Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008703.1 Hibiscus syriacus cultivar Beakdansim tig00111742_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1275178
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1221191 original size:21 final size:21
Alignment explanation
Indices: 1221160--1221216 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
1221150 AAGTCTGCCC
*
1221160 ATATTGTTTTATTTTTAATATA
1 ATATT-TTTTATTTTTAATAAA
1221182 ATATTTTTTA-TTTTAATAAA
1 ATATTTTTTATTTTTAATAAA
1221202 AGTA-TTTTTATTTTT
1 A-TATTTTTTATTTTT
1221217 TATACGATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 16 0.50
21 11 0.34
22 5 0.16
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (21 bp):
ATATTTTTTATTTTTAATAAA
Found at i:1228297 original size:20 final size:20
Alignment explanation
Indices: 1228259--1228297 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1228249 TTTTGATTTA
*
1228259 AGTTGACTTAGACCGGTTCG
1 AGTTGACTTAGACCAGTTCG
1228279 AGTTGAC-TAGAACCAGTTC
1 AGTTGACTTAG-ACCAGTTC
1228298 TAGGGGATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
AGTTGACTTAGACCAGTTCG
Found at i:1233492 original size:20 final size:20
Alignment explanation
Indices: 1233451--1233518 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
1233441 CCAGTTTAGT
* **
1233451 TTGACTCAGTTCGGTTTGGG
1 TTGACTCAGTTCAGTTCAGG
1233471 TTGACTCAGTTCAGTTCAGG
1 TTGACTCAGTTCAGTTCAGG
* * *
1233491 TTAACTCAGCTCAG-TCTGAG
1 TTGACTCAGTTCAGTTCAG-G
1233511 TTGACTCA
1 TTGACTCA
1233519 AATCGATTAG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.08
20 37 0.93
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (20 bp):
TTGACTCAGTTCAGTTCAGG
Found at i:1233988 original size:900 final size:900
Alignment explanation
Indices: 1232251--1234035 Score: 3435
Period size: 900 Copynumber: 2.0 Consensus size: 900
1232241 TGACCCTTTA
*
1232251 GTTAAATTTTTATGAACCGAGATAAATACTTAATTTACATGTGTACATTCGGGTTTAATAGTCAA
1 GTTAAATTTTTATGAACCGAGATAAATACTTAATTTACATGTGCACATTCGGGTTTAATAGTCAA
1232316 TTTAGAAGTTTTCAGTTTCAAATTTGGCAAAACAGACTTTGGATTCAGACTCATGACGTCAAAAA
66 TTTAGAAGTTTTCAGTTTCAAATTTGGCAAAACAGACTTTGGATTCAGACTCATGACGTCAAAAA
1232381 ACATAAAATATAACTTTTCAAAAAATTTGACTTTTTGGTCAAAGTCAACAGTGAAACTGGTCAAA
131 ACATAAAATATAACTTTTCAAAAAATTTGACTTTTTGGTCAAAGTCAACAGTGAAACTGGTCAAA
1232446 GTAAAAGTAAAAGTAAACATATCTGGTCAACAATGAACGGCATGGTCATCGATCAGGTCAAAGTT
196 GTAAAAGTAAAAGTAAACATATCTGGTCAACAATGAACGGCATGGTCATCGATCAGGTCAAAGTT
1232511 AAAATTTCGTATAAAGTTCAACAGCTGAGACCAGTTCAGTTTGACTCAGTTCGGTTTGGGTTGAC
261 AAAATTTCGTATAAAGTTCAACAGCTGAGACCAGTTCAGTTTGACTCAGTTCGGTTTGGGTTGAC
1232576 TCAGTTCAGTTCAAGTTAACTCAGCTCAGTCTGAGTTGACTCAAATCGATTAGATTTGACTCGAA
326 TCAGTTCAGTTCAAGTTAACTCAGCTCAGTCTGAGTTGACTCAAATCGATTAGATTTGACTCGAA
*
1232641 CTAGTTCTAGGGGATTCCAAGCGAAGAGAGGAGTCCCACGATCACACGACAGTGTGTGGCGGCAC
391 CTAGTTCTAGGAGATTCCAAGCGAAGAGAGGAGTCCCACGATCACACGACAGTGTGTGGCGGCAC
1232706 GTGATGATGGTGATGGGATCGGGGGTGGCCTTCGATTACTCCAACGCATCCAAACACACAAAACA
456 GTGATGATGGTGATGGGATCGGGGGTGGCCTTCGATTACTCCAACGCATCCAAACACACAAAACA
1232771 ATCCAATTCAACATTAAAAAATCCAAAACCATGGTAACAATTAACCAAAAATATTCAAAGCTTAC
521 ATCCAATTCAACATTAAAAAATCCAAAACCATGGTAACAATTAACCAAAAATATTCAAAGCTTAC
1232836 TGCTAATGACAGACGATGAAGACGCAATGTTGGGCGACGACAACAACGATGAGGTAGAATGGTGG
586 TGCTAATGACAGACGATGAAGACGCAATGTTGGGCGACGACAACAACGATGAGGTAGAATGGTGG
*
1232901 CTGAAATGACCAGAAATGTGGAAATTTAAGATGGTGAAGTTTTGGGTTTTAAAAAAGCTTTCAAT
651 CTGAAATGACCAGAAATGTGGAAAATTAAGATGGTGAAGTTTTGGGTTTTAAAAAAGCTTTCAAT
*
1232966 CTTTTGATCCCGATGAACGAATGCTGATACAAGGTCGTGGGAGGTCATGGTTGAGTCATTGGAGG
716 CTTTTGATCCCGATGAACGAATGCTGATACAAGGTCGTGGGAGGTCATGGTTGAGTCATCGGAGG
*
1233031 ATGCTATATCAGATGATGGCAGTGGGGAACAGTAACGGTGACCAAAACGGGGAGAATCATAGAGG
781 ATGCTATATCAGATGATGGCAGTGGGGAACAGTAACGGCGACCAAAACGGGGAGAATCATAGAGG
1233096 GATTTGACAGTTAGGGTTAGGAAGTTTGGATTTTTATTGTGGCAGTCAGGTCATG
846 GATTTGACAGTTAGGGTTAGGAAGTTTGGATTTTTATTGTGGCAGTCAGGTCATG
1233151 GTTAAATTTTTATGAACCGAGATAAATACTTAATTTACATGTGCACATTCGGGTTTAATAGTCAA
1 GTTAAATTTTTATGAACCGAGATAAATACTTAATTTACATGTGCACATTCGGGTTTAATAGTCAA
* * *
1233216 TTTAGAGGTTTTTAGTTTCAAATTTGGCAAAATAGACTTTGGATTCAGACTCATGACGTCAAAAA
66 TTTAGAAGTTTTCAGTTTCAAATTTGGCAAAACAGACTTTGGATTCAGACTCATGACGTCAAAAA
1233281 ACATAAAATATAACTTTTCAAAAAATTTGACTTTTTGGTCAAAGTCAACAGTGAAACTGGTCAAA
131 ACATAAAATATAACTTTTCAAAAAATTTGACTTTTTGGTCAAAGTCAACAGTGAAACTGGTCAAA
*
1233346 GTAAAAGTAAAAGTCAACATATCTGGTCAACAATGAACGGCATGGTCATCGATCAGGTCAAAGTT
196 GTAAAAGTAAAAGTAAACATATCTGGTCAACAATGAACGGCATGGTCATCGATCAGGTCAAAGTT
*
1233411 AAAATTTCGTATAAAGTTCAACAGCTGAGACCAGTTTAGTTTGACTCAGTTCGGTTTGGGTTGAC
261 AAAATTTCGTATAAAGTTCAACAGCTGAGACCAGTTCAGTTTGACTCAGTTCGGTTTGGGTTGAC
*
1233476 TCAGTTCAGTTCAGGTTAACTCAGCTCAGTCTGAGTTGACTCAAATCGATTAGATTTGACTCGAA
326 TCAGTTCAGTTCAAGTTAACTCAGCTCAGTCTGAGTTGACTCAAATCGATTAGATTTGACTCGAA
*
1233541 CTAGTTCTAGGATATTCCAAGCGAAGAGAGGAGTCCCACGATCACACGACAGTGTGTGGCGGCAC
391 CTAGTTCTAGGAGATTCCAAGCGAAGAGAGGAGTCCCACGATCACACGACAGTGTGTGGCGGCAC
1233606 GTGATGATGGTGATGGGATCGGGGGTGGCCTTCGATTACTCCAACGCATCCAAACACACAAAACA
456 GTGATGATGGTGATGGGATCGGGGGTGGCCTTCGATTACTCCAACGCATCCAAACACACAAAACA
1233671 ATCCAATTCAACATTAAAAAATCCAAAACCATGGTAACAATTAACCAAAAATATTCAAAGCTTAC
521 ATCCAATTCAACATTAAAAAATCCAAAACCATGGTAACAATTAACCAAAAATATTCAAAGCTTAC
1233736 TGCTAATGACAGACGATGAAGACGCAATGTTGGGCGACGACAACAACGATGAGGTAGAATGGTGG
586 TGCTAATGACAGACGATGAAGACGCAATGTTGGGCGACGACAACAACGATGAGGTAGAATGGTGG
*
1233801 CTGAAATGACCAGAAATGTGGAAAATTAAGATGGTGAAGTTTTGGGTTTTAACAAAGCTTTCAAT
651 CTGAAATGACCAGAAATGTGGAAAATTAAGATGGTGAAGTTTTGGGTTTTAAAAAAGCTTTCAAT
*
1233866 CTTTTGATCCCGATGAACGAATGCTGATACAGGGTCGTGGGAGGTCATGGTTGAGTCATCGGAGG
716 CTTTTGATCCCGATGAACGAATGCTGATACAAGGTCGTGGGAGGTCATGGTTGAGTCATCGGAGG
1233931 ATGCTATATCAGATGATGGCAGTGGGGAACAGTAACGGCGACCAAAACGGGGAGAATCATAGAGG
781 ATGCTATATCAGATGATGGCAGTGGGGAACAGTAACGGCGACCAAAACGGGGAGAATCATAGAGG
*
1233996 GATTTGGCAGTTAGGGTTAGGAAGTTTGGATTTTTATTGT
846 GATTTGACAGTTAGGGTTAGGAAGTTTGGATTTTTATTGT
1234036 TGATTCATGA
Statistics
Matches: 870, Mismatches: 15, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
900 870 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.27
Consensus pattern (900 bp):
GTTAAATTTTTATGAACCGAGATAAATACTTAATTTACATGTGCACATTCGGGTTTAATAGTCAA
TTTAGAAGTTTTCAGTTTCAAATTTGGCAAAACAGACTTTGGATTCAGACTCATGACGTCAAAAA
ACATAAAATATAACTTTTCAAAAAATTTGACTTTTTGGTCAAAGTCAACAGTGAAACTGGTCAAA
GTAAAAGTAAAAGTAAACATATCTGGTCAACAATGAACGGCATGGTCATCGATCAGGTCAAAGTT
AAAATTTCGTATAAAGTTCAACAGCTGAGACCAGTTCAGTTTGACTCAGTTCGGTTTGGGTTGAC
TCAGTTCAGTTCAAGTTAACTCAGCTCAGTCTGAGTTGACTCAAATCGATTAGATTTGACTCGAA
CTAGTTCTAGGAGATTCCAAGCGAAGAGAGGAGTCCCACGATCACACGACAGTGTGTGGCGGCAC
GTGATGATGGTGATGGGATCGGGGGTGGCCTTCGATTACTCCAACGCATCCAAACACACAAAACA
ATCCAATTCAACATTAAAAAATCCAAAACCATGGTAACAATTAACCAAAAATATTCAAAGCTTAC
TGCTAATGACAGACGATGAAGACGCAATGTTGGGCGACGACAACAACGATGAGGTAGAATGGTGG
CTGAAATGACCAGAAATGTGGAAAATTAAGATGGTGAAGTTTTGGGTTTTAAAAAAGCTTTCAAT
CTTTTGATCCCGATGAACGAATGCTGATACAAGGTCGTGGGAGGTCATGGTTGAGTCATCGGAGG
ATGCTATATCAGATGATGGCAGTGGGGAACAGTAACGGCGACCAAAACGGGGAGAATCATAGAGG
GATTTGACAGTTAGGGTTAGGAAGTTTGGATTTTTATTGTGGCAGTCAGGTCATG
Found at i:1236130 original size:2 final size:2
Alignment explanation
Indices: 1236125--1236204 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
1236115 TCAAAAAATA
1236125 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1236167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1236205 GCTTTGTCAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1237187 original size:18 final size:18
Alignment explanation
Indices: 1237164--1237207 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
1237154 CAAATTCTGG
1237164 GGTTTATGTTCATATTAA
1 GGTTTATGTTCATATTAA
1237182 GGTTTATGTTCATATTAA
1 GGTTTATGTTCATATTAA
1237200 GGTTTATG
1 GGTTTATG
1237208 GAATTGATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (18 bp):
GGTTTATGTTCATATTAA
Found at i:1249118 original size:15 final size:15
Alignment explanation
Indices: 1249098--1249127 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1249088 GAGGCAACCC
1249098 ATTTCGTTCTATTTT
1 ATTTCGTTCTATTTT
*
1249113 ATTTCGTTTTATTTT
1 ATTTCGTTCTATTTT
1249128 TGTTTTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (15 bp):
ATTTCGTTCTATTTT
Found at i:1249134 original size:11 final size:10
Alignment explanation
Indices: 1249109--1249147 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
1249099 TTTCGTTCTA
1249109 TTTTATTTCG
1 TTTTATTTCG
*
1249119 TTTTATTTTTG
1 TTTTA-TTTCG
1249130 TTTTATTTCG
1 TTTTATTTCG
1249140 TTTTATTT
1 TTTTATTT
1249148 TTAGCAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.10, C:0.05, G:0.08, T:0.77
Consensus pattern (10 bp):
TTTTATTTCG
Found at i:1249135 original size:21 final size:21
Alignment explanation
Indices: 1249109--1249149 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1249099 TTTCGTTCTA
1249109 TTTTATTTCGTTTTATTTTTG
1 TTTTATTTCGTTTTATTTTTG
1249130 TTTTATTTCGTTTTATTTTT
1 TTTTATTTCGTTTTATTTTT
1249150 AGCAAACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTATTTCGTTTTATTTTTG
Found at i:1249292 original size:24 final size:24
Alignment explanation
Indices: 1249248--1249336 Score: 83
Period size: 24 Copynumber: 3.7 Consensus size: 24
1249238 TGTTGAAAAA
1249248 AATAGTGCATAACAAAATTTGGTTCG
1 AATAGTGCAT-A-AAAATTTGGTTCG
* **
1249274 AATTGTGCATAAAAATTT-GAACAG
1 AATAGTGCATAAAAATTTGGTTC-G
* *
1249298 AACAGTGCATAAAAA-ATGGTTCG
1 AATAGTGCATAAAAATTTGGTTCG
*
1249321 AATAGTGCACAAAAAT
1 AATAGTGCATAAAAAT
1249337 ACACAACATA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
23 17 0.34
24 23 0.46
25 1 0.02
26 9 0.18
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (24 bp):
AATAGTGCATAAAAATTTGGTTCG
Found at i:1249327 original size:23 final size:23
Alignment explanation
Indices: 1249248--1249335 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 23
1249238 TGTTGAAAAA
1249248 AATAGTGCATAACAAAATTTGGTTCG
1 AATAGTGCATAA-AAAA--TGGTTCG
* * * **
1249274 AATTGTGCATAAAAATTTGAACAG
1 AATAGTGCATAAAAAATGGTTC-G
*
1249298 AACAGTGCATAAAAAATGGTTCG
1 AATAGTGCATAAAAAATGGTTCG
*
1249321 AATAGTGCACAAAAA
1 AATAGTGCATAAAAA
1249336 TACACAACAT
Statistics
Matches: 48, Mismatches: 13, Indels: 5
0.73 0.20 0.08
Matches are distributed among these distances:
23 17 0.35
24 17 0.35
25 3 0.06
26 11 0.23
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.25
Consensus pattern (23 bp):
AATAGTGCATAAAAAATGGTTCG
Found at i:1251854 original size:17 final size:14
Alignment explanation
Indices: 1251803--1251862 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
1251793 ATCTTTACTA
*
1251803 TTATAATTTATTATT
1 TTATTATTT-TTATT
*
1251818 TTATTATTTTTCTT
1 TTATTATTTTTATT
1251832 TT-TTATTTATTATT
1 TTATTATTT-TTATT
1251846 ATGTATTATATTTTATT
1 -T-TATTAT-TTTTATT
1251863 AAATCTTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
13 6 0.16
14 10 0.27
15 9 0.24
16 1 0.03
17 9 0.24
18 2 0.05
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (14 bp):
TTATTATTTTTATT
Found at i:1252404 original size:2 final size:2
Alignment explanation
Indices: 1252349--1252395 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1252339 TAATGTACAT
1252349 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1252391 TA TA T
1 TA TA T
1252396 GCATATATAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1253281 original size:415 final size:412
Alignment explanation
Indices: 1252458--1253279 Score: 1125
Period size: 415 Copynumber: 2.0 Consensus size: 412
1252448 AACAATCATT
* * * *
1252458 AAATTGGAAATAAAAAATTGAATAAATTAAGGAACACACATTGATGAGGGGTGATATTTGAATTA
1 AAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATAAGGGATGATAATTGAATTA
* * * * *
1252523 GTTATAAAATGTGAAGCTGAAATTAATATAAAATGGACTAATTTGTATACATTTATAAATTTGGT
66 ATTATAAAATGTGAAACTGAAATTAATATAAAATGGACTAAATTGTATACATTTAAAAAGTTGGT
* * *
1252588 GAACATAATTTGAAAATAAGTTGATTATGTGATTTACATTTTTAGGGTTTCTTTTAAGTAAATTA
131 GAACATAATTTGAAAAGAAATTGATTATGTGATTTACATTTTTAGCG--T-TTTTAAGTAAATTA
* * * * * * * * * *
1252653 AAAAAATATAAATTAGTATGGGTTAATTTTAGATACGAATATAATTTGAAGGACTAAATTGTATA
193 AAAAAATATAAATAAATATGGGTCAATATCAGATACAAATATAAATTGAAGAACTAAATTGAACA
* * * *
1252718 AATATGAAATTACAAATTAAAATTTAAATACAATCAACAACATGAAAGTATGAAATCAAAAAACT
258 AATATGAAATTACAAATTAAAATTTAAACACAATAAACAACATGAAAGGATCAAATCAAAAAACT
* * *
1252783 ATAAAATGTGATATAAAATGTAAAATAGATTGAATTGCATTAATTTCAAAAGTTGGGGAAAATTA
323 ATAAAATGTGATAGAAAATGTAAAATAGACTGAATTGCATTAATATCAAAAGTTGGGGAAAATTA
1252848 AAACAATTATATATATATAAACATG
388 AAACAATTATATATATATAAACATG
*
1252873 AAATTGGAAATACAAAATTGAATAAATTAAGCAACACACATTGATAAGGGATGA-AATTGAATTA
1 AAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATAAGGGATGATAATTGAATTA
** **
1252937 ATTATAAAATGTGAAACTGGTATTAATATAAAAAAATTTACTAAATTGTATACATTTAAAAAAGT
66 ATTATAAAATGTGAAACTGAAATTAATAT---AAAATGGACTAAATTGTATACATTT-AAAAAGT
* *
1253002 TGGTGAACGTAATTTGAAAAGAAATTTATTATGTGATTTACATTTTATAGCG-TTTTAAGTAAAT
127 TGGTGAACATAATTTGAAAAGAAATTGATTATGTGATTTACATTTT-TAGCGTTTTTAAGTAAAT
* *
1253066 TACAAAAATATAAATAAATATGGGTCAATATCATATACAAATATAAATTGAAGAACTAAATTGAA
191 TAAAAAAATATAAATAAATATGGGTCAATATCAGATACAAATATAAATTGAAGAACTAAATTGAA
*
1253131 CAAATATGAAATTACAAATTGAAATTTAAACACAATAAACAACAT-AAACGGATCAAAT-AAAAA
256 CAAATATGAAATTACAAATTAAAATTTAAACACAATAAACAACATGAAA-GGATCAAATCAAAAA
* * *
1253194 ATTGTAAAATGTGA-AGAAAATTGTAAAATGGACTGAATTGCATTAATATCAAAAGTTGGGG-AA
320 ACTATAAAATGTGATAGAAAA-TGTAAAATAGACTGAATTGCATTAATATCAAAAGTTGGGGAAA
*
1253257 ATTGAAACAATTATATATATATA
384 ATTAAAACAATTATATATATATA
1253280 TATATATATA
Statistics
Matches: 357, Mismatches: 43, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
413 29 0.08
414 91 0.25
415 164 0.46
417 22 0.06
418 47 0.13
419 4 0.01
ACGTcount: A:0.48, C:0.06, G:0.14, T:0.32
Consensus pattern (412 bp):
AAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATAAGGGATGATAATTGAATTA
ATTATAAAATGTGAAACTGAAATTAATATAAAATGGACTAAATTGTATACATTTAAAAAGTTGGT
GAACATAATTTGAAAAGAAATTGATTATGTGATTTACATTTTTAGCGTTTTTAAGTAAATTAAAA
AAATATAAATAAATATGGGTCAATATCAGATACAAATATAAATTGAAGAACTAAATTGAACAAAT
ATGAAATTACAAATTAAAATTTAAACACAATAAACAACATGAAAGGATCAAATCAAAAAACTATA
AAATGTGATAGAAAATGTAAAATAGACTGAATTGCATTAATATCAAAAGTTGGGGAAAATTAAAA
CAATTATATATATATAAACATG
Found at i:1253501 original size:2 final size:2
Alignment explanation
Indices: 1253494--1253631 Score: 51
Period size: 2 Copynumber: 68.0 Consensus size: 2
1253484 GTATAAAGTG
*
1253494 TA TA TA TA TA TA TA TA TA TA TA AA CTA CTA -A GTA TA -A GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA -TA TA -TA TA TA -TA TA
* * *
1253536 T- TA TA -A T- TA TA TA TA TA AA CTA TA AA GTA TA TA TA CTT TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA -TA TA
* * *
1253576 TA CTA -A AA CTT TA TA TA TA -A TA TA CTT TA TA T- TA TA TA CT-
1 TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA
1253616 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
1253632 AAGTTTTAGC
Statistics
Matches: 104, Mismatches: 13, Indels: 38
0.67 0.08 0.25
Matches are distributed among these distances:
1 9 0.09
2 82 0.79
3 13 0.12
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1253511 original size:23 final size:23
Alignment explanation
Indices: 1253448--1253505 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 23
1253438 ACTATATATA
1253448 ATATATATATAAACTAT-AAGGT
1 ATATATATATAAACTATAAAGGT
* *
1253470 ATATATACTTTAAAGTATAAAGTGT
1 ATATATA-TATAAACTATAAAG-GT
1253495 ATATATATATA
1 ATATATATATA
1253506 TATATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 7 0.23
23 8 0.27
24 6 0.20
25 9 0.30
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.40
Consensus pattern (23 bp):
ATATATATATAAACTATAAAGGT
Found at i:1253514 original size:41 final size:38
Alignment explanation
Indices: 1253469--1253566 Score: 119
Period size: 37 Copynumber: 2.5 Consensus size: 38
1253459 AACTATAAGG
* * *
1253469 TATATATACTTTAAAGTATAAAGTGTATATATATATATATA
1 TATATAAACTATAAAGTATAAAGTATAT-TATA-AT-TATA
1253510 TATATAAACTACT-AAGTAT-AAGTATATTATAATTATA
1 TATATAAACTA-TAAAGTATAAAGTATATTATAATTATA
1253547 TATATAAACTATAAAGTATA
1 TATATAAACTATAAAGTATA
1253567 TATACTTTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
36 1 0.02
37 21 0.41
38 2 0.04
39 4 0.08
40 7 0.14
41 15 0.29
42 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (38 bp):
TATATAAACTATAAAGTATAAAGTATATTATAATTATA
Found at i:1253577 original size:37 final size:35
Alignment explanation
Indices: 1253470--1253577 Score: 105
Period size: 37 Copynumber: 3.0 Consensus size: 35
1253460 ACTATAAGGT
* * * *
1253470 ATATATACTTTAAAGTATAAAGTGTATATATATAT-
1 ATATATA-TATAAACTATAAAGTATATATATTTATA
1253505 ATATATATATAAACTACT-AAGTATA-AGTATATTATA
1 ATATATATATAAACTA-TAAAGTATATA-TAT-TTATA
1253541 ATTATATATATAAACTATAAAGTATATATACTTTATA
1 A-TATATATATAAACTATAAAGTATATATA-TTTATA
1253578 CTAAAACTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
33 1 0.02
34 16 0.26
35 11 0.18
36 2 0.03
37 29 0.48
38 2 0.03
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.42
Consensus pattern (35 bp):
ATATATATATAAACTATAAAGTATATATATTTATA
Found at i:1253598 original size:29 final size:32
Alignment explanation
Indices: 1253440--1253631 Score: 108
Period size: 29 Copynumber: 6.2 Consensus size: 32
1253430 AACCATAAAC
* * **
1253440 TATATATAATATATA-TATAAAC-TATA-AGG
1 TATATATACTTTATACTATAAACTTATATATA
* * *
1253469 TATATATACTTTAAAGTATAAAGTGTATATATA
1 TATATATACTTTATACTATAAACT-TATATATA
* *
1253502 TATATATA-TATATAAACTACT-AA-GTATA-AGTA
1 TATATATACT-T-TATACTA-TAAACTTATATA-TA
*
1253534 TAT-TATAATTATATA-TATAAAC-TATA-A-A
1 TATATATACTT-TATACTATAAACTTATATATA
1253562 GTATATATACTTTATACTA-AAACTT-TATATA
1 -TATATATACTTTATACTATAAACTTATATATA
* *
1253593 TA-ATATACTTTATATTATATACTTATATATA
1 TATATATACTTTATACTATAAACTTATATATA
1253624 TATATATA
1 TATATATA
1253632 AAGTTTTAGC
Statistics
Matches: 131, Mismatches: 12, Indels: 37
0.73 0.07 0.21
Matches are distributed among these distances:
28 1 0.01
29 40 0.31
30 32 0.24
31 19 0.15
32 20 0.15
33 10 0.08
34 8 0.06
35 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (32 bp):
TATATATACTTTATACTATAAACTTATATATA
Found at i:1253696 original size:20 final size:21
Alignment explanation
Indices: 1253660--1253740 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 21
1253650 TATATACAAA
1253660 TATACTAATATAAAGTATATG
1 TATACTAATATAAAGTATATG
*
1253681 TATACT-ATATATAGTATAAT-
1 TATACTAATATAAAGTAT-ATG
1253701 TATA--AATACTAAAGTATATAAG
1 TATACTAATA-TAAAGTATAT--G
*
1253723 TATA-TAATATAAATTATA
1 TATACTAATATAAAGTATA
1253741 CCAATATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
19 5 0.10
20 21 0.42
21 8 0.16
22 12 0.24
23 4 0.08
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.40
Consensus pattern (21 bp):
TATACTAATATAAAGTATATG
Found at i:1253725 original size:8 final size:7
Alignment explanation
Indices: 1253681--1253811 Score: 51
Period size: 8 Copynumber: 17.7 Consensus size: 7
1253671 AAAGTATATG
*
1253681 TATACTA
1 TATAATA
1253688 TAT-ATA
1 TATAATA
1253694 GTATAAT-
1 -TATAATA
1253701 TATAA-A
1 TATAATA
1253707 TACTAAAGTA
1 TA-T-AA-TA
1253717 TATAAGTA
1 TATAA-TA
1253725 TATAATA
1 TATAATA
1253732 TA-AATTA
1 TATAA-TA
*
1253739 TACCAATA
1 TA-TAATA
1253747 TATAAAGTA
1 TAT-AA-TA
*
1253756 TATATACA
1 TATA-ATA
1253764 TATAA-A
1 TATAATA
*
1253770 GTGTAAGTA
1 -TATAA-TA
1253779 TATAAATA
1 TAT-AATA
1253787 TATAA-A
1 TATAATA
1253793 TAT-ATA
1 TATAATA
1253799 TATAAGTA
1 TATAA-TA
1253807 TATAA
1 TATAA
1253812 ACTAAAAAGA
Statistics
Matches: 99, Mismatches: 5, Indels: 39
0.69 0.03 0.27
Matches are distributed among these distances:
5 1 0.01
6 20 0.20
7 23 0.23
8 40 0.40
9 12 0.12
10 3 0.03
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (7 bp):
TATAATA
Found at i:1253726 original size:22 final size:22
Alignment explanation
Indices: 1253660--1254070 Score: 159
Period size: 22 Copynumber: 19.0 Consensus size: 22
1253650 TATATACAAA
1253660 TATACTAATATAAAGTATAT--G
1 TATA-TAATATAAAGTATATAAG
* *
1253681 TATACT-ATATATAG--TATAAT
1 TATA-TAATATAAAGTATATAAG
1253701 TATA-AATACTAAAGTATATAAG
1 TATATAATA-TAAAGTATATAAG
*
1253723 TATATAATATAAA-T-TAT-AC
1 TATATAATATAAAGTATATAAG
*
1253742 CA-AT-ATATAAAGTATATATA-
1 TATATAATATAAAGTATATA-AG
* * *
1253762 CATATAA-AGTGTAAGTATATAAA
1 TATATAATA-T-AAAGTATATAAG
*
1253785 TATATAA-ATATA-TATATAAG
1 TATATAATATAAAGTATATAAG
*
1253805 TATATAA-ACTAAA--A-AGAGAG
1 TATATAATA-TAAAGTATATA-AG
* * * *
1253825 TGTGT-GTATATA-TATATATAG
1 TATATAATATAAAGTATATA-AG
* * **
1253846 T-TTTAGTATAAAGTCCATATGGG
1 TATATAATATAAAGT--ATATAAG
*
1253869 TATATAATAATATAAAGTACATAAG
1 TATAT---AATATAAAGTATATAAG
*
1253894 TAT-TAAGTAT-AAGTATATAAA
1 TATATAA-TATAAAGTATATAAG
1253915 TAT-TAAATATAAAAGTATATAAG
1 TATAT-AATAT-AAAGTATATAAG
1253938 TATATAAGTAT-AAGTATATAAG
1 TATATAA-TATAAAGTATATAAG
1253960 TATA-AATACTAAAGTATATAAG
1 TATATAATA-TAAAGTATATAAG
1253982 TATATAATATAAAGTATATCAA-
1 TATATAATATAAAGTATAT-AAG
*
1254004 TATATAAAGTATATATA-CATATAAAG
1 TATAT-AA-TATA-A-AGTATAT-AAG
*
1254030 TATA-AGTATATAAA-TATATAAA
1 TATATA--ATATAAAGTATATAAG
1254052 TATAT-ATAT-AAGTATATAA
1 TATATAATATAAAGTATATAA
1254071 ACTAAAAAGA
Statistics
Matches: 307, Mismatches: 35, Indels: 97
0.70 0.08 0.22
Matches are distributed among these distances:
17 7 0.02
18 6 0.02
19 15 0.05
20 58 0.19
21 47 0.15
22 74 0.24
23 50 0.16
24 17 0.06
25 18 0.06
26 6 0.02
27 9 0.03
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.36
Consensus pattern (22 bp):
TATATAATATAAAGTATATAAG
Found at i:1253912 original size:8 final size:8
Alignment explanation
Indices: 1253868--1254070 Score: 149
Period size: 8 Copynumber: 27.0 Consensus size: 8
1253858 GTCCATATGG
1253868 GTATATAA
1 GTATATAA
1253876 -TAATATAAA
1 GT-ATAT-AA
*
1253885 GTACATAA
1 GTATATAA
1253893 GTAT-TAA
1 GTATATAA
1253900 G--TATAA
1 GTATATAA
1253906 GTATATAA
1 GTATATAA
*
1253914 ATAT-TAA
1 GTATATAA
* *
1253921 ATATAAAA
1 GTATATAA
1253929 GTATATAA
1 GTATATAA
1253937 GTATATAA
1 GTATATAA
1253945 G--TATAA
1 GTATATAA
1253951 GTATATAA
1 GTATATAA
1253959 GTATA-AA
1 GTATATAA
1253966 -TACTA-AA
1 GTA-TATAA
1253973 GTATATAA
1 GTATATAA
1253981 GTATATAA
1 GTATATAA
1253989 -TATA-AA
1 GTATATAA
1253995 GTATATCAA
1 GTATAT-AA
1254004 -TATATAAA
1 GTATAT-AA
1254012 GTATATATA
1 GTATATA-A
*
1254021 -CATATAA
1 GTATATAA
1254028 --AGTATAA
1 GTA-TATAA
1254035 GTATATAA
1 GTATATAA
*
1254043 ATATATAA
1 GTATATAA
1254051 --ATAT-A
1 GTATATAA
1254056 -TATATAA
1 GTATATAA
1254063 GTATATAA
1 GTATATAA
1254071 ACTAAAAAGA
Statistics
Matches: 163, Mismatches: 9, Indels: 46
0.75 0.04 0.21
Matches are distributed among these distances:
5 2 0.01
6 23 0.14
7 35 0.21
8 88 0.54
9 14 0.09
10 1 0.01
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.35
Consensus pattern (8 bp):
GTATATAA
Found at i:1253937 original size:44 final size:43
Alignment explanation
Indices: 1253877--1254070 Score: 217
Period size: 44 Copynumber: 4.6 Consensus size: 43
1253867 GGTATATAAT
*
1253877 AATATAAAGTACATAAGTAT-TAAGTATAAGTATATAAATATTA
1 AATATAAAGTATATAAGTATATAAGTATAAGTATATAAATA-TA
*
1253920 AATATAAAAGTATATAAGTATATAAGTATAAGTATATAAGTATA
1 AATAT-AAAGTATATAAGTATATAAGTATAAGTATATAAATATA
*
1253964 AATACTAAAGTATATAAGTATATAA-TATAAAGTATAT-CA-AT-
1 AATA-TAAAGTATATAAGTATATAAGTAT-AAGTATATAAATATA
*
1254005 -ATATAAAGTATATATA-CATATAAAGTATAAGTATATAAATATA
1 AATATAAAGTATATA-AGTATAT-AAGTATAAGTATATAAATATA
*
1254048 TAA-ATATA-TATATAAGTATATAA
1 -AATATAAAGTATATAAGTATATAA
1254071 ACTAAAAAGA
Statistics
Matches: 130, Mismatches: 8, Indels: 27
0.79 0.05 0.16
Matches are distributed among these distances:
39 15 0.12
40 14 0.11
41 4 0.03
42 7 0.05
43 18 0.14
44 51 0.39
45 21 0.16
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (43 bp):
AATATAAAGTATATAAGTATATAAGTATAAGTATATAAATATA
Found at i:1253993 original size:259 final size:259
Alignment explanation
Indices: 1253695--1254228 Score: 971
Period size: 259 Copynumber: 2.1 Consensus size: 259
1253685 CTATATATAG
* *
1253695 TATAATTATAAATACTAAAGTATATAAGTATATAATATAAATTATACCAATATATAAAGTATATA
1 TATAAGTATAAATACTAAAGTATATAAGTATATAATATAAAGTATACCAATATATAAAGTATATA
*
1253760 TACATATAAAGTGTAAGTATATAAATATATAAATATATATATAAGTATATAAACTAAAAAGAGAG
66 TACATATAAAGTATAAGTATATAAATATATAAATATATATATAAGTATATAAACTAAAAAGAGAG
1253825 TGTGTGTATATATATATATAGTTTTAGTATAAAGTCCATATGGGTATATAATAATATAAAGTACA
131 TGTGTGTATATATATATATAGTTTTAGTATAAAGTCCATATGGGTATATAATAATATAAAGTACA
*
1253890 TAAGTATTAAGTATAAGTATATAAATATTAAATATAAAAGTATATAAGTATATAAGTAT-AAGTA
196 TAAGTATTAAGTATAAGTATATAAATATTAAATATAAAAGTATATAAGTAT-TAAATATAAAGTA
*
1253954 TATAAGTATAAATACTAAAGTATATAAGTATATAATATAAAGTATATCAATATATAAAGTATATA
1 TATAAGTATAAATACTAAAGTATATAAGTATATAATATAAAGTATACCAATATATAAAGTATATA
1254019 TACATATAAAGTATAAGTATATAAATATATAAATATATATATAAGTATATAAACTAAAAAGAGAG
66 TACATATAAAGTATAAGTATATAAATATATAAATATATATATAAGTATATAAACTAAAAAGAGAG
* * *
1254084 TGTGTGTGTGTATATGTATAGTTTTAGTATAAAGTCCATATGGGTATATAATAATATAAAGTACA
131 TGTGTGTATATATATATATAGTTTTAGTATAAAGTCCATATGGGTATATAATAATATAAAGTACA
1254149 TAAGTATTAAGTATAAGTATATAAATATTAAATATAAAAGTATATAAGTATTAAATATAAAGTA
196 TAAGTATTAAGTATAAGTATATAAATATTAAATATAAAAGTATATAAGTATTAAATATAAAGTA
*
1254213 TATAAGTATATATACT
1 TATAAGTATAAATACT
1254229 TTCATATAAA
Statistics
Matches: 265, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
258 6 0.02
259 259 0.98
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.36
Consensus pattern (259 bp):
TATAAGTATAAATACTAAAGTATATAAGTATATAATATAAAGTATACCAATATATAAAGTATATA
TACATATAAAGTATAAGTATATAAATATATAAATATATATATAAGTATATAAACTAAAAAGAGAG
TGTGTGTATATATATATATAGTTTTAGTATAAAGTCCATATGGGTATATAATAATATAAAGTACA
TAAGTATTAAGTATAAGTATATAAATATTAAATATAAAAGTATATAAGTATTAAATATAAAGTA
Found at i:1254010 original size:17 final size:16
Alignment explanation
Indices: 1253868--1254057 Score: 120
Period size: 17 Copynumber: 11.9 Consensus size: 16
1253858 GTCCATATGG
1253868 GTATATAATAATATAAA
1 GTATATAAT-ATATAAA
*
1253885 GTACATAAGTAT-T-AA
1 GTATATAA-TATATAAA
*
1253900 GTATA-AGTATATAAA
1 GTATATAATATATAAA
1253915 -TAT-TAA-ATATAAAA
1 GTATATAATATAT-AAA
1253929 GTATATAAGTATAT-AA
1 GTATATAA-TATATAAA
1253945 GTATAAGTATATAAGTATAAA
1 GTAT-A-TA-AT-A-TATAAA
1253966 -TACTA-AAGTATAT-AA
1 GTA-TATAA-TATATAAA
1253981 GTATAT-A-ATATAAA
1 GTATATAATATATAAA
1253995 GTATATCAATATATAAA
1 GTATAT-AATATATAAA
*
1254012 GTATATATACATATAAA
1 GTATATA-ATATATAAA
*
1254029 GTATA-AGTATATAAA
1 GTATATAATATATAAA
1254044 -TATATAAATATATA
1 GTATAT-AATATATA
1254058 TATAAGTATA
Statistics
Matches: 139, Mismatches: 8, Indels: 53
0.69 0.04 0.26
Matches are distributed among these distances:
13 11 0.08
14 21 0.15
15 23 0.17
16 25 0.18
17 38 0.27
18 10 0.07
19 2 0.01
20 6 0.04
21 3 0.02
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.35
Consensus pattern (16 bp):
GTATATAATATATAAA
Found at i:1254161 original size:7 final size:7
Alignment explanation
Indices: 1254149--1254221 Score: 58
Period size: 7 Copynumber: 10.0 Consensus size: 7
1254139 ATAAAGTACA
1254149 TAAGTAT
1 TAAGTAT
1254156 TAAGTA-
1 TAAGTAT
1254162 TAAGTAT
1 TAAGTAT
*
1254169 ATAAATAT
1 -TAAGTAT
*
1254177 TAAATAT
1 TAAGTAT
*
1254184 AAAAGTAT
1 -TAAGTAT
1254192 ATAAGTAT
1 -TAAGTAT
*
1254200 TAAATAT
1 TAAGTAT
*
1254207 AAAGTAT
1 TAAGTAT
1254214 ATAAGTAT
1 -TAAGTAT
1254222 ATATACTTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
6 6 0.11
7 24 0.44
8 24 0.44
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (7 bp):
TAAGTAT
Found at i:1254171 original size:8 final size:8
Alignment explanation
Indices: 1254127--1254224 Score: 84
Period size: 8 Copynumber: 12.9 Consensus size: 8
1254117 GTCCATATGG
1254127 GTATATAA
1 GTATATAA
1254135 -TAATATAAA
1 GT-ATAT-AA
*
1254144 GTACATAA
1 GTATATAA
1254152 GTAT-TAA
1 GTATATAA
1254159 G--TATAA
1 GTATATAA
1254165 GTATATAA
1 GTATATAA
*
1254173 ATAT-TAA
1 GTATATAA
* *
1254180 ATATAAAA
1 GTATATAA
1254188 GTATATAA
1 GTATATAA
1254196 GTAT-TAA
1 GTATATAA
*
1254203 ATATA-AA
1 GTATATAA
1254210 GTATATAA
1 GTATATAA
1254218 GTATATA
1 GTATATA
1254225 TACTTTCATA
Statistics
Matches: 73, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
5 1 0.01
6 4 0.05
7 24 0.33
8 38 0.52
9 5 0.07
10 1 0.01
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (8 bp):
GTATATAA
Found at i:1254193 original size:23 final size:22
Alignment explanation
Indices: 1254136--1254221 Score: 129
Period size: 23 Copynumber: 3.9 Consensus size: 22
1254126 GGTATATAAT
*
1254136 AATATAAAGTACATAAGTATTA
1 AATATAAAGTATATAAGTATTA
* *
1254158 AGTAT-AAGTATATAAATATTA
1 AATATAAAGTATATAAGTATTA
1254179 AATATAAAAGTATATAAGTATTA
1 AATAT-AAAGTATATAAGTATTA
1254202 AATATAAAGTATATAAGTAT
1 AATATAAAGTATATAAGTAT
1254222 ATATACTTTC
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
21 18 0.32
22 19 0.33
23 20 0.35
ACGTcount: A:0.55, C:0.01, G:0.09, T:0.35
Consensus pattern (22 bp):
AATATAAAGTATATAAGTATTA
Found at i:1254206 original size:30 final size:31
Alignment explanation
Indices: 1254160--1254224 Score: 98
Period size: 30 Copynumber: 2.1 Consensus size: 31
1254150 AAGTATTAAG
1254160 TATAAGTATATAAATATTAAA-TATAAAAGTA
1 TATAAGTATATAAATA-TAAAGTATAAAAGTA
*
1254191 TATAAGTAT-TAAATATAAAGTATATAAGTA
1 TATAAGTATATAAATATAAAGTATAAAAGTA
1254221 TATA
1 TATA
1254225 TACTTTCATA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 4 0.12
30 19 0.59
31 9 0.28
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (31 bp):
TATAAGTATATAAATATAAAGTATAAAAGTA
Found at i:1254262 original size:2 final size:2
Alignment explanation
Indices: 1254255--1254283 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1254245 TCAGTGTATG
1254255 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 T
1254284 TGAATTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1257015 original size:13 final size:13
Alignment explanation
Indices: 1256982--1257015 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
1256972 ACCTGGTCCA
1256982 ACTTTGACCATTG
1 ACTTTGACCATTG
1256995 AC--TGACCATTG
1 ACTTTGACCATTG
1257006 ACTTTGACCA
1 ACTTTGACCA
1257016 AAAGTCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.58
13 8 0.42
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (13 bp):
ACTTTGACCATTG
Found at i:1260989 original size:3 final size:3
Alignment explanation
Indices: 1260983--1261082 Score: 150
Period size: 3 Copynumber: 33.7 Consensus size: 3
1260973 TTTTTACCCA
*
1260983 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
1261030 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TA- TAT TAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1261077 ATAT TA
1 -TAT TA
1261083 AATACATATA
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
2 4 0.05
3 81 0.92
4 3 0.03
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1273824 original size:9 final size:8
Alignment explanation
Indices: 1273810--1273862 Score: 63
Period size: 8 Copynumber: 6.6 Consensus size: 8
1273800 ATGCTTGAAG
*
1273810 AAAAAAGT
1 AAAAAAGA
1273818 AAAAAA-A
1 AAAAAAGA
*
1273825 AAAAGAGA
1 AAAAAAGA
*
1273833 AAAAAGAAA
1 AAAAA-AGA
1273842 AAAAAAGA
1 AAAAAAGA
1273850 AAAAAAGA
1 AAAAAAGA
1273858 AAAAA
1 AAAAA
1273863 GGGGGTCAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
7 5 0.13
8 26 0.68
9 7 0.18
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:1273844 original size:19 final size:18
Alignment explanation
Indices: 1273820--1273862 Score: 77
Period size: 18 Copynumber: 2.3 Consensus size: 18
1273810 AAAAAAGTAA
1273820 AAAAAAAAAGAGAAAAAAG
1 AAAAAAAAAGA-AAAAAAG
1273839 AAAAAAAAAGAAAAAAAG
1 AAAAAAAAAGAAAAAAAG
1273857 AAAAAA
1 AAAAAA
1273863 GGGGGTCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGAAAAAAAG
Found at i:1273862 original size:10 final size:10
Alignment explanation
Indices: 1273810--1273855 Score: 58
Period size: 10 Copynumber: 4.4 Consensus size: 10
1273800 ATGCTTGAAG
1273810 AAAAAAGTAAA
1 AAAAAAG-AAA
1273821 AAAAAA-AAGA
1 AAAAAAGAA-A
1273831 GAAAAAAGAAA
1 -AAAAAAGAAA
1273842 AAAAAAGAAA
1 AAAAAAGAAA
1273852 AAAA
1 AAAA
1273856 GAAAAAAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.06
10 15 0.47
11 13 0.41
12 2 0.06
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:1273863 original size:7 final size:7
Alignment explanation
Indices: 1273807--1273863 Score: 59
Period size: 6 Copynumber: 8.4 Consensus size: 7
1273797 ATTATGCTTG
1273807 AAGAAAA
1 AAGAAAA
1273814 AAGTAAAA
1 AAG-AAAA
1273822 AA-AAAA
1 AAGAAAA
1273828 AGAGAAAA
1 A-AGAAAA
1273836 AAG-AAA
1 AAGAAAA
1273842 AA-AAAA
1 AAGAAAA
*
1273848 GA-AAAA
1 AAGAAAA
1273854 AAGAAAA
1 AAGAAAA
1273861 AAG
1 AAG
1273864 GGGGTCAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
6 19 0.44
7 13 0.30
8 11 0.26
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (7 bp):
AAGAAAA
Found at i:1274208 original size:16 final size:19
Alignment explanation
Indices: 1274189--1274232 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
1274179 CTATTTCAAG
1274189 TTCAATTTA-TTT-G-AGA
1 TTCAATTTATTTTCGAAGA
1274205 TTCAATTTATTTTCGAAGA
1 TTCAATTTATTTTCGAAGA
1274224 TTCAATTTA
1 TTCAATTTA
1274233 CTCTTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.36
17 3 0.12
18 1 0.04
19 12 0.48
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (19 bp):
TTCAATTTATTTTCGAAGA
Found at i:1275135 original size:83 final size:81
Alignment explanation
Indices: 1275012--1275174 Score: 299
Period size: 83 Copynumber: 2.0 Consensus size: 81
1275002 GTACTCATAG
1275012 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAACCAATCATTGAATTTAGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTG-ACAGAACCAATCATTGAATTTAGA
*
1275077 AGATGAATTTTCCAATAT
65 AGAT-AATTTGCCAATAT
1275095 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGACAGAACCAATCATTGAATTTAGAA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGACAGAACCAATCATTGAATTTAGAA
1275160 GATAATTTGCCAATA
66 GATAATTTGCCAATA
1275175 GCAT
Statistics
Matches: 79, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
81 11 0.14
82 28 0.35
83 40 0.51
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (81 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGACAGAACCAATCATTGAATTTAGAA
GATAATTTGCCAATAT
Done.