Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005873.1 Hibiscus syriacus cultivar Beakdansim tig00013803_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: 95060
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:16482 original size:24 final size:23
Alignment explanation
Indices: 16450--16506 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
16440 TATTTAAATG
* *
16450 ATAAACGAACACATATGAACAAA
1 ATAAACGAACACAAACGAACAAA
* *
16473 CATAAACGAACATAAACGAACACA
1 -ATAAACGAACACAAACGAACAAA
16497 ATAAACGAAC
1 ATAAACGAAC
16507 GTAAGCGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.60, C:0.21, G:0.09, T:0.11
Consensus pattern (23 bp):
ATAAACGAACACAAACGAACAAA
Found at i:16504 original size:23 final size:23
Alignment explanation
Indices: 16450--16520 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
16440 TATTTAAATG
* * * *
16450 ATAAACGAACACATATGAACAAA
1 ATAAACGAACATAAACGAACACA
16473 CATAAACGAACATAAACGAACACA
1 -ATAAACGAACATAAACGAACACA
* *
16497 ATAAACGAACGTAAGCGAACACA
1 ATAAACGAACATAAACGAACACA
16520 A
1 A
16521 ATGAATAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
23 22 0.54
24 19 0.46
ACGTcount: A:0.58, C:0.21, G:0.11, T:0.10
Consensus pattern (23 bp):
ATAAACGAACATAAACGAACACA
Found at i:16540 original size:24 final size:24
Alignment explanation
Indices: 16504--16572 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
16494 ACAATAAACG
16504 AACGTAAGCGAACACAAATGAATA
1 AACGTAAGCGAACACAAATGAATA
* *
16528 AACGTAAGTGAACAC-AATGAATG
1 AACGTAAGCGAACACAAATGAATA
* *
16551 AACGTAAACGAACATAAATGAA
1 AACGTAAGCGAACACAAATGAA
16573 AATAAATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 19 0.49
24 20 0.51
ACGTcount: A:0.54, C:0.14, G:0.17, T:0.14
Consensus pattern (24 bp):
AACGTAAGCGAACACAAATGAATA
Found at i:16554 original size:23 final size:23
Alignment explanation
Indices: 16480--16564 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
16470 AAACATAAAC
* * * *
16480 GAACATAAACGAACACAATAAAC
1 GAACGTAAGCGAACACAATGAAT
16503 GAACGTAAGCGAACACAAATGAAT
1 GAACGTAAGCGAACAC-AATGAAT
* *
16527 AAACGTAAGTGAACACAATGAAT
1 GAACGTAAGCGAACACAATGAAT
*
16550 GAACGTAAACGAACA
1 GAACGTAAGCGAACA
16565 TAAATGAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 33 0.63
24 19 0.37
ACGTcount: A:0.54, C:0.18, G:0.16, T:0.12
Consensus pattern (23 bp):
GAACGTAAGCGAACACAATGAAT
Found at i:16759 original size:14 final size:14
Alignment explanation
Indices: 16742--16793 Score: 86
Period size: 14 Copynumber: 3.7 Consensus size: 14
16732 TGGGCTAAAT
*
16742 ATAAATAAACGAAC
1 ATAAATGAACGAAC
*
16756 ATAAATGAATGAAC
1 ATAAATGAACGAAC
16770 ATAAATGAACGAAC
1 ATAAATGAACGAAC
16784 ATAAATGAAC
1 ATAAATGAAC
16794 ATATTAATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.17
Consensus pattern (14 bp):
ATAAATGAACGAAC
Found at i:16773 original size:24 final size:24
Alignment explanation
Indices: 16746--16796 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
16736 CTAAATATAA
*
16746 ATAAACGAAC-ATAAATGAATGAAC
1 ATAAACGAACGA-AAATAAATGAAC
* *
16770 ATAAATGAACGAACATAAATGAAC
1 ATAAACGAACGAAAATAAATGAAC
16794 ATA
1 ATA
16797 TTAATGAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.18
Consensus pattern (24 bp):
ATAAACGAACGAAAATAAATGAAC
Found at i:18186 original size:15 final size:15
Alignment explanation
Indices: 18168--18205 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
18158 AGTGTATGAT
18168 GTATGCATGTATCTC
1 GTATGCATGTATCTC
*
18183 GTATGCACGTATCTC
1 GTATGCATGTATCTC
18198 --ATGCATGT
1 GTATGCATGT
18206 GTTCATGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 7 0.33
15 14 0.67
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (15 bp):
GTATGCATGTATCTC
Found at i:22016 original size:2 final size:2
Alignment explanation
Indices: 22009--22059 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
21999 TAACGCACAT
22009 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
22051 TA TA TA TA T
1 TA TA TA TA T
22060 TGTATTTGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25239 original size:750 final size:750
Alignment explanation
Indices: 23800--25300 Score: 2596
Period size: 750 Copynumber: 2.0 Consensus size: 750
23790 TAACTTTACC
*
23800 ACAACCGATTATGGGAGTTGATTGCAGCTCTACATTAAATACTCACCCAATGAAAACAAGGAGTG
1 ACAACCGATTATGGGAGTTGATTGCAACTCTACATTAAATACTCACCCAATGAAAACAAGGAGTG
*
23865 TGAGTGGTATTTCAAAACCAAAAATATTTCAAGCTATTGCTTGGATTGATGAAGAACCACAAAGC
66 TGAGTGGTATTTCAAAACCAAAAATATTTCAAGCTACTGCTTGGATTGATGAAGAACCACAAAGC
* * *
23930 ATCAAATAAGCATTGGTTAGTCCATATTGGAAGGCTGCTGCTCAGAATACGTATGAGGCTTTGAT
131 ATCAAACAAGCATTGGCTAGTCCATATTGGAAGGCTACTGCTCAGAATACGTATGAGGCTTTGAT
23995 AAAAAATAAAACTTGGTCTCTAGTGTCATTACCAGATGATACAAGAGCAGTAAATTGTAAATGGT
196 AAAAAATAAAACTTGGTCTCTAGTGTCATTACCAGATGATACAAGAGCAGTAAATTGTAAATGGT
** * * *
24060 TGTTCAAAATTAAGAGAAATATGGATGGCTTGATTGCTCGTTTAAAGCAAGATTAGTAGCAAAAT
261 TGTTCAAAATTAAGAGAAATACAGATGGCTCGATTGCTCGTTTAAAACAAGATTAGTAGCAAAAG
24125 GTTTCCTTCAGCAACCAGGTATTGACTTTCATGAGGTCTTAGTCTTGTTGTTAAACCAGTAAATG
326 GTTTCCTTCAGCAACCAGGTATTGACTTTCATGAGGTCTTAGTCTTGTTGTTAAACCAGTAAATG
*
24190 TTCGTTTCATTTTGACACTGGCTTTGTAGAAGGGGTGGCAGCTTAGACAGGTTGAGATTAATAAT
391 TTCGTTTCATTTTGACACTGGCTTTGTAGAAGGGGTAGCAGCTTAGACAGGTTGAGATTAATAAT
* *
24255 GTTTTTCTAAATAGAGTGCTTGAATAAGAAGTCTATATGACTCAACCTCCTGGTTTTGAGTTTGG
456 GTCTTTCTAAATAGAGTGCTTGAATAAGAAGTCTATATGACTCAACCACCTGGTTTTGAGTTTGG
24320 TGATGATAATCTGGTTTGCAAGTTACATAAGGCCATATATGGTTTAAAACTGGCACCACGTGCTT
521 TGATGATAATCTGGTTTGCAAGTTACATAAGGCCATATATGGTTTAAAACTGGCACCACGTGCTT
* *
24385 GGTTTGAGAGTTTAAGGAGTTACATAGAATCTGAAGGCCTTGTGGTAGCTAAGTCTGATTCTACT
586 GGTTTGAGAGTTTAAGAAGTTACATAGAATCTGAAGGCCTTGTGGTAGCCAAGTCTGATTCTACT
* *
24450 CTGTTTATTCAAAAGAGGGAGGATTGTTTTTTGTATTTACTTGTATATGTTGATGATATAATTCT
651 CTGTTTATTCAAAAGAGGGAGGATTATTTTTTATATTTACTTGTATATGTTGATGATATAATTCT
*
24515 CAGC-GGTAATAAAGCAAGTAAGGTGCAGTTTGTCG
716 CA-CTGGTAATAAAGCAAGTAAGGTGCAATTTGTCG
* *
24550 ACAACCGGTTATGGGAGTTGATTGCAACTCTACATTAAATACTCACCCAATGAAAACAATGAGTG
1 ACAACCGATTATGGGAGTTGATTGCAACTCTACATTAAATACTCACCCAATGAAAACAAGGAGTG
24615 TGAGTGGTATTTCAAAACCAAAAATATTTCAAGCTACTGCTTGGATTGATGAAGAACCACAAAGC
66 TGAGTGGTATTTCAAAACCAAAAATATTTCAAGCTACTGCTTGGATTGATGAAGAACCACAAAGC
* * *
24680 GTCAAACAAGCGTTGGCTAGTCCATATTGGAAGGCTACTGTTCAGAATGA-GTATGAGGCTTTGA
131 ATCAAACAAGCATTGGCTAGTCCATATTGGAAGGCTACTGCTCAGAAT-ACGTATGAGGCTTTGA
* * *
24744 TGAAAAATAAAACTTGGTCTCTAGTGTCATTA-CAGCTGATAGAAGAGCAGTAAATTGTAAATGG
195 TAAAAAATAAAACTTGGTCTCTAGTGTCATTACCAGATGATACAAGAGCAGTAAATTGTAAATGG
*
24808 TTGTTCAAAATTAAGAGAAATGCAGATGGCTCGATTGCTCGTTATAAAACAAGATTAGTAGCAAA
260 TTGTTCAAAATTAAGAGAAATACAGATGGCTCGATTGCTCGTT-TAAAACAAGATTAGTAGCAAA
* *
24873 AGGTTTCCTTCATCAACCAGGTATTGACTTTCATGAGGTGTTTAGTCTTGTTGTTAAACCAGTAA
324 AGGTTTCCTTCAGCAACCAGGTATTGACTTTCATGAGGT-CTTAGTCTTGTTGTTAAACCAGTAA
* * *
24938 ATGTTTGTTTCATTTTGACACT-GCTTTGTCGAAGGGGTAGCAGCTTAGATAGGTTGAGATTAAT
388 ATGTTCGTTTCATTTTGACACTGGCTTTGTAGAAGGGGTAGCAGCTTAGACAGGTTGAGATTAAT
25002 AATGTCTTTCTAAATAGAGTGCTTGAATAAGAAGTCTATATGACTCAACCACCTGGTTTTGAGTT
453 AATGTCTTTCTAAATAGAGTGCTTGAATAAGAAGTCTATATGACTCAACCACCTGGTTTTGAGTT
25067 TGGTGATGATAATCTGGTTTGCAAGTTACATAAGGCCATATATGGTTTAAAACTGGCACCACGTG
518 TGGTGATGATAATCTGGTTTGCAAGTTACATAAGGCCATATATGGTTTAAAACTGGCACCACGTG
*
25132 CTTGGTTTGAGAGTTTAAGAAGTTACATAGAATCTGAAGGCTTTGTGGTAGCCAAGTCTGATTCT
583 CTTGGTTTGAGAGTTTAAGAAGTTACATAGAATCTGAAGGCCTTGTGGTAGCCAAGTCTGATTCT
* * * * *
25197 TCTCTTTTTGTTCGAAAGAGTGAGGATTATTTTTTATATTTACTTGTATATGTTGATGATATAAT
648 ACTCTGTTTATTCAAAAGAGGGAGGATTATTTTTTATATTTACTTGTATATGTTGATGATATAAT
25262 TCTCACTGGTAATAAAGCAAGTAAGGTGCAATTTGTCG
713 TCTCACTGGTAATAAAGCAAGTAAGGTGCAATTTGTCG
25300 A
1 A
25301 AAAGTTGCAT
Statistics
Matches: 709, Mismatches: 38, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
749 70 0.10
750 593 0.84
751 46 0.06
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (750 bp):
ACAACCGATTATGGGAGTTGATTGCAACTCTACATTAAATACTCACCCAATGAAAACAAGGAGTG
TGAGTGGTATTTCAAAACCAAAAATATTTCAAGCTACTGCTTGGATTGATGAAGAACCACAAAGC
ATCAAACAAGCATTGGCTAGTCCATATTGGAAGGCTACTGCTCAGAATACGTATGAGGCTTTGAT
AAAAAATAAAACTTGGTCTCTAGTGTCATTACCAGATGATACAAGAGCAGTAAATTGTAAATGGT
TGTTCAAAATTAAGAGAAATACAGATGGCTCGATTGCTCGTTTAAAACAAGATTAGTAGCAAAAG
GTTTCCTTCAGCAACCAGGTATTGACTTTCATGAGGTCTTAGTCTTGTTGTTAAACCAGTAAATG
TTCGTTTCATTTTGACACTGGCTTTGTAGAAGGGGTAGCAGCTTAGACAGGTTGAGATTAATAAT
GTCTTTCTAAATAGAGTGCTTGAATAAGAAGTCTATATGACTCAACCACCTGGTTTTGAGTTTGG
TGATGATAATCTGGTTTGCAAGTTACATAAGGCCATATATGGTTTAAAACTGGCACCACGTGCTT
GGTTTGAGAGTTTAAGAAGTTACATAGAATCTGAAGGCCTTGTGGTAGCCAAGTCTGATTCTACT
CTGTTTATTCAAAAGAGGGAGGATTATTTTTTATATTTACTTGTATATGTTGATGATATAATTCT
CACTGGTAATAAAGCAAGTAAGGTGCAATTTGTCG
Found at i:26314 original size:15 final size:15
Alignment explanation
Indices: 26296--26325 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
26286 AGTGTATGAT
26296 GTATGCATGTATCTC
1 GTATGCATGTATCTC
26311 GTATGCATGTATCTC
1 GTATGCATGTATCTC
26326 ATGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (15 bp):
GTATGCATGTATCTC
Found at i:26331 original size:13 final size:14
Alignment explanation
Indices: 26298--26331 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
26288 TGTATGATGT
26298 ATGCATGTATCTCG
1 ATGCATGTATCTCG
26312 TATGCATGTATCTC-
1 -ATGCATGTATCTCG
26326 ATGCAT
1 ATGCAT
26332 ATTTGTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
15 13 0.68
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.38
Consensus pattern (14 bp):
ATGCATGTATCTCG
Found at i:29972 original size:2 final size:2
Alignment explanation
Indices: 29965--29992 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29955 AGATGTAAAC
29965 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
29993 GAATTAACGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32012 original size:22 final size:21
Alignment explanation
Indices: 31987--32043 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
31977 AGGAACCATA
31987 TTCGACCCAATGAAA-TTACTAT
1 TTCG-CCCAAT-AAACTTACTAT
*
32009 TTCGCTCAATAAACTTACTAT
1 TTCGCCCAATAAACTTACTAT
**
32030 TTCGCTTAATAAAC
1 TTCGCCCAATAAAC
32044 CTTGATATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 3 0.09
21 25 0.78
22 4 0.12
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (21 bp):
TTCGCCCAATAAACTTACTAT
Found at i:32031 original size:21 final size:21
Alignment explanation
Indices: 31994--32043 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
31984 ATATTCGACC
31994 CAATGAAA-TTACTATTTCGCT
1 CAAT-AAACTTACTATTTCGCT
32015 CAATAAACTTACTATTTCGCT
1 CAATAAACTTACTATTTCGCT
*
32036 TAATAAAC
1 CAATAAAC
32044 CTTGATATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (21 bp):
CAATAAACTTACTATTTCGCT
Found at i:36288 original size:125 final size:125
Alignment explanation
Indices: 36066--36315 Score: 491
Period size: 125 Copynumber: 2.0 Consensus size: 125
36056 GGTATATTTG
36066 AATACATTGGATATATGAATGAGATATGATTGTGACATAAAAGCCTACAGTGCCTTGAGAGTCGT
1 AATACATTGGATATATGAATGAGATATGATTGTGACATAAAAGCCTACAGTGCCTTGAGAGTCGT
36131 AGGTACAATTGGCATGTCATGAGGTGGAGTGATTATATAGTAAATATTTGTACATTCACT
66 AGGTACAATTGGCATGTCATGAGGTGGAGTGATTATATAGTAAATATTTGTACATTCACT
*
36191 AATACATTGGATATATGAATGAGATATGATTGTGACATAAAAGCCTACAGTGCTTTGAGAGTCGT
1 AATACATTGGATATATGAATGAGATATGATTGTGACATAAAAGCCTACAGTGCCTTGAGAGTCGT
36256 AGGTACAATTGGCATGTCATGAGGTGGAGTGATTATATAGTAAATATTTGTACATTCACT
66 AGGTACAATTGGCATGTCATGAGGTGGAGTGATTATATAGTAAATATTTGTACATTCACT
36316 GGTACGTAGC
Statistics
Matches: 124, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
125 124 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (125 bp):
AATACATTGGATATATGAATGAGATATGATTGTGACATAAAAGCCTACAGTGCCTTGAGAGTCGT
AGGTACAATTGGCATGTCATGAGGTGGAGTGATTATATAGTAAATATTTGTACATTCACT
Found at i:44585 original size:42 final size:40
Alignment explanation
Indices: 44539--44656 Score: 94
Period size: 40 Copynumber: 2.9 Consensus size: 40
44529 GTGGCATTTG
*
44539 TAGCGGTGTTTTTAGAACAAACATCGCTAAAGACTCGTACAA
1 TAGCGGTGTTTTTA-AACAAACATCGCTAAAGAAT-GTACAA
** * * **
44581 TAGCGGCATTTTTATAA-AAACGTCGTTAAAGAATGTACTT
1 TAGCGGTGTTTTTA-AACAAACATCGCTAAAGAATGTACAA
* * * **
44621 TAGTGGTGTTTTTATACAAACACCATTAAAGAATGT
1 TAGCGGTGTTTTTAAACAAACATCGCTAAAGAATGT
44657 CATTTAGTGG
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
39 1 0.02
40 31 0.52
41 14 0.23
42 14 0.23
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (40 bp):
TAGCGGTGTTTTTAAACAAACATCGCTAAAGAATGTACAA
Found at i:44790 original size:41 final size:41
Alignment explanation
Indices: 44563--45019 Score: 325
Period size: 41 Copynumber: 11.2 Consensus size: 41
44553 GAACAAACAT
** * * * *
44563 CGCTAAAGACTCGTACAATAGCGGCATTTTTATAAAAACGT
1 CGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGC
* * * *
44604 CGTTAAAGAAT-GTACTTTAGTGGTGTTTTTATACAAACAC
1 CGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGC
** * * *
44644 CATTAAAGAAT-GT-CATTTAGTGGCATTTTTGTACAAACGC
1 CGCTAAAGACTCGTAC-TTTAGTGGCGTTTTTATACAAACGC
* * ** *
44684 CGCTATAA-AGTCGTAATTTAGTGATGTTTTTATTGA-AAATGC
1 CGCTA-AAGACTCGTACTTTAGTGGCGTTTTTA-T-ACAAACGC
* * * *
44726 CGCTATAGACTCGTAATTTAGTGGCATTTTTATATAAACGC
1 CGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGC
* * * **
44767 CACTAAAGAATCGTACTTTAGTGGCGTTTATATACAAATAC
1 CGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGC
* *
44808 CGCTAAAGACTCGTACTTTAGTGGCGTTTATATACAAACGT
1 CGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGC
* * * * * * *
44849 CGTTAAAGACTCATAGTTTAGTGGTGTTTTTATATAAATGT
1 CGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGC
* * * * *
44890 CGCGAAATACT-GTACTTTAGTGGCGTTTTAAGCACAAACGT
1 CGCTAAAGACTCGTACTTTAGTGGCGTTTTTA-TACAAACGC
* * ** * *
44931 CGCTAAATACTTGTACTTTAGTGGCACTTTAATATAAACGC
1 CGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGC
* ** * *
44972 CGCTAAATA-TTATACTTTAATGGCGTTTTAAGTACAAACGC
1 CGCTAAAGACTCGTACTTTAGTGGCGTTTTTA-TACAAACGC
45013 CGCTAAA
1 CGCTAAA
45020 TAATCATTAT
Statistics
Matches: 333, Mismatches: 72, Indels: 22
0.78 0.17 0.05
Matches are distributed among these distances:
39 1 0.00
40 94 0.28
41 188 0.56
42 49 0.15
43 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (41 bp):
CGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGC
Found at i:47558 original size:3 final size:3
Alignment explanation
Indices: 47552--47627 Score: 66
Period size: 3 Copynumber: 24.7 Consensus size: 3
47542 TTCATTTGAA
* * * *
47552 TAT TAT T-T ATAT TAT TAT AAT AAT AAT AAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
47597 TAT ATAT TA- TAT ATAT ATAT TAT TAT TAT TA
1 TAT -TAT TAT TAT -TAT -TAT TAT TAT TAT TA
47628 AAAAATAATT
Statistics
Matches: 66, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
2 3 0.05
3 52 0.79
4 11 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:49257 original size:17 final size:17
Alignment explanation
Indices: 49225--49259 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
49215 TATTATAAAA
**
49225 AAATTATTATTTTATTT
1 AAATTATTATAATATTT
49242 AAATTATTATAATATTT
1 AAATTATTATAATATTT
49259 A
1 A
49260 TTAATATCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AAATTATTATAATATTT
Found at i:51326 original size:8 final size:7
Alignment explanation
Indices: 51302--51343 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
51292 TTTTCATACA
51302 TGCA-TT
1 TGCATTT
51308 TGCATTT
1 TGCATTT
51315 TGCATCTT
1 TGCAT-TT
51323 TGCATTT
1 TGCATTT
* *
51330 TTCATTG
1 TGCATTT
51337 TGCATTT
1 TGCATTT
51344 ATACTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:51326 original size:15 final size:14
Alignment explanation
Indices: 51302--51343 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
51292 TTTTCATACA
51302 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
51315 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
51330 TTCATTGTGCATTT
1 TGCATTTTGCATTT
51344 ATACTCTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:57686 original size:54 final size:54
Alignment explanation
Indices: 57604--57769 Score: 271
Period size: 54 Copynumber: 3.1 Consensus size: 54
57594 AATGATTGAG
*
57604 ACATCTTG-GCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGA
1 ACATC-TGAGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGA
*
57658 ACATCTGAGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACTA
1 ACATCTGAGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGA
* * *
57712 ACATCTGAGCAGAAGCCATAGGAAAGGATGAATGCGCTGTCAAATGTTTTACGA
1 ACATCTGAGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGA
57766 ACAT
1 ACAT
57770 GCTATTCTGA
Statistics
Matches: 105, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
53 2 0.02
54 103 0.98
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.25
Consensus pattern (54 bp):
ACATCTGAGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGA
Found at i:58166 original size:22 final size:22
Alignment explanation
Indices: 58138--58211 Score: 121
Period size: 22 Copynumber: 3.4 Consensus size: 22
58128 TACACTCTTC
*
58138 AAAGATGATAGATTCCCTTTTT
1 AAAGATGACAGATTCCCTTTTT
58160 AAAGATGACAGATTCCCTTTTT
1 AAAGATGACAGATTCCCTTTTT
* *
58182 AAAGATGACAGATTCTCTTTTC
1 AAAGATGACAGATTCCCTTTTT
58204 AAAGATGA
1 AAAGATGA
58212 AAGCTTTATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
AAAGATGACAGATTCCCTTTTT
Found at i:58809 original size:113 final size:114
Alignment explanation
Indices: 58611--58895 Score: 441
Period size: 113 Copynumber: 2.5 Consensus size: 114
58601 TTAGCAAAGC
*
58611 TCAAATCCATCACTTGATGGATCAGCATTACCAG-GTCGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCATTACCAGAGTAGAGTTCATAATGAGAAGAACTCATCTG
*
58675 AAGAAGGAATAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGA
66 AAGAAGGAAAAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGA
* * * *
58724 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTTATCTG
1 TCAAATCCATCACTTGATGGATCAGCATTACCAGAGTAGAGTTCATAATGAGAAGAACTCATCTG
*
58788 AAGAAGGAAAAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGT
66 AAGAAGGAAAAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGA
* * * * *
58837 TTAAATTCATCATTTGATGGATCAACATTGCCA-AGTAGAGTTCATAATGAGAAGAACTC
1 TCAAATCCATCACTTGATGGATCAGCATTACCAGAGTAGAGTTCATAATGAGAAGAACTC
58896 GTTATCTGAA
Statistics
Matches: 155, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
112 2 0.01
113 152 0.98
114 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (114 bp):
TCAAATCCATCACTTGATGGATCAGCATTACCAGAGTAGAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAAAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGA
Found at i:59008 original size:95 final size:93
Alignment explanation
Indices: 58821--59009 Score: 238
Period size: 95 Copynumber: 2.0 Consensus size: 93
58811 TGAGAAGAGC
* * *
58821 TTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAAGTAGAGTTCATAATG
1 TTGTTCAACCTTTTATTTAAATTCATCATTCGATGGATCAACATTCCCAAGTAGAGTTCATAATG
58886 AGAAGAACTCGTTATCTGAAAAAGAAGAAT
66 AGAAGAACTC--TATCTGAAAAAGAAGAAT
* ** *
58916 TTGTTCAACCTTTTATTTGAATTCATCATTCGATGGATCATTA-TCCCTAGTGAAAGAGTTCATA
1 TTGTTCAACCTTTTATTTAAATTCATCATTCGATGGATCAACATTCCCAAGT---AGAGTTCATA
*
58980 ATGAGAAGAACTC-ATCTGAAGAAGGAAGAA
63 ATGAGAAGAACTCTATCTGAA-AAAGAAGAA
59010 GAAGTTCATA
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
94 13 0.16
95 46 0.56
97 23 0.28
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (93 bp):
TTGTTCAACCTTTTATTTAAATTCATCATTCGATGGATCAACATTCCCAAGTAGAGTTCATAATG
AGAAGAACTCTATCTGAAAAAGAAGAAT
Found at i:59218 original size:212 final size:211
Alignment explanation
Indices: 58731--59580 Score: 914
Period size: 212 Copynumber: 4.0 Consensus size: 211
58721 TGATCAAATC
* ** * *
58731 CATCACTT-GATGGATCAGCTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTTATCTGAAGAAG
1 CATCA-TTCGATGGATCAGCATCCCCAGTGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAG
* * * * *
58794 GAAAAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGAT
65 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACTTGATGGAT
* ***
58859 CAACATTGCCA-AGTAGAGTTCATAATGAGAAGAACTCGTTATCTGAA-AAAGAAGAATTTGTTC
130 CAACATTGCCAGAG-AGAGTTCATAATGAGAAGAACTC---ATCTGAAGAAGGAAGAAGAAGTTC
* ***
58922 A-ACCT----TTTATTTGAATT
191 ATA-ATGAGAAGAATTTGAATT
** *
58939 CATCATTCGATGGATCATTATCCCTAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 CATCATTCGATGGATCAGCATCCCCAGTG-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAAG
*
59004 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGAT
65 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACTTGATGGAT
* * * * *
59069 CAACTTTTCCAGAAAGAGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAATTCATAA
130 CAACATTGCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
59134 TGAGAAGAATTTGAATT
195 TGAGAAGAATTTGAATT
* *
59151 CATCATTTGATGGATCAGCATCCCCAGTGAAAGAGTTCATAATGAGTAGAACTCATCTGAAGAAG
1 CATCATTCGATGGATCAGCATCCCCAGTG-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAAG
* * **
59216 GAAGAACAAGTTCATAATGAGAAGAACTTGTTCAA-CTGTTCGCTTGAATTCATCA-TTCGATGG
65 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT-TTTGCTCAAATTCATCACTT-GATGG
* * * * *
59279 ATCAGCATTGCCAGGGCGAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCAT
128 ATCAACATTGCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
59344 AATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
193 AAT--G-AGAA---G---AA-----T--TTGAATT
** ** * *
59379 CATCATTCGATGGATCAGCATTGCCAG-GGCGAGTTCATAATAAGAAGAACTCATCTGAAGAAAG
1 CATCATTCGATGGATCAGCATCCCCAGTGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * * * *
59443 AAGAAGTAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCGAATTCATCACTCGATGGATC
66 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACTTGATGGATC
* * *
59508 AACTTTTCCAGAGAGAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAAT
131 AACATTGCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
59573 GAGAAGAA
196 GAGAAGAA
59581 CTTGTTCAAT
Statistics
Matches: 542, Mismatches: 70, Indels: 51
0.82 0.11 0.08
Matches are distributed among these distances:
207 9 0.02
208 32 0.06
209 3 0.01
210 121 0.22
211 5 0.01
212 179 0.33
214 1 0.00
215 4 0.01
217 2 0.00
218 1 0.00
220 1 0.00
221 2 0.00
223 4 0.01
224 1 0.00
226 143 0.26
227 3 0.01
228 31 0.06
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (211 bp):
CATCATTCGATGGATCAGCATCCCCAGTGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACTTGATGGATC
AACATTGCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
GAGAAGAATTTGAATT
Found at i:59597 original size:113 final size:113
Alignment explanation
Indices: 59144--59595 Score: 670
Period size: 113 Copynumber: 4.0 Consensus size: 113
59134 TGAGAAGAAT
* ** * * *
59144 TTGAATTCATCATTTGATGGATCAGCATCCCCAGTGAAAGAGTTCATAATGAGTAGAACTCATCT
1 TTGAATTCATCATTCGATGGATCAGCATTGCCAG-G-GAGAGTTCATAATAAGAAGAACTCATCT
* * * *
59209 GAAGAAGGAAGAACAAGTTCATAATGAGAAGAACTTGTTCAACTGTTCGC
64 GAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
*
59259 TTGAATTCATCATTCGATGGATCAGCATTGCCAGGGCGAGTTCATAATAAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAGCATTGCCAGGGAGAGTTCATAATAAGAAGAACTCATCTGA
59324 AGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
66 AGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
*
59372 TTGAATTCATCATTCGATGGATCAGCATTGCCAGGGCGAGTTCATAATAAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAGCATTGCCAGGGAGAGTTCATAATAAGAAGAACTCATCTGA
* *
59437 AGAAAGAAGAAGTAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGC
66 AGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
* * * * * * * *
59485 TCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACACATCTGA
1 TTGAATTCATCATTCGATGGATCAGCATTGCCAGGGAGAGTTCATAATAAGAAGAACTCATCTGA
*
59550 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTT
66 AGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT
59596 GCATGATTCT
Statistics
Matches: 311, Mismatches: 25, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
113 274 0.88
114 6 0.02
115 31 0.10
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (113 bp):
TTGAATTCATCATTCGATGGATCAGCATTGCCAGGGAGAGTTCATAATAAGAAGAACTCATCTGA
AGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
Found at i:59863 original size:3 final size:3
Alignment explanation
Indices: 59857--59942 Score: 99
Period size: 3 Copynumber: 28.7 Consensus size: 3
59847 TTTATTTGAA
*
59857 TAT TAT T-T ATAT TAT TAT TAT T-T ATAA TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
59902 TAT TAT TA- TAT ATAT TAT TA- TAT ATAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT -TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
59943 AAATAATAAT
Statistics
Matches: 73, Mismatches: 2, Indels: 16
0.80 0.02 0.18
Matches are distributed among these distances:
2 6 0.08
3 60 0.82
4 7 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:59886 original size:18 final size:16
Alignment explanation
Indices: 59857--59940 Score: 124
Period size: 15 Copynumber: 5.6 Consensus size: 16
59847 TTTATTTGAA
59857 TATTATT-TATATTAT
1 TATTATTATATATTAT
*
59872 TATTATT-TATAATAT
1 TATTATTATATATTAT
59887 TATTATTAT-TATTAT
1 TATTATTATATATTAT
59902 TATTATTATATA-TAT
1 TATTATTATATATTAT
59917 TATTA-TATATATTAT
1 TATTATTATATATTAT
59932 TATTATTAT
1 TATTATTAT
59941 TAAAATAATA
Statistics
Matches: 63, Mismatches: 2, Indels: 7
0.88 0.03 0.10
Matches are distributed among these distances:
14 6 0.10
15 51 0.81
16 6 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTATTATATATTAT
Found at i:61581 original size:17 final size:17
Alignment explanation
Indices: 61556--61588 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
61546 AAATTAAATA
61556 TTATAAAAATTATTATT
1 TTATAAAAATTATTATT
*
61573 TTATTAAAATTATTAT
1 TTATAAAAATTATTAT
61589 AATATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATAAAAATTATTATT
Found at i:61594 original size:17 final size:17
Alignment explanation
Indices: 61561--61594 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
61551 AAATATTATA
**
61561 AAAATTATTATTTTATT
1 AAAATTATTATAATATT
61578 AAAATTATTATAATATT
1 AAAATTATTATAATATT
61595 TATTAATATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAAATTATTATAATATT
Found at i:62705 original size:43 final size:43
Alignment explanation
Indices: 62668--63026 Score: 438
Period size: 43 Copynumber: 8.4 Consensus size: 43
62658 CAAAATTGCT
* * *
62668 GCTATAGATTTAACCTTTTGCGGCGTTTGTGTCCAAAAACACC
1 GCTATAGATCTGACCTTTTGCGGCGTTTGTGTCCAAAAACGCC
* *
62711 GCTATAGATCTGACCTTTTGCGGCATTTGTGTCCAAAAATGCC
1 GCTATAGATCTGACCTTTTGCGGCGTTTGTGTCCAAAAACGCC
* *
62754 GCTATAGATCTGACCTTTTGCGGCGTTTGTGTCAAAAAACACC
1 GCTATAGATCTGACCTTTTGCGGCGTTTGTGTCCAAAAACGCC
* *
62797 GCTATAGATATGACCTTTTGCGGCGTTTGT-TCCAAAATCGCC
1 GCTATAGATCTGACCTTTTGCGGCGTTTGTGTCCAAAAACGCC
** * * **
62839 GCTATAGATCTGACCTTTTGTAGCGTTTGTATCAAAAAACGTT
1 GCTATAGATCTGACCTTTTGCGGCGTTTGTGTCCAAAAACGCC
* * *
62882 GCT-TAATATCTGACTTTTTGCGGCGTTTGTATCCAAAAACGCC
1 GCTAT-AGATCTGACCTTTTGCGGCGTTTGTGTCCAAAAACGCC
* * * *
62925 GCTAAATATCTAACCTTTTGCGGCGTTTGT-TCCATAAACGCC
1 GCTATAGATCTGACCTTTTGCGGCGTTTGTGTCCAAAAACGCC
* * *
62967 GCTATAGATCTCGACCTTTTGCAGCATTTGT-TCAAAAAACGCC
1 GCTATAGATCT-GACCTTTTGCGGCGTTTGTGTCCAAAAACGCC
63010 GCTATAGATCTTGACCT
1 GCTATAGATC-TGACCT
63027 AGGCGGCATT
Statistics
Matches: 273, Mismatches: 38, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
42 57 0.21
43 215 0.79
44 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (43 bp):
GCTATAGATCTGACCTTTTGCGGCGTTTGTGTCCAAAAACGCC
Found at i:62877 original size:128 final size:126
Alignment explanation
Indices: 62668--63026 Score: 468
Period size: 128 Copynumber: 2.8 Consensus size: 126
62658 CAAAATTGCT
* * *
62668 GCTATAGATTTAACCTTTTGCGGCGTTTGTGTCCAAAAACACCGCTATAGATCTGACCTTTTGCG
1 GCTATAGATATAACCTTTTGCGGCGTTTGT-TCC-AAAACGCCGCTATAGATCTGACCTTTTGCA
* * *
62733 GCATTTGTGTCCAAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTGTCAAAAAACACC
64 GCATTTGT-TCAAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTATCAAAAAACACC
* *
62797 GCTATAGATATGACCTTTTGCGGCGTTTGTTCCAAAATCGCCGCTATAGATCTGACCTTTTGTAG
1 GCTATAGATATAACCTTTTGCGGCGTTTGTTCCAAAA-CGCCGCTATAGATCTGACCTTTTGCAG
* ** * * * *
62862 CGTTTGTATCAAAAAACGTTGCT-TAATATCTGACTTTTTGCGGCGTTTGTATCCAAAAACGCC
65 CATTTGT-TCAAAAAACGCCGCTAT-AGATCTGACCTTTTGCGGCGTTTGTATCAAAAAACACC
* * *
62925 GCTAAATATCTAACCTTTTGCGGCGTTTGTTCCATAAACGCCGCTATAGATCTCGACCTTTTGCA
1 GCTATAGATATAACCTTTTGCGGCGTTTGTTCCA-AAACGCCGCTATAGATCT-GACCTTTTGCA
62990 GCATTTGTTCAAAAAACGCCGCTATAGATCTTGACCT
64 GCATTTGTTCAAAAAACGCCGCTATAGATC-TGACCT
63027 AGGCGGCATT
Statistics
Matches: 198, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
127 5 0.03
128 139 0.70
129 54 0.27
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (126 bp):
GCTATAGATATAACCTTTTGCGGCGTTTGTTCCAAAACGCCGCTATAGATCTGACCTTTTGCAGC
ATTTGTTCAAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTATCAAAAAACACC
Found at i:72684 original size:14 final size:15
Alignment explanation
Indices: 72665--72695 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
72655 CATAAGGTAT
72665 TTTTTTTAT-TTAAA
1 TTTTTTTATCTTAAA
72679 TTTTTTTATCTTAAA
1 TTTTTTTATCTTAAA
72694 TT
1 TT
72696 AATTAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTTTATCTTAAA
Found at i:72955 original size:15 final size:15
Alignment explanation
Indices: 72933--72965 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
72923 TCCAGAAGGT
72933 AATTTTTTTAT-TTA
1 AATTTTTTTATCTTA
72947 AATTTTTTTATCTTA
1 AATTTTTTTATCTTA
72962 AATT
1 AATT
72966 AATTAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
AATTTTTTTATCTTA
Found at i:73045 original size:270 final size:269
Alignment explanation
Indices: 72565--73104 Score: 992
Period size: 270 Copynumber: 2.0 Consensus size: 269
72555 ACTGAAATTG
72565 GTGGATGTATAATGTTATTACAATTGTGGGCATGACACACAATTCCATGGTTAACATCGATTAGC
1 GTGGATGTATAATGTTATTACAATTGTGGGCATGACACACAATTCCATGGTTAACATCGATTAGC
* *
72630 TGAACTGCAGTTGACTTTCCTCTTACATAAGGTATTTTTTTTATTTAAATTTTTTTATCTTAAAT
66 TGAACTGCAGTTGACTTTCCTCTTACAGAAGGTAATTTTTTTATTTAAATTTTTTTATCTTAAAT
*
72695 TAATTAAAAACTATTTTGTAAATGAAAAATAATTAGAGAATTTTATTTTGATTGGTATACATATG
131 TAATTAAAAACTATTATGTAAATGAAAAATAATTAGAGAATTTTATTTTGATTGGTATACATATG
72760 GAGGCATAAAATAGAAGGAACAGGGTTGGCGTACAATAATGTGAAAGAGTTTAGGTTTAAGATGG
196 GAGGCATAAAATAGAAGGAACAGGGTTGGCGTACAATAATGTGAAAGAGTTTAGGTTTAAGATGG
72825 AAATCAAAT
261 AAATCAAAT
*
72834 GTGGATGTATAATGTTATTACAATTGTGGGCATGACACAGAATTCCATGGTTAACATCGATTAGC
1 GTGGATGTATAATGTTATTACAATTGTGGGCATGACACACAATTCCATGGTTAACATCGATTAGC
*
72899 TGAACTGCAGTTGACTTTCCTCTTTCCAGAAGGTAATTTTTTTATTTAAATTTTTTTATCTTAAA
66 TGAACTGCAGTTGACTTTCCTC-TTACAGAAGGTAATTTTTTTATTTAAATTTTTTTATCTTAAA
72964 TTAATTAAAGAA-TATTATGTAAATGAAAAATAATTAGAGAATTTTATTTTGATTGGTATACATA
130 TTAATTAAA-AACTATTATGTAAATGAAAAATAATTAGAGAATTTTATTTTGATTGGTATACATA
*
73028 TGGAGGCATAAAATAGAAGGAACAGGGTTGGTGTACAATAATGTGAAAGAGTTTAGGTTTAAGAT
194 TGGAGGCATAAAATAGAAGGAACAGGGTTGGCGTACAATAATGTGAAAGAGTTTAGGTTTAAGAT
*
73093 GGACATCAAAT
259 GGAAATCAAAT
73104 G
1 G
73105 CAAAGTTGAG
Statistics
Matches: 262, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
269 86 0.33
270 174 0.66
271 2 0.01
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (269 bp):
GTGGATGTATAATGTTATTACAATTGTGGGCATGACACACAATTCCATGGTTAACATCGATTAGC
TGAACTGCAGTTGACTTTCCTCTTACAGAAGGTAATTTTTTTATTTAAATTTTTTTATCTTAAAT
TAATTAAAAACTATTATGTAAATGAAAAATAATTAGAGAATTTTATTTTGATTGGTATACATATG
GAGGCATAAAATAGAAGGAACAGGGTTGGCGTACAATAATGTGAAAGAGTTTAGGTTTAAGATGG
AAATCAAAT
Found at i:74222 original size:40 final size:40
Alignment explanation
Indices: 74174--74249 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
74164 AATGAAATTT
74174 ATATTTAAATATTTAA-ATAAAAATTAAAGATTTAATTTAA
1 ATATTTAAATA-TTAAGATAAAAATTAAAGATTTAATTTAA
* *
74214 ATATTTAAATATTAAGATAAAATTTAAATATTTAAT
1 ATATTTAAATATTAAGATAAAAATTAAAGATTTAAT
74250 CATTATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (40 bp):
ATATTTAAATATTAAGATAAAAATTAAAGATTTAATTTAA
Found at i:74273 original size:24 final size:24
Alignment explanation
Indices: 74246--74536 Score: 138
Period size: 24 Copynumber: 11.8 Consensus size: 24
74236 TTTAAATATT
74246 TAATCATTATTAAATCATTATTAG
1 TAATCATTATTAAATCATTATTAG
* *
74270 TAATCATTATT-AGTAATTATTA-
1 TAATCATTATTAAATCATTATTAG
* *
74292 TAATTTCATTATTAATAATCATTACTAAAT
1 TAA--TCATTATT-A-AATCATTA-T-TAG
* * * * *
74322 TAATTAGTATCAAATCATTAAATAT
1 TAATCATTATTAAATCATT-ATTAG
*
74347 TAAT-A--A-TAAACCATTATTAG
1 TAATCATTATTAAATCATTATTAG
*
74367 TAATCA-TATTAAATCATTAGTA-
1 TAATCATTATTAAATCATTATTAG
*
74389 TCAAATCATTAAATATCAAATCATTAAATTAA
1 T--AATCATT--AT-T-AAATCATT--ATTAG
*
74421 TAATAATTATTAAATCATTATTAG
1 TAATCATTATTAAATCATTATTAG
* *
74445 TAATC-GTATTAAATCATTAATA-
1 TAATCATTATTAAATCATTATTAG
** *
74467 TCAAATCATTA--AATATTTTTAAATTAA
1 T--AATCATTATTAA-ATCATT--ATTAG
* *
74494 TAATCATTACTATATCATTATTAG
1 TAATCATTATTAAATCATTATTAG
74518 TAATCATTATTAAATCATT
1 TAATCATTATTAAATCATT
74537 GGTATCACAT
Statistics
Matches: 204, Mismatches: 32, Indels: 62
0.68 0.11 0.21
Matches are distributed among these distances:
20 7 0.03
21 8 0.04
22 7 0.03
23 37 0.18
24 62 0.30
25 17 0.08
26 22 0.11
27 13 0.06
28 9 0.04
29 9 0.04
30 9 0.04
31 3 0.01
32 1 0.00
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (24 bp):
TAATCATTATTAAATCATTATTAG
Found at i:74396 original size:14 final size:14
Alignment explanation
Indices: 74372--74415 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
74362 ATTAGTAATC
*
74372 ATATTAAATCATTA
1 ATATCAAATCATTA
*
74386 GTATCAAATCATTAA
1 ATATCAAATCATT-A
74401 ATATCAAATCATTA
1 ATATCAAATCATTA
74415 A
1 A
74416 ATTAATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (14 bp):
ATATCAAATCATTA
Found at i:74407 original size:15 final size:15
Alignment explanation
Indices: 74372--74417 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
74362 ATTAGTAATC
*
74372 ATATTAAATCATT-A
1 ATATCAAATCATTAA
*
74386 GTATCAAATCATTAA
1 ATATCAAATCATTAA
74401 ATATCAAATCATTAA
1 ATATCAAATCATTAA
74416 AT
1 AT
74418 TAATAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.37
Consensus pattern (15 bp):
ATATCAAATCATTAA
Found at i:74455 original size:78 final size:78
Alignment explanation
Indices: 74329--74554 Score: 283
Period size: 78 Copynumber: 3.0 Consensus size: 78
74319 AATTAATTAG
*
74329 TATCAAATCATTAAA-T-AT--TAA-TAATAAACCATTATTAGTAATCATATTAAATCATTAGTA
1 TATCAAATCATTAAATTAATAATAATTAATAAATCATTATTAGTAATCATATTAAATCATTAGTA
74389 TCAAATCATTAAA
66 TCAAATCATTAAA
* * *
74402 TATCAAATCATTAAATTAATAATAATTATTAAATCATTATTAGTAATCGTATTAAATCATTAATA
1 TATCAAATCATTAAATTAATAATAATTAATAAATCATTATTAGTAATCATATTAAATCATTAGTA
74467 TCAAATCATTAAA
66 TCAAATCATTAAA
* * * * *
74480 TAT----T-TTTAAATTAATAATCATTACTATATCATTATTAGTAATCATTATTAAATCATTGGT
1 TATCAAATCATTAAATTAATAATAATTAATAAATCATTATTAGTAATCA-TATTAAATCATTAGT
*
74540 ATCACATCATTAAA
65 ATCAAATCATTAAA
74554 T
1 T
74555 TATTTTATTA
Statistics
Matches: 135, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
73 50 0.37
74 29 0.21
75 2 0.01
77 3 0.02
78 51 0.38
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (78 bp):
TATCAAATCATTAAATTAATAATAATTAATAAATCATTATTAGTAATCATATTAAATCATTAGTA
TCAAATCATTAAA
Found at i:74525 original size:13 final size:12
Alignment explanation
Indices: 74242--74536 Score: 102
Period size: 11 Copynumber: 24.1 Consensus size: 12
74232 AAAATTTAAA
74242 TATT-TAATCAT
1 TATTATAATCAT
74253 TATTA-AATCAT
1 TATTATAATCAT
74264 TATTAGTAATCAT
1 TATTA-TAATCAT
*
74277 TATTAGTAATTAT
1 TATTA-TAATCAT
* *
74290 TATAAT-TTCAT
1 TATTATAATCAT
74301 TATTAATAATCAT
1 TATT-ATAATCAT
* *
74314 TACTA-AATTAAT
1 TATTATAA-TCAT
*
74326 TAGTATCAA--AT
1 TATTAT-AATCAT
*
74337 CATTA-AAT-AT
1 TATTATAATCAT
* *
74347 TAATAATAAACCAT
1 T-ATTAT-AATCAT
74361 TATTAGTAATCA-
1 TATTA-TAATCAT
74373 TATTA-AATCAT
1 TATTATAATCAT
*
74384 TAGTATCAAATCAT
1 TATTAT--AATCAT
*
74398 TAAATATCAAATCAT
1 T-ATTAT--AATCAT
*
74413 TAAATTAATAATAAT
1 T--ATT-ATAATCAT
74428 TATTA-AATCAT
1 TATTATAATCAT
*
74439 TATTAGTAATC-G
1 TATTA-TAATCAT
74451 TATTA-AATCAT
1 TATTATAATCAT
*
74462 TAATATCAAATCAT
1 TATTAT--AATCAT
* **
74476 TA-AAT-ATTTT
1 TATTATAATCAT
74486 TAAATTAATAATCAT
1 T--ATT-ATAATCAT
*
74501 TACTAT-ATCAT
1 TATTATAATCAT
74512 TATTAGTAATCAT
1 TATTA-TAATCAT
74525 TATTA-AATCAT
1 TATTATAATCAT
74536 T
1 T
74537 GGTATCACAT
Statistics
Matches: 218, Mismatches: 32, Indels: 68
0.69 0.10 0.21
Matches are distributed among these distances:
9 2 0.01
10 15 0.07
11 65 0.30
12 26 0.12
13 59 0.27
14 23 0.11
15 23 0.11
16 3 0.01
17 2 0.01
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (12 bp):
TATTATAATCAT
Found at i:74985 original size:13 final size:11
Alignment explanation
Indices: 74935--75052 Score: 70
Period size: 11 Copynumber: 10.5 Consensus size: 11
74925 TTATCAAATC
74935 ATTAAAT-ATT
1 ATTAAATCATT
74945 ATTAAAT--TT
1 ATTAAATCATT
*
74954 -GTAAAT-ATT
1 ATTAAATCATT
74963 ATTAAATCATT
1 ATTAAATCATT
74974 ATTAGTAATCATT
1 ATTA--AATCATT
74987 ATTAAATCATT
1 ATTAAATCATT
*
74998 AGTTTCAACTCATT
1 A--TT-AAATCATT
*
75012 A--AATTATTATT
1 ATTAA--ATCATT
75023 ATTAAATCATTAGT
1 ATTAAATCA-T--T
75037 ATTAAATCATT
1 ATTAAATCATT
75048 ATTAA
1 ATTAA
75053 TAAATCATAT
Statistics
Matches: 87, Mismatches: 6, Indels: 29
0.71 0.05 0.24
Matches are distributed among these distances:
8 5 0.06
9 6 0.07
10 12 0.14
11 29 0.33
12 1 0.01
13 16 0.18
14 18 0.21
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (11 bp):
ATTAAATCATT
Found at i:74998 original size:21 final size:20
Alignment explanation
Indices: 74916--75000 Score: 72
Period size: 18 Copynumber: 4.2 Consensus size: 20
74906 ATCAAATTAG
*
74916 TAGTAATCATTATCAAATCAT
1 TAGTAAT-ATTATTAAATCAT
74937 TA--AATATTATTAAAT--T
1 TAGTAATATTATTAAATCAT
74953 T-GTAAATATTATTAAATCATTAT
1 TAGT-AATATTATTAAATC---AT
74976 TAGTAATCATTATTAAATCAT
1 TAGTAAT-ATTATTAAATCAT
74997 TAGT
1 TAGT
75001 TTCAACTCAT
Statistics
Matches: 53, Mismatches: 1, Indels: 20
0.72 0.01 0.27
Matches are distributed among these distances:
16 2 0.04
18 22 0.42
19 3 0.06
21 8 0.15
23 5 0.09
24 13 0.25
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.45
Consensus pattern (20 bp):
TAGTAATATTATTAAATCAT
Found at i:75026 original size:14 final size:14
Alignment explanation
Indices: 75009--75060 Score: 77
Period size: 14 Copynumber: 3.7 Consensus size: 14
74999 GTTTCAACTC
*
75009 ATTAAATTATTATT
1 ATTAAATCATTATT
*
75023 ATTAAATCATTAGT
1 ATTAAATCATTATT
75037 ATTAAATCATTATT
1 ATTAAATCATTATT
*
75051 AATAAATCAT
1 ATTAAATCAT
75061 ATCATTAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (14 bp):
ATTAAATCATTATT
Found at i:75348 original size:14 final size:14
Alignment explanation
Indices: 75284--75350 Score: 70
Period size: 14 Copynumber: 5.1 Consensus size: 14
75274 AGTTGTAATC
75284 ATTATTAAATCATT
1 ATTATTAAATCATT
*
75298 ATTAGT--A--ATT
1 ATTATTAAATCATT
*
75308 ATTATTAAATCAAT
1 ATTATTAAATCATT
**
75322 AACATTAAATCATT
1 ATTATTAAATCATT
75336 ATTATTAAATCATT
1 ATTATTAAATCATT
75350 A
1 A
75351 AATTCATTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
10 8 0.20
12 2 0.05
14 31 0.76
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.45
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:78329 original size:45 final size:45
Alignment explanation
Indices: 78278--78365 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
78268 TTTCCTCTAC
* *
78278 AACCACCAACCACTAACCTACTCGA-GTTATTAAAGGATAATTATT
1 AACCACCAACCACCAACCTA-TCGATATTATTAAAGGATAATTATT
* *
78323 AACCACCAACCACCAACCTATTGATATTATTAACGGATAATTA
1 AACCACCAACCACCAACCTATCGATATTATTAAAGGATAATTA
78366 ATGCTTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 3 0.08
45 35 0.92
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (45 bp):
AACCACCAACCACCAACCTATCGATATTATTAAAGGATAATTATT
Found at i:80036 original size:18 final size:18
Alignment explanation
Indices: 80015--80049 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
80005 CCAGTAATTT
*
80015 TATTCCCGCTGATAATCC
1 TATTCCCACTGATAATCC
*
80033 TATTCCCACTGGTAATC
1 TATTCCCACTGATAATC
80050 TTACATTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.31, G:0.11, T:0.34
Consensus pattern (18 bp):
TATTCCCACTGATAATCC
Found at i:81092 original size:12 final size:12
Alignment explanation
Indices: 81075--81108 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
81065 AATTTCCCAT
81075 GGATTAGAATTG
1 GGATTAGAATTG
81087 GGATTAGAATTG
1 GGATTAGAATTG
**
81099 ATATTAGAAT
1 GGATTAGAAT
81109 GATTCTACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.35
Consensus pattern (12 bp):
GGATTAGAATTG
Found at i:82508 original size:38 final size:39
Alignment explanation
Indices: 82421--82708 Score: 162
Period size: 38 Copynumber: 7.7 Consensus size: 39
82411 TTTCTCTTTA
* * *
82421 AAACAAAAATTTTGTCTC-CTTTGAGATAATTTT-TCTTG
1 AAACAAAATTTTTATCTCAC-TTGAGATAATTTTCTCTCG
*
82459 GAACAAAAATTTTCTATCTCACTTGAGATAATTTTC-CTC-
1 AAAC-AAAATTTT-TATCTCACTTGAGATAATTTTCTCTCG
* *
82498 AAA-AATAATTTTGT-T-TCACTTGAGACAA-ATTCTCTCG
1 AAACAA-AATTTT-TATCTCACTTGAGATAATTTTCTCTCG
* *
82535 AAACAAAATTTTTATCTCACTTGAGAT-ATTTTTTCTAG
1 AAACAAAATTTTTATCTCACTTGAGATAATTTTCTCTCG
** * * * * * *
82573 -AA-GTAATTTGTGTCTCACTCGAG-TCAGTTTCTCTCA
1 AAACAAAATTTTTATCTCACTTGAGATAATTTTCTCTCG
** * * * *
82609 AAACAAAAAATTTATCTCGCTTGAGATAGTTTTCCCTTG
1 AAACAAAATTTTTATCTCACTTGAGATAATTTTCTCTCG
* * * *
82648 ----AAAATTTTCATCTCACTCGAGATTA-TTTCACTCG
1 AAACAAAATTTTTATCTCACTTGAGATAATTTTCTCTCG
*
82682 AAACAAAA-TTTCATCTCACTTGAGATA
1 AAACAAAATTTTTATCTCACTTGAGATA
82709 TTTCCCTTTA
Statistics
Matches: 185, Mismatches: 46, Indels: 39
0.69 0.17 0.14
Matches are distributed among these distances:
34 7 0.04
35 22 0.12
36 39 0.21
37 35 0.19
38 45 0.24
39 16 0.09
40 20 0.11
41 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (39 bp):
AAACAAAATTTTTATCTCACTTGAGATAATTTTCTCTCG
Found at i:82591 original size:74 final size:72
Alignment explanation
Indices: 82428--83138 Score: 316
Period size: 74 Copynumber: 9.9 Consensus size: 72
82418 TTAAAACAAA
* * * * * *
82428 AATTTTGTCTC-CTTTGAGATAATTTTTCTTGGAACAAAAATTTTCTATCTCACTTGAGATAATT
1 AATTTTGTCTCAC-TTGAGACAGTTTCTCTCGAAAC-AAAA-TTT-TATCTCACTTGAGATATTT
* * *
82492 TTCCTCAAAAAT
62 TTTCT-AGAAGT
* **
82504 AATTTTGTTTCACTTGAGACAAATTCTCTCGAAACAAAATTTTTATCTCACTTGAGATATTTTTT
1 AATTTTGTCTCACTTGAGACAGTTTCTCTCGAAACAAAA-TTTTATCTCACTTGAGATATTTTTT
82569 CTAGAAGT
65 CTAGAAGT
* * * * *
82577 AATTTGTGTCTCACTCGAGTCAGTTTCTCTCAAAACAAAAAATTTATCTCGCTTGAGATAGTTTT
1 AATTT-TGTCTCACTTGAGACAGTTTCTCTCGAAAC-AAAATTTTATCTCACTTGAGATA-TTTT
** *
82642 CCCTTGAA--
63 TTCTAGAAGT
* * * * *
82650 AATTTTCATCTCACTCGAGATTA-TTTCACTCGAAACAAAATTTCATCTCACTTGAGATATTTCC
1 AATTTT-GTCTCACTTGAGA-CAGTTTCTCTCGAAACAAAATTTTATCTCACTTGAGATATTT--
* *
82714 CTT-TAAAAGT
62 TTTCTAGAAGT
* * * *
82724 --TTTATCGTCTCACTTGATACAGTTTCCCTTGAAACCAAAATTTCATCTCACTTGAGATATTTT
1 AATTT-T-GTCTCACTTGAGACAGTTTCTCTCGAAA-CAAAATTTTATCTCACTTGAGATATTTT
* *
82787 CTCTTGAA--
63 TTCTAGAAGT
* * ** * * * *
82795 ATTTTTCATCTCACTCAAGACATTTTCTCTC-AAAAAAAAATTCATCTCACTTGAGATATTTTTT
1 AATTTT-GTCTCACTTGAGACAGTTTCTCTCGAAACAAAATTTTATCTCACTTGAGATA-TTTTT
*
82859 TCTTGGAA--
64 TC-TAGAAGT
* * * * * * *
82867 ATTTTTGTCTCGCTTGAGACAGATTCTCT-GAAA-ATAGAGTTTTATCTCGCTCGAGATAGTTTT
1 AATTTTGTCTCACTTGAGACAGTTTCTCTCGAAACA-A-AATTTTATCTCACTTGAGATATTTTT
* * **
82930 CCTTAAAACC
64 TC-TAGAAGT
* **** * * * *
82940 AATTTTGTCTCACTTGAGATAGTTT-TCTCG-AA-TTTTTTTTATCACACTCGAGATATCTTCTC
1 AATTTTGTCTCACTTGAGACAGTTTCTCTCGAAACAAAATTTTATCTCACTTGAGATATTTTTTC
*
83002 GT-GAA-A
66 -TAGAAGT
** * * * * ** **
83008 AATTTCATTTCACTCGAGACAGCTTCTCTCGAAACAAAGTTGCATCT-ATCTTGAGATA-TTTCC
1 AATTTTGTCTCACTTGAGACAGTTTCTCTCGAAACAAAATTTTATCTCA-CTTGAGATATTTTTT
* *
83071 CTTGAA-A
65 CTAGAAGT
** * * * *
83078 AATTTTGTCTCACTCAAAATAGTTTCTCTTGAAA-TAAATTTTATCTCACTTGAGATATTTT
1 AATTTTGTCTCACTTGAGACAGTTTCTCTCGAAACAAAATTTTATCTCACTTGAGATATTTT
83139 CTTGAAAACT
Statistics
Matches: 489, Mismatches: 115, Indels: 68
0.73 0.17 0.10
Matches are distributed among these distances:
68 19 0.04
69 25 0.05
70 85 0.17
71 55 0.11
72 79 0.16
73 86 0.18
74 91 0.19
75 21 0.04
76 27 0.06
77 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.41
Consensus pattern (72 bp):
AATTTTGTCTCACTTGAGACAGTTTCTCTCGAAACAAAATTTTATCTCACTTGAGATATTTTTTC
TAGAAGT
Found at i:82734 original size:146 final size:144
Alignment explanation
Indices: 82460--82855 Score: 374
Period size: 146 Copynumber: 2.7 Consensus size: 144
82450 TTTTTCTTGG
** ** * **
82460 AACAAAAATTTTCTATCTCACTTGAGATAATTTT-CCTCAAAAATAATTTTGTTTCACTTGAGAC
1 AACAAAAA-TTTC-ATCTCACTTGAGAT-ATTTTCCCTTGAAAAT--TTTCATCTCACTCAAGAC
** * * * * *
82524 AAATTCTCTCGAAACAAAATTTTTATCTCACTTGAGATATTTTTTCTAGAAGTAATTTGTGTCTC
61 ATTTTCACTCGAAACAAAA-TTTCATCTCACTTGAGATATTTCTTCTAAAAGT-ATTTATGTCTC
*
82589 ACTCGAGT-CAGTTTCTCTCAA
124 ACTCGA-TACAGTTTCCCTCAA
* * *
82610 AACAAAAAATTT-ATCTCGCTTGAGATAGTTTTCCCTTGAAAATTTTCATCTCACTCGAGA-TTA
1 AAC-AAAAATTTCATCTCACTTGAGATA-TTTTCCCTTGAAAATTTTCATCTCACTCAAGACAT-
82673 TTTCACTCGAAACAAAATTTCATCTCACTTGAGATATTTCCCTT-TAAAAGT-TTTATCGTCTCA
63 TTTCACTCGAAACAAAATTTCATCTCACTTGAGATATTT--CTTCTAAAAGTATTTAT-GTCTCA
* **
82736 CTTGATACAGTTTCCCTTGA
125 CTCGATACAGTTTCCCTCAA
* * *
82756 AACCAAAATTTCATCTCACTTGAGATATTTTCTCTTGAAATTTTTCATCTCACTCAAGACATTTT
1 AACAAAAATTTCATCTCACTTGAGATATTTTCCCTTGAAAATTTTCATCTCACTCAAGACATTTT
* * *
82821 CTCTC-AAAAAAAAATTCATCTCACTTGAGATATTT
66 CACTCGAAACAAAATTTCATCTCACTTGAGATATTT
82856 TTTTCTTGGA
Statistics
Matches: 208, Mismatches: 28, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
144 28 0.13
145 48 0.23
146 59 0.28
147 35 0.17
148 19 0.09
149 8 0.04
150 6 0.03
151 5 0.02
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (144 bp):
AACAAAAATTTCATCTCACTTGAGATATTTTCCCTTGAAAATTTTCATCTCACTCAAGACATTTT
CACTCGAAACAAAATTTCATCTCACTTGAGATATTTCTTCTAAAAGTATTTATGTCTCACTCGAT
ACAGTTTCCCTCAA
Found at i:83091 original size:70 final size:71
Alignment explanation
Indices: 82464--83163 Score: 446
Period size: 70 Copynumber: 9.8 Consensus size: 71
82454 TCTTGGAACA
** * * **
82464 AAAATTTTCTATCTCACTTGAGATAATTTTC-CTCAAAAATAATTTTGTTTCACTTGAGACAAAT
1 AAAA-TTT-TATCTCACTTGAGAT-ATTTTCTCT-TGAAA-AATTTTGTCTCACTCGAGACAGTT
82528 TCTCTCGAAAC
61 TCTCTCGAAAC
* * * *
82539 AAAATTTTTATCTCACTTGAGATATTTTTTCTAGAAGTAATTTGTGTCTCACTCGAGTCAGTTTC
1 AAAA-TTTTATCTCACTTGAGATATTTTCTCTTGAA-AAATTT-TGTCTCACTCGAGACAGTTTC
*
82604 TCTCAAAAC
63 TCTCGAAAC
* * * * *
82613 AAAAAATTTATCTCGCTTGAGATAGTTTTCCCTTG-AAAATTTTCATCTCACTCGAGATTA-TTT
1 -AAAATTTTATCTCACTTGAGATA-TTTTCTCTTGAAAAATTTT-GTCTCACTCGAGA-CAGTTT
*
82676 CACTCGAAAC
62 CTCTCGAAAC
* * * * * *
82686 AAAATTTCATCTCACTTGAGATA-TTTCCCTTTAAAAGTTTTATCGTCTCACTTGATACAGTTTC
1 AAAATTTTATCTCACTTGAGATATTTTCTCTTGAAAA-ATTT-T-GTCTCACTCGAGACAGTTTC
* *
82750 CCTTGAAACC
63 TCTCGAAA-C
* * * * *
82760 AAAATTTCATCTCACTTGAGATATTTTCTCTTG-AAATTTTTCATCTCACTCAAGACATTTTCTC
1 AAAATTTTATCTCACTTGAGATATTTTCTCTTGAAAAATTTT-GTCTCACTCGAGACAGTTTCTC
*
82824 TC-AAAA
65 TCGAAAC
* * * * * * * *
82830 AAAAATTCATCTCACTTGAGATATTTTTTTCTTGGAAATTTTTGTCTCGCTTGAGACAGATTCTC
1 AAAATTTTATCTCACTTGAGATA-TTTTCTCTTGAAAAATTTTGTCTCACTCGAGACAGTTTCTC
82895 T-GAAA-
65 TCGAAAC
* * * * * *
82900 ATAGAGTTTTATCTCGCTCGAGATAGTTTTC-CTTAAAACCAATTTTGTCTCACTTGAGATAGTT
1 A-A-AATTTTATCTCACTTGAGATA-TTTTCTCTTGAAA--AATTTTGTCTCACTCGAGACAGTT
82964 T-TCTCG-AA-
61 TCTCTCGAAAC
**** * * * * ** * *
82972 TTTTTTTTATCACACTCGAGATATCTTCTCGTGAAAAATTTCATTTCACTCGAGACAGCTTCTCT
1 AAAATTTTATCTCACTTGAGATATTTTCTCTTGAAAAATTTTGTCTCACTCGAGACAGTTTCTCT
83037 CGAAAC
66 CGAAAC
* ** * * * *
83043 AAAGTTGCATCT-ATCTTGAGATA-TTTCCCTTGAAAAATTTTGTCTCACTCAAAATAGTTTCTC
1 AAAATTTTATCTCA-CTTGAGATATTTTCTCTTGAAAAATTTTGTCTCACTCGAGACAGTTTCTC
*
83106 TTGAAA-
65 TCGAAAC
* * *
83112 TAAATTTTATCTCACTTGAGATA-TTT-TCTTGAAAACTCTT-TCTCACTCGAGA
1 AAAATTTTATCTCACTTGAGATATTTTCTCTTGAAAAATTTTGTCTCACTCGAGA
83164 AAACTTTCCA
Statistics
Matches: 493, Mismatches: 105, Indels: 62
0.75 0.16 0.09
Matches are distributed among these distances:
67 10 0.02
68 30 0.06
69 29 0.06
70 92 0.19
71 54 0.11
72 77 0.16
73 88 0.18
74 87 0.18
75 26 0.05
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.40
Consensus pattern (71 bp):
AAAATTTTATCTCACTTGAGATATTTTCTCTTGAAAAATTTTGTCTCACTCGAGACAGTTTCTCT
CGAAAC
Found at i:83140 original size:36 final size:36
Alignment explanation
Indices: 82425--83140 Score: 232
Period size: 36 Copynumber: 19.8 Consensus size: 36
82415 TCTTTAAAAC
*
82425 AAAAATTTTGTCTC-CTTTGAGATAATTTT-TCTTGGAA
1 AAAAATTTTATCTCAC-TTGAGAT-ATTTTCTCTT-GAA
*
82462 CAAAAATTTTCTATCTCACTTGAGATAATTTTC-C-TCAA
1 -AAAAA-TTT-TATCTCACTTGAGAT-ATTTTCTCTTGAA
* * * ** *
82500 AAATAATTTTGTTTCACTTGAGACAAATTCTCTCGAA
1 AAA-AATTTTATCTCACTTGAGATATTTTCTCTTGAA
* *
82537 ACAAAATTTTTATCTCACTTGAGATATTTTTTCTAG-A
1 A-AAAA-TTTTATCTCACTTGAGATATTTTCTCTTGAA
** * * * **
82574 AGTAATTTGTGTCTCACTCGAG-TCAGTTTCTCTCAAAA
1 AAAAATTT-TATCTCACTTGAGAT-ATTTTCTCT-TGAA
* * *
82612 CAAAAAATTTATCTCGCTTGAGATAGTTTTCCCTTG--
1 -AAAAATTTTATCTCACTTGAGATA-TTTTCTCTTGAA
* * *
82648 -AAAATTTTCATCTCACTCGAGAT-TATTTCACTCGAA
1 AAAAATTTT-ATCTCACTTGAGATAT-TTTCTCTTGAA
* * *
82684 ACAAAATTTCATCTCACTTGAGATA-TTTCCCTT--T
1 A-AAAATTTTATCTCACTTGAGATATTTTCTCTTGAA
* * * * *
82718 AAAAGTTTTATCGTCTCACTTGATACAGTTTCCCTTGAA
1 AAAAATTTTA---TCTCACTTGAGATATTTTCTCTTGAA
*
82757 ACCAAAATTTCATCTCACTTGAGATATTTTCTCTTG--
1 A--AAAATTTTATCTCACTTGAGATATTTTCTCTTGAA
* ** * **
82793 -AAATTTTTCATCTCACTCAAGACATTTTCTCTCAAA
1 AAAAATTTT-ATCTCACTTGAGATATTTTCTCTTGAA
* * *
82829 AAAAAATTCATCTCACTTGAGATATTTTTTTCTTG--
1 AAAAATTTTATCTCACTTGAGATA-TTTTCTCTTGAA
* * * * * **
82864 GAAATTTTTGTCTCGCTTGAGACAGATTCTC-TGAA
1 AAAAATTTTATCTCACTTGAGATATTTTCTCTTGAA
* * *
82899 AATAGAGTTTTATCTCGCTCGAGATAGTTTTC-CTT-AA
1 AA-A-AATTTTATCTCACTTGAGATA-TTTTCTCTTGAA
* *
82936 AACCAATTTTGTCTCACTTGAGATAGTTTTCTC--G-A
1 AA-AAATTTTATCTCACTTGAGATA-TTTTCTCTTGAA
**** * * * *
82971 ATTTTTTTTATCACACTCGAGATATCTTCTCGTG--
1 AAAAATTTTATCTCACTTGAGATATTTTCTCTTGAA
* * * * ** *
83005 AAAAATTTCATTTCACTCGAGACAGCTTCTCTCGAA
1 AAAAATTTTATCTCACTTGAGATATTTTCTCTTGAA
* ** *
83041 ACAAAGTTGCATCT-ATCTTGAGATA-TTTCCCTTG--
1 A-AAAATTTTATCTCA-CTTGAGATATTTTCTCTTGAA
* ** * *
83075 AAAAATTTTGTCTCACTCAAAATAGTTTCTCTTGAA
1 AAAAATTTTATCTCACTTGAGATATTTTCTCTTGAA
*
83111 ATAAATTTTATCTCACTTGAGATATTTTCT
1 AAAAATTTTATCTCACTTGAGATATTTTCT
83141 TGAAAACTCT
Statistics
Matches: 490, Mismatches: 134, Indels: 110
0.67 0.18 0.15
Matches are distributed among these distances:
33 36 0.07
34 88 0.18
35 41 0.08
36 119 0.24
37 86 0.18
38 76 0.16
39 17 0.03
40 19 0.04
41 8 0.02
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (36 bp):
AAAAATTTTATCTCACTTGAGATATTTTCTCTTGAA
Found at i:83602 original size:21 final size:21
Alignment explanation
Indices: 83578--83617 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
83568 TTTTTTTATT
83578 ACTCGAGACAATTTTTCTCTC
1 ACTCGAGACAATTTTTCTCTC
* *
83599 ACTCGAGATAGTTTTTCTC
1 ACTCGAGACAATTTTTCTC
83618 GAAAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (21 bp):
ACTCGAGACAATTTTTCTCTC
Done.