Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003112.1 Hibiscus syriacus cultivar Beakdansim tig00006507_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: 642031
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:81 original size:50 final size:50
Alignment explanation
Indices: 1--154 Score: 290
Period size: 50 Copynumber: 3.1 Consensus size: 50
1 TATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
1 TATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
* *
51 TATTCTGTATAACCAGATCAGATAATTCAAAGAACACTTCCAGAAGATGC
1 TATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
101 TATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
1 TATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
151 TATT
1 TATT
155 AGCAAATTCA
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 100 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (50 bp):
TATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
Found at i:295 original size:130 final size:131
Alignment explanation
Indices: 61--301 Score: 448
Period size: 130 Copynumber: 1.8 Consensus size: 131
51 TATTCTGTAT
*
61 AACCAGATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAACCAGATCAGATAA
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAACCAGATCAGATAA
126 CTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCATGATTGGTTTGCC
66 CTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCATGATTGGTTTGCC
191 A
131 A
192 AACCAGATCAGATAACTCAAAGAACACTT-CAGAAGATGCTATTCTGTCTAACCAGATCAGATAA
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAACCAGATCAGATAA
* *
256 CTCAAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTCCA
66 CTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCA
302 TTTAATGTTT
Statistics
Matches: 107, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
130 79 0.74
131 28 0.26
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (131 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAACCAGATCAGATAA
CTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCATGATTGGTTTGCC
A
Found at i:1422 original size:11 final size:11
Alignment explanation
Indices: 1406--1459 Score: 63
Period size: 12 Copynumber: 4.7 Consensus size: 11
1396 CTTGACCCCC
1406 TTTTTTCTTTT
1 TTTTTTCTTTT
1417 TTTTTTCTTTT
1 TTTTTTCTTTT
*
1428 TTTTTTGGTTTT
1 TTTTTT-CTTTT
*
1440 TTTATTCTCTTT
1 TTTTTTCT-TTT
*
1452 TTTATTCT
1 TTTTTTCT
1460 CTTCAAGCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
11 18 0.47
12 20 0.53
ACGTcount: A:0.04, C:0.09, G:0.04, T:0.83
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:1455 original size:12 final size:12
Alignment explanation
Indices: 1437--1462 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1427 TTTTTTTGGT
1437 TTTTTTATTCTC
1 TTTTTTATTCTC
1449 TTTTTTATTCTC
1 TTTTTTATTCTC
1461 TT
1 TT
1463 CAAGCATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTATTCTC
Found at i:14400 original size:3 final size:3
Alignment explanation
Indices: 14392--14543 Score: 259
Period size: 3 Copynumber: 50.7 Consensus size: 3
14382 TTAATATATT
*
14392 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
14440 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
14488 TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAT TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
14536 TAA TAA TA
1 TAA TAA TA
14544 TGGATAAAAA
Statistics
Matches: 141, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 141 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:14918 original size:22 final size:21
Alignment explanation
Indices: 14876--14919 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
14866 TATTAGCCAT
* * *
14876 TAAAAGACCCCACATAGCTGG
1 TAAAAGACCCCAAAAACCTGG
14897 TAAAAGCACCCCAAAAACCTGG
1 TAAAAG-ACCCCAAAAACCTGG
14919 T
1 T
14920 TTGACCCTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.41, C:0.30, G:0.16, T:0.14
Consensus pattern (21 bp):
TAAAAGACCCCAAAAACCTGG
Found at i:16257 original size:23 final size:22
Alignment explanation
Indices: 16213--16259 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
16203 TAAAACTTTA
*
16213 AATTATAAAGTACTAAACATAT
1 AATTATAAAGTACTAAAAATAT
* *
16235 AATTATAAATTAGTTAAAAATAT
1 AATTATAAAGTA-CTAAAAATAT
16258 AA
1 AA
16260 ATGTATTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.34
Consensus pattern (22 bp):
AATTATAAAGTACTAAAAATAT
Found at i:17637 original size:28 final size:28
Alignment explanation
Indices: 17589--17657 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
17579 ATTTAATCTA
* *
17589 AAACCAATATAAATTACATCATAAACTTC
1 AAACC-ATATAAAGTACATCATAAACTCC
* *
17618 AAACCATATAAAGTATATCATAATCTCC
1 AAACCATATAAAGTACATCATAAACTCC
17646 AAACTC-TATAAA
1 AAAC-CATATAAA
17658 TTTTTATCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 29 0.83
29 6 0.17
ACGTcount: A:0.51, C:0.20, G:0.01, T:0.28
Consensus pattern (28 bp):
AAACCATATAAAGTACATCATAAACTCC
Found at i:17753 original size:20 final size:20
Alignment explanation
Indices: 17730--17783 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
17720 CATTTTTTAC
*
17730 ACATTACATGCATCATACAT
1 ACATTACATGTATCATACAT
*
17750 ACA-TATATGTATACATACAT
1 ACATTACATGTAT-CATACAT
17770 ACATT-CATGTATCA
1 ACATTACATGTATCA
17784 ATATATCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 9 0.31
20 19 0.66
21 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (20 bp):
ACATTACATGTATCATACAT
Found at i:18468 original size:287 final size:286
Alignment explanation
Indices: 17874--18620 Score: 875
Period size: 286 Copynumber: 2.6 Consensus size: 286
17864 AATTTAGTAT
*
17874 AATTTGATATTAAATTT-AGCTTTACATTTTATAATTGTTTTAATTTGATCCT-TGTGTATTGTT
1 AATTTGATATT-AATTTCAGCTTTACATTTTACAATTGTTTTAATTTGATCCTCTGTG--TTGTT
* * * * * * * *
17937 TAATTTATATAAAATTTAATTTGTAATTTCTTATTTATTCAATTTAATCCTTAAAACTTTATTTT
63 TAATTTATTTAAATTTTAGTTTGTAATTTCATGTTTGTTCAATTTAGTCCTTAAAACTATA-TTT
* *
18002 TTATCCAAAATTGGCCC---A-TA--T-T-TTTTTTG--ATTTACTCCAAACCCTATAAATCACA
127 TTATCCTAAATTAGCCCATAATTATTTCTATTTTTTGTAATTTACTCCAAACCCTATAAATCACA
* * * * * *
18057 TCATAAATTTCATTTTAAACCCTATAGATTATATCATAATCTCCCAACCTTATAAACTTTTATTC
192 TCATAAACTTCATTTCAAACCCTATAGATTATATCATAATCTCCAAACCATATAAAATTTTATTA
18122 ACAAACTTTTAAAATGAATGAAATGTATCC
257 ACAAACTTTTAAAATGAATGAAATGTATCC
* *
18152 AATTTGATATTAATTTCAGTTTTACATTTTACAATTATTTTAATTTGATCCTCATGTGTTGTTTA
1 AATTTGATATTAATTTCAGCTTTACATTTTACAATTGTTTTAATTTGATCCTC-TGTGTTGTTTA
* * *
18217 AATTATTTAAATTTTAGTTTATAATTTCATGTTTGTTCAATTTAGTCCTTAAAAGTATATTTTTA
65 ATTTATTTAAATTTTAGTTTGTAATTTCATGTTTGTTCAATTTAGTCCTTAAAACTATATTTTTA
*
18282 TCCTACATTAGCCCATAATTATTTCTATTTTTTGTAATTTACTCCAAACCCTATAAATCACATCA
130 TCCTAAATTAGCCCATAATTATTTCTATTTTTTGTAATTTACTCCAAACCCTATAAATCACATCA
* * * *
18347 TAAACTTCATTTCAAACCTTATCA-ATTATATCAT-ATTTCTAAACCATATAAAATTTTGTTAAC
195 TAAACTTCATTTCAAACCCTAT-AGATTATATCATAATCTCCAAACCATATAAAATTTTATTAAC
** * *
18410 AAACTTTTGTAATGAATGCAATTTAATCC
259 AAACTTTTAAAATGAATGAAATGT-ATCC
* * * * * * *
18439 ATTTTTATATTGA-TTCAAGCTTCACATTTTAC-TTTGTTTCAGTTTGAT-CTCTGCGTGTTGTT
1 AATTTGATATTAATTTC-AGCTTTACATTTTACAATTGTTTTAATTTGATCCTCT--GTGTTGTT
* * * *
18501 TAATTTATTTAAATTTCAGTTTGTAATTTTATGTTTGCTCAATTTAGTCCTTAAAATTATATTTT
63 TAATTTATTTAAATTTTAGTTTGTAATTTCATGTTTGTTCAATTTAGTCCTTAAAACTATATTTT
* *
18566 TATCATAAATTAGCACATAATTATTTCTA-TTTTT-TAATTTACTCCAAACCCTATA
128 TATCCTAAATTAGCCCATAATTATTTCTATTTTTTGTAATTTACTCCAAACCCTATA
18621 CAATTACAAT
Statistics
Matches: 402, Mismatches: 49, Indels: 30
0.84 0.10 0.06
Matches are distributed among these distances:
277 22 0.05
278 98 0.24
280 5 0.01
281 2 0.00
283 1 0.00
284 23 0.06
285 15 0.04
286 150 0.37
287 85 0.21
288 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.06, T:0.47
Consensus pattern (286 bp):
AATTTGATATTAATTTCAGCTTTACATTTTACAATTGTTTTAATTTGATCCTCTGTGTTGTTTAA
TTTATTTAAATTTTAGTTTGTAATTTCATGTTTGTTCAATTTAGTCCTTAAAACTATATTTTTAT
CCTAAATTAGCCCATAATTATTTCTATTTTTTGTAATTTACTCCAAACCCTATAAATCACATCAT
AAACTTCATTTCAAACCCTATAGATTATATCATAATCTCCAAACCATATAAAATTTTATTAACAA
ACTTTTAAAATGAATGAAATGTATCC
Found at i:20407 original size:2 final size:2
Alignment explanation
Indices: 20394--20427 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
20384 TAAAATTTTA
*
20394 AT AT AC AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20428 AGATAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:27362 original size:7 final size:7
Alignment explanation
Indices: 27350--27381 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
27340 ATTGATATGT
27350 ATGTATA
1 ATGTATA
27357 ATGTATA
1 ATGTATA
27364 ATGTATA
1 ATGTATA
27371 ATG-AT-
1 ATGTATA
27376 ATGTAT
1 ATGTAT
27382 GAATTGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 3 0.12
6 4 0.17
7 17 0.71
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.44
Consensus pattern (7 bp):
ATGTATA
Found at i:27406 original size:44 final size:44
Alignment explanation
Indices: 27339--27425 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
27329 CATTATTCCT
*
27339 AATTGATATGTATGTATAATGTAT-AATGTATAATGATATGTATG
1 AATTGAAATGTATGTATAATGTATGAATGTATAATG-TATGTATG
*
27383 AATTGAAATGTATGTA-AAGTGTATGCATGTATAATGTATGTAT
1 AATTGAAATGTATGTATAA-TGTATGAATGTATAATGTATGTAT
27426 AGTGTATGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 2 0.05
44 27 0.69
45 10 0.26
ACGTcount: A:0.38, C:0.01, G:0.20, T:0.41
Consensus pattern (44 bp):
AATTGAAATGTATGTATAATGTATGAATGTATAATGTATGTATG
Found at i:27418 original size:26 final size:26
Alignment explanation
Indices: 27389--27440 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
27379 TATGAATTGA
27389 AATGTATGTAAAGTGTATGCATGTAT
1 AATGTATGTAAAGTGTATGCATGTAT
* *
27415 AATGTATGTATAGTGTATGTATGTAT
1 AATGTATGTAAAGTGTATGCATGTAT
27441 GATAATGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.23, T:0.42
Consensus pattern (26 bp):
AATGTATGTAAAGTGTATGCATGTAT
Found at i:27438 original size:19 final size:20
Alignment explanation
Indices: 27416--27464 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
27406 TGCATGTATA
* * *
27416 ATGTATGTATAGTG-TATGT
1 ATGTATGTATAATGATACGC
27435 ATGTATG-ATAATGATACGC
1 ATGTATGTATAATGATACGC
27454 ATGTATGTATA
1 ATGTATGTATA
27465 TATATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 5 0.20
19 17 0.68
20 3 0.12
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.41
Consensus pattern (20 bp):
ATGTATGTATAATGATACGC
Found at i:27530 original size:7 final size:7
Alignment explanation
Indices: 27520--27586 Score: 50
Period size: 7 Copynumber: 9.6 Consensus size: 7
27510 TAATGTATAA
27520 TATACTT
1 TATACTT
27527 TATAC-T
1 TATACTT
27533 TATACTT
1 TATACTT
*
27540 TATAGTT
1 TATACTT
*
27547 TATATATT
1 TATA-CTT
27555 TATA-TAT
1 TATACT-T
*
27562 ATACACTT
1 -TATACTT
27570 TATA-TT
1 TATACTT
*
27576 TATACCT
1 TATACTT
27583 TATA
1 TATA
27587 TATATATATA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
6 13 0.27
7 25 0.51
8 10 0.20
9 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.01, T:0.54
Consensus pattern (7 bp):
TATACTT
Found at i:27558 original size:15 final size:15
Alignment explanation
Indices: 27519--27613 Score: 72
Period size: 15 Copynumber: 6.3 Consensus size: 15
27509 ATAATGTATA
*
27519 ATATACTTTATA-CT
1 ATATACTTTATATTT
27533 -TATACTTTATAGTTT
1 ATATACTTTATA-TTT
*
27548 ATATA-TTTATATAT
1 ATATACTTTATATTT
*
27562 ATACACTTTATATTT
1 ATATACTTTATATTT
*
27577 ATA-CCTTATATATATAT
1 ATATACTT-TATAT-T-T
*
27594 ATATACACTTATATTT
1 ATATAC-TTTATATTT
27610 ATAT
1 ATAT
27614 GTATATACTT
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
13 11 0.17
14 9 0.14
15 23 0.35
16 10 0.15
17 5 0.08
18 6 0.09
19 1 0.02
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.53
Consensus pattern (15 bp):
ATATACTTTATATTT
Found at i:27560 original size:2 final size:2
Alignment explanation
Indices: 27547--27812 Score: 75
Period size: 2 Copynumber: 137.0 Consensus size: 2
27537 CTTTATAGTT
* * * * **
27547 TA TA TA TT TA TA TA TA TA CA CTT TA TA TT TA TA CC T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * *
27589 TA TA TA TA TA CA CT- TA TA TT TA TA TG TA TA TA CT- TA TA CTA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * * * * *
27630 TC GA CA TA TA CTT TA TA TA -A T- TA TA TA TG TA TA TA TA TG TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
27671 TA TA TA CT- TT TA T- TA TA TA TA TA -A T- TA TA AA TA TA TA -A
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
27709 T- TA TA TA TA -A TG TA TA TA -A T- TA TA CTT TC TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * *
27747 TA -A TA CTT TA TA TA -A GTA TA TG TA TA TA CT- TA TA TG TA TA
1 TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA
* *
27787 TA TA CT- TT TA TA TA TA TA TA AA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA
27813 ATGTATGTAT
Statistics
Matches: 189, Mismatches: 45, Indels: 60
0.64 0.15 0.20
Matches are distributed among these distances:
1 19 0.10
2 160 0.85
3 10 0.05
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:27585 original size:13 final size:13
Alignment explanation
Indices: 27520--27592 Score: 65
Period size: 13 Copynumber: 5.3 Consensus size: 13
27510 TAATGTATAA
*
27520 TATACTTTATACT
1 TATACTTTATATT
27533 TATACTTTATAGTT
1 TATACTTTATA-TT
*
27547 TATATATTTATATAT
1 TATA-CTTTATAT-T
*
27562 ATACACTTTATATT
1 -TATACTTTATATT
* *
27576 TATACCTTATATA
1 TATACTTTATATT
27589 TATA
1 TATA
27593 TATATACACT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
13 25 0.51
14 7 0.14
15 14 0.29
16 3 0.06
ACGTcount: A:0.36, C:0.10, G:0.01, T:0.53
Consensus pattern (13 bp):
TATACTTTATATT
Found at i:27586 original size:36 final size:33
Alignment explanation
Indices: 27530--27612 Score: 112
Period size: 36 Copynumber: 2.4 Consensus size: 33
27520 TATACTTTAT
**
27530 ACTTATACTTTATAGTTTATATATTTATATATATAC
1 ACTTATA-TTTATACCTTATATA--TATATATATAC
27566 ACTTTATATTTATACCTTATATATATATATATAC
1 AC-TTATATTTATACCTTATATATATATATATAC
27600 ACTTATATTTATA
1 ACTTATATTTATA
27613 TGTATATACT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
33 11 0.25
34 13 0.30
36 15 0.34
37 5 0.11
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.52
Consensus pattern (33 bp):
ACTTATATTTATACCTTATATATATATATATAC
Found at i:27758 original size:17 final size:19
Alignment explanation
Indices: 27721--27760 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
27711 ATATATAATG
*
27721 TATATAATTATACTTTCTA
1 TATATAATAATACTTTCTA
*
27740 TATATAATAATACTTTATA
1 TATATAATAATACTTTCTA
27759 TA
1 TA
27761 AGTATATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (19 bp):
TATATAATAATACTTTCTA
Found at i:27875 original size:16 final size:16
Alignment explanation
Indices: 27854--27885 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27844 CTTATACTTT
*
27854 ATATATAAGTATATAC
1 ATATATAAATATATAC
27870 ATATATAAATATATAC
1 ATATATAAATATATAC
27886 TTATTTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (16 bp):
ATATATAAATATATAC
Found at i:27941 original size:20 final size:20
Alignment explanation
Indices: 27918--27955 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
27908 TATAATGTAC
27918 ATAA-CATATACATGCATCGT
1 ATAATCATA-ACATGCATCGT
*
27938 ATAATCATAACATTCATC
1 ATAATCATAACATGCATC
27956 ATACATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (20 bp):
ATAATCATAACATGCATCGT
Found at i:28025 original size:11 final size:11
Alignment explanation
Indices: 27964--28017 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
27954 TCATACATAT
27964 TATATAT-ATA
1 TATATATAATA
*
27974 TATATATATTA
1 TATATATAATA
27985 TA-AT-TAAGTA
1 TATATATAA-TA
*
27995 TAATGTATAATA
1 T-ATATATAATA
28007 TATATATAATA
1 TATATATAATA
28018 AGTATATACT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
9 2 0.06
10 12 0.34
11 14 0.40
12 4 0.11
13 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (11 bp):
TATATATAATA
Found at i:29456 original size:15 final size:14
Alignment explanation
Indices: 29432--29461 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
29422 TATTTTAATC
29432 AAATATAAATTTAT
1 AAATATAAATTTAT
29446 AAATAATAAATTTAT
1 AAAT-ATAAATTTAT
29461 A
1 A
29462 TTTAATCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATATAAATTTAT
Found at i:29466 original size:37 final size:38
Alignment explanation
Indices: 29396--29490 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 38
29386 ATCTTACTCG
* *
29396 AATATAAATTTGT-AATAATATATACATATTTTAATCA
1 AATATAAATTTATAAATAATAAATACATATTTTAATCA
**
29433 AATATAAATTTATAAATAATAAATTTATA-TTTAATCA
1 AATATAAATTTATAAATAATAAATACATATTTTAATCA
29470 AATATAAATTTATAAATAATA
1 AATATAAATTTATAAATAATA
29491 TTTTCTTATT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
37 41 0.77
38 12 0.23
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (38 bp):
AATATAAATTTATAAATAATAAATACATATTTTAATCA
Found at i:29467 original size:15 final size:15
Alignment explanation
Indices: 29436--29486 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
29426 TTAATCAAAT
**
29436 ATAAATTTATAAATA
1 ATAAATTTATATTTA
29451 ATAAATTTATATTTA
1 ATAAATTTATATTTA
* *
29466 ATCAAATATAAATTT-
1 AT-AAATTTATATTTA
29481 ATAAAT
1 ATAAAT
29487 AATATTTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
14 4 0.13
15 17 0.55
16 10 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAAATTTATATTTA
Found at i:29489 original size:22 final size:23
Alignment explanation
Indices: 29446--29489 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
29436 ATAAATTTAT
**
29446 AAATAATAAATTTATATTTAATC
1 AAATAATAAATTTATAAATAATC
29469 AAAT-ATAAATTTATAAATAAT
1 AAATAATAAATTTATAAATAAT
29490 ATTTTCTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATAATAAATTTATAAATAATC
Found at i:29501 original size:37 final size:37
Alignment explanation
Indices: 29396--29556 Score: 148
Period size: 38 Copynumber: 4.3 Consensus size: 37
29386 ATCTTACTCG
* * *
29396 AATATAAATTTGT-AATAATATATACATATTTTAATCA
1 AATATAAATTTATAAATAATATTTTCATA-TTTAATCA
*
29433 AATATAAATTTATAAATAATAAATTT-ATATTTAATCA
1 AATATAAATTTATAAATAAT-ATTTTCATATTTAATCA
*
29470 AATATAAATTTATAAATAATATTTTCTTATTTCAAT-A
1 AATATAAATTTATAAATAATATTTTCATATTT-AATCA
** * * * **
29507 GAATATAAATCCATAAATAAAATATTCAAATTTCAATGG
1 -AATATAAATTTATAAATAATATTTTCATATTT-AATCA
29546 AATATAAATTT
1 AATATAAATTT
29557 TCTCCCCTTC
Statistics
Matches: 103, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
36 4 0.04
37 46 0.45
38 51 0.50
39 2 0.02
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (37 bp):
AATATAAATTTATAAATAATATTTTCATATTTAATCA
Found at i:32316 original size:3 final size:3
Alignment explanation
Indices: 32308--32336 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
32298 AATAGATTAA
32308 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
32337 ATATATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:32691 original size:24 final size:24
Alignment explanation
Indices: 32659--32706 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
32649 GGACAACTGG
* *
32659 TTATCTATAGGTGTCACGATTCCT
1 TTATCTATAGGTGACACGAATCCT
*
32683 TTATCTATATGTGACACGAATCCT
1 TTATCTATAGGTGACACGAATCCT
32707 ACGTGATGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Consensus pattern (24 bp):
TTATCTATAGGTGACACGAATCCT
Found at i:32753 original size:40 final size:40
Alignment explanation
Indices: 32703--32841 Score: 127
Period size: 40 Copynumber: 3.4 Consensus size: 40
32693 GTGACACGAA
32703 TCCTACGTGATGAGGAGGTCTGGTCGATGGATGACACAGT
1 TCCTACGTGATGAGGAGGTCTGGTCGATGGATGACACAGT
* * * * * * **
32743 TCCTATGTGATGAGGATGACAGGTTATC-TTGGGGTGACACAAC
1 TCCTACGTGATGAGGAGGTCTGG---TCGAT-GGATGACACAGT
* **
32786 TCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAGT
1 TCCTACGTGATGAGGAGGTCTGGTCGATGGATGACACAGT
*
32826 TCCTACGCGATGAGGA
1 TCCTACGTGATGAGGA
32842 TAGTTGTCCA
Statistics
Matches: 75, Mismatches: 19, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
40 45 0.60
42 1 0.01
43 29 0.39
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.24
Consensus pattern (40 bp):
TCCTACGTGATGAGGAGGTCTGGTCGATGGATGACACAGT
Found at i:33108 original size:38 final size:37
Alignment explanation
Indices: 33052--33123 Score: 94
Period size: 36 Copynumber: 1.9 Consensus size: 37
33042 ACAATTTCAG
*
33052 AATTTGTATTTTAAAGAAA-AATTGTCTCAAGTGAGAAGA
1 AATTTGTATTTGAAAGAAACAA---TCTCAAGTGAGAAGA
33091 AATTTGT-TTTGAAAGAAACAATCTCAAGTGAGA
1 AATTTGTATTTGAAAGAAACAATCTCAAGTGAGA
33124 TTAATTTTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
36 12 0.39
38 10 0.32
39 9 0.29
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (37 bp):
AATTTGTATTTGAAAGAAACAATCTCAAGTGAGAAGA
Found at i:33158 original size:102 final size:99
Alignment explanation
Indices: 33020--33210 Score: 231
Period size: 102 Copynumber: 1.9 Consensus size: 99
33010 AGTCGAAGAT
* * * * **
33020 GATTAATTTTGTTTCCAGTGAAACAATTTCAGAATTTGTATTTTAAAGAAAAATTGTCTCAAGTG
1 GATTAATTTTGCTTCAAGTAAAACAATCTCAGAATTTGTATTCCAAAGAAAAA-TGTCTCAAGTG
33085 AGAAGAAATTTGTTTTGAAAGAAACAATCTCAAGTGA
65 AGAAGAAATTTGTTTT--AAGAAACAATCTCAAGTGA
* * * * *
33122 GATTAATTTTGCTTCAAGTAAAACAA-CTCTGAAATTTGTGTTCCGAGGGAAAATGTCTCAAGTG
1 GATTAATTTTGCTTCAAGTAAAACAATCTCAG-AATTTGTATTCCAAAGAAAAATGTCTCAAGTG
*
33186 AGACGAAATTTGTTTTAAGAAACAA
65 AGAAGAAATTTGTTTTAAGAAACAA
33211 CTGTCTCAAG
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
99 9 0.12
101 29 0.38
102 38 0.50
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (99 bp):
GATTAATTTTGCTTCAAGTAAAACAATCTCAGAATTTGTATTCCAAAGAAAAATGTCTCAAGTGA
GAAGAAATTTGTTTTAAGAAACAATCTCAAGTGA
Found at i:33625 original size:16 final size:16
Alignment explanation
Indices: 33604--33637 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
33594 TTCATGTATC
*
33604 ATGTATGTATGTGTTG
1 ATGTATGTATATGTTG
33620 ATGTATGTATATGTTG
1 ATGTATGTATATGTTG
33636 AT
1 AT
33638 CTGTGAGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (16 bp):
ATGTATGTATATGTTG
Found at i:38094 original size:13 final size:13
Alignment explanation
Indices: 38076--38108 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
38066 CTCAAAACAT
38076 GTCCAATTTTGAA
1 GTCCAATTTTGAA
38089 GTCCAATTTTGAA
1 GTCCAATTTTGAA
*
38102 GACCAAT
1 GTCCAAT
38109 AAAATCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (13 bp):
GTCCAATTTTGAA
Found at i:39184 original size:3 final size:3
Alignment explanation
Indices: 39176--39279 Score: 137
Period size: 3 Copynumber: 36.0 Consensus size: 3
39166 CCATTTGCTT
* *
39176 TTA TTA TTA TTA ATA ATA TTA TTA TTA TT- TTA TT- TGT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
*
39219 CTA TTA TTA TT- TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39265 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
39280 CCAACATGCC
Statistics
Matches: 92, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
2 8 0.09
3 84 0.91
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:40562 original size:21 final size:22
Alignment explanation
Indices: 40516--40568 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
40506 AATTACAAGT
*
40516 TTTATTACAG-TTTATATTTCA
1 TTTATTAAAGTTTTATATTTCA
* *
40537 -ATATTATAGTTTTA-ATTTCA
1 TTTATTAAAGTTTTATATTTCA
40557 TTTATTAAAGTT
1 TTTATTAAAGTT
40569 ATTGTTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.57
Consensus pattern (22 bp):
TTTATTAAAGTTTTATATTTCA
Found at i:41518 original size:2 final size:2
Alignment explanation
Indices: 41506--41551 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
41496 CTTATGGTTT
41506 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41549 TA T
1 TA T
41552 CTTTTTATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44802 original size:15 final size:15
Alignment explanation
Indices: 44782--44813 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
44772 GATTAATACC
44782 TTTTGCATACATTCA
1 TTTTGCATACATTCA
*
44797 TTTTGCATGCATTCA
1 TTTTGCATACATTCA
44812 TT
1 TT
44814 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.19, G:0.09, T:0.50
Consensus pattern (15 bp):
TTTTGCATACATTCA
Found at i:58275 original size:20 final size:20
Alignment explanation
Indices: 58250--58298 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
58240 TACAAAAAAC
58250 CTAAATCCCTAAAATCATCT
1 CTAAATCCCTAAAATCATCT
58270 CTAAATCCCTAAAATCATCT
1 CTAAATCCCTAAAATCATCT
58290 CTAAATCCC
1 CTAAATCCC
58299 AAACCCTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.29
Consensus pattern (20 bp):
CTAAATCCCTAAAATCATCT
Found at i:58468 original size:27 final size:28
Alignment explanation
Indices: 58438--58490 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
58428 GTAATAAAAG
*
58438 TTTTC-AAAGTTTTGGGTTTTTTTTAGA
1 TTTTCAAAAGTTTTGAGTTTTTTTTAGA
58465 TTTTCAAAAGTTTTGAGTTTTTTTTA
1 TTTTCAAAAGTTTTGAGTTTTTTTTA
58491 AATAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.21, C:0.04, G:0.15, T:0.60
Consensus pattern (28 bp):
TTTTCAAAAGTTTTGAGTTTTTTTTAGA
Found at i:58733 original size:27 final size:27
Alignment explanation
Indices: 58703--58759 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
58693 AAGCCAATTA
*
58703 TTAATTATAATCATT-AGATTAATAAAT
1 TTAATTATAATAATTGA-ATTAATAAAT
*
58730 TTAATTATGATAATTGAATTAATAAAT
1 TTAATTATAATAATTGAATTAATAAAT
58757 TTA
1 TTA
58760 TTTTTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (27 bp):
TTAATTATAATAATTGAATTAATAAAT
Found at i:58774 original size:40 final size:39
Alignment explanation
Indices: 58725--58830 Score: 117
Period size: 40 Copynumber: 2.7 Consensus size: 39
58715 ATTAGATTAA
*
58725 TAAATTTAATTATGATAATT-GAATTAATAAATTTA-TTTT
1 TAAA-TTAATTATGATAATTAG-ATTAATAAATTTACTTTC
** *
58764 TATATATTAATTATGACCATTAGATTAGTAAATTTACTTTC
1 TA-A-ATTAATTATGATAATTAGATTAATAAATTTACTTTC
*
58805 TAAATTAATTATGATTATTAGATTAA
1 TAAATTAATTATGATAATTAGATTAA
58831 ATAATTATTA
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 22 0.39
40 27 0.48
41 7 0.12
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.48
Consensus pattern (39 bp):
TAAATTAATTATGATAATTAGATTAATAAATTTACTTTC
Found at i:58867 original size:28 final size:28
Alignment explanation
Indices: 58824--58893 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 28
58814 TATGATTATT
58824 AGATTAAATAATTATTAAA-AAATTTTACA
1 AGATT-AA-AATTATTAAATAAATTTTACA
* **
58853 ATGATTAAAATTATTAAATTAATTTTATT
1 A-GATTAAAATTATTAAATAAATTTTACA
58882 AGATTAAAATTA
1 AGATTAAAATTA
58894 GATTATATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 21 0.58
29 11 0.31
30 4 0.11
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (28 bp):
AGATTAAAATTATTAAATAAATTTTACA
Found at i:66228 original size:14 final size:15
Alignment explanation
Indices: 66204--66232 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
66194 AACTTAAGCG
66204 TCTTCTTCTTTTTTT
1 TCTTCTTCTTTTTTT
66219 TCTT-TTCTTTTTTT
1 TCTTCTTCTTTTTTT
66233 AATTTCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TCTTCTTCTTTTTTT
Found at i:67768 original size:19 final size:19
Alignment explanation
Indices: 67746--67807 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
67736 TTAGTTATTT
67746 TTAGGGTTTAAATCTAAGG
1 TTAGGGTTTAAATCTAAGG
* * * ***
67765 TTAGGATTATTAGT-TATTT
1 TTAGGGTT-TAAATCTAAGG
67784 TTAGGGTTTAAATCTAAGG
1 TTAGGGTTTAAATCTAAGG
67803 TTAGG
1 TTAGG
67808 ATTATAAGTA
Statistics
Matches: 29, Mismatches: 12, Indels: 4
0.64 0.27 0.09
Matches are distributed among these distances:
18 3 0.10
19 23 0.79
20 3 0.10
ACGTcount: A:0.29, C:0.03, G:0.24, T:0.44
Consensus pattern (19 bp):
TTAGGGTTTAAATCTAAGG
Found at i:67771 original size:38 final size:38
Alignment explanation
Indices: 67727--67849 Score: 210
Period size: 38 Copynumber: 3.2 Consensus size: 38
67717 ACACAGACAA
67727 TTAGGATTATTAGTTATTTTTAGGGTTTAAATCTAAGG
1 TTAGGATTATTAGTTATTTTTAGGGTTTAAATCTAAGG
67765 TTAGGATTATTAGTTATTTTTAGGGTTTAAATCTAAGG
1 TTAGGATTATTAGTTATTTTTAGGGTTTAAATCTAAGG
* * *
67803 TTAGGATTATAAGTAATCTTTAGGGTTTAAATCTAAGG
1 TTAGGATTATTAGTTATTTTTAGGGTTTAAATCTAAGG
*
67841 CTAGGATTA
1 TTAGGATTA
67850 AAACTTTATT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 81 1.00
ACGTcount: A:0.31, C:0.04, G:0.21, T:0.44
Consensus pattern (38 bp):
TTAGGATTATTAGTTATTTTTAGGGTTTAAATCTAAGG
Found at i:69021 original size:31 final size:31
Alignment explanation
Indices: 68979--69071 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
68969 CAGAACGTGT
*
68979 GCATGTCAATATCATTAGGACAGAGAGACTA
1 GCATGTTAATATCATTAGGACAGAGAGACTA
69010 GCATGTTAATATCATTAGGACAGAGAGACTA
1 GCATGTTAATATCATTAGGACAGAGAGACTA
*
69041 GCATGTTAATATCATTAGGACAGAGGGACTA
1 GCATGTTAATATCATTAGGACAGAGAGACTA
69072 TTAACTGAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.25
Consensus pattern (31 bp):
GCATGTTAATATCATTAGGACAGAGAGACTA
Found at i:70270 original size:11 final size:11
Alignment explanation
Indices: 70248--70285 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
70238 GTAACAGTTC
70248 AATAA-AATTT
1 AATAATAATTT
*
70258 AATAATTATTT
1 AATAATAATTT
70269 AATAATAATTT
1 AATAATAATTT
70280 AATAAT
1 AATAAT
70286 CATGAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 5 0.20
11 20 0.80
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AATAATAATTT
Found at i:73416 original size:27 final size:27
Alignment explanation
Indices: 73378--73451 Score: 139
Period size: 27 Copynumber: 2.7 Consensus size: 27
73368 TTTCTGTAAC
*
73378 CATATACAATATACATATATATTTCTT
1 CATATGCAATATACATATATATTTCTT
73405 CATATGCAATATACATATATATTTCTT
1 CATATGCAATATACATATATATTTCTT
73432 CATATGCAATATACATATAT
1 CATATGCAATATACATATAT
73452 CATGCAGAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.42
Consensus pattern (27 bp):
CATATGCAATATACATATATATTTCTT
Found at i:74839 original size:33 final size:33
Alignment explanation
Indices: 74801--74894 Score: 154
Period size: 33 Copynumber: 2.9 Consensus size: 33
74791 ACGATGATTG
* *
74801 AAATACTTAAATACTTTCAAGTTTGATAAATTC
1 AAATACTTAAAAACTTTCAAGTTCGATAAATTC
*
74834 AAATACTTAAAAACTTCCAAGTTCGATAAATTC
1 AAATACTTAAAAACTTTCAAGTTCGATAAATTC
74867 AAATACTTAAAAAC-TTCAAGTTCGATAA
1 AAATACTTAAAAACTTTCAAGTTCGATAA
74895 TTGAAACAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 13 0.23
33 44 0.77
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.33
Consensus pattern (33 bp):
AAATACTTAAAAACTTTCAAGTTCGATAAATTC
Found at i:74913 original size:21 final size:21
Alignment explanation
Indices: 74889--74930 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
74879 ACTTCAAGTT
74889 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
74910 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
74931 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:81510 original size:10 final size:10
Alignment explanation
Indices: 81495--81519 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
81485 AAAATTAAAA
81495 TTTAATATTT
1 TTTAATATTT
81505 TTTAATATTT
1 TTTAATATTT
81515 TTTAA
1 TTTAA
81520 AATTAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTAATATTT
Found at i:81609 original size:11 final size:10
Alignment explanation
Indices: 81591--81625 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
81581 TTGTATTGAA
81591 TTTTATTCAT
1 TTTTATTCAT
81601 TTTTAATTCAT
1 TTTT-ATTCAT
*
81612 TTTTATTTAT
1 TTTTATTCAT
81622 TTTT
1 TTTT
81626 TAAAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTATTCAT
Found at i:90912 original size:29 final size:29
Alignment explanation
Indices: 90878--90936 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
90868 CCTAAATTAA
90878 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
*
90907 TTTGATGTCATTGTTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
90936 T
1 T
90937 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:99625 original size:21 final size:21
Alignment explanation
Indices: 99586--99625 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
99576 TCGTTTTTCA
*
99586 ATTTTGAAATATCATTTTTGT
1 ATTTTGAAATATCAGTTTTGT
99607 ATTTTGAAAATAT-AGTTTT
1 ATTTTG-AAATATCAGTTTT
99626 ATAATCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.55
Consensus pattern (21 bp):
ATTTTGAAATATCAGTTTTGT
Found at i:103321 original size:29 final size:29
Alignment explanation
Indices: 103287--103342 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
103277 CCTAAATTAA
103287 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
103316 TTTGATGTCATTGCTTACATCAATTTA
1 TTTGATGTCATTGCTTACATCAATTTA
103343 ATTAGGTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.48
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:103408 original size:11 final size:11
Alignment explanation
Indices: 103392--103443 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
103382 TAATGGTTTA
103392 GATTATTTAGT
1 GATTATTTAGT
*
103403 GATTATTTTAAT
1 GATTA-TTTAGT
*
103415 GAGTAGTTTA--
1 GATTA-TTTAGT
103425 GATTATTTAGT
1 GATTATTTAGT
103436 GATTATTT
1 GATTATTT
103444 TAATGAGTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 4 0.12
10 4 0.12
11 13 0.38
12 13 0.38
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (11 bp):
GATTATTTAGT
Found at i:103429 original size:33 final size:33
Alignment explanation
Indices: 103387--103461 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
103377 AATTTTAATG
103387 GTTTAGATTATTTAGTGATTATTTTAATGAGTA
1 GTTTAGATTATTTAGTGATTATTTTAATGAGTA
*
103420 GTTTAGATTATTTAGTGATTATTTTAATGAGTG
1 GTTTAGATTATTTAGTGATTATTTTAATGAGTA
103453 GTTTAGATT
1 GTTTAGATT
103462 GTTTCTTGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.28, C:0.00, G:0.20, T:0.52
Consensus pattern (33 bp):
GTTTAGATTATTTAGTGATTATTTTAATGAGTA
Found at i:106608 original size:22 final size:22
Alignment explanation
Indices: 106583--106902 Score: 376
Period size: 22 Copynumber: 14.6 Consensus size: 22
106573 CTAATTTAAA
*
106583 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
106605 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
106627 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
106649 ATTTATTTTAAAATAT-AAAAA
1 ATTTATTTTAAAATATGGATTG
* ***
106670 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
*
106692 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
* **
106714 ATTTGTTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
* *
106735 ATTTTATTTTAAAATATAGATTT
1 A-TTTATTTTAAAATATGGATTG
* *
106758 TTTTATTTTAAAATATGGATTA
1 ATTTATTTTAAAATATGGATTG
**
106780 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
106801 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
* * ***
106824 ATTTATTTTAAATTATGAAAAA
1 ATTTATTTTAAAATATGGATTG
106846 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
106868 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
106890 ATTTATTTTAAAA
1 ATTTATTTTAAAA
106903 AATTTATTAT
Statistics
Matches: 259, Mismatches: 34, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
21 20 0.08
22 238 0.92
23 1 0.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:106961 original size:31 final size:31
Alignment explanation
Indices: 106926--106984 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
106916 AGTTGTATGG
106926 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTATAAAACTAAA
*
106957 ATTATTTAAATTTCAGTATTGTAAAACT
1 ATTATTTAAATTTCAGTATTATAAAACT
106985 CTTTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTATAAAACTAAA
Found at i:109011 original size:18 final size:21
Alignment explanation
Indices: 108988--109031 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 21
108978 GTGCAAAAGA
*
108988 TTGTGGCTC-AAA-CACTTT-
1 TTGTGGATCTAAATCACTTTC
109006 TTGTGGATCTAAATCACTTTC
1 TTGTGGATCTAAATCACTTTC
109027 TTGTG
1 TTGTG
109032 TGTATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 3 0.14
20 6 0.27
21 5 0.23
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.43
Consensus pattern (21 bp):
TTGTGGATCTAAATCACTTTC
Found at i:110265 original size:20 final size:19
Alignment explanation
Indices: 110240--110293 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
110230 GCGAAATAAA
110240 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
110260 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
110280 AATCGCAACGCGAT
1 AATCGCAACGCGAT
110294 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:110304 original size:21 final size:20
Alignment explanation
Indices: 110280--110435 Score: 86
Period size: 20 Copynumber: 7.6 Consensus size: 20
110270 CAGTTCCCAG
110280 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
110300 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
110321 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTAT-GAA
*
110343 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
110363 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
* *
110383 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAA
* * *
110403 TATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGATTATG-AA
110424 AATCGCAACGCG
1 AATCGCAACGCG
110436 TATCCGTAAA
Statistics
Matches: 102, Mismatches: 22, Indels: 22
0.70 0.15 0.15
Matches are distributed among these distances:
19 2 0.02
20 50 0.49
21 46 0.45
22 3 0.03
23 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:110368 original size:20 final size:20
Alignment explanation
Indices: 110343--110577 Score: 201
Period size: 20 Copynumber: 11.7 Consensus size: 20
110333 GATTTTCCAG
* *
110343 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
110363 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
110383 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
*
110402 CTATCGCAACGAC-AATACGTAA
1 -AATCGCAACG-CGAATACGT-A
* *
110424 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
**
110444 AATCGCAACTAGAATACGTA
1 AATCGCAACGCGAATACGTA
* *
110464 AATCGCAATGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
*
110484 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
110504 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
110524 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
110545 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
110565 AATCGCAACGCGA
1 AATCGCAACGCGA
110578 TTTTTAAAGC
Statistics
Matches: 171, Mismatches: 33, Indels: 22
0.76 0.15 0.10
Matches are distributed among these distances:
18 1 0.01
19 3 0.02
20 129 0.75
21 36 0.21
22 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:110507 original size:121 final size:121
Alignment explanation
Indices: 110343--110573 Score: 331
Period size: 121 Copynumber: 1.9 Consensus size: 121
110333 GATTTTCCAG
* * * *
110343 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCG-ATTC-TGACTAT
1 AATCGCAACGCGAATATGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCGT-A-AAT
110406 CGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACTAGAATACGTA
64 CGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACTAGAATACGTA
* * * * * * *
110464 AATCGCAATGCGTATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCG
1 AATCGCAACGCGAATATGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCGTAAATCG
110529 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAAC
66 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAAC
110574 GCGATTTTTA
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
121 92 0.95
122 4 0.04
123 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (121 bp):
AATCGCAACGCGAATATGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCGTAAATCG
CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACTAGAATACGTA
Found at i:111110 original size:20 final size:20
Alignment explanation
Indices: 111085--111154 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
111075 TTAAATTAAT
111085 GCAACACGAAAATGACTATC
1 GCAACACGAAAATGACTATC
*
111105 GCAACACGAAAATGACTATA
1 GCAACACGAAAATGACTATC
* **
111125 GCAACGCG-AAATGAAAATC
1 GCAACACGAAAATGACTATC
*
111144 GCAACGCGAAA
1 GCAACACGAAA
111155 TTAAAATCGC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 16 0.36
20 28 0.64
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (20 bp):
GCAACACGAAAATGACTATC
Found at i:111138 original size:19 final size:19
Alignment explanation
Indices: 111094--111155 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
111084 TGCAACACGA
*
111094 AAATGACTATCGCAACACG
1 AAATGACTATCGCAACGCG
*
111113 AAAATGACTATAGCAACGCG
1 -AAATGACTATCGCAACGCG
**
111133 AAATGAAAATCGCAACGCG
1 AAATGACTATCGCAACGCG
111152 AAAT
1 AAAT
111156 TAAAATCGCA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 20 0.54
20 17 0.46
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.15
Consensus pattern (19 bp):
AAATGACTATCGCAACGCG
Found at i:111160 original size:19 final size:19
Alignment explanation
Indices: 111102--111168 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
111092 GAAAATGACT
* **
111102 ATCGCAACACGAAAATGACT
1 ATCGCAACGCG-AAATGAAA
*
111122 ATAGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
111141 ATCGCAACGCGAAATTAAA
1 ATCGCAACGCGAAATGAAA
111160 ATCGCAACG
1 ATCGCAACG
111169 ATTTTGGTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 32 0.78
20 9 0.22
ACGTcount: A:0.46, C:0.22, G:0.18, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:111269 original size:20 final size:20
Alignment explanation
Indices: 111207--111262 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
111197 TCGCGTTGCT
111207 ATTCTCTCATTGCGATAGTC
1 ATTCTCTCATTGCGATAGTC
* *
111227 ATT-TCCGCGTTGCGATAGTC
1 ATTCT-CTCATTGCGATAGTC
111247 ATTCTCTCATTGCGAT
1 ATTCTCTCATTGCGAT
111263 TTTCATTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTCTCTCATTGCGATAGTC
Found at i:113180 original size:21 final size:21
Alignment explanation
Indices: 113156--113222 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
113146 TCATTCTTTG
113156 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
113177 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
113198 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
113219 AGAG
1 AGAG
113223 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:113180 original size:42 final size:42
Alignment explanation
Indices: 113113--113222 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
113103 GTCATCCCTC
* * * * * *
113113 AAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCTTTG
1 AAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCA-TCGTTG
*
113156 -AGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCATCGTTG
1 AAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATCGTTG
*
113197 AAGAGGT-CCCTCCCACCATTCAAGAG
1 AAGA-GTCCCCTCCCACCGTTCAAGAG
113223 CCCGATTCAC
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
41 5 0.09
42 50 0.88
43 2 0.04
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.24
Consensus pattern (42 bp):
AAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATCGTTG
Found at i:114595 original size:14 final size:14
Alignment explanation
Indices: 114576--114611 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
114566 ATTGTTTAAT
114576 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
114590 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
114604 TGATTTGT
1 TGATTTGT
114612 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:114761 original size:18 final size:18
Alignment explanation
Indices: 114738--114773 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
114728 GAAATGAAAA
114738 TCGCAACGAGAGAATCGC
1 TCGCAACGAGAGAATCGC
*
114756 TCGCAACGAGGGAATCGC
1 TCGCAACGAGAGAATCGC
114774 AAAGCGAAAT
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:0.31, C:0.28, G:0.31, T:0.11
Consensus pattern (18 bp):
TCGCAACGAGAGAATCGC
Found at i:114893 original size:20 final size:19
Alignment explanation
Indices: 114825--114908 Score: 105
Period size: 20 Copynumber: 4.3 Consensus size: 19
114815 GCGATTTTGT
*
114825 CATTGCGATTTTCATTTCT
1 CATTGCGATTTTCATTTCG
**
114844 CATTGCGATAGTCATTTTCG
1 CATTGCGATTTTCA-TTTCG
*
114864 CGTTGCGATTTTCATATTCG
1 CATTGCGATTTTCAT-TTCG
*
114884 CGTTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
114903 CATTGC
1 CATTGC
114909 AATTCTCTCG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
19 22 0.39
20 34 0.61
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:114902 original size:39 final size:39
Alignment explanation
Indices: 114825--114908 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 39
114815 GCGATTTTGT
*
114825 CATTGCGATTTTCATTTCTCATTGCGATAGTCATTTTCG
1 CATTGCGATTTTCATTTCGCATTGCGATAGTCATTTTCG
* * **
114864 CGTTGCGATTTTCATATTCGCGTTGCGATTTTCA-TTTCG
1 CATTGCGATTTTCAT-TTCGCATTGCGATAGTCATTTTCG
114903 CATTGC
1 CATTGC
114909 AATTCTCTCG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 24 0.63
40 14 0.37
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.45
Consensus pattern (39 bp):
CATTGCGATTTTCATTTCGCATTGCGATAGTCATTTTCG
Found at i:114991 original size:20 final size:20
Alignment explanation
Indices: 114918--114991 Score: 53
Period size: 20 Copynumber: 3.6 Consensus size: 20
114908 CAATTCTCTC
* *
114918 GTTGCGATAGTAATTTCCGC
1 GTTGCGATAGTCATTTCCGT
* * **
114938 GTTGTGATAGACA-TTAAGAT
1 GTTGCGATAGTCATTTCCG-T
114958 GATTGCGA-ACGTCATTTCCGT
1 G-TTGCGATA-GTCATTTCCGT
114979 GTTGCGATAGTCA
1 GTTGCGATAGTCA
114992 AATGAATGCC
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
19 3 0.08
20 22 0.56
21 11 0.28
22 3 0.08
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:117469 original size:24 final size:24
Alignment explanation
Indices: 117442--117488 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
117432 CGAAATCCGA
117442 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
117466 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
117489 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:117497 original size:24 final size:24
Alignment explanation
Indices: 117446--117497 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
117436 ATCCGAGTAT
** *
117446 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
117470 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
117494 TGAC
1 TGAC
117498 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:118360 original size:20 final size:20
Alignment explanation
Indices: 118344--118409 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
118334 CAGAATCTCG
118344 TTGCGATTTACTAAATCGCA
1 TTGCGATTTACTAAATCGCA
*
118364 TTGCGATTTACGT-AATCGCT
1 TTGCGATTTAC-TAAATCGCA
* *
118384 TTGAGATTTACGT-ATTCGCA
1 TTGCGATTTAC-TAAATCGCA
118404 TTGCGA
1 TTGCGA
118410 ATTAGGAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 39 0.98
21 1 0.03
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACTAAATCGCA
Found at i:118425 original size:21 final size:21
Alignment explanation
Indices: 118399--118472 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
118389 ATTTACGTAT
*
118399 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* *
118420 TCGCATTGTGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* * *
118441 TCGCAACGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGGAAAA
*
118462 TCACAATGCGA
1 TCGCAATGCGA
118473 TAGTCAGAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:119042 original size:18 final size:18
Alignment explanation
Indices: 118998--119042 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
118988 TTAAAATTAT
118998 ATTAATTAAAATAATATAA
1 ATTAATT-AAATAATATAA
*
119017 ATTGATTAAATAAT-TAA
1 ATTAATTAAATAATATAA
119034 ATTTAATTA
1 A-TTAATTA
119043 TTTATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.17
18 13 0.57
19 6 0.26
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
ATTAATTAAATAATATAA
Found at i:123304 original size:3 final size:3
Alignment explanation
Indices: 123296--123378 Score: 98
Period size: 3 Copynumber: 27.3 Consensus size: 3
123286 TTAAATAAGA
* * *
123296 AAT AAT AAT AAT AAAT AA- AAT AAT TAC AAT AAT AAT AAAT GAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
123342 AAAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT A
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
123379 TATATATAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
2 4 0.06
3 56 0.81
4 9 0.13
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:123349 original size:44 final size:44
Alignment explanation
Indices: 123299--123390 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
123289 AATAAGAAAT
*
123299 AATAATAATAAATAA-AATAATTACAATAATAATAA-ATGATA-ATA
1 AATAATAAT-AATAATAATAATAACAAT-ATAATAATAT-ATATATA
*
123343 AATAATAATAATAATAATAATAATAATATAATAATATATATATA
1 AATAATAATAATAATAATAATAACAATATAATAATATATATATA
123387 AATA
1 AATA
123391 TTTTAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
43 15 0.35
44 28 0.65
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (44 bp):
AATAATAATAATAATAATAATAACAATATAATAATATATATATA
Found at i:123467 original size:27 final size:26
Alignment explanation
Indices: 123433--123484 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
123423 ATGTTTTTTT
123433 AATTATATAACATATATATTTTAAAAA
1 AATTATATAACATATAT-TTTTAAAAA
**
123460 AATTATATATTATATATTTTTAAAA
1 AATTATATAACATATATTTTTAAAA
123485 TATTTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
AATTATATAACATATATTTTTAAAAA
Found at i:123510 original size:62 final size:61
Alignment explanation
Indices: 123375--123512 Score: 140
Period size: 61 Copynumber: 2.3 Consensus size: 61
123365 ATAATATAAT
* * * * *
123375 AATATATATATAAATATTTTAAAAAACATATAATATATAATTTCCAAAATGTTTTTTTAAT
1 AATATATACATATATATTTTAAAAAACATATAATATATAATTTCCAAAATATTTTTTAAAA
* **
123436 TATATA-ACATATATATTTTAAAAAA-AT-TATATATTATATATTTTTAAAATATTTTTTAAAA
1 AATATATACATATATATTTTAAAAAACATATA-ATA-TATA-ATTTCCAAAATATTTTTTAAAA
123497 AACTATATA-ATATATA
1 AA-TATATACATATATA
123513 AATGTTTTCC
Statistics
Matches: 63, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
58 2 0.03
59 5 0.08
60 21 0.33
61 23 0.37
62 11 0.17
63 1 0.02
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.46
Consensus pattern (61 bp):
AATATATACATATATATTTTAAAAAACATATAATATATAATTTCCAAAATATTTTTTAAAA
Found at i:123542 original size:38 final size:38
Alignment explanation
Indices: 123495--123598 Score: 124
Period size: 38 Copynumber: 2.7 Consensus size: 38
123485 TATTTTTTAA
*
123495 AAAACTATATAATATATAAATGTTTTC-CAAATG-TTTTC
1 AAAACTATATAATATATAAA--TTTTCAAAAATGTTTTTC
123533 AAAACTATAT-ATCATATAAATTTTCAAAAATGTTTTTC
1 AAAACTATATAAT-ATATAAATTTTCAAAAATGTTTTTC
* **
123571 AAAACTATATATTATATACGTTTTCAAA
1 AAAACTATATAATATATAAATTTTCAAA
123599 TATATATATA
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
36 5 0.09
37 7 0.12
38 45 0.78
39 1 0.02
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (38 bp):
AAAACTATATAATATATAAATTTTCAAAAATGTTTTTC
Found at i:123603 original size:2 final size:2
Alignment explanation
Indices: 123598--123637 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
123588 ACGTTTTCAA
123598 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
123638 CATTTTCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123604 original size:25 final size:26
Alignment explanation
Indices: 123566--123614 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
123556 TCAAAAATGT
123566 TTTTCAAAACTATATAT-TATATACG
1 TTTTCAAAACTATATATATATATACG
123591 TTTTCAAATA-TATATATATATATA
1 TTTTCAAA-ACTATATATATATATA
123615 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (26 bp):
TTTTCAAAACTATATATATATATACG
Found at i:123706 original size:39 final size:37
Alignment explanation
Indices: 123623--123714 Score: 105
Period size: 37 Copynumber: 2.4 Consensus size: 37
123613 TATATATATA
* *
123623 TATATATATATTATACATTTTCAAAATGTTTTCAAAGAC
1 TATATAT-TA-TATATATTTTCAAAATGTTTTCAAAAAC
*
123662 TATATATTATATATATTTTTAAAATGTTTTCGAAAAAAAC
1 TATATATTATATATATTTTCAAAATGTTTTC---AAAAAC
123702 -ATATATTATATAT
1 TATATATTATATAT
123715 CATATAATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
37 20 0.43
38 2 0.04
39 20 0.43
40 5 0.11
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (37 bp):
TATATATTATATATATTTTCAAAATGTTTTCAAAAAC
Found at i:135810 original size:17 final size:18
Alignment explanation
Indices: 135780--135813 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
135770 TGACAAAAAA
135780 TTATTTTTAGAAAATTAT
1 TTATTTTTAGAAAATTAT
135798 TTATTTTTA-AAAATTA
1 TTATTTTTAGAAAATTA
135814 AGTAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TTATTTTTAGAAAATTAT
Found at i:136347 original size:18 final size:17
Alignment explanation
Indices: 136324--136370 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
136314 CGTTTATAAG
136324 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
* *
136342 GGAATTAGAATCTGTCA
1 GGAATTGGAATCTGTAA
*
136359 GGAATTGAAATC
1 GGAATTGGAATC
136371 CAATTCCAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:136705 original size:5 final size:5
Alignment explanation
Indices: 136695--136720 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
136685 ATAAAGTTTC
136695 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
136721 ATATATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:137130 original size:256 final size:257
Alignment explanation
Indices: 136705--137453 Score: 1100
Period size: 256 Copynumber: 2.9 Consensus size: 257
136695 ACCCGACCCG
136705 ACCCGACCCGACCCGAATATATGAATTAGAAACCCGACCCGACCCGAAATAATAAAAAAAATTAT
1 ACCCGACCCGACCCGAATATATGAATTAGAAACCCGA-CCGACCCGAAATAAT-AAAAAAATTAT
*
136770 TTTTATTCAATAAAAACA--G--TTAATTGAAAAAAATTATATATAGAGAGGTATTATTGTAATT
64 TTTTATTCAATAAAAACAGTGACTTAATTG-AAAAAATTATATATAGAGGGGTATTATTGTAATT
* *
136831 ATTTCTAAAAATATAAGGTAAAATTATATATTTTTTCGGGTCGGGTCTGGTATTTTTCACCCTAA
128 ATTCCTAAATATATAAGGTAAAATTATATATTTTTTCGGGTCGGGTCTGGTATTTTTCACCCTAA
* *
136896 ACCCGAACCCGACCCGAATATCACACTTAAAAAAACCGACCCGACCTGACCAAA-ATAAAGTTTC
193 ACCCGAACCCGACCCGAATATCACACTTAAAAAAACCGACCCGACCCGACAAAATATAAAGTTTC
*
136960 CCCCGACCCGACCCGAATATATGAATTAGAAACCCGACTCGACCCGAAATAATAAAAAAATTA-T
1 ACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC-CGACCCGAAATAATAAAAAAATTATT
* *
137024 TTTATTCAATAAAAAAAGTGACTTAATTGAAAAAATTATATATAGAGGGGTATTATTATAATTAT
65 TTTATTCAATAAAAACAGTGACTTAATTGAAAAAATTATATATAGAGGGGTATTATTGTAATTAT
137089 TCCTAAATATATAAGGTAAAATTATATATTTTTTCGGGTCGGGTCGGGTCGGGTATTTTTCACCC
130 TCCTAAATATATAAGGTAAAATTATATATTTTTTCGGGTCGGGTC---T--GGTATTTTTCACCC
* *
137154 TAAACCCGAACCCGACCCGAATATCACACTTAAAAAAA-TGACCCGACCCGATAAAATATAAAGT
190 TAAACCCGAACCCGACCCGAATATCACACTTAAAAAAACCGACCCGACCCGACAAAATATAAAGT
*
137218 TTT
255 TTC
137221 ACCCGACCCGACCCGAATATATGAATTAGAAA--C--CCGACCCGAAATAATAAAAAAA-TATTT
1 ACCCGACCCGACCCGAATATATGAATTAGAAACCCGACCGACCCGAAATAATAAAAAAATTATTT
* *
137281 TTATTCAATAAAAACAGTGACTTAATTGAAAAAATTATATAGAGAGGGGAATTATTGTAATTATT
66 TTATTCAATAAAAACAGTGACTTAATTGAAAAAATTATATATAGAGGGGTATTATTGTAATTATT
*
137346 CCTAAATATATAAGGTAAAATTATATATTTTTTCGGGTC--G---GATATTTTTCACCCTAAACC
131 CCTAAATATATAAGGTAAAATTATATATTTTTTCGGGTCGGGTCTGGTATTTTTCACCCTAAACC
* *
137406 CGAATCCGACTCGACCCGAATACCACACTTAAATAAACCCGACCCGAC
196 CGAA--C--C-CGACCCGAATATCACACTTAAA-AAAACCGACCCGAC
137454 TCGAACCATA
Statistics
Matches: 455, Mismatches: 20, Indels: 40
0.88 0.04 0.08
Matches are distributed among these distances:
246 23 0.05
248 1 0.00
250 1 0.00
251 21 0.05
252 3 0.01
253 25 0.05
254 12 0.03
255 53 0.12
256 200 0.44
257 8 0.02
259 2 0.00
260 14 0.03
261 92 0.20
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (257 bp):
ACCCGACCCGACCCGAATATATGAATTAGAAACCCGACCGACCCGAAATAATAAAAAAATTATTT
TTATTCAATAAAAACAGTGACTTAATTGAAAAAATTATATATAGAGGGGTATTATTGTAATTATT
CCTAAATATATAAGGTAAAATTATATATTTTTTCGGGTCGGGTCTGGTATTTTTCACCCTAAACC
CGAACCCGACCCGAATATCACACTTAAAAAAACCGACCCGACCCGACAAAATATAAAGTTTC
Found at i:138816 original size:25 final size:25
Alignment explanation
Indices: 138788--138865 Score: 115
Period size: 25 Copynumber: 3.2 Consensus size: 25
138778 ATTGATTCAT
138788 AAAAATAAAAGTATCACATTTATTA
1 AAAAATAAAAGTATCACATTTATTA
*
138813 AAAAATAAAAGTATCACATTCA-T-
1 AAAAATAAAAGTATCACATTTATTA
* *
138836 AAAAATAAAAGTATAACAATTATTA
1 AAAAATAAAAGTATCACATTTATTA
138861 AAAAA
1 AAAAA
138866 AAATTAACAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
23 19 0.40
24 2 0.04
25 26 0.55
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.27
Consensus pattern (25 bp):
AAAAATAAAAGTATCACATTTATTA
Found at i:138863 original size:23 final size:23
Alignment explanation
Indices: 138789--138875 Score: 81
Period size: 23 Copynumber: 3.8 Consensus size: 23
138779 TTGATTCATA
* *
138789 AAAATAAAAGTATCACATTTATT
1 AAAATAAAAGTATAACAATTATT
* *
138812 AAAAAATAAAAGTATCAC-ATTCATA
1 --AAAATAAAAGTATAACAATT-ATT
138837 AAAATAAAAGTATAACAATTATT
1 AAAATAAAAGTATAACAATTATT
*
138860 AAAA-AAAAAT-TAACAA
1 AAAATAAAAGTATAACAA
138876 AGTCAGATAC
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
21 6 0.11
22 5 0.09
23 21 0.38
24 5 0.09
25 18 0.33
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.26
Consensus pattern (23 bp):
AAAATAAAAGTATAACAATTATT
Found at i:144475 original size:3 final size:3
Alignment explanation
Indices: 144467--144530 Score: 101
Period size: 3 Copynumber: 21.0 Consensus size: 3
144457 TCATTTTGTT
**
144467 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
144516 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
144531 AATAAATATT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:148628 original size:18 final size:18
Alignment explanation
Indices: 148602--148646 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
148592 TTTACATTCC
* *
148602 ATTTGCATTCGTATTTAT
1 ATTTTCATTCGTATATAT
148620 ATTTTCATTCGTATATAT
1 ATTTTCATTCGTATATAT
148638 ATTTTCATT
1 ATTTTCATT
148647 TTTGCATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.58
Consensus pattern (18 bp):
ATTTTCATTCGTATATAT
Found at i:152019 original size:21 final size:20
Alignment explanation
Indices: 151968--152019 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
151958 TTTTCCCAAT
*
151968 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* * **
151988 TCACAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
152009 TCGCAATGCGA
1 TCGCAATGCGA
152020 TACTGACTAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:152033 original size:20 final size:20
Alignment explanation
Indices: 152008--152101 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
151998 AATTGGGAAA
152008 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
152028 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
152048 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
152069 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
152089 TTCGCAACGCGAT
1 ATCGCAATGCGAT
152102 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:152677 original size:19 final size:19
Alignment explanation
Indices: 152655--152744 Score: 144
Period size: 19 Copynumber: 4.7 Consensus size: 19
152645 GAAACCAAAA
*
152655 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
152674 TCGCGTTTCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
152693 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
152712 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
152732 TCGCGTTGCGATT
1 TCGCGTTGCGATT
152745 GTCTGGTCGC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 47 0.72
20 18 0.28
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.48
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:152736 original size:39 final size:38
Alignment explanation
Indices: 152655--152744 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
152645 GAAACCAAAA
* *
152655 TCGCATTGCGATTTTCATTTCGCGTTTCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
152693 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
152732 TCGCGTTGCGATT
1 TCGCGTTGCGATT
152745 GTCTGGTCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 21 0.44
39 27 0.56
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.48
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:152755 original size:39 final size:39
Alignment explanation
Indices: 152674--152755 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
152664 GATTTTCATT
* * **
152674 TCGC-GTTTCGATTTTCATTTCGCGTTGCGATTTTTATT
1 TCGCGGTTGCGATTTTCATTTCGCGTTGCGATTTCTAGG
152712 TCGCGGTTGCGATTTTCATTTCGCGTTGCGATTGTCT-GG
1 TCGCGGTTGCGATTTTCATTTCGCGTTGCGATT-TCTAGG
152751 TCGCG
1 TCGCG
152756 ATAGTCATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 4 0.11
39 32 0.84
40 2 0.05
ACGTcount: A:0.09, C:0.21, G:0.26, T:0.45
Consensus pattern (39 bp):
TCGCGGTTGCGATTTTCATTTCGCGTTGCGATTTCTAGG
Found at i:152764 original size:33 final size:33
Alignment explanation
Indices: 152727--152811 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
152717 GTTGCGATTT
* * *
152727 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCACGATAG
*
152760 TCATTTCGCGTTGCGATTCTCTCGTTACGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCACGATAG
152793 TCATTTCCGCGTTGCGATT
1 TCATTT-CGCGTTGCGATT
152812 TTCATTTCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 35 0.74
34 12 0.26
ACGTcount: A:0.13, C:0.24, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCACGATAG
Found at i:154840 original size:42 final size:42
Alignment explanation
Indices: 154780--154902 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
154770 GCCCGACTCG
* * *
154780 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
154822 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
154864 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
154903 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:154860 original size:21 final size:21
Alignment explanation
Indices: 154836--154902 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
154826 TCATTCCTCG
154836 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
154857 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
154878 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
154899 AGAG
1 AGAG
154903 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:156280 original size:14 final size:14
Alignment explanation
Indices: 156261--156294 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
156251 ATTGTTTAAT
156261 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
156275 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
156289 TGATTT
1 TGATTT
156295 ATTTAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:156446 original size:18 final size:18
Alignment explanation
Indices: 156423--156458 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
156413 GAAATGAAAA
156423 TCGCAACGAGAGAATCGC
1 TCGCAACGAGAGAATCGC
*
156441 TCGCAACGAGGGAATCGC
1 TCGCAACGAGAGAATCGC
156459 AAAGCGAAAT
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:0.31, C:0.28, G:0.31, T:0.11
Consensus pattern (18 bp):
TCGCAACGAGAGAATCGC
Found at i:156576 original size:39 final size:39
Alignment explanation
Indices: 156529--156616 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 39
156519 GCGATTTTGT
156529 CGTTGCGATTTTCAT-TTCGCATTGCAATAGTCATTTTCG
1 CGTTGCGATTTTCATATTCGCATTGCAATAGTCA-TTTCG
* * **
156568 CGTTGCGATTTTCATATTCGCGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATATTCGCATTGCAATAGTCATTTCG
*
156607 CATTGCGATT
1 CGTTGCGATT
156617 CTCTCGTTGC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 29 0.67
40 14 0.33
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.44
Consensus pattern (39 bp):
CGTTGCGATTTTCATATTCGCATTGCAATAGTCATTTCG
Found at i:156582 original size:20 final size:20
Alignment explanation
Indices: 156491--156616 Score: 117
Period size: 19 Copynumber: 6.8 Consensus size: 20
156481 GCGAATTTAG
*
156491 TTTCGCGTTGCGATTTT-AG
1 TTTCGCGTTGCGATTTTCAT
156510 TTTCGCGTTGCGA--TT--T
1 TTTCGCGTTGCGATTTTCAT
*
156526 TGT--CGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCAT
* * **
156543 TTTCGCATTGCAATAGTCAT
1 TTTCGCGTTGCGATTTTCAT
156563 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
156583 ATTCGCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCAT
*
156602 TTTCGCATTGCGATT
1 TTTCGCGTTGCGATT
156617 CTCTCGTTGC
Statistics
Matches: 86, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
14 8 0.09
16 4 0.05
17 4 0.05
19 36 0.42
20 34 0.40
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.46
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:158938 original size:12 final size:12
Alignment explanation
Indices: 158921--158945 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
158911 TCTTCAGGGA
158921 CTTTTTCTTCTT
1 CTTTTTCTTCTT
158933 CTTTTTCTTCTT
1 CTTTTTCTTCTT
158945 C
1 C
158946 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:159154 original size:24 final size:24
Alignment explanation
Indices: 159120--159173 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
159110 CTGAAACATC
* *
159120 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
159144 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
159168 ATCAAA
1 ATCAAA
159174 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:160295 original size:14 final size:14
Alignment explanation
Indices: 160276--160329 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
160266 GAAAATCGCA
160276 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
160290 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
160307 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
160323 TTGCGAT
1 TTGCGAT
160330 AGACATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:160295 original size:33 final size:33
Alignment explanation
Indices: 160258--160328 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
160248 AAAATGGCTA
160258 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
160291 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
160324 TGCGA
1 TGCGA
160329 TAGACATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:160329 original size:33 final size:33
Alignment explanation
Indices: 160271--160348 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
160261 GAAATGAAAA
***
160271 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGACATT
160304 TCGCATTGCGATTTTCTCGTTGCGATAGACATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGACATT
*
160337 TCGCGTTGCGAT
1 TCGCATTGCGAT
160349 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGACATT
Found at i:160455 original size:14 final size:14
Alignment explanation
Indices: 160436--160472 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
160426 CATCAATTAA
160436 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
160450 ACAAATCATCTTTT
1 ACAAATCAACATTT
160464 ACAAATCAA
1 ACAAATCAA
160473 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:162309 original size:19 final size:20
Alignment explanation
Indices: 162264--162314 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
162254 CACGAAACTT
162264 AAAATCGCAACGCGGAAATG
1 AAAATCGCAACGCGGAAATG
*** *
162284 GCTATCGCAATGC-GAAATG
1 AAAATCGCAACGCGGAAATG
162303 AAAATCGCAACG
1 AAAATCGCAACG
162315 ACAAAATCGC
Statistics
Matches: 23, Mismatches: 8, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACGCGGAAATG
Found at i:162381 original size:14 final size:14
Alignment explanation
Indices: 162362--162419 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
162352 TTTCATTTCG
162362 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
162376 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
162392 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
162408 CGTTGCGATTTT
1 CGTTGCGATTTT
162420 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:162426 original size:33 final size:33
Alignment explanation
Indices: 162345--162435 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
162335 ACAAATCGCA
*
162345 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
162378 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
162410 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
162436 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Done.