Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2601
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: 62402
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:196 original size:29 final size:29
Alignment explanation
Indices: 157--234 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
147 CTTAATAATC
*
157 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
187 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
216 AGCCCGCACACTTA-TGCCA
1 AACCCGCACACTTAGTGCCA
235 ATCTCACAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 8 0.19
29 32 0.74
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.14, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:2538 original size:49 final size:49
Alignment explanation
Indices: 2372--2774 Score: 664
Period size: 49 Copynumber: 8.4 Consensus size: 49
2362 GCTCTGTCAC
*
2372 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC--
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
*
2419 ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCAC--
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
2466 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
2515 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
*
2562 ATATATACACTTTCACATTC-TCACATCGGCCATTAGACCTTATCACATAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--AT
2612 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
*
2661 GTATATACACTTTC-CACTTCATCACATCGGCCATTAGGCCTTATCACAT
1 ATATATACACTTTCACA-TTCATCACATCGGCCATTAGGCCTTATCACAT
*
2710 ATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
2759 ATATATACA--TTCACAT
1 ATATATACACTTTCACAT
2775 CACAATTATC
Statistics
Matches: 339, Mismatches: 8, Indels: 18
0.93 0.02 0.05
Matches are distributed among these distances:
46 25 0.07
47 118 0.35
48 2 0.01
49 147 0.43
50 22 0.06
51 25 0.07
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.33
Consensus pattern (49 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
Found at i:2712 original size:195 final size:190
Alignment explanation
Indices: 2368--2774 Score: 683
Period size: 195 Copynumber: 2.1 Consensus size: 190
2358 CTCGGCTCTG
*
2368 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGACCTCATCACATATATACACTTTC
*
2433 ACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCC
66 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCC
2498 ATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
131 ATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
*
2558 TCACATATATACACTTTCACATTC-TCACATCGGCCATTAGACCTTATCACATATATATATACAC
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGACCTCATCAC----ATATATACAC
2622 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATGTATATACACTTTC-CACTTCATCAC
62 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACA--TATATACACTTTCACA-TTCATCAC
*
2686 ATCGGCCATTAGGCCTTATCACATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCT
124 ATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
2751 TA
189 TA
* *
2753 TCACATATATATACATTCACAT
1 TCACATATATACACTTTCACAT
2775 CACAATTATC
Statistics
Matches: 204, Mismatches: 6, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
189 24 0.12
190 24 0.12
193 47 0.23
194 2 0.01
195 107 0.52
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (190 bp):
TCACATATATACACTTTCACATTCATCACATCGGCCATTAGACCTCATCACATATATACACTTTC
ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCC
ATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
Found at i:2811 original size:18 final size:20
Alignment explanation
Indices: 2788--2827 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
2778 AATTATCAAA
2788 ATATACT-TCATATAT-CAC
1 ATATACTATCATATATACAC
*
2806 ATATACTATCATGTATACAC
1 ATATACTATCATATATACAC
2826 AT
1 AT
2828 TGTCTTGGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 7 0.37
20 5 0.26
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.38
Consensus pattern (20 bp):
ATATACTATCATATATACAC
Found at i:8341 original size:49 final size:49
Alignment explanation
Indices: 8122--8567 Score: 620
Period size: 49 Copynumber: 9.3 Consensus size: 49
8112 ACCTTCGGGA
* * * * *
8122 CTTATCACAT-T-TATACAC-TTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8167 CTCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CT-TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
8215 CTCATCAC--ATATATACACTTTCACATTCATCACATC-GCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8261 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8308 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8357 CTTATCAC--ATATATACACTTTCACATTC-TCACATCGGCCATTAGAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8403 CTTATCACATATCATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--AT-ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8455 CTTATCACATGTATATACACTTTC-CACTTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACA-TTCATCACATCGGCCATTAGGC
*
8504 CTTATCACATATATATACATTTTCACATTCATCACA-C-GCCATTTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCA-TTAGGC
8552 CTTATCACATATATAT
1 CTTATCACATATATAT
8568 CATTCACATA
Statistics
Matches: 368, Mismatches: 16, Indels: 31
0.89 0.04 0.07
Matches are distributed among these distances:
45 3 0.01
46 81 0.22
47 95 0.26
48 27 0.07
49 113 0.31
50 4 0.01
51 20 0.05
52 25 0.07
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:22398 original size:43 final size:42
Alignment explanation
Indices: 22351--22473 Score: 126
Period size: 41 Copynumber: 2.9 Consensus size: 42
22341 ATGCCAACAT
* *
22351 CCCAGACGTGGTCTTACATGTAATCACATATCGATGCCACTAA
1 CCCAGACGTGGTCTTACACGTAATCAAATATCGATGCCA-TAA
* **
22394 CCCAGACAG-GGTCTTGCACG-AATCAAATA-CGATGCCGATGT
1 CCCAGAC-GTGGTCTTACACGTAATCAAATATCGATGCC-ATAA
* **
22435 CCCAGACATGGTCTTACACGTAATCATTTATCGATGCCA
1 CCCAGACGTGGTCTTACACGTAATCAAATATCGATGCCA
22474 ACGTCCTAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
41 25 0.38
42 17 0.26
43 23 0.35
44 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (42 bp):
CCCAGACGTGGTCTTACACGTAATCAAATATCGATGCCATAA
Found at i:22485 original size:43 final size:43
Alignment explanation
Indices: 22341--22495 Score: 165
Period size: 43 Copynumber: 3.7 Consensus size: 43
22331 ATATCGTACA
* * * *
22341 ATGCCAACATCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATATCG
* *
22384 ATGCC-AC-TAACCCAGACAGGGTCTTGCACG-AATCAAATA-CG
1 ATGCCAACGT--CCCAGACATGGTCTTACACGTAATCAAATATCG
* * **
22425 ATGCCGATGTCCCAGACATGGTCTTACACGTAATCATTTATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATATCG
*
22468 ATGCCAACGTCCTAGACATGGTCTTACA
1 ATGCCAACGTCCCAGACATGGTCTTACA
22496 TGAGAACAAC
Statistics
Matches: 93, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
41 26 0.28
42 18 0.19
43 49 0.53
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATATCG
Found at i:27287 original size:24 final size:24
Alignment explanation
Indices: 27260--27307 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
27250 GATCGGCTTC
27260 CACCAGAACCATGACTTCTTCACT
1 CACCAGAACCATGACTTCTTCACT
27284 CACCAGAACCATGACTTCTTCACT
1 CACCAGAACCATGACTTCTTCACT
27308 TTCTTCATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.38, G:0.08, T:0.25
Consensus pattern (24 bp):
CACCAGAACCATGACTTCTTCACT
Found at i:32979 original size:27 final size:27
Alignment explanation
Indices: 32947--33154 Score: 155
Period size: 27 Copynumber: 7.7 Consensus size: 27
32937 CTCAATTTGT
*
32947 AAAATTACCAAAGTACCCTCGATTTAC
1 AAAATTACCAAATTACCCTCGATTTAC
* *** *
32974 AGAATTACCGTTTTACCCTCGATTTAT
1 AAAATTACCAAATTACCCTCGATTTAC
* *****
33001 AGAATTATTGTTTTACCCTCGATTTAC
1 AAAATTACCAAATTACCCTCGATTTAC
** *
33028 AAAATTACCATTTTACCCTCGATTTAT
1 AAAATTACCAAATTACCCTCGATTTAC
* * ***
33055 AGAATTATCGTTTTACCCTCGATTTAC
1 AAAATTACCAAATTACCCTCGATTTAC
* * * *
33082 AAAATTACTAAAATACCCTTGGTTTAC
1 AAAATTACCAAATTACCCTCGATTTAC
* ** *
33109 AAAATTACCAAAATACCCTCGATCAAT
1 AAAATTACCAAATTACCCTCGATTTAC
*
33136 AAAATTACCAAAATACCCT
1 AAAATTACCAAATTACCCT
33155 TGGCTTGTAA
Statistics
Matches: 148, Mismatches: 33, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 148 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.34
Consensus pattern (27 bp):
AAAATTACCAAATTACCCTCGATTTAC
Found at i:33099 original size:81 final size:81
Alignment explanation
Indices: 32914--33131 Score: 256
Period size: 81 Copynumber: 2.7 Consensus size: 81
32904 GAATACTTTA
* * * **
32914 ATTTACCAAATTACTGAAATGCCCTCAATTTGTAAAATTACCAAAGTACCCTCGATTTACAGAAT
1 ATTTACAAAATTACTGAAATACCCTCGATTTACAAAATTACCAAAGTACCCTCGATTTACAGAAT
32979 TACCGTTTTACCCTCG
66 TACCGTTTTACCCTCG
* * * *** *** *
32995 ATTTATAGAATTATTGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTATAGAAT
1 ATTTACAAAATTACTGAAATACCCTCGATTTACAAAATTACCAAAGTACCCTCGATTTACAGAAT
*
33060 TATCGTTTTACCCTCG
66 TACCGTTTTACCCTCG
* * * *
33076 ATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCGAT
1 ATTTACAAAATTACTGAAATACCCTCGATTTACAAAATTACCAAAGTACCCTCGAT
33132 CAATAAAATT
Statistics
Matches: 109, Mismatches: 28, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
81 109 1.00
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (81 bp):
ATTTACAAAATTACTGAAATACCCTCGATTTACAAAATTACCAAAGTACCCTCGATTTACAGAAT
TACCGTTTTACCCTCG
Found at i:33100 original size:54 final size:54
Alignment explanation
Indices: 32960--33089 Score: 233
Period size: 54 Copynumber: 2.4 Consensus size: 54
32950 ATTACCAAAG
* * *
32960 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTATTGTTT
1 TACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTATAGAATTATCGTTT
33014 TACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTATAGAATTATCGTTT
33068 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAAAATTAC
33090 TAAAATACCC
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 73 1.00
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.40
Consensus pattern (54 bp):
TACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTATAGAATTATCGTTT
Found at i:33165 original size:27 final size:27
Alignment explanation
Indices: 33082--33180 Score: 119
Period size: 27 Copynumber: 3.7 Consensus size: 27
33072 CTCGATTTAC
* * *
33082 AAAATTACTAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCTTGGATTAT
* *
33109 AAAATTACCAAAATACCC-TCGATCAAT
1 AAAATTACCAAAATACCCTTGGAT-TAT
* *
33136 AAAATTACCAAAATACCCTTGGCTTGT
1 AAAATTACCAAAATACCCTTGGATTAT
33163 AAAATTACCAAAATACCC
1 AAAATTACCAAAATACCC
33181 CTAATTTGTG
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
26 3 0.05
27 55 0.90
28 3 0.05
ACGTcount: A:0.44, C:0.23, G:0.06, T:0.26
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTTGGATTAT
Found at i:33167 original size:54 final size:54
Alignment explanation
Indices: 33068--33180 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
33058 ATTATCGTTT
** * *
33068 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTCGATCAACAAAATTACCAAAATACCCTTGGCTTACAAAATTACCAAAA
* **
33122 TACCCTCGATCAATAAAATTACCAAAATACCCTTGGCTTGTAAAATTACCAAAA
1 TACCCTCGATCAACAAAATTACCAAAATACCCTTGGCTTACAAAATTACCAAAA
33176 TACCC
1 TACCC
33181 CTAATTTGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (54 bp):
TACCCTCGATCAACAAAATTACCAAAATACCCTTGGCTTACAAAATTACCAAAA
Found at i:33189 original size:27 final size:27
Alignment explanation
Indices: 33082--33236 Score: 109
Period size: 27 Copynumber: 5.8 Consensus size: 27
33072 CTCGATTTAC
* * * **
33082 AAAATTACTAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCCTGATTTGT
***
33109 AAAATTACCAAAATA-CCCTCGATCAAT
1 AAAATTACCAAAATACCCCT-GATTTGT
* **
33136 AAAATTACCAAAATACCCTTGGCTTGT
1 AAAATTACCAAAATACCCCTGATTTGT
*
33163 AAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCCTGATTTGT
* *** *
33190 GAAATTATTGAAATA-CTCTCGATTTGT
1 AAAATTACCAAAATACCCCT-GATTTGT
*
33217 AAAA-TATCAAAATACCCCTG
1 AAAATTACCAAAATACCCCTG
33237 TAGGGTAGAA
Statistics
Matches: 98, Mismatches: 26, Indels: 9
0.74 0.20 0.07
Matches are distributed among these distances:
26 15 0.15
27 80 0.82
28 3 0.03
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.30
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGATTTGT
Found at i:33269 original size:27 final size:27
Alignment explanation
Indices: 33226--33359 Score: 187
Period size: 27 Copynumber: 5.0 Consensus size: 27
33216 TAAAATATCA
33226 AAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* * *
33253 CAATACCCCTGTCGGGTAGAATTATCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
33280 AAATACCCTTGTAGGGTAGAAATACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
33307 AAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* * * *
33334 AGATACCCTTGTGGGGTAAAATTACC
1 AAATACCCCTGTAGGGTAGAATTACC
33360 ATTTTGCCCC
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 93 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (27 bp):
AAATACCCCTGTAGGGTAGAATTACCG
Found at i:33598 original size:25 final size:25
Alignment explanation
Indices: 33564--33633 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
33554 AGGAAGTGCT
*
33564 AAAAGGGCTTTGCCCTAGTTTA-CTG
1 AAAAGGGCTTTGCCCCAGTTTATC-G
33589 AAAAGGGCTTTGCCCCAGTTTATCG
1 AAAAGGGCTTTGCCCCAGTTTATCG
*
33614 AAAAGAGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
33634 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
25 41 0.98
26 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCG
Found at i:33657 original size:50 final size:50
Alignment explanation
Indices: 33564--33658 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
33554 AGGAAGTGCT
* * **
33564 AAAAGGGCTTTGCCCTAGTTTACTGAAAAGGGCTTTGCCCCAGTTTATCG
1 AAAAGAGCTTTGCCCCAGTTTACTGAAAAGGGCTAGGCCCCAGTTTATCG
*
33614 AAAAGAGCTTTGCCCCAG-TTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 AAAAGAGCTTTGCCCCAGTTTACTGAAAAG-GGCTAGGCC-CCAGTT
33659 ATATGATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
48 6 0.16
49 10 0.26
50 22 0.58
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (50 bp):
AAAAGAGCTTTGCCCCAGTTTACTGAAAAGGGCTAGGCCCCAGTTTATCG
Found at i:43387 original size:27 final size:27
Alignment explanation
Indices: 43335--43420 Score: 111
Period size: 27 Copynumber: 3.2 Consensus size: 27
43325 CAGACACCGT
* *
43335 ATCAGGT-GGCCTTAGCCCATTAACAGA
1 ATCAGGTGGGCCTAAGCCAATT-ACAGA
* *
43362 ATCTGGTGGGCCTAATCCAATTACAGA
1 ATCAGGTGGGCCTAAGCCAATTACAGA
*
43389 ATCAGGTGGGCCTAAGCCTATTACAGA
1 ATCAGGTGGGCCTAAGCCAATTACAGA
43416 ATCAG
1 ATCAG
43421 TACCAGATGC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 40 0.78
28 11 0.22
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (27 bp):
ATCAGGTGGGCCTAAGCCAATTACAGA
Found at i:48431 original size:27 final size:27
Alignment explanation
Indices: 48375--48452 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
48365 AGAAACAAAC
* *
48375 TGGGCCTTAGCCCATTAACAGAATCTGG
1 TGGGCCTAAGCCCATT-ACAGAATCAGG
*
48403 TGGGCCTAATCCCATTACAGAATCAGG
1 TGGGCCTAAGCCCATTACAGAATCAGG
* *
48430 TGGGCCTAAGCCCTTTATAGAAT
1 TGGGCCTAAGCCCATTACAGAAT
48453 TAGTACCAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 30 0.68
28 14 0.32
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (27 bp):
TGGGCCTAAGCCCATTACAGAATCAGG
Found at i:48533 original size:19 final size:20
Alignment explanation
Indices: 48494--48533 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
48484 CCAGCCCAAT
*
48494 CCAACCAATACACCACCTGTA
1 CCAACCAACACACCA-CTGTA
48515 CCAACCAACACACCA-TGTA
1 CCAACCAACACACCACTGTA
48534 GGGATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
21 14 0.78
ACGTcount: A:0.40, C:0.42, G:0.05, T:0.12
Consensus pattern (20 bp):
CCAACCAACACACCACTGTA
Found at i:51091 original size:28 final size:28
Alignment explanation
Indices: 51051--51114 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
51041 TGGGAAGTAG
* *
51051 TTGGGCCTGATGGGCCATGTGAATGTGA
1 TTGGGCCTGATGGGCCATGTGAACGAGA
51079 TTGGGCCTGATGGGCCATGTGAACGAGA
1 TTGGGCCTGATGGGCCATGTGAACGAGA
51107 TTGGGCCT
1 TTGGGCCT
51115 AAAGGGGCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.39, T:0.27
Consensus pattern (28 bp):
TTGGGCCTGATGGGCCATGTGAACGAGA
Found at i:51460 original size:27 final size:27
Alignment explanation
Indices: 51430--51903 Score: 360
Period size: 27 Copynumber: 17.6 Consensus size: 27
51420 TAATAAAGAG
* **
51430 AAATTACTAAAATACCCTAAATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * * *
51457 AAATTACCGAAATACCCCCAATTTGTG
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
51484 GAATTATTGAAATACCCTTGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
**
51511 AAATTACCAAAATACCCTCGA-TTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* *
51537 AAATTACTGAAATACCCTCAATTTATA
1 AAATTACTGAAATACCCTCGATTTGTA
* *
51564 AAATTA-TCAAAATATCCC-CGA-TTGTG
1 AAATTACT-GAAATA-CCCTCGATTTGTA
* *
51590 AAATTA-TCAAAACACCCTCGATTTGTA
1 AAATTACT-GAAATACCCTCGATTTGTA
** *
51617 AAATTACCAAAATACCCTCAATTAT-T-
1 AAATTACTGAAATACCCTCGATT-TGTA
* *
51643 AAATTATTAAAATACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * * * *
51670 AAACTATTGAAATACCCCCTATTTGTG
1 AAATTACTGAAATACCCTCGATTTGTA
* * ** *
51697 AAATT-TTCGAAACACTTTCAATTTGTA
1 AAATTACT-GAAATACCCTCGATTTGTA
* * *
51724 AAATTAC-CAGAAGACCCTCAATTTGTA
1 AAATTACTGA-AATACCCTCGATTTGTA
*
51751 AAATTA-TCGAAACACCCTCGATTTGTA
1 AAATTACT-GAAATACCCTCGATTTGTA
* *
51778 AAATTACCGAAACACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
51805 AAATTACTGAAATACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
51832 AAATTACCGAAACACCCCCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
51859 AAATTA-TCGAAATTCCCTTG-TAGTGTA
1 AAATTACT-GAAATACCCTCGAT-TTGTA
*
51886 AAATTGACTGACATACCC
1 AAATT-ACTGAAATACCC
51904 CTGTAGGGTA
Statistics
Matches: 361, Mismatches: 67, Indels: 37
0.78 0.14 0.08
Matches are distributed among these distances:
25 4 0.01
26 68 0.19
27 275 0.76
28 13 0.04
29 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.31
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGATTTGTA
Found at i:51513 original size:54 final size:54
Alignment explanation
Indices: 51430--51876 Score: 429
Period size: 54 Copynumber: 8.3 Consensus size: 54
51420 TAATAAAGAG
* * ** * *
51430 AAATTACTAAAATACCCTAAATTTGTAAAATTACCGAAATACCCCCAATTTGTG
1 AAATTATTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCCCGATTTGTA
* * * *
51484 GAATTATTGAAATACCCTTGATTTGTAAAATTACCAAAATACCCTCGA-TTGTA
1 AAATTATTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCCCGATTTGTA
* * * * * * *
51537 AAATTACTGAAATACCCTCAATTTATAAAATTATCAAAATATCCCCGA-TTGTG
1 AAATTATTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCCCGATTTGTA
** * * * *
51590 AAATTATCAAAACACCCTCGATTTGTAAAATTACCAAAATACCCTCAATTAT-T-
1 AAATTATTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCCCGATT-TGTA
* * ** * *
51643 AAATTATTAAAATACCCTCGATTTGTAAAACTATTGAAATACCCCCTATTTGTG
1 AAATTATTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCCCGATTTGTA
* ** * * * *
51697 AAATT-TTCGAAACACTTTCAATTTGTAAAATTACC-AGAAGACCCTCAATTTGTA
1 AAATTATT-GAAATACCCTCGATTTGTAAAATTACCGA-AATACCCCCGATTTGTA
* * * *
51751 AAATTATCGAAACACCCTCGATTTGTAAAATTACCGAAACACCCTCGATTTGTA
1 AAATTATTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCCCGATTTGTA
* *
51805 AAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAACACCCCCGATTTGTA
1 AAATTATTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCCCGATTTGTA
* *
51859 AAATTATCGAAATTCCCT
1 AAATTATTGAAATACCCT
51877 TGTAGTGTAA
Statistics
Matches: 324, Mismatches: 61, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
52 1 0.00
53 132 0.41
54 188 0.58
55 3 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (54 bp):
AAATTATTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCCCGATTTGTA
Found at i:52394 original size:11 final size:11
Alignment explanation
Indices: 52378--52403 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
52368 ATTGCATGTA
52378 TGATATTATTG
1 TGATATTATTG
52389 TGATATTATTG
1 TGATATTATTG
52400 TGAT
1 TGAT
52404 GTGGGCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (11 bp):
TGATATTATTG
Found at i:61261 original size:17 final size:18
Alignment explanation
Indices: 61239--61281 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
61229 TGCTTTGAAG
61239 ATTTGG-CGCCACTATCT
1 ATTTGGACGCCACTATCT
61256 ATTTGGTGACGCCACTATCT
1 ATTT-G-GACGCCACTATCT
61276 ATTTGG
1 ATTTGG
61282 TGAGAAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 4 0.17
18 2 0.09
19 2 0.09
20 15 0.65
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (18 bp):
ATTTGGACGCCACTATCT
Found at i:61270 original size:20 final size:20
Alignment explanation
Indices: 61245--61284 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
61235 GAAGATTTGG
61245 CGCCACTATCTATTTGGTGA
1 CGCCACTATCTATTTGGTGA
61265 CGCCACTATCTATTTGGTGA
1 CGCCACTATCTATTTGGTGA
61285 GAAATGTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (20 bp):
CGCCACTATCTATTTGGTGA
Done.