Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, whole genome shotgun sequence
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: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 8 of 117
Found at i:2073739 original size:2 final size:2
Alignment explanation
Indices: 2073732--2073762 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2073722 GATAGTGCTT
2073732 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
2073763 TTAAAGGAAA
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:2077124 original size:16 final size:16
Alignment explanation
Indices: 2077103--2077158 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
2077093 TTAATGTTTC
2077103 AATTAATATATAATTT
1 AATTAATATATAATTT
*
2077119 AATTAAAAT-TAATATTT
1 AATTAATATAT-A-ATTT
* *
2077136 CAATCAATATATAATTA
1 -AATTAATATATAATTT
2077153 AATTAA
1 AATTAA
2077159 AAATAAGTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
15 1 0.03
16 14 0.45
17 7 0.23
18 8 0.26
19 1 0.03
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTAATATATAATTT
Found at i:2077137 original size:34 final size:34
Alignment explanation
Indices: 2077093--2077160 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
2077083 TATTTAACAT
* * *
2077093 TTAATGTTTCAATTAATATATAATTTAATTAAAA
1 TTAATATTTCAATCAATATATAATTAAATTAAAA
2077127 TTAATATTTCAATCAATATATAATTAAATTAAAA
1 TTAATATTTCAATCAATATATAATTAAATTAAAA
2077161 ATAAGTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.44
Consensus pattern (34 bp):
TTAATATTTCAATCAATATATAATTAAATTAAAA
Found at i:2079105 original size:27 final size:27
Alignment explanation
Indices: 2079075--2079153 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 27
2079065 TCTCCTAGAC
2079075 GATTTTTAAGAATGCATAGATATATTT
1 GATTTTTAAGAATGCATAGATATATTT
* *
2079102 GA--TTT-AG-A-G-TTA-TTATATTT
1 GATTTTTAAGAATGCATAGATATATTT
2079122 GATTTTTAAGAATGCATAGATATATTT
1 GATTTTTAAGAATGCATAGATATATTT
2079149 GATTT
1 GATTT
2079154 AGAGTTATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
20 9 0.22
21 2 0.05
22 4 0.10
23 3 0.07
24 3 0.07
25 4 0.10
26 2 0.05
27 14 0.34
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.48
Consensus pattern (27 bp):
GATTTTTAAGAATGCATAGATATATTT
Found at i:2079129 original size:47 final size:47
Alignment explanation
Indices: 2079075--2079164 Score: 180
Period size: 47 Copynumber: 1.9 Consensus size: 47
2079065 TCTCCTAGAC
2079075 GATTTTTAAGAATGCATAGATATATTTGATTTAGAGTTATTATATTT
1 GATTTTTAAGAATGCATAGATATATTTGATTTAGAGTTATTATATTT
2079122 GATTTTTAAGAATGCATAGATATATTTGATTTAGAGTTATTAT
1 GATTTTTAAGAATGCATAGATATATTTGATTTAGAGTTATTAT
2079165 TGTTATACCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (47 bp):
GATTTTTAAGAATGCATAGATATATTTGATTTAGAGTTATTATATTT
Found at i:2079325 original size:3 final size:3
Alignment explanation
Indices: 2079317--2079343 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2079307 TTTGAGTTGA
2079317 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
2079344 TTGGGAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2084862 original size:11 final size:11
Alignment explanation
Indices: 2084848--2084872 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2084838 TATTTATAAA
2084848 ATTAATAAATT
1 ATTAATAAATT
2084859 ATTAATAAATT
1 ATTAATAAATT
2084870 ATT
1 ATT
2084873 TTTATGACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTAATAAATT
Found at i:2084940 original size:23 final size:23
Alignment explanation
Indices: 2084914--2084966 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
2084904 AACTAAAAAT
2084914 TAATAAAATAATAAT-TTATTATA
1 TAATAAAAT-ATAATATTATTATA
* *
2084937 TAATAAAATTTATTATTATTATA
1 TAATAAAATATAATATTATTATA
2084960 TAATAAA
1 TAATAAA
2084967 TAAGTGGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 3 0.11
23 24 0.89
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TAATAAAATATAATATTATTATA
Found at i:2086437 original size:13 final size:13
Alignment explanation
Indices: 2086419--2086446 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2086409 TTGAAATGAT
2086419 ATTTTTATCATCA
1 ATTTTTATCATCA
2086432 ATTTTTATCATCA
1 ATTTTTATCATCA
2086445 AT
1 AT
2086447 CTTGAGACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTTTTATCATCA
Found at i:2100901 original size:22 final size:20
Alignment explanation
Indices: 2100861--2100905 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
2100851 TAGTATTATA
*
2100861 AATTGATTTGATATTGATTT
1 AATTGATTTGAAATTGATTT
2100881 AATTGATTATAGAAATTGATTT
1 AATTGATT-T-GAAATTGATTT
2100903 AAT
1 AAT
2100906 CATTATTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.36
21 1 0.05
22 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (20 bp):
AATTGATTTGAAATTGATTT
Found at i:2101552 original size:16 final size:17
Alignment explanation
Indices: 2101531--2101564 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2101521 ACGAAGCAAC
*
2101531 AAAAAG-TATGTTTGCA
1 AAAAAGTTATATTTGCA
2101547 AAAAAGTTATATTTGCA
1 AAAAAGTTATATTTGCA
2101564 A
1 A
2101565 CTTGCAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (17 bp):
AAAAAGTTATATTTGCA
Found at i:2116390 original size:5 final size:5
Alignment explanation
Indices: 2116376--2116407 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
2116366 TCTAAATATA
2116376 TTTT- TTTTC TTTTC TTTT- TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
2116408 TGATCTACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (5 bp):
TTTTC
Found at i:2116393 original size:14 final size:14
Alignment explanation
Indices: 2116376--2116408 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
2116366 TCTAAATATA
2116376 TTTTTTTTCTTTTC
1 TTTTTTTTCTTTTC
2116390 TTTTTTTTCTTTTC
1 TTTTTTTTCTTTTC
2116404 TTTTT
1 TTTTT
2116409 GATCTACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTTCTTTTC
Found at i:2117361 original size:17 final size:18
Alignment explanation
Indices: 2117326--2117367 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2117316 TTAATTTTTA
* *
2117326 TTATTTATTCCATTTATT
1 TTATTTATTACATTAATT
2117344 TTATTT-TTACATTAATT
1 TTATTTATTACATTAATT
2117361 TT-TTTAT
1 TTATTTAT
2117368 ATTTTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 3 0.14
17 12 0.57
18 6 0.29
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTATTACATTAATT
Found at i:2118210 original size:261 final size:266
Alignment explanation
Indices: 2117604--2118680 Score: 1338
Period size: 261 Copynumber: 4.0 Consensus size: 266
2117594 TATTACTAAT
* ***
2117604 ATATTGGAGTATTTTATAAAAAGTTTTCAATACAATAAAAAAATTTTTTTTTTTTTGCTATAAAG
1 ATATTGGAGTA-TTTATAAAAAGTTTTCAATACAAT-AAAAAA-TATAAATTTTTTGCTATAAAG
*
2117669 TAGTAAATAAATTTTAACTAATTTGTT-AAAATAAAAAGATAAAAATAAGGAAAAAAA--TTATC
63 TAGTAAATAAATTTTAACTAATTTGTTAAAAATAAAAATATAAAAATAAGGAAAAAAATTTTATC
* * * * ** * *
2117731 TGATGACA-AAATCTAAAAGTATTACAAGTAGTGATGCTTTACGAAATTTCTAAAT-GAAA-TTT
128 TGATGATAGGATTCTAAAAGTATTACAAGTAGTGATGCTTTAAGAAATCCCTAAATAAAAAGATT
* * * *
2117793 TTTTTTAATATTACCAATGTATTGAAATATTTATAGAAAATCTTCAACATGATAAAAATCTCTTT
193 TTTTTTAATATTATCAGTGTATTGAAATATTTATAAAAAATCTTTAACATGATAAAAATC-C---
*
2117858 TTTCTTATTATTACTAA
254 TTT-TT-TTCTTA-T-A
* * * * ***
2117875 CATATTGGAGTATTTATAGAAAGTTTTCTATACAATAAAAATTTTTCTTTTTTTTTTTTGCTATA
1 -ATATTGGAGTATTTATAAAAAGTTTTCAATACAATAAAAA-----ATATAAATTTTTTGCTATA
**
2117940 AAGTAGTAAATAAATTTTAACTAATTTGTTAAAAATAAAAAGCTAAAAATAAGGAAAAAAATTTT
60 AAGTAGTAAATAAATTTTAACTAATTTGTTAAAAATAAAAATATAAAAATAAGGAAAAAAATTTT
* ** *
2118005 ATCTGATGACAAAATTCTAAAAGTATTACAAGTAGTGATGCTTTAAGATATCCCTAAATAAAAAG
125 ATCTGATGATAGGATTCTAAAAGTATTACAAGTAGTGATGCTTTAAGAAATCCCTAAATAAAAAG
2118070 ATTTTTTTTAATATTATCAGTGTATTGAAATATTTATAAAAAATCTTTAACATGATAAAAATCCT
190 ATTTTTTTTAATATTATCAGTGTATTGAAATATTTATAAAAAATCTTTAACATGATAAAAATCCT
2118135 TTTTTTC-T-T-
255 TTTTTTCTTATA
2118144 ATATTGGAGTATTTATAAAAAGTTTTCAATACAATAAAAAA-A-AAATTTTTTGCTATAAAGTAG
1 ATATTGGAGTATTTATAAAAAGTTTTCAATACAATAAAAAATATAAATTTTTTGCTATAAAGTAG
* * *
2118207 TAAATAAATTTTAACTAATTTGTTAAAAATAAAAATATAAAAATAAGAAAAAAAAATTTATCCGA
66 TAAATAAATTTTAACTAATTTGTTAAAAATAAAAATATAAAAATAAGGAAAAAAATTTTATCTGA
* * *
2118272 TAATAGGATTCTAAAAGTATTACAAGTAGTGATACTTTACGAAATCCCTAAATAAAAAGATTTTT
131 TGATAGGATTCTAAAAGTATTACAAGTAGTGATGCTTTAAGAAATCCCTAAATAAAAAGATTTTT
*
2118337 TTTAATATTATCAGTGTACTGAAATATTTATAAAAAATCTTTAACATGATAAAAAT-CTATTTTT
196 TTTAATATTATCAGTGTATTGAAATATTTATAAAAAATCTTTAACATGATAAAAATCCT-TTTTT
2118401 TCTTATTATTACTAA
260 TC------TTA-T-A
**
2118416 CATATTGGAGTATTTATAAAAAGTTTTCAATACAATAAAAAATTTTATTTTATTTTTTGCTATAA
1 -ATATTGGAGTATTTATAAAAAGTTTTCAATACAATAAAAAA---TA-TAAATTTTTTGCTATAA
2118481 AGTAGTAAATAAATTTTAACTAATTTGTTAAAAATAAAAATATAAAAATAAGGAAAAAAAATTTT
61 AGTAGTAAATAAATTTTAACTAATTTGTTAAAAATAAAAATATAAAAATAAGG-AAAAAAATTTT
*
2118546 ATCTGATGATAGGATTCTAAAAGTATTACAAGTAGTGATGCTTTACA-AAATCCCTAAATGAAAA
125 ATCTGATGATAGGATTCTAAAAGTATTACAAGTAGTGATGCTTTA-AGAAATCCCTAAATAAAAA
* * * *
2118610 TA-TTTTTTTAATATTACCAGTGTATT-AGAATATTTATAGAAAATCTTCAACATGATAAAAATC
189 GATTTTTTTTAATATTATCAGTGTATTGA-AATATTTATAAAAAATCTTTAACATGATAAAAATC
2118673 CTTTTTTT
253 CTTTTTTT
2118681 TTCAAAAATT
Statistics
Matches: 721, Mismatches: 50, Indels: 61
0.87 0.06 0.07
Matches are distributed among these distances:
260 2 0.00
261 198 0.27
268 39 0.05
270 6 0.01
271 23 0.03
272 11 0.02
273 42 0.06
274 50 0.07
275 31 0.04
276 3 0.00
277 14 0.02
278 43 0.06
279 130 0.18
280 129 0.18
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (266 bp):
ATATTGGAGTATTTATAAAAAGTTTTCAATACAATAAAAAATATAAATTTTTTGCTATAAAGTAG
TAAATAAATTTTAACTAATTTGTTAAAAATAAAAATATAAAAATAAGGAAAAAAATTTTATCTGA
TGATAGGATTCTAAAAGTATTACAAGTAGTGATGCTTTAAGAAATCCCTAAATAAAAAGATTTTT
TTTAATATTATCAGTGTATTGAAATATTTATAAAAAATCTTTAACATGATAAAAATCCTTTTTTT
CTTATA
Found at i:2118681 original size:541 final size:537
Alignment explanation
Indices: 2117603--2118680 Score: 1673
Period size: 541 Copynumber: 2.0 Consensus size: 537
2117593 ATATTACTAA
***
2117603 TATATTGGAGTATTTTATAAAAAGTTTTCAATACAATAAAAAAATTTTTTTTTTTTTGCTATAAA
1 TATATTGGAGTATTTTATAAAAAGTTTTCAATACAATAAAAAAA---TAAATTTTTTGCTATAAA
* *
2117668 GTAGTAAATAAATTTTAACTAATTTGTTAAAATAAAAAGATAAAAATAAGGAAAAAAATTATCTG
63 GTAGTAAATAAATTTTAACTAATTTGTTAAAATAAAAAGATAAAAATAAGAAAAAAAATTATCCG
* * ** * *
2117733 ATGACAAAATCTAAAAGTATTACAAGTAGTGATGCTTTACGAAATTTCTAAATGAAATTTTTTTT
128 ATAACAAAATCTAAAAGTATTACAAGTAGTGATACTTTACGAAATCCCTAAATAAAAATTTTTTT
* * *
2117798 TAATATTACCAATGTATTGAAATATTTATAGAAAATCTTCAACATGATAAAAATCTCTTTTTTCT
193 TAATATTACCAATGTACTGAAATATTTATAAAAAATCTTCAACATGATAAAAATCTATTTTTTCT
* * * * *
2117863 TATTATTACTAACATATTGGAGTATTTATAGAAAGTTTTCTATACAATAAAAATTTTTCTTTTTT
258 TATTATTACTAACATATTGGAGTATTTATAAAAAGTTTTCAATACAATAAAAAATTTTCATTTTA
*
2117928 TTTTTTGCTATAAAGTAGTAAATAAATTTTAACTAATTTGTTAAAAATAAAAAGCTAAAAATAAG
323 TTTTTTGCTATAAAGTAGTAAATAAATTTTAACTAATTTGTTAAAAATAAAAAGATAAAAATAAG
*
2117993 GAAAAAAATTTTATCTGATGACAAAATTCTAAAAGTATTACAAGTAGTGATGCTTTAAGATATCC
388 GAAAAAAATTTTATCTGATGACAAAATTCTAAAAGTATTACAAGTAGTGATGCTTTAAGAAATCC
* *
2118058 CTAAATAAAAAGATTTTTTTTAATATTATCAGTGTATTGAAATATTTATAAAAAATCTTTAACAT
453 CTAAATAAAAAGATTTTTTTTAATATTACCAGTGTATTGAAATATTTATAAAAAATCTTCAACAT
2118123 GATAAAAATCCTTTTTTTCT
518 GATAAAAATCCTTTTTTTCT
2118143 TATATTGGAGTA-TTTATAAAAAGTTTTCAATACAATAAAAAAA-AAATTTTTTGCTATAAAGTA
1 TATATTGGAGTATTTTATAAAAAGTTTTCAATACAATAAAAAAATAAATTTTTTGCTATAAAGTA
*
2118206 GTAAATAAATTTTAACTAATTTGTTAAAAATAAAAATATAAAAATAAGAAAAAAAAATTTATCCG
66 GTAAATAAATTTTAACTAATTTGTT-AAAATAAAAAGATAAAAATAAG-AAAAAAAA-TTATCCG
* * *
2118271 ATAATAGGATTCTAAAAGTATTACAAGTAGTGATACTTTACGAAATCCCTAAATAAAAAGATTTT
128 ATAACA-AAATCTAAAAGTATTACAAGTAGTGATACTTTACGAAATCCCTAAAT-AAAA-ATTTT
* * *
2118336 TTTTAATATTATCAGTGTACTGAAATATTTATAAAAAATCTTTAACATGATAAAAATCTATTTTT
190 TTTTAATATTACCAATGTACTGAAATATTTATAAAAAATCTTCAACATGATAAAAATCTATTTTT
2118401 TCTTATTATTACTAACATATTGGAGTATTTATAAAAAGTTTTCAATACAATAAAAAATTTT-ATT
255 TCTTATTATTACTAACATATTGGAGTATTTATAAAAAGTTTTCAATACAATAAAAAATTTTCATT
*
2118465 TTATTTTTTGCTATAAAGTAGTAAATAAATTTTAACTAATTTGTTAAAAATAAAAATATAAAAAT
320 TTATTTTTTGCTATAAAGTAGTAAATAAATTTTAACTAATTTGTTAAAAATAAAAAGATAAAAAT
* **
2118530 AAGGAAAAAAAATTTTATCTGATGATAGGATTCTAAAAGTATTACAAGTAGTGATGCTTTACA-A
385 AAGG-AAAAAAATTTTATCTGATGACAAAATTCTAAAAGTATTACAAGTAGTGATGCTTTA-AGA
* * *
2118594 AATCCCTAAATGAAAATA-TTTTTTTAATATTACCAGTGTATT-AGAATATTTATAGAAAATCTT
448 AATCCCTAAATAAAAAGATTTTTTTTAATATTACCAGTGTATTGA-AATATTTATAAAAAATCTT
2118657 CAACATGATAAAAATCCTTTTTTT
512 CAACATGATAAAAATCCTTTTTTT
2118681 TTCAAAAATT
Statistics
Matches: 492, Mismatches: 37, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
535 42 0.09
536 21 0.04
537 7 0.01
538 10 0.02
539 74 0.15
540 147 0.30
541 190 0.39
542 1 0.00
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (537 bp):
TATATTGGAGTATTTTATAAAAAGTTTTCAATACAATAAAAAAATAAATTTTTTGCTATAAAGTA
GTAAATAAATTTTAACTAATTTGTTAAAATAAAAAGATAAAAATAAGAAAAAAAATTATCCGATA
ACAAAATCTAAAAGTATTACAAGTAGTGATACTTTACGAAATCCCTAAATAAAAATTTTTTTTAA
TATTACCAATGTACTGAAATATTTATAAAAAATCTTCAACATGATAAAAATCTATTTTTTCTTAT
TATTACTAACATATTGGAGTATTTATAAAAAGTTTTCAATACAATAAAAAATTTTCATTTTATTT
TTTGCTATAAAGTAGTAAATAAATTTTAACTAATTTGTTAAAAATAAAAAGATAAAAATAAGGAA
AAAAATTTTATCTGATGACAAAATTCTAAAAGTATTACAAGTAGTGATGCTTTAAGAAATCCCTA
AATAAAAAGATTTTTTTTAATATTACCAGTGTATTGAAATATTTATAAAAAATCTTCAACATGAT
AAAAATCCTTTTTTTCT
Found at i:2125671 original size:41 final size:41
Alignment explanation
Indices: 2125612--2125724 Score: 131
Period size: 41 Copynumber: 2.8 Consensus size: 41
2125602 TATGGAAATA
**
2125612 CATTTTTTCAATAGTGATATTCGAGTGTTAAAAATCACTTG
1 CATTTTTTCGGTAGTGATATTCGAGTGTTAAAAATCACTTG
* * * *
2125653 CATTTTTTCGGTAATGATATT-GAGTATTAAAAGTCATTTG
1 CATTTTTTCGGTAGTGATATTCGAGTGTTAAAAATCACTTG
* *
2125693 CATCTTTTT-GGTAGTGATATCCAAGTGTTAAA
1 CAT-TTTTTCGGTAGTGATATTCGAGTGTTAAA
2125725 GTTGCAATTA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
40 29 0.48
41 31 0.52
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (41 bp):
CATTTTTTCGGTAGTGATATTCGAGTGTTAAAAATCACTTG
Found at i:2125683 original size:40 final size:41
Alignment explanation
Indices: 2125612--2125712 Score: 125
Period size: 40 Copynumber: 2.5 Consensus size: 41
2125602 TATGGAAATA
** *
2125612 CATTTTTTCAATAGTGATATTCGAGTGTTAAAAATCACTTG
1 CATTTTTTCGGTAGTGATATTCGAGTATTAAAAATCACTTG
* * *
2125653 CATTTTTTCGGTAATGATATT-GAGTATTAAAAGTCATTTG
1 CATTTTTTCGGTAGTGATATTCGAGTATTAAAAATCACTTG
2125693 CATCTTTTT-GGTAGTGATAT
1 CAT-TTTTTCGGTAGTGATAT
2125713 CCAAGTGTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 29 0.56
41 23 0.44
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.45
Consensus pattern (41 bp):
CATTTTTTCGGTAGTGATATTCGAGTATTAAAAATCACTTG
Found at i:2125726 original size:40 final size:40
Alignment explanation
Indices: 2125612--2125724 Score: 120
Period size: 40 Copynumber: 2.8 Consensus size: 40
2125602 TATGGAAATA
** *
2125612 CATTTTTTCAATAGTGATATTCGAGTGTTAAAAATCACTTG
1 CATTTTTTCGGTAGTGATA-TCGAGTGTTAAAAGTCACTTG
* * * *
2125653 CATTTTTTCGGTAATGATATTGAGTATTAAAAGTCATTTG
1 CATTTTTTCGGTAGTGATATCGAGTGTTAAAAGTCACTTG
*
2125693 CATCTTTTT-GGTAGTGATATCCAAGTGTTAAA
1 CAT-TTTTTCGGTAGTGATAT-CGAGTGTTAAA
2125725 GTTGCAATTA
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
40 30 0.51
41 29 0.49
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (40 bp):
CATTTTTTCGGTAGTGATATCGAGTGTTAAAAGTCACTTG
Found at i:2125796 original size:42 final size:42
Alignment explanation
Indices: 2125704--2125784 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
2125694 ATCTTTTTGG
* *
2125704 TAGTGATATCCAAGTGTTAAAGTTGCAATTACATTTTCTCAA
1 TAGTGATATCCAACTGTTAAAGTTGCAATTACATTTTATCAA
* *
2125746 TAGTGATATTCAACTGTTAAAGCTTG-AATTTCATTTTAT
1 TAGTGATATCCAACTGTTAAAG-TTGCAATTACATTTTAT
2125785 TAGTGGTGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 31 0.91
43 3 0.09
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (42 bp):
TAGTGATATCCAACTGTTAAAGTTGCAATTACATTTTATCAA
Found at i:2125899 original size:23 final size:24
Alignment explanation
Indices: 2125865--2125920 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
2125855 TTCTTTCTCT
* * *
2125865 ATATTTGCATTT-TTTCAATGGTG
1 ATATTTGAATTTCCTTCAATGGTA
*
2125888 ATATTTGAATTTCCTTCGATGGTA
1 ATATTTGAATTTCCTTCAATGGTA
2125912 ATATTTGAA
1 ATATTTGAA
2125921 ATCATTTGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 11 0.39
24 17 0.61
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.48
Consensus pattern (24 bp):
ATATTTGAATTTCCTTCAATGGTA
Found at i:2126026 original size:41 final size:41
Alignment explanation
Indices: 2125975--2126094 Score: 161
Period size: 42 Copynumber: 2.9 Consensus size: 41
2125965 GAATTACATC
* * *
2125975 TTTTCAGTGGTGATATCCAAATGTTAGAAATTATTT-TAATT
1 TTTTCGGTGGTGATATCCAAGTGTTAAAAATTATTTGT-ATT
*
2126016 TTTTCGGTGGTAATATCCAAGTGTTAAAAAATTATTTGTATT
1 TTTTCGGTGGTGATATCCAAGTGTT-AAAAATTATTTGTATT
* *
2126058 TTTTTGGTGGTGATATCCAAGTGTTAAAAATCATTTG
1 TTTTCGGTGGTGATATCCAAGTGTTAAAAATTATTTG
2126095 CAGTTTCATT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
41 33 0.47
42 36 0.51
43 1 0.01
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.45
Consensus pattern (41 bp):
TTTTCGGTGGTGATATCCAAGTGTTAAAAATTATTTGTATT
Found at i:2126231 original size:41 final size:41
Alignment explanation
Indices: 2126152--2126441 Score: 161
Period size: 40 Copynumber: 7.2 Consensus size: 41
2126142 GGTGCTGTTC
* * * * *
2126152 GAGTGTTAAAACTGGATTTACATCTTATTGGTGGTGATATCT
1 GAGTGTTAAAAAT-CATTTACATCTTCTCGGTGATGATATCT
* * *
2126194 AAGTGTTAAAAATCATTTACATTTTCTCGGTGATGATATCC
1 GAGTGTTAAAAATCATTTACATCTTCTCGGTGATGATATCT
** * * *
2126235 GAGTAATAAAAATCATTT--ATCCT-TCGATGGTGATAT-T
1 GAGTGTTAAAAATCATTTACATCTTCTCGGTGATGATATCT
* * * ** *
2126272 CAAGTGTTAAAAATCATTTATAT-TTTTTTGT-AGTGATATTT
1 -GAGTGTTAAAAATCATTTACATCTTCTCGGTGA-TGATATCT
* * * *
2126313 GAGTGTTAAAAATCATTTGCATTTTCTCGATAATGATATC-
1 GAGTGTTAAAAATCATTTACATCTTCTCGGTGATGATATCT
* * * ** * *
2126353 GAGTATTAAAAGTCATTTGCATCTTCTTAGTGGTGATATCC
1 GAGTGTTAAAAATCATTTACATCTTCTCGGTGATGATATCT
* * * *
2126394 GAGAGTTAAAAAT--TTGT--ATCTTCTCGATGGTAATATCT
1 GAGTGTTAAAAATCATT-TACATCTTCTCGGTGATGATATCT
2126432 GAGTGTTAAA
1 GAGTGTTAAA
2126442 GCTTGAATTG
Statistics
Matches: 189, Mismatches: 49, Indels: 24
0.72 0.19 0.09
Matches are distributed among these distances:
38 51 0.27
39 6 0.03
40 62 0.33
41 58 0.31
42 12 0.06
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.41
Consensus pattern (41 bp):
GAGTGTTAAAAATCATTTACATCTTCTCGGTGATGATATCT
Found at i:2126283 original size:38 final size:39
Alignment explanation
Indices: 2126183--2126292 Score: 107
Period size: 38 Copynumber: 2.8 Consensus size: 39
2126173 ATCTTATTGG
** *
2126183 TGGTGATA-TCTAAGTGTTAAAAATCATTTACATTTTCTCGG
1 TGGTGATATTC-AAGTGTTAAAAATCATTT--ATCCTCTCGA
* * * **
2126224 TGATGATATCCGAGTAATAAAAATCATTTATCCT-TCGA
1 TGGTGATATTCAAGTGTTAAAAATCATTTATCCTCTCGA
2126262 TGGTGATATTCAAGTGTTAAAAATCATTTAT
1 TGGTGATATTCAAGTGTTAAAAATCATTTAT
2126293 ATTTTTTTGT
Statistics
Matches: 55, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
38 29 0.53
39 3 0.05
41 22 0.40
42 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (39 bp):
TGGTGATATTCAAGTGTTAAAAATCATTTATCCTCTCGA
Found at i:2126435 original size:119 final size:118
Alignment explanation
Indices: 2126182--2126441 Score: 285
Period size: 119 Copynumber: 2.2 Consensus size: 118
2126172 CATCTTATTG
* * *
2126182 GTGGTGATATCTAAGTGTTAAAAATCATTTACATTTTCTCGGTGATGATATCCGAGTAATAAAAA
1 GTGGTGATATCTGAGTGTTAAAAATCATTTACATTTTCTCGATAATGATATCCGAGTAATAAAAA
* * * * * *
2126247 TCATTTATCCTTCGATGGTGATATTCAAGTGTTAAAAATCATTTATATTTTTTT
66 TCATTTATCCTTAGATGGTGATATCCAAGAGTTAAAAA-CATTTATATCTTCTC
* * * * *
2126301 GTAGTGATATTTGAGTGTTAAAAATCATTTGCATTTTCTCGATAATGATAT-CGAGTATTAAAAG
1 GTGGTGATATCTGAGTGTTAAAAATCATTTACATTTTCTCGATAATGATATCCGAGTAATAAAAA
* *
2126365 TCATTTGCATCTTCTTAG-TGGTGATATCCGAGAGTT-AAAA-ATTTGTATCTTCTC
66 TCATTT--ATC--CTTAGATGGTGATATCCAAGAGTTAAAAACATTTATATCTTCTC
*
2126419 GATGGTAATATCTGAGTGTTAAA
1 G-TGGTGATATCTGAGTGTTAAA
2126442 GCTTGAATTG
Statistics
Matches: 117, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
118 28 0.24
119 63 0.54
120 7 0.06
121 15 0.13
122 4 0.03
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (118 bp):
GTGGTGATATCTGAGTGTTAAAAATCATTTACATTTTCTCGATAATGATATCCGAGTAATAAAAA
TCATTTATCCTTAGATGGTGATATCCAAGAGTTAAAAACATTTATATCTTCTC
Found at i:2128745 original size:10 final size:10
Alignment explanation
Indices: 2128730--2128767 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
2128720 AAAATTATTC
2128730 TTTTAATAAA
1 TTTTAATAAA
*
2128740 TTTTAATTAA
1 TTTTAATAAA
2128750 TTTT-A-AAA
1 TTTTAATAAA
2128758 TTTTAATAAA
1 TTTTAATAAA
2128768 AAGATATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 6 0.25
9 2 0.08
10 16 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:2145221 original size:2 final size:2
Alignment explanation
Indices: 2145214--2145238 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2145204 AGCCAAATCA
2145214 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
2145239 ATTATAACAC
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:2145796 original size:21 final size:20
Alignment explanation
Indices: 2145772--2145811 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
2145762 AAATATCAAA
2145772 ATTAAAATAAATATATAATTT
1 ATTAAAATAAATATA-AATTT
*
2145793 ATTAATATAAATATAAATT
1 ATTAAAATAAATATAAATT
2145812 CAACCCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTAAAATAAATATAAATTT
Found at i:2166268 original size:30 final size:29
Alignment explanation
Indices: 2166223--2166280 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
2166213 TTCCTCAATT
2166223 TTTTATTGCATGTAATTAAAATTATTAAC
1 TTTTATTGCATGTAATTAAAATTATTAAC
* * *
2166252 TTTTATTTCAATGTAATTATACTTATTAA
1 TTTTATTGC-ATGTAATTAAAATTATTAA
2166281 ATCTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (29 bp):
TTTTATTGCATGTAATTAAAATTATTAAC
Found at i:2178309 original size:2 final size:2
Alignment explanation
Indices: 2178302--2178337 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2178292 TCCAATTCTT
2178302 TA TA TA TA TA TA 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 TA TA TA
2178338 AAGTAAGTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2179845 original size:115 final size:115
Alignment explanation
Indices: 2179643--2179873 Score: 462
Period size: 115 Copynumber: 2.0 Consensus size: 115
2179633 AATGTAAAAT
2179643 CCATTCAGGCAGTGCAATCTGTCATTGAAGCTTATCCTTAGAAAATCTATAGCTCTCCACATTGC
1 CCATTCAGGCAGTGCAATCTGTCATTGAAGCTTATCCTTAGAAAATCTATAGCTCTCCACATTGC
2179708 CTACTTTCTTTTGTGGTAAATAATGGTTCATCTGCTACAAACGTTAGAAC
66 CTACTTTCTTTTGTGGTAAATAATGGTTCATCTGCTACAAACGTTAGAAC
2179758 CCATTCAGGCAGTGCAATCTGTCATTGAAGCTTATCCTTAGAAAATCTATAGCTCTCCACATTGC
1 CCATTCAGGCAGTGCAATCTGTCATTGAAGCTTATCCTTAGAAAATCTATAGCTCTCCACATTGC
2179823 CTACTTTCTTTTGTGGTAAATAATGGTTCATCTGCTACAAACGTTAGAAC
66 CTACTTTCTTTTGTGGTAAATAATGGTTCATCTGCTACAAACGTTAGAAC
2179873 C
1 C
2179874 TGTTGAGTGA
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 116 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.34
Consensus pattern (115 bp):
CCATTCAGGCAGTGCAATCTGTCATTGAAGCTTATCCTTAGAAAATCTATAGCTCTCCACATTGC
CTACTTTCTTTTGTGGTAAATAATGGTTCATCTGCTACAAACGTTAGAAC
Found at i:2188765 original size:16 final size:17
Alignment explanation
Indices: 2188737--2188769 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2188727 ATAAATAAAT
2188737 ATTTTATTATTTATTTA
1 ATTTTATTATTTATTTA
2188754 ATTTTA-TATTTATTTA
1 ATTTTATTATTTATTTA
2188770 TTAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTATTATTTATTTA
Found at i:2189105 original size:22 final size:22
Alignment explanation
Indices: 2189080--2189125 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2189070 TATAAAAGAA
*
2189080 TATATTT-TATTATTTATTAAAT
1 TATATTTATA-TATGTATTAAAT
*
2189102 TATATTTATATATGTATTATAT
1 TATATTTATATATGTATTAAAT
2189124 TA
1 TA
2189126 ATAAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TATATTTATATATGTATTAAAT
Found at i:2189178 original size:29 final size:29
Alignment explanation
Indices: 2189079--2189179 Score: 73
Period size: 30 Copynumber: 3.3 Consensus size: 29
2189069 ATATAAAAGA
* * * *
2189079 ATATATTTTATTATTTATTAAATTATATTT
1 ATATATTATA-TATTAATAAAAATATATTT
2189109 ATATATGTATTATATTAATAAAAATATTATTT
1 ATATAT-TA-TATATTAATAAAAATA-TATTT
2189141 A-ATCCATTA-AT-TTAATAAAAAAGTATATTT
1 ATAT--ATTATATATTAAT-AAAAA-TATATTT
2189171 ATATATTAT
1 ATATATTAT
2189180 TAAGTTATAA
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
29 9 0.16
30 19 0.33
31 18 0.31
32 10 0.17
33 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (29 bp):
ATATATTATATATTAATAAAAATATATTT
Found at i:2190590 original size:15 final size:15
Alignment explanation
Indices: 2190572--2190601 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2190562 TGATTAGAGC
2190572 TTTAAAAATTAAAAT
1 TTTAAAAATTAAAAT
*
2190587 TTTAAAAATTTAAAT
1 TTTAAAAATTAAAAT
2190602 ACATAATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTAAAAATTAAAAT
Found at i:2192456 original size:64 final size:65
Alignment explanation
Indices: 2192354--2192484 Score: 237
Period size: 64 Copynumber: 2.0 Consensus size: 65
2192344 CAAAAATCCA
2192354 TTGTCTTTCCAAATGGAGAGCTTATCCAAATCAGCGGGGTCACACGGAATATGCCACTTTGGAGC
1 TTGTCTTTCCAAATGGAGAGCTTATCCAAATCAGCGGGGTCACACGGAATATGCCACTTTGGAGC
* *
2192419 TTGTC-TTCCAAATGGAGAGCTTATCCAAATCAGCGGGGTCACCCGGAATATGCCATTTTGGAGC
1 TTGTCTTTCCAAATGGAGAGCTTATCCAAATCAGCGGGGTCACACGGAATATGCCACTTTGGAGC
2192483 TT
1 TT
2192485 CTTTTGATAC
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 59 0.92
65 5 0.08
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.27
Consensus pattern (65 bp):
TTGTCTTTCCAAATGGAGAGCTTATCCAAATCAGCGGGGTCACACGGAATATGCCACTTTGGAGC
Found at i:2194287 original size:27 final size:27
Alignment explanation
Indices: 2194250--2194315 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
2194240 TGTTTTTGGG
*
2194250 AAATAAAATTATG-ATAAAGATAAGATA
1 AAATAATATTATGAATAAA-ATAAGATA
* * *
2194277 AAATAATATTATGAATAAAATTATATT
1 AAATAATATTATGAATAAAATAAGATA
2194304 AAATAATATTAT
1 AAATAATATTAT
2194316 TTTATTTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (27 bp):
AAATAATATTATGAATAAAATAAGATA
Found at i:2196334 original size:13 final size:13
Alignment explanation
Indices: 2196316--2196341 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2196306 GATTGTCTCA
2196316 ACTAAGATTTTGG
1 ACTAAGATTTTGG
2196329 ACTAAGATTTTGG
1 ACTAAGATTTTGG
2196342 TTAAGTTAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
ACTAAGATTTTGG
Found at i:2200142 original size:64 final size:64
Alignment explanation
Indices: 2200047--2200168 Score: 226
Period size: 64 Copynumber: 1.9 Consensus size: 64
2200037 TAATAAATTT
* *
2200047 TCTCCTATAAACATGGTTATGCTGTATAATTCATTGTGATCAAAGTCAAATTTAATGCATTTTC
1 TCTCCTATAAACATGATTATGCTGTATAATTCAATGTGATCAAAGTCAAATTTAATGCATTTTC
2200111 TCTCCTATAAACATGATTATGCTGTATAATTCAATGTGATCAAAGTCAAATTTAATGC
1 TCTCCTATAAACATGATTATGCTGTATAATTCAATGTGATCAAAGTCAAATTTAATGC
2200169 TTTCACCCTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.39
Consensus pattern (64 bp):
TCTCCTATAAACATGATTATGCTGTATAATTCAATGTGATCAAAGTCAAATTTAATGCATTTTC
Found at i:2200530 original size:27 final size:27
Alignment explanation
Indices: 2200494--2200546 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
2200484 ATATGAGAGA
2200494 TTTTGAAAAGGCAATTAAAATTTTCTT
1 TTTTGAAAAGGCAATTAAAATTTTCTT
2200521 TTTTGAAAAGGCAATTAAAATTTTCT
1 TTTTGAAAAGGCAATTAAAATTTTCT
2200547 AAGTAACGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (27 bp):
TTTTGAAAAGGCAATTAAAATTTTCTT
Found at i:2201955 original size:1 final size:1
Alignment explanation
Indices: 2201949--2201978 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
2201939 TATGATCGGG
2201949 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2201979 CATTTCCTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2202239 original size:2 final size:2
Alignment explanation
Indices: 2202234--2202262 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2202224 TGATATATTG
2202234 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2202263 TTTATGTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2203090 original size:2 final size:2
Alignment explanation
Indices: 2203083--2203134 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
2203073 GCCATGCATT
2203083 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
2203125 TC TA TC TC TC
1 TC TC TC TC TC
2203135 GTCTTCAACG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.02, C:0.48, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2203533 original size:3 final size:3
Alignment explanation
Indices: 2203525--2203563 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
2203515 CAGACCCCGT
* *
2203525 CAA CAA CAA CAA CAA CAA CAA CAA CAA AAA CAA AAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
2203564 TAGTTTTAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.72, C:0.28, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:2204129 original size:21 final size:22
Alignment explanation
Indices: 2204095--2204137 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2204085 AGAGTTCAGA
2204095 TTTTGAAGAGGAAGATG-ACCC
1 TTTTGAAGAGGAAGATGTACCC
* *
2204116 TTTTGCAGATGAAGATGTACCC
1 TTTTGAAGAGGAAGATGTACCC
2204138 GATGAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (22 bp):
TTTTGAAGAGGAAGATGTACCC
Found at i:2216576 original size:24 final size:24
Alignment explanation
Indices: 2216525--2216585 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
2216515 ATTTGGTAAT
2216525 TGAAAATAAAAAATAATTTTAAAAA
1 TGAAAAT-AAAAATAATTTTAAAAA
*
2216550 TGAAAATAAAAAT-ATTTTGAAATA
1 TGAAAATAAAAATAATTTT-AAAAA
*
2216574 TGAAATTAAAAA
1 TGAAAATAAAAA
2216586 AATATTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 5 0.15
24 21 0.64
25 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (24 bp):
TGAAAATAAAAATAATTTTAAAAA
Found at i:2216610 original size:26 final size:26
Alignment explanation
Indices: 2216532--2216610 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 26
2216522 AATTGAAAAT
*
2216532 AAAAAATAATTTT-AAAAATG-AAA-A
1 AAAAAAT-ATTTTGAAATATGAAAACA
* **
2216556 TAAAAATATTTTGAAATATGAAATTA
1 AAAAAATATTTTGAAATATGAAAACA
* * *
2216582 AAAAAATATTTTTAATTGTGAAAACA
1 AAAAAATATTTTGAAATATGAAAACA
2216608 AAA
1 AAA
2216611 GATTTATATT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
23 5 0.12
24 12 0.28
25 2 0.05
26 24 0.56
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.32
Consensus pattern (26 bp):
AAAAAATATTTTGAAATATGAAAACA
Found at i:2216774 original size:20 final size:23
Alignment explanation
Indices: 2216744--2216794 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
2216734 TATTTTCCTA
2216744 TTTTATATTT-TTTAA-AAATAAT
1 TTTTAT-TTTATTTAATAAATAAT
2216766 TTTTATTTTCATTTAATAAATAAT
1 TTTTATTTT-ATTTAATAAATAAT
2216790 TTTTA
1 TTTTA
2216795 AAAAAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 3 0.12
22 6 0.23
23 5 0.19
24 12 0.46
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTATTTTATTTAATAAATAAT
Found at i:2219380 original size:2 final size:2
Alignment explanation
Indices: 2219340--2219368 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2219330 TCTCCATCTT
2219340 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2219369 TCTTTTTCTC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2220438 original size:10 final size:10
Alignment explanation
Indices: 2220423--2220452 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2220413 ATTAAGTTTT
2220423 TATATTTTAA
1 TATATTTTAA
2220433 TATATTTTAA
1 TATATTTTAA
2220443 T-TATTTTAA
1 TATATTTTAA
2220452 T
1 T
2220453 TGATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:2221526 original size:12 final size:12
Alignment explanation
Indices: 2221504--2221541 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2221494 TTTTGAATTA
2221504 TAATA-AATATT
1 TAATATAATATT
2221515 TAATATAATATT
1 TAATATAATATT
*
2221527 TATTATAATATT
1 TAATATAATATT
2221539 TAA
1 TAA
2221542 ATTATAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 5 0.21
12 19 0.79
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATATAATATT
Found at i:2221553 original size:24 final size:23
Alignment explanation
Indices: 2221499--2221555 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 23
2221489 ATGGTTTTTG
*
2221499 AATTATAATAAATATTTAATATA
1 AATTATTATAAATATTTAATATA
2221522 ATATTTATTAT-AATATTTAAATTATA
1 A-A-TTATTATAAATATTT-AA-TATA
2221548 AATTATTA
1 AATTATTA
2221556 ATTAATGTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 1 0.03
24 14 0.48
25 9 0.31
26 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATTATTATAAATATTTAATATA
Found at i:2221670 original size:16 final size:16
Alignment explanation
Indices: 2221624--2221671 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
2221614 ATAAATAATT
*
2221624 TTTAAATATCATATTA
1 TTTAAATATTATATTA
* *
2221640 ATTAATAAATT-TATTA
1 TTTAA-ATATTATATTA
2221656 TTTAAATATTATATTA
1 TTTAAATATTATATTA
2221672 AATATTTTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
15 4 0.16
16 18 0.72
17 3 0.12
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAAATATTATATTA
Found at i:2222071 original size:26 final size:28
Alignment explanation
Indices: 2222035--2222098 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 28
2222025 TGTATTTAAT
*
2222035 ATATAAAATTATG-ATAAAA-TAAAATA
1 ATATAATATTATGTATAAAATTAAAATA
*
2222061 ATATAATATTATGTATAAAATTAAATTA
1 ATATAATATTATGTATAAAATTAAAATA
2222089 A-ATAAT-TTAT
1 ATATAATATTAT
2222099 TGATTAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 16 0.47
27 11 0.32
28 7 0.21
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (28 bp):
ATATAATATTATGTATAAAATTAAAATA
Found at i:2223905 original size:2 final size:2
Alignment explanation
Indices: 2223900--2223936 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2223890 TATCTAATCC
2223900 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
2223937 ACATCACAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2224498 original size:28 final size:29
Alignment explanation
Indices: 2224458--2224524 Score: 100
Period size: 28 Copynumber: 2.3 Consensus size: 29
2224448 AATGGTTTTG
*
2224458 AATTATAATAAATATTTAATATAATATTTA
1 AATTATTA-AAATATTTAATATAATATTTA
*
2224488 AATT-TTAAAATATTTATTATAATATTTA
1 AATTATTAAAATATTTAATATAATATTTA
2224516 AATTATTAA
1 AATTATTAA
2224525 TTATTAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 24 0.71
29 6 0.18
30 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
AATTATTAAAATATTTAATATAATATTTA
Found at i:2224534 original size:28 final size:28
Alignment explanation
Indices: 2224467--2224534 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
2224457 GAATTATAAT
2224467 AAATATTTAA-TATAATATTTAAATTTTA
1 AAATA-TTAATTATAATATTTAAATTTTA
*
2224495 AAATATTTATTATAATATTTAAATTATT-
1 AAATATTAATTATAATATTTAAATT-TTA
*
2224523 AATTATTAATTA
1 AAATATTAATTA
2224535 ATGTGATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 3 0.09
28 30 0.86
29 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
AAATATTAATTATAATATTTAAATTTTA
Found at i:2225035 original size:22 final size:21
Alignment explanation
Indices: 2225000--2225041 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
2224990 AATATATAGA
*
2225000 ATTATGATAAAATAAAATAAT
1 ATTATGACAAAATAAAATAAT
2225021 ATTATGTACAAAATAAAATAA
1 ATTATG-ACAAAATAAAATAA
2225042 AATAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (21 bp):
ATTATGACAAAATAAAATAAT
Found at i:2225080 original size:20 final size:21
Alignment explanation
Indices: 2225035--2225091 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
2225025 TGTACAAAAT
2225035 AAAA-TAAAATAATTTATTTA
1 AAAATTAAAATAATTTATTTA
** *
2225055 TTAATTAAAATTATTT-TTTA
1 AAAATTAAAATAATTTATTTA
* *
2225075 AAAATTTATATAATTTA
1 AAAATTAAAATAATTTA
2225092 AATTATTAAT
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATTAAAATAATTTATTTA
Found at i:2225091 original size:17 final size:18
Alignment explanation
Indices: 2225071--2225108 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2225061 AAAATTATTT
*
2225071 TTTAAA-AATTTATATAA
1 TTTAAATAATTAATATAA
*
2225088 TTTAAATTATTAATATAA
1 TTTAAATAATTAATATAA
2225106 TTT
1 TTT
2225109 TTAAAAGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAATAATTAATATAA
Found at i:2225937 original size:19 final size:20
Alignment explanation
Indices: 2225915--2225952 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2225905 TTTTAATATA
2225915 TATACTACTATTTA-AAAAT
1 TATACTACTATTTATAAAAT
* *
2225934 TATAGTATTATTTATAAAA
1 TATACTACTATTTATAAAA
2225953 AAAATCAGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (20 bp):
TATACTACTATTTATAAAAT
Found at i:2228621 original size:18 final size:17
Alignment explanation
Indices: 2228598--2228632 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
2228588 TTTAGTATTT
2228598 TTCTTAGTACTTTTTTTC
1 TTCTTAGTA-TTTTTTTC
2228616 TTCTTAGTATTTTTTTC
1 TTCTTAGTATTTTTTTC
2228633 ATGATTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.11, C:0.14, G:0.06, T:0.69
Consensus pattern (17 bp):
TTCTTAGTATTTTTTTC
Found at i:2228726 original size:24 final size:24
Alignment explanation
Indices: 2228699--2228744 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2228689 TTAATTATCT
2228699 AATGATGAAATTTATA-AAAATTTA
1 AATGAT-AAATTTATATAAAATTTA
* *
2228723 AATGGTAAATTTTTATAAAATT
1 AATGATAAATTTATATAAAATT
2228745 CTTAAGTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (24 bp):
AATGATAAATTTATATAAAATTTA
Found at i:2233173 original size:9 final size:9
Alignment explanation
Indices: 2233157--2233225 Score: 75
Period size: 10 Copynumber: 7.0 Consensus size: 9
2233147 ATAAAGGAAG
2233157 GAAAAAAAGA
1 GAAAAAAA-A
2233167 GAAAAAAAA
1 GAAAAAAAA
2233176 GAAAAAAAGAAA
1 G--AAAAA-AAA
2233188 GAAAAAGAAA
1 GAAAAA-AAA
2233198 GAAAAAAAA
1 GAAAAAAAA
*
2233207 TGAAAAAAAT
1 -GAAAAAAAA
2233217 GAAAAAAAA
1 GAAAAAAAA
2233226 AGGTTAAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
9 13 0.25
10 31 0.58
11 5 0.09
12 4 0.08
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:2233174 original size:11 final size:11
Alignment explanation
Indices: 2233158--2233261 Score: 73
Period size: 10 Copynumber: 10.2 Consensus size: 11
2233148 TAAAGGAAGG
2233158 AAAAAAAGAGA
1 AAAAAAAGAGA
2233169 AAAAAAAGA-A
1 AAAAAAAGAGA
2233179 AAAAAGAA-AGA
1 AAAAA-AAGAGA
*
2233190 AAAAGAA-AGA
1 AAAAAAAGAGA
*
2233200 AAAAAAA-TGA
1 AAAAAAAGAGA
*
2233210 AAAAAATGA-A
1 AAAAAAAGAGA
2233220 AAAAAAAG-G-
1 AAAAAAAGAGA
**
2233229 TTAAAAA-A-A
1 AAAAAAAGAGA
*
2233238 AAAGAAAGAGA
1 AAAAAAAGAGA
*
2233249 AAAAAAATAGA
1 AAAAAAAGAGA
2233260 AA
1 AA
2233262 GGAGAGAAAA
Statistics
Matches: 72, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
9 9 0.12
10 35 0.49
11 28 0.39
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (11 bp):
AAAAAAAGAGA
Found at i:2233235 original size:32 final size:31
Alignment explanation
Indices: 2233159--2233254 Score: 54
Period size: 33 Copynumber: 2.9 Consensus size: 31
2233149 AAAGGAAGGA
* *
2233159 AAAAAAGAGAAAAAAAAGAAA-AAAAGAAAGAA
1 AAAAAAGAAAAAAAA-AGAAAGAAAAAAAAG-A
* *
2233191 AAAGAAAGAAAAAAAATGAAA-AAAATGAAA-A
1 AAA-AAAGAAAAAAAAAGAAAGAAAA-AAAAGA
*
2233222 AAAAAGGTTAAAAAAAAAAGAAAGAGAAAAAAA
1 AAAAAAG---AAAAAAAAAGAAAGA-AAAAAAA
2233255 ATAGAAAGGA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
30 3 0.06
31 4 0.08
32 11 0.21
33 27 0.52
34 4 0.08
35 3 0.06
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (31 bp):
AAAAAAGAAAAAAAAAGAAAGAAAAAAAAGA
Found at i:2233254 original size:14 final size:13
Alignment explanation
Indices: 2233157--2233215 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 13
2233147 ATAAAGGAAG
2233157 GAAAAAAAGAGAAA
1 GAAAAAAA-AGAAA
*
2233171 -AAAAAGAAAAAAA
1 GAAAAA-AAAGAAA
2233184 GAAAGAAAAAGAAA
1 GAAA-AAAAAGAAA
2233198 GAAAAAAAATGAAA
1 GAAAAAAAA-GAAA
2233212 -AAAA
1 GAAAA
2233216 TGAAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
13 18 0.46
14 19 0.49
15 2 0.05
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (13 bp):
GAAAAAAAAGAAA
Found at i:2233266 original size:18 final size:17
Alignment explanation
Indices: 2233162--2233277 Score: 61
Period size: 17 Copynumber: 6.9 Consensus size: 17
2233152 GGAAGGAAAA
* *
2233162 AAAGAGAAAAAAAAGAA
1 AAAGAGAAAAAAAATAG
* *
2233179 AAAAAGAAAGAAAA-AG
1 AAAGAGAAAAAAAATAG
2233195 -AA-AGAAAAAAAAT-G
1 AAAGAGAAAAAAAATAG
2233209 AAA-A-AAATGAAAAA-A-
1 AAAGAGAAA--AAAAATAG
*
2233224 AAAG-GTTAAAAAAAAAAG
1 AAAGAG--AAAAAAAATAG
2233242 AAAGAGAAAAAAAATAG
1 AAAGAGAAAAAAAATAG
2233259 AAAGGAGAGAAAAAGAATA
1 AAA-GAGA-AAAAA-AATA
2233278 CTCAAATTGA
Statistics
Matches: 79, Mismatches: 5, Indels: 27
0.71 0.05 0.24
Matches are distributed among these distances:
14 13 0.16
15 8 0.10
16 11 0.14
17 26 0.33
18 11 0.14
19 6 0.08
20 4 0.05
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (17 bp):
AAAGAGAAAAAAAATAG
Found at i:2234964 original size:20 final size:20
Alignment explanation
Indices: 2234941--2234989 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
2234931 AAATGTGAAT
2234941 CTTTGAACTCGAATGAAAAG
1 CTTTGAACTCGAATGAAAAG
2234961 CTTTGAACTCGAATGAAAAG
1 CTTTGAACTCGAATGAAAAG
*
2234981 CTTTAAACT
1 CTTTGAACT
2234990 TTTATATATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (20 bp):
CTTTGAACTCGAATGAAAAG
Found at i:2235408 original size:43 final size:42
Alignment explanation
Indices: 2235288--2235480 Score: 235
Period size: 42 Copynumber: 4.5 Consensus size: 42
2235278 GATTGTCAAT
* * *
2235288 GAGCATTTTATTTTTTCTAAAGTTGTGGTTGCCTCTATTTAAAG
1 GAGCAATTTA-TTTTTC-AAAGTTATGGTTGCCTCTATTTAGAG
* * *
2235332 GAGTATTTTATTTTTCAAAGTTATGCTTGCCTCTATTTAGAG
1 GAGCAATTTATTTTTCAAAGTTATGGTTGCCTCTATTTAGAG
* *
2235374 GAGCAATTTATGTTTCCAAAGTTATGGTTGCCTCTATTTAGAA
1 GAGCAATTTAT-TTTTCAAAGTTATGGTTGCCTCTATTTAGAG
*
2235417 GAGCAATTTATTTTTTAAAGTTATGGTTGCCTCTATTTA-ATG
1 GAGCAATTTATTTTTCAAAGTTATGGTTGCCTCTATTTAGA-G
* *
2235459 GAACGATTTATGTTTTCAAAGT
1 GAGCAATTTAT-TTTTCAAAGT
2235481 CGTTATTGCC
Statistics
Matches: 131, Mismatches: 15, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
41 1 0.01
42 67 0.51
43 54 0.41
44 9 0.07
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (42 bp):
GAGCAATTTATTTTTCAAAGTTATGGTTGCCTCTATTTAGAG
Found at i:2235437 original size:85 final size:85
Alignment explanation
Indices: 2235301--2235480 Score: 247
Period size: 85 Copynumber: 2.1 Consensus size: 85
2235291 CATTTTATTT
* * * *
2235301 TTTCTAAAGTTGTGGTTGCCTCTATTTAAAGGAGTATTTTATTTTTCAAAGTTATGCTTGCCTCT
1 TTTCCAAAGTTATGGTTGCCTCTATTTAAAGGAGCAATTTATTTTTCAAAGTTATGCTTGCCTCT
*
2235366 ATTTAGA-GGAGCAATTTATG
66 ATTTA-ATGGAACAATTTATG
* *
2235386 TTTCCAAAGTTATGGTTGCCTCTATTTAGAA-GAGCAATTTATTTTTTAAAGTTATGGTTGCCTC
1 TTTCCAAAGTTATGGTTGCCTCTATTTA-AAGGAGCAATTTATTTTTCAAAGTTATGCTTGCCTC
*
2235450 TATTTAATGGAACGATTTATG
65 TATTTAATGGAACAATTTATG
*
2235471 TTTTCAAAGT
1 TTTCCAAAGT
2235481 CGTTATTGCC
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
84 1 0.01
85 81 0.96
86 2 0.02
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (85 bp):
TTTCCAAAGTTATGGTTGCCTCTATTTAAAGGAGCAATTTATTTTTCAAAGTTATGCTTGCCTCT
ATTTAATGGAACAATTTATG
Found at i:2235490 original size:85 final size:85
Alignment explanation
Indices: 2235316--2235513 Score: 229
Period size: 85 Copynumber: 2.3 Consensus size: 85
2235306 AAAGTTGTGG
* * *
2235316 TTGCCTCTATTTAAAGGAGTATTTTATTTTTCAAAGTTATGCTTGCCTCTATTTAGAGGAGCAAT
1 TTGCCTCTATTTAAAGGAGCAATTTATTTTTCAAAGTTATGCTTGCCTCTATTTAGAGGAACAAT
* *
2235381 TTATGTTTCCAAAGTTATGG
66 TTATGTTTCCAAAGTCATGA
* * *
2235401 TTGCCTCTATTTAGAA-GAGCAATTTATTTTTTAAAGTTATGGTTGCCTCTATTTA-ATGGAACG
1 TTGCCTCTATTTA-AAGGAGCAATTTATTTTTCAAAGTTATGCTTGCCTCTATTTAGA-GGAACA
* * *
2235464 ATTTATGTTTTCAAAGTCGTTA
64 ATTTATGTTTCCAAAGTCATGA
* * * *
2235486 TTGCCTTTATTTATAGAAGTAATTTATT
1 TTGCCTCTATTTAAAGGAGCAATTTATT
2235514 ACCTCTATTT
Statistics
Matches: 95, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
84 2 0.02
85 91 0.96
86 2 0.02
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (85 bp):
TTGCCTCTATTTAAAGGAGCAATTTATTTTTCAAAGTTATGCTTGCCTCTATTTAGAGGAACAAT
TTATGTTTCCAAAGTCATGA
Found at i:2235512 original size:26 final size:26
Alignment explanation
Indices: 2235483--2235539 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
2235473 TTCAAAGTCG
* * *
2235483 TTATTGCCTTTATTTATAGAAGTAAT
1 TTATTACCTCTATTTAGAGAAGTAAT
*
2235509 TTATTACCTCTATTTAGAGGAGTAAT
1 TTATTACCTCTATTTAGAGAAGTAAT
2235535 TTATT
1 TTATT
2235540 TTTTCAAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (26 bp):
TTATTACCTCTATTTAGAGAAGTAAT
Found at i:2235564 original size:42 final size:42
Alignment explanation
Indices: 2235515--2235781 Score: 301
Period size: 42 Copynumber: 6.4 Consensus size: 42
2235505 TAATTTATTA
*
2235515 CCTCTATTTAGAGGAGTAATTTATTTTTTCAAAGTTATGGTG
1 CCTCTATTTAGAGGAGCAATTTATTTTTTCAAAGTTATGGTG
* * ** * *
2235557 GCTCTATTTAGATGAGTGATTTATTTTTTCAAAGTT-TTGTT
1 CCTCTATTTAGAGGAGCAATTTATTTTTTCAAAGTTATGGTG
2235598 CCTCTATTTAGAGGAGCAATTTATTTTTTCAAAGTTA-GGTTG
1 CCTCTATTTAGAGGAGCAATTTATTTTTTCAAAGTTATGG-TG
* * *
2235640 CCTCTATTTAGAGGAACAATTTATTTTTTCAAAGTTCTGTTG
1 CCTCTATTTAGAGGAGCAATTTATTTTTTCAAAGTTATGGTG
* * * *
2235682 CCTCTATTTAGAGGACCAATTTA-TTCTTCAAAGTTGTGTTG
1 CCTCTATTTAGAGGAGCAATTTATTTTTTCAAAGTTATGGTG
* * * *
2235723 CCTATATTTAAAAGAGCAATTTATTTTTTCGAAATTCTAT--TG
1 CCTCTATTTAGAGGAGCAATTTATTTTTTC-AAAGT-TATGGTG
*
2235765 CCTCTATTTAGATGAGC
1 CCTCTATTTAGAGGAGC
2235782 TTTGTTTATT
Statistics
Matches: 192, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
41 71 0.37
42 114 0.59
43 5 0.03
44 2 0.01
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (42 bp):
CCTCTATTTAGAGGAGCAATTTATTTTTTCAAAGTTATGGTG
Found at i:2235602 original size:83 final size:84
Alignment explanation
Indices: 2235515--2235781 Score: 344
Period size: 83 Copynumber: 3.2 Consensus size: 84
2235505 TAATTTATTA
* * * **
2235515 CCTCTATTTAGAGGAGTAATTTATTTTTTCAAAGTTATGGTGGCTCTATTTAGATGAGTGATTTA
1 CCTCTATTTAGAGGAGCAATTTATTTTTTCAAAGTTATGGTGCCTCTATTTAGAAGAGCAATTTA
*
2235580 TTTTTTCAAAGTTTTGTT-
66 TTTTTTCAAAGTTCTGTTG
* *
2235598 CCTCTATTTAGAGGAGCAATTTATTTTTTCAAAGTTA-GGTTGCCTCTATTTAGAGGAACAATTT
1 CCTCTATTTAGAGGAGCAATTTATTTTTTCAAAGTTATGG-TGCCTCTATTTAGAAGAGCAATTT
2235662 ATTTTTTCAAAGTTCTGTTG
65 ATTTTTTCAAAGTTCTGTTG
* * * * * *
2235682 CCTCTATTTAGAGGACCAATTTA-TTCTTCAAAGTTGTGTTGCCTATATTTAAAAGAGCAATTTA
1 CCTCTATTTAGAGGAGCAATTTATTTTTTCAAAGTTATGGTGCCTCTATTTAGAAGAGCAATTTA
*
2235746 TTTTTTCGAAA-TTCTATTG
66 TTTTTTC-AAAGTTCTGTTG
*
2235765 CCTCTATTTAGATGAGC
1 CCTCTATTTAGAGGAGC
2235782 TTTGTTTATT
Statistics
Matches: 162, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
82 2 0.01
83 134 0.83
84 26 0.16
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (84 bp):
CCTCTATTTAGAGGAGCAATTTATTTTTTCAAAGTTATGGTGCCTCTATTTAGAAGAGCAATTTA
TTTTTTCAAAGTTCTGTTG
Found at i:2235652 original size:125 final size:125
Alignment explanation
Indices: 2235510--2235776 Score: 342
Period size: 125 Copynumber: 2.1 Consensus size: 125
2235500 AGAAGTAATT
* ** * * ***
2235510 TATTACCTCTATTTAGAGGAGTAATTTATTTTTTCAAAGTTATGGTGGCTCTATTTAGATGAGTG
1 TATTGCCTCTATTTAGAGGAACAATTTATTTTTTCAAAGTTATGGTGCCTCTATTTAGAGGACCA
* * * * *
2235575 ATTTATTTTTTCAAAGTTTTGTT-CCTCTATTTAGAGGAGCAATTTATTTTTTC-AAAGT-
66 ATTTA-TTCTTCAAAGTTGTGTTGCCTATATTTAAAAGAGCAATTTATTTTTTCGAAAGTC
* *
2235633 TAGGTTGCCTCTATTTAGAGGAACAATTTATTTTTTCAAAGTTCTGTTGCCTCTATTTAGAGGAC
1 TA--TTGCCTCTATTTAGAGGAACAATTTATTTTTTCAAAGTTATGGTGCCTCTATTTAGAGGAC
*
2235698 CAATTTATTCTTCAAAGTTGTGTTGCCTATATTTAAAAGAGCAATTTATTTTTTCGAAATTC
64 CAATTTATTCTTCAAAGTTGTGTTGCCTATATTTAAAAGAGCAATTTATTTTTTCGAAAGTC
2235760 TATTGCCTCTATTTAGA
1 TATTGCCTCTATTTAGA
2235777 TGAGCTTTGT
Statistics
Matches: 123, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
123 2 0.02
124 15 0.12
125 100 0.81
126 4 0.03
127 2 0.02
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (125 bp):
TATTGCCTCTATTTAGAGGAACAATTTATTTTTTCAAAGTTATGGTGCCTCTATTTAGAGGACCA
ATTTATTCTTCAAAGTTGTGTTGCCTATATTTAAAAGAGCAATTTATTTTTTCGAAAGTC
Found at i:2236382 original size:23 final size:22
Alignment explanation
Indices: 2236323--2236383 Score: 54
Period size: 23 Copynumber: 2.6 Consensus size: 22
2236313 AAACAATTTA
*
2236323 AAAATTTTAAGAATTTTTTTTTG
1 AAAATTTTTAG-ATTTTTTTTTG
2236346 --AATTTTTGGCAGATTTTTTTTTGG
1 AAAATTTTT---AGATTTTTTTTT-G
2236370 AAAATTTTTAGATT
1 AAAATTTTTAGATT
2236384 CCAACGAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
21 6 0.19
23 15 0.48
24 3 0.10
26 7 0.23
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.56
Consensus pattern (22 bp):
AAAATTTTTAGATTTTTTTTTG
Found at i:2237051 original size:25 final size:25
Alignment explanation
Indices: 2237008--2237055 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
2236998 TTAATTATCC
2237008 AATGATGAAATTTATTAAAATTTCA
1 AATGATGAAATTTATTAAAATTTCA
*
2237033 AATGAT-AAATTTTTATAAAATTT
1 AATGATGAAATTTAT-TAAAATTT
2237056 TTAGGTGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (25 bp):
AATGATGAAATTTATTAAAATTTCA
Found at i:2241237 original size:2 final size:2
Alignment explanation
Indices: 2241230--2241262 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2241220 AATGAAATAG
2241230 AT AT AT AT 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 AT AT AT AT A
2241263 AACCAGAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2245170 original size:16 final size:15
Alignment explanation
Indices: 2245142--2245184 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
2245132 TTTACGTAAA
2245142 ATTAAAAAAAATCAT
1 ATTAAAAAAAATCAT
*
2245157 ATTAAAAGAAAATCTT
1 ATTAAAA-AAAATCAT
2245173 ATATAAAAAAAA
1 AT-TAAAAAAAA
2245185 AGAAATGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 7 0.28
16 13 0.52
17 5 0.20
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (15 bp):
ATTAAAAAAAATCAT
Found at i:2247963 original size:23 final size:22
Alignment explanation
Indices: 2247931--2247980 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 22
2247921 ACAATTGTAA
2247931 ACAAACCTCCTATATGTATTGT
1 ACAAACCTCCTATATGTATTGT
2247953 ACAAGACCTCCTATATGTATTGT
1 ACAA-ACCTCCTATATGTATTGT
2247976 ACAAA
1 ACAAA
2247981 TGAACAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 5 0.19
23 22 0.81
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (22 bp):
ACAAACCTCCTATATGTATTGT
Found at i:2249837 original size:6 final size:6
Alignment explanation
Indices: 2249826--2249861 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
2249816 TTGGCTTCTT
*
2249826 TGTTTG TGTTTG TGTTTG TGTTTG TGTTTG GGTTTG
1 TGTTTG TGTTTG TGTTTG TGTTTG TGTTTG TGTTTG
2249862 AGTCTTCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (6 bp):
TGTTTG
Found at i:2250261 original size:25 final size:24
Alignment explanation
Indices: 2250228--2250274 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
2250218 TAAAATTTAT
* *
2250228 AAATTTATATTATATTTTATATAA
1 AAATTTATATCATAATTTATATAA
2250252 AAATTATATATCATAATTTATAT
1 AAATT-TATATCATAATTTATAT
2250275 TAATATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATTTATATCATAATTTATATAA
Found at i:2251651 original size:68 final size:68
Alignment explanation
Indices: 2251542--2251677 Score: 254
Period size: 68 Copynumber: 2.0 Consensus size: 68
2251532 AAAGTTACCA
2251542 CTAAAGCCCATTCTAAATCCACAGATGGAAGCAAGCAACAGTCCAGTAATTAGAGCTCTAAAATC
1 CTAAAGCCCATTCTAAATCCACAGATGGAAGCAAGCAACAGTCCAGTAATTAGAGCTCTAAAATC
2251607 AAC
66 AAC
* *
2251610 CTAAAGCCCATTCTAAATCCACAGATGGAAGCAAGCAACAGTCCAGTAATTAGAGCTCTCAATTC
1 CTAAAGCCCATTCTAAATCCACAGATGGAAGCAAGCAACAGTCCAGTAATTAGAGCTCTAAAATC
2251675 AAC
66 AAC
2251678 AGGTTGTTAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.40, C:0.26, G:0.15, T:0.20
Consensus pattern (68 bp):
CTAAAGCCCATTCTAAATCCACAGATGGAAGCAAGCAACAGTCCAGTAATTAGAGCTCTAAAATC
AAC
Found at i:2256614 original size:14 final size:14
Alignment explanation
Indices: 2256597--2256627 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2256587 ATTATTTATT
*
2256597 AAACCTAAATAAAC
1 AAACATAAATAAAC
2256611 AAACATAAATAAAC
1 AAACATAAATAAAC
2256625 AAA
1 AAA
2256628 AATTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.16, G:0.00, T:0.13
Consensus pattern (14 bp):
AAACATAAATAAAC
Found at i:2256965 original size:21 final size:21
Alignment explanation
Indices: 2256905--2256973 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
2256895 ATTAATTTTG
*
2256905 ATAA-ATTAAAAAATAATAATA
1 ATAATATTAAAATA-AATAATA
* ** **
2256926 ATAAAATTAATTTTTATAATA
1 ATAATATTAAAATAAATAATA
2256947 ATAATATTAAAATAAATAATA
1 ATAATATTAAAATAAATAATA
2256968 A-AATAT
1 ATAATAT
2256974 ATATTTGGAT
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 5 0.14
21 27 0.73
22 5 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATAATATTAAAATAAATAATA
Found at i:2257123 original size:27 final size:27
Alignment explanation
Indices: 2257061--2257124 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
2257051 ATTAAACTTG
* *
2257061 TATTAATAAATTTTAAAATATATTTTA
1 TATTAATAAATTTAAAAATATATTATA
*
2257088 TATTTATAAATTTAATAAATA-ATTA-A
1 TATTAATAAATTTAA-AAATATATTATA
2257114 TAATTAATAAA
1 T-ATTAATAAA
2257125 ATTATTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
26 2 0.06
27 24 0.77
28 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TATTAATAAATTTAAAAATATATTATA
Found at i:2257626 original size:46 final size:44
Alignment explanation
Indices: 2257542--2257629 Score: 131
Period size: 46 Copynumber: 2.0 Consensus size: 44
2257532 CAAATCATTA
*
2257542 TAATTAATAGTTCTTTTTTTTAAATTTCAATCTGTTATATTTCT
1 TAATTAATAGTTCTTTTTTTTAAATTTCAATCTATTATATTTCT
* *
2257586 TAATTAATAGTTTTTTTCCTTTTTAATTTCAATCTATTATATTT
1 TAATTAATAGTTCTTTT--TTTTAAATTTCAATCTATTATATTT
2257630 TTTTTCTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 16 0.41
46 23 0.59
ACGTcount: A:0.27, C:0.09, G:0.03, T:0.60
Consensus pattern (44 bp):
TAATTAATAGTTCTTTTTTTTAAATTTCAATCTATTATATTTCT
Found at i:2276442 original size:24 final size:24
Alignment explanation
Indices: 2276415--2276469 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
2276405 CAACTTTTTT
*
2276415 CTCTTCCT-CTTTGGTATCTCCTTC
1 CTCTTCCTACTCTGGTATC-CCTTC
2276439 CTCTT-CTAGCTCTGGTATCCCTTC
1 CTCTTCCTA-CTCTGGTATCCCTTC
2276463 CTCTTCC
1 CTCTTCC
2276470 CTCACTACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 2 0.07
24 15 0.56
25 10 0.37
ACGTcount: A:0.05, C:0.40, G:0.09, T:0.45
Consensus pattern (24 bp):
CTCTTCCTACTCTGGTATCCCTTC
Found at i:2276686 original size:3 final size:3
Alignment explanation
Indices: 2276640--2276670 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2276630 GTTGTTGTTG
2276640 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
2276671 CTTATTACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:2279472 original size:23 final size:23
Alignment explanation
Indices: 2279446--2279489 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2279436 TTTAATTGAA
*
2279446 ATTTACAGATTTATTAAATTTTT
1 ATTTACAAATTTATTAAATTTTT
* *
2279469 ATTTATAAATTTTTTAAATTT
1 ATTTACAAATTTATTAAATTT
2279490 ACATATCATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
ATTTACAAATTTATTAAATTTTT
Found at i:2279484 original size:15 final size:15
Alignment explanation
Indices: 2279454--2279482 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2279444 AAATTTACAG
2279454 ATTTATTAAATTTTT
1 ATTTATTAAATTTTT
2279469 ATTTA-TAAATTTTT
1 ATTTATTAAATTTTT
2279483 TAAATTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTATTAAATTTTT
Found at i:2286802 original size:22 final size:22
Alignment explanation
Indices: 2286772--2286816 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2286762 GATGAAAAGA
*
2286772 ATTTTTTTAATTT-TTTAGTTTT
1 ATTTATTT-ATTTATTTAGTTTT
*
2286794 ATTTATTTATTTATTTATTTTT
1 ATTTATTTATTTATTTAGTTTT
2286816 A
1 A
2286817 CAAATGAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (22 bp):
ATTTATTTATTTATTTAGTTTT
Found at i:2298985 original size:15 final size:15
Alignment explanation
Indices: 2298965--2298994 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2298955 GAAGTTTGTC
2298965 TCTTTGTTGTGCTAA
1 TCTTTGTTGTGCTAA
2298980 TCTTTGTTGTGCTAA
1 TCTTTGTTGTGCTAA
2298995 GGATGAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.20, T:0.53
Consensus pattern (15 bp):
TCTTTGTTGTGCTAA
Found at i:2302915 original size:75 final size:74
Alignment explanation
Indices: 2302824--2303111 Score: 391
Period size: 75 Copynumber: 3.9 Consensus size: 74
2302814 TCAGAGTACA
*
2302824 AGAGAGTCAATTAGGTCAGAGCCCCAGTTCCCATATCCACGACGGCAACCACCTCAAAATATGGG
1 AGAGAGTCAGTTAGGTCAGAGCCCCAGTTCCCATATCCACGACGGCAACCACCTCAAAATATGGG
2302889 CCAGAATCTG
66 CCAGAATC-G
* * * * * * * *
2302899 AGAGAGTCAGCTAGGTCTGAGCCACAGTTCCCATATCCTCAACGGCAACCTCCACAAAGTATGGG
1 AGAGAGTCAGTTAGGTCAGAGCCCCAGTTCCCATATCCACGACGGCAACCACCTCAAAATATGGG
*
2302964 CCAGAGTCCG
66 CCAGAAT-CG
*
2302974 CA-AGAGTCAGTTAGGTCAGAGCCCCAGTTCCCATATCCACGATGGCAACCACCTCAAAATATGG
1 -AGAGAGTCAGTTAGGTCAGAGCCCCAGTTCCCATATCCACGACGGCAACCACCTCAAAATATGG
*
2303038 GCCA-AAGTACA
65 GCCAGAA-T-CG
* *
2303049 AGAGAGTCAGTTAGGTCAGAGCCCCAGTTCTCATATCCACTACGGCAACCACCTCAAAATATG
1 AGAGAGTCAGTTAGGTCAGAGCCCCAGTTCCCATATCCACGACGGCAACCACCTCAAAATATG
2303112 AATGCCTCAT
Statistics
Matches: 184, Mismatches: 25, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
74 2 0.01
75 180 0.98
76 2 0.01
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.18
Consensus pattern (74 bp):
AGAGAGTCAGTTAGGTCAGAGCCCCAGTTCCCATATCCACGACGGCAACCACCTCAAAATATGGG
CCAGAATCG
Found at i:2303086 original size:150 final size:150
Alignment explanation
Indices: 2302826--2303098 Score: 433
Period size: 150 Copynumber: 1.8 Consensus size: 150
2302816 AGAGTACAAG
2302826 AGAGTCAATTAGGTCAGAGCCCCAGTTCCCATATCCACGACGGCAACCACCTCAAAATATGGGCC
1 AGAGTCAATTAGGTCAGAGCCCCAGTTCCCATATCCACGACGGCAACCACCTCAAAATATGGGCC
* * *
2302891 AGAATCTGAGAGAGTCAGCTAGGTCTGAGCCACAGTTCCCATATCCTCAACGGCAACCTCCACAA
66 AGAATCTAAGAGAGTCAGCTAGGTCAGAGCCACAGTTCCCATATCCACAACGGCAACCTCCACAA
2302956 AGTATGGGCCAGAGTCCGCA
131 AGTATGGGCCAGAGTCCGCA
* *
2302976 AGAGTCAGTTAGGTCAGAGCCCCAGTTCCCATATCCACGATGGCAACCACCTCAAAATATGGGCC
1 AGAGTCAATTAGGTCAGAGCCCCAGTTCCCATATCCACGACGGCAACCACCTCAAAATATGGGCC
* * * *
2303041 A-AAGTAC-AAGAGAGTCAGTTAGGTCAGAGCCCCAGTTCTCATATCCACTACGGCAACC
66 AGAA-T-CTAAGAGAGTCAGCTAGGTCAGAGCCACAGTTCCCATATCCACAACGGCAACC
2303099 ACCTCAAAAT
Statistics
Matches: 112, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
149 2 0.02
150 109 0.97
151 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (150 bp):
AGAGTCAATTAGGTCAGAGCCCCAGTTCCCATATCCACGACGGCAACCACCTCAAAATATGGGCC
AGAATCTAAGAGAGTCAGCTAGGTCAGAGCCACAGTTCCCATATCCACAACGGCAACCTCCACAA
AGTATGGGCCAGAGTCCGCA
Found at i:2303743 original size:2 final size:2
Alignment explanation
Indices: 2303736--2303774 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2303726 TTGTTTGAGA
2303736 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
2303775 GTACTTGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2304051 original size:16 final size:16
Alignment explanation
Indices: 2304030--2304062 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2304020 GCTTTATTAA
2304030 TTTGGACAATGA-AATT
1 TTTGGAC-ATGATAATT
2304046 TTTGGACATGATAATT
1 TTTGGACATGATAATT
2304062 T
1 T
2304063 CTTGTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.42
Consensus pattern (16 bp):
TTTGGACATGATAATT
Found at i:2304257 original size:14 final size:13
Alignment explanation
Indices: 2304231--2304256 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2304221 AATCAATAAA
2304231 AAAAATAATTTTT
1 AAAAATAATTTTT
2304244 AAAAATAATTTTT
1 AAAAATAATTTTT
2304257 TTCTTCATCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAAATAATTTTT
Found at i:2304664 original size:3 final size:3
Alignment explanation
Indices: 2304656--2304688 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2304646 ATTCTAGGGT
2304656 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2304689 ATTTTAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2312730 original size:39 final size:39
Alignment explanation
Indices: 2312676--2312753 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
2312666 ACAGCAAGAG
*
2312676 ATAGTTGGATGATGTTTTAACCCAATGCTATGCTTGAAA
1 ATAGTTGGATGATGTTTTAACCCAAGGCTATGCTTGAAA
**
2312715 ATAGTTGGATGATGTTTTAACTTAAGGCTATGCTTGAAA
1 ATAGTTGGATGATGTTTTAACCCAAGGCTATGCTTGAAA
2312754 TCAAGGAGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (39 bp):
ATAGTTGGATGATGTTTTAACCCAAGGCTATGCTTGAAA
Found at i:2313194 original size:2 final size:2
Alignment explanation
Indices: 2313187--2313213 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2313177 CCTACTTTGA
2313187 AT 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 AT A
2313214 AAATCAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2321071 original size:4 final size:4
Alignment explanation
Indices: 2321062--2321087 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2321052 CAACGTAAGT
2321062 TCAA TCAA TCAA TCAA TCAA TCAA TC
1 TCAA TCAA TCAA TCAA TCAA TCAA TC
2321088 TATAACATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (4 bp):
TCAA
Found at i:2327090 original size:15 final size:15
Alignment explanation
Indices: 2327070--2327106 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
2327060 ATAAAAGTTG
2327070 ATCAAATTTTTTAAA
1 ATCAAATTTTTTAAA
2327085 ATCAAATTTTTTAAA
1 ATCAAATTTTTTAAA
*
2327100 ATTAAAT
1 ATCAAAT
2327107 ATTTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (15 bp):
ATCAAATTTTTTAAA
Found at i:2327111 original size:14 final size:15
Alignment explanation
Indices: 2327070--2327114 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
2327060 ATAAAAGTTG
*
2327070 ATCAAATTTTTTAAA
1 ATCAAATTATTTAAA
*
2327085 ATCAAATTTTTTAAA
1 ATCAAATTATTTAAA
*
2327100 ATTAAA-TATTTAAA
1 ATCAAATTATTTAAA
2327114 A
1 A
2327115 AAGATTTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
14 8 0.29
15 20 0.71
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (15 bp):
ATCAAATTATTTAAA
Found at i:2330260 original size:24 final size:24
Alignment explanation
Indices: 2330230--2330280 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
2330220 ACACCTGGTG
2330230 AAGACAATGCAATTATTGAAACTA
1 AAGACAATGCAATTATTGAAACTA
* *
2330254 AAGACAATGGAGTTATTGAAACTA
1 AAGACAATGCAATTATTGAAACTA
2330278 AAG
1 AAG
2330281 CCTTACCTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.24
Consensus pattern (24 bp):
AAGACAATGCAATTATTGAAACTA
Found at i:2338957 original size:26 final size:25
Alignment explanation
Indices: 2338907--2338958 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
2338897 TTATTTGTAA
*
2338907 ATAATTTTAATAAAATTCATTTTTT
1 ATAATTTTAATAAAATTCATCTTTT
*
2338932 ATAATTTTTCATAAAATTTCA-CTTTT
1 ATAA-TTTTAATAAAA-TTCATCTTTT
2338958 A
1 A
2338959 ATACTTTCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 4 0.17
26 15 0.65
27 4 0.17
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (25 bp):
ATAATTTTAATAAAATTCATCTTTT
Found at i:2349837 original size:432 final size:432
Alignment explanation
Indices: 2349034--2349897 Score: 1674
Period size: 432 Copynumber: 2.0 Consensus size: 432
2349024 AAATCTAAGC
*
2349034 TTTTGTTGACCGCTTTCTAAAAGCAGGTTTAATTTCCATTTCCATCTCCATTTGTTAGATTACCA
1 TTTTGTTGACCGCTTTCTAAAAGCAGGTTTAATTTCCATTTCCATCTCCATTTGTTAGATAACCA
2349099 CCATGGTATAACAGAAATTGTACATAACAAAAGGACTGATAATGGGATGAGAGTTCAACCAAATT
66 CCATGGTATAACAGAAATTGTACATAACAAAAGGACTGATAATGGGATGAGAGTTCAACCAAATT
2349164 GCCCTAAAGCATCTAATCCTTACCATGAATGCAATGAATTCTGTGTCTGGAGAACTTCCAATGCC
131 GCCCTAAAGCATCTAATCCTTACCATGAATGCAATGAATTCTGTGTCTGGAGAACTTCCAATGCC
2349229 GATACTCAGGGGGTTAGAAAGGAATCAGGTTTATGAGTGATTAAAAGTTCTTTTCTGTATTAGTA
196 GATACTCAGGGGGTTAGAAAGGAATCAGGTTTATGAGTGATTAAAAGTTCTTTTCTGTATTAGTA
2349294 AGGTTTTGAATTCTGTTTAGGTTTTGTTGATCTCCTTCTAAAACTAGGTGTCTATGTCTAGATAA
261 AGGTTTTGAATTCTGTTTAGGTTTTGTTGATCTCCTTCTAAAACTAGGTGTCTATGTCTAGATAA
2349359 TCTCAATGGTAGAAAAGAAGGTGAGCTTAGCAAAAAGAAGGATGACAAGGGAAGAGTGCACCGAA
326 TCTCAATGGTAGAAAAGAAGGTGAGCTTAGCAAAAAGAAGGATGACAAGGGAAGAGTGCACCGAA
*
2349424 CTTGGGGAAAGGCATCTAATCCTTACCATGAATGTGATGAAA
391 CTTGCGGAAAGGCATCTAATCCTTACCATGAATGTGATGAAA
* *
2349466 TTTTGTTGACTGCTTTCTAAAAGCTGGTTTAATTTCCATTTCCATCTCCATTTGTTAGATAACCA
1 TTTTGTTGACCGCTTTCTAAAAGCAGGTTTAATTTCCATTTCCATCTCCATTTGTTAGATAACCA
2349531 CCATGGTATAACAGAAATTGTACATAACAAAAGGACTGATAATGGGATGAGAGTTCAACCAAATT
66 CCATGGTATAACAGAAATTGTACATAACAAAAGGACTGATAATGGGATGAGAGTTCAACCAAATT
2349596 GCCCTAAAGCATCTAATCCTTACCATGAATGCAATGAATTCTGTGTCTGGAGAACTTCCAATGCC
131 GCCCTAAAGCATCTAATCCTTACCATGAATGCAATGAATTCTGTGTCTGGAGAACTTCCAATGCC
2349661 GATACTCAGGGGGTTAGAAAGGAATCAGGTTTATGAGTGATTAAAAGTTCTTTTCTGTATTAGTA
196 GATACTCAGGGGGTTAGAAAGGAATCAGGTTTATGAGTGATTAAAAGTTCTTTTCTGTATTAGTA
2349726 AGGTTTTGAATTCTGTTTAGGTTTTGTTGATCTCCTTCTAAAACTAGGTGTCTATGTCTAGATAA
261 AGGTTTTGAATTCTGTTTAGGTTTTGTTGATCTCCTTCTAAAACTAGGTGTCTATGTCTAGATAA
*
2349791 TCTCAATGGTAGAAAAGAAGGTGAGCTTAGCAAAAAGAAGGATGACAAGGGAAGAGTGCACCGAG
326 TCTCAATGGTAGAAAAGAAGGTGAGCTTAGCAAAAAGAAGGATGACAAGGGAAGAGTGCACCGAA
*
2349856 CTTGCGGAAAGGCATCTTATCCTTACCATGAATGTGATGAAA
391 CTTGCGGAAAGGCATCTAATCCTTACCATGAATGTGATGAAA
2349898 ATTGCTTCAA
Statistics
Matches: 426, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
432 426 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (432 bp):
TTTTGTTGACCGCTTTCTAAAAGCAGGTTTAATTTCCATTTCCATCTCCATTTGTTAGATAACCA
CCATGGTATAACAGAAATTGTACATAACAAAAGGACTGATAATGGGATGAGAGTTCAACCAAATT
GCCCTAAAGCATCTAATCCTTACCATGAATGCAATGAATTCTGTGTCTGGAGAACTTCCAATGCC
GATACTCAGGGGGTTAGAAAGGAATCAGGTTTATGAGTGATTAAAAGTTCTTTTCTGTATTAGTA
AGGTTTTGAATTCTGTTTAGGTTTTGTTGATCTCCTTCTAAAACTAGGTGTCTATGTCTAGATAA
TCTCAATGGTAGAAAAGAAGGTGAGCTTAGCAAAAAGAAGGATGACAAGGGAAGAGTGCACCGAA
CTTGCGGAAAGGCATCTAATCCTTACCATGAATGTGATGAAA
Found at i:2350386 original size:12 final size:12
Alignment explanation
Indices: 2350351--2350416 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
2350341 AATTTATTTT
*
2350351 TTTAATTAT-TT
1 TTTAATTATATA
*
2350362 TTTAAATTTTATA
1 TTT-AATTATATA
2350375 TTTAATTATATA
1 TTTAATTATATA
**
2350387 TATTTTTATATATA
1 T-TTAAT-TATATA
*
2350401 TTTAATTTTATA
1 TTTAATTATATA
2350413 TTTA
1 TTTA
2350417 TATTTAAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
11 3 0.07
12 23 0.53
13 10 0.23
14 7 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTAATTATATA
Found at i:2350396 original size:22 final size:22
Alignment explanation
Indices: 2350368--2350423 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
2350358 ATTTTTTAAA
2350368 TTTTATATTTAATT-ATATATAT
1 TTTTATATTTAATTAAT-TATAT
* * *
2350390 TTTTATATATATTTAATTTTAT
1 TTTTATATTTAATTAATTATAT
*
2350412 ATTTATATTTAA
1 TTTTATATTTAA
2350424 AATAATATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTATATTTAATTAATTATAT
Found at i:2350400 original size:16 final size:16
Alignment explanation
Indices: 2350381--2350419 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2350371 TATATTTAAT
*
2350381 TATATATATTTTTATA
1 TATATATAATTTTATA
*
2350397 TATATTTAATTTTATA
1 TATATATAATTTTATA
*
2350413 TTTATAT
1 TATATAT
2350420 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATATAATTTTATA
Found at i:2377878 original size:13 final size:14
Alignment explanation
Indices: 2377854--2377885 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
2377844 TTGCAATTTG
2377854 CTTTTTTCCTTTTT
1 CTTTTTTCCTTTTT
2377868 CTTTTTT-CTTTTT
1 CTTTTTTCCTTTTT
2377881 CTTTT
1 CTTTT
2377886 CTGAGTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
CTTTTTTCCTTTTT
Found at i:2388400 original size:2 final size:2
Alignment explanation
Indices: 2388393--2388424 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2388383 AATTTGCTGG
2388393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2388425 CAACTAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2398949 original size:9 final size:9
Alignment explanation
Indices: 2398935--2398960 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2398925 TAAAAAGGCA
2398935 ACTTGGGCC
1 ACTTGGGCC
2398944 ACTTGGGCC
1 ACTTGGGCC
2398953 ACTTGGGC
1 ACTTGGGC
2398961 TAATTAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.31, G:0.35, T:0.23
Consensus pattern (9 bp):
ACTTGGGCC
Found at i:2403600 original size:3 final size:3
Alignment explanation
Indices: 2403592--2403624 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2403582 CTCGTAGACA
*
2403592 AAT AAT AAT AAT AAT AAT AAT TAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2403625 TATTATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:2403625 original size:12 final size:12
Alignment explanation
Indices: 2403592--2403627 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2403582 CTCGTAGACA
*
2403592 AATAATAATAAT
1 AATAATAATTAT
2403604 AATAATAATTAT
1 AATAATAATTAT
2403616 AATAATAATTAT
1 AATAATAATTAT
2403628 TATTATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATAATAATTAT
Found at i:2403704 original size:16 final size:17
Alignment explanation
Indices: 2403678--2403712 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2403668 TAAATGTTAT
*
2403678 TTTTAATTTTTAATTTA
1 TTTTAATTTTTAATATA
2403695 TTTT-ATTTTTAATATA
1 TTTTAATTTTTAATATA
2403711 TT
1 TT
2403713 ACTAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTAATTTTTAATATA
Found at i:2404298 original size:21 final size:22
Alignment explanation
Indices: 2404259--2404306 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2404249 TTATATAATT
*
2404259 ATTTTAAAAAATATTATTTAAA
1 ATTTTAAAAAATATAATTTAAA
* *
2404281 ATTTTAAAATATA-AATTTTAA
1 ATTTTAAAAAATATAATTTAAA
2404302 ATTTT
1 ATTTT
2404307 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTTAAAAAATATAATTTAAA
Found at i:2405977 original size:19 final size:21
Alignment explanation
Indices: 2405953--2405992 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2405943 GTTGGTACTC
2405953 AATTAG-GCAAAAT-ATTTTG
1 AATTAGAGCAAAATAATTTTG
2405972 AATTAGAAGCAAAATAATTTT
1 AATTAG-AGCAAAATAATTTT
2405993 CATTTTTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.35
Consensus pattern (21 bp):
AATTAGAGCAAAATAATTTTG
Found at i:2419054 original size:18 final size:18
Alignment explanation
Indices: 2419028--2419077 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
2419018 GCTATGTAAA
2419028 ATATTATATTTATATTAT
1 ATATTATATTTATATTAT
* ** *
2419046 ATTTTATATAAAAATTAT
1 ATATTATATTTATATTAT
2419064 ATATTATAATTTAT
1 ATATTAT-ATTTAT
2419078 GTTAATATAA
Statistics
Matches: 23, Mismatches: 8, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATTATATTTATATTAT
Done.