Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011505.1 Kokia drynarioides strain JFW-HI SEQ_126490, 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: 365990
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 225 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:295140 original size:7 final size:6
Alignment explanation
Indices: 295088--295136 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
295078 TTTAATTATT
* *
295088 TTTAAA TTTAAA TTCAAA -TTAAA TTTAAA CTT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
295134 TTT
1 TTT
295137 TAAAAGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 8 0.22
6 29 0.78
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:300276 original size:58 final size:59
Alignment explanation
Indices: 300207--300425 Score: 223
Period size: 58 Copynumber: 3.7 Consensus size: 59
300197 CTTCAGGAAG
* * *
300207 AAAATGATAATTTTCAAAAGGTTCGGGGTTAAAAATGGAATTTTTAGACATTCGA-GGT
1 AAAATGGTAATTTTCGAAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATTCGAGGGT
* * *
300265 AAAATGGTAATTTTTGGAAGGTTTGAGGTTAAAAATGGAATTTTTAGACATTCGAGGGT
1 AAAATGGTAATTTTCGAAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATTCGAGGGT
* * * * *
300324 AAAATGGTAATTTTGGAAA-GTTCGAGGTCAAAAAATGG-ATTTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTCGAAAGGTTCGAGGT-TAAAAATGGAATTTTTAGACA-TTCGAGGGT
* * ** *
300383 AAAAAT-ATAATTTTTAGAAA-GTTTAAGGTAAAAAATGGAATTT
1 -AAAATGGTAA-TTTTCGAAAGGTTCGAGGTTAAAAATGGAATTT
300426 GGAAAGTTTA
Statistics
Matches: 138, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
58 66 0.48
59 48 0.35
60 24 0.17
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTCGAAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATTCGAGGGT
Found at i:300293 original size:29 final size:30
Alignment explanation
Indices: 300236--300580 Score: 230
Period size: 30 Copynumber: 11.9 Consensus size: 30
300226 GGTTCGGGGT
* * *
300236 TAAAAATGG-AATTTTTAGACA-TTCGAGG
1 TAAAAATGGTAATTTTTGGAAAGTTTGAGG
*
300264 T-AAAATGGTAATTTTTGGAAGGTTTGAGG
1 TAAAAATGGTAATTTTTGGAAAGTTTGAGG
* * *
300293 TTAAAAATGG-AATTTTTAGACA-TTCGAGGG
1 -TAAAAATGGTAATTTTTGGAAAGTTTGA-GG
*
300323 T-AAAATGGTAA-TTTTGGAAAGTTCGAGG
1 TAAAAATGGTAATTTTTGGAAAGTTTGAGG
* *
300351 TCAAAAAATGG--ATTTTTGGAAAGTTCGGGGG
1 T--AAAAATGGTAATTTTTGGAAAGTT-TGAGG
* * *
300382 TAAAAAT-ATAATTTTTAGAAAGTTTAAGG
1 TAAAAATGGTAATTTTTGGAAAGTTTGAGG
*
300411 TAAAAAATGG-AA--TTTGGAAAGTTTAAGG
1 T-AAAAATGGTAATTTTTGGAAAGTTTGAGG
*
300439 GAAAAAT-GTAATTTTTGGAAAGTTTTG-GG
1 TAAAAATGGTAATTTTTGGAAAG-TTTGAGG
300468 TCAAAAATGG-AA-TTTTGGAAAGTTTGAGGG
1 T-AAAAATGGTAATTTTTGGAAAGTTTGA-GG
* * * *
300498 TAGAAAT-ATAATTTTTGGATAA-TTCGAGC
1 TAAAAATGGTAATTTTTGGA-AAGTTTGAGG
* *
300527 TCAAAATGG-AA-TTTTGGAAAATTTGAGGG
1 TAAAAATGGTAATTTTTGGAAAGTTTGA-GG
* *
300556 TAAAAAT-ATAATTTTTGGACAGTTT
1 TAAAAATGGTAATTTTTGGAAAGTTT
300581 AGGGACCTTT
Statistics
Matches: 250, Mismatches: 35, Indels: 62
0.72 0.10 0.18
Matches are distributed among these distances:
26 1 0.00
27 17 0.07
28 57 0.23
29 73 0.29
30 81 0.32
31 21 0.08
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.34
Consensus pattern (30 bp):
TAAAAATGGTAATTTTTGGAAAGTTTGAGG
Found at i:300358 original size:59 final size:59
Alignment explanation
Indices: 300237--300580 Score: 325
Period size: 58 Copynumber: 5.9 Consensus size: 59
300227 GTTCGGGGTT
* * * *
300237 AAAAATGGAATTTTTAGACA-TTCGA-GGTAAAATGGTAATTTTTGGAAGGTTTGAGGTT
1 AAAAATGGAATTTTTGGAAAGTTCGAGGGTAAAAT-GTAATTTTTGGAAAGTTTGAGGTC
* * *
300295 AAAAATGGAATTTTTAGACA-TTCGAGGGTAAAATGGTAA-TTTTGGAAAGTTCGAGGTC
1 AAAAATGGAATTTTTGGAAAGTTCGAGGGTAAAAT-GTAATTTTTGGAAAGTTTGAGGTC
* * * * *
300353 AAAAAATGG-ATTTTTGGAAAGTTCGGGGGTAAAAATATAATTTTTAGAAAGTTTAAGGTA
1 -AAAAATGGAATTTTTGGAAAGTTCGAGGGT-AAAATGTAATTTTTGGAAAGTTTGAGGTC
** *
300413 AAAAATGGAA--TTTGGAAAGTTTAAGGGAAAAATGTAATTTTTGGAAAGTTTTG-GGTC
1 AAAAATGGAATTTTTGGAAAGTTCGAGGGTAAAATGTAATTTTTGGAAAG-TTTGAGGTC
* * * *
300470 AAAAATGGAA-TTTTGGAAAGTTTGAGGGTAGAAATATAATTTTTGGATAA-TTCGAGCTC
1 AAAAATGGAATTTTTGGAAAGTTCGAGGGTA-AAATGTAATTTTTGGA-AAGTTTGAGGTC
* * * *
300529 -AAAATGGAA-TTTTGGAAAATTTGAGGGTAAAAATATAATTTTTGGACAGTTT
1 AAAAATGGAATTTTTGGAAAGTTCGAGGGT-AAAATGTAATTTTTGGAAAGTTT
300581 AGGGACCTTT
Statistics
Matches: 246, Mismatches: 27, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
57 32 0.13
58 132 0.54
59 59 0.24
60 23 0.09
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.34
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAAGTTCGAGGGTAAAATGTAATTTTTGGAAAGTTTGAGGTC
Found at i:300485 original size:58 final size:60
Alignment explanation
Indices: 300272--300580 Score: 327
Period size: 58 Copynumber: 5.3 Consensus size: 60
300262 GGTAAAATGG
* * * * * *
300272 TAATTTTTGGAAGGTTT-GAGGTTAAAAATGGAATTTTTAGACA-TTCGAGGGT-AAAATGG
1 TAATTTTTGGAAAGTTTCGAGGTCAAAAATGGAA-TTTTGGAAAGTTTGAGGGTAAAAAT-A
* * *
300331 TAA-TTTTGGAAAG-TTCGAGGTCAAAAAATGGATTTTTGGAAAGTTCGGGGGTAAAAATA
1 TAATTTTTGGAAAGTTTCGAGGTC-AAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATA
* * * * *
300390 TAATTTTTAGAAAGTTT-AAGGTAAAAAATGGAA-TTTGGAAAGTTTAAGGG-AAAAATG
1 TAATTTTTGGAAAGTTTCGAGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATA
* *
300447 TAATTTTTGGAAAGTTTTG-GGTCAAAAATGGAATTTTGGAAAGTTTGAGGGTAGAAATA
1 TAATTTTTGGAAAGTTTCGAGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATA
* *
300506 TAATTTTTGGATAA--TTCGAGCTC-AAAATGGAATTTTGGAAAATTTGAGGGTAAAAATA
1 TAATTTTTGGA-AAGTTTCGAGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATA
*
300564 TAATTTTTGGACAGTTT
1 TAATTTTTGGAAAGTTT
300581 AGGGACCTTT
Statistics
Matches: 211, Mismatches: 26, Indels: 26
0.80 0.10 0.10
Matches are distributed among these distances:
57 38 0.18
58 98 0.46
59 53 0.25
60 20 0.09
61 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (60 bp):
TAATTTTTGGAAAGTTTCGAGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATA
Found at i:300572 original size:88 final size:86
Alignment explanation
Indices: 300257--300584 Score: 276
Period size: 88 Copynumber: 3.8 Consensus size: 86
300247 TTTTTAGACA
* * * * *
300257 TTCGAGGT-AAAATGGTAATTTTTGGAAGGTTTGAGGTTAAAAATGGAATTTTTAGACA-TTCGA
1 TTCGAGGTCAAAATGG-AATTTTTGGAAAGTTTGAGGGTAAAAATAGAATTTTTAGAAAGTT-TA
*
300320 GGGTAAAATGGTAATTTTGGAAAG
64 GGGTAAAAT-ATAATTTTGGAAAG
* * *
300344 TTCGAGGTCAAAAAATGG-ATTTTTGGAAAGTTCGGGGGTAAAAATATAATTTTTAGAAAGTTTA
1 TTCGAGGTC--AAAATGGAATTTTTGGAAAGTTTGAGGGTAAAAATAGAATTTTTAGAAAGTTTA
* *
300408 AGGTAAAAAATGGAA-TTTGGAAAG
64 GGGTAAAATAT--AATTTTGGAAAG
** ** * * * *
300432 TTTAAGGGAAAAATGTAATTTTTGGAAAGTTT-TGGGTCAAAAATGGAA-TTTTGGAAAGTTTGA
1 TTCGAGGTCAAAATGGAATTTTTGGAAAGTTTGAGGGT-AAAAATAGAATTTTTAGAAAGTTT-A
300495 GGGTAGAAATATAATTTTTGGATAA-
64 GGGTA-AAATATAA-TTTTGGA-AAG
* * * * *
300520 TTCGAGCTCAAAATGGAA-TTTTGGAAAATTTGAGGGTAAAAATATAATTTTTGGACAGTTTAGG
1 TTCGAGGTCAAAATGGAATTTTTGGAAAGTTTGAGGGTAAAAATAGAATTTTTAGAAAGTTTAGG
300584 G
66 G
300585 ACCTTTTTGG
Statistics
Matches: 192, Mismatches: 34, Indels: 30
0.75 0.13 0.12
Matches are distributed among these distances:
86 24 0.12
87 60 0.31
88 95 0.49
89 6 0.03
90 7 0.04
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (86 bp):
TTCGAGGTCAAAATGGAATTTTTGGAAAGTTTGAGGGTAAAAATAGAATTTTTAGAAAGTTTAGG
GTAAAATATAATTTTGGAAAG
Found at i:300584 original size:29 final size:29
Alignment explanation
Indices: 300272--300584 Score: 166
Period size: 29 Copynumber: 10.7 Consensus size: 29
300262 GGTAAAATGG
* * *
300272 TAATTTTTGGAAGGTTTGAGGTTAAAAATG
1 TAATTTTTGGAAAGTTT-AGGGTAAAAATA
* * * * *
300302 GAATTTTTAGACA-TTCGAGGGT-AAAATGG
1 TAATTTTTGGAAAGTT-TAGGGTAAAAAT-A
*
300331 TAA-TTTTGGAAAG-TTCGAGGTCAAAAA-A
1 TAATTTTTGGAAAGTTTAG-GGT-AAAAATA
* **
300359 TGGATTTTTGGAAAGTTCGGGGGTAAAAATA
1 T-AATTTTTGGAAAGTT-TAGGGTAAAAATA
* *
300390 TAATTTTTAGAAAGTTTAAGGTAAAAA-A
1 TAATTTTTGGAAAGTTTAGGGTAAAAATA
*
300418 TGGAA--TTTGGAAAGTTTAAGGG-AAAAATG
1 T--AATTTTTGGAAAGTTT-AGGGTAAAAATA
* *
300447 TAATTTTTGGAAAGTTTTGGGTCAAAAATG
1 TAATTTTTGGAAAGTTTAGGGT-AAAAATA
* *
300477 GAA-TTTTGGAAAGTTTGAGGGTAGAAATA
1 TAATTTTTGGAAAGTTT-AGGGTAAAAATA
* * * *
300506 TAATTTTTGGATAA--TTCGAGCTCAAAATG
1 TAATTTTTGGA-AAGTTTAG-GGTAAAAATA
* *
300535 GAA-TTTTGGAAAATTTGAGGGTAAAAATA
1 TAATTTTTGGAAAGTTT-AGGGTAAAAATA
*
300564 TAATTTTTGGACAGTTTAGGG
1 TAATTTTTGGAAAGTTTAGGG
300585 ACCTTTTTGG
Statistics
Matches: 214, Mismatches: 42, Indels: 55
0.69 0.14 0.18
Matches are distributed among these distances:
27 5 0.02
28 46 0.21
29 79 0.37
30 75 0.35
31 8 0.04
32 1 0.00
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.34
Consensus pattern (29 bp):
TAATTTTTGGAAAGTTTAGGGTAAAAATA
Found at i:302438 original size:17 final size:17
Alignment explanation
Indices: 302416--302493 Score: 70
Period size: 17 Copynumber: 4.6 Consensus size: 17
302406 TAAATAAATT
*
302416 TAAATTTAAATCTATAA
1 TAAATTTAAATCTAAAA
* **
302433 TAAATTTAAATTTCCAA
1 TAAATTTAAATCTAAAA
*
302450 TAAATTGAAA-CTTAAAA
1 TAAATTTAAATC-TAAAA
* *
302467 TAAACTT-AATTTAAAA
1 TAAATTTAAATCTAAAA
302483 TAAATTTAAAT
1 TAAATTTAAAT
302494 TTTGTTGGGC
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
16 13 0.28
17 34 0.72
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATCTAAAA
Found at i:303195 original size:201 final size:206
Alignment explanation
Indices: 302829--303348 Score: 685
Period size: 201 Copynumber: 2.5 Consensus size: 206
302819 ATTTAGTCTT
* *
302829 CTTCTCAGTATCTCATCAGGAAGATGACCT-CATCACTTGTTTCAATCTGCTTCTCTGTATTTTA
1 CTTCTCAGTATCTCATCAGGAAGATGACCTGCATCACTTGTTTCAATCTGCTTCTCTGTATCTCA
* * *
302893 TCAGAAAGACGAATTTGGTCTACTTCTCAGTATCTCATTAGGAAGCTAACCGTTTTATTGCTTCG
66 TCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCGTTTTATTGCTTCG
* * * *
302958 ACCTGCTTCTCAGTACCTTATCAGGAAGCCGGGGTTCGAAGATTTGCTCGCATTGAGCCTT-G-A
131 ACCTGCTTCTCACTACCTCATCAAGAAGCCGGGGTTCAAAGATTTGCTCGCATTGAGCCTTGGCA
303021 -G-TTGGTATA
196 TGATTGGTATA
** *
303030 CTTCTCTTTATCTCATCAGGAAGATGA-CTGCCTCACTTGTTTCAATCTGCTTCTCTGTATCTCA
1 CTTCTCAGTATCTCATCAGGAAGATGACCTGCATCACTTGTTTCAATCTGCTTCTCTGTATCTCA
* *
303094 TCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCG
66 TCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCGTTTTATTGCTTCG
* * *
303159 ACTTGCTTCTCACTATCTCATCAAGAAGCTGGGGTTCAAAGATTTGCTCGCATTGAGCCTTGGCT
131 ACCTGCTTCTCACTACCTCATCAAGAAGCCGGGGTTCAAAGATTTGCTCGCATTGAGCCTTGG--
* *
303224 TCATTGATTTGGTCTT
194 -CA-TGA-TTGGTATA
* * * * ** * * *
303240 CTTCTCAGTATCTCATTAGGAAGGTGAGC-GCATCGCTTGTTTTGATCCGCCTCTTTGTATCTCA
1 CTTCTCAGTATCTCATCAGGAAGATGACCTGCATCACTTGTTTCAATCTGCTTCTCTGTATCTCA
*
303304 TCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAG
66 TCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAG
303349 ATGACCAGCT
Statistics
Matches: 276, Mismatches: 32, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
200 2 0.01
201 170 0.62
202 1 0.00
206 1 0.00
208 1 0.00
210 100 0.36
211 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (206 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCTGCATCACTTGTTTCAATCTGCTTCTCTGTATCTCA
TCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCGTTTTATTGCTTCG
ACCTGCTTCTCACTACCTCATCAAGAAGCCGGGGTTCAAAGATTTGCTCGCATTGAGCCTTGGCA
TGATTGGTATA
Found at i:313676 original size:29 final size:30
Alignment explanation
Indices: 313623--313927 Score: 210
Period size: 29 Copynumber: 10.5 Consensus size: 30
313613 CTTCAGGAAC
313623 AAAATGGTAATTTTT-GAAAGGTTCGGGGTTA
1 AAAATGG-AATTTTTGGAAA-GTTCGGGGTTA
* *
313654 AAAATGGAATTTTTAGACA-TTCGAGGG-T-
1 AAAATGGAATTTTTGGAAAGTTCG-GGGTTA
* ** *
313682 AAAATGGTAATTTTTGGAAGGTTCAAGGTCA
1 AAAATGG-AATTTTTGGAAAGTTCGGGGTTA
* * *
313713 AAAAAGGAATTTTTAGACA-TTCGAGGG-T-
1 AAAATGGAATTTTTGGAAAGTTCG-GGGTTA
* *
313741 AAAATGGTAA-TTTTGGAAAGTTCGAGGTCAA
1 AAAATGG-AATTTTTGGAAAGTTCGGGGT-TA
*
313772 AAAATGGAA-TTTTGGAAAGTTCGGGGATA
1 AAAATGGAATTTTTGGAAAGTTCGGGGTTA
* *
313801 AAAATGTAATTTTTGGAAAGTT----TTTA
1 AAAATGGAATTTTTGGAAAGTTCGGGGTTA
*** *
313827 AAAATGGAA-TTTTGGAAAGTTTAAGGAT-
1 AAAATGGAATTTTTGGAAAGTTCGGGGTTA
* * *
313855 AAAATGTAATTTTTGGAAAGTTTGGGGTCA
1 AAAATGGAATTTTTGGAAAGTTCGGGGTTA
* *
313885 AAAATGGAA-TTTTAGAAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAAGTTCGGGGTTA
**
313914 AAAATATAATTTTT
1 AAAATGGAATTTTT
313928 TGATAGCTCA
Statistics
Matches: 214, Mismatches: 40, Indels: 41
0.73 0.14 0.14
Matches are distributed among these distances:
25 12 0.06
26 10 0.05
28 30 0.14
29 73 0.34
30 66 0.31
31 23 0.11
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAAGTTCGGGGTTA
Found at i:313947 original size:59 final size:58
Alignment explanation
Indices: 313623--313996 Score: 293
Period size: 59 Copynumber: 6.4 Consensus size: 58
313613 CTTCAGGAAC
** * *
313623 AAAATGGTAATTTTT-GAAAGGTTCGGGGTTAAAAATGGAATTTTTAGACA-TTCGAGGGT
1 AAAAT-GTAATTTTTGGAAA-GTTCATGGTCAAAAATGGAA-TTTTAGAAAGTTCGAGGGT
* * * *
313682 AAAATGGTAATTTTTGGAAGGTTCAAGGTCAAAAAAGGAATTTTTAGACA-TTCGAGGGT
1 AAAAT-GTAATTTTTGGAAAGTTCATGGTCAAAAATGGAA-TTTTAGAAAGTTCGAGGGT
*
313741 AAAATGGTAA-TTTTGGAAAGTTCGA-GGTCAAAAAATGGAATTTTGGAAAGTTCG-GGGAT
1 AAAAT-GTAATTTTTGGAAAGTTC-ATGGTC-AAAAATGGAATTTTAGAAAGTTCGAGGG-T
* * ** *
313800 AAAAATGTAATTTTTGGAAAGTT--T--TTAAAAATGGAATTTTGGAAAGTTTAAGGAT
1 -AAAATGTAATTTTTGGAAAGTTCATGGTCAAAAATGGAATTTTAGAAAGTTCGAGGGT
*** *
313855 AAAATGTAATTTTTGGAAAGTTTGGGGTCAAAAATGGAATTTTAGAAAGTTCGGGGGT
1 AAAATGTAATTTTTGGAAAGTTCATGGTCAAAAATGGAATTTTAGAAAGTTCGAGGGT
* * * * * * * *
313913 AAAAATATAATTTTTTGATAGCTCATGGTCAAAAATAGAATTCTGGAAAGGTTGGA-GGT
1 -AAAATGTAATTTTTGGAAAGTTCATGGTCAAAAATGGAATTTTAGAAA-GTTCGAGGGT
* * *
313972 AAAAATATAATTTTTGTACAGTTCA
1 -AAAATGTAATTTTTGGAAAGTTCA
313997 GGGACCTTTT
Statistics
Matches: 264, Mismatches: 36, Indels: 30
0.80 0.11 0.09
Matches are distributed among these distances:
54 22 0.08
55 23 0.09
56 3 0.01
58 51 0.19
59 141 0.53
60 24 0.09
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (58 bp):
AAAATGTAATTTTTGGAAAGTTCATGGTCAAAAATGGAATTTTAGAAAGTTCGAGGGT
Found at i:314757 original size:19 final size:19
Alignment explanation
Indices: 314729--314772 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
314719 ATCCCTTTCT
314729 CTTTTCA-TTTCTTAAAAC
1 CTTTTCATTTTCTTAAAAC
* *
314747 CGTTTTGATTTTTTTAAAAC
1 C-TTTTCATTTTCTTAAAAC
314767 CTTTTC
1 CTTTTC
314773 TCCTTTCGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
18 1 0.05
19 9 0.43
20 11 0.52
ACGTcount: A:0.23, C:0.18, G:0.05, T:0.55
Consensus pattern (19 bp):
CTTTTCATTTTCTTAAAAC
Found at i:315860 original size:17 final size:17
Alignment explanation
Indices: 315838--315917 Score: 88
Period size: 17 Copynumber: 4.7 Consensus size: 17
315828 TAAATAAATT
* *
315838 TAAATTTAAATCTATAA
1 TAAATTTAAATTTAAAA
**
315855 TAAATTTAAATTTCCAA
1 TAAATTTAAATTTAAAA
*
315872 TAAAATTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* * *
315889 TAAACTTCATTTTAAAA
1 TAAATTTAAATTTAAAA
315906 TAAATTTAAATT
1 TAAATTTAAATT
315918 CTGTTGGGCC
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:316026 original size:39 final size:39
Alignment explanation
Indices: 315983--316096 Score: 111
Period size: 39 Copynumber: 2.9 Consensus size: 39
315973 ACTCAATATA
* * *
315983 GTATTACGGTGTCTATAGTGTCACCATCAGTTCAGTGTT
1 GTATTACAGTGTCTATAGTGTCACCACCAATTCAGTGTT
* **
316022 GTATTACAGTGTTTATAGTGTCACTGCCAATTCAGTGTT
1 GTATTACAGTGTCTATAGTGTCACCACCAATTCAGTGTT
* ** * * * *
316061 GTACTGTAGTGTTTACAGTGTCACTACCAGTTCAGT
1 GTATTACAGTGTCTATAGTGTCACCACCAATTCAGT
316097 AATTTGATAA
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (39 bp):
GTATTACAGTGTCTATAGTGTCACCACCAATTCAGTGTT
Found at i:319193 original size:24 final size:23
Alignment explanation
Indices: 319151--319195 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
319141 ACATAGTTAG
*
319151 AAATGAATATGATATGAATTGGT
1 AAATGAATATGAGATGAATTGGT
*
319174 AAATGATATGTGAGATGAATTG
1 AAATGA-ATATGAGATGAATTG
319196 TTGATGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.33
Consensus pattern (23 bp):
AAATGAATATGAGATGAATTGGT
Found at i:321888 original size:15 final size:15
Alignment explanation
Indices: 321870--321900 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
321860 CTATTTTAAA
321870 TTGAATATTTTTAGT
1 TTGAATATTTTTAGT
*
321885 TTGAATTTTTTTAGT
1 TTGAATATTTTTAGT
321900 T
1 T
321901 ATGTCAGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.65
Consensus pattern (15 bp):
TTGAATATTTTTAGT
Found at i:321926 original size:2 final size:2
Alignment explanation
Indices: 321919--321951 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
321909 CATGAAATGT
321919 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 T
321952 TCACCTATGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:322039 original size:24 final size:24
Alignment explanation
Indices: 322012--322271 Score: 205
Period size: 24 Copynumber: 10.8 Consensus size: 24
322002 AAACGTATAT
* *
322012 AAGCTAATGAGCGTAAATGTGTGC
1 AAGCTGATGAGCGTAAACGTGTGC
* * ****
322036 AAGCTGACGAGCGTAAACATACAT
1 AAGCTGATGAGCGTAAACGTGTGC
* *
322060 AAGCTTATGAGTGTAAACGTGTGC
1 AAGCTGATGAGCGTAAACGTGTGC
* **
322084 AAGCTGATGAGCGTAAACGTATAT
1 AAGCTGATGAGCGTAAACGTGTGC
** * *
322108 AAGCTGACAAGCATAAGCGTGTGC
1 AAGCTGATGAGCGTAAACGTGTGC
*
322132 AAGCTAATGAGCGTAAACGTGTGC
1 AAGCTGATGAGCGTAAACGTGTGC
* * * * * **
322156 AAGTTGACGAGTGTAAACATATAT
1 AAGCTGATGAGCGTAAACGTGTGC
* *
322180 ATGCTGACGAGCGTAAACGTGTGC
1 AAGCTGATGAGCGTAAACGTGTGC
* * * **
322204 AAGCTGACGAGTGTAAACGTATAT
1 AAGCTGATGAGCGTAAACGTGTGC
*
322228 AAGCTGATGAGCATAAACGTGTGC
1 AAGCTGATGAGCGTAAACGTGTGC
* *
322252 AAGTTGACGAGCGTAAACGT
1 AAGCTGATGAGCGTAAACGT
322272 ATATGAGTCG
Statistics
Matches: 174, Mismatches: 62, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 174 1.00
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (24 bp):
AAGCTGATGAGCGTAAACGTGTGC
Found at i:322260 original size:72 final size:72
Alignment explanation
Indices: 322000--322271 Score: 247
Period size: 72 Copynumber: 3.8 Consensus size: 72
321990 ATTGAATTAC
* * * * * * ****
322000 GTAAACGTATATAAGCTAATGAGCGTAAATGTGTGCAAGCTGACGAGCGTAAACATACATAAGCT
1 GTAAACGTATACAAGCTGATGAGCGTAAACGTATACAAGCTGACGAGCGTAAACGTGTGCAAGCT
*
322065 TATGAGT
66 AATGAGT
* * * * * *
322072 GTAAACGTGTGCAAGCTGATGAGCGTAAACGTATATAAGCTGACAAGCATAAGCGTGTGCAAGCT
1 GTAAACGTATACAAGCTGATGAGCGTAAACGTATACAAGCTGACGAGCGTAAACGTGTGCAAGCT
*
322137 AATGAGC
66 AATGAGT
* * * * * * * *
322144 GTAAACGTGTGCAAGTTGACGAGTGTAAACATATATATGCTGACGAGCGTAAACGTGTGCAAGCT
1 GTAAACGTATACAAGCTGATGAGCGTAAACGTATACAAGCTGACGAGCGTAAACGTGTGCAAGCT
* *
322209 GACGAGT
66 AATGAGT
* * * * *
322216 GTAAACGTATATAAGCTGATGAGCATAAACGTGTGCAAGTTGACGAGCGTAAACGT
1 GTAAACGTATACAAGCTGATGAGCGTAAACGTATACAAGCTGACGAGCGTAAACGT
322272 ATATGAGTCG
Statistics
Matches: 158, Mismatches: 42, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
72 158 1.00
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (72 bp):
GTAAACGTATACAAGCTGATGAGCGTAAACGTATACAAGCTGACGAGCGTAAACGTGTGCAAGCT
AATGAGT
Found at i:328283 original size:3 final size:3
Alignment explanation
Indices: 328275--328333 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
328265 TTGTTTAGTG
328275 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
328323 ATA ATA ATA AT
1 ATA ATA ATA AT
328334 GAAATTAAAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:328742 original size:24 final size:24
Alignment explanation
Indices: 328678--328888 Score: 149
Period size: 24 Copynumber: 8.8 Consensus size: 24
328668 CGTTGAATTA
* *
328678 CGTAAACGTATATAAGCTAATGAG
1 CGTAAACGTATATAAGCTGACGAG
* * **
328702 CGTGAACGTGTGCAAGCTGACGAG
1 CGTAAACGTATATAAGCTGACGAG
* *
328726 CGTAAACGTACATAAGCTGATGAG
1 CGTAAACGTATATAAGCTGACGAG
* * *
328750 CGTAATA-GTGT-TCAAGCTAATGAG
1 CGTAA-ACGTATAT-AAGCTGACGAG
*
328774 TGTAAACGTATATAAGCTGACGAG
1 CGTAAACGTATATAAGCTGACGAG
* * * * *
328798 TGTAAACGTGT-CAAGCTAACAAG
1 CGTAAACGTATATAAGCTGACGAG
* *
328821 TGTAAACGTATATAAGCTGACAAG
1 CGTAAACGTATATAAGCTGACGAG
* * ** *
328845 CATAAACGTGTGCAATCTGACGAG
1 CGTAAACGTATATAAGCTGACGAG
**
328869 CGTAAACGTATGCAAGCTGA
1 CGTAAACGTATATAAGCTGA
328889 TGATGTAAGA
Statistics
Matches: 146, Mismatches: 36, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
23 21 0.14
24 123 0.84
25 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (24 bp):
CGTAAACGTATATAAGCTGACGAG
Found at i:328749 original size:48 final size:48
Alignment explanation
Indices: 328678--328888 Score: 237
Period size: 48 Copynumber: 4.4 Consensus size: 48
328668 CGTTGAATTA
* * * *
328678 CGTAAACGTATATAAGCTAATGAGCGTGAACGTGTGCAAGCTGACGAG
1 CGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTAACGAG
* * * *
328726 CGTAAACGTACATAAGCTGATGAGCGTAATA-GTGTTCAAGCTAATGAG
1 CGTAAACGTATATAAGCTGACGAGCGTAA-ACGTGTGCAAGCTAACGAG
* * *
328774 TGTAAACGTATATAAGCTGACGAGTGTAAACGTGT-CAAGCTAACAAG
1 CGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTAACGAG
* * * * *
328821 TGTAAACGTATATAAGCTGACAAGCATAAACGTGTGCAATCTGACGAG
1 CGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTAACGAG
**
328869 CGTAAACGTATGCAAGCTGA
1 CGTAAACGTATATAAGCTGA
328889 TGATGTAAGA
Statistics
Matches: 139, Mismatches: 21, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
47 43 0.31
48 95 0.68
49 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (48 bp):
CGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTAACGAG
Found at i:331403 original size:51 final size:52
Alignment explanation
Indices: 331241--331423 Score: 314
Period size: 52 Copynumber: 3.5 Consensus size: 52
331231 ATGCAAAAGA
331241 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGG
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGG
*
331293 TCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGG
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGG
* * *
331345 TCTGATGACTATGTGTCATCGTGAGTATATG-ATCCTTTTCGGATTATGAGG
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGG
*
331396 TCCGATGACAATGTGTCATCGTGAGTAT
1 TCCGATGACTATGTGTCATCGTGAGTAT
331424 TAAATGAGAA
Statistics
Matches: 124, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
51 44 0.35
52 80 0.65
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (52 bp):
TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGG
Found at i:334162 original size:26 final size:26
Alignment explanation
Indices: 334126--334177 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
334116 ATCATGGAGA
334126 ACCACTAGATTCTAATTGGATTTTTT
1 ACCACTAGATTCTAATTGGATTTTTT
*
334152 ACCACTAGATTCTATTTGGATTTTTT
1 ACCACTAGATTCTAATTGGATTTTTT
334178 TTGTTCTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (26 bp):
ACCACTAGATTCTAATTGGATTTTTT
Found at i:349948 original size:6 final size:6
Alignment explanation
Indices: 349929--350010 Score: 66
Period size: 6 Copynumber: 14.3 Consensus size: 6
349919 TTTAAAAAAA
* ** *
349929 TAAATT TTAA-T TAAATT TAAAAA TAAATT TAAATT TAGAA-- TGAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TA-AATT TAAATT
* *
349975 TAAATT CAAA-A TAAATT TAAATT TAAA-T TAAATT TA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TA
350011 GAAATAAATT
Statistics
Matches: 58, Mismatches: 12, Indels: 12
0.71 0.15 0.15
Matches are distributed among these distances:
4 2 0.03
5 13 0.22
6 41 0.71
7 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:349949 original size:17 final size:17
Alignment explanation
Indices: 349939--350010 Score: 99
Period size: 17 Copynumber: 4.2 Consensus size: 17
349929 TAAATTTTAA
349939 TTAAATTTAAAAATAAAT
1 TTAAATTT-AAAATAAAT
* *
349957 TTAAATTTAGAATGAAT
1 TTAAATTTAAAATAAAT
*
349974 TTAAATTCAAAATAAAT
1 TTAAATTTAAAATAAAT
*
349991 TTAAATTTAAATTAAAT
1 TTAAATTTAAAATAAAT
350008 TTA
1 TTA
350011 GAAATAAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
17 39 0.83
18 8 0.17
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:349957 original size:12 final size:12
Alignment explanation
Indices: 349924--349961 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
349914 GGTTTTTTAA
349924 AAAAATAAATTT
1 AAAAATAAATTT
* *
349936 -TAATTAAATTT
1 AAAAATAAATTT
349947 AAAAATAAATTT
1 AAAAATAAATTT
349959 AAA
1 AAA
349962 TTTAGAATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAAAATAAATTT
Found at i:349978 original size:23 final size:23
Alignment explanation
Indices: 349952--350027 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
349942 AATTTAAAAA
*
349952 TAAATTTAAATTTAGAATGAATT
1 TAAATTTAAATTTAGAATAAATT
* *
349975 TAAATTCAAA-ATA-AATTTAAATT
1 TAAATTTAAATTTAGAA--TAAATT
349998 TAAA-TTAAATTTAGAAATAAATT
1 TAAATTTAAATTTAG-AATAAATT
*
350021 AAAATTT
1 TAAATTT
350028 TTTAAAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
21 2 0.05
22 6 0.15
23 29 0.71
24 2 0.05
25 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (23 bp):
TAAATTTAAATTTAGAATAAATT
Found at i:350624 original size:39 final size:38
Alignment explanation
Indices: 350501--350727 Score: 138
Period size: 39 Copynumber: 5.8 Consensus size: 38
350491 ATCTAGGCTT
* ** *
350501 GGGGTAAGAGATCGGAT-AGTTGTAATCTGCC-CTAAATTT
1 GGGGTAAGAGATCGG-TGA-TTGCAATCTGCCTC-AGGTTC
* * * * * *
350540 GGGGTAAGAGATCGGATGGTTGTAATTTGCCCCAAGCTC
1 GGGGTAAGAGATCGG-TGATTGCAATCTGCCTCAGGTTC
** * *
350579 AAGGTAAGGGATCGGTCGATTGCAATCTGCCTCAGGCTC
1 GGGGTAAGAGATCGGT-GATTGCAATCTGCCTCAGGTTC
* * * *
350618 GGGGTAAGAGATCAGATGAGTGCAATCTGTCTCATGTTC
1 GGGGTAAGAGATC-GGTGATTGCAATCTGCCTCAGGTTC
* * *
350657 GAGGTAAGAGATTTGTTGA-TG-ATGATCTGCCTCAGGTTC
1 GGGGTAAGAGA-TCGGTGATTGCA--ATCTGCCTCAGGTTC
*
350696 GGGGTAAGAGATCGGATGGTTGCAATCTGCCT
1 GGGGTAAGAGATCGG-TGATTGCAATCTGCCT
350728 TAAGCTCAGG
Statistics
Matches: 148, Mismatches: 30, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
37 1 0.01
38 5 0.03
39 135 0.91
40 6 0.04
41 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (38 bp):
GGGGTAAGAGATCGGTGATTGCAATCTGCCTCAGGTTC
Found at i:350779 original size:77 final size:78
Alignment explanation
Indices: 350616--350824 Score: 244
Period size: 77 Copynumber: 2.7 Consensus size: 78
350606 TGCCTCAGGC
* * * * *
350616 TCGGGGTAAGAGATCAGATGAG-TGCAATCTGTCTCATGTTCGAGGTAAGAGATTTGTTGATGAT
1 TCGGGGTAAGAGATCGGATG-GTTGCAATCTGCCTCAAGCTCGAGGGAAGAGATTTGTTGATGAT
* * **
350680 GATCTGCCTCAGGT
65 GAGCTACCTCAAAT
*
350694 TCGGGGTAAGAGATCGGATGGTTGCAATCTGCCTTAAGCTC-AGGGAAGAGATTTGCTT-ATGAT
1 TCGGGGTAAGAGATCGGATGGTTGCAATCTGCCTCAAGCTCGAGGGAAGAGATTTG-TTGATGAT
*
350757 GAGCTACCTTAAAT
65 GAGCTACCTCAAAT
* * * *
350771 TTGGGGTAAGAGATCGGATGGTTGCAATCTGCCTCAGGGTCGAGGTAAGAGATT
1 TCGGGGTAAGAGATCGGATGGTTGCAATCTGCCTCAAGCTCGAGGGAAGAGATT
350825 CGCTGAGGAT
Statistics
Matches: 112, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
77 65 0.58
78 47 0.42
ACGTcount: A:0.25, C:0.14, G:0.32, T:0.29
Consensus pattern (78 bp):
TCGGGGTAAGAGATCGGATGGTTGCAATCTGCCTCAAGCTCGAGGGAAGAGATTTGTTGATGATG
AGCTACCTCAAAT
Found at i:350855 original size:77 final size:78
Alignment explanation
Indices: 350540--350862 Score: 298
Period size: 78 Copynumber: 4.2 Consensus size: 78
350530 CCCTAAATTT
* * * * * * *
350540 GGGGTAAGAGATCGGATGGTTGTAATTTGCCCCAAGCTCAAGGTAAGGGA-TCGGTCGAT--TGC
1 GGGGTAAGAGATCGGATGGTTGCAATCTGCCTCAAGCTCGAGGTAAGAGATTTGCT-GATGATG-
*
350602 AATCTGCCTCAGGCTC
64 -ATCTGCCTCAAGCTC
* * * * *
350618 GGGGTAAGAGATCAGATGAG-TGCAATCTGTCTCATGTTCGAGGTAAGAGATTTGTTGATGATGA
1 GGGGTAAGAGATCGGATG-GTTGCAATCTGCCTCAAGCTCGAGGTAAGAGATTTGCTGATGATGA
* *
350682 TCTGCCTCAGGTTC
65 TCTGCCTCAAGCTC
* * * *
350696 GGGGTAAGAGATCGGATGGTTGCAATCTGCCTTAAGCTC-AGGGAAGAGATTTGCTTATGATGAG
1 GGGGTAAGAGATCGGATGGTTGCAATCTGCCTCAAGCTCGAGGTAAGAGATTTGCTGATGATGAT
* * ** *
350760 CTACCTTAAATTT
66 CTGCCTCAAGCTC
* * * *
350773 GGGGTAAGAGATCGGATGGTTGCAATCTGCCTCAGGGTCGAGGTAAGAGATTCGCTGAGGATGAT
1 GGGGTAAGAGATCGGATGGTTGCAATCTGCCTCAAGCTCGAGGTAAGAGATTTGCTGATGATGAT
*
350838 TTGCCTCAAGCTC
66 CTGCCTCAAGCTC
*
350851 -GGGTAAAAGATC
1 GGGGTAAGAGATC
350863 AAAATCTTCA
Statistics
Matches: 198, Mismatches: 41, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
77 77 0.39
78 115 0.58
79 4 0.02
80 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.27
Consensus pattern (78 bp):
GGGGTAAGAGATCGGATGGTTGCAATCTGCCTCAAGCTCGAGGTAAGAGATTTGCTGATGATGAT
CTGCCTCAAGCTC
Found at i:351184 original size:50 final size:50
Alignment explanation
Indices: 351117--351874 Score: 209
Period size: 49 Copynumber: 15.4 Consensus size: 50
351107 CGTTGCGGTT
** * * * *
351117 TCAACCTTTCCTTTCATATCTTTTTAGGTACCAGGTTCGTCATTGCAGTC
1 TCAACCTTTCCCATCAAATCTTTTTAGGTACCAGGTTCGCCGTTGCAGGC
* * * * * **
351167 TCAACCTTTCCCATC--AT-ATTTCACGGAATCAGATTCGCCGTTGCATTC
1 TCAACCTTTCCCATCAAATCTTTTTA-GGTACCAGGTTCGCCGTTGCAGGC
* * * ** * * * *
351215 TCAATCTTTCCCATCACATC-TTTGAGGTACTGGGTTTGTCGTTAC-GAC
1 TCAACCTTTCCCATCAAATCTTTTTAGGTACCAGGTTCGCCGTTGCAGGC
* * * * * *
351263 ATCAACCTTTCCCTTCAAATCTTTTTAGTTACCGGGTTCACCGTTGCTGGA
1 -TCAACCTTTCCCATCAAATCTTTTTAGGTACCAGGTTCGCCGTTGCAGGC
* * * * * * *
351314 TCAATCTTTCCCATCACAT-TTTTGAGGTACCAAGTTCACCGTTGCGGGA
1 TCAACCTTTCCCATCAAATCTTTTTAGGTACCAGGTTCGCCGTTGCAGGC
* * * * *
351363 TCAACCTTTCCCTTCAAATCTTTTTAGGTATC-GAGCTCGCTGTTGC-GACC
1 TCAACCTTTCCCATCAAATCTTTTTAGGTACCAG-GTTCGCCGTTGCAG-GC
* * * ** * *** *
351413 TTAACCTTTCCCTTTAAATCTTCAT-GGTACCGGGTTTTTCGTTG-TGGCC
1 TCAACCTTTCCCATCAAATCTTTTTAGGTACCAGGTTCGCCGTTGCAGG-C
* * ** * * *** *
351462 TCAACCTTTCTCATCACAT-TTCAT-GGTATCGGGTTTTTCGTTG-TGGCC
1 TCAACCTTTCCCATCAAATCTTTTTAGGTACCAGGTTCGCCGTTGCAGG-C
* * ** * * * *
351510 TCAACCTTTCTCATCACAT-TTCAT-GGTACC-GGATTTGTCATTG-TGGTC
1 TCAACCTTTCCCATCAAATCTTTTTAGGTACCAGG-TTCGCCGTTGCAGG-C
* * * * * * * * *
351558 TCAATCTTTCCCATCACAT-TTCTGAGGTACCAAGTTCACCATTGCGGGG
1 TCAACCTTTCCCATCAAATCTTTTTAGGTACCAGGTTCGCCGTTGCAGGC
** * * * * * *
351607 TCAACCTTTCCTTTCAAATCTTCTTAAGTACCGGGTTTGTCATTGC-GGTC
1 TCAACCTTTCCCATCAAATCTTTTTAGGTACCAGGTTCGCCGTTGCAGG-C
* * ** * * * *
351657 TTAACCTTTCCCTTCAAATCTTCAT-GGTACCGGGTTTGTCGTTGCAGCC
1 TCAACCTTTCCCATCAAATCTTTTTAGGTACCAGGTTCGCCGTTGCAGGC
* * ** *
351706 TCGACCTTTCCCATCATAT-TTCAT-GGTACC-GGATTCGTCGTTGC-GGCC
1 TCAACCTTTCCCATCAAATCTTTTTAGGTACCAGG-TTCGCCGTTGCAGG-C
* * * * * * * *
351754 TCAATCTTTCTCAT-AACAT-TTCTAAGGTACCAAGTTCACCGTTGCGGGA
1 TCAACCTTTCCCATCAA-ATCTTTTTAGGTACCAGGTTCGCCGTTGCAGGC
* * * ** *
351803 TCAACCTTTCCCTTCAAATCTTTTTAGGTACCGGGGTCATCGTTGCGGGC
1 TCAACCTTTCCCATCAAATCTTTTTAGGTACCAGGTTCGCCGTTGCAGGC
*
351853 TCAACCTTTCCCTTCAAATCTT
1 TCAACCTTTCCCATCAAATCTT
351875 CCTGGTATCG
Statistics
Matches: 552, Mismatches: 128, Indels: 56
0.75 0.17 0.08
Matches are distributed among these distances:
47 10 0.02
48 162 0.29
49 190 0.34
50 189 0.34
51 1 0.00
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (50 bp):
TCAACCTTTCCCATCAAATCTTTTTAGGTACCAGGTTCGCCGTTGCAGGC
Found at i:351488 original size:48 final size:48
Alignment explanation
Indices: 351404--352157 Score: 434
Period size: 48 Copynumber: 15.4 Consensus size: 48
351394 CGAGCTCGCT
* * * * * *
351404 GTTGCGACCTTAACCTTTCCCTTTAAATCTTCATGGTACCGGGTTTTTC
1 GTTGCGGCCTCAACCTTTCCCATCACAT-TTCATGGTACCGGGTTTGTC
* * * *
351453 GTTGTGGCCTCAACCTTTCTCATCACATTTCATGGTATCGGGTTTTTC
1 GTTGCGGCCTCAACCTTTCCCATCACATTTCATGGTACCGGGTTTGTC
* * *
351501 GTTGTGGCCTCAACCTTTCTCATCACATTTCATGGTACCGGATTTGTC
1 GTTGCGGCCTCAACCTTTCCCATCACATTTCATGGTACCGGGTTTGTC
* * * * ** ***
351549 ATTGTGGTCTCAATCTTTCCCATCACATTTC-TGAGGTACCAAGTTCACC
1 GTTGCGGCCTCAACCTTTCCCATCACATTTCAT--GGTACCGGGTTTGTC
* ** ** * * *
351598 ATTGCGGGGTCAACCTTTCCTTTCAAATCTTCTTAAGTACCGGGTTTGTC
1 GTTGCGGCCTCAACCTTTCCCATCACAT-TTCAT-GGTACCGGGTTTGTC
* * * * *
351648 ATTGCGGTCTTAACCTTTCCCTTCAAATCTTCATGGTACCGGGTTTGTC
1 GTTGCGGCCTCAACCTTTCCCATCACAT-TTCATGGTACCGGGTTTGTC
* * * * *
351697 GTTGCAGCCTCGACCTTTCCCATCATATTTCATGGTACCGGATTCGTC
1 GTTGCGGCCTCAACCTTTCCCATCACATTTCATGGTACCGGGTTTGTC
* * * * ** ***
351745 GTTGCGGCCTCAATCTTTCTCATAACATTTCTAAGGTACCAAGTTCACC
1 GTTGCGGCCTCAACCTTTCCCATCACATTTC-ATGGTACCGGGTTTGTC
** * * ** * **
351794 GTTGCGGGATCAACCTTTCCCTTCAAATCTTTTTAGGTACCGGGGTCATC
1 GTTGCGGCCTCAACCTTTCCCATCACAT-TTCAT-GGTACCGGGTTTGTC
* * * * * *
351844 GTTGCGGGCTCAACCTTTCCCTTCAAATCTTCCTGGTATCGGGTTTGCC
1 GTTGCGGCCTCAACCTTTCCCATCACAT-TTCATGGTACCGGGTTTGTC
* * * * ** *
351893 GTTACGACCTCAACCTTTGCCATCACATTTCATGGTATCGGACTTGCC
1 GTTGCGGCCTCAACCTTTCCCATCACATTTCATGGTACCGGGTTTGTC
* ** ** * *** *
351941 ATTGCGGGTTCAATTTTTCCTATCACATTTC-TGACGTACTAAGTTCGTC
1 GTTGCGGCCTCAACCTTTCCCATCACATTTCATG--GTACCGGGTTTGTC
** ** * * *
351990 GTTGCGGGATCAACCTTTCCTTTCAAATTTTCATGGTACCAGGTTTGCC
1 GTTGCGGCCTCAACCTTTCCCATCACA-TTTCATGGTACCGGGTTTGTC
* * * * * * *
352039 ATTCCAGCCTTAACCTTTCCCATCACATTTCATGCT-CTCGGATTCGTC
1 GTTGCGGCCTCAACCTTTCCCATCACATTTCATGGTAC-CGGGTTTGTC
** * * *
352087 GTTGCGGCCTCAATATTTCCCATCACATCTTCTAAGGTACCGGGTTCGTT
1 GTTGCGGCCTCAACCTTTCCCATCACAT-TTC-ATGGTACCGGGTTTGTC
*
352137 GTTGCGGTCTCAACCTTTCCC
1 GTTGCGGCCTCAACCTTTCCC
352158 TTTAAATCTT
Statistics
Matches: 544, Mismatches: 146, Indels: 29
0.76 0.20 0.04
Matches are distributed among these distances:
47 4 0.01
48 209 0.38
49 208 0.38
50 119 0.22
51 4 0.01
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (48 bp):
GTTGCGGCCTCAACCTTTCCCATCACATTTCATGGTACCGGGTTTGTC
Found at i:351657 original size:99 final size:98
Alignment explanation
Indices: 351106--352157 Score: 309
Period size: 99 Copynumber: 10.7 Consensus size: 98
351096 ATCGGGTTTC
** * * * *
351106 CCGTTGCGGTTTCAACCTTTCCTTTCATATCTTTTTAGGTACCAGG-TTCGTCATTGCAGTCTCA
1 CCGTTGCGGGATCAACCTTTCCCTTCAAATCTTCTTAGGTACC-GGATTCGTCATTGCGGTCTCA
* * * *
351170 ACCTTTCCCATCATATTTC-ACGGAATC-AGATTCG
65 ACCTTTCCCATCACATTTCTA-GGTACCAAG-TTCA
**** * * * * * * * * * *
351204 CCGTTGCATTCTCAATCTTTCCCATCACATCTT-TGAGGTACTGGGTTTGTCGTTAC-GACATCA
1 CCGTTGCGGGATCAACCTTTCCCTTCAAATCTTCTTAGGTACCGGATTCGTCATTGCGGTC-TCA
* * * * **
351267 ACCTTTCCCTTCAAATCTTTTTAGTTACCGGGTTCA
65 ACCTTTCCCATCACA--TTTCTAGGTACCAAGTTCA
* * * * * ** * **
351303 CCGTTGCTGGATCAATCTTTCCCATCACAT-TT-TTGAGGTACC-AAGTTCACCGTTGCGGGATC
1 CCGTTGCGGGATCAACCTTTCCCTTCAAATCTTCTT-AGGTACCGGA-TTCGTCATTGCGGTCTC
* * * * * * *
351365 AACCTTTCCCTTCAAATCTTTTTAGGTATCGAGCTCG
64 AACCTTTCCCATCACA--TTTCTAGGTACCAAGTTCA
* *** * * * * ** * * *
351402 CTGTTGCGACCTTAACCTTTCCCTTTAAATCTTCAT-GGTACCGGGTTTTTCGTTGTGGCCTCAA
1 CCGTTGCGGGATCAACCTTTCCCTTCAAATCTTCTTAGGTACCGGATTCGTCATTGCGGTCTCAA
* * ** **
351466 CCTTTCTCATCACATTTC-ATGGTATCGGGTTTT
66 CCTTTCCCATCACATTTCTA-GGTACCAAGTTCA
* * ** * * * * * *
351499 TCGTTGTGGCCTCAACCTTTCTCATCACAT-TTCAT-GGTACCGGATTTGTCATTGTGGTCTCAA
1 CCGTTGCGGGATCAACCTTTCCCTTCAAATCTTCTTAGGTACCGGATTCGTCATTGCGGTCTCAA
*
351562 TCTTTCCCATCACATTTCTGAGGTACCAAGTTCA
66 CCTTTCCCATCACATTTCT-AGGTACCAAGTTCA
* * * * * * *
351596 CCATTGCGGGGTCAACCTTTCCTTTCAAATCTTCTTAAGTACCGGGTTTGTCATTGCGGTCTTAA
1 CCGTTGCGGGATCAACCTTTCCCTTCAAATCTTCTTAGGTACCGGATTCGTCATTGCGGTCTCAA
* * ** **
351661 CCTTTCCCTTCAAATCTTC-ATGGTACCGGGTTTG
66 CCTTTCCCATCACAT-TTCTA-GGTACCAAGTTCA
* * ** * * * * * *
351695 TCGTTGCAGCCTCGACCTTTCCCATCATAT-TTCAT-GGTACCGGATTCGTCGTTGCGGCCTCAA
1 CCGTTGCGGGATCAACCTTTCCCTTCAAATCTTCTTAGGTACCGGATTCGTCATTGCGGTCTCAA
* * *
351758 TCTTTCTCATAACATTTCTAAGGTACCAAGTTCA
66 CCTTTCCCATCACATTTCT-AGGTACCAAGTTCA
* ** * * *
351792 CCGTTGCGGGATCAACCTTTCCCTTCAAATCTTTTTAGGTACCGGGGTCATCGTTGCGGGCTCAA
1 CCGTTGCGGGATCAACCTTTCCCTTCAAATCTTCTTAGGTACCGGATTCGTCATTGCGGTCTCAA
* * * ** **
351857 CCTTTCCCTTCAAATCTTCCT-GGTATCGGGTTTG
66 CCTTTCCCATCACAT-TT-CTAGGTACCAAGTTCA
* *** * * * * * *
351891 CCGTTACGACCTCAACCTTTGCCATCACAT-TTCAT-GGTATCGGACTT-GCCATTGCGGGT-TC
1 CCGTTGCGGGATCAACCTTTCCCTTCAAATCTTCTTAGGTACCGGA-TTCGTCATTGC-GGTCTC
** * * * *
351952 AATTTTTCCTATCACATTTCTGACGTACTAAGTTCG
64 AACCTTTCCCATCACATTTCT-AGGTACCAAGTTCA
* * * * * * * * * *
351988 TCGTTGCGGGATCAACCTTTCCTTTCAAATTTTCAT-GGTACCAGG-TTTGCCATTCCAGCCTTA
1 CCGTTGCGGGATCAACCTTTCCCTTCAAATCTTCTTAGGTACC-GGATTCGTCATTGCGGTCTCA
* * *
352051 ACCTTTCCCATCACATTTC-ATGCT-CTC-GGATTCG
65 ACCTTTCCCATCACATTTCTA-GGTAC-CAAG-TTCA
* ** ** * * * * **
352085 TCGTTGCGGCCTCAATATTTCCCATCACATCTTCTAAGGTACCGGGTTCGTTGTTGCGGTCTCAA
1 CCGTTGCGGGATCAACCTTTCCCTTCAAATCTTCTTAGGTACCGGATTCGTCATTGCGGTCTCAA
352150 CCTTTCCC
66 CCTTTCCC
352158 TTTAAATCTT
Statistics
Matches: 694, Mismatches: 222, Indels: 76
0.70 0.22 0.08
Matches are distributed among these distances:
95 2 0.00
96 58 0.08
97 247 0.36
98 109 0.16
99 265 0.38
100 10 0.01
101 3 0.00
ACGTcount: A:0.18, C:0.28, G:0.17, T:0.36
Consensus pattern (98 bp):
CCGTTGCGGGATCAACCTTTCCCTTCAAATCTTCTTAGGTACCGGATTCGTCATTGCGGTCTCAA
CCTTTCCCATCACATTTCTAGGTACCAAGTTCA
Found at i:351693 original size:196 final size:194
Alignment explanation
Indices: 351415--352157 Score: 774
Period size: 196 Copynumber: 3.8 Consensus size: 194
351405 TTGCGACCTT
* * * * *
351415 AACCTTTCCCTTT-AAATCTTCATGGTACCGGGTTTTTCGTTGTGGCCTCAACCTTTCTCATCAC
1 AACCTTT-CCTTTCAAATCTTCATGGTACCGGGTTTGTCATTGCGGCCTCAACCTTTCCCATCAA
* * * *
351479 ATTTCATGGTATCGGGTTTTTCGTTGTGGCCTCAACCTTTCTCATCACATTTCATGGTACCGGAT
65 ATTTCATGGTACCGGGTTTGTCGTTGCGGCCTCAACCTTTCCCATCACATTTCATGGTACCGGAT
* * * *
351544 TTGTCATTGTGGTCTCAATCTTTCCCATCACATTTCTGAGGTACCAAGTTCACCATTGCGGGGTC
130 TCGTCATTGCGGTCTCAATCTTTCCCATCACATTTCTGAGGTACCAAGTTCACCGTTGCGGGATC
* * * * *
351609 AACCTTTCCTTTCAAATCTTCTTAAGTACCGGGTTTGTCATTGCGGTCTTAACCTTTCCCTTCAA
1 AACCTTTCCTTTCAAATCTTCAT-GGTACCGGGTTTGTCATTGCGGCCTCAACCTTTCCCATCAA
* * *
351674 ATCTTCATGGTACCGGGTTTGTCGTTGCAGCCTCGACCTTTCCCATCATATTTCATGGTACCGGA
65 AT-TTCATGGTACCGGGTTTGTCGTTGCGGCCTCAACCTTTCCCATCACATTTCATGGTACCGGA
* * * * *
351739 TTCGTCGTTGCGGCCTCAATCTTTCTCATAACATTTCTAAGGTACCAAGTTCACCGTTGCGGGAT
129 TTCGTCATTGCGGTCTCAATCTTTCCCATCACATTTCTGAGGTACCAAGTTCACCGTTGCGGGAT
351804 C
194 C
* ** * ** * * *
351805 AACCTTTCCCTTCAAATCTTTTTAGGTACCGGGGTCATCGTTGCGGGCTCAACCTTTCCCTTCAA
1 AACCTTTCCTTTCAAATCTTCAT-GGTACCGGGTTTGTCATTGCGGCCTCAACCTTTCCCATCAA
* * * * * * *
351870 ATCTTCCTGGTATCGGGTTTGCCGTTACGACCTCAACCTTTGCCATCACATTTCATGGTATCGGA
65 AT-TTCATGGTACCGGGTTTGTCGTTGCGGCCTCAACCTTTCCCATCACATTTCATGGTACCGGA
* * * * * **
351935 CTT-GCCATTGCGGGT-TCAATTTTTCCTATCACATTTCTGACGTACTAAGTTCGTCGTTGCGGG
129 -TTCGTCATTGC-GGTCTCAATCTTTCCCATCACATTTCTGAGGTACCAAGTTCACCGTTGCGGG
351998 ATC
192 ATC
* * * * * * *
352001 AACCTTTCCTTTCAAATTTTCATGGTACCAGGTTTGCCATTCCAGCCTTAACCTTTCCCATCACA
1 AACCTTTCCTTTCAAATCTTCATGGTACCGGGTTTGTCATTGCGGCCTCAACCTTTCCCATCAAA
* * * ** *
352066 TTTCATGCT-CTCGGATTCGTCGTTGCGGCCTCAATATTTCCCATCACATCTTCTAAGGTACCGG
66 TTTCATGGTAC-CGGGTTTGTCGTTGCGGCCTCAACCTTTCCCATCACAT-TTC-ATGGTACCGG
* ** *
352130 GTTCGTTGTTGCGGTCTCAACCTTTCCC
128 ATTCGTCATTGCGGTCTCAATCTTTCCC
352158 TTTAAATCTT
Statistics
Matches: 446, Mismatches: 93, Indels: 18
0.80 0.17 0.03
Matches are distributed among these distances:
193 5 0.01
194 52 0.12
195 73 0.16
196 312 0.70
197 4 0.01
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (194 bp):
AACCTTTCCTTTCAAATCTTCATGGTACCGGGTTTGTCATTGCGGCCTCAACCTTTCCCATCAAA
TTTCATGGTACCGGGTTTGTCGTTGCGGCCTCAACCTTTCCCATCACATTTCATGGTACCGGATT
CGTCATTGCGGTCTCAATCTTTCCCATCACATTTCTGAGGTACCAAGTTCACCGTTGCGGGATC
Found at i:351921 original size:392 final size:390
Alignment explanation
Indices: 351415--352155 Score: 916
Period size: 392 Copynumber: 1.9 Consensus size: 390
351405 TTGCGACCTT
* * ** * * *
351415 AACCTTTCCCTTTAAATCTTCATGGTACCGGGTTTTTCGTTGTGGCCTCAACCTTTCTCATCACA
1 AACCTTTCCCTTCAAATCTTCATGGTACCGGGGTCATCGTTGCGGCCTCAACCTTTCCCATCAAA
** ** * *
351480 TTTCATGGTATCGGGTTTTTCGTTGTGGCCTCAACCTTTCTCATCACATTTCATGGTACCGGATT
66 TTTCATGGTATCGGGTTTGCCGTTACGACCTCAACCTTTCTCATCACATTTCATGGTACCGGACT
* * * *
351545 TGTCATTG-TGGTCTCAATCTTTCCCATCACATTTCTGAGGTACCAAGTTCACCATTGCGGGGTC
131 TGCCATTGCGGGT-TCAATCTTTCCCATCACATTTCTGACGTACCAAGTTCACCATTGCGGGATC
* * * * * * *
351609 AACCTTTCCTTTCAAATCTTCTTAAGTACCGGGTTTGTCATTGCGGTCTTAACCTTTCCCTTCAA
195 AACCTTTCCTTTCAAATCTTCAT-AGTACCAGGTTTGCCATTCCAGCCTTAACCTTTCCCATCAA
* * * * * * *
351674 ATCTTCATGGTAC-CGGGTTTGTCGTTGCAGCCTCGACCTTTCCCATCATAT-TTC-ATGGTACC
259 AT-TTCATGCT-CTCGGATTCGTCGTTGCAGCCTCAACATTTCCCATCACATCTTCTAAGGTACC
*
351736 GGATTCGTCGTTGCGGCCTCAATCTTTCTCATAACATTTCTAAGGTACCAAGTTCACCGTTGCGG
322 GGATTCGTCGTTGCGGCCTCAACCTTTCTCATAACATTTCTAAGGTACCAAGTTCACCGTTGCGG
351801 GATC
387 GATC
** * *
351805 AACCTTTCCCTTCAAATCTTTTTAGGTACCGGGGTCATCGTTGCGGGCTCAACCTTTCCCTTCAA
1 AACCTTTCCCTTCAAATCTTCAT-GGTACCGGGGTCATCGTTGCGGCCTCAACCTTTCCCATCAA
* *
351870 ATCTTCCTGGTATCGGGTTTGCCGTTACGACCTCAACCTTTGC-CATCACATTTCATGGTATCGG
65 AT-TTCATGGTATCGGGTTTGCCGTTACGACCTCAACCTTT-CTCATCACATTTCATGGTACCGG
* * * ** *
351934 ACTTGCCATTGCGGGTTCAATTTTTCCTATCACATTTCTGACGTACTAAGTTCGTCGTTGCGGGA
128 ACTTGCCATTGCGGGTTCAATCTTTCCCATCACATTTCTGACGTACCAAGTTCACCATTGCGGGA
* *
351999 TCAACCTTTCCTTTCAAATTTTCATGGTACCAGGTTTGCCATTCCAGCCTTAACCTTTCCCATCA
193 TCAACCTTTCCTTTCAAATCTTCATAGTACCAGGTTTGCCATTCCAGCCTTAACCTTTCCCATCA
* * *
352064 CATTTCATGCTCTCGGATTCGTCGTTGCGGCCTCAATATTTCCCATCACATCTTCTAAGGTACCG
258 AATTTCATGCTCTCGGATTCGTCGTTGCAGCCTCAACATTTCCCATCACATCTTCTAAGGTACCG
* * *
352129 GGTTCGTTGTTGCGGTCTCAACCTTTC
323 GATTCGTCGTTGCGGCCTCAACCTTTC
352156 CCTTTAAATC
Statistics
Matches: 292, Mismatches: 52, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
389 1 0.00
390 58 0.20
391 73 0.25
392 156 0.53
393 4 0.01
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (390 bp):
AACCTTTCCCTTCAAATCTTCATGGTACCGGGGTCATCGTTGCGGCCTCAACCTTTCCCATCAAA
TTTCATGGTATCGGGTTTGCCGTTACGACCTCAACCTTTCTCATCACATTTCATGGTACCGGACT
TGCCATTGCGGGTTCAATCTTTCCCATCACATTTCTGACGTACCAAGTTCACCATTGCGGGATCA
ACCTTTCCTTTCAAATCTTCATAGTACCAGGTTTGCCATTCCAGCCTTAACCTTTCCCATCAAAT
TTCATGCTCTCGGATTCGTCGTTGCAGCCTCAACATTTCCCATCACATCTTCTAAGGTACCGGAT
TCGTCGTTGCGGCCTCAACCTTTCTCATAACATTTCTAAGGTACCAAGTTCACCGTTGCGGGATC
Found at i:351927 original size:244 final size:243
Alignment explanation
Indices: 351298--351929 Score: 728
Period size: 244 Copynumber: 2.6 Consensus size: 243
351288 TAGTTACCGG
*
351298 GTTCACCGTTGCTGGATCAATCTTTCCCATCACATTTTTGAGGTACCAAGTTCACCGTTGCGGGA
1 GTTCACCGTTGCGGGATCAATCTTTCCCATCACATTTTTGAGGTACCAAGTTCACCGTTGCGGGA
* * * * * *
351363 TCAACCTTTCCCTTCAAATCTTTTTAGGTATCGAGCTCGCTGTTGCGACCTTAACCTTTCCCTTT
66 TCAACCTTTCCCTTCAAATCTTCTTAGGTATCGGGTTTGCCGTTGCGACCTTAACCTTTCCCTTC
* ** * *
351428 AAATCTTCATGGTACCGGGTTTTTCGTTGTGGCCTCAACCTTTCTCATCACATTTCATGGTATCG
131 AAATCTTCATGGTACCGGGTTTGTCGTTGCAGCCTCAACCTTTCCCATCACATTTCATGGTACCG
* ** * * * *
351493 GGTTTTTCGTTGTGGCCTCAACCTTTCTCATCACATTTCATGGTACCG
196 GATTCGTCGTTGCGGCCTCAACCTTTCTCATAACATTTCAAGGTACCA
*** * * ** * *
351541 GATTTGTCATTGTGGTCTCAATCTTTCCCATCACATTTCTGAGGTACCAAGTTCACCATTGCGGG
1 G-TTCACCGTTGCGGGATCAATCTTTCCCATCACATTTTTGAGGTACCAAGTTCACCGTTGCGGG
* * * * * * **
351606 GTCAACCTTTCCTTTCAAATCTTCTTAAGTACCGGGTTTGTCATTGCGGTCTTAACCTTTCCCTT
65 ATCAACCTTTCCCTTCAAATCTTCTTAGGTATCGGGTTTGCCGTTGCGACCTTAACCTTTCCCTT
* *
351671 CAAATCTTCATGGTACCGGGTTTGTCGTTGCAGCCTCGACCTTTCCCATCATATTTCATGGTACC
130 CAAATCTTCATGGTACCGGGTTTGTCGTTGCAGCCTCAACCTTTCCCATCACATTTCATGGTACC
*
351736 GGATTCGTCGTTGCGGCCTCAATCTTTCTCATAACATTTCTAAGGTACCAA
195 GGATTCGTCGTTGCGGCCTCAACCTTTCTCATAACATTTC-AAGGTACC-A
* * * * ** * *
351787 GTTCACCGTTGCGGGATCAACCTTTCCCTTCAAATCTTTTTAGGTACCGGGGTCATCGTTGCGGG
1 GTTCACCGTTGCGGGATCAATCTTTCCCATCACAT-TTTTGAGGTACCAAGTTCACCGTTGCGGG
* * * * * *
351852 CTCAACCTTTCCCTTCAAATCTTCCT-GGTATCGGGTTTGCCGTTACGACCTCAACCTTTGCCAT
65 ATCAACCTTTCCCTTCAAATCTTCTTAGGTATCGGGTTTGCCGTTGCGACCTTAACCTTTCCCTT
*
351916 CACAT-TTCATGGTA
130 CAAATCTTCATGGTA
351930 TCGGACTTGC
Statistics
Matches: 315, Mismatches: 70, Indels: 7
0.80 0.18 0.02
Matches are distributed among these distances:
243 1 0.00
244 205 0.65
245 63 0.20
246 46 0.15
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (243 bp):
GTTCACCGTTGCGGGATCAATCTTTCCCATCACATTTTTGAGGTACCAAGTTCACCGTTGCGGGA
TCAACCTTTCCCTTCAAATCTTCTTAGGTATCGGGTTTGCCGTTGCGACCTTAACCTTTCCCTTC
AAATCTTCATGGTACCGGGTTTGTCGTTGCAGCCTCAACCTTTCCCATCACATTTCATGGTACCG
GATTCGTCGTTGCGGCCTCAACCTTTCTCATAACATTTCAAGGTACCA
Found at i:352015 original size:146 final size:147
Alignment explanation
Indices: 351842--352171 Score: 380
Period size: 146 Copynumber: 2.3 Consensus size: 147
351832 ACCGGGGTCA
* * * * * *
351842 TCGTTGCGGGCTCAACCTTTCCCTTCAAATCTTCCTGGTATCGGGTTTGCCGTTAC-GACCTCAA
1 TCGTTGCGGGCTCAACCTTTCCTTTCAAATCTTCATGGTACCAGGTTTGCCATTCCAG-CCTCAA
* * ** * *
351906 CCTTTGCCATCACATTTCATGGTATCGGACTT-GCCATTGCGGGTTCAATTTTTCCTATCACAT-
65 CCTTTCCCATCACATTTCATGCTATCGGA-TTCGCCATTGCGGCCTCAATATTTCCCATCACATC
* *
351969 TTCTGACGTACTAAGTTCG
129 TTCTAACGTACCAAGTTCG
* * *
351988 TCGTTGCGGGATCAACCTTTCCTTTCAAATTTTCATGGTACCAGGTTTGCCATTCCAGCCTTAAC
1 TCGTTGCGGGCTCAACCTTTCCTTTCAAATCTTCATGGTACCAGGTTTGCCATTCCAGCCTCAAC
* * *
352053 CTTTCCCATCACATTTCATGCTCTCGGATTCGTCGTTGCGGCCTCAATATTTCCCATCACATCTT
66 CTTTCCCATCACATTTCATGCTATCGGATTCGCCATTGCGGCCTCAATATTTCCCATCACATCTT
* **
352118 CTAAGGTACCGGGTTCG
131 CTAACGTACCAAGTTCG
* *
352135 TTGTTGCGGTCTCAACCTTTCCCTTT-AAATCTTCATG
1 TCGTTGCGGGCTCAACCTTT-CCTTTCAAATCTTCATG
352172 TTTTTCTCAG
Statistics
Matches: 153, Mismatches: 27, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
145 2 0.01
146 104 0.68
147 42 0.27
148 5 0.03
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.36
Consensus pattern (147 bp):
TCGTTGCGGGCTCAACCTTTCCTTTCAAATCTTCATGGTACCAGGTTTGCCATTCCAGCCTCAAC
CTTTCCCATCACATTTCATGCTATCGGATTCGCCATTGCGGCCTCAATATTTCCCATCACATCTT
CTAACGTACCAAGTTCG
Found at i:352155 original size:440 final size:438
Alignment explanation
Indices: 351107--352170 Score: 1009
Period size: 440 Copynumber: 2.4 Consensus size: 438
351097 TCGGGTTTCC
* * * * *
351107 CGTTGCGGTTTCAACCTTTCCTTTCATATCTTTTTAGGTACCAGGTTCGTCATTGCAGTCTCAAC
1 CGTTGCGGTATCAACCTTTCCTTTCAAAT-TTTAT-GGTACCAGGTTCGCCATTGCAGCCTCAAC
* * ** * * **
351172 CTTTCCCATCATATTTCACGGAATCAGATTCGCCGTTGCATTCTCAATCTTTCCCATCACATCTT
64 CTTTCCCATCAAATTTCA-AGTCTCGGATTCGTCGTTGCGGTCTCAATCTTTCCCATCACATCTT
* * * * ** * *
351237 -TGAGGTACTGGGTTTGTCGTTACGACATCAACCTTTCCCTTCAAATCTTTTTAGTTACCGGGTT
128 CTAAGGTACCGGGTTTGTCGTTGCGAC-TCAACCTTTCCCATCAAATCTTCATAGGTACCGGATT
* * *
351301 CACCGTTGCTGGATCAATCTTTCCCATCACATTTTTGAGGTACCAAGTTCACCGTTGCGGGATCA
192 CACCGTTGCTGGATCAATCTTTCCCATAACATTTCTAAGGTACCAAGTTCACCGTTGCGGGATCA
* * *
351366 ACCTTTCCCTTCAAATCTTTTTAGGTATCGAGCTCGCTGTTGCGACCTTAACCTTTCCCTTTAAA
257 ACCTTTCCCTTCAAATCTTTTTAGGTACCGAGCTCGCTGTTGCGACCTCAACCTTTCCCTTCAAA
** ** * **
351431 TCTTCATGGTACCGGGTTTTTCGTTGTGGCCTCAACCTTTCTCATCACATTTCATGGTATCGGGT
322 TCTTCATGGTACCGGGTTTGCCGTTACGACCTCAACCTTTCTCATCACATTTCATGGTATCGGAC
** * * ** *
351496 TTTTCGTTGTGGCCTCAACCTTTCTCATCACATTTCATGGTACCGGATTTGT
387 TTGCCATTGCGGCCTCAACCTTTCTCATCACATTTCATGGTACAAGATTCGT
* * * * ** * * * * **
351548 CATTGTGGTCTCAATCTTTCCCATCACATTTCTGA-GGTACCAAGTTCACCATTGCGGGGTCAAC
1 CGTTGCGGTATCAACCTTTCCTTTCAAATTT-T-ATGGTACCAGGTTCGCCATTGCAGCCTCAAC
** * * * * * * *
351612 CTTTCCTTTCAAATCTTCTTAAGTAC-CGGGTTTGTCATTGCGGTCTTAACCTTTCCCTTCAAAT
64 CTTTCCCATCAAAT-TTC--AAGT-CTCGGATTCGTCGTTGCGGTCTCAATCTTTCCCATCACAT
* * * *
351676 CTTC-ATGGTACCGGGTTTGTCGTTGCAGCCTCGACCTTTCCCATCATAT-TTCAT-GGTACCGG
125 CTTCTAAGGTACCGGGTTTGTCGTTGC-GACTCAACCTTTCCCATCAAATCTTCATAGGTACCGG
** * *
351738 ATTCGTCGTTGC-GGCCTCAATCTTTCTCATAACATTTCTAAGGTACCAAGTTCACCGTTGCGGG
189 ATTCACCGTTGCTGG-ATCAATCTTTCCCATAACATTTCTAAGGTACCAAGTTCACCGTTGCGGG
* * * **
351802 ATCAACCTTTCCCTTCAAATCTTTTTAGGTACCGGGGTC-ATCGTTGCGGGCTCAACCTTTCCCT
253 ATCAACCTTTCCCTTCAAATCTTTTTAGGTACCGAGCTCGCT-GTTGCGACCTCAACCTTTCCCT
* *
351866 TCAAATCTTCCTGGTATCGGGTTTGCCGTTACGACCTCAACCTTTGC-CATCACATTTCATGGTA
317 TCAAATCTTCATGGTACCGGGTTTGCCGTTACGACCTCAACCTTT-CTCATCACATTTCATGGTA
** **
351930 TCGGACTTGCCATTGCGGGTTCAATTTTTC-CTATCACATTTC-TGACGTACTAAG-TTCGT
381 TCGGACTTGCCATTGCGGCCTCAACCTTTCTC-ATCACATTTCATG--GTAC-AAGATTCGT
* * * *
351989 CGTTGCGGGATCAACCTTTCCTTTCAAATTTTCATGGTACCAGGTTTGCCATTCCAGCCTTAACC
1 CGTTGCGGTATCAACCTTTCCTTTCAAATTTT-ATGGTACCAGGTTCGCCATTGCAGCCTCAACC
* * * *
352054 TTTCCCATCACATTTCATGCTCTCGGATTCGTCGTTGCGGCCTCAATATTTCCCATCACATCTTC
65 TTTCCCATCAAATTTCAAG-TCTCGGATTCGTCGTTGCGGTCTCAATCTTTCCCATCACATCTTC
* * * * *
352119 TAAGGTACCGGGTTCGTTGTTGCGGTCTCAACCTTTCCCTTTAAATCTTCAT
129 TAAGGTACCGGGTTTGTCGTTGC-GACTCAACCTTTCCCATCAAATCTTCAT
352171 GTTTTTCTCA
Statistics
Matches: 486, Mismatches: 117, Indels: 40
0.76 0.18 0.06
Matches are distributed among these distances:
438 3 0.01
439 40 0.08
440 276 0.57
441 98 0.20
442 66 0.14
443 3 0.01
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.37
Consensus pattern (438 bp):
CGTTGCGGTATCAACCTTTCCTTTCAAATTTTATGGTACCAGGTTCGCCATTGCAGCCTCAACCT
TTCCCATCAAATTTCAAGTCTCGGATTCGTCGTTGCGGTCTCAATCTTTCCCATCACATCTTCTA
AGGTACCGGGTTTGTCGTTGCGACTCAACCTTTCCCATCAAATCTTCATAGGTACCGGATTCACC
GTTGCTGGATCAATCTTTCCCATAACATTTCTAAGGTACCAAGTTCACCGTTGCGGGATCAACCT
TTCCCTTCAAATCTTTTTAGGTACCGAGCTCGCTGTTGCGACCTCAACCTTTCCCTTCAAATCTT
CATGGTACCGGGTTTGCCGTTACGACCTCAACCTTTCTCATCACATTTCATGGTATCGGACTTGC
CATTGCGGCCTCAACCTTTCTCATCACATTTCATGGTACAAGATTCGT
Found at i:353064 original size:7 final size:7
Alignment explanation
Indices: 353033--353063 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
353023 TTTTCTCGTT
353033 TTTTCTA
1 TTTTCTA
353040 TTTTCTA
1 TTTTCTA
353047 TTTTCTA
1 TTTTCTA
353054 TTTTCT-
1 TTTTCTA
353060 TTTT
1 TTTT
353064 TTCTCCTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTCTA
Found at i:353064 original size:14 final size:14
Alignment explanation
Indices: 353017--353064 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
353007 CAACCTTTCC
*
353017 TTTTCTTTTTCTCGTT
1 TTTTCTATTT-TC-TT
*
353033 TTTTCTATTTTCTA
1 TTTTCTATTTTCTT
353047 TTTTCTATTTTCTT
1 TTTTCTATTTTCTT
353061 TTTT
1 TTTT
353065 TCTCCTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 18 0.62
15 2 0.07
16 9 0.31
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTTCTATTTTCTT
Found at i:353092 original size:17 final size:16
Alignment explanation
Indices: 353054--353100 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
353044 CTATTTTCTA
*
353054 TTTTCTTTTTTTCTCC
1 TTTTTTTTTTTTCTCC
353070 TCTTTTTTTGTTTT-TCC
1 T-TTTTTTT-TTTTCTCC
*
353087 TTTTTTTTCTTTCT
1 TTTTTTTTTTTTCT
353101 TATTTATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 3 0.12
16 9 0.35
17 10 0.38
18 4 0.15
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTTTTTTTTTCTCC
Found at i:359123 original size:17 final size:17
Alignment explanation
Indices: 359103--359141 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
359093 TAATTTTTAA
* * *
359103 TTAAATTTAGAATGAAT
1 TTAAATTCAAAATAAAT
359120 TTAAATTCAAAATAAAT
1 TTAAATTCAAAATAAAT
359137 TTAAA
1 TTAAA
359142 GAAATAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (17 bp):
TTAAATTCAAAATAAAT
Found at i:365865 original size:23 final size:23
Alignment explanation
Indices: 365822--365865 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
365812 ATGAAAAGAA
**
365822 ATAATTTATATTTAACCATAAAC
1 ATAATTTATATTTAAAAATAAAC
*
365845 ATAATTTATTTTTAAAAATAA
1 ATAATTTATATTTAAAAATAA
365866 TAAAGTATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (23 bp):
ATAATTTATATTTAAAAATAAAC
Found at i:365941 original size:13 final size:14
Alignment explanation
Indices: 365923--365952 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
365913 ACTTTAATTA
365923 AATTA-TTTTAAAT
1 AATTATTTTTAAAT
365936 AATTATTTTTAAAT
1 AATTATTTTTAAAT
365950 AAT
1 AAT
365953 AAACAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTATTTTTAAAT
Done.