAGACAGAAAAAAAAAACCAAACTAGGCTTGCCCG
Found at i:1240356 original size:2 final size:2
Alignment explanation
Indices: 1240351--1240378 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1240341 AGAAAAAAGG
1240351 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1240379 CTCTACAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1244442 original size:42 final size:42
Alignment explanation
Indices: 1244396--1244479 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
1244386 TATATAAAAA
* * * *
1244396 TAATTCAATGAAGTGAAAATATGCATTTAATTAA-TCTTAATG
1 TAATTAAATAAAGTCAAAACATGCATTTAA-TAAGTCTTAATG
*
1244438 TAATTAAATAAATTCAAAACATGCATTTAATAAGTCTTAATG
1 TAATTAAATAAAGTCAAAACATGCATTTAATAAGTCTTAATG
1244480 AAATATATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
41 3 0.08
42 33 0.92
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (42 bp):
TAATTAAATAAAGTCAAAACATGCATTTAATAAGTCTTAATG
Found at i:1245614 original size:5 final size:5
Alignment explanation
Indices: 1245602--1245644 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
1245592 CAGATTTGAC
* * *
1245602 CAGG- CAGGG CAGGG CAGGG CAGGA CAGGA CAGGA CAGGA CAGG
1 CAGGA CAGGA CAGGA CAGGA CAGGA CAGGA CAGGA CAGGA CAGG
1245645 CTCCACAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
4 4 0.11
5 33 0.89
ACGTcount: A:0.30, C:0.21, G:0.49, T:0.00
Consensus pattern (5 bp):
CAGGA
Found at i:1246309 original size:6 final size:6
Alignment explanation
Indices: 1246301--1246342 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
1246291 GTTTTGCATG
* * *
1246301 CATATG CATATG CATATA CATATA CATATA CATATT CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1246343 TATTCATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (6 bp):
CATATA
Found at i:1246315 original size:12 final size:12
Alignment explanation
Indices: 1246298--1246342 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
1246288 TTGGTTTTGC
*
1246298 ATGCATATGCAT
1 ATGCATATACAT
1246310 ATGCATATACAT
1 ATGCATATACAT
*
1246322 ATACATATACAT
1 ATGCATATACAT
*
1246334 ATTCATATA
1 ATGCATATA
1246343 TATTCATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.36
Consensus pattern (12 bp):
ATGCATATACAT
Found at i:1252689 original size:4 final size:4
Alignment explanation
Indices: 1252647--1252671 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1252637 CACTTGACCC
1252647 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
1252672 AAAATCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:1257597 original size:2 final size:2
Alignment explanation
Indices: 1257585--1257624 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1257575 TCTGGTTGCT
*
1257585 TA TA TA CA 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
1257625 ATGGTTATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1269537 original size:138 final size:138
Alignment explanation
Indices: 1269296--1269724 Score: 657
Period size: 138 Copynumber: 3.1 Consensus size: 138
1269286 CGTTAAGTGT
* *
1269296 GAAACTCGAGTCACCAACGAAATCAGAAACTAGTTGGGTCATCAATCCATTTTCGATCTTAAATG
1 GAAACTCGAGTCACCAGCGAAATCAGAAACTAGTTGGG---TCAATCCACTTTCGATCTTAAATG
* *
1269361 ATTTATCAACTTCGTCATCACAAGCTGTTGCTAGTGGTTCAATGGTCTTAGATGACTTATCATTC
63 ATTTATCAACCTCGTCATCACAAGCTGTTGCTAGTGGTTCAATGGTCTTAGATGACTCATCATTC
*
1269426 TCATTAAACTC
128 TCATTAAGCTC
* * *
1269437 GAAACTCGAGTCACCAGCAAAATCAGAAACTAGTTGGGTCAATCCGCTTTCTATCTTAAATGATT
1 GAAACTCGAGTCACCAGCGAAATCAGAAACTAGTTGGGTCAATCCACTTTCGATCTTAAATGATT
* *
1269502 TATCAACCTCATCATCACAAGCTGTTGCTACTGGTTCAATGGTCTTAGATGACTCATCATTCTCA
66 TATCAACCTCGTCATCACAAGCTGTTGCTAGTGGTTCAATGGTCTTAGATGACTCATCATTCTCA
1269567 TTAAGCTC
131 TTAAGCTC
*
1269575 GAAACTCGAGTCACCAAG-GAAATCAGAAA-TCAATTGGGTCAATCCACTTTCGATCTTAAATGA
1 GAAACTCGAGTCACC-AGCGAAATCAGAAACT-AGTTGGGTCAATCCACTTTCGATCTTAAATGA
1269638 TTTATCAAACCT-GTCATCACAAGCTGTTGCTAGTGGTTCAATGGTCTTAGATGACTCATCATTT
64 TTTATC-AACCTCGTCATCACAAGCTGTTGCTAGTGGTTCAATGGTCTTAGATGACTCATCA---
1269702 TTCTCATTAAGCTC
125 TTCTCATTAAGCTC
1269716 GAAACTCGA
1 GAAACTCGA
1269725 CGTTTTGTCC
Statistics
Matches: 266, Mismatches: 16, Indels: 12
0.90 0.05 0.04
Matches are distributed among these distances:
137 1 0.00
138 199 0.75
139 7 0.03
141 59 0.22
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (138 bp):
GAAACTCGAGTCACCAGCGAAATCAGAAACTAGTTGGGTCAATCCACTTTCGATCTTAAATGATT
TATCAACCTCGTCATCACAAGCTGTTGCTAGTGGTTCAATGGTCTTAGATGACTCATCATTCTCA
TTAAGCTC
Found at i:1273393 original size:25 final size:25
Alignment explanation
Indices: 1273337--1273394 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
1273327 TTGAGAAACA
*
1273337 TTTATTTTAATATTTTTAATGTATT
1 TTTATATTAATATTTTTAATGTATT
* *
1273362 TGATATATT-ATATTTTTAAATTTATT
1 T-TTATATTAATATTTTT-AATGTATT
1273388 TTTATAT
1 TTTATAT
1273395 AAAAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (25 bp):
TTTATATTAATATTTTTAATGTATT
Found at i:1276517 original size:15 final size:15
Alignment explanation
Indices: 1276499--1276546 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1276489 TTTCCTTAGA
1276499 TTATATTTTAATTAT
1 TTATATTTTAATTAT
* *
1276514 TTATATTTAAAATA-
1 TTATATTTTAATTAT
1276528 TTATATTTTAATTAT
1 TTATATTTTAATTAT
1276543 TTAT
1 TTAT
1276547 GTTAGTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATATTTTAATTAT
Found at i:1276543 original size:14 final size:14
Alignment explanation
Indices: 1276498--1276543 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
1276488 ATTTCCTTAG
1276498 ATTATATTTTAATT
1 ATTATATTTTAATT
* *
1276512 ATTTATATTTAAAAT
1 A-TTATATTTTAATT
1276527 ATTATATTTTAATT
1 ATTATATTTTAATT
1276541 ATT
1 ATT
1276544 TATGTTAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTATATTTTAATT
Found at i:1276682 original size:21 final size:22
Alignment explanation
Indices: 1276642--1276682 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1276632 TTCTTTATTT
* *
1276642 TCTATTTTCTTTTGCTTCTCAC
1 TCTATTTTCCTCTGCTTCTCAC
1276664 TCTATTTTCCTCT-CTTCTC
1 TCTATTTTCCTCTGCTTCTC
1276683 CATCTCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.07, C:0.32, G:0.02, T:0.59
Consensus pattern (22 bp):
TCTATTTTCCTCTGCTTCTCAC
Found at i:1277553 original size:31 final size:32
Alignment explanation
Indices: 1277509--1277569 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
1277499 CTATAATACT
*
1277509 ACTATAATGTAAATATTAAAAAAATAAAAAAA
1 ACTATAATATAAATATTAAAAAAATAAAAAAA
* * *
1277541 ACTA-AATATAAATTTTTAATAAATAAAAA
1 ACTATAATATAAATATTAAAAAAATAAAAA
1277570 TCTAAAATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (32 bp):
ACTATAATATAAATATTAAAAAAATAAAAAAA
Found at i:1278991 original size:24 final size:22
Alignment explanation
Indices: 1278948--1278991 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
1278938 TTGGAGGTAA
* *
1278948 ATAATATAAGTAAAATTTTGTT
1 ATAAAATAAGTAAAAGTTTGTT
1278970 ATAAAATAAGTAATTAAGTTTG
1 ATAAAATAAGTAA--AAGTTTG
1278992 ATCCCCCCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
24 6 0.33
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (22 bp):
ATAAAATAAGTAAAAGTTTGTT
Found at i:1280155 original size:3 final size:3
Alignment explanation
Indices: 1280147--1280178 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1280137 TTCTCCCATG
1280147 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1280179 GAAATTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1282448 original size:3 final size:3
Alignment explanation
Indices: 1282442--1282469 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1282432 AAATGAAAAA
1282442 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1282470 GAGAGAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1283740 original size:16 final size:17
Alignment explanation
Indices: 1283709--1283750 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1283699 TGGGATCATT
*
1283709 TATTTTAATGTTTTAATA
1 TATTTT-ATGTTTTAAAA
1283727 TATTTTAT-TTTTAAAA
1 TATTTTATGTTTTAAAA
*
1283743 TTTTTTAT
1 TATTTTAT
1283751 ATACGAGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.64
17 2 0.09
18 6 0.27
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTTTATGTTTTAAAA
Found at i:1298614 original size:152 final size:151
Alignment explanation
Indices: 1298339--1298631 Score: 473
Period size: 152 Copynumber: 1.9 Consensus size: 151
1298329 ACTAAATTTT
* * * * *
1298339 AATTTATTATGATATAATCACTAATCGATTTCTAATATTTTAGTTATTATATTATTAACGGTTAA
1 AATTTATTATGATATAACCACTAATCAATTGCTAATATTTTAGTTATTATATTATTAACAGCTAA
1298404 CGTTTATATAATTATTTTTATTATTTTTTTTAATAATTTAATTTTTTTATTATAAAAAATTTAGA
66 CGTTTATATAATTATTTTTATTATTTTTTTTAATAATTTAA-TTTTTTATTATAAAAAATTTAGA
1298469 ATATATAAATTAAAAATTATAA
130 ATATATAAATTAAAAATTATAA
1298491 AATTTATTATGATATAACCACTAATCAATTGCTAATATTTTAGTTATTATATTATTAACAGCTAA
1 AATTTATTATGATATAACCACTAATCAATTGCTAATATTTTAGTTATTATATTATTAACAGCTAA
*
1298556 CGTACGTTATATCATTATTTTTA-TATCTTTTTTTAATAATTTAA-TTTTTATTATAAAAAATTT
66 CGT---TTATATAATTATTTTTATTAT-TTTTTTTAATAATTTAATTTTTTATTATAAAAAATTT
1298619 AGAATATATAAAT
127 AGAATATATAAAT
1298632 AAGTAAAATT
Statistics
Matches: 131, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
152 63 0.48
153 32 0.24
154 3 0.02
155 33 0.25
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.50
Consensus pattern (151 bp):
AATTTATTATGATATAACCACTAATCAATTGCTAATATTTTAGTTATTATATTATTAACAGCTAA
CGTTTATATAATTATTTTTATTATTTTTTTTAATAATTTAATTTTTTATTATAAAAAATTTAGAA
TATATAAATTAAAAATTATAA
Found at i:1300482 original size:39 final size:39
Alignment explanation
Indices: 1300439--1300513 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
1300429 AATTTATACC
*
1300439 TTCTAGAATTGATAATCAACTAGCATATACACATTCACG
1 TTCTAGAATTGATAATCAACTAACATATACACATTCACG
1300478 TTCTAGAATTGATAATCAACTAACATATACACATTC
1 TTCTAGAATTGATAATCAACTAACATATACACATTC
1300514 CATAACCTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (39 bp):
TTCTAGAATTGATAATCAACTAACATATACACATTCACG
Found at i:1300985 original size:24 final size:24
Alignment explanation
Indices: 1300953--1301001 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1300943 GGCATTAATA
1300953 TGTCCACAAAAAGTTAT-CAATATT
1 TGTCCACAAAAAGTT-TCCAATATT
*
1300977 TGTCTACAAAAAGTTTCCAATATT
1 TGTCCACAAAAAGTTTCCAATATT
1301001 T
1 T
1301002 TTCTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (24 bp):
TGTCCACAAAAAGTTTCCAATATT
Found at i:1304103 original size:16 final size:16
Alignment explanation
Indices: 1304084--1304127 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1304074 AACTTAATAT
1304084 TAATAATATTTTTTAA
1 TAATAATATTTTTTAA
***
1304100 TAATAATACAATTTAA
1 TAATAATATTTTTTAA
1304116 TAATAATATTTT
1 TAATAATATTTT
1304128 AAATATATAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATAATATTTTTTAA
Found at i:1304113 original size:19 final size:19
Alignment explanation
Indices: 1304077--1304123 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1304067 ATAATTAAAC
* *
1304077 TTAATATTAATAATATTTT
1 TTAATAATAATAATATTTA
1304096 TTAATAATAATACA-ATTTA
1 TTAATAATAATA-ATATTTA
*
1304115 ATAATAATA
1 TTAATAATA
1304124 TTTTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATAATAATAATATTTA
Found at i:1307103 original size:1 final size:1
Alignment explanation
Indices: 1307097--1307129 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
1307087 TTAACCTCCT
1307097 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1307130 GAATTGATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1315162 original size:125 final size:126
Alignment explanation
Indices: 1314938--1315269 Score: 443
Period size: 125 Copynumber: 2.6 Consensus size: 126
1314928 TATATGTCCA
* * * * * * *
1314938 ACCAACATCAGAGCAAA-AAGGTAGCGAGAACAATCATGTCATCACACAGTAAACGCTAAAGCAT
1 ACCAACAACAGAGCAAACAA-GTATCGAGAACAACCGTGTCATCACACAGTTAACACTAAGGCAT
* * * *
1315002 GGCAGATATATCAAATCGATGGAATCTAGCATTGACATAGGTACAGATACATACATATCTG-
65 GGCAGAAATATCAAATCGATGGAACCTAGCATTGACATAGGTACAGATACATACAAATCCGT
*
1315063 ACCAACAACCGAGCAAACAAGTATCGAGAACAACCGTGTCATCACACAGTTAACACTAAGGCATG
1 ACCAACAACAGAGCAAACAAGTATCGAGAACAACCGTGTCATCACACAGTTAACACTAAGGCATG
* * ** * * *
1315128 GAAGAAATACCAAATCGATGGAACCTAGTGTTGACATAGGTACGGATATATATAAATCCGT
66 GCAGAAATATCAAATCGATGGAACCTAGCATTGACATAGGTACAGATACATACAAATCCGT
* * *
1315189 ACCAACAACAGAGCAAACAAGTATCGAGAACAACCGTGCCATAACACAGTTAACACCAAGGCATG
1 ACCAACAACAGAGCAAACAAGTATCGAGAACAACCGTGTCATCACACAGTTAACACTAAGGCATG
1315254 GCAGAAATATCAAATC
66 GCAGAAATATCAAATC
1315270 AACGGAATCA
Statistics
Matches: 180, Mismatches: 25, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
125 103 0.57
126 77 0.43
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (126 bp):
ACCAACAACAGAGCAAACAAGTATCGAGAACAACCGTGTCATCACACAGTTAACACTAAGGCATG
GCAGAAATATCAAATCGATGGAACCTAGCATTGACATAGGTACAGATACATACAAATCCGT
Found at i:1315305 original size:126 final size:126
Alignment explanation
Indices: 1315063--1315306 Score: 335
Period size: 126 Copynumber: 1.9 Consensus size: 126
1315053 TACATATCTG
* * * *
1315063 ACCAACAACCGAGCAAACAAGTATCGAGAACAACCGTGTCATCACACAGTTAACACTAAGGCATG
1 ACCAACAACAGAGCAAACAAGTATCGAGAACAACCGTGCCATAACACAGTTAACACCAAGGCATG
* * * ** * * *
1315128 GAAGAAATACCAAATCGATGGAACCTAGTGTTGACATAGGTACGGATATATATAAATCCGT
66 GAAGAAATACCAAATCAACGGAACCAAGTGTCAACATAGATACAGAGATATATAAATCCGT
1315189 ACCAACAACAGAGCAAACAAGTATCGAGAACAACCGTGCCATAACACAGTTAACACCAAGGCATG
1 ACCAACAACAGAGCAAACAAGTATCGAGAACAACCGTGCCATAACACAGTTAACACCAAGGCATG
* * * * *
1315254 GCAGAAATATCAAATCAACGGAATCAAGTGTCAACATTGATATAGAGATATAT
66 GAAGAAATACCAAATCAACGGAACCAAGTGTCAACATAGATACAGAGATATAT
1315307 TGAACAAATT
Statistics
Matches: 101, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
126 101 1.00
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (126 bp):
ACCAACAACAGAGCAAACAAGTATCGAGAACAACCGTGCCATAACACAGTTAACACCAAGGCATG
GAAGAAATACCAAATCAACGGAACCAAGTGTCAACATAGATACAGAGATATATAAATCCGT
Found at i:1322715 original size:24 final size:24
Alignment explanation
Indices: 1322658--1322716 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
1322648 AGGAGTAGAA
1322658 GATGCTCCAAAAGCAGGACTGCTT
1 GATGCTCCAAAAGCAGGACTGCTT
* **
1322682 GAAG-TGCCAAAAGCAGGTGTGCTT
1 GATGCT-CCAAAAGCAGGACTGCTT
1322706 GATGCTCCAAA
1 GATGCTCCAAA
1322717 TGTGCCTCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 27 0.93
25 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (24 bp):
GATGCTCCAAAAGCAGGACTGCTT
Found at i:1322830 original size:24 final size:24
Alignment explanation
Indices: 1322798--1322900 Score: 107
Period size: 24 Copynumber: 4.3 Consensus size: 24
1322788 TTCCAGTTGA
* *
1322798 ACCAAAGGCCGGGGTGCCGGTAGC
1 ACCAAAGGCAGGGGTGCCCGTAGC
*
1322822 ACCAAAGGCAGGGGTGCCCGTGGC
1 ACCAAAGGCAGGGGTGCCCGTAGC
* ** * *
1322846 ACCAAAGGCAGGAGTGCTTGTGGA
1 ACCAAAGGCAGGGGTGCCCGTAGC
* * *
1322870 ACCAAAGGCAGGAGTGCTCGTGGC
1 ACCAAAGGCAGGGGTGCCCGTAGC
1322894 ACCAAAG
1 ACCAAAG
1322901 CTACCAAATG
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.26, C:0.25, G:0.38, T:0.11
Consensus pattern (24 bp):
ACCAAAGGCAGGGGTGCCCGTAGC
Found at i:1323042 original size:24 final size:24
Alignment explanation
Indices: 1322964--1323043 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
1322954 ACTTGAAGAT
*
1322964 GCTCCAAAAGCAGGGGTGCTCGAA
1 GCTCCAAAAGCAGGAGTGCTCGAA
* * * *
1322988 CCCCCAAATGCAGGAGTGCTGGAA
1 GCTCCAAAAGCAGGAGTGCTCGAA
* * *
1323012 G-TGCCAAAAGCAGGTGTGCTTGAT
1 GCT-CCAAAAGCAGGAGTGCTCGAA
1323036 GCTCCAAA
1 GCTCCAAA
1323044 TGCGCCACCT
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
24 42 0.98
25 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.30, T:0.16
Consensus pattern (24 bp):
GCTCCAAAAGCAGGAGTGCTCGAA
Found at i:1323152 original size:24 final size:24
Alignment explanation
Indices: 1323125--1323286 Score: 207
Period size: 24 Copynumber: 6.8 Consensus size: 24
1323115 TTCCAGTCGA
* *
1323125 ACCAAAGGCAGGGGTGCTTGTGGC
1 ACCAAAGGCAGGGGTACTCGTGGC
* * * *
1323149 ACCAAAGGCTGGAGTACTCATGGA
1 ACCAAAGGCAGGGGTACTCGTGGC
*
1323173 ACCAAAGGCAGGGGTACTTGTGGC
1 ACCAAAGGCAGGGGTACTCGTGGC
* *
1323197 ACCAAAAGCAGGGGCACTCGTGGC
1 ACCAAAGGCAGGGGTACTCGTGGC
1323221 ACCAAAGGCAGGGGTACTCGTGGC
1 ACCAAAGGCAGGGGTACTCGTGGC
* *
1323245 ACCAAAAGCAGGGGTGCTCGTGGC
1 ACCAAAGGCAGGGGTACTCGTGGC
* *
1323269 ACCGAAGGCAGGAGTACT
1 ACCAAAGGCAGGGGTACT
1323287 GGAACCAAAA
Statistics
Matches: 116, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 116 1.00
ACGTcount: A:0.27, C:0.23, G:0.36, T:0.14
Consensus pattern (24 bp):
ACCAAAGGCAGGGGTACTCGTGGC
Found at i:1323160 original size:48 final size:48
Alignment explanation
Indices: 1323102--1323250 Score: 158
Period size: 48 Copynumber: 3.1 Consensus size: 48
1323092 TCCAGGGCTC
* * *
1323102 CCAAATGCTGGACTTC-CAGTCGAACCAAAGGCAGGGGTGCTTGTGGCA
1 CCAAAGGCTGGACTACTCA-TCGAACCAAAGGCAGGGGTACTTGTGGCA
* *
1323150 CCAAAGGCTGGAGTACTCATGGAACCAAAGGCAGGGGTACTTGTGGCA
1 CCAAAGGCTGGACTACTCATCGAACCAAAGGCAGGGGTACTTGTGGCA
* * * * * * *
1323198 CCAAAAGCAGGGGC-ACTCGTGGCACCAAAGGCAGGGGTACTCGTGGCA
1 CCAAAGGC-TGGACTACTCATCGAACCAAAGGCAGGGGTACTTGTGGCA
1323246 CCAAA
1 CCAAA
1323251 AGCAGGGGTG
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
48 83 0.95
49 4 0.05
ACGTcount: A:0.28, C:0.25, G:0.32, T:0.15
Consensus pattern (48 bp):
CCAAAGGCTGGACTACTCATCGAACCAAAGGCAGGGGTACTTGTGGCA
Found at i:1330061 original size:18 final size:18
Alignment explanation
Indices: 1330021--1330072 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
1330011 TTTTCAGTTG
*
1330021 TAATTAATTTAGAATT-TT
1 TAATTAA-TTAAAATTATT
*
1330039 CAATTAATTAAAATTATT
1 TAATTAATTAAAATTATT
1330057 TAATTAA--AAAATTATT
1 TAATTAATTAAAATTATT
1330073 CTCATCCCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 14 0.47
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:1331404 original size:24 final size:24
Alignment explanation
Indices: 1331369--1331416 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1331359 AATTCATATC
*
1331369 ACTTTCAATTCCAATTTCACTTTT
1 ACTTTCAATTCCAATTTCAATTTT
* *
1331393 ACTTTCATTTCCACTTTCAATTTT
1 ACTTTCAATTCCAATTTCAATTTT
1331417 GATCACAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.25, G:0.00, T:0.52
Consensus pattern (24 bp):
ACTTTCAATTCCAATTTCAATTTT
Found at i:1347702 original size:28 final size:29
Alignment explanation
Indices: 1347666--1347725 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
1347656 ATTTTTTCAA
*
1347666 TTCTCAAACTATAAA-AAAAAAT-CTAAAT
1 TTCTAAAACT-TAAAGAAAAAATACTAAAT
*
1347694 TTCTAAAACTTAAAGCAAAAATGACTAAAT
1 TTCTAAAACTTAAAGAAAAAAT-ACTAAAT
1347724 TT
1 TT
1347726 ATTAAGTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 4 0.15
28 15 0.56
30 8 0.30
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.30
Consensus pattern (29 bp):
TTCTAAAACTTAAAGAAAAAATACTAAAT
Found at i:1350296 original size:17 final size:17
Alignment explanation
Indices: 1350271--1350305 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1350261 TTATCAAACG
*
1350271 TATTTAAAAAATTAATT
1 TATTGAAAAAATTAATT
*
1350288 TATTGAAAATATTAATT
1 TATTGAAAAAATTAATT
1350305 T
1 T
1350306 TCAGTTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TATTGAAAAAATTAATT
Found at i:1366545 original size:39 final size:39
Alignment explanation
Indices: 1366500--1366577 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
1366490 AACAACACAG
1366500 GGATTAATTTACTATAACAAGTAACATATGATTGTTATT
1 GGATTAATTTACTATAACAAGTAACATATGATTGTTATT
1366539 GGATTAATTTACTATAACAAGTAACATATGATTGTTATT
1 GGATTAATTTACTATAACAAGTAACATATGATTGTTATT
1366578 TGTTGATGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (39 bp):
GGATTAATTTACTATAACAAGTAACATATGATTGTTATT
Found at i:1372560 original size:23 final size:23
Alignment explanation
Indices: 1372530--1372632 Score: 89
Period size: 23 Copynumber: 4.5 Consensus size: 23
1372520 AGTGCTGAGG
* * *
1372530 AAACAGTAAGTACATACAGTGCG
1 AAACAGTAAGCACACACAGTGCA
* *
1372553 AATCAGTAGGCACACACAGTGCA
1 AAACAGTAAGCACACACAGTGCA
* * * *
1372576 AAACAGTAAGCACACATATTACG
1 AAACAGTAAGCACACACAGTGCA
* * *
1372599 AATCAATAAGCACACACAGTGCT
1 AAACAGTAAGCACACACAGTGCA
*
1372622 TAACAGTAAGC
1 AAACAGTAAGC
1372633 GCGCTAATGT
Statistics
Matches: 60, Mismatches: 20, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (23 bp):
AAACAGTAAGCACACACAGTGCA
Found at i:1372583 original size:46 final size:46
Alignment explanation
Indices: 1372530--1372632 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 46
1372520 AGTGCTGAGG
* * * * *
1372530 AAACAGTAAGTACATACAGTGCGAATCAGTAGGCACACACAGTGCA
1 AAACAGTAAGCACACACAGTACGAATCAATAAGCACACACAGTGCA
* * *
1372576 AAACAGTAAGCACACATATTACGAATCAATAAGCACACACAGTGCT
1 AAACAGTAAGCACACACAGTACGAATCAATAAGCACACACAGTGCA
*
1372622 TAACAGTAAGC
1 AAACAGTAAGC
1372633 GCGCTAATGT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (46 bp):
AAACAGTAAGCACACACAGTACGAATCAATAAGCACACACAGTGCA
Found at i:1377647 original size:24 final size:22
Alignment explanation
Indices: 1377619--1377664 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1377609 TGTCATATAA
1377619 AATAACATTAAATTATTTTAAAAG
1 AATAA-ATTAAATT-TTTTAAAAG
**
1377643 AATAAATTTTATTTTTTAAAAG
1 AATAAATTAAATTTTTTAAAAG
1377665 TTTTTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 6 0.30
24 5 0.25
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (22 bp):
AATAAATTAAATTTTTTAAAAG
Found at i:1391105 original size:21 final size:21
Alignment explanation
Indices: 1391079--1391118 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1391069 CTAAATTGAA
* *
1391079 AATTAAAATATATTTAAATTT
1 AATTAAAATAAATATAAATTT
1391100 AATTAAAATAAATATAAAT
1 AATTAAAATAAATATAAAT
1391119 AAGAAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTAAAATAAATATAAATTT
Found at i:1394812 original size:20 final size:20
Alignment explanation
Indices: 1394772--1394812 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1394762 CTAATAACTC
* * *
1394772 TTGAGTTTAAGATTTATGGT
1 TTGAGTTTAAAATGTAAGGT
1394792 TTGAGTTTAAAATGTAAGGT
1 TTGAGTTTAAAATGTAAGGT
1394812 T
1 T
1394813 ATTAGTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.46
Consensus pattern (20 bp):
TTGAGTTTAAAATGTAAGGT
Found at i:1395631 original size:23 final size:24
Alignment explanation
Indices: 1395588--1395657 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
1395578 AAATAAATTT
**
1395588 TATAT-TTTTTATGAAAATTAAAA-
1 TATATATTTTTAT-AATTTTAAAAC
1395611 TATATATTTTTATAATTTTAATAAC
1 TATATATTTTTATAATTTTAA-AAC
1395636 T-TATATTTTTATAATTTTAAAA
1 TATATATTTTTATAATTTTAAAA
1395658 GATTAAATCA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
23 13 0.31
24 28 0.67
25 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (24 bp):
TATATATTTTTATAATTTTAAAAC
Found at i:1398555 original size:19 final size:19
Alignment explanation
Indices: 1398531--1398577 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
1398521 ATCAAAGAGC
1398531 AAATTGGTCTTTCTGTTAA
1 AAATTGGTCTTTCTGTTAA
1398550 AAATTGGTCTTTCTGTTAA
1 AAATTGGTCTTTCTGTTAA
1398569 AAATTGGTC
1 AAATTGGTC
1398578 ATTGTACCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.45
Consensus pattern (19 bp):
AAATTGGTCTTTCTGTTAA
Found at i:1400767 original size:33 final size:33
Alignment explanation
Indices: 1400725--1400791 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1400715 TGATATAAAT
1400725 TCGAATATGGTTATTTTAATATTTTCTCTAATA
1 TCGAATATGGTTATTTTAATATTTTCTCTAATA
1400758 TCGAATATGGTTATTTTAATATTTTCTCTAATA
1 TCGAATATGGTTATTTTAATATTTTCTCTAATA
1400791 T
1 T
1400792 TATATTGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (33 bp):
TCGAATATGGTTATTTTAATATTTTCTCTAATA
Found at i:1403117 original size:12 final size:12
Alignment explanation
Indices: 1403100--1403132 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1403090 AAAAATTTAA
1403100 TTTAATAATTAT
1 TTTAATAATTAT
1403112 TTTAATAA-TAT
1 TTTAATAATTAT
*
1403123 TTTATTAATT
1 TTTAATAATT
1403133 TAATATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTAATAATTAT
Found at i:1413659 original size:21 final size:21
Alignment explanation
Indices: 1413633--1413673 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1413623 TACAACAAAC
* *
1413633 AACAATCTTTAAATTTAACAA
1 AACAATATTTAAACTTAACAA
*
1413654 AACAATATTTCAACTTAACA
1 AACAATATTTAAACTTAACA
1413674 CACTTTTTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (21 bp):
AACAATATTTAAACTTAACAA
Found at i:1413758 original size:38 final size:38
Alignment explanation
Indices: 1413701--1413773 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
1413691 GTTAAATTTG
* *
1413701 ATTTTAATATTCAATTTAATA-TTTAAATTTCTTTATT
1 ATTTCAATATTCAATTTAATACTTGAAATTTCTTTATT
* *
1413738 ATTTCAATATTTCAGTTTAATACTTGAATTTTCTTT
1 ATTTCAATA-TTCAATTTAATACTTGAAATTTCTTT
1413774 TATCTTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 8 0.27
38 11 0.37
39 11 0.37
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.58
Consensus pattern (38 bp):
ATTTCAATATTCAATTTAATACTTGAAATTTCTTTATT
Found at i:1414801 original size:68 final size:68
Alignment explanation
Indices: 1414691--1414821 Score: 201
Period size: 68 Copynumber: 1.9 Consensus size: 68
1414681 TACAAATCTG
* * *
1414691 TCTCAAAGCTTAAATCTTTGAAACCCATTAACCCAAAAATTCAATAT-ATTTGATTCCATTATCG
1 TCTCAAAGCTTAAATATTTAAAACCCATTAACCCAAAAATTCAATATCA-TTGATTCCAATATCG
1414755 TCTA
65 TCTA
* *
1414759 TCTCAAAGCTTGAATATTTAAAACCCATTAACCCAAAGATTCAATATCATTGATTCCAATATC
1 TCTCAAAGCTTAAATATTTAAAACCCATTAACCCAAAAATTCAATATCATTGATTCCAATATC
1414822 TTCTTCCCGT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
68 56 0.98
69 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (68 bp):
TCTCAAAGCTTAAATATTTAAAACCCATTAACCCAAAAATTCAATATCATTGATTCCAATATCGT
CTA
Found at i:1414893 original size:17 final size:17
Alignment explanation
Indices: 1414871--1414904 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1414861 GATTCAAGCT
*
1414871 TTGAAACATATTTGTAA
1 TTGAAACAGATTTGTAA
1414888 TTGAAACAGATTTGTAA
1 TTGAAACAGATTTGTAA
1414905 CTAAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (17 bp):
TTGAAACAGATTTGTAA
Found at i:1422073 original size:31 final size:30
Alignment explanation
Indices: 1422026--1422090 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
1422016 AAAAAGATCA
* * *
1422026 AAATTCAGCTCTAATATGAGAATAATTGTC
1 AAATTCAGCTCCAATATAAGAACAATTGTC
*
1422056 AAATTCATGCTCCAATATAAGAGCAATTGTC
1 AAATTCA-GCTCCAATATAAGAACAATTGTC
1422087 AAAT
1 AAAT
1422091 CCAAAGATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (30 bp):
AAATTCAGCTCCAATATAAGAACAATTGTC
Found at i:1422148 original size:31 final size:31
Alignment explanation
Indices: 1422113--1422171 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1422103 TAAGATAAAC
*
1422113 AATTTAAGTTCCAATGTAAAAATAATTACCT
1 AATTTAAGTTCCAATATAAAAATAATTACCT
* * *
1422144 AATTTAGGTTTCAATATGAAAATAATTA
1 AATTTAAGTTCCAATATAAAAATAATTA
1422172 TCAATTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.37
Consensus pattern (31 bp):
AATTTAAGTTCCAATATAAAAATAATTACCT
Found at i:1441051 original size:40 final size:40
Alignment explanation
Indices: 1440996--1441079 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
1440986 GGTGCTGCAT
1440996 CAAATGAAGAAGAGGAAGATTCACATGATGAACTCTAAAA
1 CAAATGAAGAAGAGGAAGATTCACATGATGAACTCTAAAA
1441036 CAAATGAAGAAGAGGAAGATTCACATGATGAACTCTAAAA
1 CAAATGAAGAAGAGGAAGATTCACATGATGAACTCTAAAA
1441076 CAAA
1 CAAA
1441080 CATCTCGATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.51, C:0.13, G:0.19, T:0.17
Consensus pattern (40 bp):
CAAATGAAGAAGAGGAAGATTCACATGATGAACTCTAAAA
Found at i:1451647 original size:4 final size:4
Alignment explanation
Indices: 1451638--1451684 Score: 85
Period size: 4 Copynumber: 11.5 Consensus size: 4
1451628 GGAGTATCTG
1451638 TACA TACA TACA TACA TACA CTACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA -TACA TACA TACA TACA TACA TACA TA
1451685 TCGAAAGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 38 0.90
5 4 0.10
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:1455365 original size:16 final size:16
Alignment explanation
Indices: 1455344--1455398 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
1455334 CTCATAAAAA
*
1455344 AAAATATAAAAAGTTG
1 AAAATAAAAAAAGTTG
*
1455360 AAAATAGAAAAAG-T-
1 AAAATAAAAAAAGTTG
1455374 AAAATAAAAATAAGTATG
1 AAAATAAAAA-AAGT-TG
1455392 AAAATAA
1 AAAATAA
1455399 TATCTTTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 9 0.27
15 4 0.12
16 12 0.36
17 1 0.03
18 7 0.21
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (16 bp):
AAAATAAAAAAAGTTG
Found at i:1462734 original size:13 final size:13
Alignment explanation
Indices: 1462716--1462742 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1462706 TGCACGAGAA
1462716 TGTTCTTTAAAGT
1 TGTTCTTTAAAGT
1462729 TGTTCTTTAAAGT
1 TGTTCTTTAAAGT
1462742 T
1 T
1462743 CGTTAGAGTT
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:0.07, G:0.15, T:0.56
Consensus pattern (13 bp):
TGTTCTTTAAAGT
Found at i:1466395 original size:10 final size:10
Alignment explanation
Indices: 1466380--1466421 Score: 68
Period size: 10 Copynumber: 4.2 Consensus size: 10
1466370 TAATCATATT
1466380 TTAATTTTAA
1 TTAATTTTAA
1466390 TTAATTTTAA
1 TTAATTTTAA
1466400 TTAA-TTTAA
1 TTAATTTTAA
1466409 TTAATCTTTAA
1 TTAAT-TTTAA
1466420 TT
1 TT
1466422 GTTAATTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.30
10 14 0.47
11 7 0.23
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (10 bp):
TTAATTTTAA
Found at i:1466398 original size:16 final size:16
Alignment explanation
Indices: 1466377--1466428 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 16
1466367 AATTAATCAT
1466377 ATTTTAATTTTAATTA
1 ATTTTAATTTTAATTA
1466393 ATTTTAATTAATTTAATTA
1 ATTTTAA-T--TTTAATTA
1466412 ATCTTTAATTGTTAATT
1 AT-TTTAATT-TTAATT
1466429 TGGTACATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
16 7 0.23
17 2 0.06
18 6 0.19
19 11 0.35
20 5 0.16
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTTAATTTTAATTA
Found at i:1467177 original size:15 final size:16
Alignment explanation
Indices: 1467148--1467181 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1467138 ACACAATAAA
*
1467148 ACAATAAAAATATTTT
1 ACAATAAAAACATTTT
1467164 ACAA-AAAAACATTTT
1 ACAATAAAAACATTTT
1467179 ACA
1 ACA
1467182 TTCAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (16 bp):
ACAATAAAAACATTTT
Found at i:1470633 original size:23 final size:23
Alignment explanation
Indices: 1470590--1470633 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1470580 GCTCAATGTG
** *
1470590 AAGAAAGATTTTTTTTTTGAGTT
1 AAGAAAGATTTTTAGTATGAGTT
1470613 AAGAAAGATTTTTAGTATGAG
1 AAGAAAGATTTTTAGTATGAG
1470634 AGGAAGTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.43
Consensus pattern (23 bp):
AAGAAAGATTTTTAGTATGAGTT
Found at i:1483574 original size:18 final size:17
Alignment explanation
Indices: 1483551--1483585 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1483541 CCTTTAAACC
*
1483551 TTTCTCTTTCTTCTCCTT
1 TTTCTCCTTC-TCTCCTT
1483569 TTTCTCCTTCTCTCCTT
1 TTTCTCCTTCTCTCCTT
1483586 CCGAAATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTCTCCTTCTCTCCTT
Found at i:1485343 original size:20 final size:21
Alignment explanation
Indices: 1485307--1485345 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1485297 TCAACAAAAA
1485307 TTATAAAATAATTCAAAATAT
1 TTATAAAATAATTCAAAATAT
*
1485328 TTATAAAA-ATTTCAAAAT
1 TTATAAAATAATTCAAAAT
1485346 TTATATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
TTATAAAATAATTCAAAATAT
Found at i:1488986 original size:21 final size:20
Alignment explanation
Indices: 1488947--1488988 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1488937 CCCAGTCTTC
*
1488947 AAAAAATCAAAACATAACAA
1 AAAAAATCAAAACACAACAA
*
1488967 AAAAAATCAAAATTACAACAA
1 AAAAAATCAAAA-CACAACAA
1488988 A
1 A
1488989 TTACTTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.74, C:0.14, G:0.00, T:0.12
Consensus pattern (20 bp):
AAAAAATCAAAACACAACAA
Found at i:1496042 original size:2 final size:2
Alignment explanation
Indices: 1496037--1496109 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
1496027 AAAAAATCAA
1496037 TC TC TC TC TC TC TC TC 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 TC TC TC TC TC TC TC TC
1496079 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1496110 GTTCTTTTCT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1506107 original size:62 final size:62
Alignment explanation
Indices: 1505995--1506118 Score: 162
Period size: 62 Copynumber: 2.0 Consensus size: 62
1505985 GTGTTTGAAC
* *
1505995 TTTTTTTTGTATAAGTTAGTCCCTGAACTTTGATAATTGTTCCCATATTAGGGCTTGAACTT
1 TTTTTTTTGTATAAGTTAGTCCCTGAACTTTGACAATTGTTCCCACATTAGGGCTTGAACTT
* * * *
1506057 TTTTTTTCTGT-TCAAGTTAGTCTCTGAAC-TTGGCAATTGTTCTCACATTAGGGCTTTAACTT
1 TTTTTTT-TGTAT-AAGTTAGTCCCTGAACTTTGACAATTGTTCCCACATTAGGGCTTGAACTT
1506119 AAGGGTTTTC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
62 36 0.67
63 18 0.33
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (62 bp):
TTTTTTTTGTATAAGTTAGTCCCTGAACTTTGACAATTGTTCCCACATTAGGGCTTGAACTT
Found at i:1513000 original size:16 final size:17
Alignment explanation
Indices: 1512979--1513076 Score: 61
Period size: 15 Copynumber: 6.2 Consensus size: 17
1512969 TTATATATTA
* *
1512979 TATATTTTTATTA-AAT
1 TATATTTTAATAATAAT
1512995 TATATTTTAATAATAAT
1 TATATTTTAATAATAAT
*
1513012 TATA--TTAAGAAT-AT
1 TATATTTTAATAATAAT
** *
1513026 TATTAAGTT-AT-ATATT
1 TA-TATTTTAATAATAAT
*
1513042 TATATTTT-ATTA-AAT
1 TATATTTTAATAATAAT
1513057 TATA-TTTAATAATAAT
1 TATATTTTAATAATAAT
1513073 TATA
1 TATA
1513077 CCAAAATATA
Statistics
Matches: 65, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
14 7 0.11
15 26 0.40
16 23 0.35
17 9 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TATATTTTAATAATAAT
Found at i:1513143 original size:60 final size:60
Alignment explanation
Indices: 1512968--1513148 Score: 245
Period size: 60 Copynumber: 3.0 Consensus size: 60
1512958 TTTTTCTAAT
*
1512968 ATTATATATTATATATTTTTATTAAATTATATTTTAATAATAATTATATTAAGAATATTATTAA
1 ATTATATATT-TATA-TTTTATTAAATTATA-TTTAATAATAATTATATTAA-AATATAATTAA
* **
1513032 GTTATATATTTATATTTTATTAAATTATATTTAATAATAATTATACCAAAATATAATTAA
1 ATTATATATTTATATTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAA
* * ** *
1513092 ATTATTTATTTTTATTTTATTAAATTATATTTAATAATAATCCTATTAAAATTTAAT
1 ATTATATATTTATATTTTATTAAATTATATTTAATAATAATTATATTAAAATATAAT
1513149 AACAATAACC
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
60 59 0.56
61 18 0.17
62 15 0.14
63 4 0.04
64 9 0.09
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (60 bp):
ATTATATATTTATATTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAA
Found at i:1515983 original size:22 final size:20
Alignment explanation
Indices: 1515958--1516002 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 20
1515948 CAAAAGCATA
1515958 AAAAGCATTAAAGAAAATCATG
1 AAAAGCA-TAAA-AAAATCATG
*
1515980 AAAAGCATAAAAGAATCATG
1 AAAAGCATAAAAAAATCATG
1516000 AAA
1 AAA
1516003 GAAAATAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 4 0.18
22 7 0.32
ACGTcount: A:0.62, C:0.09, G:0.13, T:0.16
Consensus pattern (20 bp):
AAAAGCATAAAAAAATCATG
Found at i:1515998 original size:20 final size:22
Alignment explanation
Indices: 1515949--1516002 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1515939 AAAAACCACC
* *
1515949 AAAAGCATAAAAAGCATTAAAG
1 AAAATCATGAAAAGCATTAAAG
1515971 AAAATCATGAAAAGCA-TAAA-
1 AAAATCATGAAAAGCATTAAAG
*
1515991 AGAATCATGAAA
1 AAAATCATGAAA
1516003 GAAAATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 11 0.38
21 4 0.14
22 14 0.48
ACGTcount: A:0.63, C:0.09, G:0.13, T:0.15
Consensus pattern (22 bp):
AAAATCATGAAAAGCATTAAAG
Found at i:1517216 original size:62 final size:61
Alignment explanation
Indices: 1517131--1517407 Score: 250
Period size: 61 Copynumber: 4.6 Consensus size: 61
1517121 AAAATTGAAA
** * * * *
1517131 TGTTGGCCATGC-AATGATCGACACCCCTTTTTTGTAAGAAAAAAAATTTCAAAATTTTGGGG
1 TGTTGGCCAT-CAAATGGCCGACACCCCCTTTTTCT-CGAAAAAAAATTTCAAAATTTTTGGG
** *
1517193 TGTTGGCCATCAAATGGCCGACACCCCCCATTT-GC-AAAAAAAATTGT----ATTTTTGGG
1 TGTTGGCCATCAAATGGCCGACACCCCCTTTTTCTCGAAAAAAAATT-TCAAAATTTTTGGG
* * ** * * * *
1517249 TGTTAGCCATCAAATTGCCGACACTTCCTATTTCTCGAAAAAAAAATTCAAATTTTTTTGG
1 TGTTGGCCATCAAATGGCCGACACCCCCTTTTTCTCGAAAAAAAATTTCAAAATTTTTGGG
* * *
1517310 TGTTGGCCATCAAATGGCCGACA-CCCCTCTTTTCTCGAGAAAAAATTTCAAATTTTTTTGG
1 TGTTGGCCATCAAATGGCCGACACCCCCT-TTTTCTCGAAAAAAAATTTCAAAATTTTTGGG
*
1517371 TGTTAGCCATGC-AATGGCCGACACCCCC-TTTTCTCGA
1 TGTTGGCCAT-CAAATGGCCGACACCCCCTTTTTCTCGA
1517408 GAAATTTTTT
Statistics
Matches: 179, Mismatches: 25, Indels: 24
0.79 0.11 0.11
Matches are distributed among these distances:
56 36 0.20
57 2 0.01
58 9 0.05
59 10 0.06
60 13 0.07
61 78 0.44
62 31 0.17
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (61 bp):
TGTTGGCCATCAAATGGCCGACACCCCCTTTTTCTCGAAAAAAAATTTCAAAATTTTTGGG
Found at i:1517402 original size:60 final size:60
Alignment explanation
Indices: 1517170--1517411 Score: 262
Period size: 61 Copynumber: 4.0 Consensus size: 60
1517160 TTTTGTAAGA
* ** * **
1517170 AAAAAAATTTCAAAATTTTGGGGTGTTGGCCATCAAATGGCCGACACCCCCCATT-T-GCA-
1 AAAAAAA-TTCAAATTTTTTTGGTGTTAGCCATCAAATGGCCGACACCCCCTTTTCTCG-AG
** * * ** *
1517229 AAAAAAATT-GTA-TTTTTGGGTGTTAGCCATCAAATTGCCGACACTTCCTATTTCTCGAA
1 AAAAAAATTCAAATTTTTTTGGTGTTAGCCATCAAATGGCCGACACCCCCT-TTTCTCGAG
*
1517288 AAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTCTTTTCTCGAG
1 AAAAAAATTCAAATTTTTTTGGTGTTAGCCATCAAATGGCCGACACCCC-CTTTTCTCGAG
*
1517349 AAAAAATTTCAAATTTTTTTGGTGTTAGCCATGC-AATGGCCGACACCCCCTTTTCTCGAG
1 AAAAAAATTCAAATTTTTTTGGTGTTAGCCAT-CAAATGGCCGACACCCCCTTTTCTCGAG
1517409 AAA
1 AAA
1517412 TTTTTTTTTT
Statistics
Matches: 156, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
56 31 0.20
57 3 0.02
58 4 0.03
59 17 0.11
60 15 0.10
61 83 0.53
62 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (60 bp):
AAAAAAATTCAAATTTTTTTGGTGTTAGCCATCAAATGGCCGACACCCCCTTTTCTCGAG
Found at i:1520085 original size:20 final size:20
Alignment explanation
Indices: 1520060--1520113 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1520050 ATGATGGATG
1520060 AAAGTCGATCAACGGCGGAC
1 AAAGTCGATCAACGGCGGAC
*
1520080 AAAGTCGGTCAACGGCGGAC
1 AAAGTCGATCAACGGCGGAC
*
1520100 AAAATCGATCAACG
1 AAAGTCGATCAACG
1520114 ACGGTCTCGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.24, G:0.28, T:0.11
Consensus pattern (20 bp):
AAAGTCGATCAACGGCGGAC
Found at i:1520424 original size:83 final size:82
Alignment explanation
Indices: 1520280--1520800 Score: 711
Period size: 83 Copynumber: 6.3 Consensus size: 82
1520270 TAAATATAAA
* *
1520280 ATATAATAAAAATTGTAATATAAAAAAAGAATTTATTTAAAAATATAAAATTAATAAATAATGTA
1 ATATGATAAAAATTGTAATATAAAAAAA-AATTTATTTAAAGATATAAAATTAATAAATAATGTA
*
1520345 TTATCAAATCAACACATT
65 TTGTCAAATCAACACATT
*
1520363 ATATGATAAAAATTATAATATAAAAAAAGAATTTATTTAAAGATATAAAATTAATAAATAATGTA
1 ATATGATAAAAATTGTAATATAAAAAAA-AATTTATTTAAAGATATAAAATTAATAAATAATGTA
*
1520428 TTGTCAAATCGACACATT
65 TTGTCAAATCAACACATT
* * *
1520446 AGATGATAAAAATTGTAATATAAAAAAAGAATTTATTTAAAGATATAAAATTAATAAATATTATA
1 ATATGATAAAAATTGTAATATAAAAAAA-AATTTATTTAAAGATATAAAATTAATAAATAATGTA
*
1520511 TTATCAAATCAACACATT
65 TTGTCAAATCAACACATT
* *
1520529 ATATTATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAAATATTGTA
1 ATATGATAAAAATTGTAATATAA-AAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTA
*
1520594 TTGTCAAATTAACACATT
65 TTGTCAAATCAACACATT
* * *
1520612 ATATTATAAAAATTGTAATATAATAAAAAATTTATTTAAAGATATAAAATTAATAAATATTGTAT
1 ATATGATAAAAATTGTAATATAAAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTAT
*
1520677 TGTCAAATCAAAACATT
66 TGTCAAATCAACACATT
* * * * ** * *
1520694 ACATGATAAAAATTATAATATAATAATATTTTGTACTTTAAATATGA-AAAATTGATAAATAATG
1 ATATGATAAAAATTGTAATATAAAAAAAAATT-TA-TTTAAAGAT-ATAAAATTAATAAATAATG
* * *
1520758 TATTGTCAAATTAATACAAT
63 TATTGTCAAATCAACACATT
* *
1520778 ATTTGATATAAATTGTAATATAA
1 ATATGATAAAAATTGTAATATAA
1520801 TAACTATCTT
Statistics
Matches: 399, Mismatches: 35, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
82 82 0.21
83 252 0.63
84 64 0.16
85 1 0.00
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (82 bp):
ATATGATAAAAATTGTAATATAAAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTAT
TGTCAAATCAACACATT
Found at i:1524842 original size:59 final size:59
Alignment explanation
Indices: 1524659--1525163 Score: 616
Period size: 60 Copynumber: 8.5 Consensus size: 59
1524649 AGAAGAAGTT
* *
1524659 GGTGTTGGCCATTTGATGGCCAACACC-AAAAAATTTGAAATTTTTTTATTCGAGAAAAG-G
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTT--AATTTTTTT-CTCGAGAAAAGAG
* * * * * *
1524719 GGTGTCGACCATTTGATGGCCGACACTAAAAAAAATTAAATTTTTTTTCTCGAGAACAGGG
1 GGTGTCGGCCATTTGATGGCCAACAC-CAAAAAAATTTAA-TTTTTTTCTCGAGAAAAGAG
* *
1524780 GGTGTTGGCCATTTGATGGCCAACACCAAAAAAATTTAATTTTTTTCTCGAGAATAGAG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAATTTTTTTCTCGAGAAAAGAG
1524839 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAATG-G
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTT-AATTTTTTTCTCGAGAAAA-GAG
*
1524899 GGTGTCGGCCA-TTGCATGGCCAACACCAAAAAAATTTGAATTTTTTTTCTCGAGAAAATGGG
1 GGTGTCGGCCATTTG-ATGGCCAACACCAAAAAAATTT-AA-TTTTTTTCTCGAGAAAA-GAG
* *
1524961 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAAATTGAATTTTTTTCTCGAGAAAAGGG
1 GGTGTCGGCCATTTGATGGCCAACACC-AAAAAAATTTAATTTTTTTCTCGAGAAAAGAG
* **
1525021 GGTGTCGACCATTTGATGATCAACACCAAAAAAATTTAATTTTTTTCTCGAGAAATA-AG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAATTTTTTTCTCGAGAAA-AGAG
* * * *
1525080 GGATGTCGGTCATTTGATGGCCAACACC-CAAAAATGTAATTTTTTT-T-GCA-AATAGAG
1 GG-TGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAATTTTTTTCTCG-AGAAAAGAG
1525137 GGTGTCGGCCA-TTGCATGGCCAACACC
1 GGTGTCGGCCATTTG-ATGGCCAACACC
1525164 CCAAATTTTT
Statistics
Matches: 398, Mismatches: 31, Indels: 36
0.86 0.07 0.08
Matches are distributed among these distances:
55 3 0.01
56 21 0.05
57 7 0.02
58 2 0.01
59 103 0.26
60 148 0.37
61 68 0.17
62 34 0.09
63 12 0.03
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (59 bp):
GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAATTTTTTTCTCGAGAAAAGAG
Found at i:1524870 original size:120 final size:120
Alignment explanation
Indices: 1524659--1525163 Score: 649
Period size: 122 Copynumber: 4.2 Consensus size: 120
1524649 AGAAGAAGTT
* *
1524659 GGTGTTGGCCATTTGATGGCCAACACC-AAAAAATTTGAAATTTTTTTATTCGAGAAAAG-GGGT
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTG-AATTTTTTT-CTCGAGAAAAGAGGGT
* * * *
1524722 GTCGACCATTTGATGGCCGACACTAAAAAAAATTAAATTTTTTTTCTCGAGAACAGGG
64 GTCGGCCATTTGATGGCCAACACCAAAAAAAATTAAA-TTTTTTTCTCGAGAAAAGGG
* *
1524780 GGTGTTGGCCATTTGATGGCCAACACCAAAAAAATTT-AATTTTTTTCTCGAGAATAGAGGGTGT
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGAGGGTGT
* *
1524844 CGGCCATTTGATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAATGG
66 CGGCCATTTGATGGCCAACACCAAAAAAAATTAAATTTTTTTCTCGAGAAAAGGG
*
1524899 GGTGTCGGCCA-TTGCATGGCCAACACCAAAAAAATTTGAATTTTTTTTCTCGAGAAAATGGGGG
1 GGTGTCGGCCATTTG-ATGGCCAACACCAAAAAAATTTGAA-TTTTTTTCTCGAGAAAA-GAGGG
*
1524963 TGTCGGCCATTTGATGGCCAACACCAAAAAAAATTGAATTTTTTTCTCGAGAAAAGGG
63 TGTCGGCCATTTGATGGCCAACACCAAAAAAAATTAAATTTTTTTCTCGAGAAAAGGG
* **
1525021 GGTGTCGACCATTTGATGATCAACACCAAAAAAATTT-AATTTTTTTCTCGAGAAATA-AGGGAT
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAA-AGAGGG-T
* * * *
1525084 GTCGGTCATTTGATGGCCAACACC--CAAAAATGT-AATTTTTTT-T-GCA-AATAGAG
64 GTCGGCCATTTGATGGCCAACACCAAAAAAAAT-TAAATTTTTTTCTCG-AGAAAAGGG
1525137 GGTGTCGGCCA-TTGCATGGCCAACACC
1 GGTGTCGGCCATTTG-ATGGCCAACACC
1525164 CCAAATTTTT
Statistics
Matches: 347, Mismatches: 25, Indels: 29
0.87 0.06 0.07
Matches are distributed among these distances:
115 3 0.01
116 26 0.07
117 2 0.01
118 18 0.05
119 63 0.18
120 88 0.25
121 46 0.13
122 98 0.28
123 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (120 bp):
GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGAGGGTGT
CGGCCATTTGATGGCCAACACCAAAAAAAATTAAATTTTTTTCTCGAGAAAAGGG
Found at i:1525217 original size:18 final size:17
Alignment explanation
Indices: 1525196--1525229 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1525186 TCATATTTTT
1525196 GTATATCAAAAAAATACC
1 GTAT-TCAAAAAAATACC
*
1525214 GTATTTAAAAAAATAC
1 GTATTCAAAAAAATAC
1525230 ACACGTGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (17 bp):
GTATTCAAAAAAATACC
Found at i:1526836 original size:29 final size:28
Alignment explanation
Indices: 1526790--1526844 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1526780 TTTTTTAGTT
*
1526790 TTTTTTTAATTAGTTATAGCTGATATAA
1 TTTTTTTAATTAGTTATAACTGATATAA
**
1526818 TTTTTTTAATTTTTATATAACTGATAT
1 TTTTTTTAATTAGT-TATAACTGATAT
1526845 TATAAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (28 bp):
TTTTTTTAATTAGTTATAACTGATATAA
Found at i:1526906 original size:17 final size:17
Alignment explanation
Indices: 1526884--1526922 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1526874 TTTTTTATCA
1526884 TTTATATATATTT-GAAT
1 TTTATATAT-TTTAGAAT
*
1526901 TTTATATATTTTATAAT
1 TTTATATATTTTAGAAT
1526918 TTTAT
1 TTTAT
1526923 TTTATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTATATATTTTAGAAT
Found at i:1526923 original size:13 final size:13
Alignment explanation
Indices: 1526907--1526953 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
1526897 GAATTTTATA
*
1526907 TATTTTATAATTT
1 TATTTTATAAATT
1526920 TATTTTATATAATT
1 TATTTTATA-AATT
*
1526934 TATTATTATAAAAT
1 TATT-TTATAAATT
1526948 TATTTT
1 TATTTT
1526954 TAATTTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 11 0.37
14 14 0.47
15 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTTATAAATT
Found at i:1526930 original size:15 final size:16
Alignment explanation
Indices: 1526898--1526948 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
1526888 TATATATTTG
*
1526898 AATTTTATATATTTTAT
1 AATTTTAT-TATTATAT
1526915 AATTTTATT-TTATAT
1 AATTTTATTATTATAT
*
1526930 AA-TTTATTATTATAA
1 AATTTTATTATTATAT
1526945 AATT
1 AATT
1526949 ATTTTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 6 0.20
15 14 0.47
16 2 0.07
17 8 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTTTATTATTATAT
Found at i:1527296 original size:13 final size:13
Alignment explanation
Indices: 1527278--1527306 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1527268 AATTACACTC
1527278 AAATTCAATTTTA
1 AAATTCAATTTTA
1527291 AAATTCAATTTTA
1 AAATTCAATTTTA
1527304 AAA
1 AAA
1527307 AATATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATTCAATTTTA
Found at i:1533410 original size:26 final size:26
Alignment explanation
Indices: 1533377--1533426 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1533367 AAAAATAATA
*
1533377 TTACTATATTTTATGT-ATTTATTTAT
1 TTACTATATTATAT-TAATTTATTTAT
1533403 TTACTATATTATATTAATTTATTT
1 TTACTATATTATATTAATTTATTT
1533427 GTTAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (26 bp):
TTACTATATTATATTAATTTATTTAT
Found at i:1545370 original size:24 final size:25
Alignment explanation
Indices: 1545316--1545373 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
1545306 ATCAATTATA
*
1545316 TTAATTTTTAATAATAAAAATAAAT
1 TTAATTTTTAATAATAAAAACAAAT
** **
1545341 AAAATTTTTAATAA-AAGTACAAAT
1 TTAATTTTTAATAATAAAAACAAAT
1545365 TTAATTTTT
1 TTAATTTTT
1545374 TATCTAACGC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
TTAATTTTTAATAATAAAAACAAAT
Found at i:1577176 original size:29 final size:29
Alignment explanation
Indices: 1577111--1577177 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
1577101 TATGAATTAT
1577111 AATTT-AATTTG--TAATTATATACATGA
1 AATTTGAATTTGTATAATTATATACATGA
* * *
1577137 ATTTTGAATTTGTATAATTTTATATATGAA
1 AATTTGAATTTGTATAATTATATACATG-A
1577167 AATTTG-ATTTG
1 AATTTGAATTTG
1577178 ATCAAATTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
26 4 0.12
27 6 0.18
29 17 0.52
30 6 0.18
ACGTcount: A:0.37, C:0.01, G:0.10, T:0.51
Consensus pattern (29 bp):
AATTTGAATTTGTATAATTATATACATGA
Found at i:1578506 original size:103 final size:103
Alignment explanation
Indices: 1578347--1578541 Score: 300
Period size: 103 Copynumber: 1.9 Consensus size: 103
1578337 TTTTTAATTA
* * ** *
1578347 AAATTAATGTACTCAATTTTGTACATTTGTCCTACATGCATGCAACTGTATGTTTATTAGTCAAA
1 AAATTAATATACTCAAATTTGTACATTTGTCCTACATGCATGCAACTAAATATTTATTAGTCAAA
1578412 CCAAATCAATGAGCATTAAATTTAATTAAAGAGATTTT
66 CCAAATCAATGAGCATTAAATTTAATTAAAGAGATTTT
* * **
1578450 AAATTAATATACTCAAATTTGTACGTTTGTCCTACATGTATGCAGTTAAATATTTATTAGTCAAA
1 AAATTAATATACTCAAATTTGTACATTTGTCCTACATGCATGCAACTAAATATTTATTAGTCAAA
*
1578515 CCAAATCAATGAGCATTAATTTTAATT
66 CCAAATCAATGAGCATTAAATTTAATT
1578542 TCAATATTGT
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
103 82 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.38
Consensus pattern (103 bp):
AAATTAATATACTCAAATTTGTACATTTGTCCTACATGCATGCAACTAAATATTTATTAGTCAAA
CCAAATCAATGAGCATTAAATTTAATTAAAGAGATTTT
Found at i:1585023 original size:16 final size:16
Alignment explanation
Indices: 1585002--1585034 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1584992 TGCAAGATAG
1585002 TTTAAGGACCTCCTTT
1 TTTAAGGACCTCCTTT
1585018 TTTAAGGACCTCCTTT
1 TTTAAGGACCTCCTTT
1585034 T
1 T
1585035 AATTCTTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.45
Consensus pattern (16 bp):
TTTAAGGACCTCCTTT
Found at i:1589009 original size:4 final size:4
Alignment explanation
Indices: 1589000--1589042 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
1588990 ATCAATTTTA
* *
1589000 ACAT ACAT ACAT ACAT ACGT ACGT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1589043 CACACACAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.47, C:0.26, G:0.05, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:1590041 original size:45 final size:44
Alignment explanation
Indices: 1589990--1590126 Score: 119
Period size: 45 Copynumber: 3.2 Consensus size: 44
1589980 TTAAAATATT
*
1589990 AATATTATATTAATTAAGTATATTATTAGTATAAACATCAATTTA
1 AATATTATATTAATTAA-TATATTATTACTATAAACATCAATTTA
* *
1590035 AATATTAAATGTCAATATAA-AT-TTGATT-CTTTAAA-AT--A-TT-
1 AATATTATAT-T-AAT-TAATATATT-ATTACTATAAACATCAATTTA
* *
1590075 AATATTATATCAATTAAATATATTATTATTATAAACATCAATTTA
1 AATATTATATTAATT-AATATATTATTACTATAAACATCAATTTA
1590120 AATATTA
1 AATATTA
1590127 AATGTCAATA
Statistics
Matches: 72, Mismatches: 7, Indels: 26
0.69 0.07 0.25
Matches are distributed among these distances:
37 1 0.01
38 5 0.07
39 5 0.07
40 16 0.22
41 4 0.06
42 1 0.01
43 1 0.01
44 4 0.06
45 23 0.32
46 6 0.08
47 3 0.04
48 3 0.04
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (44 bp):
AATATTATATTAATTAATATATTATTACTATAAACATCAATTTA
Found at i:1590067 original size:85 final size:85
Alignment explanation
Indices: 1589977--1590143 Score: 298
Period size: 85 Copynumber: 2.0 Consensus size: 85
1589967 CTAAAATAAA
* *
1589977 TCTTTAAAATATTAATATTATATTAATTAAGTATATTATTAGTATAAACATCAATTTAAATATTA
1 TCTTTAAAATATTAATATTATATCAATTAAATATATTATTAGTATAAACATCAATTTAAATATTA
1590042 AATGTCAATATAAATTTGAT
66 AATGTCAATATAAATTTGAT
*
1590062 TCTTTAAAATATTAATATTATATCAATTAAATATATTATTATTATAAACATCAATTTAAATATTA
1 TCTTTAAAATATTAATATTATATCAATTAAATATATTATTAGTATAAACATCAATTTAAATATTA
*
1590127 AATGTCAATATGAATTT
66 AATGTCAATATAAATTT
1590144 AATGTGGAGT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 78 1.00
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (85 bp):
TCTTTAAAATATTAATATTATATCAATTAAATATATTATTAGTATAAACATCAATTTAAATATTA
AATGTCAATATAAATTTGAT
Found at i:1593918 original size:7 final size:7
Alignment explanation
Indices: 1593906--1593930 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1593896 ATATATTTAT
1593906 AATTGAA
1 AATTGAA
1593913 AATTGAA
1 AATTGAA
1593920 AATTGAA
1 AATTGAA
1593927 AATT
1 AATT
1593931 AAATACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (7 bp):
AATTGAA
Found at i:1594680 original size:102 final size:103
Alignment explanation
Indices: 1594562--1594762 Score: 332
Period size: 102 Copynumber: 2.0 Consensus size: 103
1594552 CTGGGCCTAC
1594562 TTTGAACATGTATATTTTATATAAATACCTTTGTCCAAATCTTCCCATT-TTTGAATGGATCTTC
1 TTTGAACATGTATATTTTATATAAATACCTTTGTCCAAATCTTCCCATTCTTTGAATGGATCTTC
* *
1594626 GGGTCTGATTGGATGACCCGATGCATAGATAATTTTAT
66 GAGTCTGATTGGATGACCCGATGCATAGACAATTTTAT
* * * *
1594664 TTTGAACATGTATATTTTATATAAATACTTTTGTCTAAATCTTTCCATTCTTTGGATGGATCTTC
1 TTTGAACATGTATATTTTATATAAATACCTTTGTCCAAATCTTCCCATTCTTTGAATGGATCTTC
*
1594729 GAGTCTGATTGGATGACCCGGTGCATAGACAATT
66 GAGTCTGATTGGATGACCCGATGCATAGACAATT
1594763 CTACTGATTT
Statistics
Matches: 91, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
102 46 0.51
103 45 0.49
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.41
Consensus pattern (103 bp):
TTTGAACATGTATATTTTATATAAATACCTTTGTCCAAATCTTCCCATTCTTTGAATGGATCTTC
GAGTCTGATTGGATGACCCGATGCATAGACAATTTTAT
Found at i:1594798 original size:103 final size:102
Alignment explanation
Indices: 1594562--1594765 Score: 255
Period size: 103 Copynumber: 2.0 Consensus size: 102
1594552 CTGGGCCTAC
* * * * *
1594562 TTTGAACATGTATATTTTATATAAATACCTTTGTCCAAATCTTCCCATTTTTGAATGGATCTTCG
1 TTTGAACATGCACATGTCATATAAATACTTTTGTCCAAATCTTCCCATTTTTGAATGGATCTTCG
* * *
1594627 GGTCTGATTGGATGACCCGATGCATAGATAATTTTAT
66 AGTCTGATTGGATGACCCGATGCATAGACAATTCTAT
* * * * * * *
1594664 TTTGAACATGTATATTTTATATAAATACTTTTGTCTAAATCTTTCCATTCTTTGGATGGATCTTC
1 TTTGAACATGCACATGTCATATAAATACTTTTGTCCAAATCTTCCCATT-TTTGAATGGATCTTC
*
1594729 GAGTCTGATTGGATGACCCGGTGCATAGACAATTCTA
65 GAGTCTGATTGGATGACCCGATGCATAGACAATTCTA
1594766 CTGATTTGTC
Statistics
Matches: 93, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
102 46 0.49
103 47 0.51
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (102 bp):
TTTGAACATGCACATGTCATATAAATACTTTTGTCCAAATCTTCCCATTTTTGAATGGATCTTCG
AGTCTGATTGGATGACCCGATGCATAGACAATTCTAT
Found at i:1604563 original size:22 final size:20
Alignment explanation
Indices: 1604533--1604573 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1604523 AAAAAATTAT
1604533 TAAAAAATTAATTTGAAAAATC
1 TAAAAAATT--TTTGAAAAATC
*
1604555 TAAATAATTTTTGAAAAAT
1 TAAAAAATTTTTGAAAAAT
1604574 TAATTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (20 bp):
TAAAAAATTTTTGAAAAATC
Found at i:1608172 original size:16 final size:16
Alignment explanation
Indices: 1608153--1608183 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1608143 TTACATATTA
1608153 TGTAATTTAATTTTTT
1 TGTAATTTAATTTTTT
*
1608169 TGTAATTTTATTTTT
1 TGTAATTTAATTTTT
1608184 CTTTGTGATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TGTAATTTAATTTTTT
Found at i:1611162 original size:49 final size:52
Alignment explanation
Indices: 1611102--1611213 Score: 149
Period size: 52 Copynumber: 2.2 Consensus size: 52
1611092 CCATGGCCAA
* *
1611102 CCATGGCATGGGCTACA-C-AAAAAAA-ATTATCAAATAAAGGGGGTGTCAG
1 CCATGGCATGGGCGACACCAAAAAAAATATTATCAAATAAAAGGGGTGTCAG
* * * *
1611151 CTATGGAATGGGCGACACCAAAAAAAATATTATCAGATAAAAGTGGTGTCAG
1 CCATGGCATGGGCGACACCAAAAAAAATATTATCAAATAAAAGGGGTGTCAG
1611203 CCATGGCATGG
1 CCATGGCATGG
1611214 TTGACACAAG
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
49 14 0.27
50 1 0.02
51 7 0.13
52 30 0.58
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (52 bp):
CCATGGCATGGGCGACACCAAAAAAAATATTATCAAATAAAAGGGGTGTCAG
Found at i:1613124 original size:17 final size:17
Alignment explanation
Indices: 1613102--1613144 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
1613092 ATAATAAAAA
1613102 AATAATTTTATTAT-TTT
1 AATAATTTTA-TATCTTT
1613119 AATAA-TTTATATCTTT
1 AATAATTTTATATCTTT
1613135 ATATAATTTT
1 A-ATAATTTT
1613145 TAAATGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 3 0.13
16 8 0.35
17 9 0.39
18 3 0.13
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
AATAATTTTATATCTTT
Found at i:1614983 original size:4 final size:4
Alignment explanation
Indices: 1614976--1615001 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1614966 AAAGAAAGAA
1614976 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
1615002 GAACTGTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1623188 original size:14 final size:13
Alignment explanation
Indices: 1623153--1623188 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
1623143 CTTAAAATGG
1623153 TAAATTTTTCATT
1 TAAATTTTTCATT
*
1623166 TAAATTTTTTATT
1 TAAATTTTTCATT
1623179 TAAATCTTTT
1 TAAAT-TTTT
1623189 ATAATTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (13 bp):
TAAATTTTTCATT
Found at i:1629675 original size:18 final size:18
Alignment explanation
Indices: 1629648--1629693 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1629638 CGACACGGAG
*
1629648 GAGGACGAAGAAGAACCA
1 GAGGAAGAAGAAGAACCA
* *
1629666 GAGGAAGAAGAGGAGCCA
1 GAGGAAGAAGAAGAACCA
1629684 GAGGAAGAAG
1 GAGGAAGAAG
1629694 GAGTTCAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.48, C:0.11, G:0.41, T:0.00
Consensus pattern (18 bp):
GAGGAAGAAGAAGAACCA
Found at i:1637077 original size:24 final size:24
Alignment explanation
Indices: 1637029--1637080 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1637019 GATGTGGTAA
1637029 AAAAATATAATAAATATATTTATT
1 AAAAATATAATAAATATATTTATT
*
1637053 AAAAATTTAAATAAA-AT-TTTGATT
1 AAAAATAT-AATAAATATATTT-ATT
1637077 AAAA
1 AAAA
1637081 GTGATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 3 0.12
24 16 0.64
25 6 0.24
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAAATATAATAAATATATTTATT
Found at i:1640850 original size:16 final size:17
Alignment explanation
Indices: 1640811--1640853 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
1640801 GTTTAGGGTT
1640811 TAAATTT-TTTAATTAA
1 TAAATTTATTTAATTAA
1640827 TTAAATTTATTTAATTAA
1 -TAAATTTATTTAATTAA
1640845 -AAATTTATT
1 TAAATTTATT
1640854 CTCATTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.36
17 7 0.28
18 9 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAATTTATTTAATTAA
Found at i:1651084 original size:120 final size:118
Alignment explanation
Indices: 1650950--1651326 Score: 366
Period size: 120 Copynumber: 3.1 Consensus size: 118
1650940 TTCAAATTTT
* * *
1650950 TTTCAAAAAAAAATTGCATTTTTGGGTGTTGGCTATCAAATAGTCGACACCCCCTATTTCTCGAG
1 TTTCAAAAAAAAATTGCATTTTTGGGTGTCGGCCATCAAATAGCCGACACCCCCTATTTCTCGAG
** * * **
1651015 AAAAAAATTTCAATTTTTTTTTTGTGTTGTACATTGAATGGCCGACACCCCCTA
66 AAAAAAATTTCAA-AATTTTTTGGTGTTGGACATCAAATGGCCGACACCCCCTA
* *
1651069 TTTCAAAAAATAAATTGCATTTTTGGGTGTCGGCCATCAAATGGCCGACACCCCCTATTTTTCGA
1 TTTCAAAAAA-AAATTGCATTTTTGGGTGTCGGCCATCAAATAGCCGACACCCCCTATTTCTCGA
*
1651134 GAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTA
65 GAAAAAAATTTCAAAATTTTTTGGTGTTGGACATCAAATGGCCGACACCCCCTA
** ** * * *
1651188 TTTCTCGAGAAAAAATTTTTAAATTTTTTTGGTGTTGGCCACTGC--ATGGCCGACACCCCCT-T
1 -TT-TC-A-AAAAAA-AATTGCA-TTTTTGGGTGTCGGCCA-T-CAAATAGCCGACACCCCCTAT
* ** * * ** *
1651250 TTCTCGAG-AAAAATTTTTTAATTTTTTTGGTGTTGGCCATCAAATACCCGACACCCTCTA
58 TTCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGGACATCAAATGGCCGACACCCCCTA
*
1651310 TTCTCGAGAAAAAAATT
1 TT-TC-AAAAAAAAATT
1651327 TTAAATTTTT
Statistics
Matches: 220, Mismatches: 29, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
119 45 0.20
120 70 0.32
121 9 0.04
122 47 0.21
123 16 0.07
124 31 0.14
125 1 0.00
126 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (118 bp):
TTTCAAAAAAAAATTGCATTTTTGGGTGTCGGCCATCAAATAGCCGACACCCCCTATTTCTCGAG
AAAAAAATTTCAAAATTTTTTGGTGTTGGACATCAAATGGCCGACACCCCCTA
Found at i:1651166 original size:62 final size:62
Alignment explanation
Indices: 1650968--1651366 Score: 424
Period size: 62 Copynumber: 6.5 Consensus size: 62
1650958 AAAAATTGCA
* * * * *
1650968 TTTTTGGGTGTTGGCTATCAAATAGTCGACACCCCCTATTTCTCGAGAAAAAAATTTCAATTT
1 TTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTATTTCTCGAGAAAAAAATTTCAA-AT
* ** ** * *
1651031 TTTTTTTGTGTTGTACATTGAATGGCCGACACCCCCTA-TT-TC-AAAAAATAAATTGC--A-
1 TTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTATTTCTCGAGAAAA-AAATTTCAAAT
* * * *
1651088 TTTTTGGGTGTCGGCCATCAAATGGCCGACACCCCCTATTTTTCGAGAAAAAAATTTCAAAA
1 TTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTATTTCTCGAGAAAAAAATTTCAAAT
* *
1651150 TTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTATTTCTCGAGAAAAAATTTTTAAAT
1 TTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTATTTCTCGAGAAAAAAATTTCAAAT
* **
1651212 TTTTTTGGTGTTGGCCACTGC--ATGGCCGACACCCCCT-TTTCTCGAG-AAAAATTTTTTAAT
1 TTTTTTGGTGTTGGCCA-T-CAAATGGCCGACACCCCCTATTTCTCGAGAAAAAAATTTCAAAT
** * *
1651272 TTTTTTGGTGTTGGCCATCAAATACCCGACACCCTCTA-TTCTCGAGAAAAAAATTTTAAATT
1 TTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTATTTCTCGAGAAAAAAATTTCAAA-T
* * *
1651334 TTTTTTTGTGTTGACCATCAAATGGCCGGCACC
1 TTTTTTGGTGTTGGCCATCAAATGGCCGACACC
1651367 AACTTCTCTT
Statistics
Matches: 284, Mismatches: 38, Indels: 29
0.81 0.11 0.08
Matches are distributed among these distances:
57 31 0.11
58 3 0.01
59 9 0.03
60 61 0.21
61 29 0.10
62 120 0.42
63 30 0.11
64 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.35
Consensus pattern (62 bp):
TTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTATTTCTCGAGAAAAAAATTTCAAAT
Done.