Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 12 of 31
Found at i:2780269 original size:150 final size:150
Alignment explanation
Indices: 2779998--2780350 Score: 564
Period size: 150 Copynumber: 2.4 Consensus size: 150
2779988 ATTTAGTGCC
* *
2779998 ATCTTCAGGCTCCTTCTCTCGCTTTCTCTTCGATGAAGTCTTG-TCAATCTTAACTCCAGTTTTC
1 ATCTTCAGGCTCCTTCTCTCGCTTTCTCTTCAATGAAGT-TTGATCAATCTTAACCCCAGTTTTC
* * *
2780062 TTGGAAGAACTATCTTCAGGCTCCTTTTCTTTCTTTCTCGTCGATGAAGTTTGATAAATCTTAAC
65 TTGCAAGAACTATCTTCAGGCTCCTTTTCTCTCTTTCTCGTCAATGAAGTTTGATAAATCTTAAC
*
2780127 CCTGGTTTTCTTAGAAGAACT
130 CCTGGTTTTCTCAGAAGAACT
* * *
2780148 ATCTTCAGGTTCCTTATCTCGCTTTCTCTTCAATGAAGTTTGATCAATCTTAACCCCGGTTTTCT
1 ATCTTCAGGCTCCTTCTCTCGCTTTCTCTTCAATGAAGTTTGATCAATCTTAACCCCAGTTTTCT
*
2780213 TGCAAGAACTATCTTCAGGCTCCTTTTCTCTCTTTCTCTTCAATGAAGTTTGATAAATCTTAACC
66 TGCAAGAACTATCTTCAGGCTCCTTTTCTCTCTTTCTCGTCAATGAAGTTTGATAAATCTTAACC
2780278 CTGGTTTTCTCAGAAGAACT
131 CTGGTTTTCTCAGAAGAACT
* * * *
2780298 ATCTTCACGCTCCTTCTCTCGTTTTCTCTTCAATGAAGTTCGATCACTCTTAA
1 ATCTTCAGGCTCCTTCTCTCGCTTTCTCTTCAATGAAGTTTGATCAATCTTAA
2780351 TCTCAACATC
Statistics
Matches: 186, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
149 3 0.02
150 183 0.98
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.41
Consensus pattern (150 bp):
ATCTTCAGGCTCCTTCTCTCGCTTTCTCTTCAATGAAGTTTGATCAATCTTAACCCCAGTTTTCT
TGCAAGAACTATCTTCAGGCTCCTTTTCTCTCTTTCTCGTCAATGAAGTTTGATAAATCTTAACC
CTGGTTTTCTCAGAAGAACT
Found at i:2784978 original size:258 final size:247
Alignment explanation
Indices: 2784375--2784979 Score: 663
Period size: 258 Copynumber: 2.4 Consensus size: 247
2784365 CAAAGCTAAC
*
2784375 TTGATTTCAATCTCTAATTCAATTGTAACACCACCGAGTGAGCCAATACCGGAGGTTGAACCAAT
1 TTGATTTCAATCTCTAATTCAATTGTAACACCACC--GTGAGCCAATA-CGG-GGGTGAACCAAT
* * * *
2784440 ACAACATTAACTAACTTGCTAACGACAATAACAACAACAATAACATCATTAATGACAATAAATAA
62 ACAGCCTTAACTAACTTGCTAACGACAATAACAACAACAATAACATCAATAACGACAATAAATAA
* * *
2784505 AAGACGTAAACAATTACCACTGAGGGAAATTAACTTGCTAACGACAGTAAATAAAAGATATAATC
127 AAGACGTAAACAATTACCACTCAGGGAAATTAACTTGCTAACGACAATAAATAAAAGACATAATC
* * * * *
2784570 AATTAACTCAAGTGTGGCAACCCTAAGGGAGATAAATAAACGCCAATCCCATAAAC
192 AATTAACTCAAGTGTGGCAACCATAAGGAAGACAAATAAACACCAATCCCATAAAA
* * *
2784626 TTGATTTCAATCTCTAATTCAATGGTAACTATACCA-GGTGAG-C--T---GGGG-GAACAAATA
1 TTGATTTCAATCTCTAATTCAATTGTAAC---ACCACCGTGAGCCAATACGGGGGTGAACCAATA
* *
2784683 CAGCCTTAACTAACTTGCTAACGACAATAAGGACAATAGCGACTTTAATGACATTAATGACAATA
63 CAGCCTTAACTAACTTGCTAACGACAAT-A--AC-A-A-CAAC---AAT-A-A--CAT--CAATA
* *
2784748 ACGACAATAAATAAAAGACGTAATCAATTACCAC-CACGGGAAAAATTTACTTGCTAACGACAAT
113 ACGACAATAAATAAAAGACGTAAACAATTACCACTCA-GGG--AAATTAACTTGCTAACGACAAT
*
2784812 AAATAAAAGACATAATCAATTACCTC-AGTGTGGCAACCATAAGGAAGACAAATAAACACCAATC
175 AAATAAAAGACATAATCAATTAACTCAAGTGTGGCAACCATAAGGAAGACAAATAAACACCAATC
*
2784876 CCGTAAAA
240 CCATAAAA
* *
2784884 TTGATTTCAATCTCTAATTCAATTATAACGCCACCGTGCAAGCCAATACAGGTGGGTGAACCAAT
1 TTGATTTCAATCTCTAATTCAATTGTAACACCACCGTG--AGCCAATAC-GG-GGGTGAACCAAT
2784949 ACAGCCTTAACTAACTTGCTAACGACAATAA
62 ACAGCCTTAACTAACTTGCTAACGACAATAA
2784980 ATAAGAGACA
Statistics
Matches: 294, Mismatches: 27, Indels: 53
0.79 0.07 0.14
Matches are distributed among these distances:
242 34 0.12
243 3 0.01
244 1 0.00
245 2 0.01
246 1 0.00
247 1 0.00
248 4 0.01
250 1 0.00
251 36 0.12
252 1 0.00
253 1 0.00
254 4 0.01
255 5 0.02
256 4 0.01
257 39 0.13
258 69 0.23
259 45 0.15
261 1 0.00
264 1 0.00
265 1 0.00
266 4 0.01
267 36 0.12
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.23
Consensus pattern (247 bp):
TTGATTTCAATCTCTAATTCAATTGTAACACCACCGTGAGCCAATACGGGGGTGAACCAATACAG
CCTTAACTAACTTGCTAACGACAATAACAACAACAATAACATCAATAACGACAATAAATAAAAGA
CGTAAACAATTACCACTCAGGGAAATTAACTTGCTAACGACAATAAATAAAAGACATAATCAATT
AACTCAAGTGTGGCAACCATAAGGAAGACAAATAAACACCAATCCCATAAAA
Found at i:2785152 original size:222 final size:219
Alignment explanation
Indices: 2784746--2785445 Score: 711
Period size: 222 Copynumber: 3.0 Consensus size: 219
2784736 TTAATGACAA
* * * * *
2784746 TAACGACAATAAATAAAAGACGTAATCAATTACCACCACGGGAAAAATTTACTTGCTAACGACAA
1 TAACGACAATAAATAAGAGACATAATCAATTACCACTAAGGG-AAAATTAACTTGCTAACGACAA
* * * *
2784811 TAAATAAAAGACATAATCAATTACCTCAGTGTGGCAACCATAAGGAAGACAAATAAACACCAATC
65 TAAATAAAAGACATAATCAATTATCTCAGTGTGGCAACCCTAAGGAAGATAAATAAACGCCAATC
* * * * * * **
2784876 CCGTAAAATTGATTTCAATCTCTAATTCAATTATAACGCCACCGTGCAAGCCAATACAGGTGGGT
130 CCATAAACTTGATTTCAATCTCTAATTCAAATGTAA-GCCACTGGGTGAGCCAATACAGGT-GGT
2784941 GAACCAATACAGCCTTAACTAACTTGC
193 GAACCAATACAGCCTTAACTAACTTGC
2784968 TAACGACAATAAATAAGAGACATAATCAATTACCACTAAGGGAAAATTAACTTGCTAACGACAAT
1 TAACGACAATAAATAAGAGACATAATCAATTACCACTAAGGGAAAATTAACTTGCTAACGACAAT
* *
2785033 AAATAAAGGACATTATCAATTATCTCACGTGTGGCAACCCTAAGTG-AGATAAATAAACGCCAAT
66 AAATAAAAGACATAATCAATTATCTCA-GTGTGGCAACCCTAAG-GAAGATAAATAAACGCCAAT
* * * **
2785097 CCCATAAACTTGATTTCAATCTCTAACTCAAAGGTAATGCCAGTGGGTGAGCCAATACAGGCCAG
129 CCCATAAACTTGATTTCAATCTCTAATTCAAATGTAA-GCCACTGGGTGAGCCAATACAGG-TGG
*
2785162 TAAACCAATACAGCCTTAACTAACTTGC
192 TGAACCAATACAGCCTTAACTAACTTGC
**
2785190 TAACGACAATAACAACATTAACGACAAGAATGACAATTAATAAAAGGACATAATCAATTACACTA
1 TAACGACAAT---AA-A-T------AAG-A-GAC-A-TAAT-------C--AAT---TACCACTA
* *
2785255 AGGGAAAATTAAATTGCCAACGACAATAAATAAAAAGACATAATCAATTATCTCAAGTGTGGCAA
39 AGGGAAAATTAACTTGCTAACGACAATAAAT-AAAAGACATAATCAATTATCTC-AGTGTGGCAA
* * * *
2785320 CCCTTAGGTAGATAAATAAATGACCAATCCCATAAACTTGATTTCTATCTCTAATTC-AATGTAA
102 CCCTAAGGAAGATAAATAAACG-CCAATCCCATAAACTTGATTTCAATCTCTAATTCAAATGTAA
* * * * *
2785384 CCCACTGGGTGAGTCAATACGGGTGGTGAATCAATACAGACTTAACTAACTTGC
166 GCCACTGGGTGAGCCAATACAGGTGGTGAACCAATACAGCCTTAACTAACTTGC
2785438 TAACGACA
1 TAACGACA
2785446 TTAACGACAA
Statistics
Matches: 398, Mismatches: 46, Indels: 42
0.82 0.09 0.09
Matches are distributed among these distances:
221 46 0.12
222 156 0.39
223 1 0.00
225 2 0.01
226 1 0.00
227 1 0.00
233 3 0.01
234 1 0.00
235 3 0.01
236 1 0.00
237 4 0.01
244 1 0.00
246 3 0.01
248 34 0.09
249 55 0.14
250 53 0.13
251 33 0.08
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.23
Consensus pattern (219 bp):
TAACGACAATAAATAAGAGACATAATCAATTACCACTAAGGGAAAATTAACTTGCTAACGACAAT
AAATAAAAGACATAATCAATTATCTCAGTGTGGCAACCCTAAGGAAGATAAATAAACGCCAATCC
CATAAACTTGATTTCAATCTCTAATTCAAATGTAAGCCACTGGGTGAGCCAATACAGGTGGTGAA
CCAATACAGCCTTAACTAACTTGC
Found at i:2785450 original size:9 final size:9
Alignment explanation
Indices: 2785438--2785499 Score: 61
Period size: 9 Copynumber: 6.9 Consensus size: 9
2785428 ACTAACTTGC
*
2785438 TAACGACAT
1 TAACGACAA
2785447 TAACGACAA
1 TAACGACAA
*
2785456 TAACAACAA
1 TAACGACAA
* *
2785465 TAATGACAT
1 TAACGACAA
* *
2785474 TTAGGACAA
1 TAACGACAA
*
2785483 TAACAACAA
1 TAACGACAA
2785492 TAACGACA
1 TAACGACA
2785500 CCAGGTGAGC
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.53, C:0.19, G:0.10, T:0.18
Consensus pattern (9 bp):
TAACGACAA
Found at i:2785472 original size:27 final size:27
Alignment explanation
Indices: 2785438--2785499 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
2785428 ACTAACTTGC
2785438 TAACGACATTAACGACAATAACAACAA
1 TAACGACATTAACGACAATAACAACAA
* * *
2785465 TAATGACATTTAGGACAATAACAACAA
1 TAACGACATTAACGACAATAACAACAA
2785492 TAACGACA
1 TAACGACA
2785500 CCAGGTGAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.53, C:0.19, G:0.10, T:0.18
Consensus pattern (27 bp):
TAACGACATTAACGACAATAACAACAA
Found at i:2785565 original size:9 final size:9
Alignment explanation
Indices: 2785551--2785594 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
2785541 ACTAACTTGC
2785551 TAACGACAT
1 TAACGACAT
2785560 TAACGACAT
1 TAACGACAT
* *
2785569 TAACGAAAA
1 TAACGACAT
2785578 TAACGACAT
1 TAACGACAT
2785587 TAACGACA
1 TAACGACA
2785595 ATAGATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.50, C:0.20, G:0.11, T:0.18
Consensus pattern (9 bp):
TAACGACAT
Found at i:2786066 original size:30 final size:30
Alignment explanation
Indices: 2786030--2786119 Score: 144
Period size: 30 Copynumber: 3.0 Consensus size: 30
2786020 GGCCATTTAG
*
2786030 CAGCTCCTCCCTCCACCAATCGCTGGACTT
1 CAGCTCCTCCCTCCTCCAATCGCTGGACTT
*
2786060 CAGCTCCTCTCTCCTCCAATCGCTGGACTT
1 CAGCTCCTCCCTCCTCCAATCGCTGGACTT
* *
2786090 CAGCTCCTTCCTCCTCCAATGGCTGGACTT
1 CAGCTCCTCCCTCCTCCAATCGCTGGACTT
2786120 TGTAAGAGTA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.14, C:0.43, G:0.14, T:0.28
Consensus pattern (30 bp):
CAGCTCCTCCCTCCTCCAATCGCTGGACTT
Found at i:2787258 original size:17 final size:18
Alignment explanation
Indices: 2787227--2787260 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2787217 TAATATTTTT
*
2787227 TAAAAATATTATAATAAA
1 TAAAAATAATATAATAAA
2787245 TAAAAATAAT-TAATAA
1 TAAAAATAATATAATAA
2787261 TATTAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAATAATATAATAAA
Found at i:2787267 original size:19 final size:18
Alignment explanation
Indices: 2787226--2787269 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
2787216 TTAATATTTT
2787226 TTAAAAATATTATAATAA
1 TTAAAAATATTATAATAA
*
2787244 ATAAAAATAATTAATAAT-A
1 TTAAAAAT-ATT-ATAATAA
2787263 TTAAAAA
1 TTAAAAA
2787270 ATTTTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 7 0.32
19 10 0.45
20 5 0.23
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TTAAAAATATTATAATAA
Found at i:2789041 original size:21 final size:21
Alignment explanation
Indices: 2789007--2789065 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 21
2788997 TTGCCTCATA
2789007 ACCATATATATATATGTTAATAT
1 ACCATAT-TATATAT-TTAATAT
*
2789030 ACC-TATTATATAATTTCATAT
1 ACCATATTATAT-ATTTAATAT
2789051 ACCATATTATATATT
1 ACCATATTATATATT
2789066 GTATTGCTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 17 0.52
22 13 0.39
23 3 0.09
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.46
Consensus pattern (21 bp):
ACCATATTATATATTTAATAT
Found at i:2789584 original size:63 final size:64
Alignment explanation
Indices: 2789484--2789638 Score: 149
Period size: 63 Copynumber: 2.4 Consensus size: 64
2789474 TTGGATATCA
** * * * *
2789484 TTTTTTTAA-ATCATTAAATTTATATATTTATCGTAATTTGA-TAATA-TTCTGAATATCATTT-
1 TTTTTTTAATATTTTTAAATTTATACATTCACCATAA-TTGAGTAATACTT-TGAATATCATTTC
2789545 T
64 T
* *
2789546 GTTTTTTT-ATATTTTTAAATTTGTACATTCACCATAATTGAGTAATACTTTGAATATTATTTCC
1 -TTTTTTTAATATTTTTAAATTTATACATTCACCATAATTGAGTAATACTTTGAATATCATTT-C
2789610 T
64 T
* *
2789611 TTTTTTTAATGTTTTTGAATTTATACAT
1 TTTTTTTAATATTTTTAAATTTATACAT
2789639 ATTGATATAT
Statistics
Matches: 75, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
62 5 0.07
63 43 0.57
64 9 0.12
65 18 0.24
ACGTcount: A:0.30, C:0.08, G:0.06, T:0.55
Consensus pattern (64 bp):
TTTTTTTAATATTTTTAAATTTATACATTCACCATAATTGAGTAATACTTTGAATATCATTTCT
Found at i:2790220 original size:72 final size:69
Alignment explanation
Indices: 2790073--2790459 Score: 280
Period size: 68 Copynumber: 5.6 Consensus size: 69
2790063 TATAATTTGA
* *
2790073 TAAATGTATAAATTTAAAAATAT--AAAAA-AAATAATATCCAATCACATATCAGTATTA-TCAA
1 TAAATGTATAAATTTAAAAATATAAAAAAAGAAATGATATCCAAT--CATATCAATATTACT-AA
*
2790134 ATTATGA
63 ATTATGG
*
2790141 TAAATGTATAAACTTAAAAATATAAAAAAAGGAAATGATATCCAATTGCATATCAATATTACTAA
1 TAAATGTATAAATTTAAAAATATAAAAAAA-GAAATGATATCCAA-T-CATATCAATATTACTAA
* *
2790206 ACTAGGG
63 ATTATGG
* *
2790213 TAAATGTATAAATTTAAGAATATAAAAGAAAAAGAAATGATAT---A-CATATCAATATTACCAA
1 TAAATGTATAAATTTAA-AA-ATATAA-AAAAAGAAATGATATCCAATCATATCAATATTACTAA
2790274 ATTATGG
63 ATTATGG
* * * * *
2790281 CAAATGTATAAATTT-AAAA-A-AATATAA-AAATGATATTCAATCATAT-ATCAGATTA-TCAA
1 TAAATGTATAAATTTAAAAATATAAAAAAAGAAATGATATCCAATCATATCA--ATATTACT-AA
* ***
2790340 GTTAACA
63 ATTATGG
* * * * *
2790347 TAAATGTATAAATTAAAAAATATAAAAAAAGAAATGACATACATGTACATATCAATATTACCAAA
1 TAAATGTATAAATTTAAAAATATAAAAAAAGAAATGATATCCA-AT-CATATCAATATTACTAAA
***
2790412 TTAACA
64 TTATGG
* * ** *
2790418 TAAATTTATAAATTTAAGAATATAAAAAGGGAAATGACATCC
1 TAAATGTATAAATTTAAAAATATAAAAAAAGAAATGATATCC
2790460 GATGCTTACT
Statistics
Matches: 258, Mismatches: 37, Indels: 45
0.76 0.11 0.13
Matches are distributed among these distances:
61 9 0.03
62 3 0.01
63 2 0.01
64 3 0.01
65 6 0.02
66 25 0.10
67 5 0.02
68 58 0.22
69 5 0.02
70 15 0.06
71 51 0.20
72 51 0.20
73 5 0.02
74 15 0.06
75 5 0.02
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.29
Consensus pattern (69 bp):
TAAATGTATAAATTTAAAAATATAAAAAAAGAAATGATATCCAATCATATCAATATTACTAAATT
ATGG
Found at i:2791021 original size:18 final size:18
Alignment explanation
Indices: 2790998--2791035 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2790988 ATCAAAGAAC
*
2790998 TTAATAAATGATCAAAAT
1 TTAATAAATAATCAAAAT
*
2791016 TTAATAAATAATTAAAAT
1 TTAATAAATAATCAAAAT
2791034 TT
1 TT
2791036 TTATTTTCGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (18 bp):
TTAATAAATAATCAAAAT
Found at i:2791858 original size:21 final size:22
Alignment explanation
Indices: 2791834--2791881 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
2791824 AAATGATACG
2791834 AATATAATATAA-A-ATAAAAAT
1 AATATAATATAACACA-AAAAAT
*
2791855 AATAAAATATAACACAAAAAAT
1 AATATAATATAACACAAAAAAT
2791877 AATAT
1 AATAT
2791882 GAACACAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 11 0.48
22 11 0.48
23 1 0.04
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (22 bp):
AATATAATATAACACAAAAAAT
Found at i:2792101 original size:11 final size:11
Alignment explanation
Indices: 2792078--2792124 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 11
2792068 ATTAAAAAAA
2792078 TAATTTTTA-T
1 TAATTTTTATT
2792088 TAATTTTTATT
1 TAATTTTTATT
*
2792099 TAATATTTATTT
1 TAATTTTTA-TT
2792111 TAATAATTTTATT
1 TAAT--TTTTATT
2792124 T
1 T
2792125 TTAAAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 9 0.29
11 9 0.29
12 6 0.19
13 3 0.10
14 4 0.13
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATT
Found at i:2792110 original size:27 final size:28
Alignment explanation
Indices: 2792074--2792153 Score: 76
Period size: 26 Copynumber: 3.0 Consensus size: 28
2792064 AAATATTAAA
2792074 AAAATA-ATTTTTATTAATTTT-TATTT
1 AAAATATATTTTTATTAATTTTATATTT
* * * *
2792100 AATATTTA-TTTTAATAATTTTATTTTT
1 AAAATATATTTTTATTAATTTTATATTT
* * *
2792127 AAAATATATTTTAATTAAATTAATATT
1 AAAATATATTTTTATTAATTTTATATT
2792154 ATTTAACTCA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
26 16 0.40
27 11 0.28
28 13 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
AAAATATATTTTTATTAATTTTATATTT
Found at i:2792117 original size:26 final size:27
Alignment explanation
Indices: 2792074--2792141 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
2792064 AAATATTAAA
*
2792074 AAAATA-ATTTTTATTAATTTT-TATTT
1 AAAATATA-TTTTAATAATTTTATATTT
* * *
2792100 AATATTTATTTTAATAATTTTATTTTT
1 AAAATATATTTTAATAATTTTATATTT
2792127 AAAATATATTTTAAT
1 AAAATATATTTTAAT
2792142 TAAATTAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
26 16 0.47
27 18 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
AAAATATATTTTAATAATTTTATATTT
Found at i:2792126 original size:15 final size:15
Alignment explanation
Indices: 2792080--2792128 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
2792070 TAAAAAAATA
*
2792080 ATTTTTATTAATTTT
1 ATTTTTAATAATTTT
*
2792095 -TATTTAAT-A-TTT
1 ATTTTTAATAATTTT
2792107 A-TTTTAATAATTTT
1 ATTTTTAATAATTTT
2792121 ATTTTTAA
1 ATTTTTAA
2792129 AATATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
12 9 0.33
13 2 0.07
14 10 0.37
15 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTTAATAATTTT
Found at i:2792421 original size:24 final size:26
Alignment explanation
Indices: 2792389--2792440 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
2792379 TTTATTTTAA
2792389 ATTTATATTT-AA-TAATTAAAAAAT
1 ATTTATATTTAAATTAATTAAAAAAT
* *
2792413 ATTTTTATTTAAATTAATTATAAAAT
1 ATTTATATTTAAATTAATTAAAAAAT
2792439 AT
1 AT
2792441 ATATTATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.38
25 2 0.08
26 13 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTTATATTTAAATTAATTAAAAAAT
Found at i:2792445 original size:24 final size:22
Alignment explanation
Indices: 2792387--2792445 Score: 55
Period size: 26 Copynumber: 2.5 Consensus size: 22
2792377 AATTTATTTT
*
2792387 AAATTTATATTTAATAATTAAA
1 AAATATATATTTAATAATTAAA
* *
2792409 AAATATTTTTATTTAAATTAATTATA
1 AAATA--TATATTT-AA-TAATTAAA
2792435 AAATATATATT
1 AAATATATATT
2792446 ATTACTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
22 4 0.14
24 11 0.38
25 2 0.07
26 12 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATATATATTTAATAATTAAA
Found at i:2792617 original size:22 final size:23
Alignment explanation
Indices: 2792592--2792636 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2792582 AGTGACCCAT
2792592 AAATA-TAATATTT-CTATTTTAA
1 AAATATTAAT-TTTACTATTTTAA
*
2792614 AAATATTAATTTTAGTATTTTAA
1 AAATATTAATTTTACTATTTTAA
2792637 CTTATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
AAATATTAATTTTACTATTTTAA
Found at i:2793678 original size:21 final size:21
Alignment explanation
Indices: 2793652--2793691 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2793642 TTTAAAATTT
2793652 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
2793673 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
2793692 AATAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:2793874 original size:29 final size:31
Alignment explanation
Indices: 2793834--2793916 Score: 83
Period size: 29 Copynumber: 2.9 Consensus size: 31
2793824 TTTCTATTTT
*
2793834 ATATATTA-ATTTTTTAAAA-ATAA-TTTAA
1 ATATTTTATATTTTTTAAAATATAATTTTAA
* *
2793862 AT-TTTT-TATATTTTAAAATTTAATTTTAA
1 ATATTTTATATTTTTTAAAATATAATTTTAA
2793891 ATATTTTATA--TTTTAAAATA-AATTTT
1 ATATTTTATATTTTTTAAAATATAATTTT
2793917 TTTTTACAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
27 13 0.28
28 11 0.24
29 16 0.35
30 4 0.09
31 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
ATATTTTATATTTTTTAAAATATAATTTTAA
Found at i:2793886 original size:22 final size:23
Alignment explanation
Indices: 2793855--2793907 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
2793845 TTTTAAAAAT
**
2793855 AATTTAAATTTTTTATATTTTAA
1 AATTTAAATTTTAAATATTTTAA
*
2793878 AATTT-AATTTTAAATATTTTAT
1 AATTTAAATTTTAAATATTTTAA
*
2793900 ATTTTAAA
1 AATTTAAA
2793908 ATAAATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
AATTTAAATTTTAAATATTTTAA
Found at i:2793917 original size:29 final size:29
Alignment explanation
Indices: 2793845--2793916 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
2793835 TATATTAATT
* *
2793845 TTTTAAAAAT-AA-TTTAAATTTTTTATA
1 TTTTAAAATTAAATTTTAAATATTTTATA
*
2793872 TTTTAAAATTTAATTTTAAATATTTTATA
1 TTTTAAAATTAAATTTTAAATATTTTATA
2793901 TTTTAAAA-TAAATTTT
1 TTTTAAAATTAAATTTT
2793917 TTTTTACAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 9 0.22
28 9 0.22
29 22 0.55
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTTAAAATTAAATTTTAAATATTTTATA
Found at i:2798086 original size:2 final size:2
Alignment explanation
Indices: 2798079--2798126 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
2798069 CCTATTATTA
* *
2798079 AT AT AT AT AT AT AT AT AT AT AC AC ACT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
2798122 AT AT A
1 AT AT A
2798127 AATGTTGACA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 42 0.98
3 1 0.02
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2800040 original size:13 final size:13
Alignment explanation
Indices: 2799997--2800042 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
2799987 GTTGGTTTTT
*
2799997 AATAAATTATTAA
1 AATAAATTATAAA
2800010 AATAATATTAATATAA
1 AATAA-ATT-ATA-AA
2800026 AATAAATTATAAA
1 AATAAATTATAAA
2800039 AATA
1 AATA
2800043 TTATTATGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 11 0.38
14 6 0.21
15 5 0.17
16 7 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATAAATTATAAA
Found at i:2800318 original size:18 final size:19
Alignment explanation
Indices: 2800295--2800349 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 19
2800285 AGTTTAGTAA
2800295 TTTAAAATAATTAAATT-T
1 TTTAAAATAATTAAATTAT
*
2800313 TTTAAAATAATTAGATTAT
1 TTTAAAATAATTAAATTAT
* *
2800332 TATAAATTAATTAAATTA
1 TTTAAAATAATTAAATTA
2800350 AAATTTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TTTAAAATAATTAAATTAT
Found at i:2800344 original size:37 final size:38
Alignment explanation
Indices: 2800288--2800382 Score: 106
Period size: 41 Copynumber: 2.5 Consensus size: 38
2800278 ACTTATTAGT
*
2800288 TTAG-TAATT-TAAAATAATTAAATT-TTTTAAAATAA
1 TTAGATAATTATAAATTAATTAAATTATTTTAAAATAA
* *
2800323 TTAGATTATTATAAATTAATTAAATTAAAATTTTAAAATAG
1 TTAGATAATTATAAATTAATTAAATT---ATTTTAAAATAA
*
2800364 TTAGATAATTATAATTTAA
1 TTAGATAATTATAAATTAA
2800383 AATTTAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
35 4 0.08
36 4 0.08
37 14 0.29
41 27 0.55
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (38 bp):
TTAGATAATTATAAATTAATTAAATTATTTTAAAATAA
Found at i:2800362 original size:41 final size:42
Alignment explanation
Indices: 2800303--2800382 Score: 117
Period size: 41 Copynumber: 1.9 Consensus size: 42
2800293 AATTTAAAAT
* *
2800303 AATTAAATTTTTTAAAATAATTAGATTATTATAAATTAATTA
1 AATTAAATATTTTAAAATAATTAGATAATTATAAATTAATTA
* *
2800345 AATTAAA-ATTTTAAAATAGTTAGATAATTATAATTTAA
1 AATTAAATATTTTAAAATAATTAGATAATTATAAATTAA
2800383 AATTTAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
41 27 0.79
42 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (42 bp):
AATTAAATATTTTAAAATAATTAGATAATTATAAATTAATTA
Found at i:2800392 original size:31 final size:30
Alignment explanation
Indices: 2800334--2800421 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 30
2800324 TAGATTATTA
*
2800334 TAAATTAATTAAA-TTAAAATTTTAAAATAGT
1 TAAA-TAATTAAATTTAAAA-TTTAAAATAAT
*
2800365 TAGATAATTATAATTTAAAATTTAAAATAAT
1 TAAATAATTA-AATTTAAAATTTAAAATAAT
* **
2800396 TAAATGATTAAAATTTTTAATTTAAA
1 TAAATAATT-AAATTTAAAATTTAAA
2800422 TTTAAAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 6 0.12
31 35 0.73
32 7 0.15
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (30 bp):
TAAATAATTAAATTTAAAATTTAAAATAAT
Found at i:2800430 original size:22 final size:21
Alignment explanation
Indices: 2800405--2800455 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
2800395 TTAAATGATT
*
2800405 AAAATTTTTAATTTAAATTTAA
1 AAAATTATTAATTTAAA-TTAA
* *
2800427 AAAATAATTATTTTAAATTAA
1 AAAATTATTAATTTAAATTAA
2800448 ATAAATTA
1 A-AAATTA
2800456 AACTAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAATTATTAATTTAAATTAA
Found at i:2800584 original size:19 final size:19
Alignment explanation
Indices: 2800518--2800590 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 19
2800508 TTATCATTAA
*
2800518 TTATAAATAA-AATATTTT
1 TTATAAATAATATTATTTT
*
2800536 TTA-ATAATAAAAATTATTATT
1 TTATA-AAT-AATATTATT-TT
*
2800557 ATATTTAAATAATATTATTTT
1 -T-TATAAATAATATTATTTT
2800578 TTATAAATAATAT
1 TTATAAATAATAT
2800591 AACCTCTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
17 1 0.02
18 6 0.14
19 13 0.30
20 6 0.14
21 4 0.09
22 9 0.20
23 4 0.09
24 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATAAATAATATTATTTT
Found at i:2800635 original size:27 final size:27
Alignment explanation
Indices: 2800604--2800655 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
2800594 CTCTTAAATT
*
2800604 ATTAAAAAATATCAACATAATAATATA
1 ATTAAAAAATATAAACATAATAATATA
*
2800631 ATTAAAAAATATAAATATAATAATA
1 ATTAAAAAATATAAACATAATAATA
2800656 ATTTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (27 bp):
ATTAAAAAATATAAACATAATAATATA
Found at i:2800704 original size:25 final size:26
Alignment explanation
Indices: 2800639--2800704 Score: 64
Period size: 28 Copynumber: 2.5 Consensus size: 26
2800629 TAATTAAAAA
*
2800639 ATATAAATATAATAATAATTTAATAAT
1 ATATAAATA-ATTAATAATTTAATAAT
*
2800666 ATTATCAAAAAATTAAT-ATTATAATAAT
1 A-TAT-AAATAATTAATAATT-TAATAAT
2800694 A-ATAAATAATT
1 ATATAAATAATT
2800705 TACAAATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
25 7 0.21
26 2 0.06
27 4 0.12
28 16 0.48
29 4 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
ATATAAATAATTAATAATTTAATAAT
Found at i:2800801 original size:24 final size:23
Alignment explanation
Indices: 2800773--2800836 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
2800763 GTAAATATAT
* *
2800773 TAATTAATTTAATAATTTTTTTA
1 TAATTAATTTAATAATATTTTAA
**
2800796 TAAATTAAAATAATAATATTTTAA
1 T-AATTAATTTAATAATATTTTAA
* *
2800820 TAATTTATTTAAAAATA
1 TAATTAATTTAATAATA
2800837 AAAACACTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
23 13 0.41
24 19 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TAATTAATTTAATAATATTTTAA
Found at i:2801911 original size:20 final size:19
Alignment explanation
Indices: 2801882--2801929 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
2801872 TATTATCTTA
* *
2801882 ATTTTATAATAAAAATTATT
1 ATTTTTTAAT-AAAATTAAT
*
2801902 ATTTTTTAATTAAATTAAT
1 ATTTTTTAATAAAATTAAT
*
2801921 ATTATTTAA
1 ATTTTTTAA
2801930 CTTATAATAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTTTAATAAAATTAAT
Found at i:2802786 original size:17 final size:17
Alignment explanation
Indices: 2802761--2802797 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2802751 AAAGCTCTTC
2802761 TTTCGTTTTCATTCCTT
1 TTTCGTTTTCATTCCTT
*
2802778 TTTCTTTTTCATTCCTT
1 TTTCGTTTTCATTCCTT
2802795 TTT
1 TTT
2802798 TTAAATGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.05, C:0.22, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTCGTTTTCATTCCTT
Found at i:2803774 original size:19 final size:19
Alignment explanation
Indices: 2803752--2803792 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2803742 TCAAAATTTC
*
2803752 TTTAAATATTAAATAAA-AA
1 TTTAAAT-TTAAACAAATAA
2803771 TTTAAATTTAAACAAATAA
1 TTTAAATTTAAACAAATAA
2803790 TTT
1 TTT
2803793 TTATCCTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTAAATTTAAACAAATAA
Found at i:2804335 original size:13 final size:13
Alignment explanation
Indices: 2804319--2804343 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2804309 GTTAAAATTT
2804319 AATTATATAAAAA
1 AATTATATAAAAA
2804332 AATTATATAAAA
1 AATTATATAAAA
2804344 TGTAAGATAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATTATATAAAAA
Found at i:2804926 original size:143 final size:146
Alignment explanation
Indices: 2804761--2805022 Score: 386
Period size: 144 Copynumber: 1.8 Consensus size: 146
2804751 CTAATAATTG
* ** * * *
2804761 ATATATAAAATTTTTATAAATTTATAATTTTTTTGACACGTAAAAAATAATATGAACACG-TATG
1 ATATATAAAATTTATATAAATTTATAATACTTTTAACACGAAAAAAATAATACGAACACGTTATG
* *
2804825 AATTCACAAAAGTTTCACTAAATTGAAACACGATGAAAAATTATGCAAAATATATCTTAAATTTA
66 AATGCACAAAAGTTTCACTAAATTGAAACACGATGAAAAACTATGCAAAATATATCTTAAATTTA
2804890 TATAAAAATTATTGTC
131 TATAAAAATTATTGTC
2804906 ATATA-AAAATTTATAT-AATTTATAATACTTTTAACACGAAAAAAATAATACGAACACGTTATG
1 ATATATAAAATTTATATAAATTTATAATACTTTTAACACGAAAAAAATAATACGAACACGTTATG
* * ** *
2804969 AATGCATAAAATTTTCACTAAATTGAAACACGATGATTAGCTATGCAAAATATA
66 AATGCACAAAAGTTTCACTAAATTGAAACACGATGAAAAACTATGCAAAATATA
2805023 ACATGAATTG
Statistics
Matches: 103, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
143 37 0.36
144 61 0.59
145 5 0.05
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (146 bp):
ATATATAAAATTTATATAAATTTATAATACTTTTAACACGAAAAAAATAATACGAACACGTTATG
AATGCACAAAAGTTTCACTAAATTGAAACACGATGAAAAACTATGCAAAATATATCTTAAATTTA
TATAAAAATTATTGTC
Found at i:2805147 original size:31 final size:32
Alignment explanation
Indices: 2805102--2805164 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
2805092 AACACTGTAC
* *
2805102 GAATACATGAATATATCAAAATATAGATAAAT
1 GAATAAATGAATATATAAAAATATAGATAAAT
* *
2805134 GAATAAAT-AATATATAAAAATTTATATAAAT
1 GAATAAATGAATATATAAAAATATAGATAAAT
2805165 TTATTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (32 bp):
GAATAAATGAATATATAAAAATATAGATAAAT
Found at i:2805320 original size:30 final size:30
Alignment explanation
Indices: 2805286--2805362 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 30
2805276 AATACATGAA
*
2805286 ATAAAATAAATTATTTATATATAAAAAA-AT
1 ATAAAATAAA-TATTTACATATAAAAAACAT
2805316 ATAAAAATATAATATTTTACATATAAAAAACAT
1 AT-AAAATA-AATA-TTTACATATAAAAAACAT
*
2805349 A-AATATAAATATTT
1 ATAAAATAAATATTT
2805363 TTTTCTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
29 3 0.07
30 6 0.15
31 13 0.32
32 16 0.39
33 3 0.07
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (30 bp):
ATAAAATAAATATTTACATATAAAAAACAT
Found at i:2805332 original size:31 final size:30
Alignment explanation
Indices: 2805288--2805363 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
2805278 TACATGAAAT
* *
2805288 AAAATAAAT-TATTTATATATAAAAAAATATA
1 AAAATAAATAT-TTTACATAT-AAAAAACATA
2805319 AAAATATAATATTTTACATATAAAAAACATA
1 AAAATA-AATATTTTACATATAAAAAACATA
*
2805350 AATATAAATATTTT
1 AAAATAAATATTTT
2805364 TTTCTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
30 8 0.20
31 20 0.50
32 11 0.28
33 1 0.03
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (30 bp):
AAAATAAATATTTTACATATAAAAAACATA
Found at i:2805401 original size:14 final size:13
Alignment explanation
Indices: 2805360--2805413 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 13
2805350 AATATAAATA
2805360 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
2805373 TTCTTTTTGCCCTTTTCT
1 TT-TTTTT---CTTTT-T
2805391 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
2805404 TTTTCTTTCT
1 TTTT-TTTCT
2805414 CTCTTGTCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
13 7 0.20
14 15 0.43
17 10 0.29
18 3 0.09
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTTTTTCTTTTT
Found at i:2806355 original size:21 final size:20
Alignment explanation
Indices: 2806289--2806343 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
2806279 CAAAAGGTTT
* * * *
2806289 AAATTTAAAAGTAAATAAGA
1 AAATTTTAAATTAAAAAAAA
2806309 AAATTTTAAATTAAAAAAAA
1 AAATTTTAAATTAAAAAAAA
*
2806329 AAATTTTTAATTAAA
1 AAATTTTAAATTAAA
2806344 TAAATAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
AAATTTTAAATTAAAAAAAA
Found at i:2822582 original size:72 final size:72
Alignment explanation
Indices: 2822465--2822609 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
2822455 AACAGTCTTA
2822465 TCACTTGGCATTCATCAGGCTGAAAAGATAAATTTCTAATAAAAATCACCACCATAATCCACATT
1 TCACTTGGCATTCATCAGGCTGAAAAGATAAATTTCTAATAAAAATCACCACCATAATCCACATT
2822530 CTATACC
66 CTATACC
2822537 TCACTTGGCATTCATCAGGCTGAAAAGATAAATTTCTAATAAAAATCACCACCATAATCCACATT
1 TCACTTGGCATTCATCAGGCTGAAAAGATAAATTTCTAATAAAAATCACCACCATAATCCACATT
2822602 CTATACC
66 CTATACC
2822609 T
1 T
2822610 TAGATCTCGC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.39, C:0.25, G:0.08, T:0.28
Consensus pattern (72 bp):
TCACTTGGCATTCATCAGGCTGAAAAGATAAATTTCTAATAAAAATCACCACCATAATCCACATT
CTATACC
Found at i:2824698 original size:26 final size:27
Alignment explanation
Indices: 2824643--2824706 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
2824633 AAAACATAAC
* **
2824643 ATTTTATTAATTAATTTATAAAATTTTT
1 ATTTTATT-ATTAATGTATAAAATAATT
2824671 ATTTTATTATT-ATGTATAAAATAATT
1 ATTTTATTATTAATGTATAAAATAATT
2824697 ATTTTATTAT
1 ATTTTATTAT
2824707 AATAATTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 22 0.67
27 3 0.09
28 8 0.24
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (27 bp):
ATTTTATTATTAATGTATAAAATAATT
Found at i:2824731 original size:16 final size:19
Alignment explanation
Indices: 2824671--2824722 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
2824661 TAAAATTTTT
2824671 ATTTTATTATTATGTATAA-A
1 ATTTTATT-TTAT-TATAATA
*
2824691 ATAATTATTTTATTATAATA
1 AT-TTTATTTTATTATAATA
2824711 ATTTTATTTTAT
1 ATTTTATTTTAT
2824723 AAATATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 14 0.50
20 9 0.32
21 5 0.18
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTATTTTATTATAATA
Found at i:2824937 original size:23 final size:23
Alignment explanation
Indices: 2824900--2824944 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2824890 TTAGATTTTA
* * *
2824900 TTTTTTTTATTTTATGTTTATAC
1 TTTTTTATATATTATGATTATAC
2824923 TTTTTTATATATTATGATTATA
1 TTTTTTATATATTATGATTATA
2824945 TTTAAAATAT
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:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (23 bp):
TTTTTTATATATTATGATTATAC
Found at i:2827477 original size:13 final size:15
Alignment explanation
Indices: 2827459--2827490 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
2827449 TAGTGCATCA
2827459 ACATAAAA-TCAA-C
1 ACATAAAAGTCAATC
2827472 ACATAAAAGTCAATC
1 ACATAAAAGTCAATC
2827487 ACAT
1 ACAT
2827491 TAGTATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 4 0.24
15 5 0.29
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (15 bp):
ACATAAAAGTCAATC
Found at i:2828080 original size:3 final size:3
Alignment explanation
Indices: 2828072--2828102 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2828062 TACATGTGAA
*
2828072 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2828103 TCAAGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2828973 original size:14 final size:14
Alignment explanation
Indices: 2828894--2828980 Score: 54
Period size: 14 Copynumber: 5.9 Consensus size: 14
2828884 ATTTGAGTAT
2828894 AATATAATTAATATA
1 AATATAATTAATA-A
*
2828909 TTAAAATAATT-ATAA
1 --AATATAATTAATAA
*
2828924 AATTATAAGTGTAATAT
1 AA-TATAA-T-TAATAA
*
2828941 AAT-TAAAT-ATAA
1 AATATAATTAATAA
2828953 TAATATAATTAATAA
1 -AATATAATTAATAA
*
2828968 AATATATTTAATA
1 AATATAATTAATA
2828981 TATTTATTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
12 3 0.05
13 6 0.11
14 20 0.36
15 9 0.16
16 5 0.09
17 13 0.23
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
AATATAATTAATAA
Found at i:2828979 original size:18 final size:18
Alignment explanation
Indices: 2828935--2828971 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2828925 ATTATAAGTG
*
2828935 TAATATAATTAAATATAA
1 TAATATAATTAAATAAAA
2828953 TAATATAATT-AATAAAA
1 TAATATAATTAAATAAAA
2828970 TA
1 TA
2828972 TATTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAATATAATTAAATAAAA
Found at i:2834998 original size:2 final size:2
Alignment explanation
Indices: 2834927--2834982 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
2834917 GAGATTCATG
* * * * *
2834927 TA TA TA -A TA TG TA TT TA TA TA TA TA TA TA TA CA CA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2834968 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
2834983 GTAAAATATA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2843215 original size:13 final size:12
Alignment explanation
Indices: 2843197--2843235 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2843187 TAAGTATCAC
2843197 AAATTTAATTAA
1 AAATTTAATTAA
*
2843209 TAAATTTATTTAA
1 -AAATTTAATTAA
*
2843222 AAATTTAATCAA
1 AAATTTAATTAA
2843234 AA
1 AA
2843236 TAATAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (12 bp):
AAATTTAATTAA
Found at i:2843227 original size:12 final size:13
Alignment explanation
Indices: 2843197--2843230 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2843187 TAAGTATCAC
2843197 AAATTTAATTAAT
1 AAATTTAATTAAT
*
2843210 AAATTTATTTAA-
1 AAATTTAATTAAT
2843222 AAATTTAAT
1 AAATTTAAT
2843231 CAAAATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATTTAATTAAT
Found at i:2843710 original size:16 final size:17
Alignment explanation
Indices: 2843689--2843756 Score: 63
Period size: 16 Copynumber: 4.2 Consensus size: 17
2843679 TTTATAATAA
2843689 TTATATT-TAAAATATT
1 TTATATTATAAAATATT
*
2843705 TTATATTATATAA-ATT
1 TTATATTATAAAATATT
* *
2843721 TTA-A-TATATTAATAAT
1 TTATATTATA-AAATATT
*
2843737 TTATATTATAAAAAATT
1 TTATATTATAAAATATT
2843754 TTA
1 TTA
2843757 ATAAATGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
14 4 0.10
15 4 0.10
16 18 0.43
17 12 0.29
18 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATATTATAAAATATT
Found at i:2844881 original size:15 final size:16
Alignment explanation
Indices: 2844863--2844892 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2844853 CAAAAAGGGC
2844863 AAAAGAAAAA-AAAGA
1 AAAAGAAAAAGAAAGA
2844878 AAAAGAAAAAGAAAG
1 AAAAGAAAAAGAAAG
2844893 GGAGAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAAAGA
Found at i:2845478 original size:2 final size:2
Alignment explanation
Indices: 2845471--2845495 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2845461 TTAGCATTTA
2845471 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2845496 AAAGAGTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2847200 original size:3 final size:3
Alignment explanation
Indices: 2847186--2847222 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
2847176 CCATCTTCTA
2847186 ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2847223 AGAAAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:2847395 original size:15 final size:15
Alignment explanation
Indices: 2847355--2847388 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2847345 TTATTCTTGC
2847355 AAAAAAT-ATTTTTA
1 AAAAAATAATTTTTA
2847369 AAAAAATAATTTTTA
1 AAAAAATAATTTTTA
2847384 AAAAA
1 AAAAA
2847389 TAAATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAAAATAATTTTTA
Found at i:2847531 original size:2 final size:2
Alignment explanation
Indices: 2847524--2847554 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2847514 AAGAAATCAT
*
2847524 TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2847555 TTGCTTTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2849119 original size:10 final size:10
Alignment explanation
Indices: 2849106--2849150 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
2849096 AAAGATTTGT
2849106 ATATATTTTA
1 ATATATTTTA
2849116 ATATA-TTT-
1 ATATATTTTA
2849124 ATATATTTATA
1 ATATATTT-TA
*
2849135 TTATATTTTA
1 ATATATTTTA
2849145 AT-TATT
1 ATATATT
2849151 ATGTTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
8 5 0.17
9 9 0.30
10 9 0.30
11 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATATATTTTA
Found at i:2849123 original size:20 final size:19
Alignment explanation
Indices: 2849086--2849144 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
2849076 ATATGAAGCG
* * *
2849086 ATATTTTTTAAAAGATTTGT
1 ATATATTTTAATATATTT-T
2849106 ATATATTTTAATATA-TTT
1 ATATATTTTAATATATTTT
*
2849124 ATATATTTATATTATATTTT
1 ATATATTT-TAATATATTTT
2849144 A
1 A
2849145 ATTATTATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 9 0.27
19 8 0.24
20 16 0.48
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
ATATATTTTAATATATTTT
Found at i:2849136 original size:14 final size:12
Alignment explanation
Indices: 2849117--2849167 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 12
2849107 TATATTTTAA
2849117 TATATTTATATATT
1 TATA-TTATAT-TT
2849131 TATATTATATTT
1 TATATTATATTT
2849143 TA-ATTATTATGTT
1 TATATTA-TAT-TT
2849156 TATATTATATTT
1 TATATTATATTT
2849168 AAAATTATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.12
12 9 0.26
13 13 0.38
14 8 0.24
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (12 bp):
TATATTATATTT
Found at i:2849141 original size:11 final size:11
Alignment explanation
Indices: 2849125--2849168 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
2849115 AATATATTTA
2849125 TATATTTATAT
1 TATATTTATAT
2849136 TATATTTTAATTAT
1 TATA-TTT-A-TAT
*
2849150 TATGTTTATAT
1 TATATTTATAT
2849161 TATATTTA
1 TATATTTA
2849169 AAATTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 14 0.50
12 4 0.14
13 4 0.14
14 6 0.21
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:2849160 original size:25 final size:26
Alignment explanation
Indices: 2849125--2849183 Score: 93
Period size: 25 Copynumber: 2.3 Consensus size: 26
2849115 AATATATTTA
*
2849125 TATATTTATATTATATTT-TAATTAT
1 TATATTTATATTATATTTAAAATTAT
*
2849150 TATGTTTATATTATATTTAAAATTAT
1 TATATTTATATTATATTTAAAATTAT
2849176 TATATTTA
1 TATATTTA
2849184 AATTTAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 17 0.57
26 13 0.43
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (26 bp):
TATATTTATATTATATTTAAAATTAT
Found at i:2849194 original size:15 final size:15
Alignment explanation
Indices: 2849161--2849194 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2849151 ATGTTTATAT
*
2849161 TATATTTAAAATTAT
1 TATATTTAAAATTAA
*
2849176 TATATTTAAATTTAA
1 TATATTTAAAATTAA
2849191 TATA
1 TATA
2849195 AGATATTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATTTAAAATTAA
Found at i:2850242 original size:2 final size:2
Alignment explanation
Indices: 2850229--2850258 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2850219 ATGATATGTG
*
2850229 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2850259 ATTTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2850752 original size:3 final size:3
Alignment explanation
Indices: 2850744--2850776 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2850734 AGCTTATCCA
2850744 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2850777 GAATGTTATT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2853492 original size:15 final size:16
Alignment explanation
Indices: 2853464--2853496 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2853454 CTTCGAGGGT
2853464 AAGCATTTGCAGAAAA
1 AAGCATTTGCAGAAAA
*
2853480 AAGC-TTTGGAGAAAA
1 AAGCATTTGCAGAAAA
2853495 AA
1 AA
2853497 AAATTTCAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.52, C:0.09, G:0.21, T:0.18
Consensus pattern (16 bp):
AAGCATTTGCAGAAAA
Found at i:2855785 original size:22 final size:22
Alignment explanation
Indices: 2855746--2855792 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
2855736 GAAAATTCTA
*
2855746 TTTGAAAAATAATGTTTTTAGTT
1 TTTGAAAAATAATATTTTTA-TT
2855769 TTTGAAAAATAA-ATTTTTATT
1 TTTGAAAAATAATATTTTTATT
2855790 TTT
1 TTT
2855793 ATTTGTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.22
22 6 0.26
23 12 0.52
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (22 bp):
TTTGAAAAATAATATTTTTATT
Found at i:2858014 original size:29 final size:28
Alignment explanation
Indices: 2857939--2858014 Score: 68
Period size: 27 Copynumber: 2.8 Consensus size: 28
2857929 ACATTTAAAA
* * *
2857939 TTTATT-TTTATATAACAATTATATATT
1 TTTATTATTTAAATAATAATTAAATATT
* *
2857966 TTTA-TAATTAAAT-TTAAATTAAATATTT
1 TTTATTATTTAAATAAT-AATTAAATA-TT
2857994 TTTATTATTTAAATAATAATT
1 TTTATTATTTAAATAATAATT
2858015 TAAAATTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
26 1 0.03
27 17 0.46
28 6 0.16
29 12 0.32
30 1 0.03
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTATTATTTAAATAATAATTAAATATT
Found at i:2858438 original size:11 final size:12
Alignment explanation
Indices: 2858419--2858490 Score: 55
Period size: 11 Copynumber: 6.2 Consensus size: 12
2858409 ATTTTATATG
*
2858419 TATATTATTAAA
1 TATAATATTAAA
2858431 TA-AATATT-AA
1 TATAATATTAAA
2858441 TATAATATTAAA
1 TATAATATTAAA
*
2858453 TATTTAAT-TTAAT
1 TA--TAATATTAAA
2858466 TATAATA-TATAA
1 TATAATATTA-AA
*
2858478 TAT-ATTTTAAA
1 TATAATATTAAA
2858489 TA
1 TA
2858491 AAATTTATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
10 4 0.08
11 23 0.47
12 12 0.24
13 6 0.12
14 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TATAATATTAAA
Found at i:2858454 original size:18 final size:17
Alignment explanation
Indices: 2858431--2858490 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
2858421 TATTATTAAA
2858431 TAAATATTAATATAATAT
1 TAAATATTAATAT-ATAT
*
2858449 TAAATATTTAATTTA-AT
1 TAAATA-TTAATATATAT
*
2858466 TATAATATATAATATATTT
1 TA-AATAT-TAATATATAT
2858485 TAAATA
1 TAAATA
2858491 AAATTTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
17 5 0.14
18 21 0.60
19 9 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAATATTAATATATAT
Found at i:2859345 original size:2 final size:2
Alignment explanation
Indices: 2859338--2859362 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2859328 CATAAACTTT
2859338 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2859363 GTATTGCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2864362 original size:20 final size:20
Alignment explanation
Indices: 2864337--2864377 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2864327 TCAGATAATG
2864337 TTGCTTCTATTCTGAACATT
1 TTGCTTCTATTCTGAACATT
2864357 TTGCTTCTATTCTGAACATT
1 TTGCTTCTATTCTGAACATT
2864377 T
1 T
2864378 AGCACCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.51
Consensus pattern (20 bp):
TTGCTTCTATTCTGAACATT
Found at i:2872308 original size:13 final size:13
Alignment explanation
Indices: 2872275--2872317 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2872265 GAAAATTAAA
*
2872275 TTTAATAATATAT
1 TTTAATATTATAT
2872288 ATTT-ATATTATAT
1 -TTTAATATTATAT
*
2872301 TTTAATATTTTAT
1 TTTAATATTATAT
2872314 TTTA
1 TTTA
2872318 TTATAATCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 3 0.12
13 20 0.77
14 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTAATATTATAT
Found at i:2872319 original size:18 final size:19
Alignment explanation
Indices: 2872286--2872324 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
2872276 TTAATAATAT
*
2872286 ATATTTATATTATATTTTA
1 ATATTTATATTATATTATA
*
2872305 ATATTT-TATTTTATTATA
1 ATATTTATATTATATTATA
2872323 AT
1 AT
2872325 CGTGTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATATTTATATTATATTATA
Found at i:2872364 original size:20 final size:19
Alignment explanation
Indices: 2872337--2872405 Score: 62
Period size: 18 Copynumber: 3.9 Consensus size: 19
2872327 TGTTTAAAAT
*
2872337 ATTTAATAT-TTATATAAA
1 ATTTAAAATATTATATAAA
2872355 ATTTAAAATATTA-AT--A
1 ATTTAAAATATTATATAAA
2872371 ATTT---ATATTATATAAA
1 ATTTAAAATATTATATAAA
*
2872387 TTTTAAAATATTTATATAA
1 ATTTAAAATA-TTATATAA
2872406 TTCTATTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
13 6 0.15
14 2 0.05
16 9 0.22
18 10 0.24
19 6 0.15
20 8 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTAAAATATTATATAAA
Found at i:2872375 original size:16 final size:15
Alignment explanation
Indices: 2872351--2872398 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
2872341 AATATTTATA
2872351 TAAAATTTAAAATAT
1 TAAAATTTAAAATAT
* *
2872366 TAATAATTTATATTAT
1 TAA-AATTTAAAATAT
*
2872382 ATAAATTTTAAAATAT
1 -TAAAATTTAAAATAT
2872398 T
1 T
2872399 TATATAATTC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
15 4 0.15
16 19 0.73
17 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAATTTAAAATAT
Found at i:2872382 original size:32 final size:34
Alignment explanation
Indices: 2872337--2872416 Score: 103
Period size: 32 Copynumber: 2.4 Consensus size: 34
2872327 TGTTTAAAAT
2872337 ATTTAATATTTATATAAAATTTAAAATA-TTA-ATA
1 ATTT-ATA-TTATATAAAATTTAAAATATTTATATA
*
2872371 ATTTATATTATATAAATTTTAAAATATTTATATA
1 ATTTATATTATATAAAATTTAAAATATTTATATA
*
2872405 A-TTCTATTATAT
1 ATTTATATTATAT
2872417 TGATAATACT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
32 18 0.43
33 16 0.38
34 8 0.19
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (34 bp):
ATTTATATTATATAAAATTTAAAATATTTATATA
Found at i:2872404 original size:27 final size:28
Alignment explanation
Indices: 2872329--2872404 Score: 91
Period size: 32 Copynumber: 2.6 Consensus size: 28
2872319 TATAATCGTG
2872329 TTTAAAATATTTA-ATATTTATATAAAA
1 TTTAAAATATTTATATATTTATATAAAA
* *
2872356 TTTAAAATATTAATAATTTATATTATATAAAT
1 TTTAAAATATT--T-ATATAT-TTATATAAAA
2872388 TTTAAAATATTTATATA
1 TTTAAAATATTTATATA
2872405 ATTCTATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
27 11 0.27
29 5 0.12
30 2 0.05
31 3 0.07
32 20 0.49
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TTTAAAATATTTATATATTTATATAAAA
Found at i:2872769 original size:21 final size:21
Alignment explanation
Indices: 2872732--2872775 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2872722 ACCATCTCCA
2872732 CCTCCACCACAACCACCACCT
1 CCTCCACCACAACCACCACCT
*
2872753 CCTCCACCTCTAA-CACCACCT
1 CCTCCACCAC-AACCACCACCT
2872774 CC
1 CC
2872776 ACTTGTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.25, C:0.61, G:0.00, T:0.14
Consensus pattern (21 bp):
CCTCCACCACAACCACCACCT
Found at i:2873390 original size:2 final size:2
Alignment explanation
Indices: 2873383--2873418 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2873373 TGATAATTTA
* *
2873383 AT AT AT AT AT AT AT AT GT AT AC 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
2873419 GTTACATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2875242 original size:2 final size:2
Alignment explanation
Indices: 2875235--2875265 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2875225 TTGCATTGAT
2875235 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2875266 TTAAAATTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2888144 original size:2 final size:2
Alignment explanation
Indices: 2888139--2888163 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2888129 GTGTGTGCTT
2888139 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
2888164 GGATTTCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2888769 original size:99 final size:99
Alignment explanation
Indices: 2888598--2888801 Score: 399
Period size: 99 Copynumber: 2.1 Consensus size: 99
2888588 AAAAAAAGAT
2888598 GGCTTTAGCACATCCAGCAAAGGAACAGGACATTAATTCAGGATATCCCAGAAAGGAACTACGAC
1 GGCTTTAGCACATCCAGCAAAGGAACAGGACATTAATTCAGGATATCCCAGAAAGGAACTACGAC
2888663 TTTCAGATTGAGACAAAGGTGTACCTATCTAGAA
66 TTTCAGATTGAGACAAAGGTGTACCTATCTAGAA
2888697 GGCTTTAGCACATCCAGCAAAGGAACAGGACATTAATTCAGGATATCCCAGAAAGGAACTACGAC
1 GGCTTTAGCACATCCAGCAAAGGAACAGGACATTAATTCAGGATATCCCAGAAAGGAACTACGAC
*
2888762 TTTCAGATTGGGACAAAGGTGTACCTATCTAGAA
66 TTTCAGATTGAGACAAAGGTGTACCTATCTAGAA
2888796 GGCTTT
1 GGCTTT
2888802 TGATCCATGA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 104 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (99 bp):
GGCTTTAGCACATCCAGCAAAGGAACAGGACATTAATTCAGGATATCCCAGAAAGGAACTACGAC
TTTCAGATTGAGACAAAGGTGTACCTATCTAGAA
Found at i:2892618 original size:2 final size:2
Alignment explanation
Indices: 2892611--2892654 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2892601 GGAACAGAAA
* *
2892611 AG AG AG AG AA AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2892653 AG
1 AG
2892655 GCCTTCTTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2897000 original size:16 final size:16
Alignment explanation
Indices: 2896979--2897011 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2896969 ACAGAACTGA
*
2896979 ATAAATTTCCAGAGTT
1 ATAAATTTCAAGAGTT
2896995 ATAAATTTCAAGAGTT
1 ATAAATTTCAAGAGTT
2897011 A
1 A
2897012 CAAAAGTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (16 bp):
ATAAATTTCAAGAGTT
Found at i:2899317 original size:15 final size:16
Alignment explanation
Indices: 2899294--2899328 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2899284 AATTTTGAAG
2899294 TTCTCTTTTTTTTTGT
1 TTCTCTTTTTTTTTGT
*
2899310 TTCT-TTTTTTTTTTT
1 TTCTCTTTTTTTTTGT
2899325 TTCT
1 TTCT
2899329 AATGTAAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (16 bp):
TTCTCTTTTTTTTTGT
Found at i:2905914 original size:12 final size:13
Alignment explanation
Indices: 2905878--2905931 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 13
2905868 TTTTAATAAT
* *
2905878 TAATTATATAAAA
1 TAATTATATTATA
*
2905891 TAATTTTA-TATA
1 TAATTATATTATA
2905903 TAATTA-ATTATA
1 TAATTATATTATA
2905915 TAATTATATTA-A
1 TAATTATATTATA
2905927 TAATT
1 TAATT
2905932 CAATAAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 1 0.03
12 23 0.66
13 11 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATTATATTATA
Found at i:2906271 original size:4 final size:4
Alignment explanation
Indices: 2906264--2906294 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
2906254 AAATAAAGTT
2906264 TAAA TAAA TAAA TAAA TAAA TAAA T-AA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
2906295 ATAATGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:2909064 original size:24 final size:24
Alignment explanation
Indices: 2909036--2909083 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2909026 TTGCTTTTGT
2909036 AAAACACAAAATTGCAGGTACCTG
1 AAAACACAAAATTGCAGGTACCTG
2909060 AAAACACAAAATTGCAGGTACCTG
1 AAAACACAAAATTGCAGGTACCTG
2909084 TGCCCATGGA
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:0.46, C:0.21, G:0.17, T:0.17
Consensus pattern (24 bp):
AAAACACAAAATTGCAGGTACCTG
Found at i:2909452 original size:14 final size:13
Alignment explanation
Indices: 2909433--2909462 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
2909423 AATAACTTAA
2909433 AAATAAAATATATT
1 AAATAAAATAT-TT
2909447 AAATAAAATATTT
1 AAATAAAATATTT
2909460 AAA
1 AAA
2909463 AATATCTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATAAAATATTT
Found at i:2909921 original size:27 final size:28
Alignment explanation
Indices: 2909865--2909921 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
2909855 GATCTCGATG
*
2909865 TTTTATTAATAATATTACATTAAGATTA
1 TTTTATTAATAATATTAAATTAAGATTA
*
2909893 TTTTATCTAA-AATA-TAAATTATGATTA
1 TTTTAT-TAATAATATTAAATTAAGATTA
2909920 TT
1 TT
2909922 CATATAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 13 0.50
28 10 0.38
29 3 0.12
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (28 bp):
TTTTATTAATAATATTAAATTAAGATTA
Found at i:2911322 original size:14 final size:14
Alignment explanation
Indices: 2911303--2911330 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2911293 TAAACTAACT
2911303 CCCAACTCTGACCC
1 CCCAACTCTGACCC
2911317 CCCAACTCTGACCC
1 CCCAACTCTGACCC
2911331 TGGGGATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.57, G:0.07, T:0.14
Consensus pattern (14 bp):
CCCAACTCTGACCC
Found at i:2912385 original size:45 final size:45
Alignment explanation
Indices: 2912318--2912408 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
2912308 GTATGACCAA
*
2912318 AACCATCATCCATCTCTCTTCCTTGACAGTTTAGTAATAGCTAGT
1 AACCATCATCAATCTCTCTTCCTTGACAGTTTAGTAATAGCTAGT
*
2912363 AACCATCATCAATCTCTTTTCCTTGACAGTTTAGTAATAGCTAGT
1 AACCATCATCAATCTCTCTTCCTTGACAGTTTAGTAATAGCTAGT
2912408 A
1 A
2912409 CCTGCAAGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (45 bp):
AACCATCATCAATCTCTCTTCCTTGACAGTTTAGTAATAGCTAGT
Found at i:2916972 original size:16 final size:16
Alignment explanation
Indices: 2916909--2916983 Score: 64
Period size: 16 Copynumber: 4.6 Consensus size: 16
2916899 ATTTATATTA
*
2916909 AAAATTATTAATATATT
1 AAAATTA-TAATATAAT
* *
2916926 AAAATTTTTATA-AAT
1 AAAATTATAATATAAT
* *
2916941 ATAAATTAT-TTTTAAT
1 A-AAATTATAATATAAT
2916957 AAAATTATAATATAAT
1 AAAATTATAATATAAT
2916973 AAAATATATAA
1 AAAAT-TATAA
2916984 ATGTTACTGA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
15 11 0.24
16 24 0.52
17 11 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAATTATAATATAAT
Found at i:2922733 original size:18 final size:18
Alignment explanation
Indices: 2922706--2922771 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
2922696 TTCAATTAGT
*
2922706 AAAATTTTTAAATATTCA
1 AAAATATTTAAATATTCA
*
2922724 AAAATATTTAAA-ATT-T
1 AAAATATTTAAATATTCA
*
2922740 AAAATATTTTAAAATATACA
1 AAAATA-TTT-AAATATTCA
*
2922760 AATATA-TTAAAT
1 AAAATATTTAAAT
2922772 CTAATGTCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
16 6 0.15
17 10 0.26
18 16 0.41
19 2 0.05
20 5 0.13
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATATTTAAATATTCA
Found at i:2922771 original size:17 final size:18
Alignment explanation
Indices: 2922715--2922770 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
2922705 TAAAATTTTT
* *
2922715 AAATATTCAAAAATATTTA
1 AAATATACAAATATA-TTA
* *
2922734 AAATTTA-AAATATTTTA
1 AAATATACAAATATATTA
2922751 AAATATACAAATATATTA
1 AAATATACAAATATATTA
2922769 AA
1 AA
2922771 TCTAATGTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 9 0.30
18 16 0.53
19 5 0.17
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATACAAATATATTA
Found at i:2923386 original size:3 final size:3
Alignment explanation
Indices: 2923378--2923409 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2923368 AATTGAGAGC
2923378 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2923410 ATGTAAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2926107 original size:2 final size:2
Alignment explanation
Indices: 2926100--2926128 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2926090 TTTTGGATGC
2926100 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2926129 TTTCTGGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2929091 original size:22 final size:23
Alignment explanation
Indices: 2929066--2929117 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
2929056 TATTTTTTAT
* *
2929066 ATAAAAAAATTGT-AATTTTAAA
1 ATAAAAAAATTATAAATATTAAA
2929088 ATAAAAAAATTATAAATATTAAA
1 ATAAAAAAATTATAAATATTAAA
*
2929111 ATTAAAA
1 ATAAAAA
2929118 TTTAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
ATAAAAAAATTATAAATATTAAA
Found at i:2929122 original size:13 final size:15
Alignment explanation
Indices: 2929093--2929125 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
2929083 TTAAAATAAA
2929093 AAAATTATAAATATT
1 AAAATTATAAATATT
2929108 AAAATTA-AAAT-TT
1 AAAATTATAAATATT
2929121 AAAAT
1 AAAAT
2929126 AAATTAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 4 0.22
15 7 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:2933659 original size:18 final size:18
Alignment explanation
Indices: 2933622--2933660 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2933612 TTGTTTCATG
* * *
2933622 AAAAATAAATTTATTTAA
1 AAAAATAAAATGATTCAA
2933640 AAAAATAAAATGATTCAA
1 AAAAATAAAATGATTCAA
2933658 AAA
1 AAA
2933661 TATTATCATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAAATAAAATGATTCAA
Found at i:2934115 original size:50 final size:50
Alignment explanation
Indices: 2934040--2934140 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
2934030 CTTAGGAGTC
*
2934040 AGGAAGGACCCCAATAAGTAGAAGCTACAGAAGCAGACAAATTTCATTTT
1 AGGAAGGACCACAATAAGTAGAAGCTACAGAAGCAGACAAATTTCATTTT
*
2934090 AGGAAGGACCACAGTAAGTAGAAGCTACAGAAGCAGACAAATTTCATTTT
1 AGGAAGGACCACAATAAGTAGAAGCTACAGAAGCAGACAAATTTCATTTT
2934140 A
1 A
2934141 TCTTTTATTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.20
Consensus pattern (50 bp):
AGGAAGGACCACAATAAGTAGAAGCTACAGAAGCAGACAAATTTCATTTT
Found at i:2939235 original size:14 final size:13
Alignment explanation
Indices: 2939216--2939246 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
2939206 CAAAGAAGAG
2939216 TTTTTTTTTCTCTT
1 TTTTTTTTTC-CTT
2939230 TTTTTTTTTCCTT
1 TTTTTTTTTCCTT
2939243 TTTT
1 TTTT
2939247 CAGAGAGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTTTTTCCTT
Found at i:2940259 original size:21 final size:21
Alignment explanation
Indices: 2940235--2940305 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
2940225 TAAGATAATT
2940235 TATATATTAATATTATATTTA
1 TATATATTAATATTATATTTA
* * *
2940256 TATATTTTTATGAATTATAATTA
1 TATATATTAAT--ATTATATTTA
* * *
2940279 TATTTA-AAATATTATATATTT
1 TATATATTAATATTATAT-TTA
2940300 TATATA
1 TATATA
2940306 AATTTTAAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
20 6 0.16
21 16 0.43
22 2 0.05
23 13 0.35
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (21 bp):
TATATATTAATATTATATTTA
Found at i:2940297 original size:37 final size:37
Alignment explanation
Indices: 2940253--2940328 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 37
2940243 AATATTATAT
* *
2940253 TTATATATTTT-TATGAATTATAATTATATTTAAAATA
1 TTATATATTTTATATAAATTATAA-AATATTTAAAATA
* *
2940290 TTATATATTTTATATAAATTTTAAAATATTTAATATA
1 TTATATATTTTATATAAATTATAAAATATTTAAAATA
2940327 TT
1 TT
2940329 TTTATAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 24 0.71
38 10 0.29
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (37 bp):
TTATATATTTTATATAAATTATAAAATATTTAAAATA
Found at i:2940302 original size:9 final size:9
Alignment explanation
Indices: 2940290--2940360 Score: 54
Period size: 9 Copynumber: 7.3 Consensus size: 9
2940280 ATTTAAAATA
2940290 TTATATATT
1 TTATATATT
2940299 TTATATAAATT
1 TTATAT--ATT
*
2940310 TTAAAATATT
1 TT-ATATATT
*
2940320 TAATATATT
1 TTATATATT
2940329 TT-TATAATAT
1 TTATAT-AT-T
2940339 TTATATTATT
1 TTATA-TATT
*
2940349 TTTTATATT
1 TTATATATT
2940358 TTA
1 TTA
2940361 AAATTATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
8 3 0.06
9 21 0.43
10 12 0.24
11 9 0.18
12 4 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTATATATT
Found at i:2940303 original size:7 final size:7
Alignment explanation
Indices: 2940234--2940304 Score: 51
Period size: 6 Copynumber: 10.1 Consensus size: 7
2940224 ATAAGATAAT
2940234 TTATATA
1 TTATATA
2940241 TTA-ATA
1 TTATATA
2940247 TTATAT-
1 TTATATA
2940253 TTATATA
1 TTATATA
*
2940260 TTTTTATGAA
1 -TTATAT--A
2940270 TTATA-A
1 TTATATA
2940276 TTATAT-
1 TTATATA
*
2940282 TTAAAATA
1 TT-ATATA
2940290 TTATATA
1 TTATATA
*
2940297 TTTTATA
1 TTATATA
2940304 T
1 T
2940305 AAATTTTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
6 20 0.39
7 19 0.37
8 7 0.14
9 4 0.08
10 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (7 bp):
TTATATA
Found at i:2940316 original size:28 final size:30
Alignment explanation
Indices: 2940270--2940340 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
2940260 TTTTTATGAA
2940270 TTATAATTATATTTAAAATA-TT-ATATATTT
1 TTATAA-TAT-TTTAAAATATTTAATATATTT
2940300 TATATAA-ATTTTAAAATATTTAATATATTT
1 T-TATAATATTTTAAAATATTTAATATATTT
2940330 TTATAATATTT
1 TTATAATATTT
2940341 ATATTATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
28 9 0.24
29 9 0.24
30 14 0.38
31 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TTATAATATTTTAAAATATTTAATATATTT
Found at i:2940318 original size:21 final size:20
Alignment explanation
Indices: 2940294--2940350 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
2940284 AAAATATTAT
2940294 ATATTTTATATAAATTTTAAA
1 ATATTTTATAT-AATTTTAAA
* * *
2940315 ATATTTAATATATTTTTATA
1 ATATTTTATATAATTTTAAA
*
2940335 ATA-TTTATATTATTTT
1 ATATTTTATATAATTTT
2940351 TTATATTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 10 0.33
20 10 0.33
21 10 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTTTATATAATTTTAAA
Found at i:2940348 original size:20 final size:20
Alignment explanation
Indices: 2940298--2940351 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
2940288 TATTATATAT
* *
2940298 TTTATATAAATTTTAAAATA
1 TTTATATTATTTTTAAAATA
*
2940318 TTTA-ATATATTTTTATAATA
1 TTTATAT-TATTTTTAAAATA
2940338 TTTATATTATTTTT
1 TTTATATTATTTTT
2940352 TATATTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 2 0.07
20 25 0.86
21 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTATATTATTTTTAAAATA
Found at i:2942769 original size:30 final size:30
Alignment explanation
Indices: 2942712--2942769 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
2942702 TTGACACTTA
* *
2942712 TTAACATTTTCAATATAATAAATTTAATCT
1 TTAACATTTTAAATATAATAAAATTAATCT
2942742 TTAACAATTTTAAATATAA-AAAATTAAT
1 TTAAC-ATTTTAAATATAATAAAATTAAT
2942770 TAAATTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (30 bp):
TTAACATTTTAAATATAATAAAATTAATCT
Found at i:2943230 original size:17 final size:17
Alignment explanation
Indices: 2943168--2943244 Score: 52
Period size: 16 Copynumber: 4.5 Consensus size: 17
2943158 AATTTACTCG
*
2943168 ATTTAATTTAAATTAA-
1 ATTTAATTTTAATTAAT
*
2943184 A-TTATATTTAAATATAAT
1 ATTTA-ATTTTAAT-TAAT
* *
2943202 ATTTTTTATTTAAATTAAT
1 A--TTTAATTTTAATTAAT
*
2943221 -TTTAATTTTAATTATT
1 ATTTAATTTTAATTAAT
2943237 ATTTAATT
1 ATTTAATT
2943245 AATAAAAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.06
16 22 0.44
17 10 0.20
18 1 0.02
19 4 0.08
20 8 0.16
21 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTAATTTTAATTAAT
Found at i:2944179 original size:6 final size:6
Alignment explanation
Indices: 2944159--2944199 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
2944149 TACCAATGCA
*
2944159 AAGCAGG AA-CAG AAGCAG AAGCAG TAGCAG AAGCAG -AGCAG
1 AAGCA-G AAGCAG AAGCAG AAGCAG AAGCAG AAGCAG AAGCAG
2944200 GGGCAGGAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 8 0.26
6 21 0.68
7 2 0.06
ACGTcount: A:0.46, C:0.17, G:0.34, T:0.02
Consensus pattern (6 bp):
AAGCAG
Found at i:2944182 original size:18 final size:18
Alignment explanation
Indices: 2944159--2944200 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2944149 TACCAATGCA
2944159 AAGCAGGAACAGAAGCAG
1 AAGCAGGAACAGAAGCAG
* *
2944177 AAGCAGTAGCAGAAGCAG
1 AAGCAGGAACAGAAGCAG
2944195 -AGCAGG
1 AAGCAGG
2944201 GGCAGGAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.45, C:0.17, G:0.36, T:0.02
Consensus pattern (18 bp):
AAGCAGGAACAGAAGCAG
Done.