Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008150.1 Hibiscus syriacus cultivar Beakdansim tig00110716_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: 3012591
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 14
Found at i:2298597 original size:2 final size:2
Alignment explanation
Indices: 2298590--2298620 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2298580 TTTTAACATT
2298590 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 T
2298621 TGAAATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2300566 original size:16 final size:16
Alignment explanation
Indices: 2300516--2300557 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
2300506 CGTATTATCC
2300516 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
* *
2300532 GACCTGTTATGAACCT
1 GACCTGTTTTCAACCT
2300548 GACCTGTTTT
1 GACCTGTTTT
2300558 TAACATGACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:2304091 original size:86 final size:86
Alignment explanation
Indices: 2303946--2304147 Score: 350
Period size: 86 Copynumber: 2.3 Consensus size: 86
2303936 GGTTAGCAAC
* *
2303946 CAACCTTATAAAAGTAATCCGAATGAATAAATCAACAGTAGCTACAAATTAAACAGTTTATTTAA
1 CAACCTTATAAAAGCAATCCGAATGAACAAATCAACAGTAGCTACAAATTAAACAGTTTATTTAA
2304011 ACTGTAAATAAAGGCAGCTAA
66 ACTGTAAATAAAGGCAGCTAA
* *
2304032 CAACCTTATAAAAGCAATCCGAATGAACAAATCAATAGTAGCTACAAATTAAATAGTTTATTTAA
1 CAACCTTATAAAAGCAATCCGAATGAACAAATCAACAGTAGCTACAAATTAAACAGTTTATTTAA
2304097 ACTGTAAATAAAGGCAGCTAA
66 ACTGTAAATAAAGGCAGCTAA
* *
2304118 CAACCTTATAAAATCAATCTGAATGAACAA
1 CAACCTTATAAAAGCAATCCGAATGAACAA
2304148 CCAACAACAC
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 110 1.00
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (86 bp):
CAACCTTATAAAAGCAATCCGAATGAACAAATCAACAGTAGCTACAAATTAAACAGTTTATTTAA
ACTGTAAATAAAGGCAGCTAA
Found at i:2304239 original size:102 final size:102
Alignment explanation
Indices: 2304057--2304276 Score: 379
Period size: 102 Copynumber: 2.2 Consensus size: 102
2304047 AATCCGAATG
* *
2304057 AACAAATCAATAGTAGCTACAAATTAAATAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAAC
1 AACAAATCAACAGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAAC
2304122 CTTATAAAATCAATCTGAATGAACAACCAACAACACA
66 CTTATAAAATCAATCTGAATGAACAACCAACAACACA
*
2304159 AACAAATCAACAGTAGCTACAAATTAAACAGTTTATTTAAATTGTAAATAAAGGCAGCTAACAAC
1 AACAAATCAACAGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAAC
*
2304224 CTTATAAAAGT-AATCTGAATGAACAACCAACAACGCA
66 CTTATAAAA-TCAATCTGAATGAACAACCAACAACACA
*
2304261 AATAAATCAACAGTAG
1 AACAAATCAACAGTAG
2304277 AAACGAATCA
Statistics
Matches: 112, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
102 111 0.99
103 1 0.01
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.23
Consensus pattern (102 bp):
AACAAATCAACAGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAAC
CTTATAAAATCAATCTGAATGAACAACCAACAACACA
Found at i:2304672 original size:17 final size:17
Alignment explanation
Indices: 2304650--2304694 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
2304640 TTTTGGGTTT
*
2304650 GGGTTTGGGTTCAATTC
1 GGGTTTGGGTTCAATTA
*
2304667 GGGTTTGGGTTCAGTTA
1 GGGTTTGGGTTCAATTA
2304684 GGGTTTGGGTT
1 GGGTTTGGGTT
2304695 TAGGTTTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.09, C:0.07, G:0.42, T:0.42
Consensus pattern (17 bp):
GGGTTTGGGTTCAATTA
Found at i:2304677 original size:6 final size:6
Alignment explanation
Indices: 2304603--2304660 Score: 64
Period size: 6 Copynumber: 9.8 Consensus size: 6
2304593 GTTCGGATTA
* ** * *
2304603 GGGTTT GGGTTT GAG-TT CAGTTT GGGTTT CGGTTT GGTTTT GGGTTT
1 GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT
2304650 GGGTTT GGGTT
1 GGGTTT GGGTT
2304661 CAATTCGGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
5 4 0.09
6 39 0.91
ACGTcount: A:0.03, C:0.03, G:0.43, T:0.50
Consensus pattern (6 bp):
GGGTTT
Found at i:2305443 original size:14 final size:13
Alignment explanation
Indices: 2305414--2305469 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 13
2305404 CATCCCTATA
*
2305414 TAATTTTTATTAAT
1 TAATATTTA-TAAT
2305428 TAAGTATTTATAAT
1 TAA-TATTTATAAT
2305442 TAATATTATAATAAT
1 TAATATT-T-ATAAT
2305457 T-ATATATTATAAT
1 TAATAT-TTATAAT
2305470 ATTAATTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
13 9 0.24
14 16 0.43
15 12 0.32
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (13 bp):
TAATATTTATAAT
Found at i:2305448 original size:24 final size:24
Alignment explanation
Indices: 2305410--2305521 Score: 81
Period size: 24 Copynumber: 4.8 Consensus size: 24
2305400 ATTTCATCCC
**
2305410 TATATAATTTTTATTAATTAAGTA
1 TATATAATTAATATTAATTAAGTA
* * *
2305434 TTTATAATTAATATTATAATAATTA
1 TATATAATTAATATTA-ATTAAGTA
*
2305459 TATATTA-TAATATTAATTAA-TA
1 TATATAATTAATATTAATTAAGTA
* * *
2305481 TA-AT-ATTAATATAAAATATAGTC
1 TATATAATTAATATTAATTA-AGTA
2305504 TATA-ACATTAATATTAAT
1 TATATA-ATTAATATTAAT
2305522 ATAAACTATA
Statistics
Matches: 68, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
20 1 0.01
21 12 0.18
22 5 0.07
23 7 0.10
24 22 0.32
25 21 0.31
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
TATATAATTAATATTAATTAAGTA
Found at i:2305465 original size:16 final size:15
Alignment explanation
Indices: 2305424--2305492 Score: 74
Period size: 15 Copynumber: 4.7 Consensus size: 15
2305414 TAATTTTTAT
2305424 TAATTAAGTATT-T-A
1 TAATTAA-TATTATAA
2305438 TAATTAATATTATAA
1 TAATTAATATTATAA
2305453 TAATTATATATTATAA
1 TAATTA-ATATTATAA
*
2305469 T-ATTAATTAATATAA
1 TAATTAA-TATTATAA
2305484 T-ATTAATAT
1 TAATTAATAT
2305493 AAAATATAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
13 4 0.08
14 11 0.22
15 24 0.49
16 10 0.20
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (15 bp):
TAATTAATATTATAA
Found at i:2305498 original size:28 final size:30
Alignment explanation
Indices: 2305440--2305499 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
2305430 AGTATTTATA
* *
2305440 ATTAATATTATAATAATTATATATTATAAT
1 ATTAATAATATAATAATTATATATTAAAAT
2305470 ATTAATTAATATAAT-ATTA-ATA-TAAAAT
1 ATTAA-TAATATAATAATTATATATTAAAAT
2305498 AT
1 AT
2305500 AGTCTATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 7 0.26
29 3 0.11
30 9 0.33
31 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
ATTAATAATATAATAATTATATATTAAAAT
Found at i:2305516 original size:31 final size:30
Alignment explanation
Indices: 2305481--2305543 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
2305471 TTAATTAATA
2305481 TAATATTAATATAAAATATA-GTCTATAACAT
1 TAATATTAATATAAAATATATGT-TATAA-AT
*
2305512 TAATATTAATATAAACTATATGTTATAAAT
1 TAATATTAATATAAAATATATGTTATAAAT
2305542 TA
1 TA
2305544 TATAGTATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 4 0.13
31 24 0.80
32 2 0.07
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (30 bp):
TAATATTAATATAAAATATATGTTATAAAT
Found at i:2305588 original size:15 final size:15
Alignment explanation
Indices: 2305568--2305656 Score: 56
Period size: 15 Copynumber: 5.6 Consensus size: 15
2305558 TAAACTACAT
2305568 TTAATATAATTAATA
1 TTAATATAATTAATA
*
2305583 TTAATATAATTTAATT
1 TTAATATAA-TTAATA
*
2305599 TATAAAAT-ATATACTATA
1 T-TAATATAAT-TA--ATA
*
2305617 TTAGTATAAATT-ATA
1 TTAATAT-AATTAATA
* *
2305632 GTTAAGATAATTAACA
1 -TTAATATAATTAATA
2305648 TTAATATAA
1 TTAATATAA
2305657 ACTATATAGT
Statistics
Matches: 56, Mismatches: 9, Indels: 18
0.67 0.11 0.22
Matches are distributed among these distances:
15 25 0.45
16 16 0.29
17 9 0.16
18 4 0.07
19 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (15 bp):
TTAATATAATTAATA
Found at i:2305651 original size:65 final size:66
Alignment explanation
Indices: 2305510--2305693 Score: 196
Period size: 65 Copynumber: 2.8 Consensus size: 66
2305500 AGTCTATAAC
* * * *
2305510 ATTAATATTAATATAAACTATATGTTATAAATTATATAGTATAGTTTATAAACTACATTTAATAT
1 ATTAATATTAATATAAACTATATGTTATAAAATATATACTATAGTTTATAAACTACAGTTAAGAT
2305575 A
66 A
** * *
2305576 ATTAATATTAATATAATTTA-AT-TTATAAAATATATACTATA-TTAGTATAAATTATAGTTAAG
1 ATTAATATTAATATAAACTATATGTTATAAAATATATACTATAGTT--TATAAACTACAGTTAAG
2305638 ATA
64 ATA
* * * *
2305641 ATTAACATTAATATAAACTATATAG-TACATTAATATAAACTATAGTTTATAAA
1 ATTAATATTAATATAAACTATAT-GTTATA-AAATATATACTATAGTTTATAAA
2305694 TTATATACTA
Statistics
Matches: 97, Mismatches: 14, Indels: 13
0.78 0.11 0.10
Matches are distributed among these distances:
63 2 0.02
64 17 0.18
65 35 0.36
66 20 0.21
67 9 0.09
68 12 0.12
69 2 0.02
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (66 bp):
ATTAATATTAATATAAACTATATGTTATAAAATATATACTATAGTTTATAAACTACAGTTAAGAT
A
Found at i:2305670 original size:22 final size:22
Alignment explanation
Indices: 2305645--2305746 Score: 86
Period size: 22 Copynumber: 4.7 Consensus size: 22
2305635 AAGATAATTA
2305645 ACATTAATATAAACTATATAGT
1 ACATTAATATAAACTATATAGT
2305667 ACATTAATATAAAC--TATAGT
1 ACATTAATATAAACTATATAGT
** * * *
2305687 TTATAAATTATATACTATA-GGT
1 ACATTAA-TATAAACTATATAGT
* *
2305709 -TATAAAGTATAAACTATATAGT
1 ACATTAA-TATAAACTATATAGT
*
2305731 ACACTAATATAAACTA
1 ACATTAATATAAACTA
2305747 ATGATTATAA
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
20 10 0.16
21 22 0.34
22 27 0.42
23 5 0.08
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.36
Consensus pattern (22 bp):
ACATTAATATAAACTATATAGT
Found at i:2305703 original size:21 final size:21
Alignment explanation
Indices: 2305674--2305726 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2305664 AGTACATTAA
* *
2305674 TATAAACTATAGTTTATAAAT
1 TATAAACTATAGGTTATAAAG
*
2305695 TATATACTATAGGTTATAAAG
1 TATAAACTATAGGTTATAAAG
2305716 TATAAACTATA
1 TATAAACTATA
2305727 TAGTACACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAG
Found at i:2305812 original size:41 final size:39
Alignment explanation
Indices: 2305766--2305858 Score: 98
Period size: 41 Copynumber: 2.3 Consensus size: 39
2305756 AACTATAGGT
* *
2305766 TACATATA-TAGTTTATATAACATATAAATAGATTGTATATA
1 TACATATACTAGGTTATAT-ACATATAAATAG-TT-TATACA
*
2305807 TACATATACTGTAGGTTATATATATATAAATAGTTTATACA
1 TACATATAC--TAGGTTATATACATATAAATAGTTTATACA
*
2305848 TACATGTACTA
1 TACATATACTA
2305859 TAAGTTACAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
39 2 0.04
41 21 0.47
42 2 0.04
43 11 0.24
44 9 0.20
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.41
Consensus pattern (39 bp):
TACATATACTAGGTTATATACATATAAATAGTTTATACA
Found at i:2305871 original size:41 final size:43
Alignment explanation
Indices: 2305787--2305873 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 43
2305777 TTTATATAAC
* * * *
2305787 ATATAAATAGATTGTATATATACATATACTGTAGGTTATATAT
1 ATATAAATAGATTGTATACATACATATACTATAAGTTACATAT
*
2305830 ATATAAATAG-TT-TATACATACATGTACTATAAGTTACATAT
1 ATATAAATAGATTGTATACATACATATACTATAAGTTACATAT
2305871 ATA
1 ATA
2305874 GTTTACATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 27 0.69
42 2 0.05
43 10 0.26
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (43 bp):
ATATAAATAGATTGTATACATACATATACTATAAGTTACATAT
Found at i:2305976 original size:14 final size:14
Alignment explanation
Indices: 2305936--2305988 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
2305926 TATGTATAGT
*
2305936 GTTTAGGGTTTAAA
1 GTTTAGGGTTTAGA
**
2305950 GTTTAGAATTTAGA
1 GTTTAGGGTTTAGA
* *
2305964 GTTTAGGGGTTAGG
1 GTTTAGGGTTTAGA
*
2305978 GTTTTGGGTTT
1 GTTTAGGGTTT
2305989 TTATAAACTA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (14 bp):
GTTTAGGGTTTAGA
Found at i:2306136 original size:35 final size:36
Alignment explanation
Indices: 2306096--2306169 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
2306086 TACACTATAC
* *
2306096 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACACACATATACTATAAGTTACATAT
**
2306131 ATAGTTTACATGTACACATATACTATAAGTTACATAT
1 ATAGTTTA-ATACACACATATACTATAAGTTACATAT
2306168 AT
1 AT
2306170 TAACTATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 7 0.21
37 26 0.79
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (36 bp):
ATAGTTTAATACACACATATACTATAAGTTACATAT
Found at i:2306379 original size:2 final size:2
Alignment explanation
Indices: 2306372--2306611 Score: 64
Period size: 2 Copynumber: 123.0 Consensus size: 2
2306362 TGTTTCTTTA
2306372 AT AT AT AT AT AT AT AT AT AT AT AT -T ACT -T AT AT -T AGT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT
* * * *
2306412 AC AT AC AT AT AT AT ACT AT AT -T A- AT AT AA AT A- AT AT -T TT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
2306451 AT AA ACT AT AT ACT TT TT AT AGT TT AT AC AT AT AT AGT TT AT AT
1 AT AT A-T AT AT A-T AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT
* * * * * * *
2306495 AT AT AGT -T CAC AT AA AC AT A- AT TT TT AT AT AT AT AT AT AG CT
1 AT AT A-T AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
2306537 -T AT A- AT A- AT -T AT AT AGT TT AT A- AT AT AA AT AT AGT TT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT
* *
2306576 AT AT A- AA AT TT AT AT -T 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
2306612 TTTTTTCAAT
Statistics
Matches: 174, Mismatches: 36, Indels: 56
0.65 0.14 0.21
Matches are distributed among these distances:
1 17 0.10
2 146 0.84
3 11 0.06
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2306412 original size:28 final size:28
Alignment explanation
Indices: 2306379--2306434 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
2306369 TTAATATATA
* *
2306379 TATATATATATATATATTACTTATATTAGT
1 TATACATACATATATA-TAC-TATATTAGT
2306409 TATACATACATATATATACTATATTA
1 TATACATACATATATATACTATATTA
2306435 ATATAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.29
29 3 0.12
30 14 0.58
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (28 bp):
TATACATACATATATATACTATATTAGT
Found at i:2306496 original size:13 final size:14
Alignment explanation
Indices: 2306468--2306502 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
2306458 ATATACTTTT
2306468 TATAGTTTATACATA
1 TATAGTTTATA-ATA
2306483 TATAGTTTAT-ATA
1 TATAGTTTATAATA
2306496 TATAGTT
1 TATAGTT
2306503 CACATAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.50
15 10 0.50
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (14 bp):
TATAGTTTATAATA
Found at i:2307921 original size:19 final size:19
Alignment explanation
Indices: 2307897--2307936 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2307887 TTTGACATTC
2307897 CAAAGGATGAAGAAGAAAG
1 CAAAGGATGAAGAAGAAAG
2307916 CAAAGGATGAAGAAGAAAG
1 CAAAGGATGAAGAAGAAAG
2307935 CA
1 CA
2307937 GTTTACAGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.57, C:0.07, G:0.30, T:0.05
Consensus pattern (19 bp):
CAAAGGATGAAGAAGAAAG
Found at i:2309859 original size:27 final size:26
Alignment explanation
Indices: 2309826--2309915 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 26
2309816 TTAAATACAT
2309826 AATATTTTATATAAATTAACTTTAAGA
1 AATATTTTATATAAATTAACTTTAA-A
*
2309853 AATATTTT-T-TATATTAACTTATTAAA
1 AATATTTTATATAAATTAAC-T-TTAAA
* * *
2309879 TATATTTTATTATTAACTT-ATTTTAAA
1 AATATTTTA-TA-TAAATTAACTTTAAA
2309906 AATATTTTAT
1 AATATTTTAT
2309916 TTTAATTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
25 8 0.16
26 11 0.22
27 25 0.49
28 2 0.04
29 1 0.02
30 4 0.08
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.53
Consensus pattern (26 bp):
AATATTTTATATAAATTAACTTTAAA
Found at i:2309868 original size:25 final size:25
Alignment explanation
Indices: 2309826--2309897 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
2309816 TTAAATACAT
*
2309826 AATATTTTATATAAATTAACTTTAAGA
1 AATATTTT-T-TATATTAACTTTAAGA
**
2309853 AATATTTTTTATATTAAC-TTATTA
1 AATATTTTTTATATTAACTTTAAGA
*
2309877 AATATATTTTATTATTAACTT
1 AATATTTTTTA-TATTAACTT
2309898 ATTTTAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
24 14 0.36
25 15 0.38
26 2 0.05
27 8 0.21
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (25 bp):
AATATTTTTTATATTAACTTTAAGA
Found at i:2309902 original size:16 final size:17
Alignment explanation
Indices: 2309871--2309903 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2309861 TTATATTAAC
2309871 TTATTAAATATATTTTA
1 TTATTAAATATATTTTA
*
2309888 TTATTAACT-TATTTTA
1 TTATTAAATATATTTTA
2309904 AAAATATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTAAATATATTTTA
Found at i:2309916 original size:27 final size:26
Alignment explanation
Indices: 2309846--2309934 Score: 92
Period size: 27 Copynumber: 3.3 Consensus size: 26
2309836 ATAAATTAAC
*
2309846 TTTAAGAAATATTTTTTATATTAACTTA
1 TTTAA-AAATATTTTAT-TATTAACTTA
*
2309874 -TTAAATATATTTTATTATTAACTTA
1 TTTAAAAATATTTTATTATTAACTTA
*
2309899 TTTTAAAAATATTTTATT-TTAATTTTAA
1 -TTTAAAAATATTTTATTATTAA-CTT-A
2309927 TTTAAAAA
1 TTTAAAAA
2309935 ATATATTTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
25 10 0.19
26 13 0.25
27 29 0.55
28 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (26 bp):
TTTAAAAATATTTTATTATTAACTTA
Found at i:2309966 original size:30 final size:29
Alignment explanation
Indices: 2309876--2310008 Score: 101
Period size: 30 Copynumber: 4.4 Consensus size: 29
2309866 TTAACTTATT
* *
2309876 AAATATATTTTATTATTAACT-TATTTTA
1 AAATATATTTTATTATTATCTAAATTTTA
* * *
2309904 AAA-ATATTTTATT-TTAATTTTAATTTAAA
1 AAATATATTTTATTATT-ATCTAAATTT-TA
*
2309933 AAATATATTTTATTCTTATCTAAACTTTTA
1 AAATATATTTTATTATTATCTAAA-TTTTA
* *
2309963 AAATTTATTTTTATTATTATTTTAAATTTTCA
1 AAATATA-TTTTATTATTA-TCTAAATTTT-A
2309995 AAGTATATATTTTA
1 AA--ATATATTTTA
2310009 ATCTTAATTT
Statistics
Matches: 83, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
26 2 0.02
27 12 0.14
28 7 0.08
29 4 0.05
30 22 0.27
31 19 0.23
32 8 0.10
33 5 0.06
34 4 0.05
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (29 bp):
AAATATATTTTATTATTATCTAAATTTTA
Found at i:2311015 original size:16 final size:16
Alignment explanation
Indices: 2310996--2311044 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 16
2310986 TCTGGATTTG
2310996 TTTTATTTTATTTTAT
1 TTTTATTTTATTTTAT
2311012 TTTTATATTTATTATTTAT
1 TTTTAT-TTTA-T-TTTAT
*
2311031 TATTATTTTTATTT
1 TTTTA-TTTTATTT
2311045 ATATATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 6 0.21
17 6 0.21
18 2 0.07
19 13 0.46
20 1 0.04
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTATTTTATTTTAT
Found at i:2311017 original size:6 final size:6
Alignment explanation
Indices: 2310996--2311044 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
2310986 TCTGGATTTG
* *
2310996 TTTTA- TTTTA- TTTTAT TTTTAT ATTTAT TATTTAT TATTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T-TTTAT TTTTAT TTTTAT
2311043 TT
1 TT
2311045 ATATATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
5 10 0.26
6 22 0.58
7 6 0.16
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:2311045 original size:16 final size:16
Alignment explanation
Indices: 2310997--2311046 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
2310987 CTGGATTTGT
2310997 TTTATT-TTA-TTTTA
1 TTTATTATTATTTTTA
2311011 TTT-TTA-TATTTATTA
1 TTTATTATTATTT-TTA
2311026 TTTATTATTATTTTTA
1 TTTATTATTATTTTTA
2311042 TTTAT
1 TTTAT
2311047 ATATATATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 4 0.13
14 5 0.16
15 6 0.19
16 11 0.35
17 5 0.16
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTATTATTTTTA
Found at i:2311154 original size:47 final size:43
Alignment explanation
Indices: 2311097--2311191 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 43
2311087 TTGAAAAAAA
**
2311097 ATATAATATATAATTTTTAGAAAATGGTTTTCG-AAATATATATATAT
1 ATATAATATATAA-TTTT-GAAAA--CATTTCGAAAATATATATAT-T
*
2311144 ATATATTATATAATTTTGAAAACATTTCGAAAATATATATATT
1 ATATAATATATAATTTTGAAAACATTTCGAAAATATATATATT
2311187 ATATA
1 ATATA
2311192 GTTTTGAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
43 11 0.25
44 12 0.27
45 5 0.11
46 4 0.09
47 12 0.27
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.44
Consensus pattern (43 bp):
ATATAATATATAATTTTGAAAACATTTCGAAAATATATATATT
Found at i:2311187 original size:36 final size:36
Alignment explanation
Indices: 2311140--2311439 Score: 305
Period size: 36 Copynumber: 8.3 Consensus size: 36
2311130 AAATATATAT
* *
2311140 ATATATATATTATATAATTTTGAAAACATTTCGAAA
1 ATATATATATTATATAGTTTTGAAAACATTTTGAAA
*
2311176 ATATATATATTATATAGTTTTGAAAA-TTTTTGAAA
1 ATATATATATTATATAGTTTTGAAAACATTTTGAAA
* *
2311211 ACATATATAGTATATAGTTTTTGAAAA-AGTTTTTGAAA
1 ATATATATATTATATAG-TTTTGAAAACA--TTTTGAAA
* *
2311249 ATATATA-A-TATATAGTTTTGAAAACGTTTT-TAA
1 ATATATATATTATATAGTTTTGAAAACATTTTGAAA
2311282 ATATATATA-TA-AT--TTTTGAAAACATTTTTGAAA
1 ATATATATATTATATAGTTTTGAAAACA-TTTTGAAA
* * *
2311315 ACATATATATTATATAGTTTTTAAAACGTTTTTGAAAA
1 ATATATATATTATATAGTTTTGAAAAC-ATTTTG-AAA
* *
2311353 CATATATATAATATATAGTTTTTAAAACATTTTGAAA
1 -ATATATATATTATATAGTTTTGAAAACATTTTGAAA
* *
2311390 ATATATATAATATATATACTTTTGAAAAATATTTTTGAAA
1 ATATATAT-AT-TATATAGTTTTG-AAAACA-TTTTGAAA
2311430 ATATAT-TATT
1 ATATATATATT
2311440 TAAAAAACAA
Statistics
Matches: 225, Mismatches: 21, Indels: 35
0.80 0.07 0.12
Matches are distributed among these distances:
31 10 0.04
32 4 0.02
33 21 0.09
34 9 0.04
35 33 0.15
36 49 0.22
37 20 0.09
38 34 0.15
39 31 0.14
40 14 0.06
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (36 bp):
ATATATATATTATATAGTTTTGAAAACATTTTGAAA
Found at i:2311207 original size:46 final size:43
Alignment explanation
Indices: 2311125--2311214 Score: 119
Period size: 43 Copynumber: 2.0 Consensus size: 43
2311115 AGAAAATGGT
*
2311125 TTTCGAAATATATATATATATATATTATATAATTTTGAAAACA
1 TTTCGAAATATATATATATATATATTATAAAATTTTGAAAACA
*
2311168 TTTCGAAA-ATATATATATTATATAGTTTTGAAAATTTTTGAAAACA
1 TTTCGAAATATATATATA-TATATA-TTAT-AAAA-TTTTGAAAACA
2311214 T
1 T
2311215 ATATAGTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
42 9 0.22
43 14 0.34
44 3 0.07
45 3 0.07
46 12 0.29
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (43 bp):
TTTCGAAATATATATATATATATATTATAAAATTTTGAAAACA
Found at i:2311310 original size:12 final size:12
Alignment explanation
Indices: 2311293--2311318 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2311283 TATATATATA
2311293 ATTTTTGAAAAC
1 ATTTTTGAAAAC
2311305 ATTTTTGAAAAC
1 ATTTTTGAAAAC
2311317 AT
1 AT
2311319 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (12 bp):
ATTTTTGAAAAC
Found at i:2311356 original size:141 final size:141
Alignment explanation
Indices: 2311144--2311511 Score: 422
Period size: 139 Copynumber: 2.6 Consensus size: 141
2311134 ATATATATAT
*
2311144 ATATATTATATAATTTTGAAAACA-TTTCGAAAATATATATATTATATAGTTTTGAAAA-TTTTT
1 ATATA-TATATAATTTTGAAAACATTTTTGAAAA-ATATATATTATATAGTTTTGAAAACTTTTT
*
2311207 GAAAACATATATAGTATATAGTTTTTGAAAA-AGTTTTTG-AAA-ATATAT-A-ATATATAGTTT
64 GAAAACATATATA-TATATAGTTTTT-AAAACA--TTTTGAAAATATATATAATATATATACTTT
*
2311267 TG-AAAACGTTTTT-AA
125 TGAAAAACATTTTTGAA
*
2311282 ATATATATATAATTTTTGAAAACATTTTTGAAAACATATATATTATATAGTTTTTAAAACGTTTT
1 ATATATATATAA-TTTTGAAAACATTTTTGAAAA-ATATATATTATATAGTTTTGAAAAC-TTTT
2311347 TGAAAACATATATATAATATATAGTTTTTAAAACATTTTGAAAATATATATAATATATATACTTT
63 TGAAAAC--ATATAT-ATATATAGTTTTTAAAACATTTTGAAAATATATATAATATATATACTTT
*
2311412 TGAAAAATATTTTTGAA
125 TGAAAAACATTTTTGAA
** * ** *
2311429 A-ATATAT-T-ATTTAAAAAACAATTTTTG-AAAATATAGATTATAGGGTTTTGAAAACTTTTAG
1 ATATATATATAATTTTGAAAAC-ATTTTTGAAAAATATATATTATATAGTTTTGAAAACTTTTTG
2311490 AAAACATATA-ATATATAGTTTT
65 AAAACATATATATATATAGTTTT
2311512 ATTTTTTTTT
Statistics
Matches: 202, Mismatches: 13, Indels: 31
0.82 0.05 0.13
Matches are distributed among these distances:
137 19 0.09
138 16 0.08
139 36 0.18
141 26 0.13
142 28 0.14
143 36 0.18
144 10 0.05
145 13 0.06
146 15 0.07
147 3 0.01
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.44
Consensus pattern (141 bp):
ATATATATATAATTTTGAAAACATTTTTGAAAAATATATATTATATAGTTTTGAAAACTTTTTGA
AAACATATATATATATAGTTTTTAAAACATTTTGAAAATATATATAATATATATACTTTTGAAAA
ACATTTTTGAA
Found at i:2311371 original size:39 final size:37
Alignment explanation
Indices: 2311282--2311435 Score: 175
Period size: 38 Copynumber: 4.0 Consensus size: 37
2311272 ACGTTTTTAA
*
2311282 ATATATATATAATTTTTGAAAACATTTTTGAAAACATAT
1 ATATATATATAGTTTTT-AAAAC-TTTTTGAAAACATAT
2311321 ATAT-TATATAGTTTTTAAAACGTTTTTGAAAACATAT
1 ATATATATATAGTTTTTAAAAC-TTTTTGAAAACATAT
* *
2311358 ATATAATATATAGTTTTTAAAACATTTTGAAAATATAT
1 ATAT-ATATATAGTTTTTAAAACTTTTTGAAAACATAT
* * * *
2311396 ATAATATATATACTTTTGAAAAATATTTTTGAAAATATAT
1 AT-ATATATATAGTTTT-TAAAA-CTTTTTGAAAACATAT
2311436 TATTTAAAAA
Statistics
Matches: 102, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
37 24 0.24
38 37 0.36
39 27 0.26
40 14 0.14
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (37 bp):
ATATATATATAGTTTTTAAAACTTTTTGAAAACATAT
Found at i:2311444 original size:14 final size:13
Alignment explanation
Indices: 2311409--2311459 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
2311399 ATATATATAC
2311409 TTTTGAAAAATAT
1 TTTTGAAAAATAT
2311422 TTTTGAAAATATAT
1 TTTTGAAAA-ATAT
* *
2311436 TATTTAAAAAACAAT
1 T-TTTGAAAAA-TAT
2311451 TTTTGAAAA
1 TTTTGAAAA
2311460 TATAGATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 13 0.41
15 10 0.31
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (13 bp):
TTTTGAAAAATAT
Found at i:2312018 original size:17 final size:17
Alignment explanation
Indices: 2311996--2312036 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2311986 AGCCATGTTC
2311996 ACAAGAAAAAACAAAAA
1 ACAAGAAAAAACAAAAA
* *
2312013 ACAAGAAATAGCAAAAA
1 ACAAGAAAAAACAAAAA
*
2312030 AAAAGAA
1 ACAAGAA
2312037 GCCAACCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.78, C:0.10, G:0.10, T:0.02
Consensus pattern (17 bp):
ACAAGAAAAAACAAAAA
Found at i:2313895 original size:2 final size:2
Alignment explanation
Indices: 2313890--2313952 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
2313880 TTTTTTACCT
2313890 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
2313932 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
2313953 TATCTTTATT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2313987 original size:17 final size:16
Alignment explanation
Indices: 2313942--2313989 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
2313932 TATATATATA
2313942 TATATATATATTATCTT
1 TATAT-TATATTATCTT
* *
2313959 TATTATTTTATTTTCTT
1 TA-TATTATATTATCTT
2313976 TATATCTATATTAT
1 TATAT-TATATTAT
2313990 TTATTCATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.12
17 19 0.76
18 3 0.12
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
TATATTATATTATCTT
Found at i:2314000 original size:25 final size:25
Alignment explanation
Indices: 2313953--2314001 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2313943 ATATATATAT
* *
2313953 TATCTTTATTATTTTATTTTCTTTA
1 TATCTATATTATTTTATTATCTTTA
2313978 TATCTATATTA-TTTATTCATCTTT
1 TATCTATATTATTTTATT-ATCTTT
2314002 TTTCACTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.67
Consensus pattern (25 bp):
TATCTATATTATTTTATTATCTTTA
Found at i:2314005 original size:32 final size:33
Alignment explanation
Indices: 2313942--2314005 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 33
2313932 TATATATATA
*
2313942 TATATATATATTATCTTTATTATTTTATTTTCTT
1 TATATATATATTA-CTTTATTATCTTATTTTCTT
*
2313976 TATATCTATATTA-TTTATTCATCTT-TTTTC
1 TATATATATATTACTTTATT-ATCTTATTTTC
2314006 ACTTGATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 11 0.41
33 4 0.15
34 12 0.44
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (33 bp):
TATATATATATTACTTTATTATCTTATTTTCTT
Found at i:2314108 original size:9 final size:9
Alignment explanation
Indices: 2314096--2314208 Score: 78
Period size: 9 Copynumber: 12.9 Consensus size: 9
2314086 TGTCTTTATT
2314096 TTTATTCTT-
1 TTTATT-TTA
*
2314105 TTTATTTTG
1 TTTATTTTA
2314114 TTTATTTTA
1 TTTATTTTA
2314123 TTTATTTTA
1 TTTATTTTA
2314132 TTTA-TTTA
1 TTTATTTTA
* *
2314140 TTTCTGTTTC
1 TTTAT-TTTA
2314150 TTTA--TT-
1 TTTATTTTA
* *
2314156 TTCATTTTG
1 TTTATTTTA
*
2314165 TTTATATTA
1 TTTATTTTA
2314174 TTTATTTT-
1 TTTATTTTA
2314182 TTTATCTTTA
1 TTTAT-TTTA
*
2314192 TTTTTTATTA
1 TTTATT-TTA
2314202 -TTATTTT
1 TTTATTTT
2314209 TCTTTAGCTT
Statistics
Matches: 84, Mismatches: 11, Indels: 19
0.74 0.10 0.17
Matches are distributed among these distances:
6 3 0.04
7 2 0.02
8 18 0.21
9 48 0.57
10 13 0.15
ACGTcount: A:0.17, C:0.04, G:0.03, T:0.76
Consensus pattern (9 bp):
TTTATTTTA
Found at i:2314169 original size:60 final size:60
Alignment explanation
Indices: 2314062--2314200 Score: 171
Period size: 60 Copynumber: 2.3 Consensus size: 60
2314052 TTTTCCTATA
* * *
2314062 TTTTA-TTTATTTCATTT-TTTCTCTTGTCTTTATTTTTATTCTTTTTATTTTGTTTATTT
1 TTTTATTTTATTT-ATTTATTTCTCTTGTCTTTATTTTCATTCTTTTTATATTATTTATTT
*
2314121 TATTTATTTTATTTATTTATTTCTGTT-TCTTTATTTTCATT-TTGTTTATATTATTTATTT
1 T-TTTATTTTATTTATTTATTTCTCTTGTCTTTATTTTCATTCTT-TTTATATTATTTATTT
2314181 TTTTATCTTTATTT-TTTATT
1 TTTTAT-TTTATTTATTTATT
2314201 ATTATTTTTC
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
59 14 0.20
60 43 0.61
61 14 0.20
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (60 bp):
TTTTATTTTATTTATTTATTTCTCTTGTCTTTATTTTCATTCTTTTTATATTATTTATTT
Found at i:2314191 original size:14 final size:13
Alignment explanation
Indices: 2314104--2314209 Score: 74
Period size: 14 Copynumber: 7.8 Consensus size: 13
2314094 TTTTTATTCT
2314104 TTTTATTTTGTTTA
1 TTTTATTTT-TTTA
2314118 TTTTATTTATTTTA
1 TTTTATTT-TTTTA
* *
2314132 -TTTATTTATTTC
1 TTTTATTTTTTTA
*
2314144 TGTTTCTTTATTTTCA
1 T-TTTATTT-TTTT-A
* *
2314160 TTTTGTTTATATTA
1 TTTTATTT-TTTTA
2314174 -TTTATTTTTTTA
1 TTTTATTTTTTTA
2314186 TCTTTA-TTTTTTA
1 T-TTTATTTTTTTA
2314199 TTATTATTTTT
1 TT-TTATTTTT
2314210 CTTTAGCTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
12 8 0.11
13 24 0.32
14 27 0.36
15 14 0.19
16 1 0.01
ACGTcount: A:0.17, C:0.04, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:2314206 original size:51 final size:50
Alignment explanation
Indices: 2314063--2314208 Score: 140
Period size: 51 Copynumber: 2.9 Consensus size: 50
2314053 TTTCCTATAT
* * * *
2314063 TTTATTTATTTCA-TTTTTTCTCTTGTCTTTATTTTTATTCTTTTTATTTTG
1 TTTATTTATTT-ATTTTTTTATCTT-TATTTATTTTTATTATTTTCATTTTG
*
2314114 TTTATTTTATTTATTTTATTTA--TTTATTTCTGTTTCT-TTATTTTCATTTTG
1 TTTA-TTTATTTATTTT-TTTATCTTTATTTAT-TTT-TATTATTTTCATTTTG
2314165 TTTATATTATTTATTTTTTTATCTTTATTT-TTTATTATTATTTT
1 TTTAT-TTATTTATTTTTTTATCTTTATTTATTT-TTATTATTTT
2314209 TCTTTAGCTT
Statistics
Matches: 80, Mismatches: 5, Indels: 20
0.76 0.05 0.19
Matches are distributed among these distances:
50 13 0.16
51 46 0.57
52 18 0.22
53 3 0.04
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (50 bp):
TTTATTTATTTATTTTTTTATCTTTATTTATTTTTATTATTTTCATTTTG
Found at i:2325813 original size:124 final size:123
Alignment explanation
Indices: 2325651--2326261 Score: 654
Period size: 124 Copynumber: 4.8 Consensus size: 123
2325641 ACAATACTTA
* *
2325651 GATTTCAACTTCACGATGAAGGATATCTAATTCAAGGCTCAACTTCACAATGAAGGGGCCATCCA
1 GATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCA
* * *
2325716 CGATTTCAACTTCACGACGAAGGATATCATGCCTACCAGTAACATTCATCATTAGATTG
66 CGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATTCATC-TTAGATTG
* *
2325775 GATTTCAACTTCACGATGAATGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCATCCA
1 GATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCA
2325840 CGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAGATTG
66 CGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATTCATC-TTAGATTG
* *
2325899 GATTTCAACTTCACGATGAAGGATATCCAATTCAAGGATCAACTTCACAACGAAGGGGCCATCAA
1 GATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCA
* * * * * *
2325964 AGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCATACAACTCTAGATTT
66 CGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATTCATCT-TAGATTG
* * * * **
2326023 GATTTCAACTTCACGACGAAGGATATCCAATTAAAAGCTCAACTTCACAGCGAATGAGCTTTCCA
1 GATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAA-G-G--GGCCA
* * * * *
2326088 GTTTCATTCAGAGTCCATTTCAACTTCACGGCGAAGGATATTG-GACTCGAAACAACGCAAC-TT
62 ---TC---C--A--CGATTTCAACTTCACGACGAAGGATATCGTG-C-C--CACCA-GCAACATT
*
2326151 ACA-C-AAGATTG
112 -CATCTTAGATTG
* * * * * ** *
2326162 GATTTCAACTTCACGACGAATGATATCCAATTCAAAGCTCAACCTCACGACGAAGGATCCATCTA
1 GATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCA
* *
2326227 CGATTTCAACTCCACGACGAAGGATATCGTACCCA
66 CGATTTCAACTTCACGACGAAGGATATCGTGCCCA
2326262 AAAGATTGAC
Statistics
Matches: 417, Mismatches: 48, Indels: 46
0.82 0.09 0.09
Matches are distributed among these distances:
122 1 0.00
123 1 0.00
124 278 0.67
125 27 0.06
126 1 0.00
127 1 0.00
128 3 0.01
131 2 0.00
132 2 0.00
135 4 0.01
136 1 0.00
137 2 0.00
138 27 0.06
139 55 0.13
141 6 0.01
142 6 0.01
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (123 bp):
GATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCA
CGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATTCATCTTAGATTG
Found at i:2326677 original size:15 final size:16
Alignment explanation
Indices: 2326657--2326686 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2326647 ATATTATGGG
2326657 TTACAT-TTATAATAT
1 TTACATATTATAATAT
2326672 TTACATATTATAATA
1 TTACATATTATAATA
2326687 AACATACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (16 bp):
TTACATATTATAATAT
Found at i:2327839 original size:2 final size:2
Alignment explanation
Indices: 2327834--2327866 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2327824 GTGCTTTACT
*
2327834 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2327867 TGTTTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2328301 original size:5 final size:5
Alignment explanation
Indices: 2328288--2328428 Score: 108
Period size: 5 Copynumber: 29.6 Consensus size: 5
2328278 TTCTCTTGTC
**
2328288 TTTATT TTTAT TTTAT TTTAT TTTGG TTTAT TTTA- TTTAT TTTA- -TTAT
1 TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
*
2328336 TTTAT TTTA- TTTAT TTTA- -ATAT TTTA- TTTAT GTTT-T TTTAT TTTCAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT TTTAT TTT-AT
* *
2328383 TTT-G TTTAT ATTA- TTTA- TTT-T TTTAT CTTTAT TTTAT TATTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT TTTAT T-TTAT TTT
2328429 TTCCTTTAGC
Statistics
Matches: 110, Mismatches: 10, Indels: 31
0.73 0.07 0.21
Matches are distributed among these distances:
3 5 0.05
4 27 0.25
5 56 0.51
6 22 0.20
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:2328427 original size:68 final size:68
Alignment explanation
Indices: 2328294--2328428 Score: 161
Period size: 68 Copynumber: 2.0 Consensus size: 68
2328284 TGTCTTTATT
** *
2328294 TTTATTTTATTTTATTTTGGTTTATTTTATTTATTTTATTATTTTATTTTATTTATTTTAATATT
1 TTTATTTTATTTTATTTTCATTTATTTTATTTATTTTATTATTTTATTTTATTTATATTAATATT
2328359 TTA
66 TTA
* *
2328362 TTTATGTTT-TTTTATTTTCATTT-TGTTTATATTA-TTTATTTTTTTATCTTTATTT-TATTAT
1 TTTAT-TTTATTTTATTTTCATTTAT-TTTAT-TTATTTTATTATTTTAT-TTTATTTATATTAA
2328423 TATTTT
62 TATTTT
2328429 TTCCTTTAGC
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
67 1 0.02
68 44 0.76
69 13 0.22
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.76
Consensus pattern (68 bp):
TTTATTTTATTTTATTTTCATTTATTTTATTTATTTTATTATTTTATTTTATTTATATTAATATT
TTA
Found at i:2337977 original size:18 final size:18
Alignment explanation
Indices: 2337954--2337991 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2337944 AGCCTTGTTG
2337954 TCTCTAATTTTTTTAGAT
1 TCTCTAATTTTTTTAGAT
2337972 TCTCTAATTTTTTTAGAT
1 TCTCTAATTTTTTTAGAT
2337990 TC
1 TC
2337992 AATTACTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.61
Consensus pattern (18 bp):
TCTCTAATTTTTTTAGAT
Found at i:2340581 original size:6 final size:6
Alignment explanation
Indices: 2340565--2340619 Score: 74
Period size: 6 Copynumber: 9.2 Consensus size: 6
2340555 ATAGGTGTAT
* * * *
2340565 TATAGA TATATA CATATA CATATA CATATA TATATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
2340613 TATATA T
1 TATATA T
2340620 TGAATATGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (6 bp):
TATATA
Found at i:2343804 original size:20 final size:20
Alignment explanation
Indices: 2343779--2343827 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
2343769 CGCATCTTTG
*
2343779 CATTTTTACGTTTGTATTTA
1 CATTTTTACGTTTGCATTTA
* **
2343799 CATTTTCATTTTTGCATTTA
1 CATTTTTACGTTTGCATTTA
*
2343819 CATATTTAC
1 CATTTTTAC
2343828 ATATTTGCAT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.57
Consensus pattern (20 bp):
CATTTTTACGTTTGCATTTA
Found at i:2349069 original size:119 final size:120
Alignment explanation
Indices: 2348922--2349239 Score: 543
Period size: 119 Copynumber: 2.7 Consensus size: 120
2348912 ATTTCATTTG
2348922 ACTCAAGATT-TTTTTCCTTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
2348986 AGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA-AAGATTTTATCTC
66 AGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
*
2349040 ACTCAAGATTGTTTTTCCATT-AAACAGAAGATTTTATCTCATTCAAGATTATTTTTCCTTGAAA
1 ACTCAAGATTGTTTTTCC-TTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAA
2349104 CAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
65 CAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
* * ** *
2349160 ACTCAATATTGATTTTCCTTGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTTTCTTGAAAC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
*
2349225 AAAAGATTTTATCTC
66 AGAAGATTTTATCTC
2349240 GCTTGAGATA
Statistics
Matches: 188, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
118 10 0.05
119 93 0.49
120 85 0.45
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (120 bp):
ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
AGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
Found at i:2349093 original size:20 final size:20
Alignment explanation
Indices: 2349030--2349094 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
2349020 TGAAACAAAG
*
2349030 ATTTTATCTCACTCAAGATT
1 ATTTTATCTCATTCAAGATT
* * **
2349050 GTTTT-TC-CATTAAACAGAAG
1 ATTTTATCTCATT-CA-AGATT
2349070 ATTTTATCTCATTCAAGATT
1 ATTTTATCTCATTCAAGATT
2349090 ATTTT
1 ATTTT
2349095 TCCTTGAAAC
Statistics
Matches: 32, Mismatches: 9, Indels: 8
0.65 0.18 0.16
Matches are distributed among these distances:
18 3 0.09
19 3 0.09
20 19 0.59
21 3 0.09
22 4 0.12
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (20 bp):
ATTTTATCTCATTCAAGATT
Found at i:2349242 original size:40 final size:40
Alignment explanation
Indices: 2348922--2349239 Score: 534
Period size: 40 Copynumber: 8.0 Consensus size: 40
2348912 ATTTCATTTG
2348922 ACTCAAGATT-TTTTTCCTTGAAACAGAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
*
2348961 ATTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
2349001 ACTCAAGATTGTTTTTCCTTGAAACA-AAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
2349040 ACTCAAGATTGTTTTTCCATT-AAACAGAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCC-TTGAAACAGAAGATTTTATCTC
* *
2349080 ATTCAAGATTATTTTTCCTTGAAACAGAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
2349120 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
* *
2349160 ACTCAATATTGATTTTCCTTGAAACAGAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
* * *
2349200 GCTCAAGATTGTTTTTTCTTGAAACAAAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
2349240 GCTTGAGATA
Statistics
Matches: 262, Mismatches: 13, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
39 47 0.18
40 215 0.82
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (40 bp):
ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
Found at i:2349259 original size:159 final size:159
Alignment explanation
Indices: 2348924--2349262 Score: 515
Period size: 159 Copynumber: 2.1 Consensus size: 159
2348914 TTCATTTGAC
* * *
2348924 TCAAGATT-TTTTTCCTTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAACAG
1 TCAAGATTAGTTTCCCTTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAG
*
2348988 AAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAAAGATTTTATCTCACTCAAGATTGTT
66 AAGATTTTATCTCACTCAAGATTGATTTTCCTTGAAACAAAGATTTTATCTCACTCAAGATTGTT
*
2349053 TTTCCATTAAACAGAAGATTTTATCTCAT
131 TTTCCATTAAACAAAAGATTTTATCTCAT
* *
2349082 TCAAGATTATTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAG
1 TCAAGATTAGTTTCCCTTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAG
* *
2349147 AAGATTTTATCTCACTCAATATTGATTTTCCTTGAAACAGAAGATTTTATCTCGCTCAAGATTGT
66 AAGATTTTATCTCACTCAAGATTGATTTTCCTTGAAACA-AAGATTTTATCTCACTCAAGATTGT
* *
2349212 TTTTTC-TTGAAACAAAAGATTTTATCTCGCT
130 TTTTCCATT-AAACAAAAGATTTTATCTC-AT
*
2349243 T-GAGA-TAGTTTCCCTTGAAA
1 TCAAGATTAGTTTCCCTTGAAA
2349263 AAATTTTGTC
Statistics
Matches: 167, Mismatches: 10, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
158 8 0.05
159 107 0.64
160 50 0.30
161 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.41
Consensus pattern (159 bp):
TCAAGATTAGTTTCCCTTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAG
AAGATTTTATCTCACTCAAGATTGATTTTCCTTGAAACAAAGATTTTATCTCACTCAAGATTGTT
TTTCCATTAAACAAAAGATTTTATCTCAT
Found at i:2349310 original size:36 final size:36
Alignment explanation
Indices: 2349230--2349412 Score: 273
Period size: 36 Copynumber: 5.1 Consensus size: 36
2349220 GAAACAAAAG
* *
2349230 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAA-AA
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
* *
2349265 ATTTTGTCTCTTTTGAGATAGTTTCCCTCGAAACAA
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
2349301 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
*
2349337 ATTTTGTCTCTCTTGAGACAGTTT-CCTTGAAACAA
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
*
2349372 ATTTTGTCT-TCCTTGAGATAGTTTCTCTTGAAACAA
1 ATTTTGTCTCT-CTTGAGATAGTTTCCCTTGAAACAA
*
2349408 GTTTT
1 ATTTT
2349413 TGATACAGTT
Statistics
Matches: 135, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
34 1 0.01
35 61 0.45
36 73 0.54
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (36 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
Found at i:2349317 original size:71 final size:71
Alignment explanation
Indices: 2349230--2349412 Score: 271
Period size: 71 Copynumber: 2.6 Consensus size: 71
2349220 GAAACAAAAG
* * * *
2349230 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAA-AAATTTTGTCTCTTTTGAGATAGTTTCCCTC
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTT-CCTC
2349294 GAAACAA
65 GAAACAA
*
2349301 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCTTG
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCTCG
2349366 AAACAA
66 AAACAA
* *
2349372 ATTTTGTCT-TCCTTGAGATAGTTTCTCTTGAAACAAGTTTT
1 ATTTTGTCTCT-CTTGAGATAGTTTCCCTTGAAACAAATTTT
2349413 TGATACAGTT
Statistics
Matches: 103, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
70 1 0.01
71 78 0.76
72 24 0.23
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (71 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCTCG
AAACAA
Found at i:2349550 original size:73 final size:73
Alignment explanation
Indices: 2349427--2349671 Score: 312
Period size: 73 Copynumber: 3.4 Consensus size: 73
2349417 ACAGTTTCTC
* * * * * * *
2349427 TTGAAA-AAATTTTGTCTCCCTTGATATGGGTTTTCTAAAAACCAAGTTCGTCTCACTTGAGACA
1 TTGAAACAAAATTTATCTCACTTGAGATGGGTTTTCTTAAAACCTACTTCGTCTCACTTGAGACA
*
2349491 ACTTTCCT
66 ATTTTCCT
** * * *
2349499 TTGAAACAAAATGAATCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCGTCTGACTTGAGATA
1 TTGAAACAAAATTTATCTCACTTGAGATGGGTTTTCTTAAAACCTACTTCGTCTCACTTGAGACA
*
2349564 GTTTTCCT
66 ATTTTCCT
* **
2349572 TTGAAACAAAATTTATCTCACTTGAGATGGGTTTTCTTAAAACCTACTTCGTATTGCTTGAGACA
1 TTGAAACAAAATTTATCTCACTTGAGATGGGTTTTCTTAAAACCTACTTCGTCTCACTTGAGACA
2349637 ATTTTCCT
66 ATTTTCCT
* *
2349645 TCGGAACAAAATTTATCTCACTTGAGA
1 TTGAAACAAAATTTATCTCACTTGAGA
2349672 GTGCTTCTCT
Statistics
Matches: 148, Mismatches: 24, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
72 6 0.04
73 142 0.96
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (73 bp):
TTGAAACAAAATTTATCTCACTTGAGATGGGTTTTCTTAAAACCTACTTCGTCTCACTTGAGACA
ATTTTCCT
Found at i:2349568 original size:36 final size:36
Alignment explanation
Indices: 2349514--2349623 Score: 121
Period size: 36 Copynumber: 3.0 Consensus size: 36
2349504 ACAAAATGAA
2349514 TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCG
1 TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCG
* * * * ** * **
2349550 TCTGACTTGAGATAGTTTTCCTTTGAAACAAAATTTA
1 TCTCACTTGAGATGGTTTTTC-TTAAAACCTACTTCG
*
2349587 TCTCACTTGAGATGGGTTTTCTTAAAACCTACTTCG
1 TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCG
2349623 T
1 T
2349624 ATTGCTTGAG
Statistics
Matches: 54, Mismatches: 19, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
36 28 0.52
37 26 0.48
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (36 bp):
TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCG
Found at i:2349598 original size:37 final size:37
Alignment explanation
Indices: 2349477--2349599 Score: 113
Period size: 37 Copynumber: 3.4 Consensus size: 37
2349467 ACCAAGTTCG
* ** *
2349477 TCTCACTTGAGACAACTTTCCTTTGAAACAAAATGAA
1 TCTCACTTGAGATAGTTTTCCTTTGAAACAAAATTAA
* * * ** * **
2349514 TCTCACTTGAGATGGTTTTTC-TTAAAACCTACTTCG
1 TCTCACTTGAGATAGTTTTCCTTTGAAACAAAATTAA
* *
2349550 TCTGACTTGAGATAGTTTTCCTTTGAAACAAAATTTA
1 TCTCACTTGAGATAGTTTTCCTTTGAAACAAAATTAA
2349587 TCTCACTTGAGAT
1 TCTCACTTGAGAT
2349600 GGGTTTTCTT
Statistics
Matches: 63, Mismatches: 22, Indels: 2
0.72 0.25 0.02
Matches are distributed among these distances:
36 26 0.41
37 37 0.59
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (37 bp):
TCTCACTTGAGATAGTTTTCCTTTGAAACAAAATTAA
Found at i:2350190 original size:105 final size:107
Alignment explanation
Indices: 2350061--2350347 Score: 393
Period size: 105 Copynumber: 2.7 Consensus size: 107
2350051 ACTTGAGAGA
*
2350061 TCAACATTTTCAATGAAGAGTTCATAATGAGAAGAACTTGTCCTAAAGGAGAAAGTTCATAATGA
1 TCAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTTGTCCTAAAGGAGAAAGTTCATAATGA
* *
2350126 GAAGAACTTGTTCCTTTCAAATTCACCACAGAAGGAGGTGAAC
66 GAAGAACGTGTTCCTTTCAAATCCACCACAGAAGGAGGTG-AC
* *
2350169 -CAACATTTCC-A-GAAGAGTTCATAATGAGAAGAACTCGTCCTAGAGGAGAAAGTTCATAATGA
1 TCAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTTGTCCTAAAGGAGAAAGTTCATAATGA
* *
2350231 GAAGAACGTGTTCCTTTCAAGTCCACCGCAGAAGGAGGTGAC
66 GAAGAACGTGTTCCTTTCAAATCCACCACAGAAGGAGGTGAC
* * * *
2350273 TCAAGATTTCCAATGGAGGGTTCATAATGAGAAGGACTTGTCC-AACGAGGGAGAATGAGTTCAT
1 TCAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTTGTCCTAA--A-GGAGAA--AGTTCAT
2350337 AATGAGAAGAA
61 AATGAGAAGAA
2350348 TTGACATTCA
Statistics
Matches: 158, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
104 2 0.01
105 94 0.59
106 3 0.02
107 34 0.22
108 1 0.01
109 6 0.04
111 18 0.11
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.23
Consensus pattern (107 bp):
TCAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTTGTCCTAAAGGAGAAAGTTCATAATGA
GAAGAACGTGTTCCTTTCAAATCCACCACAGAAGGAGGTGAC
Found at i:2352088 original size:2 final size:2
Alignment explanation
Indices: 2352081--2352159 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
2352071 ATAGGTGTAT
*
2352081 TA TA TA TA TA TA CA 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
2352123 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
2352160 GAATATGCTT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2353136 original size:16 final size:17
Alignment explanation
Indices: 2353105--2353142 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
2353095 GCATACCAAC
*
2353105 TTTTGTCTTAAAAATTA
1 TTTTTTCTTAAAAATTA
2353122 TTTTTTCTT-AAAATTA
1 TTTTTTCTTAAAAATTA
2353138 TTTTT
1 TTTTT
2353143 AAAAGACGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (17 bp):
TTTTTTCTTAAAAATTA
Found at i:2358531 original size:3 final size:3
Alignment explanation
Indices: 2358525--2358587 Score: 78
Period size: 3 Copynumber: 22.0 Consensus size: 3
2358515 ATTTATTATT
* *
2358525 TAA TAA T-A TAA TAA TAT TAA TAA TAA TAT TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2358571 -AA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
2358588 ATCAAAAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 6 0.12
3 45 0.88
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2358599 original size:37 final size:37
Alignment explanation
Indices: 2358527--2358599 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
2358517 TTATTATTTA
* * *
2358527 ATAATATAATAATATTAATAATAATATTAATAATAAT
1 ATAATAAAATAATATTAATAATAATATAAAAAATAAT
2358564 ATAATAAAATAAT-TATAATAATAA-ATCAAAAAATAA
1 ATAATAAAATAATAT-TAATAATAATAT-AAAAAATAA
2358600 AAAACAAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
36 3 0.10
37 28 0.90
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (37 bp):
ATAATAAAATAATATTAATAATAATATAAAAAATAAT
Found at i:2359227 original size:113 final size:112
Alignment explanation
Indices: 2359072--2359640 Score: 652
Period size: 117 Copynumber: 5.0 Consensus size: 112
2359062 ATAGAATCAA
* *
2359072 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTCATT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
* *
2359137 ATGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTC-TAGC
66 ATGAACTTTCTCTGGAAATGTTGATCCATCGAGTGATGAATTCAT-GC
* *
2359184 AAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCA
1 AAAAGG-TTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCA
* * * * *
2359249 TTATGATCTCTT-TC-GAAAATGTTGATCTGTTTCCTTC-TGTGAT-AGAGTCATGC
64 TTATGAACT-TTCTCTGGAAATGTTGA------TCCATCGAGTGATGA-ATTCATGC
* *
2359302 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
* *
2359367 ATGAACTTTCTCTGGAAATGTTGATCCATTGAGTGATGAATTCAAGC
66 ATGAACTTTCTCTGGAAATGTTGATCCATCGAGTGATGAATTCATGC
*
2359414 AAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAGG-TTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCA
* * * *
2359479 TTATGAA-TTGT-TTTGGAAATGTTGATATATCTTCTTC-TGTGAT-AGAGTCATGC
64 TTATGAACTT-TCTCTGGAAATGTTG----ATC--CATCGAGTGATGA-ATTCATGC
* * *
2359532 AAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCATATTCAGATAAGTTCTTCTCATT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
* * *
2359597 ATGAACTTTCTCTGGAAATGTTGATCCATTGAGTAATGGATTCA
66 ATGAACTTTCTCTGGAAATGTTGATCCATCGAGTGATGAATTCA
2359641 AATCTTTGCT
Statistics
Matches: 386, Mismatches: 42, Indels: 58
0.79 0.09 0.12
Matches are distributed among these distances:
111 6 0.02
112 31 0.08
113 95 0.25
114 57 0.15
115 3 0.01
116 56 0.15
117 97 0.25
118 33 0.09
119 8 0.02
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (112 bp):
AAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAATGTTGATCCATCGAGTGATGAATTCATGC
Found at i:2359329 original size:117 final size:116
Alignment explanation
Indices: 2358984--2359622 Score: 622
Period size: 117 Copynumber: 5.5 Consensus size: 116
2358974 GTTGAACAAG
* *
2358984 TTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGAACAC-TTCTAGAAATGTTGATACTGAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCGA-AAATGTTGAT-C---T
* * *
2359047 CTATCTCCTTCTGTGATAGAATCA--AAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
61 -T-T-TCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAT
* * *
2359104 TTCTTCTTCC-TCTTCAGATGAGTTATTCTCATTATGAACTTCCTCTGGAAAA-GTTGA-----T
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-T-CTTTCGAAAATGTTGATCTTTT
* * * *
2359162 CCATCGAGTGAT-GAATTC-TAGCAAAAGGTTTGAACAAATTCTTCTCATTATGAAT
64 CCTTC-TGTGATAG-AGTCAT-GCAAAAGG-TTGAACAAGTTCTTCTCATTATGAAT
* *
2359217 TTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGATCTCTTTCGAAAATGTTGATCTGTTTC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCGAAAATGTTGATCT-TTTC
*
2359282 CTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
65 CTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAT
* *
2359334 TTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACT-TTCTCTGGAAATGTTGATC----
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTT-TC-GAAAATGTTGATCTTTT
* ** * * *
2359393 CATTGAGTGAT-GAATTCAAGCAAAAGGTTTGAACAAATTCTTCTCATTATGAAT
64 CCTTCTGTGATAG-AGTCATGCAAAAGG-TTGAACAAGTTCTTCTCATTATGAAT
* * * * *
2359447 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAATTGTTTTGGAAATGTTGATATATCTT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCGAAAATGTTGATCT-T-TT
2359512 -CTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAT
64 CCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAT
* * * *
2359564 TTCTTCTT-CATATTCAGATAAGTTCTTCTCATTATGAACT-TTCTCTGGAAATGTTGATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTT-TC-GAAAATGTTGATC
2359623 CATTGAGTAA
Statistics
Matches: 436, Mismatches: 48, Indels: 73
0.78 0.09 0.13
Matches are distributed among these distances:
109 6 0.01
110 8 0.02
111 1 0.00
112 34 0.08
113 86 0.20
114 55 0.13
115 6 0.01
116 58 0.13
117 91 0.21
118 35 0.08
119 8 0.02
120 34 0.08
121 8 0.02
122 4 0.01
123 2 0.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (116 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCGAAAATGTTGATCTTTTCC
TTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAT
Found at i:2359346 original size:230 final size:231
Alignment explanation
Indices: 2358984--2359641 Score: 997
Period size: 230 Copynumber: 2.8 Consensus size: 231
2358974 GTTGAACAAG
* * *
2358984 TTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGAACAC-TTCTAGAAATGTTGATACTGAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGATCTCTTTCGA-AAATGTTGAT-CTG--
* *
2359047 CTATCTCCTTCTGTGATAGAATCA--AAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
62 -TAT-TCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
* * * * *
2359110 TTCCTCTTCAGATGAGTTATTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATG
125 TTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATTGAGTGATG
*
2359175 AATTCTAGCAAAAGGTTTGAACAAATTCTTCTCATTATGAAT
190 AATTCAAGCAAAAGGTTTGAACAAATTCTTCTCATTATGAAT
*
2359217 TTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGATCTCTTTCGAAAATGTTGATCTGT-TT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGATCTCTTTCGAAAATGTTGATCTGTATT
2359281 CCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTC
66 CCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTC
2359346 TTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATTGAGTGATGAATTCA
131 TTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATTGAGTGATGAATTCA
2359411 AGCAAAAGGTTTGAACAAATTCTTCTCATTATGAAT
196 AGCAAAAGGTTTGAACAAATTCTTCTCATTATGAAT
* * * * * *
2359447 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAT-TGTTTTGGAAATGTTGATATATCT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG-ATCTCTTTCGAAAATGTTGATCTGTAT
* *
2359511 T-CTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCAT
65 TCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT
* * *
2359575 ATTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATTGAGTAATGGATTC
130 CTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATTGAGTGATGAATTC
2359640 AA
195 AA
2359642 ATCTTTGCTA
Statistics
Matches: 396, Mismatches: 23, Indels: 15
0.91 0.05 0.03
Matches are distributed among these distances:
228 18 0.05
229 1 0.00
230 318 0.80
231 4 0.01
233 9 0.02
234 42 0.11
235 4 0.01
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.41
Consensus pattern (231 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGATCTCTTTCGAAAATGTTGATCTGTATT
CCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTC
TTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATTGAGTGATGAATTCA
AGCAAAAGGTTTGAACAAATTCTTCTCATTATGAAT
Found at i:2366272 original size:43 final size:43
Alignment explanation
Indices: 2366219--2366430 Score: 194
Period size: 43 Copynumber: 4.9 Consensus size: 43
2366209 TTTTTTTGTT
* * * *
2366219 AAAAATGCCGCTATAGGTATTGATATTTAGCGGCGTTTGTCAG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCAG
* * * *
2366262 AAAAACGCCGCAATAGGTGTTGATATTTATCAGTGTTTTTCAT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCAG
** * *
2366305 AAAAACATCGTAATAGGTGTTGATATTTAGCGGCGTTTTTTAG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCAG
* * * * **
2366348 ACAAATGCTGCAATAGGT-TATGATGTTTAGCGGCGTTTTTCTCC
1 AAAAACGCCGCAATAGGTGT-TGATATTTAGCGGCGTTTTTC-AG
* * * *
2366392 AAAAA-GCCACAGTAGGTGTTGATGTTTTGCGGCGTTTTT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTT
2366431 GCTAAAAATG
Statistics
Matches: 135, Mismatches: 31, Indels: 6
0.78 0.18 0.03
Matches are distributed among these distances:
42 1 0.01
43 129 0.96
44 5 0.04
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.36
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCAG
Found at i:2366908 original size:21 final size:21
Alignment explanation
Indices: 2366884--2366945 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
2366874 TTGTGCCGTC
* *
2366884 GCTGCTTCTTTCTCTGCTTCT
1 GCTGCTGCTCTCTCTGCTTCT
** *
2366905 GCTGCTGCTCTGGCTGCGTCT
1 GCTGCTGCTCTCTCTGCTTCT
2366926 GCTGCTGCTCTCTCTGCTTC
1 GCTGCTGCTCTCTCTGCTTC
2366946 CCTTGCTTCA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.00, C:0.35, G:0.23, T:0.42
Consensus pattern (21 bp):
GCTGCTGCTCTCTCTGCTTCT
Found at i:2376004 original size:42 final size:42
Alignment explanation
Indices: 2375912--2376004 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
2375902 ATAATATTTC
*
2375912 GCGGCGTTTGTAAACCAAACGCCACCACATGCCAACTCTACT
1 GCGGCGTTTGTAAACCAAACACCACCACATGCCAACTCTACT
* * * * * *
2375954 GTGACGTTTGTAAACCAAACACCACTATATTCCAACTCTATT
1 GCGGCGTTTGTAAACCAAACACCACCACATGCCAACTCTACT
2375996 GCGGCGTTT
1 GCGGCGTTT
2376005 ACTAAAAACG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (42 bp):
GCGGCGTTTGTAAACCAAACACCACCACATGCCAACTCTACT
Found at i:2377667 original size:41 final size:40
Alignment explanation
Indices: 2377519--2377669 Score: 151
Period size: 41 Copynumber: 3.7 Consensus size: 40
2377509 ATTTATACAA
* * * **
2377519 AAAAATGCCACAATTGATT-GCACTATTGTGGCGTTTGTT
1 AAAAACGCCACTATTGATTAACACTATTACGGCGTTTGTT
* * * *
2377558 AAAACAACGCCAGTATTGATTAAAACTATTACGGCTTTTTTTT
1 -AAA-AACGCCACTATTGATTAACACTATTACGGC-GTTTGTT
2377601 AAAAACGCCACTATTGATTAACACTATTACGGCGTTTGTCT
1 AAAAACGCCACTATTGATTAACACTATTACGGCGTTTGT-T
* * *
2377642 AAAAATGCCACTATTTATTATCACTATT
1 AAAAACGCCACTATTGATTAACACTATT
2377670 GCGACATTTT
Statistics
Matches: 91, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
40 7 0.08
41 67 0.74
42 12 0.13
43 5 0.05
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (40 bp):
AAAAACGCCACTATTGATTAACACTATTACGGCGTTTGTT
Found at i:2377730 original size:42 final size:40
Alignment explanation
Indices: 2377583--2377813 Score: 114
Period size: 42 Copynumber: 5.6 Consensus size: 40
2377573 TTGATTAAAA
* ** * *
2377583 CTATTACGGCTTTTTTTTAAAAACGCCACTAT-TGATTAACA
1 CTATTACGGCGTTTTGGTATAAACGCCACTATATG-TTAA-T
* * * * *
2377624 CTATTACGGCG-TTTGTCTAAAAATGCCACTATTTATT-AT
1 CTATTACGGCGTTTTG-GTATAAACGCCACTATATGTTAAT
* * * *
2377663 CACTATTGCGACATTTTAGGAATAAACGCCACTATATGTGTAAT
1 --CTATTACGGCGTTTT-GGTATAAACGCCACTATATGT-TAAT
* **
2377707 CTATTACGGTGTTTGTGGTATAAAAACCACTA-AT-TTACCGAT
1 CTATTACGGCGTTT-TGGTATAAACGCCACTATATGTTA---AT
* * *
2377749 CTATTGCGGCATTTTGGCTA-AAATGCCACTATATGTTAAT
1 CTATTACGGCGTTTTGG-TATAAACGCCACTATATGTTAAT
*
2377789 CTATTACGGCGTTTATCGTATAAAC
1 CTATTACGGCGTTT-TGGTATAAAC
2377814 ACTACTAATA
Statistics
Matches: 142, Mismatches: 31, Indels: 34
0.69 0.15 0.16
Matches are distributed among these distances:
39 2 0.01
40 21 0.15
41 53 0.37
42 58 0.41
43 6 0.04
44 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (40 bp):
CTATTACGGCGTTTTGGTATAAACGCCACTATATGTTAAT
Found at i:2379149 original size:3 final size:3
Alignment explanation
Indices: 2379143--2379202 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
2379133 ATTTATTATT
* *
2379143 TAA TAA TAA CAA TAA TAA TAA TAT TAA TAA TAA TATA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
*
2379188 TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA
2379203 ATCAGAAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2382719 original size:18 final size:18
Alignment explanation
Indices: 2382691--2382727 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2382681 AAAAAAATTA
2382691 TTTTGATTTTAATTGTTGT
1 TTTTGATTTTAATT-TTGT
2382710 TTTTGA-TTTAATTTTGT
1 TTTTGATTTTAATTTTGT
2382727 T
1 T
2382728 GCTTTCATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 7 0.39
19 6 0.33
ACGTcount: A:0.16, C:0.00, G:0.14, T:0.70
Consensus pattern (18 bp):
TTTTGATTTTAATTTTGT
Found at i:2384230 original size:16 final size:16
Alignment explanation
Indices: 2384209--2384264 Score: 76
Period size: 16 Copynumber: 3.3 Consensus size: 16
2384199 ATTTTGGATG
2384209 TTTGTGAATGTTTGAA
1 TTTGTGAATGTTTGAA
*
2384225 TTTGTGGATGTTTGAA
1 TTTGTGAATGTTTGAA
2384241 TTTGTTTTGAATGTTTGAA
1 TTTG---TGAATGTTTGAA
2384260 TTTGT
1 TTTGT
2384265 TTTGGATGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 20 0.57
19 15 0.43
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (16 bp):
TTTGTGAATGTTTGAA
Found at i:2384252 original size:35 final size:37
Alignment explanation
Indices: 2384207--2384278 Score: 112
Period size: 35 Copynumber: 1.9 Consensus size: 37
2384197 ACATTTTGGA
2384207 TGTTTGTGAATGTTTGAATTTG-TGGATGTTTGAATT
1 TGTTTGTGAATGTTTGAATTTGTTGGATGTTTGAATT
2384243 TGTTT-TGAATGTTTGAATTTGTTTTGGATGTTTGAA
1 TGTTTGTGAATGTTTGAATTTG--TTGGATGTTTGAA
2384279 CTTAAATGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
35 16 0.48
36 5 0.15
38 12 0.36
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.54
Consensus pattern (37 bp):
TGTTTGTGAATGTTTGAATTTGTTGGATGTTTGAATT
Found at i:2384256 original size:19 final size:19
Alignment explanation
Indices: 2384207--2384278 Score: 96
Period size: 19 Copynumber: 3.9 Consensus size: 19
2384197 ACATTTTGGA
2384207 TGTTTGTGAATGTTTGAATT
1 TGTTT-TGAATGTTTGAATT
*
2384227 TG---TGGATGTTTGAATT
1 TGTTTTGAATGTTTGAATT
2384243 TGTTTTGAATGTTTGAATT
1 TGTTTTGAATGTTTGAATT
*
2384262 TGTTTTGGATGTTTGAA
1 TGTTTTGAATGTTTGAA
2384279 CTTAAATGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
16 15 0.33
19 29 0.63
20 2 0.04
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.54
Consensus pattern (19 bp):
TGTTTTGAATGTTTGAATT
Found at i:2385872 original size:8 final size:8
Alignment explanation
Indices: 2385848--2385907 Score: 68
Period size: 8 Copynumber: 7.5 Consensus size: 8
2385838 TATATTTGTC
*
2385848 TTATACAT
1 TTATATAT
2385856 TTATAATAT
1 TTAT-ATAT
2385865 TTATATAT
1 TTATATAT
*
2385873 ATATATA-
1 TTATATAT
2385880 TTATATAT
1 TTATATAT
*
2385888 ATATATAT
1 TTATATAT
*
2385896 ATATATAT
1 TTATATAT
2385904 TTAT
1 TTAT
2385908 TACTTATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
7 6 0.13
8 32 0.71
9 7 0.16
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (8 bp):
TTATATAT
Found at i:2385873 original size:2 final size:2
Alignment explanation
Indices: 2385857--2385903 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
2385847 CTTATACATT
*
2385857 TA TA -A TA TT TA TA TA TA TA TA TA T- 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
2385897 TA TA TA T
1 TA TA TA T
2385904 TTATTACTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2387166 original size:7 final size:7
Alignment explanation
Indices: 2387154--2387198 Score: 65
Period size: 7 Copynumber: 6.3 Consensus size: 7
2387144 TATGTATATA
2387154 TTATTTT
1 TTATTTT
2387161 TTATTTT
1 TTATTTT
2387168 ATT-TTATT
1 -TTATT-TT
2387176 TTATTTT
1 TTATTTT
2387183 TTATTTT
1 TTATTTT
2387190 TTATTTT
1 TTATTTT
2387197 TT
1 TT
2387199 TTTGTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 29 0.83
8 6 0.17
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TTATTTT
Found at i:2387169 original size:5 final size:5
Alignment explanation
Indices: 2387159--2387206 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
2387149 ATATATTATT
* *
2387159 TTTTA TTTTA TTTTA TTTTA TTTT- TTATT- TTTTA TTTTT TTTTG TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTT
2387207 TTATTTAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 4 0.10
5 35 0.90
ACGTcount: A:0.12, C:0.00, G:0.02, T:0.85
Consensus pattern (5 bp):
TTTTA
Found at i:2387176 original size:17 final size:16
Alignment explanation
Indices: 2387154--2387212 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
2387144 TATGTATATA
2387154 TTATTTTTTATTTTATT
1 TTATTTTTTATTTT-TT
2387171 TTA--TTTTA--TTTT
1 TTATTTTTTATTTTTT
2387183 TTATTTTTTATTTTTTT
1 TTATTTTTTA-TTTTTT
*
2387200 TTGTTTTTTATTT
1 TTATTTTTTATTT
2387213 AGTTCCATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
12 5 0.14
13 2 0.06
14 5 0.14
15 5 0.14
16 3 0.08
17 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.85
Consensus pattern (16 bp):
TTATTTTTTATTTTTT
Found at i:2387186 original size:29 final size:29
Alignment explanation
Indices: 2387127--2387206 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
2387117 CTTTCATTGT
* * *
2387127 TTTTTTACTTTATATTATATGTATATATTA
1 TTTTTTATTTTATTTTAT-TTTATATATTA
* *
2387157 TTTTTTATTTTATTTTATTTTATTTTTTA
1 TTTTTTATTTTATTTTATTTTATATATTA
* *
2387186 TTTTTTATTTTTTTTTGTTTT
1 TTTTTTATTTTATTTTATTTT
2387207 TTATTTAGTT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 27 0.63
30 16 0.37
ACGTcount: A:0.19, C:0.01, G:0.03, T:0.78
Consensus pattern (29 bp):
TTTTTTATTTTATTTTATTTTATATATTA
Found at i:2387207 original size:10 final size:10
Alignment explanation
Indices: 2387152--2387213 Score: 63
Period size: 10 Copynumber: 6.2 Consensus size: 10
2387142 TATATGTATA
*
2387152 TATTATTTTT
1 TATTTTTTTT
*
2387162 TATTTTATTT
1 TATTTTTTTT
*
2387172 TATTTTATTT
1 TATTTTTTTT
*
2387182 T-TTATTTTT
1 TATTTTTTTT
2387191 TATTTTTTTT
1 TATTTTTTTT
*
2387201 TGTTTTTTATT
1 TATTTTTT-TT
2387212 TA
1 TA
2387214 GTTCCATTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
9 7 0.16
10 33 0.77
11 3 0.07
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (10 bp):
TATTTTTTTT
Found at i:2387297 original size:24 final size:24
Alignment explanation
Indices: 2387250--2387311 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
2387240 GTTTTTTTTG
2387250 TTTGTTTTGTTTTATTTTAACTTAT
1 TTTGTTTT-TTTTATTTTAACTTAT
*
2387275 TTTGTTTTTTTTAATTTT-CCTTAT
1 TTTGTTTTTTTT-ATTTTAACTTAT
*
2387299 TTTATTATTTTTT
1 TTTGTT-TTTTTT
2387312 TCTTTTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 14 0.42
25 19 0.58
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.76
Consensus pattern (24 bp):
TTTGTTTTTTTTATTTTAACTTAT
Found at i:2391609 original size:12 final size:13
Alignment explanation
Indices: 2391592--2391620 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2391582 CATAAGTCGA
2391592 AAAAG-AAAAAAG
1 AAAAGAAAAAAAG
2391604 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
2391617 AAAA
1 AAAA
2391621 ATCATTTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:2392664 original size:65 final size:68
Alignment explanation
Indices: 2392555--2392738 Score: 241
Period size: 65 Copynumber: 2.7 Consensus size: 68
2392545 CGACACAATT
* * *
2392555 TACTCGAGATTGGATTTTAACTTCACAACGAAAGATATCCAACTCAAAGCCAATTTGGTG-A-AA
1 TACTCAAGATTGGATTTCAACTTCACAACGAAAGATATCCAACTCAAAGCCAATTTGATGAAGAA
*
2392618 -CC
66 TAC
*
2392620 TACTCAAGATTGGATTTCAACTTCACGAA-GAAAGATATCGAACTCAAAGCCAATTTGATGAAGT
1 TACTCAAGATTGGATTTCAACTTCAC-AACGAAAGATATCCAACTCAAAGCCAATTTGATGAAG-
2392684 AATAC
64 AATAC
* * * *
2392689 AACTCTAGATTGGATTTCAACTTTACAACGAAAGATATCCAATTCAAAGC
1 TACTCAAGATTGGATTTCAACTTCACAACGAAAGATATCCAACTCAAAGC
2392739 TCAACTTTAC
Statistics
Matches: 103, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
65 53 0.51
66 3 0.03
68 4 0.04
69 43 0.42
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.27
Consensus pattern (68 bp):
TACTCAAGATTGGATTTCAACTTCACAACGAAAGATATCCAACTCAAAGCCAATTTGATGAAGAA
TAC
Found at i:2393775 original size:21 final size:21
Alignment explanation
Indices: 2393749--2393797 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
2393739 ATTATTTTTA
2393749 TTATTTATCT-TTTTTTACTGT
1 TTATTTATCTCTTTTTTA-TGT
* *
2393770 TTATTTTATTTCTTTTTTATTT
1 TTA-TTTATCTCTTTTTTATGT
2393792 TTATTT
1 TTATTT
2393798 GTTTTCCTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 6 0.25
22 11 0.46
23 7 0.29
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (21 bp):
TTATTTATCTCTTTTTTATGT
Found at i:2393790 original size:16 final size:17
Alignment explanation
Indices: 2393769--2393802 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2393759 TTTTTTACTG
2393769 TTTA-TTTTATTTCTTT
1 TTTATTTTTATTTCTTT
*
2393785 TTTATTTTTATTTGTTT
1 TTTATTTTTATTTCTTT
2393802 T
1 T
2393803 CCTAGTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTATTTTTATTTCTTT
Found at i:2393880 original size:10 final size:9
Alignment explanation
Indices: 2393860--2394061 Score: 68
Period size: 10 Copynumber: 20.9 Consensus size: 9
2393850 TATATGTATA
*
2393860 TATTATTTT
1 TATTTTTTT
2393869 TATTCTTTTT
1 TATT-TTTTT
2393879 TATTTTATTT
1 TATTTT-TTT
2393889 TATTTTTTCTTT
1 TA--TTTT-TTT
*
2393901 TATATGTTTT
1 TAT-TTTTTT
* *
2393911 TGTTTTGTT
1 TATTTTTTT
*
2393920 T-TTGTTTT
1 TATTTTTTT
*
2393928 T-GTTTTTT
1 TATTTTTTT
*
2393936 TATTTAGTTT
1 TATTT-TTTT
*
2393946 CATTATTTTT
1 TATT-TTTTT
*
2393956 TCTTTCTTCTT
1 TATTT-TT-TT
*
2393967 TCTTTTTATT
1 TATTTTT-TT
*
2393977 TTTTATTTTT
1 TATT-TTTTT
2393987 TATTATTTTT
1 TATT-TTTTT
2393997 TATTTTTTT
1 TATTTTTTT
*
2394006 GTATTATTTT
1 -TATTTTTTT
* *
2394016 CACTTATTTTG
1 TA-TT-TTTTT
* *
2394027 TATTATTTG
1 TATTTTTTT
*
2394036 TATTTTGTAT
1 TATTTT-TTT
*
2394046 TA-TTTTAT
1 TATTTTTTT
2394054 TATTTTTT
1 TATTTTTT
2394062 GTTCTATTTA
Statistics
Matches: 148, Mismatches: 29, Indels: 32
0.71 0.14 0.15
Matches are distributed among these distances:
8 17 0.11
9 36 0.24
10 69 0.47
11 17 0.11
12 9 0.06
ACGTcount: A:0.14, C:0.04, G:0.05, T:0.77
Consensus pattern (9 bp):
TATTTTTTT
Found at i:2393896 original size:7 final size:7
Alignment explanation
Indices: 2393865--2394078 Score: 59
Period size: 7 Copynumber: 28.4 Consensus size: 7
2393855 GTATATATTA
2393865 TTTTTAT
1 TTTTTAT
2393872 TCTTTT-T
1 T-TTTTAT
2393879 TATTTTA-
1 T-TTTTAT
2393886 -TTTTAT
1 TTTTTAT
*
2393892 TTTTTCT
1 TTTTTAT
*
2393899 TTTATAT
1 TTTTTAT
*
2393906 GTTTTTGT
1 -TTTTTAT
2393914 TTTGTT-T
1 TTT-TTAT
2393921 TTGTTT-T
1 TT-TTTAT
2393928 TGTTTT-T
1 T-TTTTAT
2393935 TTATTTAGT
1 TT-TTTA-T
*
2393944 TTCATTAT
1 TT-TTTAT
*
2393952 TTTTTCT
1 TTTTTAT
*
2393959 TTCTTCTTT
1 TT-TT-TAT
2393968 CTTTTTAT
1 -TTTTTAT
2393976 TTTTTAT
1 TTTTTAT
2393983 TTTTTAT
1 TTTTTAT
2393990 TATTTT-T
1 T-TTTTAT
2393997 TATTTT-T
1 T-TTTTAT
2394004 TTGTATTAT
1 TT-T-TTAT
2394013 TTTCACTTAT
1 TTT---TTAT
*
2394023 TTTGTAT
1 TTTTTAT
2394030 TATTTGTAT
1 T-TTT-TAT
*
2394039 TTTGTAT
1 TTTTTAT
2394046 TATTTTAT
1 T-TTTTAT
2394054 TATTTT-T
1 T-TTTTAT
*
2394061 TGTTCTAT
1 T-TTTTAT
*
2394069 TTATTAT
1 TTTTTAT
2394076 TTT
1 TTT
2394079 CATATTTATG
Statistics
Matches: 161, Mismatches: 22, Indels: 48
0.70 0.10 0.21
Matches are distributed among these distances:
5 5 0.03
6 2 0.01
7 84 0.52
8 44 0.27
9 17 0.11
10 9 0.06
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.77
Consensus pattern (7 bp):
TTTTTAT
Found at i:2393916 original size:5 final size:6
Alignment explanation
Indices: 2393905--2393934 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2393895 TTCTTTTATA
2393905 TGTTTT TG-TTT TGTTTT TGTTTT TGTTTT T
1 TGTTTT TGTTTT TGTTTT TGTTTT TGTTTT T
2393935 TTATTTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
TGTTTT
Found at i:2393969 original size:71 final size:71
Alignment explanation
Indices: 2393894--2394025 Score: 164
Period size: 69 Copynumber: 1.9 Consensus size: 71
2393884 TATTTTATTT
* *
2393894 TTTCTTTTATATGTTTTTGTTTTGTT-TT-TGTTTTTGTTTTTTTAT-TTAGTTTCA-TTATTTT
1 TTTCTTTT-TAT-TTTTTATTTT-TTATTAT-TTTTTATTTTTTTATATTAGTTTCACTTATTTT
2393955 TTCTTTCTTC
62 TTCTTTCTTC
* *
2393965 TTTCTTTTTATTTTTTATTTTTTATTATTTTTTATTTTTTTGTATTATTTTCACTTATTTT
1 TTTCTTTTTATTTTTTATTTTTTATTATTTTTTATTTTTTTATATTAGTTTCACTTATTTT
2394026 GTATTATTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
68 2 0.04
69 24 0.45
70 12 0.23
71 15 0.28
ACGTcount: A:0.11, C:0.06, G:0.05, T:0.77
Consensus pattern (71 bp):
TTTCTTTTTATTTTTTATTTTTTATTATTTTTTATTTTTTTATATTAGTTTCACTTATTTTTTCT
TTCTTC
Found at i:2393979 original size:24 final size:24
Alignment explanation
Indices: 2393948--2394004 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
2393938 TTTAGTTTCA
* *
2393948 TTATTTTTTCTTTCTTCTT-TCTTT
1 TTATTTTTTATTTCTTATTAT-TTT
*
2393972 TTATTTTTTATTTTTTATTATTTT
1 TTATTTTTTATTTCTTATTATTTT
2393996 TTATTTTTT
1 TTATTTTTT
2394005 TGTATTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 28 0.97
25 1 0.03
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (24 bp):
TTATTTTTTATTTCTTATTATTTT
Found at i:2394010 original size:20 final size:19
Alignment explanation
Indices: 2393972--2394078 Score: 93
Period size: 20 Copynumber: 5.7 Consensus size: 19
2393962 TTCTTTCTTT
2393972 TTATTTTTTA-TTTTT-TA
1 TTATTTTTTATTTTTTGTA
2393989 TTATTTTTTATTTTTTTGTA
1 TTATTTTTTA-TTTTTTGTA
*
2394009 TTA-TTTTCACTTATTTTGTA
1 TTATTTTTTA-TT-TTTTGTA
*
2394029 TTA-TTTGTA--TTTTGTA
1 TTATTTTTTATTTTTTGTA
2394045 TTATTTTATTATTTTTTGT-
1 TTATTTT-TTATTTTTTGTA
*
2394064 TCTATTTATTATTTT
1 T-TATTTTTTATTTT
2394079 CATATTTATG
Statistics
Matches: 75, Mismatches: 6, Indels: 16
0.77 0.06 0.16
Matches are distributed among these distances:
16 10 0.13
17 13 0.17
18 2 0.03
19 20 0.27
20 30 0.40
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.75
Consensus pattern (19 bp):
TTATTTTTTATTTTTTGTA
Found at i:2394041 original size:16 final size:15
Alignment explanation
Indices: 2394019--2394054 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
2394009 TTATTTTCAC
2394019 TTATTTTGTATTATT
1 TTATTTTGTATTATT
2394034 TGTATTTTGTATTATT
1 T-TATTTTGTATTATT
2394050 TTATT
1 TTATT
2394055 ATTTTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.72
Consensus pattern (15 bp):
TTATTTTGTATTATT
Found at i:2401695 original size:27 final size:27
Alignment explanation
Indices: 2401626--2401701 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
2401616 TGTTGGTTGA
* *
2401626 TGAGACAGATC-GTGTTGAGGTTGTTGC
1 TGAGACAGA-CAGTGTTGAGGCTGGTGC
** *
2401653 TGAGGTAGGCCA-TGTTGAGGCTGGTGC
1 TGAGACA-GACAGTGTTGAGGCTGGTGC
2401680 TGAGACAGACAGTGTTGAGGCT
1 TGAGACAGACAGTGTTGAGGCT
2401702 ACCTCAGTCT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.20, C:0.13, G:0.39, T:0.28
Consensus pattern (27 bp):
TGAGACAGACAGTGTTGAGGCTGGTGC
Found at i:2404170 original size:2 final size:2
Alignment explanation
Indices: 2404159--2404196 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2404149 TACCCTTATG
2404159 TA TA TA -A 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 T
2404197 TATTTGTGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2405239 original size:64 final size:64
Alignment explanation
Indices: 2405163--2405300 Score: 222
Period size: 64 Copynumber: 2.2 Consensus size: 64
2405153 CCTGAAGCCA
*
2405163 ACCTGCATCCGATATGAGAATGACCTGAACCCAAATTGAACCGATAATATGATAATTGAACTCG
1 ACCTGCATCCGATATGAGAATGACCTGAACCCAAATTGAACCGATAATATGATAATTGAACGCG
* ** *
2405227 ACCTGCATCCGATCTGAGAATGACCTGAACCTGAATTGAACTGATAATATGATAATTGAACGCG
1 ACCTGCATCCGATATGAGAATGACCTGAACCCAAATTGAACCGATAATATGATAATTGAACGCG
*
2405291 ACATGCATCC
1 ACCTGCATCC
2405301 AAATGATATA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 68 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (64 bp):
ACCTGCATCCGATATGAGAATGACCTGAACCCAAATTGAACCGATAATATGATAATTGAACGCG
Found at i:2405371 original size:16 final size:16
Alignment explanation
Indices: 2405350--2405392 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
2405340 AACTGATATT
2405350 ACCTGACCTATTATCA
1 ACCTGACCTATTATCA
* * *
2405366 ACCTGACATTTTATGA
1 ACCTGACCTATTATCA
2405382 ACCTGACCTAT
1 ACCTGACCTAT
2405393 AATTGACTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (16 bp):
ACCTGACCTATTATCA
Found at i:2414610 original size:18 final size:18
Alignment explanation
Indices: 2414587--2414630 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
2414577 GCGATAGTGT
2414587 TATTATTATTTAATAAAA
1 TATTATTATTTAATAAAA
*
2414605 TATTATTATTTGATAAAA
1 TATTATTATTTAATAAAA
2414623 TATTATTA
1 TATTATTA
2414631 CTAAATGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TATTATTATTTAATAAAA
Found at i:2417286 original size:8 final size:8
Alignment explanation
Indices: 2417275--2417300 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2417265 TATTTATTCA
2417275 TTTATAAT
1 TTTATAAT
2417283 TTTATAAT
1 TTTATAAT
2417291 TTTATAAT
1 TTTATAAT
2417299 TT
1 TT
2417301 CATATCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTATAAT
Found at i:2426360 original size:32 final size:33
Alignment explanation
Indices: 2426299--2426367 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
2426289 CTTAATATTA
*
2426299 AAAAATAAATAAATATTATTAAAACATTTATCT
1 AAAAATAAATAAATAATATTAAAACATTTATCT
* * * *
2426332 AAAAATAATTATATAAT-TTAAAATATTTATTT
1 AAAAATAAATAAATAATATTAAAACATTTATCT
2426364 AAAA
1 AAAA
2426368 TATCTGAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (33 bp):
AAAAATAAATAAATAATATTAAAACATTTATCT
Found at i:2427516 original size:3 final size:3
Alignment explanation
Indices: 2427497--2427576 Score: 94
Period size: 3 Copynumber: 27.0 Consensus size: 3
2427487 GATCTGTTTG
*
2427497 TAA TAA TAT TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2427542 TAA TAG TGA TAA TTAA -AA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
2427577 AAACAAATGG
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
2 6 0.09
3 54 0.82
4 6 0.09
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2428216 original size:192 final size:194
Alignment explanation
Indices: 2427886--2428294 Score: 608
Period size: 192 Copynumber: 2.1 Consensus size: 194
2427876 TCTTTATATG
* * * * *
2427886 AGTTCTTCTCATTATGAAC-ACTTCTGGAAATGTTGATGCTAATCTATCTTCTTCTGTGATAGAG
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATG--AATCTATCTCCTTCTGTGATAGAA
* * *
2427950 TCATATAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATAAGTTCTT
64 TCAGACAAAAGGTTGAACAAGCTCTTCTCATTATAAACTTCTTCTTCCTATTCAGATAAGTTCTT
* *
2428015 CTCATTATGAATTTTCTCTGGAAAAGCTGATCCATCGAGTGATTAATTAAAGCGAAAGGTTAAAC
129 CTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGAATTAAAGCGAAAGGTTAAAC
2428080 A
194 A
2428081 AGTTCTTCTCATTATGAACTTCCTCTGGAAAAG-TGATG-ATCTATCTCCTTCTGTGATAGAATC
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATGAATCTATCTCCTTCTGTGATAGAATC
* *
2428144 AGGCAAAAGGTTGAACAAGCTCTTCTCATTATAAACTTCTTCTTCCTCTTCAGATAAGTTCTTCT
66 AGACAAAAGGTTGAACAAGCTCTTCTCATTATAAACTTCTTCTTCCTATTCAGATAAGTTCTTCT
* * ** *
2428209 CATTATGAACTTTCTCTGGAAAAGCTGATCCCTTGAGTGATGAATTCGAGCGAAAGGTTGAACA
131 CATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGAATTAAAGCGAAAGGTTAAACA
* *
2428273 AATTCTTCTCATTTTGAACTTC
1 AGTTCTTCTCATTATGAACTTC
2428295 TTCTTCCTTC
Statistics
Matches: 194, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
192 160 0.82
195 24 0.12
196 10 0.05
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (194 bp):
AGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATGAATCTATCTCCTTCTGTGATAGAATC
AGACAAAAGGTTGAACAAGCTCTTCTCATTATAAACTTCTTCTTCCTATTCAGATAAGTTCTTCT
CATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGAATTAAAGCGAAAGGTTAAACA
Found at i:2428293 original size:112 final size:113
Alignment explanation
Indices: 2428149--2428368 Score: 334
Period size: 113 Copynumber: 2.0 Consensus size: 113
2428139 GAATCAGGCA
*
2428149 AAAGGTTGAACAAGCTCTTCTCATTATAAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATT
1 AAAGGTTGAACAAACTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
*
2428213 ATGAACTTTCTCTGGAAAAGCTGATCCCTTGAGTGATGAATTCGAGCG
66 ATGAACTTTCTCTGGAAAAGCTGATCCATTGAGTGATGAATTCGAGCG
* * * * *
2428261 AAAGGTTGAACAAATTCTTCTCATTTTGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATT
1 AAAGGTTGAACAAACTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
* * * *
2428326 ATGAACTTTCTCTGGCAATGTTGATCCATTGAGTGATGGATTC
66 ATGAACTTTCTCTGGAAAAGCTGATCCATTGAGTGATGAATTC
2428369 AAATCTTGCT
Statistics
Matches: 96, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
112 37 0.39
113 59 0.61
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (113 bp):
AAAGGTTGAACAAACTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGCTGATCCATTGAGTGATGAATTCGAGCG
Found at i:2429933 original size:16 final size:16
Alignment explanation
Indices: 2429884--2429943 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
2429874 ATCTTGGCCC
*
2429884 TCATTTTCTTTCATTTT
1 TCATTTTTTTTCA-TTT
* **
2429901 TCATTTCATCATCATTT
1 TCATTT-TTTTTCATTT
*
2429918 TTATTTTTTTTCATTT
1 TCATTTTTTTTCATTT
2429934 TCATTTTTTT
1 TCATTTTTTT
2429944 CTTCTTTAAG
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
16 16 0.48
17 14 0.42
18 3 0.09
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (16 bp):
TCATTTTTTTTCATTT
Found at i:2437315 original size:16 final size:16
Alignment explanation
Indices: 2437283--2437316 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2437273 TGAAATGAAT
*
2437283 AATGAATGTGTGAAAA
1 AATGAATGTATGAAAA
*
2437299 AATGAATGTATGCAAA
1 AATGAATGTATGAAAA
2437315 AA
1 AA
2437317 GATATTGATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.21, T:0.24
Consensus pattern (16 bp):
AATGAATGTATGAAAA
Found at i:2440045 original size:3 final size:3
Alignment explanation
Indices: 2440026--2440100 Score: 82
Period size: 3 Copynumber: 25.0 Consensus size: 3
2440016 GATCTATTTG
* * *
2440026 TAA TAA TAT TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAG
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2440072 TGA TAAA TAA -AA TAA TAA TAA T-A TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
2440101 AAACAAATGG
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
2 4 0.07
3 51 0.85
4 5 0.08
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2440158 original size:23 final size:23
Alignment explanation
Indices: 2440132--2440183 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
2440122 AATATCTTCA
* *
2440132 CCATTTAATTTGCTACAACATTT
1 CCATTTAATTTGCCACAACATAT
** *
2440155 CCATCCAATTTGCCACGACATAT
1 CCATTTAATTTGCCACAACATAT
2440178 CCATTT
1 CCATTT
2440184 GCTACCATAC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.37
Consensus pattern (23 bp):
CCATTTAATTTGCCACAACATAT
Found at i:2442601 original size:23 final size:22
Alignment explanation
Indices: 2442575--2442623 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
2442565 CTGACTTTAA
*
2442575 CTTTCTTCTCTTATTCTTTCTTT
1 CTTTCTTCTCTTATTCCTTC-TT
*
2442598 CTTTTTTCTCTTATTCCTTCTT
1 CTTTCTTCTCTTATTCCTTCTT
2442620 CTTT
1 CTTT
2442624 TCTATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (22 bp):
CTTTCTTCTCTTATTCCTTCTT
Found at i:2442626 original size:20 final size:22
Alignment explanation
Indices: 2442575--2442632 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
2442565 CTGACTTTAA
*
2442575 CTTTCTTCTCTTATTCTTTCTTT
1 CTTT-TTCTCTTATTCCTTCTTT
2442598 CTTTTTTCTCTTATTCCTTC-TT
1 C-TTTTTCTCTTATTCCTTCTTT
*
2442620 C-TTTTCTATTATT
1 CTTTTTCTCTTATT
2442633 TATTTTCTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 11 0.34
22 3 0.09
23 15 0.47
24 3 0.09
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (22 bp):
CTTTTTCTCTTATTCCTTCTTT
Found at i:2442648 original size:24 final size:25
Alignment explanation
Indices: 2442614--2442660 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2442604 TCTCTTATTC
2442614 CTTCTTCTTTTCTATTATTTATTTT
1 CTTCTTCTTTTCTATTATTTATTTT
* *
2442639 CTTCTT-TTTTCTTTTCTTTATT
1 CTTCTTCTTTTCTATTATTTATT
2442661 CTTTTTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (25 bp):
CTTCTTCTTTTCTATTATTTATTTT
Found at i:2442657 original size:12 final size:12
Alignment explanation
Indices: 2442580--2442665 Score: 56
Period size: 12 Copynumber: 7.2 Consensus size: 12
2442570 TTTAACTTTC
2442580 TTCTCTTATTC-T
1 TTCT-TTATTCTT
*
2442592 TTCTTTCTT-TT
1 TTCTTTATTCTT
2442603 TTCTCTTATTCCTT
1 TTCT-TTATT-CTT
*
2442617 CTTC-TT-TTCTA
1 -TTCTTTATTCTT
*
2442628 TTATTTATT-TT
1 TTCTTTATTCTT
*
2442639 CTTCTTTTTTCTT
1 -TTCTTTATTCTT
2442652 TTCTTTATTCTT
1 TTCTTTATTCTT
2442664 TT
1 TT
2442666 TCATTTCTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 18
0.69 0.10 0.22
Matches are distributed among these distances:
10 2 0.04
11 14 0.25
12 32 0.56
13 4 0.07
14 2 0.04
15 3 0.05
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (12 bp):
TTCTTTATTCTT
Found at i:2442937 original size:38 final size:41
Alignment explanation
Indices: 2442844--2442991 Score: 155
Period size: 39 Copynumber: 3.8 Consensus size: 41
2442834 TGGCAGGTAT
* ** *
2442844 GGGA-GAGACACATAGAGTGCAATGTGTCTTCG-GGAGAAA
1 GGGAGGAGACACATGGAGTGCAATGCATCTTCGAGGGGAAA
*
2442883 -CGAGGAGACACATGGAGTGCAATGCATCTTC-AGGGG-AA
1 GGGAGGAGACACATGGAGTGCAATGCATCTTCGAGGGGAAA
* * * *
2442921 GGG-GGAGACTCATGGAGTGCAATGCGTATTCGGGGGGAAA
1 GGGAGGAGACACATGGAGTGCAATGCATCTTCGAGGGGAAA
* *
2442961 GGGAAGAGACACATGTAGTGCAATGCATCTT
1 GGGAGGAGACACATGGAGTGCAATGCATCTT
2442992 TCGTGTGTAC
Statistics
Matches: 88, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
38 29 0.33
39 32 0.36
40 5 0.06
41 22 0.25
ACGTcount: A:0.30, C:0.15, G:0.36, T:0.18
Consensus pattern (41 bp):
GGGAGGAGACACATGGAGTGCAATGCATCTTCGAGGGGAAA
Done.