Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007744.1 Hibiscus syriacus cultivar Beakdansim tig00110007_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: 4276731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 16
Found at i:547600 original size:21 final size:22
Alignment explanation
Indices: 547543--547611 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 22
547533 AGGGTCTTAT
* *
547543 TGGTCATT-TGGAC-AATTATG
1 TGGTCATTCGGGACAAACTATG
547563 TGGTCATTCGGGACAAA-TATG
1 TGGTCATTCGGGACAAACTATG
547584 TGG-CACTTCGGTG-CAAACCTATG
1 TGGTCA-TTCGG-GACAAA-CTATG
547607 TGGTC
1 TGGTC
547612 CTTTGATATA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
20 10 0.24
21 20 0.49
22 3 0.07
23 7 0.17
24 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (22 bp):
TGGTCATTCGGGACAAACTATG
Found at i:548096 original size:39 final size:38
Alignment explanation
Indices: 548053--548153 Score: 127
Period size: 35 Copynumber: 2.7 Consensus size: 38
548043 TTTTGATATA
*
548053 AAATGGTTATTTTATGAAAAAAGGTTTCATTTACAAATT
1 AAATGGTTATTTTATG-AAAAAGGTTTAATTTACAAATT
** *
548092 AAATGGTTATTTTATG---TTGTTTTAATTTACAAATT
1 AAATGGTTATTTTATGAAAAAGGTTTAATTTACAAATT
*
548127 AAATGGTTATTTTATGAAAGAGGTTTA
1 AAATGGTTATTTTATGAAAAAGGTTTA
548154 TGCTGTTTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
35 31 0.60
38 5 0.10
39 16 0.31
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.46
Consensus pattern (38 bp):
AAATGGTTATTTTATGAAAAAGGTTTAATTTACAAATT
Found at i:553410 original size:20 final size:21
Alignment explanation
Indices: 553356--553415 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
553346 TGGGAAATAA
*
553356 TTAAGGGTAGTATTGATACCTG
1 TTAAGGGTAGTATCGATA-CTG
*
553378 TTGAAGTG-A-TATCGATACTG
1 TT-AAGGGTAGTATCGATACTG
553398 -TAAGGGTAGTATCGATAC
1 TTAAGGGTAGTATCGATAC
553416 ATGAAGGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 4 0.12
19 2 0.06
20 12 0.38
21 7 0.22
22 3 0.09
23 4 0.12
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.33
Consensus pattern (21 bp):
TTAAGGGTAGTATCGATACTG
Found at i:553429 original size:20 final size:20
Alignment explanation
Indices: 553387--553435 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
553377 GTTGAAGTGA
*
553387 TATCGATACTGTAAGGGTAG
1 TATCGATACTGTAAGGATAG
*
553407 TATCGATACATG-AAGGATGG
1 TATCGATAC-TGTAAGGATAG
*
553427 TATCAATAC
1 TATCGATAC
553436 CCTTAAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (20 bp):
TATCGATACTGTAAGGATAG
Found at i:554201 original size:23 final size:23
Alignment explanation
Indices: 554146--554266 Score: 151
Period size: 23 Copynumber: 5.3 Consensus size: 23
554136 TTTGAGAAAG
*
554146 TATGTGGTCCTTCGG-GACAAA--
1 TATGTGGTACTTCGGTG-CAAACC
*
554167 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGTACTTCGGTGCAAACC
554190 TATGTGGTACTTCGGTGCAAACC
1 TATGTGGTACTTCGGTGCAAACC
*
554213 TATGTGGTACTTCGGTGCAAACT
1 TATGTGGTACTTCGGTGCAAACC
* *
554236 TATGT-GTCACTTCAGTGCAAAAC
1 TATGTGGT-ACTTCGGTGCAAACC
554259 TATGTGGT
1 TATGTGGT
554267 TATTCGGGAC
Statistics
Matches: 88, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
21 17 0.19
22 3 0.03
23 66 0.75
24 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (23 bp):
TATGTGGTACTTCGGTGCAAACC
Found at i:556707 original size:23 final size:23
Alignment explanation
Indices: 556652--556772 Score: 151
Period size: 23 Copynumber: 5.3 Consensus size: 23
556642 TTTGAGAAAG
*
556652 TATGTGGTCCTTCGG-GACAAA--
1 TATGTGGTACTTCGGTG-CAAACC
*
556673 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGTACTTCGGTGCAAACC
556696 TATGTGGTACTTCGGTGCAAACC
1 TATGTGGTACTTCGGTGCAAACC
*
556719 TATGTGGTACTTCGGTGCAAACT
1 TATGTGGTACTTCGGTGCAAACC
* *
556742 TATGT-GTCACTTCAGTGCAAAAC
1 TATGTGGT-ACTTCGGTGCAAACC
556765 TATGTGGT
1 TATGTGGT
556773 TATTCGGGAC
Statistics
Matches: 88, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
21 17 0.19
22 3 0.03
23 66 0.75
24 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (23 bp):
TATGTGGTACTTCGGTGCAAACC
Found at i:561838 original size:272 final size:275
Alignment explanation
Indices: 561338--561885 Score: 1066
Period size: 272 Copynumber: 2.0 Consensus size: 275
561328 GTGCCATCAA
561338 ATACTATATTTTTCTTTTCTTTAAATGGATAATTGAACATCATGGGCTTCTCTTTACGAGGTCTC
1 ATACTATA-TTTTCTTTTCTTTAAATGGATAATTGAACATCATGGGCTTCTCTTTACGAGGTCTC
561403 ATAATCAGATGGACACATACCTTGTGTTTTAACAAAGCCTTTAAACACAATATGCATCTCTAATT
65 ATAATCAGATGGACACATACCTTGTGTTTTAACAAAGCCTTTAAACACAATATGCATCTCTAATT
561468 GCAAAAATACTTTATTTTATCCATGTTTGCTTAGAAAAGTTATAAATATATCTGATACATGAATG
130 GCAAAAATACTTTATTTTATCCATGTTTGCTTAGAAAAGTTATAAATATATCTGATACATGAATG
561533 CCTTGATTCTTTGCTATGAATTTTGATATTGGAACATCCTAGACTAAACCATA-TCCTCTTATCA
195 CCTTGATTCTTTGCTATGAATTTTGATATTGGAACATCCTAGACTAAACCATACTCCTCTTATCA
561597 AGGATACCATGTTCTC
260 AGGATACCATGTTCTC
561613 ATACTATA-TTT-TTTTCTTTAAATGGATAATTGAACATCATGGGCTTCTCTTTACGAGGTCTCA
1 ATACTATATTTTCTTTTCTTTAAATGGATAATTGAACATCATGGGCTTCTCTTTACGAGGTCTCA
561676 TAATCAGATGGACACATACCTTGTGTTTTAACAAAGCCTTTAAACACAATATGCATCTCTAATTG
66 TAATCAGATGGACACATACCTTGTGTTTTAACAAAGCCTTTAAACACAATATGCATCTCTAATTG
561741 CAAAAATACTTTATTTTATCCATGTTTGCTTAGAAAAGTTATAAATATATCTGATACATGAATGC
131 CAAAAATACTTTATTTTATCCATGTTTGCTTAGAAAAGTTATAAATATATCTGATACATGAATGC
561806 CTTGATTCTTTGCTATGAATTTTGATATTGGAACATCCTAGACTAAACCATACTCCTCTTATCAA
196 CTTGATTCTTTGCTATGAATTTTGATATTGGAACATCCTAGACTAAACCATACTCCTCTTATCAA
561871 GGATACCATGTTCTC
261 GGATACCATGTTCTC
561886 TCTAGTCTGT
Statistics
Matches: 272, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
272 234 0.86
273 30 0.11
275 8 0.03
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (275 bp):
ATACTATATTTTCTTTTCTTTAAATGGATAATTGAACATCATGGGCTTCTCTTTACGAGGTCTCA
TAATCAGATGGACACATACCTTGTGTTTTAACAAAGCCTTTAAACACAATATGCATCTCTAATTG
CAAAAATACTTTATTTTATCCATGTTTGCTTAGAAAAGTTATAAATATATCTGATACATGAATGC
CTTGATTCTTTGCTATGAATTTTGATATTGGAACATCCTAGACTAAACCATACTCCTCTTATCAA
GGATACCATGTTCTC
Found at i:568423 original size:2 final size:2
Alignment explanation
Indices: 568412--568451 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
568402 TTTCGGGTAT
568412 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
568452 TACAAAAAAA
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):
TA
Found at i:574574 original size:28 final size:28
Alignment explanation
Indices: 574520--574578 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
574510 TGACTTAGTA
* * *
574520 AACTCATATGATTCAACTCTTCCGAGTC
1 AACTCATATGAATCAACTCATACGAGTC
* *
574548 AACTCATCTGAATCAACTCATATGAGTC
1 AACTCATATGAATCAACTCATACGAGTC
574576 AAC
1 AAC
574579 CCGTTAACTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.29
Consensus pattern (28 bp):
AACTCATATGAATCAACTCATACGAGTC
Found at i:574577 original size:14 final size:14
Alignment explanation
Indices: 574520--574578 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
574510 TGACTTAGTA
*
574520 AACTCATATGATTC
1 AACTCATATGAGTC
* **
574534 AACTCTTCCGAGTC
1 AACTCATATGAGTC
* *
574548 AACTCATCTGAATC
1 AACTCATATGAGTC
574562 AACTCATATGAGTC
1 AACTCATATGAGTC
574576 AAC
1 AAC
574579 CCGTTAACTT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.29
Consensus pattern (14 bp):
AACTCATATGAGTC
Found at i:588043 original size:19 final size:19
Alignment explanation
Indices: 588016--588060 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
588006 TTCCGTAGAA
*
588016 GACCACCGAATTATGAAAT
1 GACCTCCGAATTATGAAAT
588035 GACCTCCGAATTATGAAAT
1 GACCTCCGAATTATGAAAT
*
588054 GTCCTCC
1 GACCTCC
588061 ATGGGACTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
GACCTCCGAATTATGAAAT
Found at i:592367 original size:16 final size:16
Alignment explanation
Indices: 592346--592404 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
592336 GAACGTTTGG
592346 AGAAAAATTCAAATGA
1 AGAAAAATTCAAATGA
* *
592362 AGAAAAACTTGAACGTTTGA
1 AGAAAAA-TTCAA---ATGA
*
592382 AGGAAAATTCAAATGA
1 AGAAAAATTCAAATGA
592398 AGAAAAA
1 AGAAAAA
592405 CTTTTTGAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 16 0.48
17 4 0.12
19 4 0.12
20 9 0.27
ACGTcount: A:0.58, C:0.07, G:0.17, T:0.19
Consensus pattern (16 bp):
AGAAAAATTCAAATGA
Found at i:592419 original size:37 final size:36
Alignment explanation
Indices: 592336--592407 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
592326 AATTGAAAGA
* *
592336 GAACGTTTGGAGAAAAATTCAAATGAAGAAAAACTT
1 GAACGTTTGAAGGAAAATTCAAATGAAGAAAAACTT
592372 GAACGTTTGAAGGAAAATTCAAATGAAGAAAAACTT
1 GAACGTTTGAAGGAAAATTCAAATGAAGAAAAACTT
592408 TTTGAAGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.22
Consensus pattern (36 bp):
GAACGTTTGAAGGAAAATTCAAATGAAGAAAAACTT
Found at i:592524 original size:14 final size:14
Alignment explanation
Indices: 592505--592532 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
592495 TAACCAATTT
592505 TATCTACCTTACTC
1 TATCTACCTTACTC
592519 TATCTACCTTACTC
1 TATCTACCTTACTC
592533 CTTCTCCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.43
Consensus pattern (14 bp):
TATCTACCTTACTC
Found at i:595292 original size:2 final size:2
Alignment explanation
Indices: 595285--595555 Score: 97
Period size: 2 Copynumber: 142.5 Consensus size: 2
595275 TATTTAGAAT
* * *
595285 TA TA TA TA -A TG TT TA TA -A TA TA TA T- TA TA TT TA -A TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
595322 TA TA T- TA TA TA GTA TA -A TG TA TA T- TA T- TA TA T- TA TA T-
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* ** * *
595359 TG TA TA CG T- TA TA T- TA TA TA GCA TT TA TA GTA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA
* *
595400 TA TA TA -A TA TA TA -A TA TA TA AA TA CTA TG TA -A 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
* * *
595440 TA TA TA T- TA CA TA GTA TT TA TA TA TA CTA TA GTA TT TA GTA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA -TA TA TA -TA TA
* *
595483 GTA TA CA -A TA TA -A AA TA T- TA T- TA TA T- TA TA 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
* * *
595520 TA GA -A TA TA TA TA -A TA TCA CA TA TA CA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA T
595556 TACGTATGAT
Statistics
Matches: 201, Mismatches: 32, Indels: 72
0.66 0.10 0.24
Matches are distributed among these distances:
1 25 0.12
2 156 0.78
3 20 0.10
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:595313 original size:7 final size:7
Alignment explanation
Indices: 595298--595475 Score: 55
Period size: 7 Copynumber: 24.9 Consensus size: 7
595288 ATATAATGTT
*
595298 TATAATA
1 TATATTA
595305 TATATTA
1 TATATTA
595312 TAT-TTA
1 TATATTA
595318 -ATATTA
1 TATATTA
595324 TATTATATA
1 TA-TAT-TA
* *
595333 GTATAATG
1 -TATATTA
595341 TATATTA
1 TATATTA
595348 TTATATTA
1 -TATATTA
595356 TAT-TGTA
1 TATAT-TA
**
595363 TACGTTA
1 TATATTA
595370 TAT-TATA
1 TATAT-TA
*
595377 TAGCATT-
1 TA-TATTA
*
595384 TATAGTA
1 TATATTA
595391 TATAGTATA
1 TATA-T-TA
*
595400 TATATAA
1 TATATTA
*
595407 TATATAA
1 TATATTA
595414 TATA-TA
1 TATATTA
* *
595420 AATACTA
1 TATATTA
* *
595427 TGTAATA
1 TATATTA
595434 TATATATA
1 TATAT-TA
595442 TATATTA
1 TATATTA
* *
595449 CATAGTA
1 TATATTA
*
595456 TTTA-TA
1 TATATTA
*
595462 TATACTA
1 TATATTA
595469 TAGTATT
1 TA-TATT
595476 TAGTATAGTA
Statistics
Matches: 128, Mismatches: 25, Indels: 35
0.68 0.13 0.19
Matches are distributed among these distances:
5 2 0.02
6 19 0.15
7 70 0.55
8 24 0.19
9 11 0.09
10 2 0.02
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (7 bp):
TATATTA
Found at i:597585 original size:3 final size:3
Alignment explanation
Indices: 597579--597684 Score: 85
Period size: 3 Copynumber: 35.0 Consensus size: 3
597569 GTAATATTAT
* * * *
597579 TAA TAA TAA TAA TAA TATA TCA TAA T-A TCA TATA TAA TAA TAG TAG
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA TAA TAA TAA
* *
597625 T-A TAA TATA TAA TTA TATA TAA TAA TAA AAA T-A TAA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
597670 T-A TAA TTAA TAA TAA
1 TAA TAA -TAA TAA TAA
597685 AAACATACAA
Statistics
Matches: 85, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
2 7 0.08
3 64 0.75
4 14 0.16
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:597605 original size:10 final size:10
Alignment explanation
Indices: 597570--597683 Score: 81
Period size: 10 Copynumber: 10.8 Consensus size: 10
597560 TTGGGCTTTG
*
597570 TAATATTAT-
1 TAATAATATA
597579 TAATAATA-A
1 TAATAATATA
597588 TAATAATATA
1 TAATAATATA
*
597598 TCATAATATCA
1 TAATAATAT-A
597609 TATATAATAATA
1 TA-ATAAT-ATA
597621 GTAGTATAATATA
1 -TA--ATAATATA
*
597634 TAATTATATA
1 TAATAATATA
*
597644 TAATAATAAA
1 TAATAATATA
*
597654 AATATAATA-A
1 TA-ATAATATA
597664 TAATAATATAA
1 TAATAATAT-A
597675 TTAATAATA
1 -TAATAATA
597684 AAAACATACA
Statistics
Matches: 86, Mismatches: 8, Indels: 19
0.76 0.07 0.17
Matches are distributed among these distances:
9 21 0.24
10 27 0.31
11 9 0.10
12 16 0.19
13 7 0.08
14 6 0.07
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (10 bp):
TAATAATATA
Found at i:597616 original size:31 final size:29
Alignment explanation
Indices: 597581--597684 Score: 106
Period size: 31 Copynumber: 3.4 Consensus size: 29
597571 AATATTATTA
597581 ATAATAATAATAATATATCATAATATCATAT
1 ATAATAATAATAATATAT-ATAATAT-ATAT
*
597612 ATAATAATAGTAGTATAATATATAAT-TATAT
1 ATAATAATAATA--AT-ATATATAATATATAT
*
597643 ATAATAATAAAAATATA-ATAATA-ATAAT
1 ATAATAATAATAATATATATAATATAT-AT
597671 ATAATTAATAATAA
1 ATAA-TAATAATAA
597685 AAACATACAA
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
27 7 0.11
28 9 0.14
29 10 0.16
31 25 0.40
32 1 0.02
33 7 0.11
34 4 0.06
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (29 bp):
ATAATAATAATAATATATATAATATATAT
Found at i:597634 original size:28 final size:27
Alignment explanation
Indices: 597570--597683 Score: 87
Period size: 28 Copynumber: 4.3 Consensus size: 27
597560 TTGGGCTTTG
* *
597570 TAATATTATTAATAATAATAATAATATA
1 TAATAATA-TAATTATAATAATAATATA
* * *
597598 TCATAATATCATATATAATAATAGTAGTA
1 TAATAATATAAT-TATAATAATAATA-TA
597627 TAAT-ATATAATTAT-AT-ATAATA-A
1 TAATAATATAATTATAATAATAATATA
* *
597650 TAAAAATATAATAATAATAAT-ATA-A
1 TAATAATATAATTATAATAATAATATA
597675 TTAATAATA
1 -TAATAATA
597684 AAAACATACA
Statistics
Matches: 69, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
23 4 0.06
24 9 0.13
25 11 0.16
26 11 0.16
27 6 0.09
28 23 0.33
29 5 0.07
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (27 bp):
TAATAATATAATTATAATAATAATATA
Found at i:607869 original size:37 final size:37
Alignment explanation
Indices: 607828--607969 Score: 173
Period size: 37 Copynumber: 3.9 Consensus size: 37
607818 GTTTCTCTTG
* *
607828 AAACAAATTTTGTCTCGCTAGAGACAATTTTTCTTAA
1 AAACAAATTTTGTCTCACTTGAGACAATTTTTCTTAA
* * *
607865 AAACAAATTTTATCTCACTTGAGA-GAGTTTTCTCTAA
1 AAACAAATTTTGTCTCACTTGAGACAATTTTTCT-TAA
* * *
607902 AAACAAATTTTGTCTCACTTGAGATAATTTCTC-TCA
1 AAACAAATTTTGTCTCACTTGAGACAATTTTTCTTAA
*
607938 AAACAAATTTTGTCTCGCTTGAGAC-ATTTTTC
1 AAACAAATTTTGTCTCACTTGAGACAATTTTTC
607970 CTTTCAAATG
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
35 6 0.07
36 32 0.36
37 47 0.52
38 5 0.06
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.39
Consensus pattern (37 bp):
AAACAAATTTTGTCTCACTTGAGACAATTTTTCTTAA
Found at i:607941 original size:36 final size:36
Alignment explanation
Indices: 607810--607961 Score: 169
Period size: 37 Copynumber: 4.2 Consensus size: 36
607800 TCTATCACCT
** ** *
607810 TTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGC
1 TTGAGATAATTTCTCTAAAAACAAATTTTGTCTCAC
* * * *
607846 TAGAGACAATTTTTCTTAAAAACAAATTTTATCTCAC
1 TTGAGATAATTTCTC-TAAAAACAAATTTTGTCTCAC
* *
607883 TTGAGAGAGTTTTCTCTAAAAACAAATTTTGTCTCAC
1 TTGAGATA-ATTTCTCTAAAAACAAATTTTGTCTCAC
* *
607920 TTGAGATAATTTCTCTCAAAACAAATTTTGTCTCGC
1 TTGAGATAATTTCTCTAAAAACAAATTTTGTCTCAC
607956 TTGAGA
1 TTGAGA
607962 CATTTTTCCT
Statistics
Matches: 96, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
36 41 0.43
37 50 0.52
38 5 0.05
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (36 bp):
TTGAGATAATTTCTCTAAAAACAAATTTTGTCTCAC
Found at i:608373 original size:29 final size:30
Alignment explanation
Indices: 608336--608443 Score: 82
Period size: 29 Copynumber: 3.5 Consensus size: 30
608326 CTTGAGACAA
608336 TTTCTCTTGAAACATCATCTTTGAGATCGT
1 TTTCTCTTGAAACATCATCTTTGAGATCGT
*
608366 TTTC-CTTGAAACAAATTTGTC-TCTCTTGAGATAG-
1 TTTCTCTTGAAAC--A----TCATCT-TTGAGATCGT
*
608400 TTTCTCTTGAAACATCATATTTGAG-TC-T
1 TTTCTCTTGAAACATCATCTTTGAGATCGT
*
608428 GTTTCCCTTGAAACAT
1 -TTTCTCTTGAAACAT
608444 TATCCCTAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 23
0.70 0.04 0.26
Matches are distributed among these distances:
28 1 0.02
29 29 0.46
30 6 0.10
31 1 0.02
33 1 0.02
34 7 0.11
35 18 0.29
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (30 bp):
TTTCTCTTGAAACATCATCTTTGAGATCGT
Found at i:608404 original size:64 final size:65
Alignment explanation
Indices: 608291--608442 Score: 211
Period size: 64 Copynumber: 2.4 Consensus size: 65
608281 AACTTAAACC
* * *
608291 TTGAGATTG-TTTCTCTTGAAACAAGTTGTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATC
1 TTGAGATCGTTTTC-CTTGAAACAAATTGTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATA
608355 T
65 T
* *
608356 TTGAGATCGTTTTCCTTGAAACAAATT-TGTCTCTCTTGAGATAGTTTCTCTTGAAACATCATAT
1 TTGAGATCGTTTTCCTTGAAACAAATTGTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATAT
*
608420 TTGAG-TCTGTTTCCCTTGAAACA
1 TTGAGATC-GTTTTCCTTGAAACA
608443 TTATCCCTAA
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
63 2 0.03
64 53 0.67
65 20 0.25
66 4 0.05
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (65 bp):
TTGAGATCGTTTTCCTTGAAACAAATTGTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATAT
Found at i:608967 original size:3 final size:3
Alignment explanation
Indices: 608959--609042 Score: 168
Period size: 3 Copynumber: 28.0 Consensus size: 3
608949 GTCTTAAAAA
608959 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
609007 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
609043 TCTAATAAAA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:609452 original size:20 final size:20
Alignment explanation
Indices: 609410--609453 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
609400 ATAGTGATAG
* * *
609410 AAACATCAACCTAATCAGCC
1 AAACAACAACCAAATCAACC
*
609430 AAACAACAACCAAATCAATC
1 AAACAACAACCAAATCAACC
609450 AAAC
1 AAAC
609454 CCGATTTGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.32, G:0.02, T:0.11
Consensus pattern (20 bp):
AAACAACAACCAAATCAACC
Found at i:609566 original size:2 final size:2
Alignment explanation
Indices: 609559--609623 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
609549 GCAATGAACC
609559 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
609601 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
609624 GAGGGGGGAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:612034 original size:3 final size:3
Alignment explanation
Indices: 611949--612025 Score: 57
Period size: 3 Copynumber: 25.0 Consensus size: 3
611939 ATTTTATTTA
* * *
611949 AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAGT -AT ATT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
* * **
611994 ACTT AAT AAAG AAT AAT GTT AAT AAT AAT AAT
1 A-AT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
612026 GGATAATAAC
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
2 1 0.02
3 50 0.89
4 5 0.09
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:619591 original size:22 final size:22
Alignment explanation
Indices: 619566--619627 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
619556 GTGAAATTCT
*
619566 TCCCGAAGGACCTATGTATATG
1 TCCCGAATGACCTATGTATATG
* *
619588 TCCCGAATAACCTCTGTATATG
1 TCCCGAATGACCTATGTATATG
619610 TCCCGAATGACCTATGTA
1 TCCCGAATGACCTATGTA
619628 ACCCTCGACT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (22 bp):
TCCCGAATGACCTATGTATATG
Found at i:623884 original size:13 final size:13
Alignment explanation
Indices: 623866--623899 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
623856 ATTATTTTAT
623866 AAAAAGCACAAAA
1 AAAAAGCACAAAA
*
623879 AAAAAGAACAAAA
1 AAAAAGCACAAAA
*
623892 GAAAAGCA
1 AAAAAGCA
623900 ATAATAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.76, C:0.12, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAGCACAAAA
Found at i:625788 original size:23 final size:24
Alignment explanation
Indices: 625745--625791 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
625735 TAAACAAAAT
*
625745 TTTATTAATCCGAAAATTCCTAAG
1 TTTATTAATCCGAAAAATCCTAAG
625769 TTTATTAATCC-AAAAATCCTAAG
1 TTTATTAATCCGAAAAATCCTAAG
625792 GAGAAAAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.36
Consensus pattern (24 bp):
TTTATTAATCCGAAAAATCCTAAG
Found at i:626580 original size:28 final size:28
Alignment explanation
Indices: 626526--626583 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
626516 CTTCAATTAT
*
626526 AATATTATGTCGTAGAGTCATTCTTTGA
1 AATATTATGTCGTAGAGTCAGTCTTTGA
* * *
626554 AATATTATGTCGTCGAGTTAGTGTTTGA
1 AATATTATGTCGTAGAGTCAGTCTTTGA
626582 AA
1 AA
626584 GCAACGATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (28 bp):
AATATTATGTCGTAGAGTCAGTCTTTGA
Found at i:627314 original size:78 final size:76
Alignment explanation
Indices: 627192--627422 Score: 385
Period size: 75 Copynumber: 3.0 Consensus size: 76
627182 AATTTTATCC
* * *
627192 TCAATTATTTAAATTTACTT-TTTTTTAGCACTTAAATGTATAATTATATTGTTTATTTTTTTAG
1 TCAATTATTTAAATTTAATTATTTTTTAACACTTAAATGTATAATTATATTGTTTATTTTTTGAG
*
627256 TTTATTAATTT
66 TTTATTAATGT
*
627267 TCAATTATTTAAATTTAATTAGTTTTTATAACACTAAAATGTATAATTATATTGTTTATTTTTTG
1 TCAATTATTTAAATTTAATTA-TTTTT-TAACACTTAAATGTATAATTATATTGTTTATTTTTTG
627332 AGTTTATTAATGT
64 AGTTTATTAATGT
627345 TCAATTATTT-AATTTAATTATTTTTTAACACTTAAATGTATAATTATATTGTTTATTTTTTGAG
1 TCAATTATTTAAATTTAATTATTTTTTAACACTTAAATGTATAATTATATTGTTTATTTTTTGAG
627409 TTTATTAATGT
66 TTTATTAATGT
627420 TCA
1 TCA
627423 TATTTATTAC
Statistics
Matches: 147, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
75 71 0.48
76 5 0.03
77 15 0.10
78 56 0.38
ACGTcount: A:0.32, C:0.05, G:0.06, T:0.57
Consensus pattern (76 bp):
TCAATTATTTAAATTTAATTATTTTTTAACACTTAAATGTATAATTATATTGTTTATTTTTTGAG
TTTATTAATGT
Found at i:627419 original size:36 final size:36
Alignment explanation
Indices: 627304--627419 Score: 114
Period size: 36 Copynumber: 3.1 Consensus size: 36
627294 ATAACACTAA
627304 AATGTATAATTATATTGTTTATTTTTTGAGTTTATT
1 AATGTATAATTATATTGTTTATTTTTTGAGTTTATT
* **
627340 AATGT-TCAATTATTTAATT-TAATTATTTTTTAACACTTA--
1 AATGTAT-AATTA--T-ATTGT--TTATTTTTTGA-GTTTATT
627379 AATGTATAATTATATTGTTTATTTTTTGAGTTTATT
1 AATGTATAATTATATTGTTTATTTTTTGAGTTTATT
627415 AATGT
1 AATGT
627420 TCATATTTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 22
0.69 0.07 0.24
Matches are distributed among these distances:
34 3 0.05
35 11 0.17
36 18 0.29
37 2 0.03
38 2 0.03
39 13 0.21
40 11 0.17
41 3 0.05
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.58
Consensus pattern (36 bp):
AATGTATAATTATATTGTTTATTTTTTGAGTTTATT
Found at i:639769 original size:19 final size:18
Alignment explanation
Indices: 639733--639767 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
639723 GCTCCAAATC
* *
639733 TTTTTCAAGATTCATTTG
1 TTTTTCAAAATCCATTTG
639751 TTTTTCAAAATCCATTT
1 TTTTTCAAAATCCATTT
639768 TGCTTTCAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.14, G:0.06, T:0.54
Consensus pattern (18 bp):
TTTTTCAAAATCCATTTG
Found at i:649268 original size:25 final size:25
Alignment explanation
Indices: 649240--649299 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
649230 TCATAAACAA
649240 AATATGAGTTCATAATACATACCAT
1 AATATGAGTTCATAATACATACCAT
649265 AATATGAGTTCATAATACATACCAT
1 AATATGAGTTCATAATACATACCAT
649290 AATATGAGTT
1 AATATGAGTT
649300 AAAGTCCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (25 bp):
AATATGAGTTCATAATACATACCAT
Found at i:651883 original size:23 final size:23
Alignment explanation
Indices: 651841--651884 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
651831 TACATTTATG
* *
651841 GCACGTATGTGATATTGGTGCCT
1 GCACATATGTGATATCGGTGCCT
*
651864 GCACATATGTGATGTCGGTGC
1 GCACATATGTGATATCGGTGC
651885 GATGTATTCC
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:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (23 bp):
GCACATATGTGATATCGGTGCCT
Found at i:652316 original size:19 final size:20
Alignment explanation
Indices: 652292--652329 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
652282 TGTCACACAT
*
652292 ATTTACTTAT-TTTTATATG
1 ATTTACATATGTTTTATATG
652311 ATTTACATATGTTTTATAT
1 ATTTACATATGTTTTATAT
652330 TTATTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (20 bp):
ATTTACATATGTTTTATATG
Found at i:652341 original size:20 final size:20
Alignment explanation
Indices: 652291--652344 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
652281 TTGTCACACA
652291 TATTTACTTAT-TTTTATAT
1 TATTTACTTATGTTTTATAT
* *
652310 GATTTACATATGTTTTATATT
1 TATTTACTTATGTTTTATA-T
652331 TATTTA-TTATGTTT
1 TATTTACTTATGTTT
652345 GCATAGCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 9 0.31
20 14 0.48
21 6 0.21
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.65
Consensus pattern (20 bp):
TATTTACTTATGTTTTATAT
Found at i:654774 original size:36 final size:36
Alignment explanation
Indices: 654727--654806 Score: 151
Period size: 36 Copynumber: 2.2 Consensus size: 36
654717 TTTGGTGATA
654727 AAAAAAATGAATTCTAGTTACAATCACCCAAACTTC
1 AAAAAAATGAATTCTAGTTACAATCACCCAAACTTC
654763 AAAAAAATGAATTCTAGTTACAATCACCCAAACTTC
1 AAAAAAATGAATTCTAGTTACAATCACCCAAACTTC
*
654799 AAACAAAT
1 AAAAAAAT
654807 ATGTTTTATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (36 bp):
AAAAAAATGAATTCTAGTTACAATCACCCAAACTTC
Found at i:659356 original size:2 final size:2
Alignment explanation
Indices: 659349--659435 Score: 156
Period size: 2 Copynumber: 43.5 Consensus size: 2
659339 TTAAACATAC
659349 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
659391 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
659433 AT A
1 AT A
659436 CATGAATAAC
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:660476 original size:8 final size:9
Alignment explanation
Indices: 660454--660489 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
660444 AATGGAAGTG
*
660454 TTTTTTCTCT
1 TTTTTT-TCC
660464 TTTTTTTCC
1 TTTTTTTCC
660473 TTTTTTTCC
1 TTTTTTTCC
660482 TTTTTTTC
1 TTTTTTTC
660490 AAATGGTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 19 0.76
10 6 0.24
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTCC
Found at i:661172 original size:3 final size:3
Alignment explanation
Indices: 661166--661219 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
661156 TTAGTAGTAG
661166 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
661214 TAA TAA
1 TAA TAA
661220 CTTGGACGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:663231 original size:81 final size:81
Alignment explanation
Indices: 663093--663982 Score: 1289
Period size: 81 Copynumber: 11.0 Consensus size: 81
663083 ATTGTTTTAA
* * *
663093 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGATAGAAAGGTGTTAATCATGTCAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
*
663158 AGGCTAAATACCTTTG
66 AGGTTAAATACCTTTG
*
663174 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTAAATCATGCCAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
*
663239 ATGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * *
663255 AGTAAAACATTAATTGTCTAGCTGTGCATTTGACAGAAATGTGTTAATCATGCCAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
663320 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * * * * * *
663336 AGTAAAACATTAATTGCCTAGTTCTGCATTTGAAAGAAATGTATCAATAATG-CAGTAAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
663400 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * * *
663416 AGTAAAAGATTCATTACCTAGCTGTGCATTTTACAAAAAGGTGTCAATCATGCTAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
* *
663481 AGGCTGAATACCTTTG
66 AGGTTAAATACCTTTG
* * ** * *
663497 AGTAAAAGATTCATTGCCTAGCTGTGCATTTGACATAAATATGTCAGTCATGCCAATTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
*
663562 AGGTTAAATACCTTTT
66 AGGTTAAATACCTTTG
663578 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCGAA-CATGCCAGTTAGATGA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTC-AATCATGCCAGTTAGATGA
663642 AAGGTTAAATACCTTTG
65 AAGGTTAAATACCTTTG
* *
663659 TGTAAAAGATTAATTGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATCATGCCAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
*
663724 AGGTTAAATATCTTTG
66 AGGTTAAATACCTTTG
* * * *
663740 AGTAAAAGATTAATTGCCTAGCTGTGCATTTAATATAAAGGTGTCAATCATGCCAATTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
* *
663805 ATGTTAAATACATTTG
66 AGGTTAAATACCTTTG
* * * *
663821 AGTAAAAGATTAATTGCCTAGTTTTTCATTTGACAGAAAGGTGTCAATCATACCAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
663886 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
** * * * *
663902 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGGTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
*
663967 AGGTTAAATTCCTTTG
66 AGGTTAAATACCTTTG
663983 GCATGAAAAG
Statistics
Matches: 724, Mismatches: 82, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
80 70 0.10
81 653 0.90
82 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (81 bp):
AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Found at i:664049 original size:46 final size:46
Alignment explanation
Indices: 663982--664245 Score: 341
Period size: 46 Copynumber: 5.7 Consensus size: 46
663972 AAATTCCTTT
*
663982 GGCATGAAAAGATGCCATAAATGAAAATGCATAACGGTGCATTATA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
* *
664028 GGCATGAAAGGATTG-CATAAATGAAAATGCATAATGGTACATTATA
1 GGCATGAAAGGA-TGCCATAAATGAAAATGCATAACGGTGCATTATA
* * *
664074 GGCATGAAAGGATGCCATAAATGAAAATGCATAATGGTGAATTATC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
* * * *
664120 GACATGAAAGGATGTCGTAAATGAAAATGCATAACGGTACATTATA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
* * * * *
664166 GGCATGAAAGGATGCAATAAATGAAAATGCTTAACGGTGAATAATT
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
* ** *
664212 GGCATAAAAGGATGCCACCAATGAAAATACATAA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAA
664246 TGGTATATTA
Statistics
Matches: 188, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
45 2 0.01
46 184 0.98
47 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (46 bp):
GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
Found at i:664096 original size:92 final size:92
Alignment explanation
Indices: 663982--664255 Score: 379
Period size: 92 Copynumber: 3.0 Consensus size: 92
663972 AAATTCCTTT
* *
663982 GGCATGAAAAGATGCCATAAATGAAAATGCATAACGGTGCATTATAGGCATGAAAGGATTG-CAT
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGAATTATAGGCATGAAAGGA-TGCCAT
664046 AAATGAAAATGCATAATGGTACATTATA
65 AAATGAAAATGCATAATGGTACATTATA
* * * * *
664074 GGCATGAAAGGATGCCATAAATGAAAATGCATAATGGTGAATTATCGACATGAAAGGATGTCGTA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGAATTATAGGCATGAAAGGATGCCATA
*
664139 AATGAAAATGCATAACGGTACATTATA
66 AATGAAAATGCATAATGGTACATTATA
* * * * * **
664166 GGCATGAAAGGATGCAATAAATGAAAATGCTTAACGGTGAATAATTGGCATAAAAGGATGCCACC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGAATTATAGGCATGAAAGGATGCCATA
* *
664231 AATGAAAATACATAATGGTATATTA
66 AATGAAAATGCATAATGGTACATTA
664256 ACAACATATA
Statistics
Matches: 160, Mismatches: 21, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
91 2 0.01
92 158 0.99
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (92 bp):
GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGAATTATAGGCATGAAAGGATGCCATA
AATGAAAATGCATAATGGTACATTATA
Found at i:664235 original size:138 final size:138
Alignment explanation
Indices: 663984--664249 Score: 392
Period size: 138 Copynumber: 1.9 Consensus size: 138
663974 ATTCCTTTGG
*
663984 CATGAAAAGATGCCATAAATGAAAATGCATAACGGTGCATTATAGGCATGAAAGGATTGCATAAA
1 CATGAAAAGATGCCATAAATGAAAATGCATAACGGTACATTATAGGCATGAAAGGATTGCATAAA
* * * * *
664049 TGAAAATGCATAATGGTACATTATAGGCATGAAAGGATGCCATAAATGAAAATGCATAATGGTGA
66 TGAAAATGCATAACGGTACATAATAGGCATAAAAGGATGCCACAAATGAAAATACATAATGGTGA
664114 ATTATCGA
131 ATTATCGA
* * *
664122 CATGAAAGGATGTCGTAAATGAAAATGCATAACGGTACATTATAGGCATGAAAGGA-TGCAATAA
1 CATGAAAAGATGCCATAAATGAAAATGCATAACGGTACATTATAGGCATGAAAGGATTGC-ATAA
* * *
664186 ATGAAAATGCTTAACGGTGA-ATAATTGGCATAAAAGGATGCCACCAATGAAAATACATAATGGT
65 ATGAAAATGCATAACGGT-ACATAATAGGCATAAAAGGATGCCACAAATGAAAATACATAATGGT
664250 ATATTAACAA
Statistics
Matches: 114, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
137 3 0.03
138 110 0.96
139 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (138 bp):
CATGAAAAGATGCCATAAATGAAAATGCATAACGGTACATTATAGGCATGAAAGGATTGCATAAA
TGAAAATGCATAACGGTACATAATAGGCATAAAAGGATGCCACAAATGAAAATACATAATGGTGA
ATTATCGA
Found at i:670509 original size:2 final size:2
Alignment explanation
Indices: 670497--670545 Score: 82
Period size: 2 Copynumber: 24.5 Consensus size: 2
670487 CAAAAGAAAC
670497 AT AT CAT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
670539 AT AT AT A
1 AT AT AT A
670546 CATTACACCT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 42 0.93
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:672811 original size:81 final size:81
Alignment explanation
Indices: 672676--673162 Score: 587
Period size: 81 Copynumber: 6.0 Consensus size: 81
672666 AATGTTTTAA
** * * * * * * *
672676 AGTAAAAGATTAATTGTGTTGCTATGCATTTTACAAAAATGTGCCAATCATGCCAGTTATATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
* *
672741 CGGTTAAATAACTTTG
66 AGGTTAAATACCTTTG
* * *
672757 AGTAAAAGATTAATTGCCTAGCTGGGCATTTGCCAGAAAGGTGTCAATCATGCCAGATAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
*
672822 AGGTTAAATACCTTTA
66 AGGTTAAATACCTTTG
* * *
672838 AGTAAAAGATTAATTGCCTAGCTATGCATTTGACAGAAATGTGTCAATCATTCCAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
672903 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * * ***
672919 AGTAAAATATTAACTGCCTAGCTGTGCATTTGACATAAATGTGTCAATCATAAAAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
672984 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * * *
673000 AATAAAAGATTAATTACCTAGTTGTGCATTTGACAAGAAAGGTGTCAATCATGTCAGTTACATGA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGAC-AGAAAGGTGTCAATCATGCCAGTTAGATGA
*
673065 AAGGTTAAATACCTATG
65 AAGGTTAAATACCTTTG
* * ** * * * * **
673082 AGTAATAGATTAATTGCCTAACAATGTATTTGGCAGAAAGGTGCCAATAATGTAAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
*
673147 AGGTTAAATGCCTTTG
66 AGGTTAAATACCTTTG
673163 GCATGAAAAG
Statistics
Matches: 349, Mismatches: 56, Indels: 2
0.86 0.14 0.00
Matches are distributed among these distances:
81 284 0.81
82 65 0.19
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (81 bp):
AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Found at i:673142 original size:244 final size:243
Alignment explanation
Indices: 672700--673162 Score: 640
Period size: 244 Copynumber: 1.9 Consensus size: 243
672690 TGTGTTGCTA
* *** * * *
672700 TGCATTTTACAAAAATGTGCCAATCATGCCAGTTATATGAACGGTTAAATAACTTTGAGTAAAAG
1 TGCATTTGACAAAAATGTGCCAATCATAAAAGTTAGATGAAAGGTTAAATAACTTTGAATAAAAG
* * *
672765 ATTAATTGCCTAGCTGGGCATTTGCCAGAAAGGTGTCAATCATGCCAGATAGATGAAAGGTTAAA
66 ATTAATTACCTAGCTGGGCATTTGCAAGAAAGGTGTCAATCATGCCAGATACATGAAAGGTTAAA
* * * * * * *
672830 TACCTTTAAGTAAAAGATTAATTGCCTAGCTATGCATTTGACAGAAATGTGTCAATCATTCCAGT
131 TACCTATAAGTAAAAGATTAATTGCCTAACAATGCATTTGACAGAAAGGTGCCAATAATTCAAGT
672895 TAGATGAAAGGTTAAATACCTTTGAGTAAAATATTAACTGCCTAGCTG
196 TAGATGAAAGGTTAAATACCTTTGAGTAAAATATTAACTGCCTAGCTG
* * *
672943 TGCATTTGACATAAATGTGTCAATCATAAAAGTTAGATGAAAGGTTAAATACCTTTGAATAAAAG
1 TGCATTTGACAAAAATGTGCCAATCATAAAAGTTAGATGAAAGGTTAAATAACTTTGAATAAAAG
* * * *
673008 ATTAATTACCTAGTTGTGCATTTGACAAGAAAGGTGTCAATCATGTCAGTTACATGAAAGGTTAA
66 ATTAATTACCTAGCTGGGCATTTG-CAAGAAAGGTGTCAATCATGCCAGATACATGAAAGGTTAA
* * * *
673073 ATACCTATGAGTAATAGATTAATTGCCTAACAATGTATTTGGCAGAAAGGTGCCAATAATGT-AA
130 ATACCTATAAGTAAAAGATTAATTGCCTAACAATGCATTTGACAGAAAGGTGCCAATAAT-TCAA
*
673137 GTTAGATGAAAGGTTAAATGCCTTTG
194 GTTAGATGAAAGGTTAAATACCTTTG
673163 GCATGAAAAG
Statistics
Matches: 189, Mismatches: 29, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
243 76 0.40
244 112 0.59
245 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (243 bp):
TGCATTTGACAAAAATGTGCCAATCATAAAAGTTAGATGAAAGGTTAAATAACTTTGAATAAAAG
ATTAATTACCTAGCTGGGCATTTGCAAGAAAGGTGTCAATCATGCCAGATACATGAAAGGTTAAA
TACCTATAAGTAAAAGATTAATTGCCTAACAATGCATTTGACAGAAAGGTGCCAATAATTCAAGT
TAGATGAAAGGTTAAATACCTTTGAGTAAAATATTAACTGCCTAGCTG
Found at i:673233 original size:46 final size:46
Alignment explanation
Indices: 673162--673404 Score: 265
Period size: 46 Copynumber: 5.3 Consensus size: 46
673152 AAATGCCTTT
* *
673162 GGCATGAAAAGATGCCATAAATGAAAATGCATAACGGTGCAATATA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
* * * **
673208 GGCATGAAAGAATGCCATAATTGAAAATACATAACGGTATATTATA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
* *
673254 GGCATGAAAGGATGCCATAAATGAAAATGTATAACAGTGCATTAT-
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
* *** * *
673299 TG-ATGTTAAAGGATGTGGTAAATGAAAATTCATAACGGTACATTATA
1 GGCATG--AAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
* * * * * *
673346 GGCATGGAAGGATGCAATAAATGAATATGCTTAACGGTGCATAATT
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
673392 GGCATGAAAGGAT
1 GGCATGAAAGGAT
673405 ACCACCAATA
Statistics
Matches: 159, Mismatches: 34, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
44 3 0.02
45 1 0.01
46 151 0.95
47 1 0.01
48 3 0.02
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (46 bp):
GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
Found at i:673278 original size:92 final size:90
Alignment explanation
Indices: 673162--673435 Score: 291
Period size: 92 Copynumber: 3.0 Consensus size: 90
673152 AAATGCCTTT
* *
673162 GGCATGAAAAGATGCCATAAATGAAAATGCATAACGGTGCAATATAGGCATGAAAGAATGCCATA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCAATAT-GGCATGAAAGGATGCCATA
673227 ATTGAAAATACATAACGGTATATTATA
65 A-TGAAAATACATAACGGTATATTATA
* * * * ***
673254 GGCATGAAAGGATGCCATAAATGAAAATGTATAACAGTGCATTATTG-ATGTTAAAGGATGTGGT
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCAATATGGCATG--AAAGGATGCCAT
* *
673318 AAATGAAAATTCATAACGGTACATTATA
64 -AATGAAAATACATAACGGTATATTATA
* * * * *
673346 GGCATGGAAGGATGCAATAAATGAATATGCTTAACGGTGC-ATAATTGGCATGAAAGGATACCAC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCAAT-A-TGGCATGAAAGGATGCCA-
* * *
673410 CAATAAAAATACATAATGGTATATTA
63 TAATGAAAATACATAACGGTATATTA
673436 ACGGCATATA
Statistics
Matches: 147, Mismatches: 28, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
90 3 0.02
91 2 0.01
92 135 0.92
93 4 0.03
94 3 0.02
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (90 bp):
GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCAATATGGCATGAAAGGATGCCATAA
TGAAAATACATAACGGTATATTATA
Found at i:678897 original size:18 final size:19
Alignment explanation
Indices: 678853--678902 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 19
678843 TGTGATTAAT
*
678853 AGTATCGATACTGATGCAATT
1 AGTATCGATACTGATG--ATG
678874 AGTATCGATACTGATG-TG
1 AGTATCGATACTGATGATG
678892 AGTATCGATAC
1 AGTATCGATAC
678903 AAAAAGAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 12 0.43
21 16 0.57
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (19 bp):
AGTATCGATACTGATGATG
Found at i:679548 original size:81 final size:81
Alignment explanation
Indices: 679413--680619 Score: 1589
Period size: 81 Copynumber: 14.9 Consensus size: 81
679403 ACTTTTTTAA
* *
679413 AGTAAAAGATTAATTGCCTAGCTGTACATTTGACAGAAAGGTGTCAATCATGCCAATTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
679478 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * * *
679494 AGTAAAAGATTAATTGCCTAGTTGTGCATTTGTCAGAACA-ATGTCAATCGTGCCAATTAGATGA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAA-AGGTGTCAATCATGCCAGTTAGATGA
679558 AAGGTTAAATACCTTTG
65 AAGGTTAAATACCTTTG
* * * * * * * *
679575 AGTAAAAGATTAATTGTCTACCTTTGCATTTGACAAAAAGGTGTCAATCTTTCCAGCTAAATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
679640 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * * *
679656 AGTAAAAGATTAATTGCCTAACTATGCATTTGGA-AGAATGGTGTCAATTATGCAAGTTAGATGA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTT-GACAGAAAGGTGTCAATCATGCCAGTTAGATGA
679720 AAGGTTAAATACCTTTG
65 AAGGTTAAATACCTTTG
* * * *
679737 ACTAAAATATTAATTGCCTAGTTGTGCATTTGATAGAAAGGTGTCAATCATGCCAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
* * *
679802 ATGTTAAATACATTTT
66 AGGTTAAATACCTTTG
* * * * **
679818 AGTAAAAGATTAATTACCTAGCTGTGCATTTGGCAGGAAGATGTCAATCATGGTAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
*
679883 AGGTTAAATACATTTG
66 AGGTTAAATACCTTTG
* * * * * * *
679899 AGTAAAACATCAATTGTCTAGCTATGCATTTGACAGAAAGGTGTTAATCATACCAATTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
679964 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* *
679980 AGTAAAAGATTAATTGCCTAGCTGCGCATTTGACAGAAAGGT-TCAATAATGCCAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
*
680044 AGATTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * * * *
680060 AGTAAAACATTAATTGCCTAGTTGTGCATTTAAAAGAAATGTGTCAATCATGCTAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
*
680125 AGGTTAAATAGCTTTG
66 AGGTTAAATACCTTTG
* * * * * *
680141 AGTAAAAGATTAATTGCCTAGTTGTGCATTTTACAGAAAAGTGTCGAGCATGCTAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
680206 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * *
680222 AGTAAAAGATTAGA-TGCCTAGTTGTGCATTTGACAGAAAAGTGTCAATCATGCCAGTTATATGA
1 AGTAAAAGATTA-ATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGA
*
680286 AAGGTTAAATACATTTG
65 AAGGTTAAATACCTTTG
* * * * *
680303 AGTAAAAGATTAATTACATAGCTGTGCATTTGATAGAAAGGTTTCAATCATGCCAGTTAGATAAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
680368 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
*
680384 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAACATGCCAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
680449 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * ** * *
680465 AGTAAAAGATTAATTGCCTAG-TGTTGCGTTTGACAGAAAGGTGTAAATTATTTCAATTAAATGA
1 AGTAAAAGATTAATTGCCTAGCTG-TGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGA
* *
680529 AATGTTAAATACCTTGG
65 AAGGTTAAATACCTTTG
* * * * * *
680546 AGTAAATGATTAATTGCCTAACTGTGCATTTTG-TAGAAAGGTGCCAATAATGCAAGTTAGATGA
1 AGTAAAAGATTAATTGCCTAGCTGTGCA-TTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGA
680610 AAGGTTAAAT
65 AAGGTTAAAT
680620 GTCTTTGTCA
Statistics
Matches: 980, Mismatches: 136, Indels: 20
0.86 0.12 0.02
Matches are distributed among these distances:
80 75 0.08
81 895 0.91
82 10 0.01
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (81 bp):
AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Found at i:680695 original size:46 final size:46
Alignment explanation
Indices: 680628--680972 Score: 347
Period size: 46 Copynumber: 7.6 Consensus size: 46
680618 ATGTCTTTGT
* * * * *
680628 CATGAAAAGAGGCCATAAATGAAAATGCATAACAGTGTATTATATG
1 CATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATAGG
* *
680674 CATGAAAGGATGCCATAAATGAAAATGCATAACGTTACATTATAGG
1 CATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATAGG
* * * *
680720 CATGAAAGGATGTCATAAATGAAAATGCATAATGGTGCATCAAAGG
1 CATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATAGG
* * * * *
680766 AATGAAAGGATGCCATAAATAAAAATGTATAACTGTACATTATAGG
1 CATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATAGG
* * * *
680812 AATGAAATGATGCCATAAATGAAAATGCATACCGGTGCATTATCA-A
1 CATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTAT-AGG
* * **
680858 CATGGAAGGATGCCATAATTGAAAAT--ATAACGGTATATTATAGG
1 CATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATAGG
* * * ** * *
680902 CCTGAAAGGATGCAATAAATGAAAATG-TTAACATTGCATAATTGG
1 CATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATAGG
* **
680947 CTTGAAAGGATGCCACCAATGAAAAT
1 CATGAAAGGATGCCATAAATGAAAAT
680973 ATATAATGGT
Statistics
Matches: 244, Mismatches: 52, Indels: 7
0.81 0.17 0.02
Matches are distributed among these distances:
43 1 0.00
44 34 0.14
45 33 0.14
46 175 0.72
47 1 0.00
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (46 bp):
CATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATAGG
Found at i:681494 original size:136 final size:135
Alignment explanation
Indices: 681341--681686 Score: 485
Period size: 136 Copynumber: 2.5 Consensus size: 135
681331 ACATTACTCC
* * * *
681341 TTTTCATTAAGGAGATCTGGTCGGTGGATGACATTGTTCCTTTGTGTTGAGGACGTCTAGCCGTA
1 TTTTCATTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGACGTTTAGCCGTA
* * * * * *
681406 TTAGGAGATTTGGAGACAACACGGTTCCTTCGTGTTGAGTAAATCGGATTGTCTGAGGATGACAC
66 TTTGGAGATTTGGAGACAACACGGTTCCTTCATGCTGAGGAAATCAGATTGTCTAAGGATGACAC
681471 TGCTA
131 TGCTA
* *
681476 TTTTGCATTGAGGAGATCTGGTCGGTAGACGACATTGTTCCTTCGTGTTGAGGACGTTTAGCTGT
1 TTTT-CATTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGACGTTTAGCCGT
* * * * *
681541 ATTTGTAGATTTGGAGACAACATGGTTCTTTCATGCTGAGGAAATCAGATTGTTTAAGGATGTCA
65 ATTTGGAGATTTGGAGACAACACGGTTCCTTCATGCTGAGGAAATCAGATTGTCTAAGGATGACA
*
681606 CTGCTCC
130 CTGCT-A
* * *
681613 TTTACGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGACGTTTAGTCGTA
1 TTTTCATTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGACGTTTAGCCGTA
681678 TTTGGAGAT
66 TTTGGAGAT
681687 AACATTGTTC
Statistics
Matches: 185, Mismatches: 24, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
135 4 0.02
136 178 0.96
137 3 0.02
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (135 bp):
TTTTCATTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGACGTTTAGCCGTA
TTTGGAGATTTGGAGACAACACGGTTCCTTCATGCTGAGGAAATCAGATTGTCTAAGGATGACAC
TGCTA
Found at i:684116 original size:10 final size:9
Alignment explanation
Indices: 684101--684218 Score: 74
Period size: 10 Copynumber: 11.4 Consensus size: 9
684091 ATATGTTCTC
684101 TTTCTTATTT
1 TTTCTT-TTT
684111 TTTCTTTCTT
1 TTTCTTT-TT
*
684121 ATTTTTTCTTT
1 -TTTCTT-TTT
684132 TTTCTATTTT
1 TTTCT-TTTT
*
684142 CTTCTGTTTCT
1 TTTCT-TTT-T
684153 GTTTCTTTTT
1 -TTTCTTTTT
*
684163 TTCTTTTTCTT
1 TT-TCTTT-TT
684174 TTTCTCTCTTT
1 TTTCT-T-TTT
684185 TTTCTTTTCT
1 TTTCTTTT-T
684195 TTTCTTTCTT
1 TTTCTTT-TT
684205 TTTCTTCTTT
1 TTTCTT-TTT
684215 TTTC
1 TTTC
684219 CTCGCCTTTA
Statistics
Matches: 88, Mismatches: 7, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
9 5 0.06
10 51 0.58
11 26 0.30
12 6 0.07
ACGTcount: A:0.03, C:0.18, G:0.02, T:0.78
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:684118 original size:14 final size:14
Alignment explanation
Indices: 684099--684131 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
684089 TAATATGTTC
684099 TCTTTCTTATTTTT
1 TCTTTCTTATTTTT
684113 TCTTTCTTATTTTT
1 TCTTTCTTATTTTT
684127 TCTTT
1 TCTTT
684132 TTTCTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (14 bp):
TCTTTCTTATTTTT
Found at i:684141 original size:8 final size:7
Alignment explanation
Indices: 684108--684218 Score: 75
Period size: 7 Copynumber: 15.0 Consensus size: 7
684098 CTCTTTCTTA
684108 TTTTTTC
1 TTTTTTC
* *
684115 TTTCTTA
1 TTTTTTC
684122 TTTTTTC
1 TTTTTTC
684129 TTTTTTC
1 TTTTTTC
*
684136 TATTTTC
1 TTTTTTC
684143 TTCTGTTTC
1 TT-T-TTTC
*
684152 -TGTTTC
1 TTTTTTC
684158 TTTTTT-
1 TTTTTTC
684164 TCTTTTTC
1 T-TTTTTC
684172 TTTTTCTCTC
1 -TTTT-T-TC
684182 TTTTTTC
1 TTTTTTC
684189 TTTTCTT-
1 TTTT-TTC
*
684196 TTCTTTC
1 TTTTTTC
684203 TTTTTCTTC
1 -TTTT-TTC
684212 TTTTTTC
1 TTTTTTC
684219 CTCGCCTTTA
Statistics
Matches: 82, Mismatches: 10, Indels: 24
0.71 0.09 0.21
Matches are distributed among these distances:
6 7 0.09
7 45 0.55
8 15 0.18
9 13 0.16
10 2 0.02
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (7 bp):
TTTTTTC
Found at i:684141 original size:14 final size:13
Alignment explanation
Indices: 684109--684218 Score: 84
Period size: 14 Copynumber: 8.0 Consensus size: 13
684099 TCTTTCTTAT
684109 TTTTTCTTTCTTAT-
1 TTTTTCTTT-TT-TC
684123 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
684136 TATTTTCTTCTGTTTC
1 T-TTTTCTT-T-TTTC
*
684152 TGTTTCTTTTTTTC
1 TTTTTC-TTTTTTC
684166 TTTTTCTTTTTCTC
1 TTTTTCTTTTT-TC
684180 TCTTTT-TTCTTTTC
1 T-TTTTCTT-TTTTC
684194 -TTTTCTTTCTTT-
1 TTTTTCTTT-TTTC
*
684206 TTCTTCTTTTTTC
1 TTTTTCTTTTTTC
684219 CTCGCCTTTA
Statistics
Matches: 81, Mismatches: 3, Indels: 25
0.74 0.03 0.23
Matches are distributed among these distances:
12 9 0.11
13 20 0.25
14 32 0.40
15 13 0.16
16 7 0.09
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:684151 original size:23 final size:20
Alignment explanation
Indices: 684108--684215 Score: 94
Period size: 23 Copynumber: 5.0 Consensus size: 20
684098 CTCTTTCTTA
684108 TTTTTTCTTTCTTATT-TTTTC
1 TTTTTTCTTT-TT-TTCTTTTC
684129 TTTTTTCTATTTTCTTCTGTTTC
1 TTTTTTCT-TTTT-TTCT-TTTC
*
684152 -TGTTTCTTTTTTTCTTTTTC
1 TTTTTTCTTTTTTTC-TTTTC
684172 TTTTTCTCTCTTTTTTCTTTTC
1 TTTTT-TCT-TTTTTTCTTTTC
684194 TTTTCTTTCTTTTTCTTCTTTT
1 -TTT-TTTCTTTTT-TTCTTTT
684216 TTCCTCGCCT
Statistics
Matches: 74, Mismatches: 3, Indels: 18
0.78 0.03 0.19
Matches are distributed among these distances:
20 7 0.09
21 20 0.27
22 21 0.28
23 24 0.32
24 2 0.03
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTTTTCTTTTTTTCTTTTC
Found at i:684163 original size:37 final size:37
Alignment explanation
Indices: 684122--684216 Score: 115
Period size: 36 Copynumber: 2.5 Consensus size: 37
684112 TTCTTTCTTA
684122 TTTTTTCTTTTTTCTATTTTCT-TC-TGTTTCTGTTTCT
1 TTTTTTCTTTTTTCT-TTTTCTCTCTTGTTTCT-TTTCT
*
684159 TTTTTTC-TTTTTCTTTTTCTCTCTTTTTTCTTTTCT
1 TTTTTTCTTTTTTCTTTTTCTCTCTTGTTTCTTTTCT
684195 TTTCTTTCTTTTTCTTCTTTTT
1 TTT-TTTC-TTTT-TTCTTTTT
684217 TCCTCGCCTT
Statistics
Matches: 51, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
35 6 0.12
36 17 0.33
37 17 0.33
39 3 0.06
40 8 0.16
ACGTcount: A:0.01, C:0.18, G:0.02, T:0.79
Consensus pattern (37 bp):
TTTTTTCTTTTTTCTTTTTCTCTCTTGTTTCTTTTCT
Found at i:684193 original size:51 final size:51
Alignment explanation
Indices: 684108--684216 Score: 132
Period size: 51 Copynumber: 2.1 Consensus size: 51
684098 CTCTTTCTTA
*
684108 TTTTTTCTTTCTTATTTTTTCTTTTTTCTATTTTCTTCTGTTTCTGTTTCT
1 TTTTTTCTTTCTTATTTTTTCTTTTTTCTATTTTCTTCTCTTTCTGTTTCT
* * * *
684159 TTTTTTCTTT-TTCTTTTTCTCTCTTTTT-TCTTTTCTTTTCTTTCTTTTTCT
1 TTTTTTCTTTCTTATTTTT-TCT-TTTTTCTATTTTCTTCTCTTTCTGTTTCT
684210 TCTTTTT
1 T-TTTTT
684217 TCCTCGCCTT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
50 7 0.14
51 33 0.66
52 10 0.20
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (51 bp):
TTTTTTCTTTCTTATTTTTTCTTTTTTCTATTTTCTTCTCTTTCTGTTTCT
Found at i:689532 original size:2 final size:2
Alignment explanation
Indices: 689525--689554 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
689515 TAATATACCA
689525 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
689555 CCATGCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:692155 original size:56 final size:56
Alignment explanation
Indices: 692069--692187 Score: 211
Period size: 56 Copynumber: 2.1 Consensus size: 56
692059 CATCGTCGGT
* * *
692069 GACCATTGATTTTGTAGGGAAAATTAGGGTGAAAATCCTATTCTTTGGTAAACCTG
1 GACCATTGATTTTGCAGGGAAAATTAGGGTGAAAATCATATTCTTTGGTAAACCTA
692125 GACCATTGATTTTGCAGGGAAAATTAGGGTGAAAATCATATTCTTTGGTAAACCTA
1 GACCATTGATTTTGCAGGGAAAATTAGGGTGAAAATCATATTCTTTGGTAAACCTA
692181 GACCATT
1 GACCATT
692188 TATCTTCATC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (56 bp):
GACCATTGATTTTGCAGGGAAAATTAGGGTGAAAATCATATTCTTTGGTAAACCTA
Found at i:692333 original size:3 final size:3
Alignment explanation
Indices: 692314--692402 Score: 117
Period size: 3 Copynumber: 29.7 Consensus size: 3
692304 GTAACCAAAA
*
692314 AAT AAT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
692359 AAT AAT AAT AAT AAC GAT AAT AAT GAT AAT AAT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
692403 CTCAGATGAA
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.01
3 73 0.99
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:699871 original size:2 final size:2
Alignment explanation
Indices: 699864--699938 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
699854 TGTGCCTATT
699864 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
699906 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
699939 GGTGTATGAC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:700556 original size:38 final size:38
Alignment explanation
Indices: 700502--700581 Score: 133
Period size: 38 Copynumber: 2.1 Consensus size: 38
700492 ACTGTCACAG
* * *
700502 TATATTGTTTGTTAATTAATTTCAACTTTGAAACGCCA
1 TATATTGTTTGATAATTAATTTCAACTATGAAACGACA
700540 TATATTGTTTGATAATTAATTTCAACTATGAAACGACA
1 TATATTGTTTGATAATTAATTTCAACTATGAAACGACA
700578 TATA
1 TATA
700582 CGATCAAACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.42
Consensus pattern (38 bp):
TATATTGTTTGATAATTAATTTCAACTATGAAACGACA
Found at i:704355 original size:12 final size:12
Alignment explanation
Indices: 704340--704406 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
704330 ATAATACTAC
704340 TAATAATAATTA
1 TAATAATAATTA
* * *
704352 TAATTATTATTG
1 TAATAATAATTA
704364 TAATAATTATGATTA
1 TAATAA-TA--ATTA
*
704379 TAATAATTATTA
1 TAATAATAATTA
*
704391 TTATAATAA-TA
1 TAATAATAATTA
704402 TAATA
1 TAATA
704407 TTTATAACCC
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
11 6 0.14
12 25 0.60
13 1 0.02
14 1 0.02
15 9 0.21
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (12 bp):
TAATAATAATTA
Found at i:704371 original size:15 final size:15
Alignment explanation
Indices: 704351--704400 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
704341 AATAATAATT
*
704351 ATAATTATTATTGTA
1 ATAATTATTATTATA
*
704366 ATAATTATGATTATA
1 ATAATTATTATTATA
704381 ATAATTATTATTATA
1 ATAATTATTATTATA
704396 ATAAT
1 ATAAT
704401 ATAATATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (15 bp):
ATAATTATTATTATA
Found at i:704745 original size:55 final size:55
Alignment explanation
Indices: 704677--705182 Score: 689
Period size: 55 Copynumber: 9.3 Consensus size: 55
704667 TTTAGGGCAT
** * * *
704677 GACTCGAACAATCTTCAACAATCGCATTTGTTCCCTATTTCTTCAGAGAGTATAA
1 GACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGA
**
704732 GACTCGAGTAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGA
1 GACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGA
* * ** *
704787 GACTCGAACAATCTTCAATAATCGTGTCTACTCCCTATTT-TT-TTAGAGTATAA
1 GACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGA
* * *
704840 GACTCGAACAATCTTTAAC-ATCGTGTCTGCTCCTTATTTCTTCAAAGAGTATGA
1 GACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGA
* *
704894 GACTCGATCAATCTTCAACAATCGTGTTTGCTCCCTATTTCTTCAGAGAGTATGA
1 GACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGA
704949 GACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGA
1 GACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGA
* * ** * * *
705004 GACTTGAACAATCTTCAATAATCGTGAATGCACCCTATTTTTTCAGAGAGTATAA
1 GACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGA
* * * *
705059 GACTCGAAAAATCTTCAACAATCGTGTCTGTTCCCTATTT-TTTAGAGAGTATAA
1 GACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGA
* * *
705113 GACTCGAACAATCTTCAAC-ATCGTGTATGCTCCCAATTTCTTCAAAGAGTATGA
1 GACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGA
*
705167 GACTCGAATAATCTTC
1 GACTCGAACAATCTTC
705183 TGTAAACGGG
Statistics
Matches: 396, Mismatches: 51, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
52 18 0.05
53 44 0.11
54 84 0.21
55 250 0.63
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (55 bp):
GACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGA
Found at i:704942 original size:217 final size:218
Alignment explanation
Indices: 704677--705182 Score: 766
Period size: 217 Copynumber: 2.3 Consensus size: 218
704667 TTTAGGGCAT
** * * *
704677 GACTCGAACAATCTTCAACAATCGCATTTGTTCCCTATTTCTTCAGAGAGTATAAGACTCGAGTA
1 GACTCGAACAATCTTCAACAATCGTGTTTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAATA
704742 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAATA
66 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAATA
** * * * *
704807 ATCGTGTCTACTCCCTATTTTTT-TAGAGTATAAGACTCGAACAATCTTTAAC-ATCGTGTCTGC
131 ATCGTGAATACACCCTATTTTTTAGAGAGTATAAGACTCGAAAAATCTTCAACAATCGTGTCTGC
* *
704870 TCCTTATTTCTTCAAAGAGTATGA
196 TCCCTATTT-TTCAAAGAGTATAA
* *
704894 GACTCGATCAATCTTCAACAATCGTGTTTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACA
1 GACTCGAACAATCTTCAACAATCGTGTTTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAATA
*
704959 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTTGAACAATCTTCAATA
66 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAATA
*
705024 ATCGTGAATGCACCCTATTTTTTCAGAGAGTATAAGACTCGAAAAATCTTCAACAATCGTGTCTG
131 ATCGTGAATACACCCTATTTTTT-AGAGAGTATAAGACTCGAAAAATCTTCAACAATCGTGTCTG
* * *
705089 TTCCCTATTTTTTAGAGAGTATAA
195 CTCCCTATTTTTCAAAGAGTATAA
* * *
705113 GACTCGAACAATCTTCAAC-ATCGTGTATGCTCCCAATTTCTTCAAAGAGTATGAGACTCGAATA
1 GACTCGAACAATCTTCAACAATCGTGTTTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAATA
705177 ATCTTC
66 ATCTTC
705183 TGTAAACGGG
Statistics
Matches: 261, Mismatches: 25, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
217 141 0.54
218 47 0.18
219 55 0.21
220 18 0.07
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (218 bp):
GACTCGAACAATCTTCAACAATCGTGTTTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAATA
ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAATA
ATCGTGAATACACCCTATTTTTTAGAGAGTATAAGACTCGAAAAATCTTCAACAATCGTGTCTGC
TCCCTATTTTTCAAAGAGTATAA
Found at i:705277 original size:54 final size:54
Alignment explanation
Indices: 705159--705668 Score: 564
Period size: 54 Copynumber: 9.4 Consensus size: 54
705149 TTTCTTCAAA
* *
705159 GAGTAT-GAGACTCGAATAATCTTCTGT-AAACGGGTTCGCT-CCT-TTT-TTCAGG
1 GAGTATGGA-ACTCGAA-CATCTTCT-TCAAACGGGTTCGCTCCCTCTTTCTTTAGG
** *
705211 GAGTATAAAACTCGAACATCTTCTTCAAAAGGGTTCGCTCCCTCTTTCTTTAGG
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGG
** * *
705265 GAGTATGGAACTC-AGACATCTTCTTCTTACAGGTTCGGTCCCTCTTTCTTTAGG
1 GAGTATGGAACTCGA-ACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGG
* ** * *
705319 AAGTATGGAACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTCTTTCTCTAGA
1 GAGTATGGAACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGG
* ** * *
705374 GAGTATGGAACTCGGACATCTTCTTCTTACGGGTTCCCTCCCTCTTTCTTCAGG
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGG
* * * *
705428 GAGTATGGAACTCAAACAATCTGCTGCAAACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGG
* ** * * * *
705483 GAGTATGGAACTCGGACATCTTCTTCTTACGAGTTCACTCCCTCTTTCTTCAAG
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGG
* * * * *
705537 GAGTATAGAACTCGAAAATCTTCTGCGAACGGGTTCACTCCCTCTTTCTTTAGG
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGG
* *
705591 GAGTATGGAACTCGAATAATCTTCTTCAAATGGGTTCGCTCCCTCTTTCTTTAGG
1 GAGTATGGAACTCGAA-CATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGG
* *
705646 GAGTATAGAACTCGAAAATCTTC
1 GAGTATGGAACTCGAACATCTTC
705669 ATTTGCTTCA
Statistics
Matches: 383, Mismatches: 65, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
50 1 0.00
51 19 0.05
52 16 0.04
53 5 0.01
54 203 0.53
55 139 0.36
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (54 bp):
GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGG
Found at i:705364 original size:109 final size:109
Alignment explanation
Indices: 705191--705668 Score: 619
Period size: 109 Copynumber: 4.4 Consensus size: 109
705181 TCTGTAAACG
* * * *
705191 GGTTCGCT-CCT-TTT-TTCAGGGAGTATAAAACTCGAAC-ATCTTCTTCAAAAGGGTTCGCTCC
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCC
* *
705252 CTCTTTCTTTAGGGAGTATGGAACTCAGACATCTTCTTCTTACA
66 CTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCTTACA
* * * **
705296 GGTTCGGTCCCTCTTTCTTTAGGAAGTATGGAACTCGAACAATCTTCAACAAACGGGTTCGCTCC
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCC
* *
705361 CTCTTTCTCTAGAGAGTATGGAACTCGGACATCTTCTTCTTACG
66 CTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCTTACA
* * * * *
705405 GGTTCCCTCCCTCTTTCTTCAGGGAGTATGGAACTCAAACAATCTGCTGCAAACGGGTTCGCTCC
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCC
705470 CTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCTTAC-
66 CTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCTTACA
* * * * *
705513 GAGTTCACTCCCTCTTTCTTCAAGGAGTATAGAACTCGAA-AATCTTCTGCGAACGGGTTCACTC
1 G-GTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTC
* * * ** **
705577 CCTCTTTCTTTAGGGAGTATGGAACTCGAATAATCTTCTTCAAATG
65 CCTCTTTCTCTAGGGAGTATGGAACTCGGA-CATCTTCTTCTTACA
705623 GGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAA-AATCTTC
1 GGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACAATCTTC
705669 ATTTGCTTCA
Statistics
Matches: 329, Mismatches: 37, Indels: 10
0.88 0.10 0.03
Matches are distributed among these distances:
105 7 0.02
106 3 0.01
107 3 0.01
108 69 0.21
109 246 0.75
110 1 0.00
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.33
Consensus pattern (109 bp):
GGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCC
CTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCTTACA
Found at i:705366 original size:55 final size:55
Alignment explanation
Indices: 704677--705669 Score: 612
Period size: 55 Copynumber: 18.3 Consensus size: 55
704667 TTTAGGGCAT
* ** * * * *
704677 GACTCGAACAATCTTCAACAATCGCATTTGTTCCCTATTTCTTCAGAGAGTATAA
1 GACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTATTTCTTTAGAGAGTATGA
** * * *
704732 GACTCGAGTAATCTTCAACAATCGTG-TCTGCTCCCTATTTCTTCAGAGAGTATGA
1 GACTCGAACAATCTTCAACAAACGGGTTC-GCTCCCTATTTCTTTAGAGAGTATGA
* * * * * *
704787 GACTCGAACAATCTTCAATAATCGTG-TCTACTCCCTATTT-TTT-TAGAGTATAA
1 GACTCGAACAATCTTCAACAAACGGGTTC-GCTCCCTATTTCTTTAGAGAGTATGA
* * * * * *
704840 GACTCGAACAATCTTTAAC-ATCGTG-TCTGCTCCTTATTTCTTCAAAGAGTATGA
1 GACTCGAACAATCTTCAACAAACGGGTTC-GCTCCCTATTTCTTTAGAGAGTATGA
* * * * *
704894 GACTCGATCAATCTTCAACAATCGTGTTTGCTCCCTATTTCTTCAGAGAGTATGA
1 GACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTATTTCTTTAGAGAGTATGA
* * *
704949 GACTCGAACAATCTTCAACAATCGTG-TCTGCTCCCTATTTCTTCAGAGAGTATGA
1 GACTCGAACAATCTTCAACAAACGGGTTC-GCTCCCTATTTCTTTAGAGAGTATGA
* * * ** * *
705004 GACTTGAACAATCTTCAATAATCGTGAAT-GCACCCTATTT-TTTCAGAGAGTATAA
1 GACTCGAACAATCTTCAACAAACG-GGTTCGCTCCCTATTTCTTT-AGAGAGTATGA
* * * * *
705059 GACTCGAAAAATCTTCAACAATCGTG-TCTGTTCCCTATTT-TTTAGAGAGTATAA
1 GACTCGAACAATCTTCAACAAACGGGTTC-GCTCCCTATTTCTTTAGAGAGTATGA
* * * * *
705113 GACTCGAACAATCTTCAAC-ATCGTGTAT-GCTCCCAATTTCTTCAAAGAGTATGA
1 GACTCGAACAATCTTCAACAAACGGGT-TCGCTCCCTATTTCTTTAGAGAGTATGA
* *** * * *
705167 GACTCGAATAATCTTCTGTAAACGGGTTCGCT-CCT-TTT-TTCAGGGAGTATAA
1 GACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTATTTCTTTAGAGAGTATGA
* ** * * *
705219 AACTCGAAC-ATCTTCTTCAAAAGGGTTCGCTCCCTCTTTCTTTAGGGAGTATG-
1 GACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTATTTCTTTAGAGAGTATGA
** ** * * *
705272 GAACTC-AGAC-ATCTTCTTCTTACAGGTTCGGTCCCTCTTTCTTTAG-GAAGTATG-
1 G-ACTCGA-ACAATCTTCAACAAACGGGTTCGCTCCCTATTTCTTTAGAG-AGTATGA
* *
705326 GAACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTCTTTCTCTAGAGAGTATG-
1 G-ACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTATTTCTTTAGAGAGTATGA
* ** ** * * * *
705381 GAACTCGGAC-ATCTTCTTCTTACGGGTTCCCTCCCTCTTTCTTCAGGGAGTATG-
1 G-ACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTATTTCTTTAGAGAGTATGA
* * ** * * *
705435 GAACTCAAACAATCTGCTGCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATG-
1 G-ACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTATTTCTTTAGAGAGTATGA
* ** ** * * * *
705490 GAACTCGGAC-ATCTTCTTCTTACGAGTTCACTCCCTCTTTCTTCA-AGGAGTAT-A
1 G-ACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTATTTCTTTAGA-GAGTATGA
** * * * *
705544 GAACTCGAA-AATCTTCTGCGAACGGGTTCACTCCCTCTTTCTTTAGGGAGTATG-
1 G-ACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTATTTCTTTAGAGAGTATGA
* ** * * *
705598 GAACTCGAATAATCTTCTTCAAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTAT-A
1 G-ACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTATTTCTTTAGAGAGTATGA
705653 GAACTCGAA-AATCTTCA
1 G-ACTCGAACAATCTTCA
705670 TTTGCTTCAC
Statistics
Matches: 786, Mismatches: 119, Indels: 67
0.81 0.12 0.07
Matches are distributed among these distances:
51 19 0.02
52 39 0.05
53 51 0.06
54 288 0.37
55 386 0.49
56 2 0.00
57 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (55 bp):
GACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTATTTCTTTAGAGAGTATGA
Found at i:705431 original size:163 final size:161
Alignment explanation
Indices: 705159--705669 Score: 550
Period size: 163 Copynumber: 3.2 Consensus size: 161
705149 TTTCTTCAAA
* *** * *
705159 GAGTAT-GAGACTCGAATAATCTTCTGTAAACGGGTTCGCT-CCT-TTTTTCAGGGAGTATAAAA
1 GAGTATGGA-ACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTCTTTCTCA-GGAGTATAGAA
* *
705221 CTCGAACATCTTCTTCAAAAGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCAGACATCT
64 CTCGAACATCTTCTTCAAACGGGTTCACTCCCTCTTTCTTTAGGGAGTATGGAACTCAGACATCT
*
705286 TCTTCTTACAGGTTCGGTCCCTCTTTCTTTAGG
129 TCTTCTTACAGGTTCGCTCCCTCTTTCTTTAGG
* *
705319 AAGTATGGAACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTCTTTCTCTAGAGAGTATGGAA
1 GAGTATGGAACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTCTTTCTC-AG-GAGTATAGAA
* ** * * *
705384 CTCGGACATCTTCTTCTTACGGGTTCCCTCCCTCTTTCTTCAGGGAGTATGGAACTCAAACAATC
64 CTCGAACATCTTCTTCAAACGGGTTCACTCCCTCTTTCTTTAGGGAGTATGGAACTCAGAC-ATC
* * ** * *
705449 TGCTGCAAACGGGTTCGCTCCCTCTTTCTCTAGG
128 TTCTTCTTACAGGTTCGCTCCCTCTTTCTTTAGG
* ** ** * *
705483 GAGTATGGAACTCGGAC-ATCTTCTTCTTACGAGTTCACTCCCTCTTTCTTCAAGGAGTATAGAA
1 GAGTATGGAACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTCTTTC-TC-AGGAGTATAGAA
* * * **
705547 CTCGAAAATCTTCTGCGAACGGGTTCACTCCCTCTTTCTTTAGGGAGTATGGAACTC-GA-ATAA
64 CTCGAACATCTTCTTCAAACGGGTTCACTCCCTCTTTCTTTAGGGAGTATGGAACTCAGACATCT
*
705610 TCTTCTTCAAATGGGTTCGCTCCCTCTTTCTTTAGG
129 TCTTCTT-ACA--GGTTCGCTCCCTCTTTCTTTAGG
*
705646 GAGTATAGAACTCGAA-AATCTTCA
1 GAGTATGGAACTCGAACAATCTTCA
705670 TTTGCTTCAC
Statistics
Matches: 288, Mismatches: 52, Indels: 19
0.80 0.14 0.05
Matches are distributed among these distances:
160 37 0.13
161 6 0.02
162 7 0.02
163 189 0.66
164 49 0.17
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (161 bp):
GAGTATGGAACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTCTTTCTCAGGAGTATAGAACT
CGAACATCTTCTTCAAACGGGTTCACTCCCTCTTTCTTTAGGGAGTATGGAACTCAGACATCTTC
TTCTTACAGGTTCGCTCCCTCTTTCTTTAGG
Found at i:705745 original size:37 final size:37
Alignment explanation
Indices: 705669--705752 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 37
705659 GAAAATCTTC
*
705669 ATTTGCTTCACTACTTCTTTATGAAGGCTTCTAGATG
1 ATTTGCTTCACTACTTCTTTATGAAGGCTTCAAGATG
* * *
705706 ATTTGTTTCACTAC-TCTTTCGTGAAGGCTT-AAGTTTG
1 ATTTGCTTCACTACTTCTTT-ATGAAGGCTTCAAG-ATG
705743 ATTTGCTTCA
1 ATTTGCTTCA
705753 AAGGTCAAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
36 7 0.17
37 33 0.82
ACGTcount: A:0.20, C:0.18, G:0.17, T:0.45
Consensus pattern (37 bp):
ATTTGCTTCACTACTTCTTTATGAAGGCTTCAAGATG
Found at i:706122 original size:37 final size:37
Alignment explanation
Indices: 706066--706198 Score: 187
Period size: 37 Copynumber: 3.6 Consensus size: 37
706056 TTGTTCCAAC
* * *
706066 ACTCTTCTGAGAAGGCTTAAAATGGATTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAGATGGATTTGCTTCACT
* *
706103 ACTCTTTGGTGAAGACTTAAGATGG-TTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAGATGGATTTGCTTCACT
* *
706139 ACTCTTCGGTGAAGGCTTAAGATTGATTTACTTCACT
1 ACTCTTCGGTGAAGGCTTAAGATGGATTTGCTTCACT
*
706176 ACTCTTCAGTGAAGGCTTAAGAT
1 ACTCTTCGGTGAAGGCTTAAGAT
706199 TGACTTTTCT
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
36 33 0.39
37 52 0.61
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (37 bp):
ACTCTTCGGTGAAGGCTTAAGATGGATTTGCTTCACT
Found at i:706138 original size:36 final size:36
Alignment explanation
Indices: 706050--706198 Score: 176
Period size: 37 Copynumber: 4.1 Consensus size: 36
706040 CTGATGGTCT
* *
706050 GATGGTTTG-TTCCAAC-ACTCTTCTGAGAAGGCTTAA
1 GATGGTTTGCTT-C-ACTACTCTTCGGTGAAGGCTTAA
* * *
706086 AATGGATTTGCTTCACTACTCTTTGGTGAAGACTTAA
1 GATGG-TTTGCTTCACTACTCTTCGGTGAAGGCTTAA
706123 GATGGTTTGCTTCACTACTCTTCGGTGAAGGCTTAA
1 GATGGTTTGCTTCACTACTCTTCGGTGAAGGCTTAA
* * *
706159 GATTGATTTACTTCACTACTCTTCAGTGAAGGCTTAA
1 GA-TGGTTTGCTTCACTACTCTTCGGTGAAGGCTTAA
706196 GAT
1 GAT
706199 TGACTTTTCT
Statistics
Matches: 98, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
36 38 0.39
37 58 0.59
38 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (36 bp):
GATGGTTTGCTTCACTACTCTTCGGTGAAGGCTTAA
Found at i:706173 original size:73 final size:73
Alignment explanation
Indices: 706050--706198 Score: 194
Period size: 73 Copynumber: 2.0 Consensus size: 73
706040 CTGATGGTCT
* * **
706050 GATGGTTTGTTCCAACACTCTTCTGAGAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGTGA
1 GATGGTTTGTTCCAACACTCTTCGGAGAAGGCTTAAAATGGATTTACTTCACTACTCTTCAGTGA
706115 AGACTTAA
66 AGACTTAA
* * *
706123 GATGGTTTGCTT-C-ACTACTCTTCGGTGAAGGCTTAAGATTGATTTACTTCACTACTCTTCAGT
1 GATGGTTTG-TTCCAAC-ACTCTTCGGAGAAGGCTTAAAATGGATTTACTTCACTACTCTTCAGT
*
706186 GAAGGCTTAA
64 GAAGACTTAA
706196 GAT
1 GAT
706199 TGACTTTTCT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
72 2 0.03
73 62 0.94
74 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (73 bp):
GATGGTTTGTTCCAACACTCTTCGGAGAAGGCTTAAAATGGATTTACTTCACTACTCTTCAGTGA
AGACTTAA
Found at i:708848 original size:2 final size:2
Alignment explanation
Indices: 708837--708871 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
708827 TTGTATACAC
708837 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
708872 TTTGTTGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:715925 original size:14 final size:14
Alignment explanation
Indices: 715906--715935 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
715896 AAATATTTAT
715906 TATTTGAAAATCGG
1 TATTTGAAAATCGG
715920 TATTTGAAAATCGG
1 TATTTGAAAATCGG
715934 TA
1 TA
715936 AAAATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (14 bp):
TATTTGAAAATCGG
Found at i:716050 original size:92 final size:92
Alignment explanation
Indices: 715946--716136 Score: 310
Period size: 92 Copynumber: 2.1 Consensus size: 92
715936 AAAATTTTTA
*
715946 ACAATAAAATCAAAACTACTTAATCGTGTAAAATCAAAATATATTATGTCAACATCCAAATCAAC
1 ACAATAAAATCAAAACTACTTAATCGTGTAAAATCAAAATATATTATGTCAACATCAAAATCAAC
* * *
716011 TCCATTTTCAGGCAGCAAGATGACAAT
66 TCCACTTTCAAGCAGCAACATGACAAT
* *
716038 ACAATAAAATCAAAATTACTTAATCGTGTAAAATCAAAATATATTATGTCAACATCAAAATCAAG
1 ACAATAAAATCAAAACTACTTAATCGTGTAAAATCAAAATATATTATGTCAACATCAAAATCAAC
*
716103 TCCACTTTCAAGCATCAACATGACAAT
66 TCCACTTTCAAGCAGCAACATGACAAT
*
716130 TCAATAA
1 ACAATAA
716137 TGTTTCATAC
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.27
Consensus pattern (92 bp):
ACAATAAAATCAAAACTACTTAATCGTGTAAAATCAAAATATATTATGTCAACATCAAAATCAAC
TCCACTTTCAAGCAGCAACATGACAAT
Found at i:731160 original size:2 final size:2
Alignment explanation
Indices: 731148--731179 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
731138 TTCCATTGAA
*
731148 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
731180 CAAACCAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:733585 original size:29 final size:29
Alignment explanation
Indices: 733551--733728 Score: 157
Period size: 29 Copynumber: 6.2 Consensus size: 29
733541 CCGTTGATCG
* *
733551 GGTGATATTTTAGTTATTATTTTGAAAAT
1 GGTGATATTTTGGTAATTATTTTGAAAAT
733580 GGTGATATTTTGGTAATTATTTTGAAAAT
1 GGTGATATTTTGGTAATTATTTTGAAAAT
* * *
733609 GGTGTTATTTTTGTAATT-TTTTTAAAA-
1 GGTGATATTTTGGTAATTATTTTGAAAAT
* * ** * *
733636 AGTGATAATTCCGTAA--ATTTTAAAAAA
1 GGTGATATTTTGGTAATTATTTTGAAAAT
** *
733663 CATGATATTTTGGTAATTATTTTGAAAAG
1 GGTGATATTTTGGTAATTATTTTGAAAAT
* * * *
733692 GGTGATATTTTTGTAAATTTTTTTAAAAAG
1 GGTGATATTTTGGT-AATTATTTTGAAAAT
733722 GGTGATA
1 GGTGATA
733729 AATGTATAAA
Statistics
Matches: 121, Mismatches: 23, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
26 8 0.07
27 22 0.18
28 8 0.07
29 63 0.52
30 20 0.17
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (29 bp):
GGTGATATTTTGGTAATTATTTTGAAAAT
Found at i:740802 original size:18 final size:18
Alignment explanation
Indices: 740779--740817 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
740769 ACCGGTTCCA
740779 ACCCGACCCAACCCGTTG
1 ACCCGACCCAACCCGTTG
*
740797 ACCCGACCCGACCCGTTG
1 ACCCGACCCAACCCGTTG
740815 ACC
1 ACC
740818 GTTGACCGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.51, G:0.18, T:0.10
Consensus pattern (18 bp):
ACCCGACCCAACCCGTTG
Found at i:748065 original size:21 final size:21
Alignment explanation
Indices: 748041--748080 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
748031 ACCGTCAACT
*
748041 AAATCCACTTCCAAATCCTCA
1 AAATCCAATTCCAAATCCTCA
*
748062 AAATCCAATTCCTAATCCT
1 AAATCCAATTCCAAATCCT
748081 AATCTCATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATCCAATTCCAAATCCTCA
Found at i:749333 original size:24 final size:23
Alignment explanation
Indices: 749283--749333 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
749273 GCTTCAACTT
* *
749283 TTTGGATTGTTTGATTTTGTGAC
1 TTTGGATTGTTTGATGTTGTGAA
749306 TTTGGATTTGTTTGGATGTT-TGAA
1 TTTGGA-TTGTTT-GATGTTGTGAA
749330 TTTG
1 TTTG
749334 TGGATTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.25
24 13 0.54
25 5 0.21
ACGTcount: A:0.14, C:0.02, G:0.27, T:0.57
Consensus pattern (23 bp):
TTTGGATTGTTTGATGTTGTGAA
Found at i:754664 original size:85 final size:85
Alignment explanation
Indices: 754546--754777 Score: 349
Period size: 85 Copynumber: 2.7 Consensus size: 85
754536 AATAATATAA
* * * *
754546 TAAATCCTAATTAAAACACTTAAGA-CTACTTAAACTAAAATACCTAAAACAAAGATAAAATAAA
1 TAAATCCTAATTGAAATAC-TAACATCTATTTAAACTAAAATACCTAAAACAAAGATAAAATAAA
*
754610 ATATTATTTAAAATAACATCC
65 ATACTATTTAAAATAACATCC
*
754631 TAAATCCTAATTGAAATACTAACATCTATTTAAACGAAAATACCTAAAACAAAGATAAAATAAAA
1 TAAATCCTAATTGAAATACTAACATCTATTTAAACTAAAATACCTAAAACAAAGATAAAATAAAA
*
754696 TACTATTTAAAATAATATCC
66 TACTATTTAAAATAACATCC
* * * *
754716 TAAATACTAATTGAAATACCAACATCTATTTAAACTAAAATATCTAAAATAAAGATAAAATA
1 TAAATCCTAATTGAAATACTAACATCTATTTAAACTAAAATACCTAAAACAAAGATAAAATA
754778 TAATGTTTAA
Statistics
Matches: 134, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
84 4 0.03
85 130 0.97
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.28
Consensus pattern (85 bp):
TAAATCCTAATTGAAATACTAACATCTATTTAAACTAAAATACCTAAAACAAAGATAAAATAAAA
TACTATTTAAAATAACATCC
Found at i:764160 original size:13 final size:13
Alignment explanation
Indices: 764142--764175 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
764132 AATGAGATAA
764142 AAATTAAATAAAC
1 AAATTAAATAAAC
*
764155 AAATTAAATAAAT
1 AAATTAAATAAAC
764168 AAA-TAAAT
1 AAATTAAAT
764176 TGGGATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (13 bp):
AAATTAAATAAAC
Found at i:764922 original size:86 final size:86
Alignment explanation
Indices: 764826--765055 Score: 369
Period size: 85 Copynumber: 2.7 Consensus size: 86
764816 GTTAAAACTT
*
764826 TTTAAACTAAAATACCTAAAACAAAGATAAAATAAAATACTATTTAAAATAGTATCCTAAAAACC
1 TTTAAACTAAAATACCTAAAACAAAGATAAAATAAAATACTATTTAAAATAATATCCTAAAAACC
764891 TAATTGAAATACTAACATCTA
66 TAATTGAAATACTAACATCTA
*
764912 TTTAAACTAAAATACCTAAAACAAAGATAAAATAAAATACTATTTAAAATAATATCCT-AAATCC
1 TTTAAACTAAAATACCTAAAACAAAGATAAAATAAAATACTATTTAAAATAATATCCTAAAAACC
764976 TAATTGAAATACTAACATCTA
66 TAATTGAAATACTAACATCTA
* * * * *
764997 TTTAAACTAAAATATCTAAAATAAAGATAAAAT---ATAATGTTTAAAATATTATCCTAAAA
1 TTTAAACTAAAATACCTAAAACAAAGATAAAATAAAATACTATTTAAAATAATATCCTAAAA
765056 CTTGAGTTTA
Statistics
Matches: 136, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
82 19 0.14
83 3 0.02
85 57 0.42
86 57 0.42
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (86 bp):
TTTAAACTAAAATACCTAAAACAAAGATAAAATAAAATACTATTTAAAATAATATCCTAAAAACC
TAATTGAAATACTAACATCTA
Found at i:784612 original size:49 final size:46
Alignment explanation
Indices: 784501--784622 Score: 138
Period size: 49 Copynumber: 2.6 Consensus size: 46
784491 GTAACCATGC
*
784501 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAAA
* * * **
784547 AAATAAGCTTACGAGCTTATGGAATTTTAAATGGTAAGTATTTTG-GTAA
1 AAATAAGCTTATGAGCTTATGGAA---T-AATGGCAAGTATATTGAAAAA
*
784596 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
784623 AAGGTAAGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
45 2 0.03
46 23 0.36
49 25 0.39
50 14 0.22
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.31
Consensus pattern (46 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAAA
Found at i:793578 original size:17 final size:18
Alignment explanation
Indices: 793556--793589 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
793546 TTGAAAGGTC
*
793556 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
793573 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
793590 ACAGAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:796195 original size:49 final size:45
Alignment explanation
Indices: 796098--796213 Score: 142
Period size: 49 Copynumber: 2.5 Consensus size: 45
796088 GTAACCATGC
*
796098 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAA
* * * **
796143 AAATAAGCTTACGAGCTTATGGAATTTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA---T-AATGGCAAGTATATTGAAAA
796192 AAATAAGCTTATGAGCTTATGG
1 AAATAAGCTTATGAGCTTATGG
796214 GGTAAAAGGT
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
45 22 0.37
48 1 0.02
49 37 0.62
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAA
Found at i:796967 original size:18 final size:18
Alignment explanation
Indices: 796952--796989 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
796942 CCTTACACAC
796952 TTTGCCACAACAACACCA
1 TTTGCCACAACAACACCA
* *
796970 TTTGCCACGACAACGCCA
1 TTTGCCACAACAACACCA
796988 TT
1 TT
796990 CATACTTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.37, G:0.11, T:0.21
Consensus pattern (18 bp):
TTTGCCACAACAACACCA
Found at i:799610 original size:2 final size:2
Alignment explanation
Indices: 799603--799639 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
799593 ATAACTCTAG
799603 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
799640 GCAACAACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:806468 original size:15 final size:15
Alignment explanation
Indices: 806448--806477 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
806438 TTCCTGGTAA
806448 GGTTGTTATAAAACC
1 GGTTGTTATAAAACC
806463 GGTTGTTATAAAACC
1 GGTTGTTATAAAACC
806478 ATGAAAGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (15 bp):
GGTTGTTATAAAACC
Found at i:810269 original size:36 final size:35
Alignment explanation
Indices: 810194--810274 Score: 110
Period size: 38 Copynumber: 2.2 Consensus size: 35
810184 ATTCTTAATG
810194 ATATTATTAGTTTAAATATTAAAAATTTATAAAAATA
1 ATATTA-TAGTTTAAATATTAAAAATTTAT-AAAATA
*
810231 ATATTATAGTTTATAAATATTAAAAATTTAT-AATTA
1 ATATTATAG-TT-TAAATATTAAAAATTTATAAAATA
810267 ATATTATA
1 ATATTATA
810275 AACATAATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
36 15 0.37
37 8 0.20
38 18 0.44
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (35 bp):
ATATTATAGTTTAAATATTAAAAATTTATAAAATA
Found at i:810285 original size:38 final size:37
Alignment explanation
Indices: 810206--810294 Score: 90
Period size: 38 Copynumber: 2.3 Consensus size: 37
810196 ATTATTAGTT
** *
810206 TAAATATTAAAAATTTATAAAAATAATATTATAGTTTA
1 TAAATATTAAAAATTTAT-AAAATAATATTATACATAA
*
810244 TAAATATTAAAAATTTAT-AATTAATATTATAAACATAA
1 TAAATATTAAAAATTTATAAAATAATATTAT--ACATAA
*
810282 TAAAAAATTAAAA
1 T-AAATATTAAAA
810295 CATAACATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
36 11 0.26
38 22 0.51
39 10 0.23
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (37 bp):
TAAATATTAAAAATTTATAAAATAATATTATACATAA
Found at i:814890 original size:45 final size:45
Alignment explanation
Indices: 814673--814891 Score: 260
Period size: 45 Copynumber: 4.9 Consensus size: 45
814663 ACTATAACAT
* * * **
814673 CTTTTCTGTTAATAATGCACCCATATGTATTTCAACTATTTTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* * * * *
814718 CTTTTATGTTGATGATGTACCCATATACATCTCAAC-CATAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTC-TAGTATA
* * * *
814763 CTTTTCTGTTGAGAATGTACCCATATACATTTCAACTCTAGCATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* * *
814808 CTTTTCTGTTGAAAATACACCCATATGCATTTAAACTCTAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
*
814853 CTTTTCTGTTGATAATGCACCCATATGTATTTCAACTCT
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCT
814892 GGCATCCTTT
Statistics
Matches: 147, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
45 146 0.99
46 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.41
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
Found at i:814919 original size:90 final size:90
Alignment explanation
Indices: 814673--815008 Score: 268
Period size: 90 Copynumber: 3.9 Consensus size: 90
814663 ACTATAACAT
* * *** * * * *
814673 CTTTTCTGTTAATAATGCACCCATATGTATTTCAACTATTTTATACTTTTATGTTGATGATGTAC
1 CTTTTCTGTTGATAATGCACCCATATGTATTTCAACTCTAGCATCCTTTCATGTTGATAATGCAC
* * *
814738 CCATATACATCTCAACCATAGTATA
66 CCATATGCATTTAAACCATAGTATA
* * ** * * *
814763 CTTTTCTGTTGAGAATGTACCCATATACATTTCAACTCTAGCATACTTTTC-TGTTGAAAATACA
1 CTTTTCTGTTGATAATGCACCCATATGTATTTCAACTCTAGCAT-CCTTTCATGTTGATAATGCA
814827 CCCATATGCATTTAAACTC-TAGTATA
65 CCCATATGCATTTAAAC-CATAGTATA
* **
814853 CTTTTCTGTTGATAATGCACCCATATGTATTTCAACTCTGGCATCCTTTCATG-CCATTAATGCA
1 CTTTTCTGTTGATAATGCACCCATATGTATTTCAACTCTAGCATCCTTTCATGTTGA-TAATGCA
814917 CCCATATGCA--T------TA-T-T-
65 CCCATATGCATTTAAACCATAGTATA
* * * ** * * * *
814932 CTTTTATGTTGACAATGTACCCATATACATTACAACTATGGCATCCTTTCATGTCGATAATGCAC
1 CTTTTCTGTTGATAATGCACCCATATGTATTTCAACTCTAGCATCCTTTCATGTTGATAATGCAC
814997 CCATATGCATTT
66 CCATATGCATTT
815009 TTCTTTTCAA
Statistics
Matches: 202, Mismatches: 37, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
79 63 0.31
80 3 0.01
81 2 0.01
82 2 0.01
88 1 0.00
89 6 0.03
90 121 0.60
91 4 0.02
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (90 bp):
CTTTTCTGTTGATAATGCACCCATATGTATTTCAACTCTAGCATCCTTTCATGTTGATAATGCAC
CCATATGCATTTAAACCATAGTATA
Found at i:814984 original size:79 final size:79
Alignment explanation
Indices: 814853--815015 Score: 229
Period size: 79 Copynumber: 2.1 Consensus size: 79
814843 CTCTAGTATA
* * ** * *
814853 CTTTTCTGTTGATAATGCACCCATATGTATTTCAACTCTGGCATCCTTTCATG-CCATTAATGCA
1 CTTTTATGTTGACAATGCACCCATATACATTACAACTATGGCATCCTTTCATGTCCA-TAATGCA
814917 CCCATATGCATTATT
65 CCCATATGCATTATT
* *
814932 CTTTTATGTTGACAATGTACCCATATACATTACAACTATGGCATCCTTTCATGTCGATAATGCAC
1 CTTTTATGTTGACAATGCACCCATATACATTACAACTATGGCATCCTTTCATGTCCATAATGCAC
*
814997 CCATATGCATTTTT
66 CCATATGCATTATT
815011 CTTTT
1 CTTTT
815016 CAATTTGTTC
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
79 72 0.97
80 2 0.03
ACGTcount: A:0.25, C:0.24, G:0.11, T:0.40
Consensus pattern (79 bp):
CTTTTATGTTGACAATGCACCCATATACATTACAACTATGGCATCCTTTCATGTCCATAATGCAC
CCATATGCATTATT
Found at i:820443 original size:45 final size:45
Alignment explanation
Indices: 820383--820612 Score: 246
Period size: 45 Copynumber: 5.1 Consensus size: 45
820373 ATACATTTTA
* *
820383 AACTATAACAT-CTTTTCTGTTGATAATGCACCCATATGTATTTC
1 AACTATAATATACTTTTCTGTTGATAATGCACCCATATGCATTTC
** * * * ** * *
820427 AACTATTGTATACTTTTATGTTGATGATGTAAACATATACATCTC
1 AACTATAATATACTTTTCTGTTGATAATGCACCCATATGCATTTC
* * * *
820472 AACCATAATATACTTTTCTGTTGAGAATGTACCCATATACATTTC
1 AACTATAATATACTTTTCTGTTGATAATGCACCCATATGCATTTC
* ** * *
820517 AACTCTAGCATACTTTTCTGTTGATAATACATCCATATGCATTTC
1 AACTATAATATACTTTTCTGTTGATAATGCACCCATATGCATTTC
*
820562 AACTATAATATATTTTTTTCTGTTGATAATGCACCCATATGCATTTC
1 AACTATAATATA--CTTTTCTGTTGATAATGCACCCATATGCATTTC
820609 AACT
1 AACT
820613 CTGGCATCCT
Statistics
Matches: 148, Mismatches: 35, Indels: 3
0.80 0.19 0.02
Matches are distributed among these distances:
44 8 0.05
45 106 0.72
47 34 0.23
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (45 bp):
AACTATAATATACTTTTCTGTTGATAATGCACCCATATGCATTTC
Found at i:820495 original size:90 final size:91
Alignment explanation
Indices: 820392--820612 Score: 273
Period size: 90 Copynumber: 2.4 Consensus size: 91
820382 AAACTATAAC
* * * * **
820392 ATCTTTTCTGTTGATAATGCACCCATATGTATTTCAACTATTGTATACTTTTATGTTGATGATGT
1 ATCTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTATGTTGATAATAC
820457 AAACATATACATCTCAACCATAATAT
66 AAACATATACATCTCAACCATAATAT
* * * * *
820483 A-CTTTTCTGTTGAGAATGTACCCATATACATTTCAACTCTAGCATACTTTTCTGTTGATAATAC
1 ATCTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTATGTTGATAATAC
** * * *
820547 ATCCATATGCATTTCAACTATAATAT
66 AAACATATACATCTCAACCATAATAT
*
820573 ATTTTTTTCTGTTGATAATGCACCCATATGCATTTCAACT
1 A-TCTTTTCTGTTGATAATGCACCCATATGCATTTCAACT
820613 CTGGCATCCT
Statistics
Matches: 108, Mismatches: 20, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
90 74 0.69
91 1 0.01
92 33 0.31
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.42
Consensus pattern (91 bp):
ATCTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTATGTTGATAATAC
AAACATATACATCTCAACCATAATAT
Found at i:820645 original size:92 final size:90
Alignment explanation
Indices: 820394--820651 Score: 259
Period size: 90 Copynumber: 2.8 Consensus size: 90
820384 ACTATAACAT
* * * * * * * *
820394 CTTTTCTGTTGATAATGCACCCATATGTATTTCAACTATTGTATACTTTTATGTTGATGATGTAA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATCCTTTCATGTTGATAATGCAA
* * *
820459 ACATATACATCTCAACCATAATATA
66 CCATATGCATTTCAACCATAATATA
* * * * *
820484 CTTTTCTGTTGAGAATGTACCCATATACATTTCAACTCTAGCATACTTTTC-TGTTGATAATACA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCAT-CCTTTCATGTTGATAATGCA
* *
820548 TCCATATGCATTTCAACTATAATATA
65 ACCATATGCATTTCAACCATAATATA
* * **
820574 TTTTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTGGCATCCTTTCATG-CCACTAATG
1 --CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATCCTTTCATGTTGA-TAATG
*
820638 CACCCATATGCATT
63 CAACCATATGCATT
820652 ATTCTTTGAT
Statistics
Matches: 135, Mismatches: 28, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
90 68 0.50
91 9 0.07
92 58 0.43
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (90 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATCCTTTCATGTTGATAATGCAA
CCATATGCATTTCAACCATAATATA
Found at i:824239 original size:26 final size:28
Alignment explanation
Indices: 824179--824240 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
824169 GAGTATTGCT
*
824179 GAGCTCGACTCGACTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTG--A-C
824210 GAGCTCGACTCGACTCGAAAACTC-G-C
1 GAGCTCGACTCGACTCGAAAACTCTGAC
824236 GAGCT
1 GAGCT
824241 TAAAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
30 1 0.03
31 24 0.80
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTCTGAC
Found at i:830152 original size:18 final size:18
Alignment explanation
Indices: 830131--830168 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
830121 AAGAGTCCCC
830131 AGCCTGCTGA-ACCTGAAG
1 AGCCTGCTGACA-CTGAAG
830149 AGCCTGCTGACACTGAAG
1 AGCCTGCTGACACTGAAG
830167 AG
1 AG
830169 ACTAATGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.16
Consensus pattern (18 bp):
AGCCTGCTGACACTGAAG
Found at i:831760 original size:20 final size:20
Alignment explanation
Indices: 831735--831786 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
831725 TGTATCCTGT
831735 TATCGATACCCTCAT-AATGG
1 TATCGATACCCT-ATCAATGG
*
831755 TATCGATATCCCTATGCTATGG
1 TATCGATA-CCCTAT-CAATGG
831777 TATCGATACC
1 TATCGATACC
831787 TAATTTGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 10 0.36
21 6 0.21
22 12 0.43
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (20 bp):
TATCGATACCCTATCAATGG
Found at i:831818 original size:34 final size:34
Alignment explanation
Indices: 831775--831855 Score: 135
Period size: 34 Copynumber: 2.4 Consensus size: 34
831765 CCTATGCTAT
*
831775 GGTATCGATACCTAATTTGGAATCGATATTTACA
1 GGTATCGATACCCAATTTGGAATCGATATTTACA
* *
831809 GGTATCGATACCCAATTTGGATTCGATGTTTACA
1 GGTATCGATACCCAATTTGGAATCGATATTTACA
831843 GGTATCGATACCC
1 GGTATCGATACCC
831856 TTACCATGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (34 bp):
GGTATCGATACCCAATTTGGAATCGATATTTACA
Found at i:832518 original size:2 final size:2
Alignment explanation
Indices: 832511--832540 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
832501 TATTTCTCTA
832511 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
832541 CTACCATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:833757 original size:32 final size:32
Alignment explanation
Indices: 833707--833814 Score: 168
Period size: 32 Copynumber: 3.4 Consensus size: 32
833697 ACTAGGGTGA
833707 CCTTGGGTA-GCTCTGAGGCCCCAAGGAATTT
1 CCTTGGGTAGGCTCTGAGGCCCCAAGGAATTT
833738 CCTTGGGTAGGCTCTGAGGCCCCAAGGAATTT
1 CCTTGGGTAGGCTCTGAGGCCCCAAGGAATTT
* *
833770 CCTTGGGTAGGCTCTAAGGCCCCAA-G-ATACT
1 CCTTGGGTAGGCTCTGAGGCCCCAAGGAAT-TT
833801 CCTTGGGTAGGCTC
1 CCTTGGGTAGGCTC
833815 ATTTCAATAT
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
30 2 0.03
31 25 0.34
32 46 0.63
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTGAGGCCCCAAGGAATTT
Found at i:835284 original size:55 final size:55
Alignment explanation
Indices: 835198--835309 Score: 179
Period size: 55 Copynumber: 2.0 Consensus size: 55
835188 ATTTTAAACA
* * *
835198 CTATTTTTATTATCAACATGTTGTTGGGAAATTATTTTAATCTTTGTTTCTCTCT
1 CTATTTTTATTATCAACATGATGTTGAGAAATTATTTTAATCTTTGATTCTCTCT
* *
835253 CTATTTTTATTATTAAGATGATGTTGAGAAATTATTTTAATCTTTGATTCTCTCT
1 CTATTTTTATTATCAACATGATGTTGAGAAATTATTTTAATCTTTGATTCTCTCT
835308 CT
1 CT
835310 CTAGACATTC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.24, C:0.12, G:0.11, T:0.54
Consensus pattern (55 bp):
CTATTTTTATTATCAACATGATGTTGAGAAATTATTTTAATCTTTGATTCTCTCT
Found at i:840606 original size:310 final size:312
Alignment explanation
Indices: 840016--840638 Score: 1189
Period size: 310 Copynumber: 2.0 Consensus size: 312
840006 AGTTTTCAGC
840016 TTCATCTTTAATCTTTAGGAGATAAACTTTTGTATATCTTGAATAATCAATTACAAAAGTTATGT
1 TTCATCTTTAATCTTTAGGAGATAAACTTTTGTATATCTTGAATAATCAATTACAAAAGTTATGT
* *
840081 AGTAGTGTTTTCCTCCTTTACTTTCAGTGTTTCTAAAATCTACTAGATCAGTATGAATAAGTTCT
66 AGTAATGTTTTCCTCCTTTACTTTCAGTGTTTCTAAAATCTACTAGATCAGTATAAATAAGTTCT
*
840146 AACAATTCAGTCTTTCTATTAGAAATAGTCTTAAAGTGAGGTCTAGTATGCTTAGCTTATACACA
131 AACAATTCAGTCTTTCTATTAGAAACAGTCTTAAAGTGAGGTCTAGTATGCTTAGCTTATACACA
840211 AATCTCACATTTGATAAAGCTAGTTGTGTCTAGTTTAGGCAGAACATTCATATTTATTAATTTCT
196 AATCTCACATTTGATAAAGCTAGTTGTGTCTAGTTTAGGCAGAACATTCATATTTATTAATTTCT
840276 TTAAAGAATGAATATCACGTGTCCTAATCTAGCATGCCACATATCAATGGAT
261 TTAAAGAATGAATATCACGTGTCCTAATCTAGCATGCCACATATCAATGGAT
840328 TTCATCTTTAATC-TTAGGAGATAAACTTTTGTATATCTTGAATAATC-ATTACAAAAGTTATGT
1 TTCATCTTTAATCTTTAGGAGATAAACTTTTGTATATCTTGAATAATCAATTACAAAAGTTATGT
840391 AGTAATGTTTTCCTCCTTTACTTTCAGTGTTTCTAAAATCTACTAGATCAGTATAAATAAGTTCT
66 AGTAATGTTTTCCTCCTTTACTTTCAGTGTTTCTAAAATCTACTAGATCAGTATAAATAAGTTCT
840456 AACAATTCAGTCTTTCTATTAGAAACAGTCTTAAAGTGAGGTCTAGTATGCTT-GCTTATACACA
131 AACAATTCAGTCTTTCTATTAGAAACAGTCTTAAAGTGAGGTCTAGTATGCTTAGCTTATACACA
840520 AATCTCACATTTGATAAAGCTAGTTGTGTCTAGTTTAGGCAGAACATTCATATTTATTAATTTCT
196 AATCTCACATTTGATAAAGCTAGTTGTGTCTAGTTTAGGCAGAACATTCATATTTATTAATTTCT
840585 TTAAAGAATGAATATTCACGTGTCCTAATCTAGCATGCCACATATCAATGGAT
261 TTAAAGAATGAATA-TCACGTGTCCTAATCTAGCATGCCACATATCAATGGAT
840638 T
1 T
840639 CAACAATATA
Statistics
Matches: 307, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
309 90 0.29
310 170 0.55
311 34 0.11
312 13 0.04
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (312 bp):
TTCATCTTTAATCTTTAGGAGATAAACTTTTGTATATCTTGAATAATCAATTACAAAAGTTATGT
AGTAATGTTTTCCTCCTTTACTTTCAGTGTTTCTAAAATCTACTAGATCAGTATAAATAAGTTCT
AACAATTCAGTCTTTCTATTAGAAACAGTCTTAAAGTGAGGTCTAGTATGCTTAGCTTATACACA
AATCTCACATTTGATAAAGCTAGTTGTGTCTAGTTTAGGCAGAACATTCATATTTATTAATTTCT
TTAAAGAATGAATATCACGTGTCCTAATCTAGCATGCCACATATCAATGGAT
Found at i:842519 original size:22 final size:22
Alignment explanation
Indices: 842491--842542 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
842481 ATTCAGCTCT
*
842491 TATAACTCCTGAAATTATATCA
1 TATAACTCCTGAAATTAAATCA
* *
842513 TATAACTGCTGGAATTAAATCA
1 TATAACTCCTGAAATTAAATCA
*
842535 AATAACTC
1 TATAACTC
842543 TTGTAACTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (22 bp):
TATAACTCCTGAAATTAAATCA
Found at i:844815 original size:11 final size:11
Alignment explanation
Indices: 844799--844839 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
844789 AGAACTGAAA
844799 ATCAACATGTC
1 ATCAACATGTC
*
844810 ATCAACATGCC
1 ATCAACATGTC
* *
844821 ATTAACATGTA
1 ATCAACATGTC
844832 ATCAACAT
1 ATCAACAT
844840 AAAGACTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (11 bp):
ATCAACATGTC
Found at i:862628 original size:12 final size:12
Alignment explanation
Indices: 862613--862639 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
862603 AGAGAAATTC
862613 CTCAAGAATTTT
1 CTCAAGAATTTT
862625 CTCAAGAATTTT
1 CTCAAGAATTTT
862637 CTC
1 CTC
862640 TAAAAAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (12 bp):
CTCAAGAATTTT
Found at i:867465 original size:263 final size:265
Alignment explanation
Indices: 866989--867525 Score: 1001
Period size: 263 Copynumber: 2.0 Consensus size: 265
866979 CACTCTGTAT
866989 ATTAAACCTATGAAATACCTTTTCAATGTACCCCTTTTGATTTAGGTACAATTTACATGTTTTCT
1 ATTAAACCTATGAAATACCTTTTCAATGTACCCCTTTTGATTTAGGTACAATTTACATGTTTTCT
867054 GTCTCTTCTAATATCTATTTTGAGTATCTTCTTCACATGAACCAGATCTTTCATCTTAAACTACT
66 GTCTCTTCTAATATCTATTTTGAGTATCTTCTTCACATGAACCAGATCTTTCATCTTAAACTACT
867119 TATTCAATGAGTTTTATATGTCTAATCTATTCTTTATTGTTCGTAGCTTTCAACATATCATTAAC
131 TATTCAATGAGTTTTATATGTCTAATCTATTCTTTATTGTTCGTAGCTTTCAACATATCATTAAC
867184 ATAAAGAAGCATATATATAGGCGAA-CTCACGAATCCTTTTCAAGT-AA-ATAGTTGTCAAAATT
196 ATAAAGAAGCA-ATATATAGGCGAACCTCACGAATCCTTTTCAAGTAAACATAGTTGTCAAAATT
867246 ACTTCA
260 ACTTCA
867252 ATTAAA-CTATGAAATACCTTTTCAATGTACCCCTTTTGATTTAGGTACAATTTACATGTTTTTC
1 ATTAAACCTATGAAATACCTTTTCAATGTACCCCTTTTGATTTAGGTACAATTTACATG-TTTTC
867316 TGTCTCTTCTAATATCTATTTTGAGTATCTTCTTCACATGAACCAGATCTTTCATCTTAAACTAC
65 TGTCTCTTCTAATATCTATTTTGAGTATCTTCTTCACATGAACCAGATCTTTCATCTTAAACTAC
867381 TTATTCAGATGAGTTTTTATATGTCTAATCTATTCTTTATTGTTCGTAGCTTTCAACATATCATT
130 TTATTCA-ATGAG-TTTTATATGTCTAATCTATTCTTTATTGTTCGTAGCTTTCAACATATCATT
867446 AACATAAAGAAGCATATATATAGGCGAACCTCACGAATCCTTTTCAAGTAAACATAGTTGTCAAA
193 AACATAAAGAAGCA-ATATATAGGCGAACCTCACGAATCCTTTTCAAGTAAACATAGTTGTCAAA
867511 ATTACTTCA
257 ATTACTTCA
867520 ATTAAA
1 ATTAAA
867526 ACTAAGAGAA
Statistics
Matches: 268, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
262 52 0.19
263 83 0.31
264 5 0.02
265 79 0.29
266 20 0.07
267 2 0.01
268 27 0.10
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (265 bp):
ATTAAACCTATGAAATACCTTTTCAATGTACCCCTTTTGATTTAGGTACAATTTACATGTTTTCT
GTCTCTTCTAATATCTATTTTGAGTATCTTCTTCACATGAACCAGATCTTTCATCTTAAACTACT
TATTCAATGAGTTTTATATGTCTAATCTATTCTTTATTGTTCGTAGCTTTCAACATATCATTAAC
ATAAAGAAGCAATATATAGGCGAACCTCACGAATCCTTTTCAAGTAAACATAGTTGTCAAAATTA
CTTCA
Found at i:871351 original size:16 final size:16
Alignment explanation
Indices: 871330--871385 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
871320 AAAAATTCTT
871330 TTTTATTTTAAATTAA
1 TTTTATTTTAAATTAA
*
871346 TTTTA-TTT-AATTCA
1 TTTTATTTTAAATTAA
*
871360 -TTTACTTTTAAAATAA
1 TTTTA-TTTTAAATTAA
*
871376 TTGTATTTTA
1 TTTTATTTTA
871386 TTATTATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 4 0.12
14 5 0.16
15 6 0.19
16 14 0.44
17 3 0.09
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (16 bp):
TTTTATTTTAAATTAA
Found at i:872097 original size:2 final size:2
Alignment explanation
Indices: 872090--872132 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
872080 TATGAAGGAT
*
872090 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
872131 TA
1 TA
872133 AACTAGATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:883935 original size:27 final size:27
Alignment explanation
Indices: 883904--883956 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
883894 TTTGGACCCT
883904 TAACTTTTCAAAAATTACATAATAGTA
1 TAACTTTTCAAAAATTACATAATAGTA
883931 TAACTTTTCAAAAATTACATAATAGT
1 TAACTTTTCAAAAATTACATAATAGT
883957 GCCCAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (27 bp):
TAACTTTTCAAAAATTACATAATAGTA
Done.