Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003959.1 Hibiscus syriacus cultivar Beakdansim tig00008560_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: 74019
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:523 original size:43 final size:43
Alignment explanation
Indices: 435--556 Score: 127
Period size: 43 Copynumber: 2.8 Consensus size: 43
425 TGTACACTAA
** * ***
435 AAACGCCGCTAAATGTCAAAACCTATTGTAGCGTTTGTCTTAC
1 AAACGCCGCTAAATGTCAAAACCTATTGCGGCGTTTATAAGAC
* * *
478 AAATGTCGCTAACTGTCAAAACCTATTGCGGCGTTTATAAGAC
1 AAACGCCGCTAAATGTCAAAACCTATTGCGGCGTTTATAAGAC
* * * *
521 AAACGCCGCTAAATATCAGAACTTGTTGCGGCGTTT
1 AAACGCCGCTAAATGTCAAAACCTATTGCGGCGTTT
557 GTTGAACAAC
Statistics
Matches: 63, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAATGTCAAAACCTATTGCGGCGTTTATAAGAC
Found at i:1540 original size:2 final size:2
Alignment explanation
Indices: 1533--1565 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1523 TGAAATAATC
1533 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
1566 CAAATGATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2362 original size:19 final size:21
Alignment explanation
Indices: 2319--2362 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
2309 TCAAAAATAT
*
2319 TAAAAAATATTATTGTTTTATA
1 TAAAAAATA-TATTGTTTTAAA
2341 TAAAAAATA-ATT-TTTTAAA
1 TAAAAAATATATTGTTTTAAA
2360 TAA
1 TAA
2363 TTTTTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 3 0.14
22 9 0.43
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TAAAAAATATATTGTTTTAAA
Found at i:7431 original size:18 final size:18
Alignment explanation
Indices: 7400--7445 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
7390 TTCGCGGAAT
* *
7400 ATAAGATTATCAGTGGGA
1 ATAAGATTACCAGTGAGA
*
7418 ATAGGATTACCAGTGAGA
1 ATAAGATTACCAGTGAGA
7436 ATAAGATTAC
1 ATAAGATTAC
7446 TGAGAATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (18 bp):
ATAAGATTACCAGTGAGA
Found at i:7597 original size:11 final size:11
Alignment explanation
Indices: 7581--7606 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
7571 TAACAAGTTG
7581 AATTCTACTAT
1 AATTCTACTAT
7592 AATTCTACTAT
1 AATTCTACTAT
7603 AATT
1 AATT
7607 AATTTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTCTACTAT
Found at i:8502 original size:56 final size:57
Alignment explanation
Indices: 8433--8551 Score: 154
Period size: 57 Copynumber: 2.1 Consensus size: 57
8423 GGTGCATCGA
* * *
8433 TGCATCAAGTGCATTCGATG-TTTCA-AAATAGCCAT-GGTGCATTGATGCATGGCTGG
1 TGCATCAAATGCATTCGATGTTTTCATAAA-AGCC-TCAGTGCATCGATGCATGGCTGG
* *
8489 TGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGCTGG
1 TGCATCAAATGCATTCGATGTTTTCATAAAAGCCTCAGTGCATCGATGCATGGCTGG
8546 TGCATC
1 TGCATC
8552 GATTCATGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
56 20 0.36
57 32 0.58
58 3 0.05
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (57 bp):
TGCATCAAATGCATTCGATGTTTTCATAAAAGCCTCAGTGCATCGATGCATGGCTGG
Found at i:14245 original size:117 final size:117
Alignment explanation
Indices: 14026--14246 Score: 266
Period size: 117 Copynumber: 1.9 Consensus size: 117
14016 TTTCAAATTA
* * * *
14026 AAATTTTCTTTTTCAATATTTTCAAATTTCATTTTTGAAAGTTCTAAATCCTTCTTCAATAGTTC
1 AAATTTTCTTTTTCAATATTTTCAAATTTCAGTTTTGAAAGCTCTAAATCATTCTTCAACAGTTC
* *
14091 ATTTTGATTTTCAAAATCCATTTTCGTTTCTATAAGAAGTTTGTTTAATTTG
66 ATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
* * * * *
14143 AAATTTTCTTTTTCAA-AGTTTTCATATTTTAGTTTTGAAAGCTCTAACTCATTTTTCAACATTT
1 AAATTTTCTTTTTCAATA-TTTTCAAATTTCAGTTTTGAAAGCTCTAAATCATTCTTCAACAGTT
* * * **
14207 CATTTTGTTTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
65 CATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
14247 ATCATTTTTA
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
116 1 0.01
117 81 0.94
118 4 0.05
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.50
Consensus pattern (117 bp):
AAATTTTCTTTTTCAATATTTTCAAATTTCAGTTTTGAAAGCTCTAAATCATTCTTCAACAGTTC
ATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
Found at i:15596 original size:18 final size:17
Alignment explanation
Indices: 15542--15590 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
15532 TTGGACTCTC
* *
15542 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
15560 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
15578 AGTGCATTCGATG
1 AGTGCA-TCGATG
15591 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:17645 original size:3 final size:3
Alignment explanation
Indices: 17637--17751 Score: 230
Period size: 3 Copynumber: 38.3 Consensus size: 3
17627 CATTTCCTTA
17637 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17685 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17733 TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
17752 TCCATATTTT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 112 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:17856 original size:22 final size:22
Alignment explanation
Indices: 17805--17849 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
17795 CAAATCTCAA
*
17805 CCAAACCCACCCGGTTTTGGCC
1 CCAAACCCACCCGATTTTGGCC
17827 CCAAACCCACCCGATTTTGGCC
1 CCAAACCCACCCGATTTTGGCC
17849 C
1 C
17850 AAGACCCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.47, G:0.16, T:0.18
Consensus pattern (22 bp):
CCAAACCCACCCGATTTTGGCC
Found at i:21703 original size:11 final size:11
Alignment explanation
Indices: 21689--21757 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 11
21679 AATTTAAGGC
*
21689 AAATAAGATAA
1 AAATAAAATAA
21700 AAATAAAATAA
1 AAATAAAATAA
*
21711 ATA-AAAATAA
1 AAATAAAATAA
* *
21721 TAATAAATATAC
1 AAATAAA-ATAA
* *
21733 TAAT-AAATATG
1 AAATAAAATA-A
21744 AAATAAAATAA
1 AAATAAAATAA
21755 AAA
1 AAA
21758 ACAACATGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
10 11 0.24
11 23 0.50
12 12 0.26
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.23
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:21710 original size:16 final size:15
Alignment explanation
Indices: 21689--21756 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 15
21679 AATTTAAGGC
21689 AAATAAGATAAAAATA
1 AAATAA-ATAAAAATA
21705 AAATAAATAAAAATA
1 AAATAAATAAAAATA
*
21720 ATAATAAATATACTAATA
1 A-AATAAATA-A-AAATA
21738 AATATGAAAT-AAAATA
1 AA-AT-AAATAAAAATA
21754 AAA
1 AAA
21757 AACAACATGA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
15 11 0.24
16 20 0.44
17 3 0.07
18 7 0.16
19 4 0.09
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (15 bp):
AAATAAATAAAAATA
Found at i:21740 original size:12 final size:12
Alignment explanation
Indices: 21696--21754 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
21686 GGCAAATAAG
*
21696 ATAA-AAATAAA
1 ATAATAAATATA
*
21707 ATAAATAAAAATA
1 AT-AATAAATATA
21720 ATAATAAATATA
1 ATAATAAATATA
* *
21732 CTAATAAATATG
1 ATAATAAATATA
21744 A-AATAAA-ATA
1 ATAATAAATATA
21754 A
1 A
21755 AAAACAACAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
10 3 0.08
11 8 0.21
12 21 0.54
13 7 0.18
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (12 bp):
ATAATAAATATA
Found at i:23084 original size:3 final size:3
Alignment explanation
Indices: 23076--23132 Score: 73
Period size: 3 Copynumber: 19.3 Consensus size: 3
23066 AAAAAGCATA
*
23076 AAT AAT AAT AAGA AAT AA- AAT AA- AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
23120 AAT AAT AGT AAT A
1 AAT AAT AAT AAT A
23133 CTATATATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 4 0.09
3 41 0.87
4 2 0.04
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:23321 original size:29 final size:29
Alignment explanation
Indices: 23220--23333 Score: 88
Period size: 34 Copynumber: 3.6 Consensus size: 29
23210 CATGTTTTTA
*
23220 AAAACGTTTTAAAAACTTTATAATATATATTT
1 AAAATGTTTTAAAAA--TTAT-ATATATATTT
*
23252 CAGAAACGGTTTTAAAAATTATATATATATATTTTT
1 -A-AAA-TGTTTTAAAAA-T-TATATATATA--TTT
23288 AAAATGTTTTTCAAAAATTATATA-ATATTT
1 AAAATG-TTTT-AAAAATTATATATATATTT
23318 -AAATGTTTTAAAAATT
1 AAAATGTTTTAAAAATT
23334 CAAAACAATA
Statistics
Matches: 72, Mismatches: 2, Indels: 20
0.77 0.02 0.21
Matches are distributed among these distances:
27 7 0.10
28 4 0.06
29 5 0.07
30 3 0.04
32 3 0.04
33 8 0.11
34 20 0.28
35 19 0.26
36 3 0.04
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (29 bp):
AAAATGTTTTAAAAATTATATATATATTT
Found at i:23383 original size:38 final size:38
Alignment explanation
Indices: 23147--23577 Score: 286
Period size: 38 Copynumber: 11.8 Consensus size: 38
23137 ATATATATAT
* * * *
23147 AAAT-ATTTTCAAAAA-TATGTAATATATAA-ATTTCCA
1 AAATGATTTT-AAAAACTATATATTATATAAGTTTTCAA
* * * *
23183 AAATGCTTTTAAAAACTATATATTATACATGTTTTTAA
1 AAATGATTTTAAAAACTATATATTATATAAGTTTTCAA
* * * *
23221 AAACG-TTTTAAAAACTTTATAATATAT-A--TTTCAG
1 AAATGATTTTAAAAACTATATATTATATAAGTTTTCAA
* * * *
23255 AAACGGTTTTAAAAATTATATA-TATAT-A-TTTT-TA
1 AAATGATTTTAAAAACTATATATTATATAAGTTTTCAA
* * * *
23289 AAATGTTTTTCAAAAATTATATAATATTTAAATGTTTT--A
1 AAATGATTTT-AAAAACTATATATTATAT-AA-GTTTTCAA
* *
23328 AAA--A--TTCAAAACAATATATTATATAAGTTTTCAA
1 AAATGATTTTAAAAACTATATATTATATAAGTTTTCAA
*
23362 AAATGATTTTAAAAACTATATATTATATATA-TTTTCTA
1 AAATGATTTTAAAAACTATATATTATATA-AGTTTTCAA
*
23400 AAATG-TTTTTAAAA--ATATATTATAT-AGTTTTCAA
1 AAATGATTTTAAAAACTATATATTATATAAGTTTTCAA
*
23434 AAAT-ATTTTTAAAACTATATATTATATACA-TTTTC-A
1 AAATGATTTTAAAAACTATATATTATATA-AGTTTTCAA
* *
23470 AAATG-TTTTCAAAAATTATGTA-TATTATAAGTTTTCAA
1 AAATGATTTT-AAAAACTATATATTA-TATAAGTTTTCAA
* * *
23508 AAATGTTTTTCAAAACTATATATTATATACGTTTTCAAA
1 AAATGATTTTAAAAACTATATATTATATAAGTTTTC-AA
* *
23547 AAATGCTTTTAAAAAAATATATATATATATA
1 AAATGATTTT-AAAAACTATATAT-TATATA
23578 TATATATATA
Statistics
Matches: 318, Mismatches: 43, Indels: 63
0.75 0.10 0.15
Matches are distributed among these distances:
32 5 0.02
33 3 0.01
34 59 0.19
35 42 0.13
36 37 0.12
37 64 0.20
38 65 0.20
39 22 0.07
40 15 0.05
41 6 0.02
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (38 bp):
AAATGATTTTAAAAACTATATATTATATAAGTTTTCAA
Found at i:23568 original size:2 final size:2
Alignment explanation
Indices: 23563--23598 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
23553 TTTTAAAAAA
23563 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23599 CATTTTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23605 original size:62 final size:58
Alignment explanation
Indices: 23524--23638 Score: 158
Period size: 62 Copynumber: 1.9 Consensus size: 58
23514 TTTTCAAAAC
*
23524 TATATATTATATACGTTTTCAAAAAATGCTTTTAAAAAAATATATATATATATATATATATA
1 TATATATTATATACATTTTC--AAAATG-TTTTAAAAAAATATATAT-TATATATATATATA
* * *
23586 TATATATTATATACATTTTCAAAATGTTTTCAAAGACTATATATTATATATAT
1 TATATATTATATACATTTTCAAAATGTTTTAAAAAAATATATATTATATATAT
23639 TTTTAAAATG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 9 0.18
59 15 0.31
60 6 0.12
62 19 0.39
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (58 bp):
TATATATTATATACATTTTCAAAATGTTTTAAAAAAATATATATTATATATATATATA
Found at i:23615 original size:99 final size:97
Alignment explanation
Indices: 23501--23690 Score: 253
Period size: 98 Copynumber: 1.9 Consensus size: 97
23491 ATATTATAAG
*
23501 TTTTCAAAAATGTTTTTCAAA-ACTATATATTATATACGTTTTCAAAAAATGCTTTT-AAAAAAA
1 TTTTCAAAAATG-TTTTCAAAGACTATATATTATATACATTTT--AAAAATG-TTTTCAAAAAAA
*
23564 TATATATATATATAT-ATATATATATATATTATATACA
62 CATATAT-TATATATCATATA-ATATATATTATATACA
* *
23601 TTTTC-AAAATGTTTTCAAAGACTATATATTATATATATTTTTAAAATGTTTTCGAAAAAAACAT
1 TTTTCAAAAATGTTTTCAAAGACTATATATTATATACATTTTAAAAATGTTTTC-AAAAAAACAT
23665 ATATTATATATCATATAATATATATT
65 ATATTATATATCATATAATATATATT
23691 TTTCAAAAAG
Statistics
Matches: 82, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
96 4 0.05
97 22 0.27
98 26 0.32
99 25 0.30
100 5 0.06
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (97 bp):
TTTTCAAAAATGTTTTCAAAGACTATATATTATATACATTTTAAAAATGTTTTCAAAAAAACATA
TATTATATATCATATAATATATATTATATACA
Found at i:23641 original size:37 final size:38
Alignment explanation
Indices: 23586--23675 Score: 121
Period size: 37 Copynumber: 2.4 Consensus size: 38
23576 TATATATATA
* *
23586 TATATATTATATACATTTTCAAAATGTTTTC-AAAGAC
1 TATATATTATATATATTTTCAAAATGTTTTCAAAAAAC
*
23623 TATATATTATATATATTTTTAAAATGTTTTCGAAAAAAAC
1 TATATATTATATATATTTTCAAAATGTTTTC--AAAAAAC
23663 -ATATATTATATAT
1 TATATATTATATAT
23676 CATATAATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
37 29 0.62
39 13 0.28
40 5 0.11
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (38 bp):
TATATATTATATATATTTTCAAAATGTTTTCAAAAAAC
Found at i:24434 original size:84 final size:83
Alignment explanation
Indices: 24318--25029 Score: 711
Period size: 84 Copynumber: 8.6 Consensus size: 83
24308 ACAATTTTAT
* * * * * * * *
24318 TGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATGTTGTGCCTTTGAGCTGAGTGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* *
24383 GACCTCAAAGGTCTTCTGG
66 GAACTCGAAGGTCTT-TGG
* * * *
24402 TGACAAATAACCCTCCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
24467 GAACTCGAAGGTCTTTGG
66 GAACTCGAAGGTCTTTGG
* * * * *
24485 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGAAAATGATATGCCTTGGAGCTGAGCGTAGT
1 -TGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGT
24550 CGAACTCGAAGGTCTTTGG
65 CGAACTCGAAGGTCTTTGG
* * * * * * * * *
24569 TGACAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAGTGATATGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTG-CCTTGGAGCTGAGCGTAGT
**
24634 CGAACTCGGGGGTCTTTGG
65 CGAACTCGAAGGTCTTTGG
* * * * * *
24653 T---AGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT-GAGCTGAGTGTAGT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGCC-TTGGAGCTGAGCGTAGT
* *
24714 CGAACTCAAAGGTCTTTTGT
65 CGAACTCGAAGGTC-TTTGG
** * * *
24734 TGGTAGACAACCCTTCTAGACTTAAGTTGTGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
*
24799 GAACTTGAAGGTCTTTGG
66 GAACTCGAAGGTCTTTGG
* * * * * * ** *
24817 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTATAA
1 -TGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTG-CCTTGGAGCTGAGCGTAG
* **
24882 TCGAACCCGGGGGTCTTT-G
64 TCGAACTCGAAGGTCTTTGG
* * * *
24901 -G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGCC-TTGGAGCTGAGCGTAGT
*
24963 CGAACTCAAAGGTCTTTTGG
65 CGAACTCGAAGGTC-TTTGG
* * *
24983 TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGCC
25030 CTCGAAGTTG
Statistics
Matches: 516, Mismatches: 97, Indels: 30
0.80 0.15 0.05
Matches are distributed among these distances:
80 47 0.09
81 80 0.16
82 2 0.00
83 46 0.09
84 314 0.61
85 27 0.05
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (83 bp):
TGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
GAACTCGAAGGTCTTTGG
Found at i:24955 original size:249 final size:248
Alignment explanation
Indices: 24429--25029 Score: 925
Period size: 249 Copynumber: 2.4 Consensus size: 248
24419 AGCCTTGAGT
* * *
24429 TATGCTGTAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGA
1 TATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGA
*
24493 CAACCCTTCTAGACTTAAGTTGTGCTGAAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCG
65 CAACCCTTCTAGACTTAAGTTGTGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCG
* * * * *
24558 AAGGTCTTTGGTGACAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAGTGATATGCCCTCGAAG
130 AAGGTCTTTGGTGACAAATAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGCCCTCGAAG
* * *
24623 CTGAGTGTAATCGAACTCGGGGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGC
195 CTGAGTATAATCGAACCCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGC
* * *
24677 TATACTGCAAATGATGTGCCGTTGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTTGTTGGTAGAC
1 TATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGAC
*
24742 AACCCTTCTAGACTTAAGTTGTGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTTGA
66 AACCCTTCTAGACTTAAGTTGTGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGA
* * * *
24807 AGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAG
131 AGGTCTTTGG-TGACAAATAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGCCCTCGAAG
24872 CTGAGTATAATCGAACCCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGC
195 CTGAGTATAATCGAACCCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGC
* ** *
24926 TATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGAT
1 TATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGAC
* * * *
24991 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCC
66 AACCCTTCTAGACTTAAGTTGTGCTGTAAATGATATGCC
25030 CTCGAAGTTG
Statistics
Matches: 320, Mismatches: 31, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
248 129 0.40
249 191 0.60
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (248 bp):
TATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGAC
AACCCTTCTAGACTTAAGTTGTGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGA
AGGTCTTTGGTGACAAATAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGCCCTCGAAGC
TGAGTATAATCGAACCCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGC
Found at i:24962 original size:165 final size:164
Alignment explanation
Indices: 24369--25102 Score: 679
Period size: 165 Copynumber: 4.4 Consensus size: 164
24359 TGTGCCTTTG
* * * * * * * *
24369 AGCTGAGTGTAGTCGACCTCAAAGGTCTTCTGGTGACAAATAACCCTCCTAGCCTTGAGTTATGC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTT-T-G-G-CAGATAACCCTTCTAGACTTAAGCTATGC
* *
24434 TGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGACAACCC
62 TGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGGCAGATAACCC
* * * * * *
24499 TTCTAGACTTAAGTTGTGCTGAAAATGATATG-CCTTGG
126 TTCTAGACTTAAGTTATACTGCAAATGATGTGCCCTCGA
* * * * * *
24537 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAAATAACCCTTCTAGCCTTGAGTTATGCT
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTT-G-G-CAGATAACCCTTCTAGACTTAAGCTATGCT
* * * * * ** *
24602 GTAAGTGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGT---AGATAGCCCT
63 GTAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCT
* * * *
24664 TCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTG-
127 TCTAGACTTAAGTTATACTGCAAATGATGTGCCCTCGA
* * * * * *
24701 AGCTGAGTGTAGTCGAACTCAAAGGTCTTTTGTTGGTAGACAACCCTTCTAGACTTAAGTTGTGC
1 AGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTAGACTTAAGCTATGC
*
24766 TGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTGGTTGGCAGATAACCC
62 TGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGGCAGATAACCC
*
24831 TTCTCGACTTAAGTTATACTGCAAATGATGTGCCCTCGA
126 TTCTAGACTTAAGTTATACTGCAAATGATGTGCCCTCGA
* * ** * * *
24870 AGCTGAGTATAATCGAACCCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGTA
* * **
24935 AATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTC
66 AATGATATGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTC
* * * *
24999 TAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
129 TAGACTTAAGTTATACTGCAAATGATGTGCCCTCGA
* ** * * * * * * *
25035 AGTTGAGTGTAATCGAACTCGGGGGTCTTCGGCAGATAGCCCCTATCGACTTTAGCTATGCTGCA
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGTA
25100 AAT
66 AAT
25103 AGTTTGTTTA
Statistics
Matches: 482, Mismatches: 71, Indels: 29
0.83 0.12 0.05
Matches are distributed among these distances:
164 89 0.18
165 212 0.44
166 9 0.02
167 48 0.10
168 103 0.21
169 21 0.04
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (164 bp):
AGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGTA
AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTA
GACTTAAGTTATACTGCAAATGATGTGCCCTCGA
Found at i:25246 original size:66 final size:66
Alignment explanation
Indices: 25140--25271 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
25130 AACGGGTCGA
25140 AGCCGGTCATGATTCTTCAGGTGGTTCCTCTGAGCGAGAACCAAGTAAGACAATCTTTGGATGAC
1 AGCCGGTCATGATTCTTCAGGTGGTTCCTCTGAGCGAGAACCAAGTAAGACAATCTTTGGATGAC
25205 T
66 T
25206 AGCCGGTCATGATTCTTCAGGTGGTTCCTCTGAGCGAGAACCAAGTAAGACAATCTTTGGATGAC
1 AGCCGGTCATGATTCTTCAGGTGGTTCCTCTGAGCGAGAACCAAGTAAGACAATCTTTGGATGAC
25271 T
66 T
25272 CCCATTTTAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (66 bp):
AGCCGGTCATGATTCTTCAGGTGGTTCCTCTGAGCGAGAACCAAGTAAGACAATCTTTGGATGAC
T
Found at i:28567 original size:18 final size:19
Alignment explanation
Indices: 28526--28570 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
28516 AGTTAATGTG
28526 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
28545 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
28563 AATGCAAA
1 AATGCAAA
28571 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:30482 original size:16 final size:15
Alignment explanation
Indices: 30461--30501 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
30451 AATTTAAGGC
30461 AAATAAGATAAAAATG
1 AAATAA-ATAAAAATG
*
30477 AAATAAATAAAAATA
1 AAATAAATAAAAATG
30492 ATAATAAATA
1 A-AATAAATA
30502 TACTAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (15 bp):
AAATAAATAAAAATG
Found at i:32022 original size:72 final size:72
Alignment explanation
Indices: 31946--32340 Score: 290
Period size: 75 Copynumber: 5.3 Consensus size: 72
31936 CCAAAATGCT
* * *
31946 TTTAAAAACTATATATTATACATGTTTTTAAAAACG-TTTTAAAAACTT-TATAATATATATTTT
1 TTTAAAAACTATATATTATATATGTTTTCAAAAATGATTTTAAAAACTTATATAATATATATTTT
32009 CAGAAAAGG
66 CA-AAAA-G
* * * * *
32018 TTTAAAAATTATATATTATATATATTTT-TAAAATGTTTTTCAAAAA-TTATATAATATTTAAAT
1 TTTAAAAACTATATATTATATATGTTTTCAAAAATGATTTT-AAAAACTTATATAATA--TATAT
*
32081 GTTTTAAAAA-
63 -TTTCAAAAAG
* * * *
32091 -TTCAAAACAATATATTATATAAGTTTTCAAAAATGATTTTAAAAACTATATATTATATATATTT
1 TTTAAAAACTATATATTATATATGTTTTCAAAAATGATTTTAAAAACT-TATATAATATATATTT
*
32155 TCTAAAATG
65 TC-AAAAAG
* * * *
32164 TTTTTAAAAACTATATATTATATA-GTTTTCAAAAAAT-ATTTTTAAAACTATATATTATTTACA
1 --TTTAAAAACTATATATTATATATGTTTTC-AAAAATGATTTTAAAAACT-TATATAATATATA
*
32227 TTTTCAAAATG
62 TTTTCAAAAAG
* * * *
32238 TTTTCAAAAATTATGTATATTATA-A-GTTTTCAAAAATGTTTTTCAAAAC-TATATATTATATA
1 -TTT-AAAAACTA--TATATTATATATGTTTTCAAAAATGATTTTAAAAACTTATATAATATATA
32300 CGTTTTCAAAAAATG
62 --TTTTC-AAAAA-G
*
32315 CTTTTAAAAAATATATATATATATAT
1 --TTTAAAAACTATATAT-TATATAT
32341 ATATATTATA
Statistics
Matches: 264, Mismatches: 32, Indels: 48
0.77 0.09 0.14
Matches are distributed among these distances:
71 8 0.03
72 66 0.25
73 36 0.14
74 27 0.10
75 68 0.26
76 46 0.17
77 9 0.03
78 4 0.02
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (72 bp):
TTTAAAAACTATATATTATATATGTTTTCAAAAATGATTTTAAAAACTTATATAATATATATTTT
CAAAAAG
Found at i:32065 original size:38 final size:36
Alignment explanation
Indices: 31890--32342 Score: 284
Period size: 38 Copynumber: 12.2 Consensus size: 36
31880 ATAGTAATAC
* * * * *
31890 TATATATATATATAAATAT-TTTCAAAAA-TATGTAA
1 TATATATAT-TTTAAAAATGTTTTAAAAACTATATAT
* **
31925 TATATAAATTTCCAAAATGCTTTTAAAAACTATATAT
1 TATATATATTTTAAAAATG-TTTTAAAAACTATATAT
* * *
31962 TATACATGTTTTTAAAAACGTTTTAAAAACT-T-TAT
1 TATATAT-ATTTTAAAAATGTTTTAAAAACTATATAT
* * *
31997 AATATATATTTTCAGAAAA-GGTTTAAAAATTATATAT
1 TATATATATTTT-A-AAAATGTTTTAAAAACTATATAT
* *
32034 TATATATATTTTTAAAATGTTTTTCAAAAATTATATAAT
1 TATATATATTTTAAAAATG-TTTT-AAAAACTATAT-AT
* * * * *
32073 ATTTAAATGTTTTAAAAA----TTCAAAACAATATAT
1 -TATATATATTTTAAAAATGTTTTAAAAACTATATAT
32106 TATATA-AGTTTTCAAAAATGATTTTAAAAACTATATAT
1 TATATATA-TTTT-AAAAATG-TTTTAAAAACTATATAT
*
32144 TATATATATTTTCTAAAATGTTTTTAAAAACTATATAT
1 TATATATATTTT-AAAAATG-TTTTAAAAACTATATAT
* * *
32182 TATATAGT-TTTCAAAAAATATTTTTAAAACTATATAT
1 TATATA-TATTT-TAAAAATGTTTTAAAAACTATATAT
* * * *
32219 TATTTACATTTTCAAAATGTTTTCAAAAATTATGTATAT
1 TATATATATTTTAAAAATGTTTT-AAAAACTA--TATAT
* *
32258 TATA-AGT-TTTCAAAAATGTTTTTCAAAACTATATAT
1 TATATA-TATTTTAAAAATG-TTTTAAAAACTATATAT
** *
32294 TATATACGTTTTCAAAAAATGCTTTTAAAAAATATATAT
1 TATATATATTTT--AAAAATG-TTTTAAAAACTATATAT
32333 ATATATATAT
1 -TATATATAT
32343 ATATTATATA
Statistics
Matches: 324, Mismatches: 60, Indels: 63
0.72 0.13 0.14
Matches are distributed among these distances:
32 8 0.02
33 7 0.02
34 17 0.05
35 33 0.10
36 33 0.10
37 72 0.22
38 96 0.30
39 38 0.12
40 20 0.06
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
TATATATATTTTAAAAATGTTTTAAAAACTATATAT
Found at i:32080 original size:29 final size:29
Alignment explanation
Indices: 32032--32092 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
32022 AAAATTATAT
*
32032 ATTATATATATTTTTAAAATGTTTTTCAAAA
1 ATTATATATATATTTAAAATG-TTTT-AAAA
32063 ATTATATA-ATATTT-AAATGTTTTAAAA
1 ATTATATATATATTTAAAATGTTTTAAAA
32090 ATT
1 ATT
32093 CAAAACAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 7 0.24
28 4 0.14
29 5 0.17
30 5 0.17
31 8 0.28
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (29 bp):
ATTATATATATATTTAAAATGTTTTAAAA
Found at i:32364 original size:51 final size:51
Alignment explanation
Indices: 32287--32390 Score: 140
Period size: 53 Copynumber: 2.0 Consensus size: 51
32277 TTTTCAAAAC
*
32287 TATATATTATATACGTTTTCAAAAAATGCTTTT-AAAAAATATATATATATATA
1 TATATATTATATACATTTTC-AAAAATG-TTTTCAAAAAATATATAT-TATATA
* *
32340 TATATATTATATACATTTTC-AAAATGTTTTCAAAGACTATATATTATATA
1 TATATATTATATACATTTTCAAAAATGTTTTCAAAAAATATATATTATATA
32390 T
1 T
32391 TTTTAAAATG
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
50 11 0.23
51 17 0.36
53 19 0.40
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (51 bp):
TATATATTATATACATTTTCAAAAATGTTTTCAAAAAATATATATTATATA
Found at i:32368 original size:90 final size:86
Alignment explanation
Indices: 32258--32450 Score: 230
Period size: 87 Copynumber: 2.2 Consensus size: 86
32248 TTATGTATAT
32258 TATAAGTTTTCAAAAATGTTTTTCAAA-ACTATATATTATATACGTTTTCAAAAAATGCTTTT-A
1 TATAA-TTTTC-AAAATG-TTTTCAAAGACTATATATTATATA--TTTT--AAAAATG-TTTTCA
* * *
32321 AAAAATATATATATATATAT-ATATATTA
58 AAAAAAACATATATATATATCATATAATA
*
32349 TATACATTTTCAAAATGTTTTCAAAGACTATATATTATATATTTTTAAAATGTTTTCGAAAAAAA
1 TATA-ATTTTCAAAATGTTTTCAAAGACTATATATTATATATTTTAAAAATGTTTTC-AAAAAAA
32414 ACATATATATATATCATATAATA
64 ACATATATATATATCATATAATA
*
32437 TATATTTTTCAAAA
1 TATAATTTTCAAAA
32451 AGCTATTCTC
Statistics
Matches: 92, Mismatches: 5, Indels: 14
0.83 0.05 0.13
Matches are distributed among these distances:
85 4 0.04
86 6 0.07
87 28 0.30
88 15 0.16
89 8 0.09
90 21 0.23
91 9 0.10
92 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (86 bp):
TATAATTTTCAAAATGTTTTCAAAGACTATATATTATATATTTTAAAAATGTTTTCAAAAAAAAC
ATATATATATATCATATAATA
Found at i:32425 original size:37 final size:36
Alignment explanation
Indices: 32347--32427 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 36
32337 ATATATATAT
* * ** *
32347 TATATACATTTTCAAAATGTTTTCAAAGACTATATA
1 TATATATATTTTCAAAATGTTTTCAAAAAAAACATA
*
32383 T-TATATATTTTTAAAATGTTTTCGAAAAAAAACATA
1 TATATATATTTTCAAAATGTTTTC-AAAAAAAACATA
32419 TATATATAT
1 TATATATAT
32428 CATATAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
35 20 0.54
36 10 0.27
37 7 0.19
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.43
Consensus pattern (36 bp):
TATATATATTTTCAAAATGTTTTCAAAAAAAACATA
Found at i:33425 original size:2 final size:2
Alignment explanation
Indices: 33420--33448 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33410 ATTATACAGA
33420 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33449 AGTAATACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41479 original size:31 final size:31
Alignment explanation
Indices: 41424--41551 Score: 86
Period size: 31 Copynumber: 4.2 Consensus size: 31
41414 TTAAGGGATT
* *
41424 AAATAGCAAAAATAGAAATATAAAGTACCAA
1 AAATAGCAAAAACAGAAATATAAAGGACCAA
* *
41455 AAATAGCACAAACAGAAACT-TAAAGGACTAA
1 AAATAGCAAAAACAGAAA-TATAAAGGACCAA
** * *
41486 AAA-AATAAAAACAGAGAAT-TATAGGA-CTA
1 AAATAGCAAAAACAGA-AATATAAAGGACCAA
* * *
41515 AAATAGTAAAAATAGAAAGT-TAAAAGACCAA
1 AAATAGCAAAAACAGAAA-TATAAAGGACCAA
41546 ACAATA
1 A-AATA
41552 ATTAAATTGA
Statistics
Matches: 76, Mismatches: 15, Indels: 11
0.75 0.15 0.11
Matches are distributed among these distances:
29 6 0.08
30 32 0.42
31 33 0.43
32 5 0.07
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.16
Consensus pattern (31 bp):
AAATAGCAAAAACAGAAATATAAAGGACCAA
Found at i:41500 original size:30 final size:29
Alignment explanation
Indices: 41464--41538 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
41454 AAAATAGCAC
41464 AAACAGAAACTTAAAGGACTAAAAAAATAA
1 AAACAGAAA-TTAAAGGACTAAAAAAATAA
* * *
41494 AAACAGAGAATTATAGGACTAAAATAGTAA
1 AAACAGA-AATTAAAGGACTAAAAAAATAA
*
41524 AAATAGAAAGTTAAA
1 AAACAGAAA-TTAAA
41539 AGACCAAACA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
29 2 0.05
30 34 0.89
31 2 0.05
ACGTcount: A:0.63, C:0.07, G:0.13, T:0.17
Consensus pattern (29 bp):
AAACAGAAATTAAAGGACTAAAAAAATAA
Found at i:45695 original size:14 final size:14
Alignment explanation
Indices: 45664--45702 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
45654 TTTTTACTTA
*
45664 TTTAATTTCAGT-C
1 TTTAATTTCATTAC
45677 TTTAATTTCATTAC
1 TTTAATTTCATTAC
45691 TTTAATTT-ATTA
1 TTTAATTTCATTA
45703 TTTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.59
Consensus pattern (14 bp):
TTTAATTTCATTAC
Found at i:57189 original size:22 final size:21
Alignment explanation
Indices: 57148--57190 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
57138 TGAAAAAACG
*
57148 TTAAGAAAAAATAAATAAATA
1 TTAACAAAAAATAAATAAATA
57169 TTAACAAAGAAATCAAA-AAATA
1 TTAACAAA-AAAT-AAATAAATA
57191 AGTAAAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 9 0.47
23 3 0.16
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.21
Consensus pattern (21 bp):
TTAACAAAAAATAAATAAATA
Found at i:58166 original size:16 final size:15
Alignment explanation
Indices: 58141--58170 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
58131 TGGTGAGGTC
58141 GGTCGTCCCGGGATG
1 GGTCGTCCCGGGATG
58156 GGTCAGTCCCGGGAT
1 GGTC-GTCCCGGGAT
58171 TATCGGCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.10, C:0.27, G:0.43, T:0.20
Consensus pattern (15 bp):
GGTCGTCCCGGGATG
Found at i:58373 original size:26 final size:26
Alignment explanation
Indices: 58343--58394 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
58333 AAAATGAGAG
*
58343 AAAAAAACGAAATTA-AATAAATAAATT
1 AAAAAAA-GAAATAATAAT-AATAAATT
58370 AAAAAAAGAAATAATAATAATAAAT
1 AAAAAAAGAAATAATAATAATAAAT
58395 ACCAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (26 bp):
AAAAAAAGAAATAATAATAATAAATT
Found at i:58640 original size:37 final size:35
Alignment explanation
Indices: 58439--58670 Score: 138
Period size: 36 Copynumber: 6.3 Consensus size: 35
58429 CAAAAACACT
*
58439 TTATAT-TATTTTTCTAAAAAT-TTTCCAAAAACTATA
1 TTATATATATTTTTC--AAAATGTTT-TAAAAACTATA
* * *
58475 -TATTATATAGTTTCCAAAAATGATTTAAAAA--ATA
1 TTA-TATATATTTTTC-AAAATGTTTTAAAAACTATA
* * *
58509 TTATAT-GAGTTTTCAAAAATGTTTTTACAAAATATATA
1 TTATATATATTTTTC-AAAATG-TTTTA-AAAA-CTATA
*
58547 TTATATA-ATTTTTCAAAAATTCTTTTTATTTAAAACCATATA
1 TTATATATATTTTTC-AAAA-T-GTTTTA---AAAA-C-TATA
*
58589 TTATATA-ATTTTTCAAAAATGTTTTAAGAACTATA
1 TTATATATATTTTTC-AAAATGTTTTAAAAACTATA
*
58624 TTATATATTTATTTTCAAAATGTTTTAAAAACTATA
1 TTATATATAT-TTTTCAAAATGTTTTAAAAACTATA
58660 TATATATATAT
1 T-TATATATAT
58671 ATATATATAT
Statistics
Matches: 161, Mismatches: 17, Indels: 35
0.76 0.08 0.16
Matches are distributed among these distances:
33 13 0.08
34 10 0.06
35 19 0.12
36 36 0.22
37 24 0.15
38 20 0.12
39 6 0.04
40 5 0.03
41 5 0.03
42 23 0.14
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (35 bp):
TTATATATATTTTTCAAAATGTTTTAAAAACTATA
Found at i:58663 original size:2 final size:2
Alignment explanation
Indices: 58656--58688 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
58646 TTTTAAAAAC
58656 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
58689 TTCCAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58803 original size:2 final size:2
Alignment explanation
Indices: 58793--58839 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
58783 AAAATTACAC
58793 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58836 TA TA
1 TA TA
58840 ATAATAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:59504 original size:81 final size:81
Alignment explanation
Indices: 59355--60735 Score: 825
Period size: 81 Copynumber: 16.9 Consensus size: 81
59345 GGTGTCATCG
* * * * * * * *
59355 AGCTGAATGGAATCGAACTCGACA-AT-TTTATTGACAGATAGCCCTTCTTGCCTTGAGCTATGC
1 AGCTGAGTGTAATCGAACTCGA-AGGTCTTT-TTGGCAGATAACCCTTCTAGCCTTGAGTTATAC
* * *
59418 TGTAAATGATATACCTTGG
64 TGCAAATGATATGCCTT-A
* * * * ** *
59437 AGCTGAGCGTAGTCGAACTCGAAGGT-TTTTTTGCAGAGAACCCTTCTAGCCTTGAGCCATACCG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTTGGCAGATAACCCTTCTAGCCTTGAGTTATACTG
* * *
59501 TAAATGATATGTCGTTG
66 CAAATGATATG-CCTTA
* * * * *
59518 AGTTGAGTGTAATC-AGACTCAAAGGTCTTTGTTGGCAGATAACTCTTATAGCCTTGAGTTATAA
1 AGCTGAGTGTAATCGA-ACTCGAAGGTCTTT-TTGGCAGATAACCCTTCTAGCCTTGAGTTATAC
* *
59582 TGCAAATGATGTGCCCTCAA
64 TGCAAATGATATG-CCT-TA
* * * * * *
59602 AGCTGAGTGTAATCAAACTTGAGGGTC--TTTGGCAGATAGCCCTTCTAGCCTTGAGCTATACCG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTTGGCAGATAACCCTTCTAGCCTTGAGTTATACTG
*
59665 CAAATGATATGCCGTTG
66 CAAATGATATGCC-TTA
* * * *
59682 AGTTGAGTGTAATCGAACTCAAAGGTCTTTATTAGCAGATAACCCTTCTAGCCTTGAGTTATGCT
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTT-TTGGCAGATAACCCTTCTAGCCTTGAGTTATACT
* *
59747 GCAAATGATGTGCCCTCAA
65 GCAAATGATATG-CCT-TA
* * **
59766 AGCTGAGTGTAATTGAACTCGAAGGTC--TTTGGCAGATAGCCCTTCTAGCCTTGAGTTATACCA
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTTGGCAGATAACCCTTCTAGCCTTGAGTTATACTG
* *
59829 CAAATGATGTGCCATTG
66 CAAATGATATGCC-TTA
*
59846 AGCTGAGTGTAATCGAACTC-AAGGTCTTTGTT-GCAGATAACCCTTCTAGCCTTGAGTTATGCT
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTT-TTGGCAGATAACCCTTCTAGCCTTGAGTTATACT
* *
59909 GCAAATGATGTGCCCTCAA
65 GCAAATGATATG-CCT-TA
* * * * * *
59928 AGTTGAGTGTAATCGAACTCG-AGTGTC--TTTGGCAGATAGCCCTTCTCGACTTAAGCTATACT
1 AGCTGAGTGTAATCGAACTCGAAG-GTCTTTTTGGCAGATAACCCTTCTAGCCTTGAGTTATACT
* *
59990 GCAAATAATGTGCCTTTA
65 GCAAATGATATGCC-TTA
* * * * * * * * *
60008 AGCTGAGCGTAGTTGAACTCGCAGGTC--TTTGGCAGATAGCCCTTTTCGACTTAAGTTATACTG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTTGGCAGATAACCCTTCTAGCCTTGAGTTATACTG
* *
60071 TAAATG--AT-CTTTA
66 CAAATGATATGCCTTA
** * * *
60084 AGCTGAGCATAGTCGAACTCGAAGGTCTTTTAGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTT--TGGCAGATAACCCTTCTAGCCTTGAGTTATAC
* *
60149 TGTAAATGATATGCCTCTG
64 TGCAAATGATATGCCT-TA
* * * * *
60168 AGCTGAGCGTAGTCGAACTCAAAGGTC-TTTTGGTCACAGATAACCCTTCTAGCCTTGGGTTATG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTTGG---CAGATAACCCTTCTAGCCTTGAGTTATA
* * * **
60232 CTGTAAATGATGTTCCCACGA
63 CTGCAAATGAT-ATGCC-TTA
* * * * * * * * **
60253 AGCTGAGTGTTATCGAACTTGAGGGTC--TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTTGGCAGATAACCCTTCTAGCCTTGAGTTATACTG
* * *
60316 CAAATGATGTACCTTGG
66 CAAATGATATGCCTT-A
* * * * * * * *
60333 AGTTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAAATAACCCTTCTCGACTTAAGTTATGC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTT--TTGGCAGATAACCCTTCTAGCCTTGAGTTATAC
** *
60398 TTTAAATGATATGCCCTCGA
64 TGCAAATGATATG-CCT-TA
* * * * ** * * * * * * *
60418 ATCTGAGTGTAATTGAACTTG-AGG-GTTTTTGATATATAGCCCTTCTCGACTTAAGCTATGCTG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTTGGCAGATAACCCTTCTAGCCTTGAGTTATACTG
*
60481 CAAATGA-AGTGCCTTGG
66 CAAATGATA-TGCCTT-A
* * * * * * *
60498 AGCTGAGCGTAGTCAAACTCGAAGGTATTTTGGTGACAAATAACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTT--TGGCAGATAACCCTTCTAGCCTTGAGTTATAC
** * *
60563 TATAAATGATGTGCCCTCGA
64 TGCAAATGATATG-CCT-TA
* * * * * * * * * * *
60583 AGCTGAGTGTAATCGAATTTGAGGGTC--TTTGGCATATAGCCCTTCTCGACATAAGCTATGCTG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTTGGCAGATAACCCTTCTAGCCTTGAGTTATACTG
* *
60646 CAAATGATGTGCCTTGG
66 CAAATGATATGCCTT-A
* * * * * * *
60663 AGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTT--TTGGCAGATAACCCTTCTAGCCTTGAGTTATAC
60728 TGCAAATG
64 TGCAAATG
60736 TTGTCTTAAA
Statistics
Matches: 1026, Mismatches: 215, Indels: 114
0.76 0.16 0.08
Matches are distributed among these distances:
76 27 0.03
77 1 0.00
78 3 0.00
79 6 0.01
80 209 0.20
81 330 0.32
82 64 0.06
83 92 0.09
84 228 0.22
85 66 0.06
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (81 bp):
AGCTGAGTGTAATCGAACTCGAAGGTCTTTTTGGCAGATAACCCTTCTAGCCTTGAGTTATACTG
CAAATGATATGCCTTA
Found at i:59675 original size:164 final size:164
Alignment explanation
Indices: 59389--60735 Score: 1225
Period size: 165 Copynumber: 8.2 Consensus size: 164
59379 ATTTTATTGA
* * * * * *** * *
59389 CAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATGATAT-ACCTTGGAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
* * * * * * * * * * *
59453 ACTCGAAGGTTTTTTTGCAGAGAACCCTTCTAGCCTTGAGCCATACCGTAAATGATATGTCGTTG
66 ACTTG-AGGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGCTATACTGCAAATGATATGCCCTTG
* * *
59518 AGTTGAGTGTAATC-AGACTCAAAGGTCTTTGTTGG
130 AGCTGAGCGTAGTCGA-ACTCAAAGGTCTTTGTTGG
* * ** * *
59553 CAGATAACTCTTATAGCCTTGAGTTATAATGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
* *
59618 ACTTGAGGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGCTATACCGCAAATGATATGCCGTTGA
66 ACTTGAGGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGCTATACTGCAAATGATATGCCCTTGA
* * * * *
59683 GTTGAGTGTAATCGAACTCAAAGGTCTTTATTAG
131 GCTGAGCGTAGTCGAACTCAAAGGTCTTTGTTGG
* *
59717 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATTGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
* * * ** * *
59782 ACTCGAAGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGTTATACCACAAATGATGTGCCATTGA
66 ACTTGAGGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGCTATACTGCAAATGATATGCCCTTGA
* *
59847 GCTGAGTGTAATCGAACTC-AAGGTCTTTGTT-G
131 GCTGAGCGTAGTCGAACTCAAAGGTCTTTGTTGG
* *
59879 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGTTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
* * * * * * * * *
59944 ACTCGAGTGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATAATGTGCCTTTAA
66 ACTTGAGGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGCTATACTGCAAATGATATGCCCTTGA
* **
60009 GCTGAGCGTAGTTGAACTCGCAGGTC--T-TTGG
131 GCTGAGCGTAGTCGAACTCAAAGGTCTTTGTTGG
* * * * * * ** ** *
60040 CAGATAGCCCTTTTCGACTTAAGTTATACTGTAAATGA--T---CTTTAAGCTGAGCATAGTCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
* * * * * *
60100 ACTCGAAGGTCTTTTAGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATG-CC
66 ACTTGAGGGTC-TTT-G-G-CAGATAGCCCTTCTAGCCTTGAGCTATACTGCAAATGATATGCCC
* **
60164 TCTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCA
127 T-TGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGTTGG
* * * * *
60204 CAGATAACCCTTCTAGCCTTGGGTTATGCTGTAAATGATGTTCCCACGAAGCTGAGTGTTATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
* * * ** * *
60269 ACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGATGT-ACCTTGG
66 ACTTGAGGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGCTATACTGCAAATGATATGCCCTT-G
* *
60333 AGTTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
130 AGCTGAGCGTAGTCGAACTCAAAGGTCTTT-GTTGG
* * * * * * * * *
60369 CAAATAACCCTTCTCGACTTAAGTTATGCTTTAAATGATATGCCCTCGAATCTGAGTGTAATTGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
* ** * * * * *
60434 ACTTGAGGGTTTTTGATATATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA-AGTG-CCTTG
66 ACTTGAGGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGCTATACTGCAAATGATA-TGCCCTT-
* * * * *
60497 GAGCTGAGCGTAGTCAAACTCGAAGGTATTTTGGTGA
129 GAGCTGAGCGTAGTCGAACTCAAAGGT-CTTTGTTGG
* * *
60534 CAAATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
* * * * * * * *
60599 ATTTGAGGGTCTTTGGCATATAGCCCTTCTCGACATAAGCTATGCTGCAAATGATGTG-CCTTGG
66 ACTTGAGGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGCTATACTGCAAATGATATGCCCTT-G
* *
60663 AGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTTGG
130 AGCTGAGCGTAGTCGAACTCAAAGGTCTTT-GTTGG
* * * *
60699 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
60736 TTGTCTTAAA
Statistics
Matches: 992, Mismatches: 165, Indels: 51
0.82 0.14 0.04
Matches are distributed among these distances:
156 24 0.02
157 3 0.00
158 1 0.00
159 4 0.00
160 60 0.06
161 33 0.03
162 134 0.14
163 17 0.02
164 289 0.29
165 395 0.40
166 5 0.01
167 1 0.00
168 3 0.00
169 23 0.02
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (164 bp):
CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
ACTTGAGGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGCTATACTGCAAATGATATGCCCTTGA
GCTGAGCGTAGTCGAACTCAAAGGTCTTTGTTGG
Found at i:60343 original size:165 final size:163
Alignment explanation
Indices: 59534--60735 Score: 1272
Period size: 165 Copynumber: 7.3 Consensus size: 163
59524 GTGTAATCAG
* * * * **
59534 ACTCAAAGGTCTTTGTTGGCAGATAACTCTTATAGCCTTGAGTTATAATGCAAATGATGTGCCCT
1 ACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCT
* * * * * *
59599 CAAAGCTGAGTGTAATCAAACTTGAGGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGCTATACC
66 CAAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCT
* * * *
59664 GCAAATGATATGCCGTTGAGTTGAGTGTAATCGA
131 GCAAATGATGTGCC-TTGAGCTGAGCGTAGTCGA
* ** *
59698 ACTCAAAGGTCTTTATTAGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCT
1 ACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCT
* * * * * * * * *
59763 CAAAGCTGAGTGTAATTGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGTTATACC
66 CAAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCT
* * *
59828 ACAAATGATGTGCCATTGAGCTGAGTGTAATCGA
131 GCAAATGATGTGCC-TTGAGCTGAGCGTAGTCGA
*
59862 ACTC-AAGGTCTTT-GTTGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCT
1 ACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCT
* * * *
59925 CAAAGTTGAGTGTAATCGAACTCGAGTGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACT
66 CAAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCT
* * *
59990 GCAAATAATGTGCCTTTAAGCTGAGCGTAGTTGA
131 GCAAATGATGTGCC-TTGAGCTGAGCGTAGTCGA
* * * * * * * *
60024 ACTCGCAGGTC-TT--TGGCAGATAGCCCTTTTCGACTTAAGTTATACTGTAAATGA--T---CT
1 ACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCT
** ** * * * * * * * *
60081 TTAAGCTGAGCATAGTCGAACTCGAAGGTCTTTTAGTGACAGATAACCCTTCTAGCCTTGAGTTA
66 CAAAGCTGAGTGTAATCGAACTTGAGGGTC-TTT-G-G-CAGATAGCCCTTCTCGACTTAAGCTA
* *
60146 TGCTGTAAATGATATGCCTCTGAGCTGAGCGTAGTCGA
127 TGCTGCAAATGATGTGCCT-TGAGCTGAGCGTAGTCGA
* ** * * *
60184 ACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGGGTTATGCTGTAAATGATGTTCCC
1 ACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCC
* * * *
60249 ACGAAGCTGAGTGTTATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGT
65 TCAAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
* *
60314 TGCAAATGATGTACCTTGGAGTTGAGCGTAGTCGA
130 TGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGA
* * * * ** *
60349 ACTCGAAGGTCTTTGGTTGGCAAATAACCCTTCTCGACTTAAGTTATGCTTTAAATGATATGCCC
1 ACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCC
* * * * ** *
60414 TCGAATCTGAGTGTAATTGAACTTGAGGGTTTTTGATATATAGCCCTTCTCGACTTAAGCTATGC
65 TCAAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
* *
60479 TGCAAATGAAGTGCCTTGGAGCTGAGCGTAGTCAA
130 TGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGA
* * * **
60514 ACTCGAAGGTATTTTGGTGACAAATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCC
1 ACTCGAAGGT-CTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCC
* * * *
60579 TCGAAGCTGAGTGTAATCGAATTTGAGGGTCTTTGGCATATAGCCCTTCTCGACATAAGCTATGC
65 TCAAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
60644 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
130 TGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGA
* * * *
60679 ACTCGAAGGTATTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
1 ACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
60736 TTGTCTTAAA
Statistics
Matches: 880, Mismatches: 139, Indels: 37
0.83 0.13 0.04
Matches are distributed among these distances:
156 24 0.03
157 3 0.00
158 1 0.00
159 3 0.00
160 60 0.07
161 33 0.04
162 139 0.16
163 14 0.02
164 196 0.22
165 373 0.42
166 7 0.01
167 1 0.00
168 3 0.00
169 23 0.03
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (163 bp):
ACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCT
CAAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCT
GCAAATGATGTGCCTTGAGCTGAGCGTAGTCGA
Found at i:60587 original size:330 final size:326
Alignment explanation
Indices: 59389--60735 Score: 1392
Period size: 330 Copynumber: 4.1 Consensus size: 326
59379 ATTTTATTGA
* * * * * * *** * * *
59389 CAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATGATAT-ACCTTGGAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCCTCAAAGCTGAGTGTAATTGA
* * * ** * * * *
59453 ACTCGAAGGTTTTTTTG-CAGAGAACCCTTCTAGCCTTGAGCCATACCGTAAATGATA-TGTCGT
66 ACTCG-AGG-GTTTTTGACAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGA-AGTG-CCT
* * * * * * * *
59516 TGAGTTGAGTGTAATC-AGACTCAAAGGTCTTTGTTGGCAGATAACTCTTATAGCCTTGAGTTAT
127 TGAGCTGAGCGTAGTCGA-ACTC-AAGGTTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTAT
** *
59580 AATGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCAAACTTGAGGGTCTTTGGCAGATAGCCCT
190 GCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCT
* * * * * * * * *
59645 TCTAGCCTTGAGCTATACCGCAAATGATATGCCGTT-GAGTTGAGTGTAATCGAACTCAAAGGTC
255 TCTCGACTTAAGCTATACTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
* *
59709 TTTATTAG
319 TTTGTTGG
* * * * *
59717 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATTGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCCTCAAAGCTGAGTGTAATTGA
* * * * ** *
59782 ACTCGAAGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGTTATACCACAAATGATGTGCCATTGA
66 ACTCGAGGGTTTTTGACAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGAAGTGCC-TTGA
* * * *
59847 GCTGAGTGTAATCGAACTCAAGGTCTTTGTTG-CAGATAACCCTTCTAGCCTTGAGTTATGCTGC
130 GCTGAGCGTAGTCGAACTCAAGGTTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGC
* * *
59911 AAATGATGTGCCCTCAAAGTTGAGTGTAATCGAACTCGAGTGTCTTTGGCAGATAGCCCTTCTCG
195 AAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCG
* ** * *
59976 ACTTAAGCTATACTGCAAATAATGTGCCTTTAAGCTGAGCGTAGTTGAACTCGCAGGTC--T-TT
260 ACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTT
60038 GG
325 GG
* * * ** ** * *
60040 CAGATAGCCCTTTTCGACTTAAGTTATACTGTAAATG--AT---CTTTAAGCTGAGCATAGTCGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCCTCAAAGCTGAGTGTAATTGA
* * *
60100 ACTCGAAGGTCTTTTAGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATA-TGCC
66 ACTCG-AGG-GTTTT--TGACAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGA-AGTGCC
* *
60164 TCTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGGGTT
126 T-TGAGCTGAGCGTAGTCGAACTC-AAGGT-TTTTGGTGACAGATAACCCTTCTAGCCTTGAGTT
* * * * *
60229 ATGCTGTAAATGATGTTCCCACGAAGCTGAGTGTTATCGAACTTGAGGGTCTTTGGCAGATAGCC
188 ATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCC
** * *
60294 CTTCTCGACTTAAGCTATGTTGCAAATGATGTACCTTGGAGTTGAGCGTAGTCGAACTCGAAGGT
253 CTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
60359 CTTTGGTTGG
318 CTTT-GTTGG
* * * *
60369 CAAATAACCCTTCTCGACTTAAGTTATGCTTTAAATGATATGCCCTCGAATCTGAGTGTAATTGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCCTCAAAGCTGAGTGTAATTGA
* * * * * * *
60434 ACTTGAGGGTTTTTGATATATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAAGTGCCTTGGA
66 ACTCGAGGGTTTTTGACAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGAAGTGCCTT-GA
* *
60499 GCTGAGCGTAGTCAAACTCGAAGGTATTTTGGTGACAAATAACCCTTCTAGCCTTGAGTTATGCT
130 GCTGAGCGTAGTCGAACTC-AAGGT-TTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
** * * *
60564 ATAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAATTTGAGGGTCTTTGGCATATAGCCCTTCT
193 GCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCT
* * *
60629 CGACATAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTG
258 CGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-
60694 GTTGG
322 GTTGG
*
60699 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATG
60736 TTGTCTTAAA
Statistics
Matches: 858, Mismatches: 135, Indels: 50
0.82 0.13 0.05
Matches are distributed among these distances:
318 20 0.02
319 2 0.00
320 3 0.00
321 2 0.00
322 59 0.07
323 38 0.04
324 6 0.01
325 140 0.16
326 132 0.15
327 20 0.02
328 92 0.11
329 60 0.07
330 257 0.30
331 2 0.00
332 4 0.00
333 3 0.00
334 18 0.02
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (326 bp):
CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCCTCAAAGCTGAGTGTAATTGA
ACTCGAGGGTTTTTGACAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGAAGTGCCTTGAG
CTGAGCGTAGTCGAACTCAAGGTTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCA
AATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGA
CTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTG
G
Found at i:61960 original size:83 final size:86
Alignment explanation
Indices: 61833--62059 Score: 257
Period size: 95 Copynumber: 2.6 Consensus size: 86
61823 GGCTAGCTGA
*
61833 ATCCATAAAGCCGGGGCGTTTAGCCAATTGCTCTAGAGGGACAGCTCAA-TATA-T-AAA-CACC
1 ATCCATAAAGCC-GGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAATTATAGTAAAATCACC
* *
61894 TTTATCAGGTTAGCTGAATCTT
65 TTTATCAGGCTAGCTGAATATT
*
61916 ATCCATAAAGCCAGGGCGTTTAACCTATTGC-CTTAGAGGGACAGCTCAAGCTTTATTGTATAGT
1 ATCCATAAAGCC-GGGCGTTTAACCAATTGCTC-TAGAGGGACAGCTC-A-----A-T-TATAGT
*
61980 AAAATTACCTTTATCAGGCTAGCTGAATATT
56 AAAATCACCTTTATCAGGCTAGCTGAATATT
*
62011 ATCCATAAAGCCGGAGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA
1 ATCCATAAAGCCGG-GCGTTTAACCAATTGCTCTAGAGGGACAGCTCAA
62060 GCTTTACTGT
Statistics
Matches: 121, Mismatches: 8, Indels: 24
0.79 0.05 0.16
Matches are distributed among these distances:
82 1 0.01
83 42 0.35
84 1 0.01
89 2 0.02
92 4 0.03
93 1 0.01
94 6 0.05
95 63 0.52
96 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (86 bp):
ATCCATAAAGCCGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAATTATAGTAAAATCACCT
TTATCAGGCTAGCTGAATATT
Found at i:62059 original size:95 final size:95
Alignment explanation
Indices: 61891--62072 Score: 287
Period size: 95 Copynumber: 1.9 Consensus size: 95
61881 ATATATAAAC
* * *
61891 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCCAGGGCGTTTAACCTATTGCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTGCCTTAGAGGG
* *
61956 ACAGCTCAAGCTTTATTGTATAGTAAAATT
66 ACAACTCAAGCTTTACTGTATAGTAAAATT
61986 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCC-GGAGCGTTTAACCAATTG-CTCTAGAG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGG-GCGTTTAACCAATTGCCT-TAGAG
62049 GGACAACTCAAGCTTTACTGTATA
64 GGACAACTCAAGCTTTACTGTATA
62073 TATATAATAT
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
94 4 0.05
95 76 0.95
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTACTGTATAGTAAAATT
Found at i:66222 original size:37 final size:38
Alignment explanation
Indices: 66114--66346 Score: 200
Period size: 37 Copynumber: 6.2 Consensus size: 38
66104 TTTTTTAACT
* **
66114 TTATATTATTTTTCTAAAAAT-TTTCCAAAAACTATATA
1 TTATATAATTTTTC-AAAAATGTTTTTAAAAACTATATA
* * *
66152 TTATAT-AGTTTCCAAAAATG-ATTT-AAAA--A-ATA
1 TTATATAATTTTTCAAAAATGTTTTTAAAAACTATATA
* *
66184 TTATATGAGTTTTCAAAAATGTTTTTAAAAA-TATATA
1 TTATATAATTTTTCAAAAATGTTTTTAAAAACTATATA
*
66221 TTATATAATTTTTCAAAAATGTTTTTTATTTAAAACCATATA
1 TTATATAATTTTTCAAAAATG-TTTTTA---AAAACTATATA
*
66263 TTATATAATTTTTCAAAATTG-TTTTAAAAACTATATA
1 TTATATAATTTTTCAAAAATGTTTTTAAAAACTATATA
* *
66300 TTATATATTTATTTTC-AAAGTG-TTTTAAAAACTATAATA
1 TTATATA-AT-TTTTCAAAAATGTTTTTAAAAACTAT-ATA
66339 TATATATA
1 T-TATATA
66347 TATATATATA
Statistics
Matches: 166, Mismatches: 14, Indels: 28
0.80 0.07 0.13
Matches are distributed among these distances:
32 9 0.05
33 14 0.08
34 3 0.02
35 8 0.05
36 8 0.05
37 44 0.27
38 31 0.19
39 9 0.05
40 11 0.07
41 4 0.02
42 25 0.15
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (38 bp):
TTATATAATTTTTCAAAAATGTTTTTAAAAACTATATA
Found at i:66254 original size:42 final size:42
Alignment explanation
Indices: 66207--66287 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
66197 CAAAAATGTT
*
66207 TTTAAAAATATATATTATATAATTTTTCAAAAATGTTTTTTA
1 TTTAAAAACATATATTATATAATTTTTCAAAAATGTTTTTTA
* *
66249 TTTAAAACCATATATTATATAATTTTTCAAAATTGTTTT
1 TTTAAAAACATATATTATATAATTTTTCAAAAATGTTTT
66288 AAAAACTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (42 bp):
TTTAAAAACATATATTATATAATTTTTCAAAAATGTTTTTTA
Found at i:68183 original size:2 final size:2
Alignment explanation
Indices: 68176--68206 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
68166 ACTGTGTCTT
68176 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
68207 CCATTCAAAG
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:69243 original size:31 final size:29
Alignment explanation
Indices: 69203--69260 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 29
69193 TTTTAGTACC
69203 TATTCTGACTAAAAATATAACTTTAGGTATT
1 TATTCTGACTAAAAA-ATAA-TTTAGGTATT
*
69234 TATTTTGACTAAAAAATAATTTAGGTA
1 TATTCTGACTAAAAAATAATTTAGGTA
69261 CTTAAATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 8 0.31
30 4 0.15
31 14 0.54
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (29 bp):
TATTCTGACTAAAAAATAATTTAGGTATT
Found at i:70256 original size:61 final size:61
Alignment explanation
Indices: 70184--70304 Score: 206
Period size: 61 Copynumber: 2.0 Consensus size: 61
70174 CGACGCCGTT
70184 TTTCACCCGGGCGGGAAAAGATTGATATTGACTTTAGAGTTTTCCTTTGAAAAGAATTTTC
1 TTTCACCCGGGCGGGAAAAGATTGATATTGACTTTAGAGTTTTCCTTTGAAAAGAATTTTC
* ** *
70245 TTTCACTCGGGCGGGAAAAGATTGATATTGACTTTAGAGTTTTTTTTTTAAAAGAATTTT
1 TTTCACCCGGGCGGGAAAAGATTGATATTGACTTTAGAGTTTTCCTTTGAAAAGAATTTT
70305 AAAATGTGAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.40
Consensus pattern (61 bp):
TTTCACCCGGGCGGGAAAAGATTGATATTGACTTTAGAGTTTTCCTTTGAAAAGAATTTTC
Found at i:73351 original size:18 final size:18
Alignment explanation
Indices: 73328--73366 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
73318 AGATGTTTAC
*
73328 TTAAATTTTAATTGATAA
1 TTAAATTATAATTGATAA
* *
73346 TTAAATTATATTTTATAA
1 TTAAATTATAATTGATAA
73364 TTA
1 TTA
73367 GCGACGTGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTAAATTATAATTGATAA
Done.