Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1329
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: 37405
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Found at i:100 original size:27 final size:26
Alignment explanation
Indices: 59--109 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
49 AAATTACCGG
* *
59 AAATACCCCTGTAGGGTAGAATTACTA
1 AAATAACCCTATAGGGT-GAATTACTA
86 AAATAACCCTATAGGGTGAATTAC
1 AAATAACCCTATAGGGTGAATTAC
110 CGATAACCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (26 bp):
AAATAACCCTATAGGGTGAATTACTA
Found at i:493 original size:25 final size:25
Alignment explanation
Indices: 454--521 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
444 AGGAAGTGCT
*
454 AAAGGGC-ATGCCCCAGTTT-ACCGA
1 AAAGGGCTTTGCCCCAGTTTAACC-A
*
478 AAAGGGCTTTGCCCCAGTTTAATCA
1 AAAGGGCTTTGCCCCAGTTTAACCA
*
503 AAAAGGCTTTGCCCCAGTT
1 AAAGGGCTTTGCCCCAGTT
522 AATCTAAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
24 7 0.18
25 30 0.77
26 2 0.05
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (25 bp):
AAAGGGCTTTGCCCCAGTTTAACCA
Found at i:530 original size:25 final size:24
Alignment explanation
Indices: 462--531 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 24
452 CTAAAGGGCA
* * *
462 TGCCCCAGTTTACCGAAAAGGGCTT
1 TGCCCCAGTTAATC-AAAAAGGCTT
487 TGCCCCAGTTTAATCAAAAAGGCTT
1 TGCCCCAG-TTAATCAAAAAGGCTT
*
512 TGCCCCAGTTAATCTAAAAG
1 TGCCCCAGTTAATCAAAAAG
532 AGGCAGGCTC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
24 11 0.28
25 25 0.62
26 4 0.10
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (24 bp):
TGCCCCAGTTAATCAAAAAGGCTT
Found at i:3175 original size:26 final size:25
Alignment explanation
Indices: 3103--3174 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 25
3093 AGTACCCTCA
*
3103 ATTTATAGAATTATTGTTTTACCCTTG
1 ATTTATAGAA-TACTGTTTTA-CCTTG
**
3130 ATTTATAGAATAACCATTTTACCTTG
1 ATTTATAGAAT-ACTGTTTTACCTTG
3156 ATTTATAGAATACTGTTTT
1 ATTTATAGAATACTGTTTT
3175 TCCCTCGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
25 6 0.15
26 17 0.44
27 16 0.41
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.49
Consensus pattern (25 bp):
ATTTATAGAATACTGTTTTACCTTG
Found at i:3184 original size:26 final size:26
Alignment explanation
Indices: 3097--3186 Score: 83
Period size: 26 Copynumber: 3.4 Consensus size: 26
3087 TACGAAAGTA
* * *
3097 CCCTCAATTTATAGAATTATTGTTTTA
1 CCCTCGATTTATAGAA-TACTGTTTTT
* **
3124 CCCTTGATTTATAGAATAAC-CATTTT
1 CCCTCGATTTATAGAAT-ACTGTTTTT
* *
3150 ACCTTGATTTATAGAATACTGTTTTT
1 CCCTCGATTTATAGAATACTGTTTTT
3176 CCCTCGATTTA
1 CCCTCGATTTA
3187 CAAATTACCA
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
25 2 0.04
26 33 0.66
27 15 0.30
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.46
Consensus pattern (26 bp):
CCCTCGATTTATAGAATACTGTTTTT
Found at i:3185 original size:52 final size:52
Alignment explanation
Indices: 3103--3203 Score: 141
Period size: 52 Copynumber: 1.9 Consensus size: 52
3093 AGTACCCTCA
* * *
3103 ATTTATAGAATTATTGTTTTACCCTTGATTTATAGAATAACCATTTTACCTTG
1 ATTTATAGAATTACTGTTTTACCCTCGATTTACA-AATAACCATTTTACCTTG
* *
3156 ATTTATAGAA-TACTGTTTTTCCCTCGATTTACAAATTACCATTTTACC
1 ATTTATAGAATTACTGTTTTACCCTCGATTTACAAATAACCATTTTACC
3204 ATTTTACCCT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 14 0.33
52 19 0.44
53 10 0.23
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.46
Consensus pattern (52 bp):
ATTTATAGAATTACTGTTTTACCCTCGATTTACAAATAACCATTTTACCTTG
Found at i:3246 original size:27 final size:27
Alignment explanation
Indices: 3210--3344 Score: 150
Period size: 27 Copynumber: 5.1 Consensus size: 27
3200 TACCATTTTA
*
3210 CCCTATAGGGTAGAATTACCGAGATAC
1 CCCTATAGGGTAGAATTACCGAAATAC
*
3237 CCCTATAGGGT--AATTACTGAAATAC
1 CCCTATAGGGTAGAATTACCGAAATAC
* *
3262 CCCTACAGGGTAGAATTACCAAAATAC
1 CCCTATAGGGTAGAATTACCGAAATAC
* * **
3289 CCCTTGTAGGGTAGAAATACTAAAATAC
1 CCC-TATAGGGTAGAATTACCGAAATAC
* *
3317 CCCTGTA-GGTAGAATTACCGAGATAC
1 CCCTATAGGGTAGAATTACCGAAATAC
3343 CC
1 CC
3345 TGTGGGGGTG
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
25 22 0.24
26 17 0.18
27 30 0.33
28 23 0.25
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (27 bp):
CCCTATAGGGTAGAATTACCGAAATAC
Found at i:3648 original size:24 final size:25
Alignment explanation
Indices: 3571--3665 Score: 129
Period size: 25 Copynumber: 3.8 Consensus size: 25
3561 AGGAAGTGCA
**
3571 AAAAGGGCAATGCCCCAGTTTAACG
1 AAAAGGGCTTTGCCCCAGTTTAACG
* * *
3596 AAAAAGGCTTTGCCCTAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTAACG
*
3621 AAAAGGGCTTTGCCCCAGTTTATC-
1 AAAAGGGCTTTGCCCCAGTTTAACG
3645 AAAAGGGCTTTGCCCCAGTTT
1 AAAAGGGCTTTGCCCCAGTTT
3666 TTAAAAGAGG
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
24 21 0.34
25 41 0.66
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.25
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTAACG
Found at i:3922 original size:27 final size:29
Alignment explanation
Indices: 3883--3946 Score: 105
Period size: 27 Copynumber: 2.2 Consensus size: 29
3873 CGCTTACAGT
3883 AAAGGCATCGGCCAGTGATATGA-TTATGA
1 AAAGGC-TCGGCCAGTGATATGATTTATGA
3912 AAAGGCT-GGCCAGTGATATGATTTATGA
1 AAAGGCTCGGCCAGTGATATGATTTATGA
3940 AAAGGCT
1 AAAGGCT
3947 TTGGCCCAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
27 14 0.41
28 14 0.41
29 6 0.18
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.25
Consensus pattern (29 bp):
AAAGGCTCGGCCAGTGATATGATTTATGA
Found at i:4966 original size:20 final size:20
Alignment explanation
Indices: 4941--4984 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
4931 TATCATGTAC
4941 TATCCACACATCCAACATGT
1 TATCCACACATCCAACATGT
4961 TATCCACACATCCAACATGT
1 TATCCACACATCCAACATGT
4981 TATC
1 TATC
4985 AAGCATAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.27
Consensus pattern (20 bp):
TATCCACACATCCAACATGT
Found at i:8011 original size:46 final size:47
Alignment explanation
Indices: 7625--8010 Score: 708
Period size: 47 Copynumber: 8.3 Consensus size: 47
7615 CTGGCCCTGT
7625 ACATATATAC-CTTTCACATTCATCACATCGGCCATTAGGCCTTATC
1 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
7671 ACATATATACACTTTCACATTCATCACATCGG-CATTAGGCCTTATC
1 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
7717 ACATATATACACTTTCACATTCATCACATCGG-CATTAGGCCTTATC
1 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
*
7763 ACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
1 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
7810 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
1 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
*
7857 ACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATC
1 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
*
7904 ACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
1 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
*
7951 ACACATATACAC-TTCACATTCATCACATCGGCCATTAGGCCTTATC
1 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
7997 ACATATATACACTT
1 ACATATATACACTT
8011 CTTGGCTGAA
Statistics
Matches: 331, Mismatches: 6, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
46 146 0.44
47 185 0.56
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
Found at i:11646 original size:40 final size:40
Alignment explanation
Indices: 11550--11692 Score: 204
Period size: 40 Copynumber: 3.7 Consensus size: 40
11540 AGCCCGGCAC
* * *
11550 GAATGCTCTTCGGG-TTTAGCACGGATATATCACTAGCA-
1 GAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCAT
* *
11588 CAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCAT
1 GAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCAT
*
11628 GAATGCTCTTCGGGACTTAGCCCGGATACATCGCTAGCAT
1 GAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCAT
11668 GAATGCTCTTC-GGACTTAG-CCGGAT
1 GAATGCTCTTCGGGACTTAGCCCGGAT
11693 TTAGTAACTC
Statistics
Matches: 95, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
38 18 0.19
39 29 0.31
40 48 0.51
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (40 bp):
GAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCAT
Found at i:11758 original size:118 final size:118
Alignment explanation
Indices: 11550--11771 Score: 281
Period size: 118 Copynumber: 1.9 Consensus size: 118
11540 AGCCCGGCAC
** *
11550 GAATGCTCTTCGGGTTTAGCACGGATATATCACTAGCACAATGCTCTTCGGAACTTAGCCCGGAT
1 GAATGCTCTTCGGACTTAGCACGGATATATAACTAGCACAATGCTCTTCGGAACTTAGCCCGGAT
* *
11615 ACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCGCTAGCAT
66 ACATCACTAGCATCAAAGCTCTTCGGGACTTAGCCCGGATACATCGCTAGCAT
* * * *
11668 GAATGCTCTTCGGACTTAGC-CGGATTTAGTAACTCGCACCAATGC-CTTCGGATCTTAGTCCGG
1 GAATGCTCTTCGGACTTAGCACGGATATA-TAACTAGCA-CAATGCTCTTCGGAACTTAGCCCGG
**
11731 ATATGGTCACTTAGCA-CAAAGC-CTTCGGGACTTAGCCCGGA
64 ATA-CATCAC-TAGCATCAAAGCTCTTCGGGACTTAGCCCGGA
11772 CATCATTCGA
Statistics
Matches: 89, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
117 7 0.08
118 63 0.71
119 14 0.16
120 5 0.06
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (118 bp):
GAATGCTCTTCGGACTTAGCACGGATATATAACTAGCACAATGCTCTTCGGAACTTAGCCCGGAT
ACATCACTAGCATCAAAGCTCTTCGGGACTTAGCCCGGATACATCGCTAGCAT
Found at i:12118 original size:29 final size:29
Alignment explanation
Indices: 12079--12157 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
12069 CTTAATAATC
*
12079 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
12109 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
12138 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
12158 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:12200 original size:43 final size:43
Alignment explanation
Indices: 12139--12241 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
12129 TGCATTTCAA
12139 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
12182 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
12225 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
12242 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:14152 original size:37 final size:37
Alignment explanation
Indices: 14102--14180 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
14092 TTATTACGAA
* *
14102 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
14139 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
14176 GTCTT
1 GTCTT
14181 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:14370 original size:46 final size:47
Alignment explanation
Indices: 14314--14833 Score: 682
Period size: 47 Copynumber: 11.1 Consensus size: 47
14304 CACATTTATG
* * * * * * *
14314 CACTTTCACATCCATCACGTTGGCCACT-CGCCCTGTCACATATATA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACACATATA
* *
14360 CACTTTCACATTCATCACATCGGCCATTAGGCCTTAT-ACATATATA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACACATATA
* * *
14406 CACTTTCACATTCATCACATCATCACATCGGCTATTAGGCCTTATCACATATAT-
1 CACTTT--CA--CAT----TCATCACATCGGCCATTAGGCCCTATCACACATATA
* *
14460 CACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACACATATA
* *
14507 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACACATATA
*
14554 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACACATATA
*
14601 CACTTTCACATTCATCACATCGG-CATTAGGCCTTAT--CACATATA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACACATATA
*
14645 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACACATATA
*
14692 CACTTTCACATTCATCACATCGG-CATTAGGCCTTAT--CACATATA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACACATATA
*
14736 CACTTTCACATTCATCACATCGGCTATTAGG-CCTATCACACATATA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACACATATA
* * *
14782 CACTTTCACATTCATCACATCGGTCATTAGGCCTTATCACATATATA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACACATATA
14829 CACTT
1 CACTT
14834 CTTGGCGAAT
Statistics
Matches: 438, Mismatches: 18, Indels: 35
0.89 0.04 0.07
Matches are distributed among these distances:
44 66 0.15
45 19 0.04
46 136 0.31
47 168 0.38
48 2 0.00
50 6 0.01
52 2 0.00
54 31 0.07
55 8 0.02
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACACATATA
Found at i:14529 original size:47 final size:47
Alignment explanation
Indices: 14420--14833 Score: 695
Period size: 47 Copynumber: 9.0 Consensus size: 47
14410 TTCACATTCA
*
14420 TCACA-TCATCACATCGGCTATTAGGCCTTATCACATATAT-CACTT
1 TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTT
14465 TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTT
1 TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTT
* *
14512 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
1 TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTT
*
14559 TCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTT
1 TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTT
14606 TCACATTCATCACATCGGC-ATTAGGCCTTAT--CACATATACACTT
1 TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTT
*
14650 TCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTT
1 TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTT
14697 TCACATTCATCACATCGGC-ATTAGGCCTTAT--CACATATACACTT
1 TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTT
14741 TCACATTCATCACATCGGCTATTAGGCC-TATCACACATATACACTT
1 TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTT
*
14787 TCACATTCATCACATCGG-TCATTAGGCCTTATCACATATATACACTT
1 TCACATTCATCACATCGGCT-ATTAGGCCTTATCACACATATACACTT
14834 CTTGGCGAAT
Statistics
Matches: 354, Mismatches: 5, Indels: 18
0.94 0.01 0.05
Matches are distributed among these distances:
44 67 0.19
45 26 0.07
46 97 0.27
47 164 0.46
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTT
Found at i:14685 original size:91 final size:91
Alignment explanation
Indices: 14420--14826 Score: 728
Period size: 91 Copynumber: 4.4 Consensus size: 91
14410 TTCACATTCA
14420 TCACA-TCATCACATCGGCTATTAGGCCTTATCACATATATCACTTTCACATTCATCACATCGGC
1 TCACATTCATCACATCGGC-ATTAGGCCTTATCACATATA-CACTTTCACATTCATCACATCGGC
*
14484 TATTAGGCCTTATCACACATATACACTT
64 CATTAGGCCTTATCACACATATACACTT
14512 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
1 TCACATTCATCACATCGG-CATTAGGCCTTATCAC--ATATACACTTTCACATTCATCACATCGG
14577 CCATTAGGCCTTATCACACATATACACTT
63 CCATTAGGCCTTATCACACATATACACTT
14606 TCACATTCATCACATCGGCATTAGGCCTTATCACATATACACTTTCACATTCATCACATCGGCCA
1 TCACATTCATCACATCGGCATTAGGCCTTATCACATATACACTTTCACATTCATCACATCGGCCA
14671 TTAGGCCTTATCACACATATACACTT
66 TTAGGCCTTATCACACATATACACTT
*
14697 TCACATTCATCACATCGGCATTAGGCCTTATCACATATACACTTTCACATTCATCACATCGGCTA
1 TCACATTCATCACATCGGCATTAGGCCTTATCACATATACACTTTCACATTCATCACATCGGCCA
14762 TTAGGCC-TATCACACATATACACTT
66 TTAGGCCTTATCACACATATACACTT
14787 TCACATTCATCACATCGGTCATTAGGCCTTATCACATATA
1 TCACATTCATCACATCGG-CATTAGGCCTTATCACATATA
14827 TACACTTCTT
Statistics
Matches: 308, Mismatches: 2, Indels: 11
0.96 0.01 0.03
Matches are distributed among these distances:
90 36 0.12
91 149 0.48
92 5 0.02
93 43 0.14
94 70 0.23
95 5 0.02
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (91 bp):
TCACATTCATCACATCGGCATTAGGCCTTATCACATATACACTTTCACATTCATCACATCGGCCA
TTAGGCCTTATCACACATATACACTT
Found at i:19466 original size:6 final size:6
Alignment explanation
Indices: 19457--19522 Score: 57
Period size: 6 Copynumber: 11.2 Consensus size: 6
19447 AATAAAATTG
* *
19457 AAATAA AAATAA AAATAA AAAT-A AAATAA ATAA-ATT AAAT-T AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA A-AATA-A AAATAA AAATAA
* *
19504 AAATAA GAATAA GAATAA A
1 AAATAA AAATAA AAATAA A
19523 TAAAAAAAGG
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
5 10 0.20
6 38 0.75
7 3 0.06
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (6 bp):
AAATAA
Found at i:19502 original size:41 final size:40
Alignment explanation
Indices: 19443--19526 Score: 116
Period size: 41 Copynumber: 2.1 Consensus size: 40
19433 TTCAAAAGAA
19443 AAATAATAAAATTGAAATAAAAATAAAAATAAAAATAAAAT
1 AAATAATAAAATTGAAATAAAAATAAAAATAAAAAT-AAAT
* * *
19484 AAATAAATTAAATT-AAATAAAAATAAGAATAAGAATAAAT
1 AAAT-AATAAAATTGAAATAAAAATAAAAATAAAAATAAAT
19524 AAA
1 AAA
19527 AAAAGGAGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
40 7 0.18
41 24 0.62
42 8 0.21
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (40 bp):
AAATAATAAAATTGAAATAAAAATAAAAATAAAAATAAAT
Found at i:27002 original size:26 final size:26
Alignment explanation
Indices: 26973--27032 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
26963 TCCCTTTGAA
* * *
26973 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
26999 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
27027 CCATTC
1 TCATTC
27033 TCAATATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:27048 original size:28 final size:28
Alignment explanation
Indices: 26980--27058 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
26970 GAATCATTCG
*
26980 ATATTTTGCACACTAAGTGTCATTCTCA
1 ATATTTTGCACACTAAGTGCCATTCTCA
* *
27008 ATATCTCGCACACTAAGTGCCATTCTCA
1 ATATTTTGCACACTAAGTGCCATTCTCA
* * *
27036 ATATTTTGTACACTGAGTACCAT
1 ATATTTTGCACACTAAGTGCCAT
27059 ATGTGATTGC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (28 bp):
ATATTTTGCACACTAAGTGCCATTCTCA
Done.