Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold98
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: 1546936
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 25 characters in sequence are not A, C, G, or T
File 13 of 13
Found at i:1514091 original size:28 final size:27
Alignment explanation
Indices: 1514059--1514118 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
1514049 TTTATTTTAT
1514059 ATTATATAACATATAATAAAAATTATAA
1 ATTATATAACATATAAT-AAAATTATAA
** * *
1514087 ATTATATATTATATTATATAATTATAA
1 ATTATATAACATATAATAAAATTATAA
1514114 ATTAT
1 ATTAT
1514119 TATATAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
ATTATATAACATATAATAAAATTATAA
Found at i:1514244 original size:23 final size:23
Alignment explanation
Indices: 1514218--1514285 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
1514208 TTTTTAAAAC
*
1514218 TAAATTTACTT-AATCAAATTAAT
1 TAAATTTAATTAAATC-AATTAAT
*
1514241 TAAATTTAATTAAATCAATTGAT
1 TAAATTTAATTAAATCAATTAAT
*
1514264 TAAA-TCAATTCAAATCAATTAA
1 TAAATTTAATT-AAATCAATTAA
1514286 CACTCACTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.13
23 30 0.77
24 4 0.10
ACGTcount: A:0.50, C:0.09, G:0.01, T:0.40
Consensus pattern (23 bp):
TAAATTTAATTAAATCAATTAAT
Found at i:1514267 original size:13 final size:13
Alignment explanation
Indices: 1514249--1514273 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1514239 ATTAAATTTA
1514249 ATTAAATCAATTG
1 ATTAAATCAATTG
1514262 ATTAAATCAATT
1 ATTAAATCAATT
1514274 CAAATCAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (13 bp):
ATTAAATCAATTG
Found at i:1514484 original size:2 final size:2
Alignment explanation
Indices: 1514472--1514510 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1514462 GTGCAGCTCA
1514472 AT AT A- AT AT AT 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 AT AT AT AT AT AT
1514511 TCACGCACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1518087 original size:22 final size:22
Alignment explanation
Indices: 1518062--1518105 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1518052 CAGATTAAAT
1518062 TTATTCCTAATGAGATATCAAC
1 TTATTCCTAATGAGATATCAAC
1518084 TTATTCCTAATGAGATATCAAC
1 TTATTCCTAATGAGATATCAAC
1518106 GATGGTTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
TTATTCCTAATGAGATATCAAC
Found at i:1521945 original size:23 final size:23
Alignment explanation
Indices: 1521915--1521969 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
1521905 GCTATTATCG
*
1521915 AATA-ACAACAAAAA-TATAGTAA
1 AATACACAACAAAAAGTA-AATAA
1521937 AATACACAACAAAAAGTAAATAA
1 AATACACAACAAAAAGTAAATAA
*
1521960 AAGACACAAC
1 AATACACAAC
1521970 TAGACTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 4 0.14
23 23 0.79
24 2 0.07
ACGTcount: A:0.67, C:0.15, G:0.05, T:0.13
Consensus pattern (23 bp):
AATACACAACAAAAAGTAAATAA
Found at i:1525878 original size:52 final size:51
Alignment explanation
Indices: 1525800--1525948 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
1525790 CGAAATATGA
1525800 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
1525852 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
* **
1525904 AAATTTTCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
1525949 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:1525955 original size:13 final size:13
Alignment explanation
Indices: 1525937--1525961 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1525927 CAAAGATCAG
1525937 TGTATCGATACAA
1 TGTATCGATACAA
1525950 TGTATCGATACA
1 TGTATCGATACA
1525962 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1526039 original size:33 final size:33
Alignment explanation
Indices: 1526002--1526068 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1525992 AGTAGCTTAA
1526002 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1526035 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1526068 A
1 A
1526069 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1526042 original size:13 final size:13
Alignment explanation
Indices: 1526024--1526048 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1526014 CAAAAAAATA
1526024 TGTATCGATACAT
1 TGTATCGATACAT
1526037 TGTATCGATACA
1 TGTATCGATACA
1526049 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1527016 original size:52 final size:51
Alignment explanation
Indices: 1526947--1527095 Score: 188
Period size: 52 Copynumber: 3.0 Consensus size: 51
1526937 AAAAGGATTT
*
1526947 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAA-GTGC
* *
1526999 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A--G----GTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGTGC
*
1527042 CAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAA-GTGC
1527094 CA
1 CA
1527096 CCGACTTGTG
Statistics
Matches: 82, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
43 36 0.44
44 2 0.02
45 1 0.01
47 1 0.01
48 1 0.01
50 1 0.01
51 2 0.02
52 38 0.46
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (51 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGTGC
Found at i:1527056 original size:43 final size:43
Alignment explanation
Indices: 1526995--1527080 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
1526985 GATGGAAAAT
*
1526995 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* *
1527038 GTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1527081 ATGGAAAAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (43 bp):
GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
Found at i:1527125 original size:30 final size:30
Alignment explanation
Indices: 1527084--1527562 Score: 374
Period size: 30 Copynumber: 16.1 Consensus size: 30
1527074 CTTAAAGATG
* **
1527084 GAAAA-GGTGCCACCGACTTGTGGGCTTCG
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*
1527113 GAAAAGGGTGCCACTGATTTGTGGGC-TTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*
1527142 G--AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*
1527170 --AAAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
***
1527198 GAAAAATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*
1527228 GAAAAGGGTGCCACTAACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
* *
1527258 --AAAGGTTGCCGCTGACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
***
1527286 GAAAAATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
* * ***
1527316 GAAAATGGTGCCACTAACTTGTGGGCTGAAAAA
1 GAAAAGGGTGCCACTGACTTGTGGGCT---TTT
* * * * **
1527349 GAAAAAGAGTGCTA-TAGAGTTGTGAGCTTACAAAA
1 G-AAAAGGGTGCCACT-GACTTGTGGGCTT----TT
* * * * *
1527384 GAAAAAGAGTGCCACGGAGTTGTGGACTTTG
1 G-AAAAGGGTGCCACTGACTTGTGGGCTTTT
* * **
1527415 GAAAA-GATGCCACCGACTTGTGGGCTTCG
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*
1527444 GAAAAGGGTGCCACTGATTTGTGGGC-TTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*
1527473 G--AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
***
1527501 GAAAAAAATGCCACTGACTTGTGGGC-TTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*** *
1527530 GAAAAAAATGCCACTGACTTGTGGACTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
1527560 GAA
1 GAA
1527563 GGGTGATGAA
Statistics
Matches: 371, Mismatches: 57, Indels: 43
0.79 0.12 0.09
Matches are distributed among these distances:
27 42 0.11
28 59 0.16
29 60 0.16
30 163 0.44
31 1 0.00
33 2 0.01
34 18 0.05
35 26 0.07
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (30 bp):
GAAAAGGGTGCCACTGACTTGTGGGCTTTT
Found at i:1527273 original size:58 final size:59
Alignment explanation
Indices: 1527086--1527562 Score: 343
Period size: 58 Copynumber: 8.0 Consensus size: 59
1527076 TAAAGATGGA
* ** *
1527086 AAAGG-TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
*
1527143 -AAGGTTGCCACTGACTTGTGGGCTTTT--AAAGGTTGCCACTGACTTGTGGGCTTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
** *
1527199 AAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTT-
1 AAAGGT-TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
* ***
1527258 AAAGGTTGCCGCTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
* *** * * * *
1527317 AAAATGG-TGCCACTAACTTGTGGGCTGAAAAAGAAAAAGAGTGCTA-TAGAGTTGTGAGCTTAC
1 -AAA-GGTTGCCACTGACTTGTGGGCT---TTTG-AAAAGGGTGCCACT-GACTTGTGGGCTT--
**
1527380 AAAAG
57 --TTG
* * * * * * **
1527385 AAAAAGAG-TGCCACGGAGTTGTGGACTTTGGAAAA-GATGCCACCGACTTGTGGGCTTCGG
1 --AAAG-GTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
* * *
1527445 AAAAGGGTGCCACTGATTTGTGGGC-TTTG--AAGGTTGCCACTGACTTGTGGGCTTTTG
1 -AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
*** *** *
1527502 AAAAAAATGCCACTGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGACTTTTG
1 -AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
1527561 AA
1 AA
1527563 GGGTGATGAA
Statistics
Matches: 335, Mismatches: 60, Indels: 49
0.75 0.14 0.11
Matches are distributed among these distances:
55 22 0.07
56 10 0.03
57 68 0.20
58 75 0.22
59 48 0.14
60 47 0.14
61 2 0.01
63 2 0.01
64 34 0.10
65 4 0.01
66 1 0.00
68 2 0.01
69 20 0.06
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (59 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
Found at i:1527275 original size:88 final size:88
Alignment explanation
Indices: 1527086--1527342 Score: 387
Period size: 88 Copynumber: 3.0 Consensus size: 88
1527076 TAAAGATGGA
* ** *** *
1527086 AAAGG-TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG--AAGG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
* *
1527147 TTGCCACTGACTTGTGGGCTTTT
66 GTGCCACTAACTTGTGGGCTTTT
1527170 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
1527235 GTGCCACTAACTTGTGGGCTTTT
66 GTGCCACTAACTTGTGGGCTTTT
* *
1527258 AAAGGTTGCCGCTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAATG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
1527323 GTGCCACTAACTTGTGGGCT
66 GTGCCACTAACTTGTGGGCT
1527343 GAAAAAGAAA
Statistics
Matches: 158, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
84 5 0.03
85 41 0.26
86 4 0.03
88 108 0.68
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.32
Consensus pattern (88 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
GTGCCACTAACTTGTGGGCTTTT
Found at i:1527485 original size:27 final size:27
Alignment explanation
Indices: 1527393--1527564 Score: 119
Period size: 29 Copynumber: 6.0 Consensus size: 27
1527383 AGAAAAAGAG
* * * *
1527393 TGCCACGGAGTTGTGGACTTTGGAAAAGA
1 TGCCACTGACTTGTGGGCTTT-G-AAGGA
* * *
1527422 TGCCACCGACTTGTGGGCTTCGGAAAAGGG
1 TGCCACTGACTTGTGGGCTT-TG--AAGGA
* *
1527452 TGCCACTGATTTGTGGGCTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTGAAGGA
**
1527479 TGCCACTGACTTGTGGGCTTTTGAAAAAAA
1 TGCCACTGACTTGTGGGC-TTTG--AAGGA
**
1527509 TGCCACTGACTTGTGGGCTTTGAAAAAAA
1 TGCCACTGACTTGTGGGCTTTG--AAGGA
*
1527538 TGCCACTGACTTGTGGACTTTTGAAGG
1 TGCCACTGACTTGTGGGC-TTTGAAGG
1527565 GTGATGAATG
Statistics
Matches: 120, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
27 21 0.17
28 6 0.05
29 47 0.39
30 46 0.38
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.28
Consensus pattern (27 bp):
TGCCACTGACTTGTGGGCTTTGAAGGA
Found at i:1529004 original size:1 final size:1
Alignment explanation
Indices: 1529000--1529107 Score: 72
Period size: 1 Copynumber: 108.0 Consensus size: 1
1528990 CCGGACCCCC
* * * * * * * * *
1529000 TTTTTTTGTTTTTGTTTGTTTTTTTATTATTTTTGTTTTTTTTTGTTGTTTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** ** * * *
1529065 CATTTTTTTCGTTTTTTTTGTTTTGTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1529108 GGAGGACGCC
Statistics
Matches: 77, Mismatches: 30, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 77 1.00
ACGTcount: A:0.03, C:0.02, G:0.10, T:0.85
Consensus pattern (1 bp):
T
Found at i:1529046 original size:31 final size:29
Alignment explanation
Indices: 1529000--1529108 Score: 107
Period size: 31 Copynumber: 3.6 Consensus size: 29
1528990 CCGGACCCCC
* *
1529000 TTTTTTTGTTTTTGTTTGTTTTTTTATTAT
1 TTTTTTTTTTTTTGTTTGTTTTTTT-TTGT
1529030 TTTTGTTTTTTTTTG-TTGTTTTTTTTTTGT
1 TTTT-TTTTTTTTTGTTTG-TTTTTTTTTGT
*
1529060 TTTTTCATTTTTTTCGTTT-TTTTTGTTTTGT
1 TTTTT--TTTTTTTTGTTTGTTTTT-TTTTGT
1529091 TTTTTTTTTGTTTT-TTTG
1 TTTTTTTTT-TTTTGTTTG
1529109 GAGGACGCCG
Statistics
Matches: 67, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
29 8 0.12
30 22 0.33
31 35 0.52
32 2 0.03
ACGTcount: A:0.03, C:0.02, G:0.11, T:0.84
Consensus pattern (29 bp):
TTTTTTTTTTTTTGTTTGTTTTTTTTTGT
Found at i:1529079 original size:26 final size:25
Alignment explanation
Indices: 1529000--1529107 Score: 98
Period size: 25 Copynumber: 4.2 Consensus size: 25
1528990 CCGGACCCCC
**
1529000 TTTTTTTGTTTTTGTTTGTTTTTTTAT
1 TTTTTTTG-TTTTGTTT-TTTTTTCGT
*
1529027 TATTTTTGTTTT-TTTTTGTTGTT--T
1 TTTTTTTGTTTTGTTTTT-TT-TTCGT
1529051 TTTTTTTGTTTT-TTCATTTTTTTCGT
1 TTTTTTTGTTTTGTT--TTTTTTTCGT
*
1529077 TTTTTTTGTTTTGTTTTTTTTTTGT
1 TTTTTTTGTTTTGTTTTTTTTTCGT
1529102 TTTTTT
1 TTTTTT
1529108 GGAGGACGCC
Statistics
Matches: 71, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
24 18 0.25
25 22 0.31
26 22 0.31
27 9 0.13
ACGTcount: A:0.03, C:0.02, G:0.10, T:0.85
Consensus pattern (25 bp):
TTTTTTTGTTTTGTTTTTTTTTCGT
Found at i:1538813 original size:10 final size:10
Alignment explanation
Indices: 1538798--1538824 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1538788 ATGTATCAAG
1538798 CAAAAACAAA
1 CAAAAACAAA
1538808 CAAAAACAAA
1 CAAAAACAAA
1538818 CAAAAAC
1 CAAAAAC
1538825 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:1543028 original size:52 final size:51
Alignment explanation
Indices: 1542950--1543098 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
1542940 CGAAATATGA
1542950 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
1543002 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
* **
1543054 AAATTTTCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
1543099 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:1543105 original size:13 final size:13
Alignment explanation
Indices: 1543087--1543111 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1543077 CAAAGATCAG
1543087 TGTATCGATACAA
1 TGTATCGATACAA
1543100 TGTATCGATACA
1 TGTATCGATACA
1543112 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1543189 original size:33 final size:33
Alignment explanation
Indices: 1543152--1543218 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1543142 AGTAGCTTAA
1543152 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1543185 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1543218 A
1 A
1543219 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1543192 original size:13 final size:13
Alignment explanation
Indices: 1543174--1543198 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1543164 CAAAAAAATA
1543174 TGTATCGATACAT
1 TGTATCGATACAT
1543187 TGTATCGATACA
1 TGTATCGATACA
1543199 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1544776 original size:477 final size:476
Alignment explanation
Indices: 1543494--1545527 Score: 2605
Period size: 477 Copynumber: 4.3 Consensus size: 476
1543484 GGTGTCTACA
* * *
1543494 ATGGTGCCTAATCCTAAAGGGAATGGGGATTAGTATGAGTATTCACGTTTGGCTTATTTAAGAGA
1 ATGGTGCCTAATCCTAAA-AGAATGGGGATTAGTATGAGTATTCATGTTTGTCTTATTTAAGAGA
* * *
1543559 CAAACATTGATTCTATCAAAAACAGTAGGAAGAAAAGCTTTTCTTGAGACACCAAAGCATCAATG
65 CAAACTTTGATTCTATCAAAAACGGCAGGAAGAAAAGCTTTTCTTGAGACACCAAAGCATCAATG
*
1543624 TC-TGGTATCCTAACAAAGGCAATGTGTTTTGGCTTCCCAATCTTGAAAAAAATGGAGACTGTTA
130 TCATGGTATCCTAACAAAGGCAATGTGTTTTGGCTTCCCAATCTTGAAAAGAATGGAGACTGTTA
* * * * *
1543688 GGAGAATCGATGCTTGTCTTATTCAAGGGATGGACTTTCATTTTAAGGAAAATAAGGCGAAGAAA
195 CGAGAATCGATGCTTGTCTTATTCAAGGGATGAACTTTGATTTTAAGGAAAATAGGGCAAAGAAA
* * * * * * * * *
1543753 AGATTTCCAGGAAAAAGAAAAACTTCATTGTCTTTTGTCCTAATTAGGAGAATGTGTTTATAGTG
260 AGATTTCCATGCAAAAGAAAATCGTCAATGTCATTTATCCAAATGAGGAGAATGTGTTTATAGTG
* * * * * * *
1543818 CTTTATCAAAAAAAGAATGCAGGTCATTACTAGAATCCATATTTGTCTCATTCGAGGAACGAACT
325 CCTTATCACAAAAAGAATGAAGATCATTACTAGAATCCATGTTTGTCTCATTTGAGGCACGAACT
* *
1543883 TAGACTTTACAACGATTGGTGGGAAGAAAGCCTTTGTTGCGAAACTAAAGCATCAATATCGTGTA
390 TAGACTTTACAACAATTGGTGGGAAGAAAGCCTTTGTTGCGAAACCAAAGCATCAATATCGTGTA
* *
1543948 TCTTAATGAGAAGACTATGTAT
455 TCCTAATGAGAAGACTATGTTT
** * * *
1543970 ATGGTGCCTAAAACTAAAAGGAACGAGGATTAGTATGAGTATTCATGTTTGGCTTATTTAAGAGA
1 ATGGTGCCTAATCCTAAAA-GAATGGGGATTAGTATGAGTATTCATGTTTGTCTTATTTAAGAGA
* *
1544035 CAAACGTTGTTTCTATCAAAAACGGC-GCGAAGAAAAGCTTTTCTTGAGACA-CAAA-CTATCAA
65 CAAACTTTGATTCTATCAAAAACGGCAG-GAAGAAAAGCTTTTCTTGAGACACCAAAGC-ATCAA
* *
1544097 TGTCA-GGTATCCTAACAAAGGCAATGTGTTTTGGCATCCCAATCTTGAAAAGAAAGGAGACTGT
128 TGTCATGGTATCCTAACAAAGGCAATGTGTTTTGGCTTCCCAATCTTGAAAAGAATGGAGACTGT
* ** * ** *
1544161 TACGAGAATCGATGCTTGTCTTTTTCGGGGGATGAACTTTGATTTTAAGGATAATTTGGCAAAGC
193 TACGAGAATCGATGCTTGTCTTATTCAAGGGATGAACTTTGATTTTAAGGAAAATAGGGCAAAGA
* *
1544226 AAAGATTTCCATGCAAAAGAAAATCATCAATGTCATTTATCCTAATGAGGAGAATGTGTTTATAG
258 AAAGATTTCCATGCAAAAGAAAATCGTCAATGTCATTTATCCAAATGAGGAGAATGTGTTTATAG
* * *
1544291 TGCCTTATCACAGAAAGAATGAAGATCATTACTAGAATCTATGTTTGTCTAATTTGAGGCACGAA
323 TGCCTTATCACAAAAAGAATGAAGATCATTACTAGAATCCATGTTTGTCTCATTTGAGGCACGAA
* * *** * **
1544356 CTTAGAATTTACAAAAATTGGAAAGAAGAAAGCCTTTGTTACGAAACCAAAATATCAATATCGTG
388 CTTAGACTTTACAACAATTGGTGGGAAGAAAGCCTTTGTTGCGAAACCAAAGCATCAATATCGTG
*
1544421 TATCCTAATGAGAGGACTATGTTT
453 TATCCTAATGAGAAGACTATGTTT
*
1544445 ATGGTGCCTAATCCTGAAAAGAATGGGGATTAGTGTGAGTATTCATGTTTGTCTTATTTAAGAGA
1 ATGGTGCCTAATCCT-AAAAGAATGGGGATTAGTATGAGTATTCATGTTTGTCTTATTTAAGAGA
* * * * *
1544510 CAAACTTTTGACTCTATTAAAAATGGCAGGAAGAAAAGCTTTTCGTGCGACACCAAAGCATCAAT
65 CAAAC-TTTGATTCTATCAAAAACGGCAGGAAGAAAAGCTTTTCTTGAGACACCAAAGCATCAAT
* * * * ** * *
1544575 GTCATGG-GTCCTAACGAAGGCAATGTGTTTTAGCTTTCCAATCTTGAAATCAAGGGAGACGGTT
129 GTCATGGTATCCTAACAAAGGCAATGTGTTTTGGCTTCCCAATCTTGAAAAGAATGGAGACTGTT
* * * ** *
1544639 ACGAGAATCGAAGCTTCTCTTATTCAAGGGATGAACTTTGATTTTAAGGATAACT-GGGTGAGGA
194 ACGAGAATCGATGCTTGTCTTATTCAAGGGATGAACTTTGATTTTAAGGA-AAATAGGGCAAAGA
*
1544703 AAAGATTTCCATGCAAAAGAAAATCGTCAATGTCATTTATCCAAAT-ACAGAGAATGTGTTTATA
258 AAAGATTTCCATGCAAAAGAAAATCGTCAATGTCATTTATCCAAATGA-GGAGAATGTGTTTATA
* * * * *
1544767 GTTCCTTATCACAAAAAGAATGAAGATCGTTACTAGAATCCATGTGTGCCTCATTTGAGGCATGA
322 GTGCCTTATCACAAAAAGAATGAAGATCATTACTAGAATCCATGTTTGTCTCATTTGAGGCACGA
*
1544832 ACTTAGACTTTACAACAATTGGTGGGAAGAAAGCCTTTGTTGTGAAACCAAAGCATCAATATCGT
387 ACTTAGACTTTACAACAATTGGTGGGAAGAAAGCCTTTGTTGCGAAACCAAAGCATCAATATCGT
* *
1544897 ATATCCTAATGATAAGACTATGTTT
452 GTATCCTAATGAGAAGACTATGTTT
* * * * *
1544922 ATGGTTCCTAATCCTGAAAAGAATTGGGATTAGTGTAAGTATTCATGTTTGTCTTCTTTAAGAGA
1 ATGGTGCCTAATCCT-AAAAGAATGGGGATTAGTATGAGTATTCATGTTTGTCTTATTTAAGAGA
* * * * *
1544987 CAAATTTTTGTTTCTATCAAAAAGGGCTA-GAAGAAAAGCTTTTCTTGTGACACCAAAGCATTAA
65 CAAA-CTTTGATTCTATCAAAAACGGC-AGGAAGAAAAGCTTTTCTTGAGACACCAAAGCATCAA
* * *
1545051 TGTCGT-GTATCCTAACGAAGGCAATGTGTTTTGGCTTCCCAATCTTGAAATGAATGGAGACTGT
128 TGTCATGGTATCCTAACAAAGGCAATGTGTTTTGGCTTCCCAATCTTGAAAAGAATGGAGACTGT
* * * * **
1545115 TACAAGAATCGATGCTTATCATATTGAAGGGATGAACACTGATTTTAAGGAAAATAGGGCAAAGA
193 TACGAGAATCGATGCTTGTCTTATTCAAGGGATGAACTTTGATTTTAAGGAAAATAGGGCAAAGA
* ** * * * *
1545180 AACGATTTCCATGCAAAAGAAAATCGTTGATGTCATTTATCCTATTGAGGAGATTGCGTTTATAG
258 AAAGATTTCCATGCAAAAGAAAATCGTCAATGTCATTTATCCAAATGAGGAGAATGTGTTTATAG
* ** * * * * *
1545245 TGCATTATCACAAAAAGTGTGAAAATCATTACTAGGATCCATGTTTGTCTCTTTTGTGGCATGAA
323 TGCCTTATCACAAAAAGAATGAAGATCATTACTAGAATCCATGTTTGTCTCATTTGAGGCACGAA
* * * * *
1545310 CTTAGACTTTACAACAATTGGTGGGAAGAAAGCTTTTTTTGCAAAATCAAAGCATCAATATCGTT
388 CTTAGACTTTACAACAATTGGTGGGAAGAAAGCCTTTGTTGCGAAACCAAAGCATCAATATCGTG
*
1545375 TATCCTATTGAGAAGACTATGTTT
453 TATCCTAATGAGAAGACTATGTTT
* * * *
1545399 ATGGCGCCTAATCCTAAAAAGAATGGGGAAATAGTATGAGTATTCTTATTTGTCTTATTTAAGAG
1 ATGGTGCCTAATCCT-AAAAGAATGGGG-ATTAGTATGAGTATTCATGTTTGTCTTATTTAAGAG
** * *
1545464 ACAAACTTTGATTCTATCAAAAGGGGC-GAGAAGAAAAGCTTTTCTTGCGACACCACCAGCATCA
64 ACAAACTTTGATTCTATCAAAAACGGCAG-GAAGAAAAGCTTTTCTTGAGACACCA-AAGCATCA
1545528 CCATATGATT
Statistics
Matches: 1352, Mismatches: 185, Indels: 40
0.86 0.12 0.03
Matches are distributed among these distances:
474 1 0.00
475 371 0.27
476 149 0.11
477 783 0.58
478 48 0.04
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (476 bp):
ATGGTGCCTAATCCTAAAAGAATGGGGATTAGTATGAGTATTCATGTTTGTCTTATTTAAGAGAC
AAACTTTGATTCTATCAAAAACGGCAGGAAGAAAAGCTTTTCTTGAGACACCAAAGCATCAATGT
CATGGTATCCTAACAAAGGCAATGTGTTTTGGCTTCCCAATCTTGAAAAGAATGGAGACTGTTAC
GAGAATCGATGCTTGTCTTATTCAAGGGATGAACTTTGATTTTAAGGAAAATAGGGCAAAGAAAA
GATTTCCATGCAAAAGAAAATCGTCAATGTCATTTATCCAAATGAGGAGAATGTGTTTATAGTGC
CTTATCACAAAAAGAATGAAGATCATTACTAGAATCCATGTTTGTCTCATTTGAGGCACGAACTT
AGACTTTACAACAATTGGTGGGAAGAAAGCCTTTGTTGCGAAACCAAAGCATCAATATCGTGTAT
CCTAATGAGAAGACTATGTTT
Done.