Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009036.1 Hibiscus syriacus cultivar Beakdansim tig00112443_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: 1934717
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1064324 original size:34 final size:33
Alignment explanation
Indices: 1064244--1064332 Score: 92
Period size: 34 Copynumber: 2.6 Consensus size: 33
1064234 AATAAATGTT
*
1064244 AAAAGAGAAAATAAAAATAAAACCAAATTAAAAA
1 AAAAGAGAAAAT-AAAATAAAACCAAAATAAAAA
**
1064278 AAGTGAGAAAATAAAGATAAAA-CAAAATAAGATAA
1 AAAAGAGAAAATAAA-ATAAAACCAAAATAA-A-AA
*
1064313 AAAAGAG-AAATATAATAAAA
1 AAAAGAGAAAATAAAATAAAA
1064333 TAATAAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
33 16 0.35
34 23 0.50
35 7 0.15
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.13
Consensus pattern (33 bp):
AAAAGAGAAAATAAAATAAAACCAAAATAAAAA
Found at i:1064419 original size:18 final size:18
Alignment explanation
Indices: 1064384--1064422 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1064374 GTTATTTTTA
* *
1064384 AAATAAAATATAAGAATT
1 AAATAAAAGAAAAGAATT
*
1064402 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
1064420 AAA
1 AAA
1064423 GAAATAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:1064440 original size:13 final size:13
Alignment explanation
Indices: 1064384--1064440 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
1064374 GTTATTTTTA
*
1064384 AAATAAAATATAAG
1 AAATAATATA-AAG
*
1064398 AATTAA-ATAAAAG
1 AAATAATAT-AAAG
1064411 AAAATAAT-TAAAG
1 -AAATAATATAAAG
1064424 AAATAATATAAAG
1 AAATAATATAAAG
1064437 AAAT
1 AAAT
1064441 TGAGATAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
12 7 0.19
13 18 0.49
14 12 0.32
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (13 bp):
AAATAATATAAAG
Found at i:1065813 original size:200 final size:199
Alignment explanation
Indices: 1065388--1065970 Score: 717
Period size: 200 Copynumber: 2.9 Consensus size: 199
1065378 GGAATGTGGC
* * * * * * *
1065388 TTCTTGTTGCCAAATCGTAGTCAACCTTGATCTTCTTCTT-AGTTTAAAGACCTCGGTTTGAAAA
1 TTCTTGTTGCTAAATCGCAGCCAACCTAGGTCTTCTTCTTGA-CTTAAAGACCTC-GTTT-AAAC
* * * * ** *
1065452 TTCAGCCGGAAAGTAGTTCCTTGATGCTACCATATGGTTGATATGCTCTCGAGCTGAATGAAATC
63 TTCAACCGAAAAGTAGTTCCTCGTTGCTACCATGCGGTTGATATG-TCTCGAGCTGAATGGAATC
* *** * * ** *
1065517 GAACTTGAAGGCTTTTATTGACATATAGGTCATCTCGCCTTGAGTTATATTGTAAATTTGGCTGG
127 GAACTTGAAAGCTTTTATTGACATATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTCGGCTGG
1065582 GAGATAGT
192 GAGATAGT
* * *
1065590 TTCTTGTTGCTAAATCACAGCCAACATAGGTCTTCTTCTTGACTTAAAGATCTCAGTTTAAACTT
1 TTCTTGTTGCTAAATCGCAGCCAACCTAGGTCTTCTTCTTGACTTAAAGACCTC-GTTTAAACTT
*
1065655 CAACCGAAAAGTAGTTCATCGTTGCTACCATGCGGTTGATATGTCATCGAGCTGAATGGAATCGA
65 CAACCGAAAAGTAGTTCCTCGTTGCTACCATGCGGTTGATATGTC-TCGAGCTGAATGGAATCGA
* * *
1065720 ACTCGAAAG-TTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTCGGCTGGGA
129 ACTTGAAAGCTTTTATTGACATATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTCGGCTGGGA
1065784 GATAG-
194 GATAGT
1065789 TTCATTGTTGCTAAATCGCAGCCAACCTAGG-CATTCTTCTTGACTTAAAGACCTCGATTTAAAC
1 TTC-TTGTTGCTAAATCGCAGCCAACCTAGGTC-TTCTTCTTGACTTAAAGACCTCG-TTTAAAC
* *
1065853 TTTAACCGGAAAA-TAGTTCCTCGTTGCTACCATGCGGTTGATATGCCTTCGAGCTGAATGGAAT
63 TTCAACC-GAAAAGTAGTTCCTCGTTGCTACCATGCGGTTGATATGTC-TCGAGCTGAATGGAAT
* * *
1065917 CGAACTTGAAAGTTTTTTTTGACATATAACCCTTATCGCCTTGAGCTATGCTGT
126 CGAACTTGAAAGCTTTTATTGACATATAACCCTTCTCGCCTTGAGCTATGCTGT
1065971 GAACAGTTCC
Statistics
Matches: 332, Mismatches: 42, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
199 5 0.02
200 170 0.51
201 109 0.33
202 47 0.14
203 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (199 bp):
TTCTTGTTGCTAAATCGCAGCCAACCTAGGTCTTCTTCTTGACTTAAAGACCTCGTTTAAACTTC
AACCGAAAAGTAGTTCCTCGTTGCTACCATGCGGTTGATATGTCTCGAGCTGAATGGAATCGAAC
TTGAAAGCTTTTATTGACATATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTCGGCTGGGAGA
TAGT
Found at i:1066141 original size:86 final size:85
Alignment explanation
Indices: 1066028--1066227 Score: 283
Period size: 86 Copynumber: 2.3 Consensus size: 85
1066018 CGGTCATAAT
* * *
1066028 TCTTTAGATGACTCCCCTTCACAGGAAAGCCAAGTGGTATATTCTTTAGGTGGTTCCCCTTCGCA
1 TCTTTGGATGACTCCCCTTCACGGGAAAGCCAAGTGATATATTCTTTAGGTGGTTCCCCTTCGCA
*
1066093 GGTATGAACCAGGTGAGATGA
66 GGTAT-AAACAGGTGAGATGA
* * * *
1066114 TCTTTGGATGACACCCCTTCACGGGAAAGTCATGTGATATATTCTTTAGGTGGTTCCCCTTCGCG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGCCAAGTGATATATTCTTTAGGTGGTTCCCCTTCGCA
* *
1066179 GGTCTAAACAGGTGAGATTA
66 GGTATAAACAGGTGAGATGA
* *
1066199 TCTTTGGATGACTCCCTTTCACGAGAAAG
1 TCTTTGGATGACTCCCCTTCACGGGAAAG
1066228 TCATGTGAGA
Statistics
Matches: 101, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
85 39 0.39
86 62 0.61
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.30
Consensus pattern (85 bp):
TCTTTGGATGACTCCCCTTCACGGGAAAGCCAAGTGATATATTCTTTAGGTGGTTCCCCTTCGCA
GGTATAAACAGGTGAGATGA
Found at i:1066173 original size:42 final size:42
Alignment explanation
Indices: 1066026--1066180 Score: 109
Period size: 42 Copynumber: 3.6 Consensus size: 42
1066016 GCCGGTCATA
* * *
1066026 ATTCTTTAGATGACTCCCCTTCACAGGAAAGCCAAGTGGTAT
1 ATTCTTTAGGTGACTCCCCTTCACGGGAAAGCCAAGTGATAT
** * * * *
1066068 ATTCTTTAGGTGGTTCCCCTTCGCAGGTATGAA-CCAGGTGAGAT
1 ATTCTTTAGGTGACTCCCCTTCAC-GGGA--AAGCCAAGTGATAT
* * *
1066112 GA-TCTTT-GGATGACACCCCTTCACGGGAAAGTCATGTGATAT
1 -ATTCTTTAGG-TGACTCCCCTTCACGGGAAAGCCAAGTGATAT
** *
1066154 ATTCTTTAGGTGGTTCCCCTTCGCGGG
1 ATTCTTTAGGTGACTCCCCTTCACGGG
1066181 TCTAAACAGG
Statistics
Matches: 84, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
41 3 0.04
42 46 0.55
43 9 0.11
44 23 0.27
45 3 0.04
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.31
Consensus pattern (42 bp):
ATTCTTTAGGTGACTCCCCTTCACGGGAAAGCCAAGTGATAT
Found at i:1066227 original size:85 final size:85
Alignment explanation
Indices: 1065998--1066244 Score: 300
Period size: 85 Copynumber: 2.9 Consensus size: 85
1065988 GAAGAATGGC
* * * * * * * *
1065998 TCCCCTTCGCGGGTCTAAGCCGGTCATAAT-TCTTTAGATGACTCCCCTTCAC-AGGAAAGCCAA
1 TCCCCTTCGCGGGTCTAAACAGGTGAGATTATCTTTGGATGACTCCCCTTCACGA-GAAAGTCAT
*
1066061 GTGGTATATTCTTTAGGTGGT
65 GTGATATATTCTTTAGGTGGT
* * * * * *
1066082 TCCCCTTCGCAGGTATGAACCAGGTGAGATGATCTTTGGATGACACCCCTTCACGGGAAAGTCAT
1 TCCCCTTCGCGGGTCT-AAACAGGTGAGATTATCTTTGGATGACTCCCCTTCACGAGAAAGTCAT
1066147 GTGATATATTCTTTAGGTGGT
65 GTGATATATTCTTTAGGTGGT
*
1066168 TCCCCTTCGCGGGTCTAAACAGGTGAGATTATCTTTGGATGACTCCCTTTCACGAGAAAGTCATG
1 TCCCCTTCGCGGGTCTAAACAGGTGAGATTATCTTTGGATGACTCCCCTTCACGAGAAAGTCATG
* *
1066233 TGAGATGTTCTT
66 TGATATATTCTT
1066245 CGGGGTGACT
Statistics
Matches: 137, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
84 14 0.10
85 62 0.45
86 61 0.45
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (85 bp):
TCCCCTTCGCGGGTCTAAACAGGTGAGATTATCTTTGGATGACTCCCCTTCACGAGAAAGTCATG
TGATATATTCTTTAGGTGGT
Found at i:1070384 original size:10 final size:10
Alignment explanation
Indices: 1070369--1070433 Score: 64
Period size: 10 Copynumber: 6.6 Consensus size: 10
1070359 AAATTTCAAA
1070369 AAAAAAATAT
1 AAAAAAATAT
1070379 AAAAAAATAT
1 AAAAAAATAT
1070389 AAAAAAATAT
1 AAAAAAATAT
* * *
1070399 TAAAAGAGA-
1 AAAAAAATAT
1070408 AAATAAAA-AT
1 AAA-AAAATAT
1070418 AAAATAAA-AT
1 AAAA-AAATAT
1070428 AAAAAA
1 AAAAAA
1070434 TGAGAAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
9 6 0.13
10 41 0.87
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (10 bp):
AAAAAAATAT
Found at i:1070384 original size:11 final size:11
Alignment explanation
Indices: 1070368--1070459 Score: 57
Period size: 10 Copynumber: 7.9 Consensus size: 11
1070358 TAAATTTCAA
1070368 AAAAAAAATAT
1 AAAAAAAATAT
1070379 -AAAAAAATAT
1 AAAAAAAATAT
1070389 -AAAAAAATATT
1 AAAAAAAATA-T
1070400 AAAAGAGAAA-AT
1 AAAA-A-AAATAT
1070412 AAAAATAAA-AT
1 AAAAA-AAATAT
*
1070423 AAAATAAAAAAT
1 AAAA-AAAATAT
*
1070435 GAGAAAATAAAGAT
1 -A-AAAA-AAATAT
1070449 AAAACAAAATA
1 AAAA-AAAATA
1070460 AGATAAAAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 19
0.76 0.03 0.21
Matches are distributed among these distances:
10 19 0.28
11 14 0.21
12 18 0.26
13 6 0.09
14 11 0.16
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.16
Consensus pattern (11 bp):
AAAAAAAATAT
Found at i:1070416 original size:31 final size:31
Alignment explanation
Indices: 1070381--1070460 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
1070371 AAAAATATAA
*
1070381 AAAAATATAAA-AAAATATTAAAA-GAGAAAAT
1 AAAAATA-AAACAAAATA-AAAAATGAGAAAAT
*
1070412 AAAAATAAAATAAAATAAAAAATGAGAAAAT
1 AAAAATAAAACAAAATAAAAAATGAGAAAAT
*
1070443 AAAGATAAAACAAAATAA
1 AAAAATAAAACAAAATAA
1070461 GATAAAAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 7 0.16
31 37 0.84
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.16
Consensus pattern (31 bp):
AAAAATAAAACAAAATAAAAAATGAGAAAAT
Found at i:1070421 original size:5 final size:5
Alignment explanation
Indices: 1070407--1070467 Score: 52
Period size: 5 Copynumber: 11.8 Consensus size: 5
1070397 ATTAAAAGAG
* * *
1070407 AAAAT AAAAAT AAAAT AAAAT AAAA- AATGAG AAAAT AAAGAT AAAAC
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAA-AT AAAAT
*
1070454 AAAAT AAGAT AAAA
1 AAAAT AAAAT AAAA
1070468 AAGGGAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
4 2 0.04
5 31 0.69
6 12 0.27
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:1071266 original size:12 final size:12
Alignment explanation
Indices: 1071251--1071275 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1071241 AAAATAATAT
1071251 TTTAAATACTAA
1 TTTAAATACTAA
1071263 TTTAAATACTAA
1 TTTAAATACTAA
1071275 T
1 T
1071276 ATCTATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTAAATACTAA
Found at i:1071537 original size:87 final size:87
Alignment explanation
Indices: 1071391--1071575 Score: 255
Period size: 87 Copynumber: 2.1 Consensus size: 87
1071381 GTTCACAGCG
* * * *
1071391 GGAATAGGAGATGAGGTCGTGGGTCACATTGTATTTGGCATGGAATTTTGAATGTAATTCGCTTG
1 GGAATAGGAGACGAGGTCGTGGGTCACACTGCATTTGGCATGGAATTTTGAACGTAATTCGCTTG
*
1071456 CAATTGTTCATACCGCACGGCC
66 CAACTGTTCATACCGCACGGCC
* *
1071478 GGAATAGGAGACGAGGAT-GTGGGTCCCACTGCATTTGGCATGGAATTTTGGACGTAATTCGCTT
1 GGAATAGGAGACGAGG-TCGTGGGTCACACTGCATTTGGCATGGAATTTTGAACGTAATTCGCTT
* * * *
1071542 GCAGCTGTTCATATCGCACGTCT
65 GCAACTGTTCATACCGCACGGCC
1071565 GGAATAGGAGA
1 GGAATAGGAGA
1071576 TGGGGGTTTT
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
87 85 0.99
88 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (87 bp):
GGAATAGGAGACGAGGTCGTGGGTCACACTGCATTTGGCATGGAATTTTGAACGTAATTCGCTTG
CAACTGTTCATACCGCACGGCC
Found at i:1072251 original size:13 final size:13
Alignment explanation
Indices: 1072222--1072256 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1072212 ATAACTAATA
*
1072222 ATATTAAAT-ATT
1 ATATTAAATAAAT
1072234 ATATTAAATAAAT
1 ATATTAAATAAAT
1072247 ATATTAAATA
1 ATATTAAATA
1072257 TATTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:1075261 original size:8 final size:8
Alignment explanation
Indices: 1075248--1075288 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1075238 CTCATTTTCA
1075248 GAGAATTT
1 GAGAATTT
1075256 GAGAATTT
1 GAGAATTT
*
1075264 -AGAGTTT
1 GAGAATTT
*
1075271 GGGAATTT
1 GAGAATTT
1075279 GAGAATTT
1 GAGAATTT
1075287 GA
1 GA
1075289 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1075583 original size:126 final size:126
Alignment explanation
Indices: 1075356--1075960 Score: 1183
Period size: 126 Copynumber: 4.8 Consensus size: 126
1075346 CTATAATCGG
1075356 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
1075421 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
1075482 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAAAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
1075547 TCATTGCCCTATTATGTCACTCATGTCCCTCAGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1075608 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1075673 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1075734 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1075799 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1075860 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1075925 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
1075961 ATAACTTAAA
Statistics
Matches: 474, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 474 1.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:1076406 original size:33 final size:34
Alignment explanation
Indices: 1076345--1076444 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
1076335 AAATTTAATG
*
1076345 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
1076379 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
1076412 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
1076445 ACATTTATCA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:1076991 original size:21 final size:21
Alignment explanation
Indices: 1076967--1077047 Score: 128
Period size: 21 Copynumber: 3.9 Consensus size: 21
1076957 ATAAAACCCT
*
1076967 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
*
1076988 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
1077009 GCGGGCTAGGAATGTAACCT-
1 GCGGGCTAGGAATGTAACCTG
*
1077029 GCGGGCTCGGAATGTAACC
1 GCGGGCTAGGAATGTAACC
1077048 CTGCGGAGAT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
20 18 0.31
21 40 0.69
ACGTcount: A:0.21, C:0.23, G:0.37, T:0.19
Consensus pattern (21 bp):
GCGGGCTAGGAATGTAACCTG
Found at i:1077083 original size:21 final size:21
Alignment explanation
Indices: 1077057--1077104 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1077047 CCTGCGGAGA
*
1077057 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
1077078 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
1077099 GGGCAT
1 TGGCAT
1077105 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:1078903 original size:31 final size:33
Alignment explanation
Indices: 1078826--1078903 Score: 99
Period size: 31 Copynumber: 2.4 Consensus size: 33
1078816 TTAATAATTC
*
1078826 TAAATAAATAATAATTATATAAATATTATTTTAATA
1 TAAA-AAATAAT-ATTACATAAATATTA-TTTAATA
1078862 -AAAAAATAATATTACATAAATA-TA-TTAATA
1 TAAAAAATAATATTACATAAATATTATTTAATA
1078892 TAAAAAATAATA
1 TAAAAAATAATA
1078904 ACTATTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 6 0.15
31 11 0.28
32 2 0.05
33 11 0.28
34 7 0.17
35 3 0.08
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (33 bp):
TAAAAAATAATATTACATAAATATTATTTAATA
Found at i:1089556 original size:23 final size:23
Alignment explanation
Indices: 1089525--1089568 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1089515 AAACACACAA
1089525 AAACAGGAAAGGCGTACTGATAG
1 AAACAGGAAAGGCGTACTGATAG
*
1089548 AAACCGGAAAGGCGTACTGAT
1 AAACAGGAAAGGCGTACTGAT
1089569 TGAAGACACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.16, G:0.30, T:0.14
Consensus pattern (23 bp):
AAACAGGAAAGGCGTACTGATAG
Found at i:1089618 original size:3 final size:3
Alignment explanation
Indices: 1089610--1089673 Score: 85
Period size: 3 Copynumber: 21.0 Consensus size: 3
1089600 ATATTTATAT
*
1089610 TTA TTA TTA TTT TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
*
1089656 -AA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
1089674 ATTACAAGCC
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
2 1 0.02
3 47 0.87
4 6 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1089640 original size:34 final size:36
Alignment explanation
Indices: 1089594--1089673 Score: 98
Period size: 34 Copynumber: 2.3 Consensus size: 36
1089584 TTTACATTTG
*
1089594 ATTT-TTA-TATTTA-TATTTATTATTATT-TTTATT
1 ATTTATTATTATTTATTA-TTATTATTATTAATTATT
1089627 A-TTATTATTATTTATTATTATTATTATTAAATTATT
1 ATTTATTATTATTTATTATTATTATTATT-AATTATT
1089663 ATTTATTATTA
1 ATTTATTATTA
1089674 ATTACAAGCC
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
32 2 0.05
33 4 0.10
34 17 0.43
35 2 0.05
36 6 0.15
37 9 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (36 bp):
ATTTATTATTATTTATTATTATTATTATTAATTATT
Found at i:1089677 original size:28 final size:28
Alignment explanation
Indices: 1089598--1089673 Score: 111
Period size: 27 Copynumber: 2.8 Consensus size: 28
1089588 CATTTGATTT
* *
1089598 TTATATTTA-TATTTATTATTATTTTTA
1 TTATAATTATTATTTATTATTATTATTA
*
1089625 TTATTATTATTATTTATTATTATTATTA
1 TTATAATTATTATTTATTATTATTATTA
1089653 TTA-AATTATTATTTATTATTA
1 TTATAATTATTATTTATTATTA
1089674 ATTACAAGCC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 24 0.55
28 20 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (28 bp):
TTATAATTATTATTTATTATTATTATTA
Found at i:1091284 original size:27 final size:27
Alignment explanation
Indices: 1091253--1091307 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
1091243 ATATTTCTAA
1091253 ATAAATAAATATTTTATTT-ATAAATAT
1 ATAAATAAATATTTT-TTTCATAAATAT
* *
1091280 ATAAATTAATATTTTTTTCATAATTAT
1 ATAAATAAATATTTTTTTCATAAATAT
1091307 A
1 A
1091308 ATTTTGAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (27 bp):
ATAAATAAATATTTTTTTCATAAATAT
Found at i:1091289 original size:120 final size:119
Alignment explanation
Indices: 1091060--1091282 Score: 299
Period size: 120 Copynumber: 1.9 Consensus size: 119
1091050 TTTTAATATA
* *
1091060 TATTTATTTATTTTTCAATATTAAGAAAGGGCAGTCTTAAAACAACTAGATGTCCATTTTCTGAT
1 TATTTATTTATTTTTCAATATGAAGAAAGGGCAGTCTTAAAACAACTAGAAGTCCATTTTCTGAT
* *
1091125 ATTTTTAAATAAATAAATATCCTATTTTTTAAATCATATATTAATTGTTTTAAT
66 ATTTCTAAATAAATAAATATCCTATTTTATAAATCATATATTAATTGTTTTAAT
* * * ** *
1091179 TATTTATTTATTTTTTAATATCGAAGAAAATGGCTGTCTTAAGGCACCTAGAAGT-CATTTTCTG
1 TATTTATTTATTTTTCAATAT-GAAG-AAAGGGCAGTCTTAAAACAACTAGAAGTCCATTTTCTG
**
1091243 ATATTTCTAAATAAATAAATATTTTA-TTTATAAAT-ATATA
64 ATATTTCTAAATAAATAAATATCCTATTTTATAAATCATATA
1091283 AATTAATATT
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
118 5 0.06
119 28 0.31
120 35 0.39
121 22 0.24
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (119 bp):
TATTTATTTATTTTTCAATATGAAGAAAGGGCAGTCTTAAAACAACTAGAAGTCCATTTTCTGAT
ATTTCTAAATAAATAAATATCCTATTTTATAAATCATATATTAATTGTTTTAAT
Found at i:1093404 original size:14 final size:14
Alignment explanation
Indices: 1093385--1093414 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1093375 TTTTAAATAA
1093385 TTTACATTTACATT
1 TTTACATTTACATT
*
1093399 TTTACATTTGCATT
1 TTTACATTTACATT
1093413 TT
1 TT
1093415 GCATCCTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.60
Consensus pattern (14 bp):
TTTACATTTACATT
Found at i:1093440 original size:14 final size:14
Alignment explanation
Indices: 1093395--1093442 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1093385 TTTACATTTA
1093395 CATTTTTACA-TTTG
1 CATTTTT-CATTTTG
* *
1093409 CATTTTGCATCCTTG
1 CATTTTTCAT-TTTG
1093424 CATTTTTCATTTTG
1 CATTTTTCATTTTG
1093438 CATTT
1 CATTT
1093443 ATACTTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 2 0.07
14 14 0.50
15 12 0.43
ACGTcount: A:0.17, C:0.19, G:0.08, T:0.56
Consensus pattern (14 bp):
CATTTTTCATTTTG
Found at i:1093510 original size:6 final size:6
Alignment explanation
Indices: 1093501--1093569 Score: 59
Period size: 6 Copynumber: 11.7 Consensus size: 6
1093491 ACATTCACAT
* * * * *
1093501 ATTTAC ATTTGC ATTTAC ATTTGC ATTTAC ATTTGC ATTT-T TTTTAC
1 ATTTAC ATTTAC ATTTAC ATTTAC ATTTAC ATTTAC ATTTAC ATTTAC
** *
1093548 ATTTGT ATTTAC ATTTTC ATTT
1 ATTTAC ATTTAC ATTTAC ATTT
1093570 TTACATAATT
Statistics
Matches: 48, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
5 3 0.06
6 45 0.94
ACGTcount: A:0.23, C:0.13, G:0.06, T:0.58
Consensus pattern (6 bp):
ATTTAC
Found at i:1093549 original size:29 final size:29
Alignment explanation
Indices: 1093514--1093571 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1093504 TACATTTGCA
1093514 TTTACATTTGCATTTACATTTGCATTTTT
1 TTTACATTTGCATTTACATTTGCATTTTT
* *
1093543 TTTACATTTGTATTTACATTTTCATTTTT
1 TTTACATTTGCATTTACATTTGCATTTTT
1093572 ACATAATTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.62
Consensus pattern (29 bp):
TTTACATTTGCATTTACATTTGCATTTTT
Found at i:1093569 original size:12 final size:12
Alignment explanation
Indices: 1093501--1093540 Score: 80
Period size: 12 Copynumber: 3.3 Consensus size: 12
1093491 ACATTCACAT
1093501 ATTTACATTTGC
1 ATTTACATTTGC
1093513 ATTTACATTTGC
1 ATTTACATTTGC
1093525 ATTTACATTTGC
1 ATTTACATTTGC
1093537 ATTT
1 ATTT
1093541 TTTTTACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.53
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:1095872 original size:68 final size:68
Alignment explanation
Indices: 1095763--1095915 Score: 306
Period size: 68 Copynumber: 2.2 Consensus size: 68
1095753 GGTAAAGGAT
1095763 ATTGGGGGACAAGGTAATCAAGAATAATTTTTCTTCTAATTCAACCTTAACCAAGGATCACCCTC
1 ATTGGGGGACAAGGTAATCAAGAATAATTTTTCTTCTAATTCAACCTTAACCAAGGATCACCCTC
1095828 TAC
66 TAC
1095831 ATTGGGGGACAAGGTAATCAAGAATAATTTTTCTTCTAATTCAACCTTAACCAAGGATCACCCTC
1 ATTGGGGGACAAGGTAATCAAGAATAATTTTTCTTCTAATTCAACCTTAACCAAGGATCACCCTC
1095896 TAC
66 TAC
1095899 ATTGGGGGACAAGGTAA
1 ATTGGGGGACAAGGTAA
1095916 AGGATATTGA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 85 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (68 bp):
ATTGGGGGACAAGGTAATCAAGAATAATTTTTCTTCTAATTCAACCTTAACCAAGGATCACCCTC
TAC
Found at i:1095989 original size:90 final size:90
Alignment explanation
Indices: 1095831--1096014 Score: 350
Period size: 90 Copynumber: 2.0 Consensus size: 90
1095821 CACCCTCTAC
*
1095831 ATTGGGGGACAAGGTAATCAAGAATAATTTTTCTTCTAATTCAACCTTAACCAAGGATCACCCTC
1 ATTGAGGGACAAGGTAATCAAGAATAATTTTTCTTCTAATTCAACCTTAACCAAGGATCACCCTC
1095896 TACATTGGGGGACAAGGTAAAGGAT
66 TACATTGGGGGACAAGGTAAAGGAT
*
1095921 ATTGAGGGACAAGGTAATCAAGAATAATTTTTCTTCTAATTCAACCTTAACTAAGGATCACCCTC
1 ATTGAGGGACAAGGTAATCAAGAATAATTTTTCTTCTAATTCAACCTTAACCAAGGATCACCCTC
1095986 TACATTGGGGGACAAGGTAAAGGAT
66 TACATTGGGGGACAAGGTAAAGGAT
1096011 ATTG
1 ATTG
1096015 GCTCACAAGA
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 92 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.28
Consensus pattern (90 bp):
ATTGAGGGACAAGGTAATCAAGAATAATTTTTCTTCTAATTCAACCTTAACCAAGGATCACCCTC
TACATTGGGGGACAAGGTAAAGGAT
Found at i:1098701 original size:114 final size:114
Alignment explanation
Indices: 1098500--1098833 Score: 553
Period size: 114 Copynumber: 2.9 Consensus size: 114
1098490 CATGTTCTCG
* * *
1098500 TAGTAGAAATAAGGAGCCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTT
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
* *
1098565 GGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAA-TTTGCTCA
66 GGTATGAACCCCAAAACTAATCATTGGATTTGAAAGATGAATTTTG-TCA
1098614 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
* *
1098679 AGTATGAACCCCAAAACTAATCATTGGATTTAAAAGATGAATTTTGTCA
66 GGTATGAACCCCAAAACTAATCATTGGATTTGAAAGATGAATTTTGTCA
* *
1098728 TAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
* *
1098793 GGTAGGAACCCCAAAACTAATCATTGGAATTGAAAGATGAA
66 GGTATGAACCCCAAAACTAATCATTGGATTTGAAAGATGAA
1098834 CTGCATGATC
Statistics
Matches: 206, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
114 202 0.98
115 4 0.02
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (114 bp):
TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
GGTATGAACCCCAAAACTAATCATTGGATTTGAAAGATGAATTTTGTCA
Found at i:1100050 original size:151 final size:150
Alignment explanation
Indices: 1099757--1100103 Score: 604
Period size: 151 Copynumber: 2.3 Consensus size: 150
1099747 AAGATCCATA
* *
1099757 TGGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAGGAATATTGATATATTTTGAACGTTTGTAT
1 TGGGGTATGCTGAAA-ACCCTTTCAATCAGAATCAGGAATATTGATATATTTTGAACGTTTGTAT
* *
1099822 TAGCAAATGATGGGGTATATCAAAACCCATTTCAGACAGATCCATGTGGGGCATTTTGAAGGCTC
65 TAGCAAATGATGGGGCATATCAAAACCCATTTCAGACAGATCCATGTGGGGCATTTTGAACGCTC
1099887 ATATCAACAAGAAGCAAATGT
130 ATATCAACAAGAAGCAAATGT
1099908 TGGGGTATGCTGAAAACCCTTTCAATCAGAATCAGGAATATTGATATATTTTGAACGTTTGTATT
1 TGGGGTATGCTGAAAACCCTTTCAATCAGAATCAGGAATATTGATATATTTTGAACGTTTGTATT
*
1099973 AGCAAATGATGGGGCATATCGAAAGCCCATTTCAGACAGATCCATGTGGGGCATTTTGAACGCTC
66 AGCAAATGATGGGGCATATC-AAAACCCATTTCAGACAGATCCATGTGGGGCATTTTGAACGCTC
*
1100038 ATATCAATAAGAAGCAAATGT
130 ATATCAACAAGAAGCAAATGT
*
1100059 TGGGGTATGCTGAAAACCCATTTCAATCATAATCAGGAATATTGA
1 TGGGGTATGCTGAAAACCC-TTTCAATCAGAATCAGGAATATTGA
1100104 CGCGTTTTGA
Statistics
Matches: 187, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
150 68 0.36
151 95 0.51
152 24 0.13
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (150 bp):
TGGGGTATGCTGAAAACCCTTTCAATCAGAATCAGGAATATTGATATATTTTGAACGTTTGTATT
AGCAAATGATGGGGCATATCAAAACCCATTTCAGACAGATCCATGTGGGGCATTTTGAACGCTCA
TATCAACAAGAAGCAAATGT
Found at i:1101576 original size:22 final size:22
Alignment explanation
Indices: 1101545--1101599 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1101535 ATCTACACTC
*
1101545 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
1101567 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
1101589 TTCAAAGATGA
1 TTCAAAGATGA
1101600 AAACTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:1102800 original size:113 final size:113
Alignment explanation
Indices: 1102035--1102785 Score: 1263
Period size: 113 Copynumber: 6.6 Consensus size: 113
1102025 ATTTCTGGAA
*
1102035 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGCAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1102100 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
* *
1102148 GAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1102213 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
* * *
1102261 GAGTTCATAATGAGAAGAAGTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAAAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1102326 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
* *
1102374 GAGCTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1102439 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
* *
1102487 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATTAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * *
1102552 CAACTTTTCGCTTGAATTTATCATTCGATGGAT-AGCATTGCCAGGGC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
* *
1102599 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * * * *
1102664 CAACTTTTTGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAG-A
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAG-GTC
*
1102712 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAAAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1102777 CAATCTTTT
66 CAA-CTTTT
1102786 GCATGATTCT
Statistics
Matches: 602, Mismatches: 33, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
112 102 0.17
113 494 0.82
114 6 0.01
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.27
Consensus pattern (113 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
Found at i:1103063 original size:3 final size:3
Alignment explanation
Indices: 1103055--1103122 Score: 66
Period size: 3 Copynumber: 22.0 Consensus size: 3
1103045 TTTTTTATAT
* *
1103055 TTA TTA TTA -TA TTTA TTA TTT TTA TTA TTTA TTT TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* *
1103101 ATA ATA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA
1103123 ATTACAAGCC
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
2 2 0.04
3 45 0.82
4 8 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1103083 original size:28 final size:29
Alignment explanation
Indices: 1103046--1103122 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 29
1103036 TACATTTGAT
1103046 TTTTTA-TATTTATTATTA-TATTTATT-A
1 TTTTTATTATTTATTATTATTA-TTATTAA
*
1103073 TTTTTATTATTTATTTTTATTATTATTAA
1 TTTTTATTATTTATTATTATTATTATTAA
*
1103102 TAATATTATTATTTATTATTA
1 T--TTTTATTATTTATTATTA
1103123 ATTACAAGCC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 6 0.14
28 16 0.38
29 4 0.10
31 16 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (29 bp):
TTTTTATTATTTATTATTATTATTATTAA
Found at i:1103086 original size:25 final size:24
Alignment explanation
Indices: 1103056--1103122 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
1103046 TTTTTATATT
1103056 TATTATTATATTTATTATT-TT--
1 TATTATTATATTTATTATTATTAA
*
1103077 TATTATTTATTTTTATTATTATTAA
1 TATTA-TTATATTTATTATTATTAA
*
1103102 TAATATTATTATTTATTATTA
1 TATTATTA-TATTTATTATTA
1103123 ATTACAAGCC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
21 5 0.13
22 13 0.34
23 2 0.05
24 3 0.08
25 15 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TATTATTATATTTATTATTATTAA
Found at i:1104348 original size:3 final size:3
Alignment explanation
Indices: 1104342--1104386 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
1104332 TTATTTGCAA
* *
1104342 TAT TAT T-T TAT TAT TAT TACT TTT TAT TAT TAT TCT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
1104387 ATATATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 32 0.89
4 2 0.06
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:1104368 original size:16 final size:15
Alignment explanation
Indices: 1104347--1104386 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
1104337 TGCAATATTA
1104347 TTTTATTATTATTACT
1 TTTTATTATTATT-CT
1104363 TTTTATTATTATTCT
1 TTTTATTATTATTCT
*
1104378 TATTATTAT
1 TTTTATTAT
1104387 ATATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTATTATTATTCT
Found at i:1104696 original size:27 final size:27
Alignment explanation
Indices: 1104666--1104720 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
1104656 ATATTTCTAA
1104666 ATAAATAAATATTTTATTT-ATAAATAT
1 ATAAATAAATATTTT-TTTCATAAATAT
* *
1104693 ATAAATTAATATTTTTTTCATAATTAT
1 ATAAATAAATATTTTTTTCATAAATAT
1104720 A
1 A
1104721 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (27 bp):
ATAAATAAATATTTTTTTCATAAATAT
Found at i:1104702 original size:120 final size:119
Alignment explanation
Indices: 1104473--1104695 Score: 290
Period size: 120 Copynumber: 1.9 Consensus size: 119
1104463 TTTTAATATA
* *
1104473 TATTTATTTATTTTTCAATATTAAGAAATGGCAGTCTTAAAACAACTAGATGTCCATTTTCTGAT
1 TATTTATTTATTTTTCAATATGAAGAAATGGCAGTCTTAAAACAACTAGAAGTCCATTTTCTGAT
* *
1104538 ATTTTTAAATAAATAAATATCCTATTTTTTAAATCATATATTAATTGTTTTAAT
66 ATTTCTAAATAAATAAATATCCTATTTTATAAATCATATATTAATTGTTTTAAT
* ** ** * *
1104592 TATTTATTTATTTTTTAATATCGAAGAAAATGGTTGTCTTAAGGCACCTAGAAGTTC-TTTTCTG
1 TATTTATTTATTTTTCAATAT-GAAG-AAATGGCAGTCTTAAAACAACTAGAAGTCCATTTTCTG
**
1104656 ATATTTCTAAATAAATAAATATTTTA-TTTATAAAT-ATATA
64 ATATTTCTAAATAAATAAATATCCTATTTTATAAATCATATA
1104696 AATTAATATT
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
118 5 0.06
119 28 0.31
120 33 0.37
121 23 0.26
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.47
Consensus pattern (119 bp):
TATTTATTTATTTTTCAATATGAAGAAATGGCAGTCTTAAAACAACTAGAAGTCCATTTTCTGAT
ATTTCTAAATAAATAAATATCCTATTTTATAAATCATATATTAATTGTTTTAAT
Found at i:1106479 original size:24 final size:23
Alignment explanation
Indices: 1106452--1106532 Score: 63
Period size: 24 Copynumber: 3.4 Consensus size: 23
1106442 ACGGAGATAT
1106452 CAGAAATCAAAACAGAATTCAACA
1 CAGAAATCAAAACAGAATTCAA-A
* * * * *
1106476 CAGATATCATAATAGAATCCAGAT
1 CAGAAATCAAAACAGAATTCA-AA
* *
1106500 CAGAAATCAGAACATAATTCAAA
1 CAGAAATCAAAACAGAATTCAAA
*
1106523 TCGGAAATCA
1 -CAGAAATCA
1106533 GATAAAATAT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
23 1 0.02
24 41 0.95
25 1 0.02
ACGTcount: A:0.52, C:0.19, G:0.11, T:0.19
Consensus pattern (23 bp):
CAGAAATCAAAACAGAATTCAAA
Found at i:1111099 original size:12 final size:12
Alignment explanation
Indices: 1111056--1111133 Score: 52
Period size: 12 Copynumber: 6.5 Consensus size: 12
1111046 TATATATCAT
*
1111056 AAATCAAAACAG
1 AAATCAGAACAG
* * *
1111068 AATTCAGCACAT
1 AAATCAGAACAG
*
1111080 ATATCAGAACAG
1 AAATCAGAACAG
*
1111092 -AATCCAGATCAG
1 AAAT-CAGAACAG
*
1111104 AAATCAGAACAT
1 AAATCAGAACAG
*
1111116 AATTCA-AATCAG
1 AAATCAGAA-CAG
1111128 AAATCA
1 AAATCA
1111134 AATAAAACAT
Statistics
Matches: 48, Mismatches: 15, Indels: 6
0.70 0.22 0.09
Matches are distributed among these distances:
11 4 0.08
12 41 0.85
13 3 0.06
ACGTcount: A:0.53, C:0.19, G:0.10, T:0.18
Consensus pattern (12 bp):
AAATCAGAACAG
Found at i:1111109 original size:24 final size:24
Alignment explanation
Indices: 1111051--1111133 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
1111041 AAACATATAT
* *
1111051 ATCATAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
1111075 CA-CATATATCAGAACAGAATCCAG
1 -ATCAGAAATCAGAACAGAATTCAG
* *
1111099 ATCAGAAATCAGAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAG
1111123 ATCAGAAATCA
1 ATCAGAAATCA
1111134 AATAAAACAT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
23 1 0.02
24 47 0.96
25 1 0.02
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:1111983 original size:12 final size:13
Alignment explanation
Indices: 1111957--1112032 Score: 65
Period size: 12 Copynumber: 6.3 Consensus size: 13
1111947 ACAGAGATAT
*
1111957 CAGAA-ATCAAAA
1 CAGAATATCATAA
*
1111969 CAGAAT-TCATCA
1 CAGAATATCATAA
1111981 CAG-ATATCATAA
1 CAGAATATCATAA
* * *
1111993 CAGAAT-CCAGAT
1 CAGAATATCATAA
1112005 CAGAA-ATCATAA
1 CAGAATATCATAA
1112017 CAGAA-ATCATAA
1 CAGAATATCATAA
1112029 CAGA
1 CAGA
1112033 TTTCAAATCG
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
11 2 0.04
12 47 0.92
13 2 0.04
ACGTcount: A:0.53, C:0.20, G:0.11, T:0.17
Consensus pattern (13 bp):
CAGAATATCATAA
Found at i:1111989 original size:24 final size:24
Alignment explanation
Indices: 1111957--1112032 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 24
1111947 ACAGAGATAT
*
1111957 CAGAAATCAAAACAGAATTCATCA
1 CAGAAATCAAAACAGAATTCATAA
* * * * *
1111981 CAGATATCATAACAGAATCCAGAT
1 CAGAAATCAAAACAGAATTCATAA
* *
1112005 CAGAAATCATAACAGAAATCATAA
1 CAGAAATCAAAACAGAATTCATAA
1112029 CAGA
1 CAGA
1112033 TTTCAAATCG
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.53, C:0.20, G:0.11, T:0.17
Consensus pattern (24 bp):
CAGAAATCAAAACAGAATTCATAA
Found at i:1112049 original size:36 final size:36
Alignment explanation
Indices: 1111964--1112045 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
1111954 TATCAGAAAT
* * * *
1111964 CAAAACAGAATTCATCACAGATATCATAACAGAATC
1 CAAATCAGAAATCATAACAGAAATCATAACAGAATC
* * *
1112000 CAGATCAGAAATCATAACAGAAATCATAACAGATTT
1 CAAATCAGAAATCATAACAGAAATCATAACAGAATC
1112036 CAAATC-GAAA
1 CAAATCAGAAA
1112046 ATCAGATAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
35 4 0.11
36 34 0.89
ACGTcount: A:0.51, C:0.20, G:0.10, T:0.20
Consensus pattern (36 bp):
CAAATCAGAAATCATAACAGAAATCATAACAGAATC
Found at i:1112363 original size:905 final size:897
Alignment explanation
Indices: 1110388--1112096 Score: 2359
Period size: 905 Copynumber: 1.9 Consensus size: 897
1110378 CGACCCATTA
** * * * * *
1110388 TAAAAATAACAGAAAATT-TAAATTTTTTATCATAACATGTAAACTCATAAAATCATTTATTAGT
1 TAAAAATAGTAGAAAATTCAAAACTTTTTATCAT-ACAGGTAAACTCATAAAATCATTTATCAAT
* ** * * * * *
1110452 ATTCAGAAATAAAGTATAT-TTTAGAATCGTATATATAAAACAAAATACAATTATATTCC-CCTA
65 ATTAAGAAATAAAACAGATATTCAAAATCG-ATATAT--AACAAAATACAATTACATGCCACCT-
* * * * * *
1110515 ATCACATCTACCATACTCTGCAAACAACACCGGAAGAACTCCCGTACTGAAGTTGATAGCTACAC
126 ATCAGATATACCAAACTCTGGAAACAATACAGGAAGAACTCCCGTACTGAAGTTGATAGCTACAC
1110580 TGGTACAATTCTTTTAACCTGCAATGGTGAGTAATAAAGTGAGCTTCGGAAAGCTCAGTAATACA
191 TGGTACAATTCTTTTAACCTGCAATGGTGAGTAATAAAGTGAGCTTCGGAAAGCTCAGTAATACA
* * * *
1110645 GAACTACCAGATGATGCTGAAGAACGTGCAGATATAAATAAGCATATATTTCCTTATCGGATCAG
256 GAACTACCAGATGATGCTGAAGAACATGCAAATACAAATAAACATATATTTCCTTATCGGATCAG
* *
1110710 ACATCTACAAATCCTTATGTTGAGCAGAGATCTTACTGATATTTCAGGTAGTAACAAATAGTGAG
321 ACATCTACAAATCCTTATATTGAGCAGAGATCCTACTGATATTTCAGGTAGTAACAAATAGTGAG
* *
1110775 CTTTCAACTCAGATGGAAATAATTCGAATGTCTAGGTTCAGGAGATCAGAATAGGTTATCTAGTG
386 CTTTCAACTCAAATGGAAATAATTCGAATGTCTAGGTTCAAGAGATCAGAATAGGTTATCTAGTG
1110840 TGTTCTCATAAAACCAATAAAAAGAAACAAATCTTTTTAAAACATATTTTTACCCCCATCCTTTC
451 TGTTCTCATAAAACCAATAAAAAGAAACAAATCTTTTTAAAACATATTTTTACCCCCATCCTTTC
*
1110905 ACAATCTGTTTGTGTAGGTTCCCCAGAACCATACACCCAACCCACGCAACCTGTAAGGCCCTGAG
516 ACAATCTGTTTGTGTAGGTTCCCCAGAACCATACACCCAACCCACACAACCTGTAAGGCCCTGAG
** *
1110970 CACAAAGCCGAGAAACCTACAGAAATACATCCTTCAACAATACCCCCCAATTAAAACATTTTTTC
581 CACAAAGCAAAGAAACCTACAGAAATACATCCTTCAACAATACCCCCCAATTAAAACATTTTTCC
* * * *
1111035 TTCAGTAAACATATATATCATAAATCAAAACAGAATTCAGCACATATATCAGAACAGAATCCAGA
646 TTCAGTAAACAGAGATATCAGAAATCAAAACAGAATTCAGCACAGATATCAGAACAGAATCCAGA
*
1111100 TCAGAAATCAGAACATAATTCAAATCAGAAATCAAATAAAACATTCATGTAATTAGGGAACACAC
711 TCAGAAATCAGAACATAATTCAAATCAGAAATCAAATAAAACATTCATGTAATTAGAGAACACAC
* * * *
1111165 TAGTGTTTACAGATATAATAGCATTAGCTAATGAATTTCTGATAAAGATGTAACCCCCTCAGACC
776 TAGTGTTTACAGATATAATAGCATTAGATAAT-AATTTCTGAGAAAGATGTAA-CACATCAGACC
** * * * * * *** *
1111230 GATGCGGGTAACCTGATCTGATCTGGGTTGTCACATTAGGACCACCGGAGCGACCCACTG
839 GATAAGGGTAACATGATATGATCAGAGTTGTAACATTAGGA-CAAAAGAGCGACCAACTG
* * * *
1111290 TAAAAATAGTGGAAAATTTAAAACTTTTTATCATAACATGTAAACTCATAAAATCATTTATCAGT
1 TAAAAATAGTAGAAAATTCAAAACTTTTTATCAT-ACAGGTAAACTCATAAAATCATTTATCAAT
* * * *
1111355 ATTAAGAAATAAAACAGATTTTCAGACTCGTATATATAAAACAAAATACAATTACATGCCCCCTA
65 ATTAAGAAATAAAACAGATATTCAAAATCG-ATATAT--AACAAAATACAATTACATGCCACCT-
* * * * * * *
1111420 ATCATATGTACCATACTCTGGAAACAATACCGGAAGAACTCCCTTACTGAAGTTGATAGTTGCAC
126 ATCAGATATACCAAACTCTGGAAACAATACAGGAAGAACTCCCGTACTGAAGTTGATAGCTACAC
*
1111485 TGGTACAATTCTTTTAACCTGCAATGGTGAGTAATAAATTGAGCTTCGGAAAGCTCAGTAATACA
191 TGGTACAATTCTTTTAACCTGCAATGGTGAGTAATAAAGTGAGCTTCGGAAAGCTCAGTAATACA
* *
1111550 GTACTACCAGATGATGCTGAAGAACATGCAAATACAGATAAACATATATTTCCTTATCGGATCAG
256 GAACTACCAGATGATGCTGAAGAACATGCAAATACAAATAAACATATATTTCCTTATCGGATCAG
*
1111615 ACATCTACAAATCCTTATATTGAGCAGAGATCCTACTGATATTTCAGGTAGTAACATATAGTGAG
321 ACATCTACAAATCCTTATATTGAGCAGAGATCCTACTGATATTTCAGGTAGTAACAAATAGTGAG
** * *
1111680 CTTTCAGTTCAAATGGAAATATTTCGGATGTCTAGGTTCAAGAGATCAGAATAGGTTATCTAGTG
386 CTTTCAACTCAAATGGAAATAATTCGAATGTCTAGGTTCAAGAGATCAGAATAGGTTATCTAGTG
* *
1111745 TGTTTTCATAAAACCAGTAAAAAGAAACAAATCTTTTTAAAACATATTTTTACCCCCATCCTTTC
451 TGTTCTCATAAAACCAATAAAAAGAAACAAATCTTTTTAAAACATATTTTTACCCCCATCCTTTC
*
1111810 ACAATCTGTTTGTGTAGGTTTCCCAGAACCATACACCCAACCCACACAACCTGTAAGGCCCTGAG
516 ACAATCTGTTTGTGTAGGTTCCCCAGAACCATACACCCAACCCACACAACCTGTAAGGCCCTGAG
* * * *
1111875 CACAAAGCAAAGGAACCTGCAGAAATACTTCCTTCAATAATA-CCCCCAATTAAAACATTTTTCC
581 CACAAAGCAAAGAAACCTACAGAAATACATCCTTCAACAATACCCCCCAATTAAAACATTTTTCC
* *
1111939 GTT-AGTAAACAGAGATATCAGAAATCAAAACAGAATTCATCACAGATATCATAACAGAATCCAG
646 -TTCAGTAAACAGAGATATCAGAAATCAAAACAGAATTCAGCACAGATATCAGAACAGAATCCAG
*
1112003 ATCAGAAATCATAACAGAAATCATAACAGATTTCAAATC-GAAAATCAGATAAAACATTCATGTA
710 ATCAG-AA--AT--CAG-AA-CAT---A-A-TTCAAATCAG-AAATCAAATAAAACATTCATGTA
1112067 ATTAGAGAACACACTAGTGTTTACAGATAT
762 ATTAGAGAACACACTAGTGTTTACAGATAT
1112097 TATTCAGAGT
Statistics
Matches: 734, Mismatches: 56, Indels: 20
0.91 0.07 0.02
Matches are distributed among these distances:
902 15 0.02
903 58 0.08
904 117 0.16
905 472 0.64
907 2 0.00
909 3 0.00
910 2 0.00
911 3 0.00
914 1 0.00
915 2 0.00
916 59 0.08
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.28
Consensus pattern (897 bp):
TAAAAATAGTAGAAAATTCAAAACTTTTTATCATACAGGTAAACTCATAAAATCATTTATCAATA
TTAAGAAATAAAACAGATATTCAAAATCGATATATAACAAAATACAATTACATGCCACCTATCAG
ATATACCAAACTCTGGAAACAATACAGGAAGAACTCCCGTACTGAAGTTGATAGCTACACTGGTA
CAATTCTTTTAACCTGCAATGGTGAGTAATAAAGTGAGCTTCGGAAAGCTCAGTAATACAGAACT
ACCAGATGATGCTGAAGAACATGCAAATACAAATAAACATATATTTCCTTATCGGATCAGACATC
TACAAATCCTTATATTGAGCAGAGATCCTACTGATATTTCAGGTAGTAACAAATAGTGAGCTTTC
AACTCAAATGGAAATAATTCGAATGTCTAGGTTCAAGAGATCAGAATAGGTTATCTAGTGTGTTC
TCATAAAACCAATAAAAAGAAACAAATCTTTTTAAAACATATTTTTACCCCCATCCTTTCACAAT
CTGTTTGTGTAGGTTCCCCAGAACCATACACCCAACCCACACAACCTGTAAGGCCCTGAGCACAA
AGCAAAGAAACCTACAGAAATACATCCTTCAACAATACCCCCCAATTAAAACATTTTTCCTTCAG
TAAACAGAGATATCAGAAATCAAAACAGAATTCAGCACAGATATCAGAACAGAATCCAGATCAGA
AATCAGAACATAATTCAAATCAGAAATCAAATAAAACATTCATGTAATTAGAGAACACACTAGTG
TTTACAGATATAATAGCATTAGATAATAATTTCTGAGAAAGATGTAACACATCAGACCGATAAGG
GTAACATGATATGATCAGAGTTGTAACATTAGGACAAAAGAGCGACCAACTG
Found at i:1117712 original size:22 final size:22
Alignment explanation
Indices: 1117670--1117712 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1117660 ACTCGAATTA
*
1117670 TTATTAATAATTAAGTTAAAAT
1 TTATTAATAATTAAGTAAAAAT
*
1117692 TTATT-ATAATGTTAGTAAAAA
1 TTATTAATAAT-TAAGTAAAAA
1117713 GTTGTACAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (22 bp):
TTATTAATAATTAAGTAAAAAT
Found at i:1118361 original size:59 final size:59
Alignment explanation
Indices: 1118247--1118425 Score: 152
Period size: 59 Copynumber: 3.0 Consensus size: 59
1118237 ATCATATATC
* * * *
1118247 CCTAAAGCTATAATC-TTCATTTTAAATTAATCTTTAAACTTTTAATATTTCAGTTTTA-T
1 CCTAAA-CTATAA-CATTCATTTTAAATTAGTCCTTAAACTTTTAACATTTCAGTTTCATT
* *
1118306 CCTTAAACTATGA-TTATCATTTTAAATTAGTCCTT-AACTTTTGAACATATT-AGTTTCATT
1 CC-TAAACTATAACAT-TCATTTTAAATTAGTCCTTAAACTTTT-AACAT-TTCAGTTTCATT
* ** * *
1118366 CCTAAACTATAACATTCATTCTAAATTAGTCCCCAAACTTTTTGAACATTCCAATTTCAT
1 CCTAAACTATAACATTCATTTTAAATTAGTCCTTAAAC-TTTT-AACATTTCAGTTTCAT
1118426 CCCAACTATA
Statistics
Matches: 98, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
58 8 0.08
59 59 0.60
60 14 0.14
61 17 0.17
ACGTcount: A:0.34, C:0.18, G:0.04, T:0.44
Consensus pattern (59 bp):
CCTAAACTATAACATTCATTTTAAATTAGTCCTTAAACTTTTAACATTTCAGTTTCATT
Found at i:1123983 original size:21 final size:21
Alignment explanation
Indices: 1123954--1123993 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1123944 ATTTTACACT
1123954 GAGTATACCGATACACCTAGA
1 GAGTATACCGATACACCTAGA
*
1123975 GAGTGTACCGATACACCTA
1 GAGTATACCGATACACCTA
1123994 TGCTCCCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (21 bp):
GAGTATACCGATACACCTAGA
Found at i:1125800 original size:29 final size:31
Alignment explanation
Indices: 1125768--1125827 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1125758 AAATTTTGAA
*
1125768 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1125797 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1125828 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1127121 original size:19 final size:20
Alignment explanation
Indices: 1127078--1127125 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1127068 TCTAAATCCT
*
1127078 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1127098 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1127117 TTTTCAAAA
1 TTTTCAAAA
1127126 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1128364 original size:21 final size:21
Alignment explanation
Indices: 1128338--1128379 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1128328 CCAGAATGGG
* *
1128338 GGGAATTGGTATCCCTTCATA
1 GGGAATCGATATCCCTTCATA
1128359 GGGAATCGATATCCCTTCATA
1 GGGAATCGATATCCCTTCATA
1128380 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (21 bp):
GGGAATCGATATCCCTTCATA
Found at i:1128563 original size:29 final size:31
Alignment explanation
Indices: 1128531--1128590 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1128521 AAATTTTGAA
*
1128531 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1128560 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1128591 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1132710 original size:2 final size:2
Alignment explanation
Indices: 1132703--1132746 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1132693 ATATTTCATT
1132703 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1132744 TA T
1 TA T
1132747 CAAAGATCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1133217 original size:22 final size:22
Alignment explanation
Indices: 1133191--1133249 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
1133181 TTTCCTTTAT
1133191 GGGGAATCGGTTCCCTCCTGTG
1 GGGGAATCGGTTCCCTCCTGTG
1133213 GGGGAATCGGTTCCCTCCTGTG
1 GGGGAATCGGTTCCCTCCTGTG
* *
1133235 GGGGTATCAGTTCCC
1 GGGGAATCGGTTCCC
1133250 CCATGACATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.10, C:0.27, G:0.36, T:0.27
Consensus pattern (22 bp):
GGGGAATCGGTTCCCTCCTGTG
Found at i:1137521 original size:2 final size:2
Alignment explanation
Indices: 1137514--1137550 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1137504 ATATTTCATT
1137514 TA TA TA 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 TA TA TA T
1137551 CAAAGATCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1141852 original size:13 final size:14
Alignment explanation
Indices: 1141822--1141854 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1141812 ATTATGATTC
*
1141822 TTCAAACATTGTTT
1 TTCAAACATAGTTT
1141836 TTCAAACATAG-TT
1 TTCAAACATAGTTT
1141849 TTCAAA
1 TTCAAA
1141855 TTTGCCATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.42
Consensus pattern (14 bp):
TTCAAACATAGTTT
Found at i:1143635 original size:13 final size:13
Alignment explanation
Indices: 1143613--1143646 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1143603 GAGGAGAGTA
*
1143613 ATTTTCAAAATTG
1 ATTTTCAAAAATG
1143626 A-TTTCAAAAATG
1 ATTTTCAAAAATG
1143638 ATTTTCAAA
1 ATTTTCAAA
1143647 TAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:1144022 original size:20 final size:20
Alignment explanation
Indices: 1143994--1144045 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1143984 ATGCATTTTG
*
1143994 TGTATCGATACACTGGATGA
1 TGTACCGATACACTGGATGA
*
1144014 TGTACCGATGCACTGGATGA
1 TGTACCGATACACTGGATGA
1144034 TGTACCGATACA
1 TGTACCGATACA
1144046 ATCTTGGCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (20 bp):
TGTACCGATACACTGGATGA
Found at i:1147128 original size:21 final size:21
Alignment explanation
Indices: 1147104--1147147 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1147094 CGGTAAAAAA
* * *
1147104 TTATTTAAAATATTATTATTT
1 TTATCTAAAATATCAATATTT
1147125 TTATCTAAAATATCAATATTT
1 TTATCTAAAATATCAATATTT
1147146 TT
1 TT
1147148 TAATATTTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATCTAAAATATCAATATTT
Found at i:1152564 original size:15 final size:15
Alignment explanation
Indices: 1152544--1152573 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1152534 GCTGGGAGGA
*
1152544 CGGATGCGGGTCGGG
1 CGGATGCGGGGCGGG
1152559 CGGATGCGGGGCGGG
1 CGGATGCGGGGCGGG
1152574 TAATATCTCA
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:0.07, C:0.20, G:0.63, T:0.10
Consensus pattern (15 bp):
CGGATGCGGGGCGGG
Found at i:1155485 original size:16 final size:18
Alignment explanation
Indices: 1155464--1155508 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
1155454 AACATTCTCA
1155464 GTAATCTTATT-CC-CTG
1 GTAATCTTATTCCCACTG
1155480 GTAATCTTACATTCCCACTG
1 GTAATCTT--ATTCCCACTG
1155500 GTAATCTTA
1 GTAATCTTA
1155509 CATTCCGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 4 0.16
19 2 0.08
20 11 0.44
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.40
Consensus pattern (18 bp):
GTAATCTTATTCCCACTG
Found at i:1155502 original size:20 final size:20
Alignment explanation
Indices: 1155477--1155514 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1155467 ATCTTATTCC
1155477 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
1155497 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1155515 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1167031 original size:23 final size:23
Alignment explanation
Indices: 1166963--1167031 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
1166953 CATATATATA
* *
1166963 TGGCACTACGGTGCATTTCTACA
1 TGGCACTTCGGTGCATTTCTACG
* * * *
1166986 CGACACTTCGGTGCAATCCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
1167009 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
1167032 AGCTATGGTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:1175076 original size:36 final size:34
Alignment explanation
Indices: 1175033--1175165 Score: 151
Period size: 34 Copynumber: 3.7 Consensus size: 34
1175023 ACGTTTCGAG
1175033 AATATATATTATATAGTTTTGAAAGCATTTTGAAA
1 AATATATATTATATAGTTTTGAAA-CATTTTGAAA
*
1175068 ACATATATATAATATATAGTTTTTTAAAACATTTTGAAA
1 A-ATATATAT--TATATAG--TTTTGAAACATTTTGAAA
* **
1175107 ATATATATAATATATAGTTTTCGAAATTTTTTG-AA
1 A-ATATATATTATATAGTTTT-GAAACATTTTGAAA
1175142 AATATATATTATATAGTTTTGAAA
1 AATATATATTATATAGTTTTGAAA
1175166 ACATATATTA
Statistics
Matches: 85, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
33 4 0.05
34 18 0.21
35 8 0.09
36 16 0.19
37 7 0.08
38 7 0.08
39 18 0.21
40 7 0.08
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (34 bp):
AATATATATTATATAGTTTTGAAACATTTTGAAA
Found at i:1175094 original size:73 final size:72
Alignment explanation
Indices: 1175003--1175169 Score: 200
Period size: 73 Copynumber: 2.3 Consensus size: 72
1174993 TTTTGAAAAA
* * *
1175003 ATAATATATAGCTTTTTAAAACGTTTCGAGAATATATAT-TATATAGTTTT-GAAAGCATTTTGA
1 ATAATATATAGTTTTTTAAAACATTTCGAAAATATATATATATATAGTTTTCGAAA-CATTTTG-
1175066 AAACATATAT
64 AAA-ATATAT
* **
1175076 ATAATATATAGTTTTTTAAAACATTTTGAAAATATATATAATATATAGTTTTCGAAATTTTTTGA
1 ATAATATATAGTTTTTTAAAACATTTCGAAAATATATAT-ATATATAGTTTTCGAAACATTTTGA
1175141 AAATATAT
65 AAATATAT
*
1175149 AT--TATATAG-TTTTGAAAACAT
1 ATAATATATAGTTTTTTAAAACAT
1175170 ATATTATATA
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
70 11 0.13
71 7 0.08
73 43 0.51
74 3 0.04
75 16 0.19
76 4 0.05
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.44
Consensus pattern (72 bp):
ATAATATATAGTTTTTTAAAACATTTCGAAAATATATATATATATAGTTTTCGAAACATTTTGAA
AATATAT
Found at i:1175147 original size:34 final size:33
Alignment explanation
Indices: 1174993--1175223 Score: 146
Period size: 34 Copynumber: 6.9 Consensus size: 33
1174983 TTGAAAATAT
* *
1174993 TTTTGAAAA-A-ATAATATATAGCTTTTTAAAACG
1 TTTTGAAAATATATAATATATAG--TTTTGAAACA
* * *
1175026 TTTCGAGAATATATATTATATAGTTTTGAAAGCA
1 TTTTGAAAATATATAATATATAGTTTTGAAA-CA
*
1175060 TTTTGAAAACATATATATAATATATAGTTTTTTAAAACA
1 TTTTG--AA-A-ATATATAATATATAG--TTTTGAAACA
**
1175099 TTTTGAAAATATATATAATATATAGTTTTCGAAATT
1 TTTTG-AAA-ATATATAATATATAGTTTT-GAAACA
*
1175135 TTTTGAAAATATATATTATATAGTTTTGAAAACA
1 TTTTGAAAATATATAATATATAGTTTTG-AAACA
1175169 ---T----ATAT-T-ATATA-A-TTTTGAAAACA
1 TTTTGAAAATATATAATATATAGTTTTG-AAACA
*
1175192 TTTTTGAAAATATATATTATATAGTTTTGAAA
1 -TTTTGAAAATATATAATATATAGTTTTGAAA
1175224 ACATATATTA
Statistics
Matches: 158, Mismatches: 17, Indels: 45
0.72 0.08 0.20
Matches are distributed among these distances:
23 11 0.07
24 1 0.01
25 4 0.03
26 1 0.01
27 5 0.03
31 5 0.03
32 1 0.01
33 19 0.12
34 31 0.20
35 22 0.14
36 9 0.06
37 18 0.11
38 17 0.11
39 7 0.04
40 7 0.04
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (33 bp):
TTTTGAAAATATATAATATATAGTTTTGAAACA
Found at i:1175165 original size:23 final size:23
Alignment explanation
Indices: 1175135--1175192 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
1175125 TTTCGAAATT
* *
1175135 TTTTGAAAATATATATTATATAG
1 TTTTGAAAACATATATTATATAA
1175158 TTTTGAAAACATATATTATATAA
1 TTTTGAAAACATATATTATATAA
1175181 TTTTGAAAACAT
1 TTTTGAAAACAT
1175193 TTTTGAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (23 bp):
TTTTGAAAACATATATTATATAA
Found at i:1175172 original size:59 final size:56
Alignment explanation
Indices: 1175099--1175285 Score: 248
Period size: 59 Copynumber: 3.2 Consensus size: 56
1175089 TTTTAAAACA
* * *
1175099 TTTTGAAAATATATATAATATATAGTTTTCGAAATTTTTTGAAAATATATATTATATAG
1 TTTTGAAAACATATAT--TATATAATTTT-GAAAATTTTTGAAAATATATATTATATAG
1175158 TTTTGAAAACATATATTATATAATTTTGAAAACATTTTTGAAAATATATATTATATAG
1 TTTTGAAAACATATATTATATAATTTTG-AAA-ATTTTTGAAAATATATATTATATAG
* * *
1175216 TTTTGAAAACATATATTATATACTTTTAAAAACAATTTTTGAAAATATATATTATATGG
1 TTTTGAAAACATATATTATATAATTTT--GAA-AATTTTTGAAAATATATATTATATAG
1175275 TTTTGAAAACA
1 TTTTGAAAACA
1175286 ATTTTTGAGA
Statistics
Matches: 117, Mismatches: 6, Indels: 10
0.88 0.05 0.08
Matches are distributed among these distances:
56 1 0.01
57 13 0.11
58 50 0.43
59 52 0.44
60 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (56 bp):
TTTTGAAAACATATATTATATAATTTTGAAAATTTTTGAAAATATATATTATATAG
Found at i:1175197 original size:35 final size:35
Alignment explanation
Indices: 1175158--1175227 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
1175148 TATTATATAG
1175158 TTTTGAAAACATATATTATATAATTTTGAAAACAT
1 TTTTGAAAACATATATTATATAATTTTGAAAACAT
* *
1175193 TTTTGAAAATATATATTATATAGTTTTGAAAACAT
1 TTTTGAAAACATATATTATATAATTTTGAAAACAT
1175228 ATATTATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (35 bp):
TTTTGAAAACATATATTATATAATTTTGAAAACAT
Found at i:1175217 original size:58 final size:58
Alignment explanation
Indices: 1175099--1175285 Score: 270
Period size: 58 Copynumber: 3.2 Consensus size: 58
1175089 TTTTAAAACA
* * *
1175099 TTTTGAAAATATATATAATATATAGTTTTCG-AAA-TTTTTTGAAAATATATATTATATAG
1 TTTTGAAAACATATAT--TATATAATTTT-GAAAACATTTTTGAAAATATATATTATATAG
1175158 TTTTGAAAACATATATTATATAATTTTGAAAACATTTTTGAAAATATATATTATATAG
1 TTTTGAAAACATATATTATATAATTTTGAAAACATTTTTGAAAATATATATTATATAG
* * *
1175216 TTTTGAAAACATATATTATATACTTTTAAAAACAATTTTTGAAAATATATATTATATGG
1 TTTTGAAAACATATATTATATAATTTTGAAAAC-ATTTTTGAAAATATATATTATATAG
1175275 TTTTGAAAACA
1 TTTTGAAAACA
1175286 ATTTTTGAGA
Statistics
Matches: 119, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
56 1 0.01
57 13 0.11
58 55 0.46
59 50 0.42
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (58 bp):
TTTTGAAAACATATATTATATAATTTTGAAAACATTTTTGAAAATATATATTATATAG
Found at i:1175220 original size:23 final size:23
Alignment explanation
Indices: 1175193--1175249 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
1175183 TTGAAAACAT
* *
1175193 TTTTGAAAATATATATTATATAG
1 TTTTGAAAACATATATTATATAC
1175216 TTTTGAAAACATATATTATATAC
1 TTTTGAAAACATATATTATATAC
*
1175239 TTTTAAAAACA
1 TTTTGAAAACA
1175250 ATTTTTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (23 bp):
TTTTGAAAACATATATTATATAC
Found at i:1175266 original size:36 final size:36
Alignment explanation
Indices: 1175216--1175318 Score: 134
Period size: 36 Copynumber: 2.9 Consensus size: 36
1175206 TATTATATAG
*
1175216 TTTTGAAAACATATATTATATACTTTTAAAAACAAT
1 TTTTGAAAACATATATTATATAATTTTAAAAACAAT
* ** *
1175252 TTTTGAAAATATATATTATATGGTTTTGAAAACAAT
1 TTTTGAAAACATATATTATATAATTTTAAAAACAAT
* * *
1175288 TTTTGAGAGCATATATAATATAATTTTAAAA
1 TTTTGAAAACATATATTATATAATTTTAAAA
1175319 TGATTTTTAT
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.43
Consensus pattern (36 bp):
TTTTGAAAACATATATTATATAATTTTAAAAACAAT
Found at i:1175339 original size:11 final size:12
Alignment explanation
Indices: 1175325--1175374 Score: 54
Period size: 11 Copynumber: 4.4 Consensus size: 12
1175315 AAAATGATTT
1175325 TTATTT-TTATA
1 TTATTTATTATA
1175336 TTA--TATTATTA
1 TTATTTATTA-TA
1175347 TTATTTATT-TA
1 TTATTTATTATA
*
1175358 TTATTTATTATT
1 TTATTTATTATA
1175370 TTATT
1 TTATT
1175375 AATATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
9 1 0.03
10 3 0.09
11 19 0.58
12 6 0.18
13 4 0.12
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTATTTATTATA
Found at i:1175361 original size:7 final size:7
Alignment explanation
Indices: 1175324--1175375 Score: 52
Period size: 8 Copynumber: 7.0 Consensus size: 7
1175314 TAAAATGATT
*
1175324 TTTATTT
1 TTTATTA
1175331 TTATATTA
1 TT-TATTA
1175339 TATTATTA
1 T-TTATTA
1175347 -TTATTTA
1 TTTA-TTA
1175354 TTTATTA
1 TTTATTA
1175361 TTTATTA
1 TTTATTA
1175368 TTTTATTA
1 -TTTATTA
1175376 ATATTTTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
6 3 0.08
7 15 0.38
8 20 0.51
9 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTATTA
Found at i:1175380 original size:18 final size:18
Alignment explanation
Indices: 1175344--1175381 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1175334 TATTATATTA
*
1175344 TTATTATTTATTTATTAT
1 TTATTATTTATTTAATAT
1175362 TTATTATTT-TATTAATAT
1 TTATTATTTAT-TTAATAT
1175380 TT
1 TT
1175382 TTTCTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTATTTATTTAATAT
Found at i:1175380 original size:29 final size:30
Alignment explanation
Indices: 1175324--1175381 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
1175314 TAAAATGATT
* *
1175324 TTTATTTTTATATTATATTATTATTATTTA
1 TTTATTATTATATTATATTATTAATATTTA
*
1175354 TTTATTATT-TATTATTTTATTAATATTT
1 TTTATTATTATATTATATTATTAATATTT
1175382 TTTCTTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (30 bp):
TTTATTATTATATTATATTATTAATATTTA
Found at i:1177538 original size:15 final size:17
Alignment explanation
Indices: 1177518--1177550 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1177508 GATTAATTAC
1177518 AAAT-AAAATTAT-TTT
1 AAATAAAAATTATATTT
1177533 AAATAAAAATTATATTT
1 AAATAAAAATTATATTT
1177550 A
1 A
1177551 TGAGGATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATAAAAATTATATTT
Found at i:1178328 original size:25 final size:25
Alignment explanation
Indices: 1178294--1178343 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1178284 GTAGTATTAC
1178294 CGGTATTTGAATTAAATTTTAAGAT
1 CGGTATTTGAATTAAATTTTAAGAT
1178319 CGGTATTTGAATTAAATTTTAAGAT
1 CGGTATTTGAATTAAATTTTAAGAT
1178344 TCTTTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44
Consensus pattern (25 bp):
CGGTATTTGAATTAAATTTTAAGAT
Found at i:1182647 original size:32 final size:32
Alignment explanation
Indices: 1182611--1182711 Score: 103
Period size: 32 Copynumber: 3.2 Consensus size: 32
1182601 ACTCAAACCG
1182611 AAAATCAACCGATCTGATATTAACCCGACCCA
1 AAAATCAACCGATCTGATATTAACCCGACCCA
* * * *** *
1182643 AAAATCAATCGATATGATATTGATATGAACCA
1 AAAATCAACCGATCTGATATTAACCCGACCCA
* * * *
1182675 AAAAACAACCGATCTGATAATCACCCTACCCA
1 AAAATCAACCGATCTGATATTAACCCGACCCA
1182707 AAAAT
1 AAAAT
1182712 TGACCGGACC
Statistics
Matches: 51, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.46, C:0.25, G:0.09, T:0.21
Consensus pattern (32 bp):
AAAATCAACCGATCTGATATTAACCCGACCCA
Found at i:1183694 original size:83 final size:83
Alignment explanation
Indices: 1183598--1183837 Score: 355
Period size: 80 Copynumber: 2.9 Consensus size: 83
1183588 GGAAATATAT
1183598 GTTTAATA-TTTAAATTTAAAAGATATTATTATCTATTTAAATTTAGATATTAAAAGAGTTTTGG
1 GTTTAATATTTTAAATTTAAAAGATATTATTAT-TATTTAAATTTAGATATTAAAAGAGTTTTGG
*
1183662 TTTAAGTAAAACTT-TCAG
65 TTGAAGTAAAACTTCTCAG
* *
1183680 GTTTAATATTTTAAATTTAAAAGATATTA-TA-TGTTTAAATTTATATATTAAAAGAGTTTTGGT
1 GTTTAATATTTTAAATTTAAAAGATATTATTATTATTTAAATTTAGATATTAAAAGAGTTTTGGT
*
1183743 TGAAGTAAAA-TTCTTAG
66 TGAAGTAAAACTTCTCAG
* * *
1183760 GTTTAATATTTTAAATTTAAAAGATATTATTATTTATCTAAATTTTGATATTAAAAGAGTTTTAG
1 GTTTAATATTTTAAATTTAAAAGATATTATTA-TTATTTAAATTTAGATATTAAAAGAGTTTTGG
*
1183825 TTGGAGTAAAACT
65 TTGAAGTAAAACT
1183838 CTGTCTAAAT
Statistics
Matches: 142, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
79 2 0.01
80 71 0.50
81 2 0.01
82 10 0.07
83 56 0.39
84 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.46
Consensus pattern (83 bp):
GTTTAATATTTTAAATTTAAAAGATATTATTATTATTTAAATTTAGATATTAAAAGAGTTTTGGT
TGAAGTAAAACTTCTCAG
Found at i:1185875 original size:22 final size:22
Alignment explanation
Indices: 1185850--1185896 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1185840 TATATTATTT
1185850 AAATTATTTACATTTATGTGTA
1 AAATTATTTACATTTATGTGTA
**
1185872 AAATTATTTATGTTTATGTGTA
1 AAATTATTTACATTTATGTGTA
1185894 AAA
1 AAA
1185897 ATTTTATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (22 bp):
AAATTATTTACATTTATGTGTA
Found at i:1189273 original size:13 final size:13
Alignment explanation
Indices: 1189255--1189283 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1189245 AAGTCCAACA
1189255 AAATTAACAAAAT
1 AAATTAACAAAAT
1189268 AAATTAACAAAAT
1 AAATTAACAAAAT
1189281 AAA
1 AAA
1189284 GTAAGTATTA
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:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATTAACAAAAT
Found at i:1189484 original size:3 final size:3
Alignment explanation
Indices: 1189478--1189524 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
1189468 ATCATCACCA
*
1189478 TCG TCG TCG TCG TCA TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
1189525 AGGAGCAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.02, C:0.34, G:0.30, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:1191592 original size:29 final size:29
Alignment explanation
Indices: 1191558--1191629 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
1191548 AAAAAAATTA
* *
1191558 ATTAAATAAAATATTA-AAAATCTTAAAT
1 ATTAAATAAAATATAACAAAATATTAAAT
1191586 AGTTAAATAAAATACTAACAAAATATTAAAT
1 A-TTAAATAAAATA-TAACAAAATATTAAAT
1191617 A-T-AATAAAATATA
1 ATTAAATAAAATATA
1191630 CCTTAACGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 2 0.05
28 10 0.26
29 13 0.33
30 2 0.05
31 12 0.31
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (29 bp):
ATTAAATAAAATATAACAAAATATTAAAT
Found at i:1191627 original size:17 final size:18
Alignment explanation
Indices: 1191595--1191628 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1191585 TAGTTAAATA
1191595 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
1191613 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
1191629 ACCTTAACGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:1193996 original size:28 final size:28
Alignment explanation
Indices: 1193965--1194018 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1193955 CATGCTTAAA
* *
1193965 TGTAAGAAATCGTATTTTATAAAAAAAT
1 TGTAAGAAATCATATTTAATAAAAAAAT
* *
1193993 TGTATGATATCATATTTAATAAAAAA
1 TGTAAGAAATCATATTTAATAAAAAA
1194019 TGATAAAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (28 bp):
TGTAAGAAATCATATTTAATAAAAAAAT
Found at i:1196781 original size:21 final size:20
Alignment explanation
Indices: 1196746--1196786 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1196736 GATTAAGATA
1196746 CTTTCGTATCTTTCTTTCTTT
1 CTTTCGTATCTTTC-TTCTTT
1196767 CTTTCGTAT-TCTTCTTCTTT
1 CTTTCGTATCT-TTCTTCTTT
1196787 TTCTTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.05, C:0.24, G:0.05, T:0.66
Consensus pattern (20 bp):
CTTTCGTATCTTTCTTCTTT
Found at i:1197333 original size:2 final size:2
Alignment explanation
Indices: 1197326--1197376 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1197316 GTTCATGGCC
1197326 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
1197368 AT AT AT AT A
1 AT AT AT AT A
1197377 CAATATTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1197752 original size:29 final size:29
Alignment explanation
Indices: 1197701--1197789 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 29
1197691 ATTATAATAT
** *
1197701 TATTAAATATTTTACAAAAATATAGTTATTA
1 TATTAAATATTTT--AAAAATATAAATATCA
** *
1197732 TATTAAATATTTTAATTATATAAATATCC
1 TATTAAATATTTTAAAAATATAAATATCA
*
1197761 TATTAAATATTTTATCAAAACATAAATAT
1 TATTAAATATTTTA--AAAATATAAATAT
1197790 AAACGCAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 24 0.51
31 23 0.49
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (29 bp):
TATTAAATATTTTAAAAATATAAATATCA
Found at i:1197789 original size:31 final size:29
Alignment explanation
Indices: 1197701--1197789 Score: 81
Period size: 31 Copynumber: 2.9 Consensus size: 29
1197691 ATTATAATAT
* *
1197701 TATTAAATATTTTACAAAAATATAGTTATTA
1 TATTAAATATTTTACAAAAATA-A-ATATCA
* * *
1197732 TATTAAATATTTTA-ATTATATAAATATCC
1 TATTAAATATTTTACA-AAAATAAATATCA
1197761 TATTAAATATTTTATCAAAACATAAATAT
1 TATTAAATATTTTA-CAAAA-ATAAATAT
1197790 AAACGCAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
29 17 0.36
30 3 0.06
31 27 0.57
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (29 bp):
TATTAAATATTTTACAAAAATAAATATCA
Found at i:1199496 original size:31 final size:31
Alignment explanation
Indices: 1199461--1199566 Score: 124
Period size: 31 Copynumber: 3.4 Consensus size: 31
1199451 ATTCAATGCC
* * *
1199461 TAAGTGATCAAAACT-TATTAAAACGATAATA
1 TAAGTGACCAAAA-TGTAATAAAACAATAATA
* *
1199492 TAAGTGACCAAAATGTAATAAAATAATGATA
1 TAAGTGACCAAAATGTAATAAAACAATAATA
**
1199523 TAAGTGACCAAAATGTAATAAAACAATAACG
1 TAAGTGACCAAAATGTAATAAAACAATAATA
*
1199554 TAAGTGACAAAAA
1 TAAGTGACCAAAA
1199567 CTTATGTTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 1 0.02
31 63 0.98
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (31 bp):
TAAGTGACCAAAATGTAATAAAACAATAATA
Found at i:1207092 original size:22 final size:21
Alignment explanation
Indices: 1207050--1207089 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1207040 GAGTTTGTTT
*
1207050 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1207071 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1207090 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1208943 original size:18 final size:19
Alignment explanation
Indices: 1208907--1208943 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1208897 TGGAGCGTGG
1208907 GGGGAATCGGTACTCCCTAT
1 GGGGAATCGGTA-TCCCTAT
1208927 GGGGAATCGGT-TCCCTA
1 GGGGAATCGGTATCCCTA
1208944 AGTGTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.24
Consensus pattern (19 bp):
GGGGAATCGGTATCCCTAT
Found at i:1219166 original size:59 final size:59
Alignment explanation
Indices: 1219070--1219203 Score: 148
Period size: 59 Copynumber: 2.3 Consensus size: 59
1219060 AAATGACCAA
* * *
1219070 CAAATTCGCAACGCG-ATCTCAAATTCGTAACGCGAATTGC-AATTTCGCAACCCAGTTT
1 CAAATTCGCAACGCGAAACTCAAATTCGCAACGCGAATTGCAAATTT-GCAACCCAATTT
* * * * **
1219128 CCAATTTCGCAACGCGAAAGTCAAATTCGCAAC-TGAATTTCAAATTTGCAACTGAATTT
1 -CAAATTCGCAACGCGAAACTCAAATTCGCAACGCGAATTGCAAATTTGCAACCCAATTT
1219187 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
1219204 TTTAATTTCG
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
58 16 0.25
59 29 0.46
60 18 0.29
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (59 bp):
CAAATTCGCAACGCGAAACTCAAATTCGCAACGCGAATTGCAAATTTGCAACCCAATTT
Found at i:1219206 original size:20 final size:20
Alignment explanation
Indices: 1219070--1219217 Score: 135
Period size: 19 Copynumber: 7.6 Consensus size: 20
1219060 AAATGACCAA
*
1219070 CAAATTCGCAACGCG-ATCT
1 CAAATTCGCAACGCGAATTT
* *
1219089 CAAATTCGTAACGCGAATTG
1 CAAATTCGCAACGCGAATTT
* * *
1219109 CAATTTCGCAAC-CCAGTTT
1 CAAATTCGCAACGCGAATTT
* **
1219128 CCAATTTCGCAACGCGAAAGT
1 -CAAATTCGCAACGCGAATTT
*
1219149 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
* *
1219168 CAAATTTGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
1219187 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
1219207 -AATTTCGCAAC
1 CAAATTCGCAAC
1219218 ACAAATGTTT
Statistics
Matches: 105, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
19 61 0.58
20 41 0.39
21 3 0.03
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:1219217 original size:38 final size:39
Alignment explanation
Indices: 1219070--1219217 Score: 101
Period size: 40 Copynumber: 3.8 Consensus size: 39
1219060 AAATGACCAA
* * *
1219070 CAAATTCGCAACGCG-ATCTCAAA-TTCGTAACGCG-AATT
1 CAAATTCGCAAC-CGAAT-TTAAATTTCGCAACGCGAAAGT
* * * *
1219108 GCAATTTCGCAACCCAGTTTCCAATTTCGCAACGCGAAAGT
1 -CAAATTCGCAACCGAATTT-AAATTTCGCAACGCGAAAGT
* * **
1219149 CAAATTCGCAACTGAATTTCAAATTT-GCAAC-TGAATTT
1 CAAATTCGCAACCGAATTT-AAATTTCGCAACGCGAAAGT
1219187 CAAATTCGCAACGCGAATTT-AATTTCGCAAC
1 CAAATTCGCAAC-CGAATTTAAATTTCGCAAC
1219218 ACAAATGTTT
Statistics
Matches: 87, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
37 5 0.06
38 23 0.26
39 25 0.29
40 31 0.36
41 3 0.03
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (39 bp):
CAAATTCGCAACCGAATTTAAATTTCGCAACGCGAAAGT
Found at i:1220131 original size:24 final size:24
Alignment explanation
Indices: 1220104--1220157 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1220094 GTATTCGAAA
1220104 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1220128 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1220152 TTTGAT
1 TTTGAT
1220158 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1222422 original size:18 final size:18
Alignment explanation
Indices: 1222399--1222434 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1222389 AAACAAAAGG
*
1222399 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1222417 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1222435 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1222902 original size:25 final size:25
Alignment explanation
Indices: 1222864--1222913 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1222854 AAATCAATTA
*
1222864 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
1222889 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
1222914 GAAACATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:1223321 original size:18 final size:18
Alignment explanation
Indices: 1223300--1223336 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1223290 GTAATTGGAG
1223300 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1223318 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1223336 T
1 T
1223337 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1223343 original size:24 final size:24
Alignment explanation
Indices: 1223292--1223344 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1223282 TTTCATATGT
* * *
1223292 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
1223316 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1223340 AATTT
1 AATTT
1223345 CGACTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1223648 original size:39 final size:39
Alignment explanation
Indices: 1223605--1223691 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
1223595 TCTGATGCTC
1223605 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
* *
1223644 ATCAAAATCCAAATCTCATATGGTGCCAAGTAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1223683 ATCAAAATC
1 ATCAAAATC
1223692 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:1224122 original size:61 final size:63
Alignment explanation
Indices: 1223991--1224131 Score: 171
Period size: 61 Copynumber: 2.2 Consensus size: 63
1223981 TTTTAGAAAC
*
1223991 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAAATCTTATTTACAAATCAAATT
1224056 A
63 A
* * ** *
1224057 AACAAATCAACTTTTACAAATCAATT-AATC-AAAAAATAAATCTTATTTCCTCATC-AATTGT
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATT-A
1224118 AACAAATCAACTTT
1 AACAAATCAACTTT
1224132 CAATGTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
60 4 0.06
61 35 0.51
62 3 0.04
66 26 0.38
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.31
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATTA
Found at i:1225530 original size:21 final size:21
Alignment explanation
Indices: 1225506--1225578 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
1225496 GGCGGGACCA
*
1225506 CTTGAACGATGACAGTGGCCT
1 CTTGAACGATGACAGGGGCCT
* ** *
1225527 CTTGAACGGTGGGAGGGGCTT
1 CTTGAACGATGACAGGGGCCT
* *
1225548 CTTCG-ATGATGATAGGGGCCT
1 CTT-GAACGATGACAGGGGCCT
1225569 CTTGAACGAT
1 CTTGAACGAT
1225579 AGGAGACGCC
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
20 1 0.03
21 37 0.95
22 1 0.03
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.26
Consensus pattern (21 bp):
CTTGAACGATGACAGGGGCCT
Found at i:1225599 original size:42 final size:42
Alignment explanation
Indices: 1225506--1225605 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
1225496 GGCGGGACCA
* * * * * ** *
1225506 CTTGAACGATGACAGTGGCCTCTTGAACGGTGGGAGGGGCTT
1 CTTGAATGATGATAGGGGCCTCTTGAACGATAGGAGACGCCT
1225548 CTTCG-ATGATGATAGGGGCCTCTTGAACGATAGGAGACGCCT
1 CTT-GAATGATGATAGGGGCCTCTTGAACGATAGGAGACGCCT
1225590 CTTGAATGATGATAGG
1 CTTGAATGATGATAGG
1225606 TGCATCGGGC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
41 1 0.02
42 46 0.96
43 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (42 bp):
CTTGAATGATGATAGGGGCCTCTTGAACGATAGGAGACGCCT
Found at i:1228243 original size:18 final size:17
Alignment explanation
Indices: 1228220--1228253 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1228210 CAGTCTGTAT
1228220 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
1228238 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
1228254 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:1230693 original size:18 final size:17
Alignment explanation
Indices: 1230670--1230703 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1230660 CAGTCTGTAT
1230670 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
1230688 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
1230704 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:1232197 original size:19 final size:20
Alignment explanation
Indices: 1232175--1232215 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1232165 AATTCGCAAC
1232175 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
*
1232194 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
1232214 GC
1 GC
1232216 AAATTTGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (20 bp):
GCGATTTTCAGTTTCGCGTT
Found at i:1232505 original size:22 final size:22
Alignment explanation
Indices: 1232477--1232571 Score: 145
Period size: 22 Copynumber: 4.3 Consensus size: 22
1232467 GATGGAGATA
*
1232477 GATGGATTTCGTCGGAAATGGG
1 GATGGATTTCGTCAGAAATGGG
1232499 GATGGATTTCGTCAGAAATGGG
1 GATGGATTTCGTCAGAAATGGG
1232521 GATGGATTTCGTCAGAAATGGG
1 GATGGATTTCGTCAGAAATGGG
* * *
1232543 GACGGATTTCGTCGGAGATGGG
1 GATGGATTTCGTCAGAAATGGG
*
1232565 GACGGAT
1 GATGGAT
1232572 GTCGCCGTAG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 69 1.00
ACGTcount: A:0.24, C:0.11, G:0.40, T:0.25
Consensus pattern (22 bp):
GATGGATTTCGTCAGAAATGGG
Found at i:1232724 original size:20 final size:20
Alignment explanation
Indices: 1232699--1232742 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1232689 GCGTAAAAAC
*
1232699 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
1232719 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
1232739 ATTT
1 ATTT
1232743 TGAAAATCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:1234609 original size:32 final size:32
Alignment explanation
Indices: 1234567--1234631 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
1234557 TATTGATTAC
1234567 AAATAGTCATTAAAT-TTATAATTTCTTTTATA
1 AAATAGTCATTAAATCTTATAATTT-TTTTATA
* *
1234599 AAATATTCATTAAATCTTATTATTTTTTTATA
1 AAATAGTCATTAAATCTTATAATTTTTTTATA
1234631 A
1 A
1234632 CATTGTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 22 0.73
33 8 0.27
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (32 bp):
AAATAGTCATTAAATCTTATAATTTTTTTATA
Found at i:1239021 original size:2 final size:2
Alignment explanation
Indices: 1239014--1239040 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1239004 TTGCATCCAT
1239014 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1239041 AAAAGAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1240089 original size:13 final size:13
Alignment explanation
Indices: 1240071--1240095 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1240061 CTATTACTAA
1240071 TAGTAATAATAAT
1 TAGTAATAATAAT
1240084 TAGTAATAATAA
1 TAGTAATAATAA
1240096 GCAAGAGGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
TAGTAATAATAAT
Found at i:1246218 original size:17 final size:16
Alignment explanation
Indices: 1246196--1246251 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
1246186 CTGTTTAAGG
*
1246196 TATATTTTATTATATTT
1 TATATTTAATT-TATTT
1246213 TATATTTAATTTATTT
1 TATATTTAATTTATTT
* *
1246229 AAGTATTTAAATTATTT
1 TA-TATTTAATTTATTT
*
1246246 AATATT
1 TATATT
1246252 GTATTTAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
16 10 0.29
17 25 0.71
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TATATTTAATTTATTT
Done.