Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001707.1 Hibiscus syriacus cultivar Beakdansim tig00003427_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: 92961
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:3578 original size:7 final size:7
Alignment explanation
Indices: 3566--3591 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3556 CTAATTTATA
3566 AAAATTT
1 AAAATTT
3573 AAAATTT
1 AAAATTT
3580 AAAATTT
1 AAAATTT
3587 AAAAT
1 AAAAT
3592 CACTCAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAAATTT
Found at i:4296 original size:14 final size:15
Alignment explanation
Indices: 4266--4299 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
4256 ATAATGTTAT
*
4266 TAATATTATTATTAA
1 TAATACTATTATTAA
4281 TAATACTATT-TTAA
1 TAATACTATTATTAA
4295 TAATA
1 TAATA
4300 AAATTCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATACTATTATTAA
Found at i:5014 original size:5 final size:5
Alignment explanation
Indices: 5004--5029 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4994 CGAAATTAAT
5004 TCGAG TCGAG TCGAG TCGAG TCGAG T
1 TCGAG TCGAG TCGAG TCGAG TCGAG T
5030 AAAAAAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.23
Consensus pattern (5 bp):
TCGAG
Found at i:6583 original size:19 final size:19
Alignment explanation
Indices: 6559--6611 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
6549 ACAAGCCCGA
*
6559 GTGCATCGATGCATAGTCT
1 GTGCATCGATGCATAGTAT
* * *
6578 GTGCATTGATGTATGGTAT
1 GTGCATCGATGCATAGTAT
*
6597 GTACATCGATGCATA
1 GTGCATCGATGCATA
6612 AAATGCATTC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (19 bp):
GTGCATCGATGCATAGTAT
Found at i:9665 original size:21 final size:23
Alignment explanation
Indices: 9610--9690 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 23
9600 ACCCGACGGA
9610 TGCATCGATGCACATTCAAGGAG
1 TGCATCGATGCACATTCAAGGAG
* * *
9633 TGCATCGGTGCACCTTC-ATG-G
1 TGCATCGATGCACATTCAAGGAG
* *
9654 TGTATCGATGCAAATTCAAAGG-G
1 TGCATCGATGCACATTC-AAGGAG
9677 ATGCATCGATGCAC
1 -TGCATCGATGCAC
9691 TGTTAAGTGT
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
21 14 0.31
22 2 0.04
23 18 0.40
24 11 0.24
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGAG
Found at i:15545 original size:19 final size:19
Alignment explanation
Indices: 15521--15573 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
15511 ACAAGCCCGA
* *
15521 GTGCATCGATACATAGTCT
1 GTGCATCGATGCATAGTAT
* *
15540 GTGCATCGATGTATGGTAT
1 GTGCATCGATGCATAGTAT
15559 GTGCATCGATGCATA
1 GTGCATCGATGCATA
15574 AAATGCATTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (19 bp):
GTGCATCGATGCATAGTAT
Found at i:16069 original size:16 final size:17
Alignment explanation
Indices: 16029--16072 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
16019 TCCTACTTGA
16029 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** *
16046 TTTTATATTT-TTAAAT
1 TTAAATATTTAATAAAT
16062 TTAAATATTTA
1 TTAAATATTTA
16073 TTTTTATATG
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:16867 original size:51 final size:50
Alignment explanation
Indices: 16794--16950 Score: 133
Period size: 50 Copynumber: 3.1 Consensus size: 50
16784 TTAGCAGTAA
* * *
16794 AGCGCACCCCTTACACCACGCTATACGATGATTTGACGTCACGTGGGGTAT
1 AGCGCGCCCCCTACACCGCGCTATACGATGATTTGACG-CACGTGGGGTAT
* * ** * *
16845 AGCGCGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGC-CATGTGGGTAT
1 AGCGCGCCCCCTACACCGCGCTATACGATGATTTGACGCACGTG-GGGTAT
* * *
16895 AGCGCGGCCCCTACAGCGCGCTATGC-ATGTATATCTGA--CACGTGGGGTAT
1 AGCGCGCCCCCTACACCGCGCTATACGATG-AT-T-TGACGCACGTGGGGTAT
16945 AGCGCG
1 AGCGCG
16951 GTGCAGGGGG
Statistics
Matches: 83, Mismatches: 18, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
49 5 0.06
50 43 0.52
51 33 0.40
52 2 0.02
ACGTcount: A:0.19, C:0.31, G:0.30, T:0.20
Consensus pattern (50 bp):
AGCGCGCCCCCTACACCGCGCTATACGATGATTTGACGCACGTGGGGTAT
Found at i:17072 original size:12 final size:10
Alignment explanation
Indices: 17031--17071 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
17021 TTTATCACAC
17031 CAAATTCTCT
1 CAAATTCTCT
17041 CAAATTCTCT
1 CAAATTCTCT
17051 -AAATTTCTCT
1 CAAA-TTCTCT
*
17061 CAAATACTCT
1 CAAATTCTCT
17071 C
1 C
17072 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:21416 original size:3 final size:3
Alignment explanation
Indices: 21410--21472 Score: 54
Period size: 3 Copynumber: 21.0 Consensus size: 3
21400 ATAATATATT
* * * * * **
21410 TAA TAA TAA TAA TAA TAA TAA TAA TTA TTA TTA TTA TTA TAA TAA TTT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
21458 TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA
21473 AAACAAAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (3 bp):
TAA
Found at i:22370 original size:76 final size:76
Alignment explanation
Indices: 21630--22343 Score: 1302
Period size: 76 Copynumber: 9.4 Consensus size: 76
21620 GATGTCTTAA
* *
21630 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
21695 AGGCTTTTTGG
66 AGGCTTTTTGG
** *
21706 AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
21771 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
21782 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
21847 AGGCTTTTTGG
66 AGGCTTTTTGG
* * * *
21858 AAATATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
21923 AGGCTTTTTGG
66 AGGCTTTTTGG
*
21934 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGG
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
21999 AGGCTTTTTGG
66 AGGCTTTTTGG
22010 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
22075 AGGCTTTTTGG
66 AGGCTTTTTGG
22086 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
22151 AGGCTTTTTGG
66 AGGCTTTTTGG
*
22162 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
22227 AGGTTTTTTGG
66 AGGCTTTTTGG
22238 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
22303 AGGCTTTTTGG
66 AGGCTTTTTGG
22314 AAACATCATGCACTGTAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
22344 TGGGAAATAG
Statistics
Matches: 624, Mismatches: 14, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 624 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:22637 original size:167 final size:168
Alignment explanation
Indices: 22347--22652 Score: 506
Period size: 167 Copynumber: 1.8 Consensus size: 168
22337 ACAGATGTGG
* *
22347 GAAATAGTTTACTAAGTAAAAAAACTAAGGAAATCATTTTCTTACTTTTCAACAATTTCATTTTT
1 GAAATAATTTACTAAGTAAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTT
** *
22412 AGAAAAGATTGAATGAGAAACTAGGAAAATCGTTTTCTCATTATGTTTTTCAAAATAACATGTTG
66 AGAAAAGATAAAATGAGAAACTAGGAAAATCGTTTTCTCATTATGTTTTTCAAAATAACATATTG
22477 ATTGGGTAAAATGCCCCAATCTCAAGATAAGGCTGTTA
131 ATTGGGTAAAATGCCCCAATCTCAAGATAAGGCTGTTA
*
22515 GAAATAATTTACTAAGTAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCA-TTTT
1 GAAATAATTTACTAAGTAAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTT
* * * **
22579 AGAAAAGATAAAATGAGAAACTATGAAAATTGTTTTCTCATTCTGTTTTTTGAAATAACATATTG
66 AGAAAAGATAAAATGAGAAACTAGGAAAATCGTTTTCTCATTATGTTTTTCAAAATAACATATTG
22644 ATTGGGTAA
131 ATTGGGTAA
22653 CATTACCCAA
Statistics
Matches: 127, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
167 70 0.55
168 57 0.45
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (168 bp):
GAAATAATTTACTAAGTAAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTT
AGAAAAGATAAAATGAGAAACTAGGAAAATCGTTTTCTCATTATGTTTTTCAAAATAACATATTG
ATTGGGTAAAATGCCCCAATCTCAAGATAAGGCTGTTA
Found at i:23213 original size:22 final size:23
Alignment explanation
Indices: 23188--23242 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 23
23178 AATAAAGCTT
23188 TCATCTTTGAAAAA-AGAATCTA
1 TCATCTTTGAAAAAGAGAATCTA
*
23210 TCAT-TTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAAGAGAATCTA
23232 TCATCTTTGAA
1 TCATCTTTGAA
23243 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 8 0.28
22 16 0.55
23 5 0.17
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (23 bp):
TCATCTTTGAAAAAGAGAATCTA
Found at i:23691 original size:54 final size:54
Alignment explanation
Indices: 23609--23762 Score: 281
Period size: 54 Copynumber: 2.9 Consensus size: 54
23599 AATAGCATGG
* *
23609 TCGTAAAACATTTGACAGCGCATTCATCCTTTCCTGTGGCTTCTGCTCAGATGT
1 TCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGATGT
*
23663 TCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGTTCAGATGT
1 TCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGATGT
23717 TCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
1 TCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
23763 CAAGATTTCT
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 96 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.36
Consensus pattern (54 bp):
TCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGATGT
Found at i:26042 original size:114 final size:114
Alignment explanation
Indices: 25842--26067 Score: 380
Period size: 114 Copynumber: 2.0 Consensus size: 114
25832 GATCATATAG
* * *
25842 TTCATCTTTCAATTCCAATAATTGGTTATGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATAATTGGTTATGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
25907 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* *
25956 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATAATTGGTTATGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* **
26021 ACACTTCCAGAAGATGCTATTGGGTTTTTTTATTTCTACTATGAGCA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCA
26068 CATGGCACTT
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 104 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATAATTGGTTATGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:31117 original size:14 final size:14
Alignment explanation
Indices: 31100--31138 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
31090 TAAAAGTATG
31100 AATGCAAAATGAAA
1 AATGCAAAATGAAA
*
31114 AATGCAAAGATGCAA
1 AATGCAAA-ATGAAA
31129 AATG-AAAATG
1 AATGCAAAATG
31139 CATATATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 11 0.48
15 9 0.39
ACGTcount: A:0.59, C:0.08, G:0.18, T:0.15
Consensus pattern (14 bp):
AATGCAAAATGAAA
Found at i:35388 original size:3 final size:3
Alignment explanation
Indices: 35382--35438 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
35372 ATAATATATT
* * * * * **
35382 TAA TAA TAA TAA TTA TTA TTA TTA TTA TAA TAA TAA TAA TTT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35430 TAA TAA TAA
1 TAA TAA TAA
35439 AAACAAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (3 bp):
TAA
Found at i:36115 original size:64 final size:67
Alignment explanation
Indices: 36006--36133 Score: 201
Period size: 64 Copynumber: 2.0 Consensus size: 67
35996 ATTTTCATCT
*
36006 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
1 TTTAATGGAGGTATGCATCAATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
36071 TA
66 TA
*
36073 TTTAATGG-GG-ATGCATCAATGCACT-C-CTTATGCATCGATGCATAAATCCTATTCGATGTTT
1 TTTAATGGAGGTATGCATCAATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGATGTTT
36134 TCTTTTTAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
63 1 0.02
64 33 0.57
65 14 0.24
66 2 0.03
67 8 0.14
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (67 bp):
TTTAATGGAGGTATGCATCAATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
TA
Found at i:36151 original size:64 final size:63
Alignment explanation
Indices: 36018--36178 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 63
36008 TAATGGAGGT
* * * * *
36018 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCAATGCACTCCA-TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* * *
36083 ATGCATCAATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCAATGCACTCCATATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* * *
36147 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCAATGCACTCCATATGCATCGATGCA
36179 CCTTAAACAA
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 57 0.70
65 22 0.27
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.34
Consensus pattern (63 bp):
ATGCATCAATGCACTCCATATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:39360 original size:49 final size:51
Alignment explanation
Indices: 39255--39375 Score: 176
Period size: 49 Copynumber: 2.4 Consensus size: 51
39245 ATACAAAACA
*
39255 CGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGTCG
1 CGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGATATGTCG
39306 CGGTACCTGCCCCGCGCTATATAAAATTAT-T-AGGAGTAAAGATATAG-CG
1 CGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGATAT-GTCG
* **
39355 TGGTACCTGATCCGCGCTATA
1 CGGTACCTGCCCCGCGCTATA
39376 CCCCTACGTG
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
49 33 0.51
50 2 0.03
51 30 0.46
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (51 bp):
CGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGATATGTCG
Found at i:41226 original size:22 final size:22
Alignment explanation
Indices: 41196--41237 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
41186 AGTCGAGGGT
* *
41196 TTCATAGGTCCTTCGGGACATA
1 TTCACAGGTCCTTAGGGACATA
41218 TTCACAGGTCCTTAGGGACA
1 TTCACAGGTCCTTAGGGACA
41238 AATCTCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (22 bp):
TTCACAGGTCCTTAGGGACATA
Found at i:42283 original size:2 final size:2
Alignment explanation
Indices: 42278--42342 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
42268 TATTAGGATG
42278 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
42320 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
42343 TGCATTTAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:47093 original size:16 final size:16
Alignment explanation
Indices: 47072--47105 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
47062 TTACTATTCA
*
47072 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
47088 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
47104 CG
1 CG
47106 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:55823 original size:17 final size:17
Alignment explanation
Indices: 55789--55822 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
55779 TGCTGTGTTC
55789 TCTTTCTCTGTTTTTTT
1 TCTTTCTCTGTTTTTTT
55806 TCTTT-TCTGTTTTTTT
1 TCTTTCTCTGTTTTTTT
55822 T
1 T
55823 TTCTTGTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (17 bp):
TCTTTCTCTGTTTTTTT
Found at i:56230 original size:3 final size:3
Alignment explanation
Indices: 56222--56331 Score: 163
Period size: 3 Copynumber: 37.7 Consensus size: 3
56212 TTATTTATTA
*
56222 AAT AAT AAT AAT -AT AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
56269 -AT AAT AAT AA- AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
56315 TTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
56332 ATTTAAATGA
Statistics
Matches: 96, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
2 6 0.06
3 90 0.94
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:57354 original size:76 final size:76
Alignment explanation
Indices: 56463--57328 Score: 1662
Period size: 76 Copynumber: 11.4 Consensus size: 76
56453 GAAATGTTGA
*
56463 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
56528 AGGCTTTTTGG
66 AGGCTTTTTGG
56539 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
56604 AGGCTTTTTGG
66 AGGCTTTTTGG
56615 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
56680 AGGCTTTTTGG
66 AGGCTTTTTGG
56691 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
56756 AGGCTTTTTGG
66 AGGCTTTTTGG
*
56767 AAACATCATGCACTGAAGGAATTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
56832 AGGCTTTTTGG
66 AGGCTTTTTGG
*
56843 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
56907 AGGCTTTTTGG
66 AGGCTTTTTGG
*
56918 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
56983 AGGCTTTTTGG
66 AGGCTTTTTGG
56994 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
57059 AGGCTTTTTGG
66 AGGCTTTTTGG
57070 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
57135 AGGCTTTTTGG
66 AGGCTTTTTGG
57146 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
57211 AGGCTTTTTGG
66 AGGCTTTTTGG
*
57222 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAGAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
57287 AGGCTTTTTTGG
66 AGGC-TTTTTGG
*
57299 AAACATCATGCACTGAAGGGCTTACAGATG
1 AAACATCATGCACTGAAGGACTTACAGATG
57329 TGAGAAATAG
Statistics
Matches: 781, Mismatches: 7, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
75 75 0.10
76 670 0.86
77 36 0.05
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.21
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:58027 original size:22 final size:22
Alignment explanation
Indices: 58002--58056 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
57992 CATAAAGTTT
*
58002 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
58024 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
58046 TCATCTTTGAA
1 TCATCTTTGAA
58057 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:60684 original size:83 final size:83
Alignment explanation
Indices: 60514--60807 Score: 518
Period size: 83 Copynumber: 3.5 Consensus size: 83
60504 GTTCCTACCA
* * *
60514 AACCATATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTC-TATTCATCTTCCAAA
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAG-CACATTCATCTTCCAAA
60578 TTCAATGATTGGTTCTGTCC
64 TTCAATGATTGGTTCTGTCC
*
60598 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATT
60663 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
*
60681 AACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATT
60746 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
60764 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
60808 GATCTCCTTA
Statistics
Matches: 202, Mismatches: 7, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
82 1 0.00
83 161 0.80
84 40 0.20
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (83 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATT
CAATGATTGGTTCTGTCC
Found at i:69032 original size:17 final size:17
Alignment explanation
Indices: 68998--69031 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
68988 TGCTGTGTTC
68998 TCTTTCTCTGTTTTTTT
1 TCTTTCTCTGTTTTTTT
69015 TCTTT-TCTGTTTTTTT
1 TCTTTCTCTGTTTTTTT
69031 T
1 T
69032 TTCTTGTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (17 bp):
TCTTTCTCTGTTTTTTT
Found at i:69439 original size:3 final size:3
Alignment explanation
Indices: 69431--69551 Score: 172
Period size: 3 Copynumber: 39.7 Consensus size: 3
69421 TTATTTATTA
*
69431 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
69477 AAAT AAT AAT AAT AAT AAAT AA- AAT AAT AAT AAT AAT ACT AAT AAT
1 -AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
69523 AAT AAT AAT AAT TTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
69552 ATTTAAATGA
Statistics
Matches: 106, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
2 2 0.02
3 95 0.90
4 9 0.08
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:69809 original size:76 final size:76
Alignment explanation
Indices: 69683--70592 Score: 1727
Period size: 76 Copynumber: 12.0 Consensus size: 76
69673 GAAATGTTGA
*
69683 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
69748 AGGCTTTTTGG
66 AGGCTTTTTGG
69759 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
69824 AGGCTTTTTGG
66 AGGCTTTTTGG
69835 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
69900 AGGC-TTTTGG
66 AGGCTTTTTGG
69910 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
69975 AGGCTTTTTGG
66 AGGCTTTTTGG
*
69986 AAACATCATGCACTGAAGGAATTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
70051 AGGCTTTTTGG
66 AGGCTTTTTGG
*
70062 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
70127 AGGCTTTTTGG
66 AGGCTTTTTGG
*
70138 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
70203 AGGCTTTTTGG
66 AGGCTTTTTGG
70214 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
70279 AGGC-TTTTGG
66 AGGCTTTTTGG
70289 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
70354 AGGCTTTTTGG
66 AGGCTTTTTGG
70365 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
70430 AGGCTTTTTGG
66 AGGCTTTTTGG
*
70441 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAGAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
70506 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
70517 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAGAACATCAAAAAGCTCCCCA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
70582 AGG-TTGTTTGG
66 AGGCTT-TTTGG
70593 CCAAGAACAC
Statistics
Matches: 824, Mismatches: 7, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
75 152 0.18
76 672 0.82
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.21
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:70289 original size:303 final size:303
Alignment explanation
Indices: 69683--70592 Score: 1718
Period size: 303 Copynumber: 3.0 Consensus size: 303
69673 GAAATGTTGA
*
69683 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
69748 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAA
69813 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
69878 AAAAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
196 -AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
69942 CCGAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
260 CCGAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
*
69986 AAACATCATGCACTGAAGGAATTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
*
70051 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAA
70116 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
70181 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
196 -AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
70246 CCGAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGC-TTTTGG
260 CCGAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
70289 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
70354 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAA
70419 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
70484 AAGAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
196 AA-AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
* *
70549 CCGAAGGCTTTAAGAACATCAAAAAGCTCCCCAAGG-TTGTTTGG
260 CCGAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTT-TTTGG
70593 CCAAGAACAC
Statistics
Matches: 595, Mismatches: 8, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
302 2 0.00
303 513 0.86
304 80 0.13
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.21
Consensus pattern (303 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
CGAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
Found at i:70382 original size:379 final size:378
Alignment explanation
Indices: 69683--70592 Score: 1743
Period size: 379 Copynumber: 2.4 Consensus size: 378
69673 GAAATGTTGA
69683 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
69748 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT-AAAACATCAA
69813 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
130 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
69878 AAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
195 AAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
69943 CGAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGAAT
260 CGAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGAAT
70008 TACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
325 TACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
70062 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
70127 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT-AAAACATCAA
70192 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
130 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
70257 AAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
195 AAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
*
70322 CGAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACT
260 CGAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGAAT
70387 TACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
325 TACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
70441 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT-AAGAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAA-AACATCAAAAAGCTCCCG
70505 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAGAACATCA
65 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAA-AACATCA
*
70570 AAAAGCTCCCCAAGG-TTGTTTGG
129 AAAAGCTCCCGAAGGCTT-TTTGG
70593 CCAAGAACAC
Statistics
Matches: 525, Mismatches: 3, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
378 6 0.01
379 519 0.99
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.21
Consensus pattern (378 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAACATCAAA
AAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTA
AAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
GAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGAATT
ACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
Found at i:72398 original size:17 final size:17
Alignment explanation
Indices: 72364--72397 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
72354 TGCTGTGTTC
72364 TCTTTCTCTGTTTTTTT
1 TCTTTCTCTGTTTTTTT
72381 TCTTT-TCTGTTTTTTT
1 TCTTTCTCTGTTTTTTT
72397 T
1 T
72398 TTCTTGTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (17 bp):
TCTTTCTCTGTTTTTTT
Found at i:72805 original size:3 final size:3
Alignment explanation
Indices: 72797--72914 Score: 166
Period size: 3 Copynumber: 38.7 Consensus size: 3
72787 TTATTTATTA
*
72797 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
*
72844 AAT AAT AAT AAT AAAT AA- AAT AAT AAT AAT AAT ACT AAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
72889 AAT AAT AAT TTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
72915 ATTTAAATGA
Statistics
Matches: 103, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
2 2 0.02
3 92 0.89
4 9 0.09
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:75192 original size:14 final size:12
Alignment explanation
Indices: 75162--75195 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
75152 CTGCTGCTCA
75162 AATATATGCAAC
1 AATATATGCAAC
75174 AATATATGCAAC
1 AATATATGCAAC
75186 AATATATGCA
1 AATATATGCA
75196 TTATTCATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (12 bp):
AATATATGCAAC
Found at i:78527 original size:13 final size:13
Alignment explanation
Indices: 78509--78539 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
78499 GAAATTATTT
78509 AATTTTGAGTTGA
1 AATTTTGAGTTGA
78522 AATTTTGAGTTGA
1 AATTTTGAGTTGA
78535 AATTT
1 AATTT
78540 GATTATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.48
Consensus pattern (13 bp):
AATTTTGAGTTGA
Found at i:79615 original size:3 final size:3
Alignment explanation
Indices: 79602--79634 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
79592 TAACCCAAAT
*
79602 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
79635 AGGTAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:80489 original size:101 final size:101
Alignment explanation
Indices: 80309--80609 Score: 514
Period size: 101 Copynumber: 3.0 Consensus size: 101
80299 ACTTTATTTT
* **
80309 CAGGGTTTGTGGAATTATCAGACACCATGTCCCCATACGTTGCTATTTGTTTCTCGGTCATCTTC
1 CAGGGTTTGTGAAATTATCAGACACCATGTCCCCATACGTTGCTATTTGTTTCTTTGTCATCTTC
*
80374 TTTACTTTCCCATTCCACAATCTCTTTCCTTTCTTA
66 CTTACTTTCCCATTCCACAATCTCTTTCCTTTCTTA
80410 CAGGGTTTGTGAAATTATCAGACACCATGTCCCCATACGTTGCT-TTGTGTTTCTTTGTCATCTT
1 CAGGGTTTGTGAAATTATCAGACACCATGTCCCCATACGTTGCTATT-TGTTTCTTTGTCATCTT
*
80474 CCTTACTTTCTCATTCCACAATCTCTTTCCTTTCTTA
65 CCTTACTTTCCCATTCCACAATCTCTTTCCTTTCTTA
* *
80511 CAGGGTTTGTGAAATTATCAGACACCATGTCCCCATACGTTCCTCTTTGTTTCTTTGTCATCTTC
1 CAGGGTTTGTGAAATTATCAGACACCATGTCCCCATACGTTGCTATTTGTTTCTTTGTCATCTTC
*
80576 CTTGCTTTCCCATTCCACAATCTCTTTCCTTTCT
66 CTTACTTTCCCATTCCACAATCTCTTTCCTTTCT
80610 GTTTCTCTAC
Statistics
Matches: 190, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
100 2 0.01
101 186 0.98
102 2 0.01
ACGTcount: A:0.17, C:0.28, G:0.12, T:0.43
Consensus pattern (101 bp):
CAGGGTTTGTGAAATTATCAGACACCATGTCCCCATACGTTGCTATTTGTTTCTTTGTCATCTTC
CTTACTTTCCCATTCCACAATCTCTTTCCTTTCTTA
Found at i:85060 original size:31 final size:31
Alignment explanation
Indices: 85018--85093 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
85008 TTAAAAAATA
*
85018 TAAGATTTAGTCACTTTTGTTTCTATTTAAT
1 TAAGATGTAGTCACTTTTGTTTCTATTTAAT
* *
85049 TAAGATGTAGTCGCTTTTGTTTTTATTTAAT
1 TAAGATGTAGTCACTTTTGTTTCTATTTAAT
*
85080 TAAGATGTGGTCAC
1 TAAGATGTAGTCAC
85094 CCTGAGTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.50
Consensus pattern (31 bp):
TAAGATGTAGTCACTTTTGTTTCTATTTAAT
Done.