Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold222
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: 1154749
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.31
Warning! 71027 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:590849 original size:26 final size:26
Alignment explanation
Indices: 590814--590867 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
590804 CATCAATAGC
*
590814 ATCGCAGCAAAGCTGTCAACAACAGT
1 ATCGCAGCAAAGCTGCCAACAACAGT
*
590840 ATCGCAGCAAAGCTGCCAATAACAGT
1 ATCGCAGCAAAGCTGCCAACAACAGT
590866 AT
1 AT
590868 ATGTGACCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.17
Consensus pattern (26 bp):
ATCGCAGCAAAGCTGCCAACAACAGT
Found at i:591041 original size:24 final size:24
Alignment explanation
Indices: 590982--591068 Score: 111
Period size: 24 Copynumber: 3.6 Consensus size: 24
590972 GCCATGCACG
**
590982 AAATCAGTCATACAAATCACAGAC
1 AAATCAGTCATTTAAATCACAGAC
591006 AAATCAGTCATTTAAATCACAGAC
1 AAATCAGTCATTTAAATCACAGAC
* * *
591030 AAATCAGTCATTTACATCTCGGAC
1 AAATCAGTCATTTAAATCACAGAC
* *
591054 AAATCAATCGTTTAA
1 AAATCAGTCATTTAA
591069 CCCCAAGGGG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (24 bp):
AAATCAGTCATTTAAATCACAGAC
Found at i:591119 original size:27 final size:27
Alignment explanation
Indices: 591089--591314 Score: 229
Period size: 27 Copynumber: 8.4 Consensus size: 27
591079 CAAAATAGTT
*
591089 ATTTTACCCTACAAGGGTATTACGATC
1 ATTTTACCCTACAGGGGTATTACGATC
* *
591116 ATTTTACCCTACAGGGGCATTACGGTC
1 ATTTTACCCTACAGGGGTATTACGATC
* * *
591143 ATTTTACCCTAAAGGGGCATTACGGTC
1 ATTTTACCCTACAGGGGTATTACGATC
* * *
591170 ATTTTACCCTACAGGGGCATTACGGTT
1 ATTTTACCCTACAGGGGTATTACGATC
* *
591197 ATTTTACCTTACAGGGGCATTAC-AGTC
1 ATTTTACCCTACAGGGGTATTACGA-TC
*** *
591224 ATTTTACCCTTTGGGGGTATTTCGATC
1 ATTTTACCCTACAGGGGTATTACGATC
*** *
591251 ATTTTACCCTTTGGGGGTATTTCGATC
1 ATTTTACCCTACAGGGGTATTACGATC
* * * *
591278 ATTTTACCTTTCAGGGGTATTTCGATA
1 ATTTTACCCTACAGGGGTATTACGATC
591305 ATTTTACCCT
1 ATTTTACCCT
591315 TCGAGGGTAT
Statistics
Matches: 177, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
27 176 0.99
28 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (27 bp):
ATTTTACCCTACAGGGGTATTACGATC
Found at i:591315 original size:81 final size:81
Alignment explanation
Indices: 591089--591327 Score: 264
Period size: 81 Copynumber: 3.0 Consensus size: 81
591079 CAAAATAGTT
* * * *
591089 ATTTTACCCTACAAGGGTATTACGATCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTA
1 ATTTTACCCTACAGGGGTATTACGATCATTTTACCTTACAGGGGCATTACGATCATTTTACCCTT
* * * *
591154 AAGGGGCATTACGGTC
66 AGGGGGTATTTCGATC
* * *
591170 ATTTTACCCTACAGGGGCATTACGGTTATTTTACCTTACAGGGGCATTAC-AGTCATTTTACCCT
1 ATTTTACCCTACAGGGGTATTACGATCATTTTACCTTACAGGGGCATTACGA-TCATTTTACCCT
*
591234 TTGGGGGTATTTCGATC
65 TAGGGGGTATTTCGATC
*** * * * * *
591251 ATTTTACCCTTTGGGGGTATTTCGATCATTTTACCTTTCAGGGGTATTTCGATAATTTTACCCTT
1 ATTTTACCCTACAGGGGTATTACGATCATTTTACCTTACAGGGGCATTACGATCATTTTACCCTT
* *
591316 CGAGGGTATTTC
66 AGGGGGTATTTC
591328 ATTAATTTTA
Statistics
Matches: 131, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
81 130 0.99
82 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (81 bp):
ATTTTACCCTACAGGGGTATTACGATCATTTTACCTTACAGGGGCATTACGATCATTTTACCCTT
AGGGGGTATTTCGATC
Found at i:591322 original size:27 final size:27
Alignment explanation
Indices: 591224--591337 Score: 133
Period size: 27 Copynumber: 4.2 Consensus size: 27
591214 CATTACAGTC
* * *
591224 ATTTTACCCTTTGGGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
591251 ATTTTACCCTTTGGGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATA
*
591278 ATTTTACCTTTC-AGGGGTATTTCGATA
1 ATTTTACCCTTCGA-GGGTATTTCGATA
591305 ATTTTACCCTTCGAGGGTATTTC-ATTA
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
591332 ATTTTA
1 ATTTTA
591338 TAACCTCTTT
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
26 1 0.01
27 77 0.97
28 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.18, T:0.46
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATA
Found at i:591336 original size:54 final size:54
Alignment explanation
Indices: 591224--591337 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
591214 CATTACAGTC
* * * * *
591224 ATTTTACCCTTTGGGGGTATTTCGATCATTTTACCCTTTGGGGGTATTTCGATC
1 ATTTTACCCTTTAGGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGATA
591278 ATTTTA-CCTTTCAGGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTC-ATTA
1 ATTTTACCCTTT-AGGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGA-TA
591332 ATTTTA
1 ATTTTA
591338 TAACCTCTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
53 6 0.11
54 47 0.89
ACGTcount: A:0.19, C:0.17, G:0.18, T:0.46
Consensus pattern (54 bp):
ATTTTACCCTTTAGGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGATA
Found at i:599964 original size:49 final size:50
Alignment explanation
Indices: 599724--599965 Score: 170
Period size: 50 Copynumber: 4.7 Consensus size: 50
599714 GGTAAAGAGA
* * *
599724 TCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCATCGAGGTTATGAGAAG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--C-A--ATATGAGAAC
* * * * * * ** *
599780 TCTCACGCAAGACCATGTCAGGGACATGCCGTTGGCACTGAGATGAGAGA-
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAATATGAGA-AC
* *
599830 TCTC-TCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATGAGAAC
1 TCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACCAATATGAGAAC
* * * **
599880 TCCCATGTAAGACCATATCTGGGATATGACATTGGCAGTACA-A-GA-AAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA-ATATGAGAAC
* *
599928 ATCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 -TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
599966 TGTTATTATC
Statistics
Matches: 148, Mismatches: 32, Indels: 19
0.74 0.16 0.10
Matches are distributed among these distances:
48 3 0.02
49 35 0.24
50 76 0.51
51 3 0.02
55 1 0.01
56 30 0.20
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAATATGAGAAC
Found at i:611442 original size:12 final size:12
Alignment explanation
Indices: 611425--611452 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
611415 GAGGGCAAGG
611425 CCGTACATACAT
1 CCGTACATACAT
611437 CCGTACATACAT
1 CCGTACATACAT
611449 CCGT
1 CCGT
611453 TTTATGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.36, G:0.11, T:0.25
Consensus pattern (12 bp):
CCGTACATACAT
Found at i:613316 original size:42 final size:44
Alignment explanation
Indices: 613219--613317 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 44
613209 ATTATGTGTC
* *
613219 TTATCCAATGGTAAACCAACCACTTGGAACAAATGTTTTGTCAA
1 TTATCCAATGGTAAAACAACCACTTGGAACAAATGTTTTGTAAA
* *
613263 --ATCCAACGGTAAAACAACTGA-TTGGAACAAATG-TTT-TAAA
1 TTATCCAATGGTAAAACAAC-CACTTGGAACAAATGTTTTGTAAA
*
613303 TTATCTAATGGTAAA
1 TTATCCAATGGTAAA
613318 CCATCAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
40 3 0.07
41 3 0.07
42 39 0.85
43 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (44 bp):
TTATCCAATGGTAAAACAACCACTTGGAACAAATGTTTTGTAAA
Found at i:619763 original size:42 final size:43
Alignment explanation
Indices: 619673--619778 Score: 139
Period size: 42 Copynumber: 2.5 Consensus size: 43
619663 ATTATGTGTC
*
619673 TTATCCAATGGTAAACCAACCACTTGGAACAAATGTTTTGTCAA
1 TTATCCAATGGTAAACCAACCA-TTGGAACAAATGTTTTGTAAA
* *
619717 --ATCCAATGATAAAACAACCGATTGGAACAAATG-TTT-TAAA
1 TTATCCAATGGTAAACCAACC-ATTGGAACAAATGTTTTGTAAA
619757 TTATCCAATGGTAAACCAACCA
1 TTATCCAATGGTAAACCAACCA
619779 ATTGAAACTT
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
40 3 0.06
41 4 0.07
42 46 0.85
43 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (43 bp):
TTATCCAATGGTAAACCAACCATTGGAACAAATGTTTTGTAAA
Found at i:626494 original size:42 final size:43
Alignment explanation
Indices: 626447--626560 Score: 126
Period size: 42 Copynumber: 2.7 Consensus size: 43
626437 TGAAAAAGAA
* * *
626447 GTTCCAATTGGTTGGTTTACCATTAGATAATT-TAAAACATTT
1 GTTCCAACTGGTTGGTTTACCATTGGATAATTACAAAACATTT
** * *
626489 GTTCCAACCAGTTGTTTTACCTTTGGAT--TTGACAAAACATTT
1 GTTCCAACTGGTTGGTTTACCATTGGATAATT-ACAAAACATTT
*
626531 GTTCCAAGTGGTTGGTTTACCATTGGATAA
1 GTTCCAACTGGTTGGTTTACCATTGGATAA
626561 GACACATAAT
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
40 2 0.04
42 54 0.96
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (43 bp):
GTTCCAACTGGTTGGTTTACCATTGGATAATTACAAAACATTT
Found at i:636234 original size:23 final size:22
Alignment explanation
Indices: 636191--636234 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
636181 TTCTAAGTCG
636191 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
636214 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
636235 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:638476 original size:1 final size:1
Alignment explanation
Indices: 638472--638505 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
638462 CTCCAATCGC
*
638472 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
638506 CCAATCGGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:640843 original size:17 final size:17
Alignment explanation
Indices: 640821--640853 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
640811 TATGAATCAC
640821 TAAGCTAAACCTTCAAT
1 TAAGCTAAACCTTCAAT
640838 TAAGCTAAACCTTCAA
1 TAAGCTAAACCTTCAA
640854 AGGGTACTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.27
Consensus pattern (17 bp):
TAAGCTAAACCTTCAAT
Found at i:642808 original size:31 final size:29
Alignment explanation
Indices: 642738--642809 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
642728 ACTTCAGATT
*
642738 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTGAAATGTA
* ***
642767 ACGTTTTAGTCACTTATGTTATCGTGTTGTA
1 ACATTTTAGTCACTTATGTT-T-GAAATGTA
642798 ACATTTTAGTCA
1 ACATTTTAGTCA
642810 TTGAGCCATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 19 0.54
30 1 0.03
31 15 0.43
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTGAAATGTA
Found at i:643368 original size:31 final size:29
Alignment explanation
Indices: 643333--643409 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
643323 TTAATAGCTC
*
643333 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
* * ***
643364 AGTGACAAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
643393 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
643410 CTAAGGTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 21 0.55
30 1 0.03
31 16 0.42
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:646585 original size:35 final size:35
Alignment explanation
Indices: 646480--646585 Score: 131
Period size: 35 Copynumber: 3.0 Consensus size: 35
646470 TCTATGGAGT
* * * *
646480 GACACCGTGTAAACGATATATAGGTCATTTGGGGC
1 GACAACGTGTAAACGGTACATAGGTCCTTTGGGGC
* * * *
646515 AATAACATGTAAATGGTACATAGGTCCTTTGGGGC
1 GACAACGTGTAAACGGTACATAGGTCCTTTGGGGC
*
646550 GACAACGTGTAAACGGTACATAGGTCCTTCGGGGC
1 GACAACGTGTAAACGGTACATAGGTCCTTTGGGGC
646585 G
1 G
646586 GCACCTCGAA
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (35 bp):
GACAACGTGTAAACGGTACATAGGTCCTTTGGGGC
Found at i:648863 original size:29 final size:29
Alignment explanation
Indices: 648821--648877 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
648811 TAATAATGTT
* *
648821 ATTATTTTCTTATATTAT-AAATTAAATTG
1 ATTATATTATTATATTATGAAA-TAAATTG
648850 ATTATATTATTATATTATGAAATAAATT
1 ATTATATTATTATATTATGAAATAAATT
648878 AAGAAAAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (29 bp):
ATTATATTATTATATTATGAAATAAATTG
Found at i:649397 original size:25 final size:26
Alignment explanation
Indices: 649311--649397 Score: 74
Period size: 26 Copynumber: 3.4 Consensus size: 26
649301 ATGAAAGCAT
* **
649311 AAAAAGAAACAAAA-AGAAATAGAAAG
1 AAAAAGAAAGAAAACA-AAATAGGGAG
*
649337 AAACAGAATA-AAAACAAAATAGGGAG
1 AAAAAGAA-AGAAAACAAAATAGGGAG
*
649363 AAAAAGAAAGAAAAGAAAA-AGGGA-
1 AAAAAGAAAGAAAACAAAATAGGGAG
649387 AAGAAAGAAAG
1 AA-AAAGAAAG
649398 GAGAAATAGG
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
24 2 0.04
25 14 0.27
26 34 0.65
27 2 0.04
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.03
Consensus pattern (26 bp):
AAAAAGAAAGAAAACAAAATAGGGAG
Found at i:650062 original size:14 final size:14
Alignment explanation
Indices: 650045--650082 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
650035 TAACTTTATT
650045 AAATTGAATTTAGA
1 AAATTGAATTTAGA
650059 AAATTGAATTTAGA
1 AAATTGAATTTAGA
650073 AAATTGAATT
1 AAATTGAATT
650083 GAATGAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (14 bp):
AAATTGAATTTAGA
Found at i:656264 original size:27 final size:27
Alignment explanation
Indices: 656205--656278 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
656195 CATAAATCGT
*
656205 CACAAAGGCTTCAATTTCATAAACAGC
1 CACAAAGGCTTCAATTTCATAAACAGA
* * *
656232 CACAAAGGCTTCCATTTCATAGATA-A
1 CACAAAGGCTTCAATTTCATAAACAGA
* *
656258 CAGCAAAGGTTTCTATTTCAT
1 CA-CAAAGGCTTCAATTTCAT
656279 GTCATGTTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
26 2 0.05
27 38 0.95
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.28
Consensus pattern (27 bp):
CACAAAGGCTTCAATTTCATAAACAGA
Found at i:659371 original size:21 final size:21
Alignment explanation
Indices: 659347--659386 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
659337 TAACTTTGAT
*
659347 AAATCATTATAAATTGTAAAA
1 AAATAATTATAAATTGTAAAA
* *
659368 AAATAATTGTAATTTGTAA
1 AAATAATTATAAATTGTAA
659387 TTTATATGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (21 bp):
AAATAATTATAAATTGTAAAA
Found at i:660521 original size:43 final size:43
Alignment explanation
Indices: 660460--660607 Score: 176
Period size: 43 Copynumber: 3.5 Consensus size: 43
660450 ACAGTAATTT
660460 CGTGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTA
*
660503 CGTGTAAGACCATGTCTGGGACATTGGCACCGTATAT-A-ATT-
1 CGTGTAAGACCATGTCTGGGACATTGGCATCG-ATATGAGATTA
* * ** * *
660544 CGTGTAAGACCCTGTCTGAGACAGAGGCATCGATATGTGATAA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTA
* * *
660587 CATGTAAAACCATATCTGGGA
1 CGTGTAAGACCATGTCTGGGA
660608 TATGACATTG
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
40 4 0.05
41 27 0.31
42 5 0.06
43 48 0.55
44 4 0.05
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTA
Found at i:674188 original size:18 final size:18
Alignment explanation
Indices: 674165--674201 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
674155 GGTGGCAATT
*
674165 TGTTCTTCAAGAACGCAC
1 TGTTCTACAAGAACGCAC
674183 TGTTCTACAAGAACGCAC
1 TGTTCTACAAGAACGCAC
674201 T
1 T
674202 ACACTCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (18 bp):
TGTTCTACAAGAACGCAC
Found at i:676904 original size:27 final size:27
Alignment explanation
Indices: 676866--677198 Score: 485
Period size: 27 Copynumber: 12.4 Consensus size: 27
676856 GGACCTTTCA
*
676866 TAGGGTAAAATGATCGAATTACCCTCG
1 TAGGGTAAAATGACCGAATTACCCTCG
**
676893 TAGGGTAAAATGACTAAATTACCCTCG
1 TAGGGTAAAATGACCGAATTACCCTCG
676920 TAGGGTAAAATGACCGAATTAGCCCT-G
1 TAGGGTAAAATGACCGAATTA-CCCTCG
* *
676947 TAGGGTAAAATGACCAAATTACCC-AG
1 TAGGGTAAAATGACCGAATTACCCTCG
* *
676973 TAAGGTAAAATGATCGAATTACCCTCG
1 TAGGGTAAAATGACCGAATTACCCTCG
*
677000 TAGGGTAAAATGACCGAATTACCCTTG
1 TAGGGTAAAATGACCGAATTACCCTCG
*
677027 TAGGGTAAAATTACCGAATTACCCTCG
1 TAGGGTAAAATGACCGAATTACCCTCG
677054 TAGGGTAAAATGACCGAATTACCCTCG
1 TAGGGTAAAATGACCGAATTACCCTCG
*
677081 TAGGGTAAAATGATCGAATTACCCTCG
1 TAGGGTAAAATGACCGAATTACCCTCG
* *
677108 TAGGGTAAAATGACTGAATTACCCCCG
1 TAGGGTAAAATGACCGAATTACCCTCG
*
677135 TAGGGTAAAATGACCGAATTACCTTC-
1 TAGGGTAAAATGACCGAATTACCCTCG
* *
677161 TAGGGTAAAATGACTGAAATACCC-CG
1 TAGGGTAAAATGACCGAATTACCCTCG
677187 ATAGGGTAAAAT
1 -TAGGGTAAAAT
677199 AATGACTGTT
Statistics
Matches: 275, Mismatches: 26, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
25 1 0.00
26 46 0.17
27 224 0.81
28 4 0.01
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (27 bp):
TAGGGTAAAATGACCGAATTACCCTCG
Found at i:679322 original size:45 final size:45
Alignment explanation
Indices: 679258--679445 Score: 202
Period size: 45 Copynumber: 4.2 Consensus size: 45
679248 TACTACGTGT
* * *
679258 ACCGGGTACCATTGATTATAAAGGTGGTTGTTGTGTGTTAATTCC
1 ACCGGGTATCATTGATTATAAAGGTGGTTGCTGTGTGTTGATTCC
* * *
679303 ACCGGGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTAC
1 ACCGGGTATCATTGATTATAAAGGTGGTTGCTGTGTGTTGATTCC
* * * *
679348 ACCGGGTA-CTATTGATTATGATGGTGGTTGCTATGTGATGATTCC
1 ACCGGGTATC-ATTGATTATAAAGGTGGTTGCTGTGTGTTGATTCC
** * * *
679393 ACCTAGTATCATTGACTATAAGGGTGG-TACTGTGTGTTGA-TCC
1 ACCGGGTATCATTGATTATAAAGGTGGTTGCTGTGTGTTGATTCC
*
679436 ACCGTGTATC
1 ACCGGGTATC
679446 TGTTATTATT
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
43 11 0.09
44 11 0.09
45 98 0.81
46 1 0.01
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (45 bp):
ACCGGGTATCATTGATTATAAAGGTGGTTGCTGTGTGTTGATTCC
Found at i:683891 original size:81 final size:79
Alignment explanation
Indices: 683748--683976 Score: 287
Period size: 81 Copynumber: 2.8 Consensus size: 79
683738 AGGTAAAATG
* * * *
683748 ACCAAAATACCACCATAAGGTAAAATGACTGAAATACCCTCATAAGGTAAAATGACTGAAATACC
1 ACCAAAATACC-CCATAAGGTAGAATGACT-AAATACCCCCATAGGGTAAAATGACCGAAATACC
683813 CCCATAAAGTAGAATA
64 CCCATAAAGTAGAATA
** *
683829 ACTGAAATACCCCTATAAGGTAGAATGACCTAAATACCCCCATAGGGTAAAATGACCAAAATACC
1 ACCAAAATACCCC-ATAAGGTAGAATGA-CTAAATACCCCCATAGGGTAAAATGACCGAAATACC
* *
683894 CCCATAAGGTAGAATG
64 CCCATAAAGTAGAATA
* * * *
683910 ACCAAAATAACCCCATAGGGTAGAATGATCAAAATACCCCCATAGGGTAGAATGATCGAAATACC
1 ACCAAAAT-ACCCCATAAGGTAGAATGA-CTAAATACCCCCATAGGGTAAAATGACCGAAATACC
683975 CC
64 CC
683977 TATAGGGTAA
Statistics
Matches: 128, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
80 2 0.02
81 119 0.93
82 7 0.05
ACGTcount: A:0.44, C:0.23, G:0.15, T:0.18
Consensus pattern (79 bp):
ACCAAAATACCCCATAAGGTAGAATGACTAAATACCCCCATAGGGTAAAATGACCGAAATACCCC
CATAAAGTAGAATA
Found at i:683991 original size:81 final size:78
Alignment explanation
Indices: 683738--683992 Score: 285
Period size: 81 Copynumber: 3.2 Consensus size: 78
683728 ACCCTAAAAT
* * * *
683738 AGGTAAAATGACCAAAATACCACCATAAGGTAAAATGACTGAAATACCCTCATAAGGTAAAATGA
1 AGGTAAAATGACCAAAATACC-CCATAAGGTAGAATGAC-AAAATACCCCCATAGGGTAAAATGA
683803 CTGAAATACCCCCATA
64 C-GAAATACCCCCATA
* * * ** *
683819 AAGTAGAATAACTGAAATACCCCTATAAGGTAGAATGACCTAAATACCCCCATAGGGTAAAATGA
1 AGGTAAAATGACCAAAATACCCC-ATAAGGTAGAATGA-CAAAATACCCCCATAGGGTAAAATGA
*
683884 CCAAAATACCCCCATA
64 -CGAAATACCCCCATA
* * *
683900 AGGTAGAATGACCAAAATAACCCCATAGGGTAGAATGATCAAAATACCCCCATAGGGTAGAATGA
1 AGGTAAAATGACCAAAAT-ACCCCATAAGGTAGAATGA-CAAAATACCCCCATAGGGTAAAATGA
*
683965 TCGAAATACCCCTATA
64 -CGAAATACCCCCATA
*
683981 GGGTAAAATGAC
1 AGGTAAAATGAC
683993 TGTTATACCC
Statistics
Matches: 147, Mismatches: 23, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
80 2 0.01
81 138 0.94
82 7 0.05
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.18
Consensus pattern (78 bp):
AGGTAAAATGACCAAAATACCCCATAAGGTAGAATGACAAAATACCCCCATAGGGTAAAATGACG
AAATACCCCCATA
Found at i:684005 original size:27 final size:27
Alignment explanation
Indices: 683738--684003 Score: 259
Period size: 27 Copynumber: 9.9 Consensus size: 27
683728 ACCCTAAAAT
* ** *
683738 AGGTAAAATGACCAAAATACCACCATA
1 AGGTAGAATGACTGAAATACCCCCATA
* *
683765 AGGTAAAATGACTGAAATACCCTCATA
1 AGGTAGAATGACTGAAATACCCCCATA
*
683792 AGGTAAAATGACTGAAATACCCCCATA
1 AGGTAGAATGACTGAAATACCCCCATA
* * *
683819 AAGTAGAATAACTGAAATACCCCTATA
1 AGGTAGAATGACTGAAATACCCCCATA
683846 AGGTAGAATGACCT-AAATACCCCCATA
1 AGGTAGAATGA-CTGAAATACCCCCATA
* * **
683873 GGGTAAAATGACCAAAATACCCCCATA
1 AGGTAGAATGACTGAAATACCCCCATA
** *
683900 AGGTAGAATGACCAAAATAACCCCATA
1 AGGTAGAATGACTGAAATACCCCCATA
* *
683927 GGGTAGAATGA-TCAAAATACCCCCATA
1 AGGTAGAATGACT-GAAATACCCCCATA
* *
683954 GGGTAGAATGA-TCGAAATACCCCTATA
1 AGGTAGAATGACT-GAAATACCCCCATA
* * **
683981 GGGTAAAATGACTGTTATACCCC
1 AGGTAGAATGACTGAAATACCCC
684004 TAGGAGATGA
Statistics
Matches: 209, Mismatches: 26, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
26 1 0.00
27 205 0.98
28 3 0.01
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (27 bp):
AGGTAGAATGACTGAAATACCCCCATA
Found at i:684427 original size:29 final size:31
Alignment explanation
Indices: 684385--684451 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
684375 AACTGCATAT
* *
684385 CTGCATTGATTAATGATATT-GTACTGTT-A
1 CTGCATCGATTAATGATATTAATACTGTTCA
684414 CTGCATCGATTAATGATATTACATACTGTTCA
1 CTGCATCGATTAATGATATTA-ATACTGTTCA
684446 CTGCAT
1 CTGCAT
684452 GACTGATATC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 19 0.58
31 7 0.21
32 7 0.21
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.40
Consensus pattern (31 bp):
CTGCATCGATTAATGATATTAATACTGTTCA
Found at i:696597 original size:42 final size:40
Alignment explanation
Indices: 696541--696827 Score: 315
Period size: 42 Copynumber: 6.8 Consensus size: 40
696531 GCGTTTATAG
696541 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTT
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTT
* *
696581 GAAAAAAGACGACGCTAAAGATCATGTTCTTTAGCGGCGCTTA
1 -AAAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCG-TTT
* * *
696624 ACAAAAAACGCCGCTAAAGAACATGCTCTTTAGCGGCGCTTAA
1 A-AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG-TT-T
*
696667 AAAAAAGACGCCGCTAAAGATCATGTTCTTTAGCGGCGGTT
1 AAAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTT
* * * * *
696708 ACAAAAAATCGCCACTAAAGATAATGTTCTTTAGCTGCACTTA
1 A-AAAAAA-CGCCGCTAAAGATCATGTTCTTTAGCGGC-GTTT
* *
696751 AAGAAAAATGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTGGT
1 AA-AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG-TT--T
696795 AAAAAAACGCCGCTATAA-ATCATGTTCTTTAGC
1 AAAAAAACGCCGCTA-AAGATCATGTTCTTTAGC
696828 CGCGCTTTCA
Statistics
Matches: 211, Mismatches: 22, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
41 8 0.04
42 128 0.61
43 71 0.34
44 4 0.02
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (40 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTT
Found at i:696686 original size:127 final size:127
Alignment explanation
Indices: 696541--696827 Score: 388
Period size: 127 Copynumber: 2.3 Consensus size: 127
696531 GCGTTTATAG
* * *
696541 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGA-AAAAAGA-CGACGCTAAAGATC
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGGTT-ACAAAAA-ATCGACACTAAAGATA
*
696604 ATGTTCTTTAGCGGCGCTTAACA-AAAAACGCCGCTAAAGA-ACATGCTCTTTAGCGGCGCTT-A
64 ATGTTCTTTAGCGGCACTTAA-AGAAAAACGCCGCTAAAGATA-ATGCTCTTTAGCGGCGCTTGA
696666 A
127 A
*
696667 AAAAAAGACGCCGCTAAAGATCATGTTCTTTAGCGGCGGTTACAAAAAATCGCCACTAAAGATAA
1 AAAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCGGTTACAAAAAATCGACACTAAAGATAA
* * * **
696732 TGTTCTTTAGCTGCACTTAAAGAAAAATGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTGGT
65 TGTTCTTTAGCGGCACTTAAAGAAAAACGCCGCTAAAGATAATGCTCTTTAGCGGCGCTTGAA
696795 AAAAAAACGCCGCTATAA-ATCATGTTCTTTAGC
1 AAAAAAACGCCGCTA-AAGATCATGTTCTTTAGC
696828 CGCGCTTTCA
Statistics
Matches: 144, Mismatches: 10, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
126 9 0.06
127 126 0.88
128 9 0.06
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (127 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGGTTACAAAAAATCGACACTAAAGATAAT
GTTCTTTAGCGGCACTTAAAGAAAAACGCCGCTAAAGATAATGCTCTTTAGCGGCGCTTGAA
Found at i:696692 original size:85 final size:84
Alignment explanation
Indices: 696542--696834 Score: 362
Period size: 85 Copynumber: 3.5 Consensus size: 84
696532 CGTTTATAGA
* ** *
696542 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG-TTTGAAAAAAGACGACGCTAAAGATCAT
1 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAAAAAAAGACGCCGCTAAAGATCAT
696606 GTTCTTTAGCGGCGCTTAAC
66 GTTCTTTAGCGGCGCTT-AC
*
696626 AAAAAACGCCGCTAAAGAACATGCTCTTTAGCGGCGCTTAAAAAAAAGACGCCGCTAAAGATCAT
1 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAAAAAAAGACGCCGCTAAAGATCAT
*
696691 GTTCTTTAGCGGCGGTTAC
66 GTTCTTTAGCGGCGCTTAC
* * * * * *
696710 AAAAAATCGCCACTAAAGATA-ATGTTCTTTAGCTGCACTTAAAGAAAA-ATGCCGCTAAAGATA
1 AAAAAA-CGCCGCTAAAGA-ACATGTTCTTTAGCGGCGCTTAAAAAAAAGACGCCGCTAAAGATC
696773 ATGTTCTTTAGCGGCGCTTGGTA-
64 ATGTTCTTTAGCGGCGC-T--TAC
* *
696796 AAAAAACGCCGCTATAA-ATCATGTTCTTTAGCCGCGCTT
1 AAAAAACGCCGCTA-AAGAACATGTTCTTTAGCGGCGCTT
696835 TCATCGCGAA
Statistics
Matches: 183, Mismatches: 18, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
84 71 0.39
85 101 0.55
86 9 0.05
87 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (84 bp):
AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAAAAAAAGACGCCGCTAAAGATCAT
GTTCTTTAGCGGCGCTTAC
Found at i:697306 original size:21 final size:21
Alignment explanation
Indices: 697295--697350 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
697285 CTTCTCGCGC
*
697295 TGCAGCCTCTGCTTCACTTGT
1 TGCAGCCTCTGCTTCACTCGT
*
697316 TGCAGCCTCTGCTTCCCTCGT
1 TGCAGCCTCTGCTTCACTCGT
*
697337 TGCCGCCTCTGCTT
1 TGCAGCCTCTGCTT
697351 TAAGTTGTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.05, C:0.39, G:0.20, T:0.36
Consensus pattern (21 bp):
TGCAGCCTCTGCTTCACTCGT
Found at i:705580 original size:19 final size:19
Alignment explanation
Indices: 705556--705597 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
705546 GGTCGGGTTT
*
705556 GGGGAGCTGTTAGGGATTA
1 GGGGAGATGTTAGGGATTA
* *
705575 GGGGAGATTTTAGGGATTT
1 GGGGAGATGTTAGGGATTA
705594 GGGG
1 GGGG
705598 GAGAATGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.02, G:0.50, T:0.29
Consensus pattern (19 bp):
GGGGAGATGTTAGGGATTA
Found at i:707037 original size:7 final size:7
Alignment explanation
Indices: 707027--707067 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
707017 ACCCCAAAAT
707027 CAAACCC
1 CAAACCC
707034 CAAACCC
1 CAAACCC
707041 CAAACCC
1 CAAACCC
*
707048 TAAACCC
1 CAAACCC
*
707055 CAAATCC
1 CAAACCC
707062 CAAACC
1 CAAACC
707068 ATAATATTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.44, C:0.51, G:0.00, T:0.05
Consensus pattern (7 bp):
CAAACCC
Found at i:707434 original size:14 final size:14
Alignment explanation
Indices: 707423--707462 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
707413 TTCTAACCCT
707423 TAACCCCAAACCAC
1 TAACCCCAAACCAC
* *
707437 TAACCCCTAACTAC
1 TAACCCCAAACCAC
*
707451 TAACCCTAAACC
1 TAACCCCAAACC
707463 TTATTTAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.40, C:0.45, G:0.00, T:0.15
Consensus pattern (14 bp):
TAACCCCAAACCAC
Found at i:708367 original size:113 final size:114
Alignment explanation
Indices: 708009--708663 Score: 562
Period size: 114 Copynumber: 5.8 Consensus size: 114
707999 AAACGCTTTT
* * * * * * * * * *
708009 TAAAAATGCCGCTAAAGCCCTAAAAGTTTAGAAAACGACGCCGTTGGGCTTAGG-TTTTTTGCGA
1 TAAAAACGCCACTAAATCCCTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTTGGTTTTTTTGCGG
* * * * *
708073 CGC-TTCAACAAAAACGCCGCTAAAGCCCTAAACATTAGCAGCGCATT--C
66 CGCTTTC-TCGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGC-TTACC
* ** * * * * * * *
708121 TTAAAACGCCGGTAAAGCCCACGAATTG-TCAGAAAACGGTGTAGTTTGGC-TTAGTTTTTGTTG
1 TAAAAACGCCACTAAATCCC-TGAA-AGCTCAGAAAACGGCGTCGTTGGGCTTTGGTTTTT-TTG
* * * * * * *
708184 CGGCGCTTTCTCAAAAACGCCGCTGAAGGCCTGAACATTAGCAGCACTTACT
63 CGGCGCTTTCTCGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACC
* * * * *
708236 TATAAATGCCACTGAATCCCTGAAAGCTCAAAAAACGGCGTCGTTGGGCTTTGGTTTTTTTGTGG
1 TAAAAACGCCACTAAATCCCTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTTGGTTTTTTTGCGG
* *
708301 CGCTTTCTC-AAAAGTGCTGCTAAAG-CCTGAGCATTAGCGGCGCTTACC
66 CGCTTTCTCGAAAA-CGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACC
* * *
708349 TAAAAACGCCACTAAATCCCTGAATGCTCAGAAAACAGCGTCGTTGGGCTTAGGTATTTTTT-CG
1 TAAAAACGCCACTAAATCCCTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTTGGT-TTTTTTGCG
* * *
708413 GCGCTTTCCCGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGTTTACG
65 GCGCTTTCTCGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACC
* * * * *
708463 AAAAAATGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTTAGTTTTTTTGTGG
1 TAAAAACGCCACTAAATCCCTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTTGGTTTTTTTGCGG
* * * * *
708528 CGCTTTCTCGAAAACGCCGCAAAAGCCCAGGGCATTAGCGACGCTTTCC
66 CGCTTTCTCGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACC
* * * * *
708577 TAAAAACGCCGCTAAAT-CCTCGAAAAGCTTAGAAAACGGTGTCGTTGTG-TTTAGG-TATTTTG
1 TAAAAACGCCACTAAATCCCT-G-AAAGCTCAGAAAACGGCGTCGTTGGGCTTT-GGTTTTTTTG
* * *
708639 CGGTGCTTTAT-GGAAACGCCGCTAA
63 CGGCGCTTTCTCGAAAACGCCGCTAA
708664 TGCTTATTTT
Statistics
Matches: 440, Mismatches: 86, Indels: 33
0.79 0.15 0.06
Matches are distributed among these distances:
112 19 0.04
113 135 0.31
114 238 0.54
115 48 0.11
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.26
Consensus pattern (114 bp):
TAAAAACGCCACTAAATCCCTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTTGGTTTTTTTGCGG
CGCTTTCTCGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACC
Found at i:708417 original size:227 final size:231
Alignment explanation
Indices: 708149--708638 Score: 627
Period size: 227 Copynumber: 2.1 Consensus size: 231
708139 CCACGAATTG
* * * *
708149 TCAGAAAACGGTGTAGTTTGGCTTA-GT-TTTTGTTGCGGCGCTTTCTCAAAAACGCCGCTGAAG
1 TCAGAAAACGGTGTCGTTGGGCTTAGGTATTTTGTTGCGGCGCTTTCCCAAAAACGCCGCTAAAG
* ** * * *
708212 GCCTGAACATTAGCAGCACTTACTTATAAATGCCACTGAATCCCTGAAAGCTCAAAAAACGGCGT
66 CCCTGAACATTAGCAGCACTTACGAAAAAATGCCACTAAATCCCCGAAAGCTCAAAAAACGGCGT
* * * * *
708277 CGTTGGGCTTTGGTTTTTTTGTGGCGCTTTCTC-AAAAGTGCTGCTAAAG-CCTGAGCATTAGCG
131 CGTTGGGCTTTAGTTTTTTTGTGGCGCTTTCTCGAAAA-CGCCGCAAAAGCCCAGAGCATTAGCG
* *
708340 GCGCTTACCTAAAAACGCCACTAAATCC-CTG-AATGC
195 ACGCTTACCTAAAAACGCCACTAAATCCTC-GAAAAGC
* * *
708376 TCAGAAAACAGCGTCGTTGGGCTTAGGTATTTT-TT-CGGCGCTTTCCCGAAAACGCCGCTAAAG
1 TCAGAAAACGGTGTCGTTGGGCTTAGGTATTTTGTTGCGGCGCTTTCCCAAAAACGCCGCTAAAG
* * ** *
708439 CCCTGAGCATTAGCGGCGTTTACGAAAAAATGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGT
66 CCCTGAACATTAGCAGCACTTACGAAAAAATGCCACTAAATCCCCGAAAGCTCAAAAAACGGCGT
*
708504 CGTTGGGCTTTAGTTTTTTTGTGGCGCTTTCTCGAAAACGCCGCAAAAGCCCAGGGCATTAGCGA
131 CGTTGGGCTTTAGTTTTTTTGTGGCGCTTTCTCGAAAACGCCGCAAAAGCCCAGAGCATTAGCGA
* *
708569 CGCTTTCCTAAAAACGCCGCTAAATCCTCGAAAAGC
196 CGCTTACCTAAAAACGCCACTAAATCCTCGAAAAGC
* * *
708605 TTAGAAAACGGTGTCGTTGTGTTTAGGTATTTTG
1 TCAGAAAACGGTGTCGTTGGGCTTAGGTATTTTG
708639 CGGTGCTTTA
Statistics
Matches: 223, Mismatches: 33, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
227 140 0.63
228 46 0.21
229 37 0.17
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27
Consensus pattern (231 bp):
TCAGAAAACGGTGTCGTTGGGCTTAGGTATTTTGTTGCGGCGCTTTCCCAAAAACGCCGCTAAAG
CCCTGAACATTAGCAGCACTTACGAAAAAATGCCACTAAATCCCCGAAAGCTCAAAAAACGGCGT
CGTTGGGCTTTAGTTTTTTTGTGGCGCTTTCTCGAAAACGCCGCAAAAGCCCAGAGCATTAGCGA
CGCTTACCTAAAAACGCCACTAAATCCTCGAAAAGC
Found at i:711242 original size:27 final size:27
Alignment explanation
Indices: 711212--711370 Score: 210
Period size: 27 Copynumber: 5.9 Consensus size: 27
711202 GCAGACCTTT
711212 CGTAGGGTAAAATGACCGAATTACCCC
1 CGTAGGGTAAAATGACCGAATTACCCC
* *
711239 CGTAGGGTAAAATCATCGAATTACCCC
1 CGTAGGGTAAAATGACCGAATTACCCC
* **
711266 TGTAGGGTAAAATGACCGAATTACCGT
1 CGTAGGGTAAAATGACCGAATTACCCC
* * *
711293 CGTACGGTAAAATGACTGAATTACCCT
1 CGTAGGGTAAAATGACCGAATTACCCC
* * *
711320 CATAGGGTAAAATGACCAAATTAGCCC
1 CGTAGGGTAAAATGACCGAATTACCCC
*
711347 CGTAGGGTAAAATGACCAAATTAC
1 CGTAGGGTAAAATGACCGAATTAC
711371 ACGTGAGCAG
Statistics
Matches: 113, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 113 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (27 bp):
CGTAGGGTAAAATGACCGAATTACCCC
Found at i:711317 original size:81 final size:81
Alignment explanation
Indices: 711211--711370 Score: 232
Period size: 81 Copynumber: 2.0 Consensus size: 81
711201 TGCAGACCTT
* * * *
711211 TCGTAGGGTAAAATGACCGAATTACCCCCGTAGGGTAAAATCATCGAATTA-CCCCTGTAGGGTA
1 TCGTACGGTAAAATGACCGAATTACCCCCATAGGGTAAAATCACCAAATTAGCCCC-GTAGGGTA
*
711275 AAATGACCGAATTACCG
65 AAATGACCAAATTACCG
* * *
711292 TCGTACGGTAAAATGACTGAATTACCCTCATAGGGTAAAATGACCAAATTAGCCCCGTAGGGTAA
1 TCGTACGGTAAAATGACCGAATTACCCCCATAGGGTAAAATCACCAAATTAGCCCCGTAGGGTAA
711357 AATGACCAAATTAC
66 AATGACCAAATTAC
711371 ACGTGAGCAG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
81 66 0.94
82 4 0.06
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (81 bp):
TCGTACGGTAAAATGACCGAATTACCCCCATAGGGTAAAATCACCAAATTAGCCCCGTAGGGTAA
AATGACCAAATTACCG
Found at i:711620 original size:26 final size:26
Alignment explanation
Indices: 711540--711620 Score: 110
Period size: 26 Copynumber: 3.1 Consensus size: 26
711530 TGGAGGAAGT
* *
711540 ATACTATTACTAGCAGCTTT-TCTACG
1 ATACTATTACTGGCAGCTTTGT-TGCG
* *
711566 ATACTATTACTGGCAGCTTTGCTGTG
1 ATACTATTACTGGCAGCTTTGTTGCG
711592 ATACTATTACTGGCAGCTTTGTTGCG
1 ATACTATTACTGGCAGCTTTGTTGCG
711618 ATA
1 ATA
711621 TTGGTGTGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGTTGCG
Found at i:711789 original size:27 final size:28
Alignment explanation
Indices: 711732--711815 Score: 109
Period size: 27 Copynumber: 3.1 Consensus size: 28
711722 TACCAATATC
* * *
711732 GTATTGGGTTAAGGCCCACATTATTACT
1 GTATTGGGCTAAGGCCCACATTGTTATT
*
711760 GTATTGTGCTAAGG-CCACATTGTTATT
1 GTATTGGGCTAAGGCCCACATTGTTATT
*
711787 GTATTGGGCTAAGGCCCACACTG-TATT
1 GTATTGGGCTAAGGCCCACATTGTTATT
711814 GT
1 GT
711816 TTCTAAAAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
27 30 0.61
28 19 0.39
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.36
Consensus pattern (28 bp):
GTATTGGGCTAAGGCCCACATTGTTATT
Found at i:712105 original size:17 final size:17
Alignment explanation
Indices: 712083--712124 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
712073 TTAATTGGGC
712083 TTTTCAAAAGGTAACTA
1 TTTTCAAAAGGTAACTA
712100 TTTTCAAAAGGTAACTA
1 TTTTCAAAAGGTAACTA
712117 TTTTCAAA
1 TTTTCAAA
712125 GACACCACGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (17 bp):
TTTTCAAAAGGTAACTA
Found at i:717222 original size:3 final size:3
Alignment explanation
Indices: 717216--717254 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
717206 TATATGTTTT
717216 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
717255 GAAAGTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:718424 original size:17 final size:17
Alignment explanation
Indices: 718395--718427 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
718385 AAGTTCTATA
718395 ATTGATATAGAAATGAC
1 ATTGATATAGAAATGAC
718412 ATTG-TATATGAAATGA
1 ATTGATATA-GAAATGA
718428 AAATGAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.33
Consensus pattern (17 bp):
ATTGATATAGAAATGAC
Found at i:719477 original size:252 final size:251
Alignment explanation
Indices: 719027--719526 Score: 788
Period size: 252 Copynumber: 2.0 Consensus size: 251
719017 TTGATAGGTG
* * *
719027 TATGTGAACTTAAGCTTAATGTTTTAGGTAGATATATGTTAGGCTATACTGAGTGGTTTGGTATG
1 TATGTAAACTTAAGCTTAATGTTTTAGGTAGATATATGTTAGGCTAAACTGAGTGATTTGGTATG
* *
719092 CTTGAAATTTTGATTTGAATGTTGTATTGATGATATGTTTTGATGATATAAATTGTGGTACCAAT
66 CTTGAAATCTTGATTTGAATGTTGCATTGATGATATGTTTTGATGATATAAATTGTGGTACCAAT
* * *
719157 AAGGGTACATTGGTGACACACCTAAGATGATTGTTTCAGCATGTTTTGAGTATGTTTGATCGTAT
131 AAGGGTACATTAGTGACACACCTAAGATGATTGTTTCAGCATGTTCTGAGTATGTTTGACCGTAT
* *
719222 TTTGAATAGGTTAAATGTTTGGTTTTTGAGTTGCTTAATGCCCAAGAAAGTAGATA
196 TTTGAATAGGTTAAATATTTGGTTTTTGAGTTGCATAATGCCCAAGAAAGTAGATA
* *
719278 TATGTAAACTTAAGCTTGATGTTTTAGGTAGATATATGTTAGGCTAAATTGAGTGATTTGGTATG
1 TATGTAAACTTAAGCTTAATGTTTTAGGTAGATATATGTTAGGCTAAACTGAGTGATTTGGTATG
*
719343 CTTGAAATCTTGATTTGAATGTTGCATTGGTGATATGTTTTTGATGATATAAATTGTGGTACCAA
66 CTTGAAATCTTGATTTGAATGTTGCATTGATGATATG-TTTTGATGATATAAATTGTGGTACCAA
* * **
719408 TGAGGGTACATTAGT-TCAGCACCTAAGATGATTGTTTTGGCATGTTCTGAGTATGTTTCG-CCG
130 TAAGGGTACATTAGTGACA-CACCTAAGATGATTGTTTCAGCATGTTCTGAGTATGTTT-GACCG
* *
719471 TATTTTGAATAGGTTAAATATTTGGTTTTTGAGTTTCATAATGCCCAAGCAAGTAG
193 TATTTTGAATAGGTTAAATATTTGGTTTTTGAGTTGCATAATGCCCAAGAAAGTAG
719527 GAATTTGTAG
Statistics
Matches: 227, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
251 96 0.42
252 130 0.57
253 1 0.00
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.41
Consensus pattern (251 bp):
TATGTAAACTTAAGCTTAATGTTTTAGGTAGATATATGTTAGGCTAAACTGAGTGATTTGGTATG
CTTGAAATCTTGATTTGAATGTTGCATTGATGATATGTTTTGATGATATAAATTGTGGTACCAAT
AAGGGTACATTAGTGACACACCTAAGATGATTGTTTCAGCATGTTCTGAGTATGTTTGACCGTAT
TTTGAATAGGTTAAATATTTGGTTTTTGAGTTGCATAATGCCCAAGAAAGTAGATA
Found at i:738950 original size:27 final size:27
Alignment explanation
Indices: 738914--739082 Score: 230
Period size: 27 Copynumber: 6.3 Consensus size: 27
738904 AGAGGTCAAT
*
738914 AAATGACCAAAATACCCCCATATGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* *
738941 AAATGACCAAAATACCCTCATAGGGTG
1 AAATGACCAAAATACCCCCATAGGGTA
* * * *
738968 AAATGGCCGAAATACCCCTATACGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
*
738995 AAATGACCAAAATACCCCCATAAGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* * *
739022 AAATGACCTAAATACCCCAATTGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
*
739049 AAATGACCAAAATACACCCATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
739076 AAATGAC
1 AAATGAC
739083 TGTTATACCC
Statistics
Matches: 121, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 121 1.00
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATACCCCCATAGGGTA
Found at i:739107 original size:54 final size:52
Alignment explanation
Indices: 738938--739109 Score: 161
Period size: 54 Copynumber: 3.2 Consensus size: 52
738928 CCCCCATATG
* * * *
738938 GTAAAATGACCAAAATACCCTCATAGGGTGAAATGGCCGAAATACCCCTA-TA
1 GTAAAATGACCAAAATACCC-CATAGGGTAAAATGACTGAAATACCCCTAGGA
* *
738990 CGGTAAAATGACCAAAATACCCCCATAAGGTAAAATGACCT-AAATACCCCAATTGG-
1 --GTAAAATGACCAAAATA-CCCCATAGGGTAAAATGA-CTGAAATACCCC--TAGGA
**
739046 GTAAAATGACCAAAATACACCCATAGGGTAAAATGACTGTTATACCCCTAGGA
1 GTAAAATGACCAAAATAC-CCCATAGGGTAAAATGACTGAAATACCCCTAGGA
*
739099 GATGAAATGAC
1 G-TAAAATGAC
739110 TGATATGGTC
Statistics
Matches: 98, Mismatches: 11, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
52 3 0.03
53 4 0.04
54 86 0.88
55 4 0.04
56 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (52 bp):
GTAAAATGACCAAAATACCCCATAGGGTAAAATGACTGAAATACCCCTAGGA
Found at i:739338 original size:26 final size:26
Alignment explanation
Indices: 739230--739336 Score: 142
Period size: 26 Copynumber: 4.1 Consensus size: 26
739220 TGGAGGAAGT
* * *
739230 ATACTGATACTGGCAGCTTTGCTACG
1 ATACTGTTACTGGCAGCTTTACTGCG
*
739256 ATACTGTTACTGGCAGCTTTACCGCG
1 ATACTGTTACTGGCAGCTTTACTGCG
739282 ATACTGTTACTGGCAGCTTTACTGCG
1 ATACTGTTACTGGCAGCTTTACTGCG
* * * *
739308 ATATTATAACTGGCAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTACTGCG
739334 ATA
1 ATA
739337 TTGGTGTGTT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTACTGCG
Found at i:746473 original size:23 final size:19
Alignment explanation
Indices: 746416--746475 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 19
746406 GTCAATTATT
*
746416 TAAATCAAAAGAAGAGAAAA
1 TAAATGAAAAGAA-AGAAAA
746436 TAAATGAAAAG-AAGAAAA
1 TAAATGAAAAGAAAGAAAA
746454 GTAATGATAGAAAAGAAAGAAA
1 -TAA--AT-GAAAAGAAAGAAA
746476 TAATAGATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
18 6 0.18
19 4 0.12
20 10 0.29
21 2 0.06
22 6 0.18
23 6 0.18
ACGTcount: A:0.68, C:0.02, G:0.18, T:0.12
Consensus pattern (19 bp):
TAAATGAAAAGAAAGAAAA
Found at i:754273 original size:3 final size:3
Alignment explanation
Indices: 754265--754297 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
754255 ATATTGTTAA
754265 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
754298 CTCTTAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:754469 original size:20 final size:20
Alignment explanation
Indices: 754427--754468 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
754417 GTTAACAATT
*
754427 AAATAATTTTTTAAATATAA
1 AAATAATTTTTAAAATATAA
*
754447 AAATTATTTTTAAAAT-TAA
1 AAATAATTTTTAAAATATAA
754466 AAA
1 AAA
754469 AGTATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATAATTTTTAAAATATAA
Found at i:754990 original size:18 final size:17
Alignment explanation
Indices: 754940--754990 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
754930 GATTTTTAAA
*
754940 ATTTAAAAATTAGAAAATT
1 ATTTAAAAA-TA-TAAATT
*
754959 -TTTAAAAATTTAAATT
1 ATTTAAAAATATAAATT
754975 ATTTAAAAAGTATAAA
1 ATTTAAAAA-TATAAA
754991 AAAATATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 5 0.19
17 9 0.33
18 13 0.48
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (17 bp):
ATTTAAAAATATAAATT
Found at i:755395 original size:30 final size:30
Alignment explanation
Indices: 755361--755425 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
755351 ACTTATTTTA
755361 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
755391 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
755421 TTGTT
1 TTGTT
755426 TGTTAAGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:755561 original size:11 final size:11
Alignment explanation
Indices: 755545--755575 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
755535 TATATATATT
755545 TAAAAATTATA
1 TAAAAATTATA
*
755556 TAAAAATAATA
1 TAAAAATTATA
755567 TAAAAATTA
1 TAAAAATTA
755576 ATACGGGCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:755838 original size:13 final size:13
Alignment explanation
Indices: 755804--755836 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
755794 TTTAACAAAC
755804 AATTCAAATAGAAA
1 AATT-AAATAGAAA
755818 AATTAAAT-GAAA
1 AATTAAATAGAAA
755830 AATTAAA
1 AATTAAA
755837 ATATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 4 0.21
14 4 0.21
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (13 bp):
AATTAAATAGAAA
Found at i:769154 original size:107 final size:107
Alignment explanation
Indices: 768968--769181 Score: 419
Period size: 107 Copynumber: 2.0 Consensus size: 107
768958 TTTCATTGTT
768968 TGTTCAATTTCCAGCAAGTTGTTTTTCTATGTTGTAGTCACTAAATTATTTTTATCTGGAGCTAC
1 TGTTCAATTTCCAGCAAGTTGTTTTTCTATGTTGTAGTCACTAAATTATTTTTATCTGGAGCTAC
769033 AGGGCTCCAAATTAAGTTCTGTTATTTTTTCCTAAAACTAGA
66 AGGGCTCCAAATTAAGTTCTGTTATTTTTTCCTAAAACTAGA
769075 TGTTCAATTTCCAGCAAGTTGTTTTTCTATGTTGTAGTCACTAAATTATTTTTATCTGGAGCTAC
1 TGTTCAATTTCCAGCAAGTTGTTTTTCTATGTTGTAGTCACTAAATTATTTTTATCTGGAGCTAC
*
769140 AGGGTTCCAAATTAAGTTCTGTTATTTTTTCCTAAAACTAGA
66 AGGGCTCCAAATTAAGTTCTGTTATTTTTTCCTAAAACTAGA
769182 CTCACATATA
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 106 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (107 bp):
TGTTCAATTTCCAGCAAGTTGTTTTTCTATGTTGTAGTCACTAAATTATTTTTATCTGGAGCTAC
AGGGCTCCAAATTAAGTTCTGTTATTTTTTCCTAAAACTAGA
Found at i:775474 original size:19 final size:19
Alignment explanation
Indices: 775439--775506 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 19
775429 TCAATTTCTT
775439 TTTC-TTTTTCATTCTCTCA
1 TTTCTTTTTTC-TTCTCTCA
* *
775458 TTTCTTTTTTCTCCTCTTGA
1 TTTCTTTTTTCTTCTC-TCA
* *
775478 ATTCTTTTATTTTTCTCTCA
1 TTTCTTTT-TTCTTCTCTCA
775498 TTTTCTTTT
1 -TTTCTTTT
775507 ATCAACAACT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
19 8 0.21
20 17 0.45
21 13 0.34
ACGTcount: A:0.09, C:0.22, G:0.01, T:0.68
Consensus pattern (19 bp):
TTTCTTTTTTCTTCTCTCA
Found at i:778668 original size:14 final size:14
Alignment explanation
Indices: 778643--778678 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
778633 TTTCTCCTCG
778643 TTCTTTTCCTTTTCT
1 TTCTTTT-CTTTTCT
778658 TTCTTTTCTTTTCT
1 TTCTTTTCTTTTCT
778672 TT-TTTTC
1 TTCTTTTC
778679 ATGAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.24
14 9 0.43
15 7 0.33
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTCTTTTCTTTTCT
Found at i:781308 original size:21 final size:20
Alignment explanation
Indices: 781273--781317 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
781263 AATAGAAATC
781273 AATAGAATTGTTATTTTAAAA
1 AATAGAATTGTTA-TTTAAAA
*
781294 AATAGAATT-TATATTTAGAA
1 AATAGAATTGT-TATTTAAAA
781314 AATA
1 AATA
781318 AAATCTCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (20 bp):
AATAGAATTGTTATTTAAAA
Found at i:783525 original size:50 final size:50
Alignment explanation
Indices: 783470--783567 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 50
783460 AACATACCTC
783470 ATATGCATATTCAACTACTATTTTACCTTTCATCCTCCAACCACAAATCA
1 ATATGCATATTCAACTACTATTTTACCTTTCATCCTCCAACCACAAATCA
*
783520 ATATGCATATTCAACTACTATTTTACCTTTCATCCTTCAACCACAAAT
1 ATATGCATATTCAACTACTATTTTACCTTTCATCCTCCAACCACAAAT
783568 TAATCCACAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.36
Consensus pattern (50 bp):
ATATGCATATTCAACTACTATTTTACCTTTCATCCTCCAACCACAAATCA
Found at i:797955 original size:26 final size:26
Alignment explanation
Indices: 797917--797968 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
797907 TTCTAAAATG
797917 GATACATGCTATGATATTGTGAAACT
1 GATACATGCTATGATATTGTGAAACT
* * *
797943 GATATATGTTATGATATTTTGAAACT
1 GATACATGCTATGATATTGTGAAACT
797969 ACTGTAGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (26 bp):
GATACATGCTATGATATTGTGAAACT
Found at i:804572 original size:33 final size:35
Alignment explanation
Indices: 804535--804602 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
804525 GCATTTTTGA
* *
804535 CACTG-TACTGAGATGGGCTAAGGCCCAA-ACTGT
1 CACTGATACTGAAAAGGGCTAAGGCCCAAGACTGT
* *
804568 CACTGATACTGAAAAGGGCTTAGGCCTAAGACTGT
1 CACTGATACTGAAAAGGGCTAAGGCCCAAGACTGT
804603 TCAACTGTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.17
34 19 0.66
35 5 0.17
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.22
Consensus pattern (35 bp):
CACTGATACTGAAAAGGGCTAAGGCCCAAGACTGT
Found at i:810270 original size:16 final size:17
Alignment explanation
Indices: 810249--810283 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
810239 ATTTTAAACA
*
810249 AATTAATTAA-TTTCTC
1 AATTAAATAATTTTCTC
810265 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
810282 AA
1 AA
810284 CCCAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:811453 original size:20 final size:20
Alignment explanation
Indices: 811428--811511 Score: 100
Period size: 20 Copynumber: 4.2 Consensus size: 20
811418 GCGCTTGTAC
*
811428 CTGTTTGCACTTTGGTGCCT
1 CTGTTTGCACTTCGGTGCCT
*
811448 CTGTTTGGACTTCGGTGCCT
1 CTGTTTGCACTTCGGTGCCT
*
811468 CTGATTGCACATT--GTGCCT
1 CTGTTTGCAC-TTCGGTGCCT
* *
811487 CTGTCTGCACCTCGGTGCCT
1 CTGTTTGCACTTCGGTGCCT
811507 CTGTT
1 CTGTT
811512 ACACATTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
18 1 0.02
19 14 0.26
20 36 0.68
21 2 0.04
ACGTcount: A:0.07, C:0.29, G:0.25, T:0.39
Consensus pattern (20 bp):
CTGTTTGCACTTCGGTGCCT
Found at i:811487 original size:39 final size:39
Alignment explanation
Indices: 811432--811518 Score: 113
Period size: 39 Copynumber: 2.2 Consensus size: 39
811422 TTGTACCTGT
* * * *
811432 TTGCACTTTGGTGCCTCTGTTTGGACTTCGGTGCCTCTG
1 TTGCACATTGGTGCCTCTGTCTGCACCTCGGTGCCTCTG
811471 ATTGCACATT-GTGCCTCTGTCTGCACCTCGGTGCCTCTG
1 -TTGCACATTGGTGCCTCTGTCTGCACCTCGGTGCCTCTG
*
811510 TTACACATT
1 TTGCACATT
811519 TTTGATGCCT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
38 8 0.19
39 26 0.62
40 8 0.19
ACGTcount: A:0.10, C:0.29, G:0.23, T:0.38
Consensus pattern (39 bp):
TTGCACATTGGTGCCTCTGTCTGCACCTCGGTGCCTCTG
Found at i:815599 original size:20 final size:20
Alignment explanation
Indices: 815565--815606 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
815555 AACTATTTAA
** *
815565 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
815585 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
815605 AT
1 AT
815607 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:818641 original size:15 final size:16
Alignment explanation
Indices: 818621--818656 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
818611 GTTAATTAAA
*
818621 TTTTAAATATA-ATAT
1 TTTTAAACATATATAT
818636 TTTTAAACATATATAT
1 TTTTAAACATATATAT
818652 TTTTA
1 TTTTA
818657 TAAATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTAAACATATATAT
Found at i:819286 original size:3 final size:3
Alignment explanation
Indices: 819278--819302 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
819268 NNNNNNNNNN
819278 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
819303 TTTAGAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:819490 original size:23 final size:23
Alignment explanation
Indices: 819464--819508 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
819454 CTCCTTTGCA
* *
819464 TTATTAAAATTTAGTTAATAAAT
1 TTATCAAAATTTAATTAATAAAT
*
819487 TTATCAATATTTAATTAATAAA
1 TTATCAAAATTTAATTAATAAA
819509 AAATAATAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TTATCAAAATTTAATTAATAAAT
Found at i:824099 original size:21 final size:21
Alignment explanation
Indices: 824074--824114 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
824064 GGTAACTGGT
824074 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCGATACTTTTTG
*
824095 AAAAGGTGTCGATACTTTTT
1 AAAAGGTATCGATACTTTTT
824115 TATAATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.39
Consensus pattern (21 bp):
AAAAGGTATCGATACTTTTTG
Found at i:841857 original size:52 final size:51
Alignment explanation
Indices: 841774--841873 Score: 164
Period size: 52 Copynumber: 1.9 Consensus size: 51
841764 TATTAATCTG
* *
841774 AACAGCATAATAATTAACTGTTTAAAATTAAATAATTTGATAATATTTTATT
1 AACAGCATAATAATTAACGGTTTAAAATTAAATAA-TTAATAATATTTTATT
*
841826 AACATCATAATAATTAACGGTTTAAAATTAAATAATTAATAATATTTT
1 AACAGCATAATAATTAACGGTTTAAAATTAAATAATTAATAATATTTT
841874 CTTACCATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 12 0.27
52 33 0.73
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (51 bp):
AACAGCATAATAATTAACGGTTTAAAATTAAATAATTAATAATATTTTATT
Found at i:853036 original size:20 final size:21
Alignment explanation
Indices: 853011--853062 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
853001 GTATCGATCC
*
853011 GGTATCGATACT-TTT-CTTAA
1 GGTATCGATA-TATTTCCTAAA
853031 GGTATCGATATATTTCCTAAA
1 GGTATCGATATATTTCCTAAA
853052 GGTATCGATAT
1 GGTATCGATAT
853063 TCCTGCTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 1 0.03
20 13 0.45
21 15 0.52
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (21 bp):
GGTATCGATATATTTCCTAAA
Found at i:855633 original size:21 final size:21
Alignment explanation
Indices: 855584--855633 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
855574 GTCCAACGAC
* *
855584 GGTGGTCAATGATGGCCCAAT
1 GGTGGTCGATGATGACCCAAT
* *
855605 GGTGGTCGATGATGACTCGAT
1 GGTGGTCGATGATGACCCAAT
855626 GGTGGTCG
1 GGTGGTCG
855634 GTAATGACGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.18, C:0.16, G:0.40, T:0.26
Consensus pattern (21 bp):
GGTGGTCGATGATGACCCAAT
Found at i:857388 original size:248 final size:249
Alignment explanation
Indices: 857014--857488 Score: 684
Period size: 248 Copynumber: 1.9 Consensus size: 249
857004 TCTTATGTTG
* * * * * *
857014 GTATACCAAAGGATTGTGAGCGCTCACTTCTCAGTTTTTGTGATTTTGGGCGTTGAGGCCCTAGA
1 GTATACCAAAGGATTGTGAGCACTAACCTATCAGTTTTTGTGATTTTGAGCATTGAGGCCCTAGA
* * * *
857079 ACATGTGGAGAGATAAGGGAATGTCGAGCTATACTCTATTTATCGGGACATGTTACTATACAAGA
66 ACATGTGGAGAGATAAGGGAATGTCAAGCTATACTCTATTCACCAGGACATGTTACTATACAAGA
*
857144 GAGTGTATTGCTTTGCGCTGCACTTATGGGACATGTTATAAGGACTCTTCAAGTCACTCTGAGGC
131 GAGTGTATTGCTTTGCGCTGCACTTATGGAACATGTTATAAGGACTCTTCAAGTCACTCTGAGGC
* *
857209 GTTATAAGGAGATCTGCATATCCAACGAGACTTAAGTTATTTTATTATTTATTT
196 ATTATAAGGAGATCTACATATCCAACGAGACTTAAGTTATTTTATTATTTATTT
* * *
857263 GTATACCAAAGGATTGTGAGTACTAACCTATCAG-TTTTGTGATTTTGAGCATTGATGCTCT-GT
1 GTATACCAAAGGATTGTGAGCACTAACCTATCAGTTTTTGTGATTTTGAGCATTGAGGCCCTAG-
* * * * *
857326 GACATGTGGAGAGATAAGGGAATGTCAAGCTTTGCTCTATTCACCAGGACATGTTTCTATACATG
65 AACATGTGGAGAGATAAGGGAATGTCAAGCTATACTCTATTCACCAGGACATGTTACTATACAAG
* ** *
857391 AGAGTGTATTGCTTTGTGCTGCACTTATGGAACATGTTATAAGGACTCTTTGAGTCACTTTGAGG
130 AGAGTGTATTGCTTTGCGCTGCACTTATGGAACATGTTATAAGGACTCTTCAAGTCACTCTGAGG
* *
857456 CATTGTAAGGAGATTTACATATCCAACGAGACT
195 CATTATAAGGAGATCTACATATCCAACGAGACT
857489 GATAAAATAA
Statistics
Matches: 198, Mismatches: 27, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
247 1 0.01
248 168 0.85
249 29 0.15
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (249 bp):
GTATACCAAAGGATTGTGAGCACTAACCTATCAGTTTTTGTGATTTTGAGCATTGAGGCCCTAGA
ACATGTGGAGAGATAAGGGAATGTCAAGCTATACTCTATTCACCAGGACATGTTACTATACAAGA
GAGTGTATTGCTTTGCGCTGCACTTATGGAACATGTTATAAGGACTCTTCAAGTCACTCTGAGGC
ATTATAAGGAGATCTACATATCCAACGAGACTTAAGTTATTTTATTATTTATTT
Found at i:858016 original size:43 final size:43
Alignment explanation
Indices: 857912--858054 Score: 225
Period size: 43 Copynumber: 3.3 Consensus size: 43
857902 TTATGTGAAA
* * *
857912 AAACGCCGCTAAAGATCATGACCTGTAGCGGCACTTTTATCAC
1 AAACGCCGCTAAAGATCTTGACCTTTAGCGGCGCTTTTATCAC
857955 -AACGCCGCTAAAGATCTTGACCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGATCTTGACCTTTAGCGGCGCTTTTATCAC
** *
857997 AAACGCAACTAAAGATCTTGACCTTTAGCGGCGTTTTTATCAC
1 AAACGCCGCTAAAGATCTTGACCTTTAGCGGCGCTTTTATCAC
858040 AAACGCCGCTAAAGA
1 AAACGCCGCTAAAGA
858055 ACAAACCTTT
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 39 0.43
43 52 0.57
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCTTGACCTTTAGCGGCGCTTTTATCAC
Found at i:858094 original size:85 final size:85
Alignment explanation
Indices: 857910--858094 Score: 219
Period size: 85 Copynumber: 2.2 Consensus size: 85
857900 GTTTATGTGA
* **
857910 AAAAACGCCGCTAAAGATCATGACCTGTAGCGGCACTTTTATCACAACGCCGCTAAAGATCTTGA
1 AAAAACGCCGCTAAAGATCATGACCTGTAGCGGCACTTTTATCACAACGCCGCTAAAGAACTAAA
* * *
857975 CCTTTAGCGGCGCTTTTATC
66 CCTTTAGCGACGCTTCTAGC
* ** * * **
857995 ACAAACGCAACTAAAGATCTTGACCTTTAGCGGCGTTTTTATCACAAACGCCGCTAAAGAAC-AA
1 AAAAACGCCGCTAAAGATCATGACCTGTAGCGGCACTTTTATCAC-AACGCCGCTAAAGAACTAA
*
858059 ACCTTTAGCGACGCTTCTCGC
65 ACCTTTAGCGACGCTTCTAGC
*
858080 AAAAACACCGCTAAA
1 AAAAACGCCGCTAAA
858095 AACATAACCT
Statistics
Matches: 81, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
85 66 0.81
86 15 0.19
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (85 bp):
AAAAACGCCGCTAAAGATCATGACCTGTAGCGGCACTTTTATCACAACGCCGCTAAAGAACTAAA
CCTTTAGCGACGCTTCTAGC
Found at i:863920 original size:7 final size:7
Alignment explanation
Indices: 863908--864090 Score: 72
Period size: 7 Copynumber: 25.7 Consensus size: 7
863898 CTTAATCTTT
863908 TAAACCC
1 TAAACCC
863915 TAAACCC
1 TAAACCC
* *
863922 TAAAACA
1 TAAACCC
863929 TAAACCC
1 TAAACCC
863936 TAAACCC
1 TAAACCC
863943 -ATAACCC
1 TA-AACCC
863950 -ATAACCC
1 TA-AACCC
*
863957 ATAACCCC
1 -TAAACCC
*
863965 TAAACCT
1 TAAACCC
863972 TAAACACC
1 TAAAC-CC
863980 --AACCC
1 TAAACCC
*
863985 TTAAACCA
1 -TAAACCC
*
863993 TAAACCA
1 TAAACCC
* *
864000 TAATCCA
1 TAAACCC
* *
864007 TAATCCA
1 TAAACCC
*
864014 TAATCCC
1 TAAACCC
*
864021 TAAACACA
1 TAAAC-CC
* *
864029 TAATCCT
1 TAAACCC
*
864036 TAAACCT
1 TAAACCC
*
864043 TAAA--A
1 TAAACCC
864048 TAGTAACTCC
1 TA--AAC-CC
* *
864058 TAAATCT
1 TAAACCC
864065 TAAACCC
1 TAAACCC
*
864072 TAAACCA
1 TAAACCC
864079 TAAACCC
1 TAAACCC
864086 TAAAC
1 TAAAC
864091 TATAATGATA
Statistics
Matches: 139, Mismatches: 24, Indels: 26
0.74 0.13 0.14
Matches are distributed among these distances:
5 4 0.03
6 4 0.03
7 112 0.81
8 16 0.12
9 1 0.01
10 2 0.01
ACGTcount: A:0.46, C:0.33, G:0.01, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:863932 original size:21 final size:21
Alignment explanation
Indices: 863908--864090 Score: 106
Period size: 21 Copynumber: 8.6 Consensus size: 21
863898 CTTAATCTTT
*
863908 TAAACCCTAAACCCTAAAACA
1 TAAACCCTAAACCCTAAACCA
*
863929 TAAACCCTAAACCCATAACCCA
1 TAAACCCTAAACCC-TAAACCA
* *
863951 T-AACCCATAACCCCTAAACCT
1 TAAACCC-TAAACCCTAAACCA
863972 TAAACACC--AACCCTTAAACCA
1 TAAAC-CCTAAACCC-TAAACCA
* * * *
863993 TAAACCATAATCCATAATCCA
1 TAAACCCTAAACCCTAAACCA
* * * *
864014 TAATCCCTAAACACATAATCCT
1 TAAACCCTAAAC-CCTAAACCA
* * *
864036 TAAACCTTAAA--ATAGTAACTCC
1 TAAACCCTAAACCCTA--AAC-CA
* *
864058 TAAATCTTAAACCCTAAACCA
1 TAAACCCTAAACCCTAAACCA
864079 TAAACCCTAAAC
1 TAAACCCTAAAC
864091 TATAATGATA
Statistics
Matches: 125, Mismatches: 24, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
19 3 0.02
20 5 0.04
21 64 0.51
22 49 0.39
23 2 0.02
24 2 0.02
ACGTcount: A:0.46, C:0.33, G:0.01, T:0.20
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAACCA
Found at i:864073 original size:14 final size:14
Alignment explanation
Indices: 864065--864095 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
864055 TCCTAAATCT
864065 TAAACCCTAAACCA
1 TAAACCCTAAACCA
*
864079 TAAACCCTAAACTA
1 TAAACCCTAAACCA
864093 TAA
1 TAA
864096 TGATAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:864187 original size:21 final size:22
Alignment explanation
Indices: 864158--864200 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
864148 TAGCGGCGCT
*
864158 TCTTCAAAAA-CGCCGCTAAAG
1 TCTTCAAAAAGAGCCGCTAAAG
*
864179 TCTTGAAAAAGAGCCGCTAAAG
1 TCTTCAAAAAGAGCCGCTAAAG
864201 CCCCAAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (22 bp):
TCTTCAAAAAGAGCCGCTAAAG
Found at i:864297 original size:40 final size:40
Alignment explanation
Indices: 864220--864331 Score: 111
Period size: 40 Copynumber: 2.8 Consensus size: 40
864210 CTCTAAAAAT
* * * ***
864220 GCCGCTAATGCTC-ATTTTTAGCGGCATTTTCCAAAAAGC
1 GCCGCTAATGCTCGATCTTTAGCTGCGTTTTTTGAAAAGC
**
864259 GGGGCTAATGCTCGATCTTTAGC-GACGTTTTTTGAAAAGC
1 GCCGCTAATGCTCGATCTTTAGCTG-CGTTTTTTGAAAAGC
* *
864299 GCCGCTAATGCTTGATTTTTAGCTGCGTTTTTT
1 GCCGCTAATGCTCGATCTTTAGCTGCGTTTTTT
864332 TATCCAAATG
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
39 12 0.20
40 46 0.78
41 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (40 bp):
GCCGCTAATGCTCGATCTTTAGCTGCGTTTTTTGAAAAGC
Found at i:864354 original size:12 final size:12
Alignment explanation
Indices: 864337--864362 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
864327 TTTTTTATCC
864337 AAATGCCGCTAA
1 AAATGCCGCTAA
864349 AAATGCCGCTAA
1 AAATGCCGCTAA
864361 AA
1 AA
864363 GCCTATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (12 bp):
AAATGCCGCTAA
Found at i:869690 original size:18 final size:18
Alignment explanation
Indices: 869669--869715 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
869659 CTGCAATAAG
869669 AAAATGTTTTG-AAATTGA
1 AAAATGTTTTGTAAA-TGA
* *
869687 AAAACGATTTGTAAATGA
1 AAAATGTTTTGTAAATGA
*
869705 ATAATGTTTTG
1 AAAATGTTTTG
869716 GAAACGAACG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.43, C:0.02, G:0.17, T:0.38
Consensus pattern (18 bp):
AAAATGTTTTGTAAATGA
Found at i:870717 original size:20 final size:20
Alignment explanation
Indices: 870692--870796 Score: 65
Period size: 20 Copynumber: 5.3 Consensus size: 20
870682 TGTACTTCGA
870692 TGCCTCTGATTGCACAATTG
1 TGCCTCTGATTGCACAATTG
* *
870712 TGCCTCTGTTTTCAC--TTCGG
1 TGCCTCTGATTGCACAATT--G
* *
870732 TGCCTCTAATTGCAAAATTG
1 TGCCTCTGATTGCACAATTG
* *
870752 TGCCTCCG-TTGCAC-TTTG
1 TGCCTCTGATTGCACAATTG
* * * *
870770 ATGCCTCTAATTTCATAATCG
1 -TGCCTCTGATTGCACAATTG
870791 TGCCTC
1 TGCCTC
870797 AATTTGCACT
Statistics
Matches: 62, Mismatches: 16, Indels: 14
0.67 0.17 0.15
Matches are distributed among these distances:
18 5 0.08
19 11 0.18
20 42 0.68
21 2 0.03
22 2 0.03
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (20 bp):
TGCCTCTGATTGCACAATTG
Found at i:870778 original size:39 final size:40
Alignment explanation
Indices: 870679--870817 Score: 154
Period size: 40 Copynumber: 3.5 Consensus size: 40
870669 GGTTGTATAG
* * * *
870679 GTTTGTACTTCGATGCCTCTGATTGCACAATTGTGCCTCT
1 GTTTGCACTTCGATGCCTCTAATTGCAAAATTGTGCCTCC
* *
870719 GTTTTCACTTCGGTGCCTCTAATTGCAAAATTGTGCCTCC
1 GTTTGCACTTCGATGCCTCTAATTGCAAAATTGTGCCTCC
* * * * *
870759 G-TTGCACTTTGATGCCTCTAATTTCATAATCGTGCCTCA
1 GTTTGCACTTCGATGCCTCTAATTGCAAAATTGTGCCTCC
* *
870798 ATTTGCACTTCGGTGCCTCT
1 GTTTGCACTTCGATGCCTCT
870818 GATAGCACTA
Statistics
Matches: 82, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
39 31 0.38
40 51 0.62
ACGTcount: A:0.17, C:0.27, G:0.18, T:0.39
Consensus pattern (40 bp):
GTTTGCACTTCGATGCCTCTAATTGCAAAATTGTGCCTCC
Found at i:880032 original size:16 final size:16
Alignment explanation
Indices: 880007--880040 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
879997 GTTTCCTGTA
880007 CTGCCAATGCCATATC
1 CTGCCAATGCCATATC
* *
880023 CTGCCCATGCCATGTC
1 CTGCCAATGCCATATC
880039 CT
1 CT
880041 AAACATGGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.41, G:0.15, T:0.26
Consensus pattern (16 bp):
CTGCCAATGCCATATC
Found at i:880156 original size:50 final size:50
Alignment explanation
Indices: 880031--880166 Score: 200
Period size: 50 Copynumber: 2.7 Consensus size: 50
880021 TCCTGCCCAT
* * ** *
880031 GCCATGTCCTAAACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTGCCAAC
* *
880081 GTCATGTCCCAGACATGGTCTTACATAGGACCTCTTATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTGCCAAC
*
880131 GCCATGTCCCAGACATGGTCTTACATGGGATCTCTT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
880167 TACCCAAATG
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 76 1.00
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTGCCAAC
Found at i:887847 original size:50 final size:50
Alignment explanation
Indices: 887772--888013 Score: 258
Period size: 50 Copynumber: 4.9 Consensus size: 50
887762 CATTTGGGTA
* **
887772 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
*
887822 AAGAGGTCCCATGTAAGATCATGTCTGGGACATGGCATTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
** * * *
887872 AAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* ** * * * *
887922 GAGAACTCCCATGTAAGACCATATCTAGGATATGGCATTGGCAGTAC-AGGA-
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA--CCGA-GAT
* * *
887973 AACA--TCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
888014 TGTTATTATC
Statistics
Matches: 161, Mismatches: 28, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
49 32 0.20
50 124 0.77
51 3 0.02
52 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
Found at i:894754 original size:50 final size:48
Alignment explanation
Indices: 894674--894912 Score: 178
Period size: 50 Copynumber: 4.8 Consensus size: 48
894664 TGGGTAAAGC
* *
894674 GATCACATGTAAGACCATGTCTTGGACATGGCATTGGCATTGAGATAA
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTGAGATAA
* * *
894722 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGATATGAGA
1 GA--TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTGAGAT-A-A
* * *** * *
894774 TATCCC-TCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATGA
1 GATCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCATTGAGATAA
* * * * * *
894822 GAACTCTCATGAAAGACCATATCTGGGATATGGTATTGGTAGTACTG-GA-AA
1 G-A-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-T--TGAGATAA
* * *
894873 CATCCCATGTAAGACTATGTCTGGGACATGGCTTTGGCAT
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
894913 GTTATTATCA
Statistics
Matches: 147, Mismatches: 33, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
48 4 0.03
49 31 0.21
50 106 0.72
51 3 0.02
52 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (48 bp):
GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTGAGATAA
Found at i:897749 original size:9 final size:9
Alignment explanation
Indices: 897731--897773 Score: 59
Period size: 9 Copynumber: 4.6 Consensus size: 9
897721 TTAATTTAGA
*
897731 TAAAACTAT
1 TAAAATTAT
897740 TAAAATTATT
1 TAAAATTA-T
897750 TAAAATATAT
1 TAAAAT-TAT
897760 TAAAATTAT
1 TAAAATTAT
897769 TAAAA
1 TAAAA
897774 ATATAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 15 0.48
10 14 0.45
11 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (9 bp):
TAAAATTAT
Found at i:897760 original size:20 final size:20
Alignment explanation
Indices: 897737--897778 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
897727 TAGATAAAAC
*
897737 TATTAAAATTATTTAAAATA
1 TATTAAAATTATTAAAAATA
897757 TATTAAAATTATTAAAAATA
1 TATTAAAATTATTAAAAATA
897777 TA
1 TA
897779 AAAAATTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TATTAAAATTATTAAAAATA
Found at i:898213 original size:10 final size:10
Alignment explanation
Indices: 898153--898253 Score: 52
Period size: 10 Copynumber: 10.3 Consensus size: 10
898143 AAAAATCAAT
898153 AAAAA-TAT-
1 AAAAATTATA
898161 AAAAA-TAT-
1 AAAAATTATA
898169 AAAAATCTATA
1 AAAAAT-TATA
*
898180 AAAAAATAT-
1 AAAAATTATA
** *
898189 TTAAATTAGA
1 AAAAATTATA
*
898199 TAAAATTATA
1 AAAAATTATA
*
898209 AAAAAATATA
1 AAAAATTATA
*
898219 TCAAAATTATTA
1 -AAAAATTA-TA
*
898231 TAAAA-TATA
1 AAAAATTATA
898240 AAAAATTCATA
1 AAAAATT-ATA
898251 AAA
1 AAA
898254 GTTTTCCTTA
Statistics
Matches: 72, Mismatches: 13, Indels: 13
0.73 0.13 0.13
Matches are distributed among these distances:
8 13 0.18
9 11 0.15
10 25 0.35
11 21 0.29
12 2 0.03
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (10 bp):
AAAAATTATA
Found at i:898214 original size:31 final size:31
Alignment explanation
Indices: 898153--898244 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 31
898143 AAAAATCAAT
* * *
898153 AAAAATAT-AAAAATAT-A-AAAATCTATAA
1 AAAAATATCAAAATTATGATAAAATATAAAA
**
898181 AAAAATATTTAAATTA-GATAAAATTATAAAA
1 AAAAATATCAAAATTATGATAAAA-TATAAAA
* *
898212 AAATATATCAAAATTATTATAAAATATAAAA
1 AAAAATATCAAAATTATGATAAAATATAAAA
898243 AA
1 AA
898245 TTCATAAAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
28 8 0.16
29 6 0.12
30 4 0.08
31 27 0.53
32 6 0.12
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.29
Consensus pattern (31 bp):
AAAAATATCAAAATTATGATAAAATATAAAA
Found at i:898225 original size:39 final size:41
Alignment explanation
Indices: 898151--898253 Score: 95
Period size: 39 Copynumber: 2.6 Consensus size: 41
898141 TAAAAAATCA
* * **
898151 ATAAAA-ATATAAAAATATAAAAATCTATAAAAAAA-TATT
1 ATAAAATAGATAAAATTATAAAAAAATATAAAAAAATTATT
* **
898190 -TAAATTAGATAAAATTATAAAAAAATATATCAAAATTATT
1 ATAAAATAGATAAAATTATAAAAAAATATAAAAAAATTATT
* *
898230 ATAAAATATAAAAAATTCATAAAA
1 ATAAAATAGATAAAATT-ATAAAA
898254 GTTTTCCTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
38 4 0.08
39 23 0.46
40 4 0.08
41 13 0.26
42 6 0.12
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (41 bp):
ATAAAATAGATAAAATTATAAAAAAATATAAAAAAATTATT
Found at i:898235 original size:11 final size:10
Alignment explanation
Indices: 898157--898246 Score: 60
Period size: 10 Copynumber: 9.0 Consensus size: 10
898147 ATCAATAAAA
*
898157 ATATAAAAAT
1 ATATAAAATT
898167 ATA-AAAATCT
1 ATATAAAAT-T
* *
898177 ATAAAAAAAT
1 ATATAAAATT
*
898187 AT-TTAAATT
1 ATATAAAATT
*
898196 AGATAAAATT
1 ATATAAAATT
* *
898206 ATAAAAAAAT
1 ATATAAAATT
898216 ATATCAAAATT
1 ATAT-AAAATT
898227 ATTATAAAA-T
1 A-TATAAAATT
*
898237 ATAAAAAATT
1 ATATAAAATT
898247 CATAAAAGTT
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
9 15 0.25
10 29 0.48
11 14 0.23
12 3 0.05
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.32
Consensus pattern (10 bp):
ATATAAAATT
Found at i:899366 original size:17 final size:17
Alignment explanation
Indices: 899319--899374 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 17
899309 NNNNNNNNNA
899319 AAAATAAAAATATATAAT
1 AAAATAAAAAT-TATAAT
*
899337 AAAATAGAAAATTATAGT
1 AAAATA-AAAATTATAAT
899355 AAAATAAAAATTATAA-
1 AAAATAAAAATTATAAT
899371 AAAA
1 AAAA
899375 AATCATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 4 0.11
17 9 0.26
18 17 0.49
19 5 0.14
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (17 bp):
AAAATAAAAATTATAAT
Found at i:902346 original size:13 final size:13
Alignment explanation
Indices: 902328--902386 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
902318 CTAAAATTTT
902328 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
902341 TCAAAAGCACTTT
1 TCAAAAGCACTTC
*
902354 TCTACAA-CACTTC
1 TC-AAAAGCACTTC
*
902367 TCAAAAGCACTTT
1 TCAAAAGCACTTC
902380 TCAAAAG
1 TCAAAAG
902387 TAATGAAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
12 3 0.08
13 33 0.85
14 3 0.08
ACGTcount: A:0.39, C:0.27, G:0.07, T:0.27
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:902633 original size:10 final size:9
Alignment explanation
Indices: 902615--902713 Score: 54
Period size: 10 Copynumber: 10.0 Consensus size: 9
902605 GAACACTTAC
902615 AAAATTTTA
1 AAAATTTTA
902624 AAAGATTTTA
1 AAA-ATTTTA
902634 AAAACTTTTGA
1 AAAA-TTTT-A
*
902645 AATATTTTTA
1 AA-AATTTTA
902655 ATAAATTTTA
1 A-AAATTTTA
* *
902665 AATATTTTTCT
1 AA-AATTTT-A
* *
902676 ACATTTTTA
1 AAAATTTTA
*
902685 ATATATTTTA
1 A-AAATTTTA
902695 TAAAATTTTA
1 -AAAATTTTA
*
902705 ATAATTTTA
1 AAAATTTTA
902714 TATCTATATA
Statistics
Matches: 70, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
9 14 0.20
10 45 0.64
11 10 0.14
12 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (9 bp):
AAAATTTTA
Found at i:902706 original size:20 final size:19
Alignment explanation
Indices: 902615--902715 Score: 73
Period size: 20 Copynumber: 5.1 Consensus size: 19
902605 GAACACTTAC
*
902615 AAAATTTTAAAAGATTTTA-
1 AAAATTTT-AAATATTTTAT
902634 AAAACTTTTGAAATATTTT-T
1 AAAA-TTTT-AAATATTTTAT
*
902654 AATAAATTTTAAATATTTTTCT
1 -A-AAATTTTAAATA-TTTTAT
* *
902676 ACATTTTTAATATATTTTAT
1 AAAATTTTAA-ATATTTTAT
902696 AAAATTTT-AATAATTTTAT
1 AAAATTTTAAAT-ATTTTAT
902715 A
1 A
902716 TCTATATATG
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
18 2 0.03
19 13 0.19
20 35 0.52
21 13 0.19
22 4 0.06
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (19 bp):
AAAATTTTAAATATTTTAT
Found at i:902712 original size:30 final size:30
Alignment explanation
Indices: 902619--902712 Score: 86
Period size: 30 Copynumber: 3.1 Consensus size: 30
902609 ACTTACAAAA
*
902619 TTTTAA-AAGATTTTAAAAACTTTTGAA-ATAT
1 TTTTAATAA-ATTTTAAAAA-TTTT-AATACAT
* **
902650 TTTTAATAAATTTTAAATATTTTTCTACAT
1 TTTTAATAAATTTTAAAAATTTTAATACAT
*
902680 TTTTAATATATTTTATAAAATTTTAATA-AT
1 TTTTAATAAATTTTA-AAAATTTTAATACAT
902710 TTT
1 TTT
902713 ATATCTATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
30 26 0.50
31 24 0.46
32 2 0.04
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTTAATAAATTTTAAAAATTTTAATACAT
Found at i:903889 original size:20 final size:20
Alignment explanation
Indices: 903851--903890 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
903841 TGAATTTTGA
*
903851 GACTAAATTTTGGGAAGTTT
1 GACTAAATTTTAGGAAGTTT
903871 GACTAAAATTTTAGG-AGTTT
1 GACT-AAATTTTAGGAAGTTT
903891 AATAAGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.40
Consensus pattern (20 bp):
GACTAAATTTTAGGAAGTTT
Found at i:904938 original size:2 final size:2
Alignment explanation
Indices: 904931--904958 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
904921 TTTGCTGCAG
904931 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
904959 TTTGTTGGTA
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):
AT
Found at i:905219 original size:6 final size:6
Alignment explanation
Indices: 905204--905323 Score: 60
Period size: 6 Copynumber: 19.5 Consensus size: 6
905194 TGGTAACCTG
* * * * * * *
905204 TAAGCAA TAACAA TAAGAA TAAGAA CAATAA TAACAA TAATAA CAATAA
1 TAAG-AA TAAGAA TAAGAA TAAGAA TAAGAA TAAGAA TAAGAA TAAGAA
* * * * * * * * * *
905253 TAACAACA AAAGAA TAACAA GAAGAA CAAGAA CAATAA TAACAA CAATAA
1 TAA-GA-A TAAGAA TAAGAA TAAGAA TAAGAA TAAGAA TAAGAA TAAGAA
905303 TAAGAA TAAGAA TAAGAA TAA
1 TAAGAA TAAGAA TAAGAA TAA
905324 TAATTATAAT
Statistics
Matches: 87, Mismatches: 24, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
6 79 0.91
7 5 0.06
8 3 0.03
ACGTcount: A:0.67, C:0.10, G:0.08, T:0.15
Consensus pattern (6 bp):
TAAGAA
Found at i:905236 original size:12 final size:12
Alignment explanation
Indices: 905209--905305 Score: 76
Period size: 12 Copynumber: 8.4 Consensus size: 12
905199 ACCTGTAAGC
* *
905209 AATAACAATAAG
1 AATAACAACAAT
*
905221 AATAAGAACAAT
1 AATAACAACAAT
905233 AAT---AACAAT
1 AATAACAACAAT
*
905242 AATAACAATAAT
1 AATAACAACAAT
* *
905254 AACAACAA-AAG
1 AATAACAACAAT
* *
905265 AATAACAAGAAG
1 AATAACAACAAT
* *
905277 AACAAGAACAAT
1 AATAACAACAAT
905289 AATAACAACAAT
1 AATAACAACAAT
905301 AATAA
1 AATAA
905306 GAATAAGAAT
Statistics
Matches: 68, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
9 9 0.13
11 9 0.13
12 50 0.74
ACGTcount: A:0.68, C:0.11, G:0.06, T:0.14
Consensus pattern (12 bp):
AATAACAACAAT
Found at i:905239 original size:9 final size:9
Alignment explanation
Indices: 905215--905258 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
905205 AAGCAATAAC
*
905215 AATAAGAAT
1 AATAACAAT
*
905224 AAGAACAAT
1 AATAACAAT
905233 AATAACAAT
1 AATAACAAT
905242 AATAACAAT
1 AATAACAAT
905251 AATAACAA
1 AATAACAA
905259 CAAAAGAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.68, C:0.09, G:0.05, T:0.18
Consensus pattern (9 bp):
AATAACAAT
Found at i:905325 original size:9 final size:9
Alignment explanation
Indices: 905215--905326 Score: 64
Period size: 9 Copynumber: 12.6 Consensus size: 9
905205 AAGCAATAAC
905215 AATAAGAAT
1 AATAAGAAT
* *
905224 AAGAACAAT
1 AATAAGAAT
*
905233 AATAACAAT
1 AATAAGAAT
*
905242 AATAACAAT
1 AATAAGAAT
* *
905251 AATAACAAC
1 AATAAGAAT
905260 AA-AAGAAT
1 AATAAGAAT
* *
905268 AACAAGAAG
1 AATAAGAAT
* *
905277 AACAAGAAC
1 AATAAGAAT
* *
905286 AATAATAAC
1 AATAAGAAT
* *
905295 AACAATAAT
1 AATAAGAAT
* * *
905304 AAGAATAAG
1 AATAAGAAT
905313 AATAAGAAT
1 AATAAGAAT
905322 AATAA
1 AATAA
905327 TTATAATATA
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
8 6 0.07
9 79 0.93
ACGTcount: A:0.68, C:0.09, G:0.08, T:0.15
Consensus pattern (9 bp):
AATAAGAAT
Found at i:918314 original size:19 final size:18
Alignment explanation
Indices: 918282--918317 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
918272 TTGGGATTTT
*
918282 ATAAATAAAGGAATAAAA
1 ATAAATAAAAGAATAAAA
918300 ATAACATAAAAGAATAAA
1 ATAA-ATAAAAGAATAAA
918318 CTTTGGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (18 bp):
ATAAATAAAAGAATAAAA
Found at i:923595 original size:6 final size:6
Alignment explanation
Indices: 923584--923612 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
923574 GGGGAAGTAA
923584 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
923613 AAATGAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:934705 original size:15 final size:16
Alignment explanation
Indices: 934673--934705 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
934663 TTTTAATAAT
934673 GGAATTGTAATATTTA
1 GGAATTGTAATATTTA
934689 GGAATTGTAAT-TTTA
1 GGAATTGTAATATTTA
934704 GG
1 GG
934706 CAGATTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.42
Consensus pattern (16 bp):
GGAATTGTAATATTTA
Found at i:947114 original size:12 final size:13
Alignment explanation
Indices: 947097--947125 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
947087 CTCATACATG
947097 AATAAATAAA-GC
1 AATAAATAAATGC
947109 AATAAATAAATGC
1 AATAAATAAATGC
947122 AATA
1 AATA
947126 GTTATAGCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:950009 original size:7 final size:7
Alignment explanation
Indices: 949979--950016 Score: 55
Period size: 6 Copynumber: 5.9 Consensus size: 7
949969 GGTTTTCTCA
949979 AAATG-G
1 AAATGAG
949985 AAATGA-
1 AAATGAG
949991 AAATGA-
1 AAATGAG
949997 AAATGAG
1 AAATGAG
950004 AAATGAG
1 AAATGAG
950011 AAATGA
1 AAATGA
950017 ATTCATTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 17 0.57
7 13 0.43
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.16
Consensus pattern (7 bp):
AAATGAG
Found at i:952398 original size:29 final size:28
Alignment explanation
Indices: 952336--952434 Score: 146
Period size: 28 Copynumber: 3.5 Consensus size: 28
952326 AAAAATAAAA
*
952336 ATTTACCAAAATAGTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
*
952364 ATTTACGAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAAC-TTTTTTTT
*
952393 ATTTACCAAGATATATA-AACTTTTTTTT
1 ATTTACCAAAATAT-TACAACTTTTTTTT
952421 ATTTACCAAAATAT
1 ATTTACCAAAATAT
952435 ATCAAAAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
28 39 0.61
29 23 0.36
30 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.47
Consensus pattern (28 bp):
ATTTACCAAAATATTACAACTTTTTTTT
Found at i:952663 original size:37 final size:37
Alignment explanation
Indices: 952619--952689 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
952609 CTCATTTTTT
* *
952619 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAAATCTATTTTAATTTAATAAAATATTCTC
*
952656 ATTTAATAAATTTATTTTAATTTAATAAAATATT
1 ATTTAATAAATCTATTTTAATTTAATAAAATATT
952690 AAGTAATACT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (37 bp):
ATTTAATAAATCTATTTTAATTTAATAAAATATTCTC
Found at i:952684 original size:19 final size:19
Alignment explanation
Indices: 952614--952684 Score: 90
Period size: 19 Copynumber: 3.8 Consensus size: 19
952604 TTCAACTCAT
* *
952614 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAAATCTA
952633 TTTTAATTTAATAAA-CTA
1 TTTTAATTTAATAAATCTA
* * *
952651 TTCTCATTTAATAAATTTA
1 TTTTAATTTAATAAATCTA
952670 TTTTAATTTAATAAA
1 TTTTAATTTAATAAA
952685 ATATTAAGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 16 0.36
19 28 0.64
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTAATTTAATAAATCTA
Found at i:952838 original size:27 final size:27
Alignment explanation
Indices: 952800--953288 Score: 951
Period size: 27 Copynumber: 18.1 Consensus size: 27
952790 CCCTTTTGAA
952800 AATTTATTTGGCACCAATGGTGCCACC
1 AATTTATTTGGCACCAATGGTGCCACC
952827 AATTTATTTGGCACCAATGGTGCCACC
1 AATTTATTTGGCACCAATGGTGCCACC
952854 AATTTATTTGGCACCAATGGTGCCACC
1 AATTTATTTGGCACCAATGGTGCCACC
952881 AATTTATTTGGCACCAATGGTGCCACC
1 AATTTATTTGGCACCAATGGTGCCACC
952908 AATTTATTTGGCACCAATGGTGCCACC
1 AATTTATTTGGCACCAATGGTGCCACC
952935 AATTTATTTGGCACCAATGGTGCCACC
1 AATTTATTTGGCACCAATGGTGCCACC
952962 AATTTATTTGGCACCAATGGTGCCACC
1 AATTTATTTGGCACCAATGGTGCCACC
952989 AATTTATTTGGCACCAATGGTGCCACC
1 AATTTATTTGGCACCAATGGTGCCACC
953016 AATTTATTTGGCACCAATGGTGCCACC
1 AATTTATTTGGCACCAATGGTGCCACC
953043 AATTTATTTGGCACCAATGGTGCCACC
1 AATTTATTTGGCACCAATGGTGCCACC
953070 AATTTATTTGGCACCAATGGTGCCACC
1 AATTTATTTGGCACCAATGGTGCCACC
953097 AATTTATTTGGCACCAATGGTGCCACC
1 AATTTATTTGGCACCAATGGTGCCACC
953124 AATTTATTTGGCACCAATGGTGCCACC
1 AATTTATTTGGCACCAATGGTGCCACC
953151 AATTTATTTGGCACCAATGGTGCCACC
1 AATTTATTTGGCACCAATGGTGCCACC
953178 AATTTATTTGGCACCAATGGTGCCACC
1 AATTTATTTGGCACCAATGGTGCCACC
953205 AATTTATTTGGCACCAATGGTGCCACC
1 AATTTATTTGGCACCAATGGTGCCACC
953232 AATTTATTTGGCACCAATGGTGCCACC
1 AATTTATTTGGCACCAATGGTGCCACC
** *
953259 AATTTATTTGGCACCTTTGGTGCCGCC
1 AATTTATTTGGCACCAATGGTGCCACC
953286 AAT
1 AAT
953289 ACCATTGGGG
Statistics
Matches: 459, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
27 459 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (27 bp):
AATTTATTTGGCACCAATGGTGCCACC
Found at i:953381 original size:28 final size:27
Alignment explanation
Indices: 953351--953448 Score: 151
Period size: 28 Copynumber: 3.5 Consensus size: 27
953341 TTTTTTTGAT
953351 ATATTTTGGTAAATAAAAAAAATTTTA
1 ATATTTTGGTAAATAAAAAAAATTTTA
953378 TATATTTTGGTAAATAAAAAAAAATTTTA
1 -ATATTTTGGTAAAT-AAAAAAAATTTTA
* *
953407 ATATTTTCGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAA-TTTTA
953435 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
953449 TTTTATTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
27 8 0.12
28 44 0.68
29 13 0.20
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.41
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAATTTTA
Found at i:956338 original size:8 final size:7
Alignment explanation
Indices: 956312--956336 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
956302 AATACATTAA
956312 TTTTATT
1 TTTTATT
956319 TTTTATT
1 TTTTATT
956326 TTTTATT
1 TTTTATT
956333 TTTT
1 TTTT
956337 TAAAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:958236 original size:20 final size:20
Alignment explanation
Indices: 958202--958310 Score: 96
Period size: 20 Copynumber: 5.5 Consensus size: 20
958192 AGCATGATTA
*
958202 TGCTATCAGAGGCACCGTAG
1 TGCTATCAGAAGCACCGTAG
* * **
958222 TGCTAACAAAAGCA-CAAATG
1 TGCTATCAGAAGCACCGTA-G
*
958242 TGCTATCAGGAGCACCGTAG
1 TGCTATCAGAAGCACCGTAG
* *
958262 TGTTATCAGAAGCACCGTAA
1 TGCTATCAGAAGCACCGTAG
* *
958282 TGCTATCAGGAGCA-CGAATG
1 TGCTATCAGAAGCACCGTA-G
958302 TGCTATCAG
1 TGCTATCAG
958311 GGGTACGAAT
Statistics
Matches: 69, Mismatches: 17, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
19 5 0.07
20 62 0.90
21 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (20 bp):
TGCTATCAGAAGCACCGTAG
Done.