Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_pilon, 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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 56 of 62
Found at i:13366753 original size:71 final size:71
Alignment explanation
Indices: 13366656--13366817 Score: 288
Period size: 71 Copynumber: 2.3 Consensus size: 71
13366646 TGGGCTGCAA
* *
13366656 AATAAGATAAGAAATTAATGATTAATAATGGAATTAATAAAGGGGATAATAATATAAGTAATGAA
1 AATAAGA-ATGAAATAAATGATTAATAATGGAATTAATAAAGGGGATAATAATATAAGTAATGAA
13366721 AAGAAAT
65 AAGAAAT
13366728 AATAAGAATGAAATAAATGATTAATAATGGAATTAATAAAGGGGATAATAATATAAGTAATGAAA
1 AATAAGAATGAAATAAATGATTAATAATGGAATTAATAAAGGGGATAATAATATAAGTAATGAAA
13366793 AGAAAT
66 AGAAAT
13366799 AATAAGAATGAAATGAAAT
1 AATAAGAATGAAAT-AAAT
13366818 AAGGATTGGA
Statistics
Matches: 87, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
71 76 0.87
72 11 0.13
ACGTcount: A:0.58, C:0.00, G:0.17, T:0.25
Consensus pattern (71 bp):
AATAAGAATGAAATAAATGATTAATAATGGAATTAATAAAGGGGATAATAATATAAGTAATGAAA
AGAAAT
Found at i:13366808 original size:19 final size:20
Alignment explanation
Indices: 13366780--13366819 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
13366770 GGATAATAAT
13366780 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
13366800 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
13366819 A
1 A
13366820 GGATTGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:13366816 original size:24 final size:24
Alignment explanation
Indices: 13366715--13366816 Score: 68
Period size: 24 Copynumber: 4.3 Consensus size: 24
13366705 TAATATAAGT
13366715 AATGAAAAGAAATAATAAGAATGA
1 AATGAAAAGAAATAATAAGAATGA
* * *
13366739 AAT-AAATGATTAATAAT-GGAAT-T
1 AATGAAAAGA--AATAATAAGAATGA
* ** * * *
13366762 AAT-AAAGGGGATAATAATATAAGT
1 AATGAAAAGAAATAATAAGA-ATGA
13366786 AATGAAAAGAAATAATAAGAATGA
1 AATGAAAAGAAATAATAAGAATGA
13366810 AATGAAA
1 AATGAAA
13366817 TAAGGATTGG
Statistics
Matches: 57, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
21 5 0.09
22 1 0.02
23 13 0.23
24 20 0.35
25 18 0.32
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.23
Consensus pattern (24 bp):
AATGAAAAGAAATAATAAGAATGA
Found at i:13367272 original size:19 final size:21
Alignment explanation
Indices: 13367228--13367280 Score: 74
Period size: 19 Copynumber: 2.6 Consensus size: 21
13367218 GAAACCCCTT
13367228 TGAAAATACATGATTTTTTAAA
1 TGAAAATACATGA-TTTTTAAA
13367250 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
13367269 TGAAGATACATG
1 TGAAAATACATG
13367281 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
22 13 0.43
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:13376425 original size:17 final size:17
Alignment explanation
Indices: 13376405--13376437 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
13376395 TTATATTCTG
13376405 ATTTTTTTTCTTTTTGT
1 ATTTTTTTTCTTTTTGT
13376422 ATTTTTTTTCTTTTTG
1 ATTTTTTTTCTTTTTG
13376438 CACTCCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.82
Consensus pattern (17 bp):
ATTTTTTTTCTTTTTGT
Found at i:13376776 original size:61 final size:67
Alignment explanation
Indices: 13376640--13376785 Score: 207
Period size: 61 Copynumber: 2.3 Consensus size: 67
13376630 TGGGCTGCAA
* *
13376640 AATAAGATAAGAAAGGAATGATTAATAATGGAATTAATAAAGGGGATAATAATAGTAATGAAAGA
1 AATAAGA-ATGAAATGAATGATTAATAATGGAATTAATAAAGGGGATAATAATAGTAATGAAAGA
13376705 AAT
65 AAT
13376708 AATAAGAATG-AATGAATGATTAAT-ATGGAATTAAT-AA-GGGATAAT-ATA-T-ATGAAAAGA
1 AATAAGAATGAAATGAATGATTAATAATGGAATTAATAAAGGGGATAATAATAGTAATG-AAAGA
13376766 AAT
65 AAT
13376769 AATAAGAATGAAATGAA
1 AATAAGAATGAAATGAA
13376786 ATAAGGATGG
Statistics
Matches: 74, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
60 3 0.04
61 19 0.26
62 9 0.12
63 8 0.11
64 2 0.03
65 11 0.15
66 13 0.18
67 2 0.03
68 7 0.09
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.25
Consensus pattern (67 bp):
AATAAGAATGAAATGAATGATTAATAATGGAATTAATAAAGGGGATAATAATAGTAATGAAAGAA
AT
Found at i:13381162 original size:12 final size:13
Alignment explanation
Indices: 13381144--13381173 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
13381134 ATTTTTGGAA
13381144 ATTTTGGCTTTTT
1 ATTTTGGCTTTTT
13381157 -TTTTGGCTTTTT
1 ATTTTGGCTTTTT
13381169 ATTTT
1 ATTTT
13381174 TTGAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.07, C:0.07, G:0.13, T:0.73
Consensus pattern (13 bp):
ATTTTGGCTTTTT
Found at i:13387137 original size:19 final size:21
Alignment explanation
Indices: 13387093--13387145 Score: 74
Period size: 19 Copynumber: 2.6 Consensus size: 21
13387083 GAAACCCCTT
13387093 TGAAAATACATGATTTTTTAAA
1 TGAAAATACATGA-TTTTTAAA
13387115 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
13387134 TGAAGATACATG
1 TGAAAATACATG
13387146 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
22 13 0.43
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:13390591 original size:24 final size:24
Alignment explanation
Indices: 13390563--13390664 Score: 77
Period size: 24 Copynumber: 4.3 Consensus size: 24
13390553 AAGGAATTTT
13390563 TAATAATGGAATTAATAAAGGGGA
1 TAATAATGGAATTAATAAAGGGGA
** * * **
13390587 TAATAATATAAGTAATGAAAAGAAA
1 TAATAATGGAATTAAT-AAAGGGGA
* *
13390612 TAATAA--GAATGAAATAAA--TGA
1 TAATAATGGAAT-TAATAAAGGGGA
13390633 TTAATAATGGAATTAATAAAGGGGA
1 -TAATAATGGAATTAATAAAGGGGA
13390658 TAATAAT
1 TAATAAT
13390665 ATAAGTAATG
Statistics
Matches: 58, Mismatches: 13, Indels: 14
0.68 0.15 0.16
Matches are distributed among these distances:
21 1 0.02
22 6 0.10
23 11 0.19
24 27 0.47
25 13 0.22
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (24 bp):
TAATAATGGAATTAATAAAGGGGA
Found at i:13390639 original size:71 final size:72
Alignment explanation
Indices: 13390562--13390702 Score: 275
Period size: 71 Copynumber: 2.0 Consensus size: 72
13390552 AAAGGAATTT
13390562 TTAATAATGGAATTAATAAAGGGGATAATAATATAAGTAATGAAAAGAAATAATAAGAATGAAAT
1 TTAATAATGGAATTAATAAAGGGGATAATAATATAAGTAATGAAAAGAAATAATAAGAATGAAAT
13390627 -AAATGA
66 GAAATGA
13390633 TTAATAATGGAATTAATAAAGGGGATAATAATATAAGTAATGAAAAGAAATAATAAGAATGAAAT
1 TTAATAATGGAATTAATAAAGGGGATAATAATATAAGTAATGAAAAGAAATAATAAGAATGAAAT
13390698 GAAAT
66 GAAAT
13390703 AAGGATGGGA
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 65 0.94
72 4 0.06
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.26
Consensus pattern (72 bp):
TTAATAATGGAATTAATAAAGGGGATAATAATATAAGTAATGAAAAGAAATAATAAGAATGAAAT
GAAATGA
Found at i:13390693 original size:19 final size:20
Alignment explanation
Indices: 13390665--13390704 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
13390655 GGATAATAAT
13390665 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
13390685 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
13390704 A
1 A
13390705 GGATGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:13390701 original size:24 final size:24
Alignment explanation
Indices: 13390600--13390701 Score: 68
Period size: 24 Copynumber: 4.3 Consensus size: 24
13390590 TAATATAAGT
13390600 AATGAAAAGAAATAATAAGAATGA
1 AATGAAAAGAAATAATAAGAATGA
* * *
13390624 AAT-AAATGATTAATAAT-GGAAT-T
1 AATGAAAAGA--AATAATAAGAATGA
* ** * * *
13390647 AAT-AAAGGGGATAATAATATAAGT
1 AATGAAAAGAAATAATAAGA-ATGA
13390671 AATGAAAAGAAATAATAAGAATGA
1 AATGAAAAGAAATAATAAGAATGA
13390695 AATGAAA
1 AATGAAA
13390702 TAAGGATGGG
Statistics
Matches: 57, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
21 5 0.09
22 1 0.02
23 13 0.23
24 20 0.35
25 18 0.32
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.23
Consensus pattern (24 bp):
AATGAAAAGAAATAATAAGAATGA
Found at i:13391162 original size:19 final size:21
Alignment explanation
Indices: 13391118--13391170 Score: 74
Period size: 19 Copynumber: 2.6 Consensus size: 21
13391108 GAAACCCCTT
13391118 TGAAAATACATGATTTTTTAAA
1 TGAAAATACATGA-TTTTTAAA
13391140 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
13391159 TGAAGATACATG
1 TGAAAATACATG
13391171 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
22 13 0.43
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:13393477 original size:13 final size:13
Alignment explanation
Indices: 13393459--13393484 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13393449 ACTATATGTT
13393459 CATCACCATTTTC
1 CATCACCATTTTC
13393472 CATCACCATTTTC
1 CATCACCATTTTC
13393485 ACGCCTATAA
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:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (13 bp):
CATCACCATTTTC
Found at i:13394240 original size:17 final size:17
Alignment explanation
Indices: 13394218--13394250 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13394208 ATCCTACCCC
13394218 TATACCATAACCATTTA
1 TATACCATAACCATTTA
*
13394235 TATACCCTAACCATTT
1 TATACCATAACCATTT
13394251 TTTTAAGCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.36
Consensus pattern (17 bp):
TATACCATAACCATTTA
Found at i:13397990 original size:15 final size:17
Alignment explanation
Indices: 13397954--13397987 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
13397944 TTTGATATCA
13397954 TTTC-TATCTATTTCCT
1 TTTCTTATCTATTTCCT
13397970 TTTCTTATC-ATTTCCT
1 TTTCTTATCTATTTCCT
13397986 TT
1 TT
13397988 CTTCTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCTTATCTATTTCCT
Found at i:13404712 original size:11 final size:13
Alignment explanation
Indices: 13404680--13404709 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
13404670 TGGCCAAAGA
13404680 TGAAAAGGTATGT
1 TGAAAAGGTATGT
13404693 TGAAAAGGTATG-
1 TGAAAAGGTATGT
13404705 TGAAA
1 TGAAA
13404710 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:13407651 original size:19 final size:19
Alignment explanation
Indices: 13407609--13407719 Score: 56
Period size: 19 Copynumber: 6.1 Consensus size: 19
13407599 TATGCCATCC
*
13407609 TTATTTCATTTCATTCTTA
1 TTATTTCATTTCATTATTA
*
13407628 TTATTTCTTTTCATTAATTA
1 TTATTTCATTTCATT-ATTA
* **
13407648 -TATTATTATCCCA-T-TTA
1 TTATT-TCATTTCATTATTA
* **
13407665 TTAATTCCGTT-ATTA--A
1 TTATTTCATTTCATTATTA
* *
13407681 TCA-TTCATTTCATTCTTA
1 TTATTTCATTTCATTATTA
13407699 TTATTTCATTTCATTACTTA
1 TTATTTCATTTCATTA-TTA
13407719 T
1 T
13407720 ATTATTATCC
Statistics
Matches: 64, Mismatches: 18, Indels: 19
0.63 0.18 0.19
Matches are distributed among these distances:
15 5 0.08
16 7 0.11
17 5 0.08
18 6 0.09
19 30 0.47
20 11 0.17
ACGTcount: A:0.25, C:0.15, G:0.01, T:0.59
Consensus pattern (19 bp):
TTATTTCATTTCATTATTA
Found at i:13413798 original size:20 final size:20
Alignment explanation
Indices: 13413773--13413810 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
13413763 CATTCATTAA
13413773 CTCATGTCATGTTATTCTAG
1 CTCATGTCATGTTATTCTAG
13413793 CTCATGTCATGTTATTCT
1 CTCATGTCATGTTATTCT
13413811 TCATTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.47
Consensus pattern (20 bp):
CTCATGTCATGTTATTCTAG
Found at i:13414288 original size:19 final size:19
Alignment explanation
Indices: 13414246--13414285 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
13414236 TATCCCATCC
*
13414246 TTATTTCATTTCATTCTTA
1 TTATTTCATTTCATTATTA
*
13414265 TTATTTCTTTTCATTAATTA
1 TTATTTCATTTCATT-ATTA
13414285 T
1 T
13414286 ATTATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTTCATTTCATTATTA
Found at i:13414313 original size:24 final size:24
Alignment explanation
Indices: 13414262--13414387 Score: 78
Period size: 24 Copynumber: 5.2 Consensus size: 24
13414252 CATTTCATTC
* * *
13414262 TTATTATTTCTTTTCATTAATTATA
1 TTATTATTCCCTTT-ATTAATTACA
*
13414287 TTATTATTCCCTTTATTAATTCCA
1 TTATTATTCCCTTTATTAATTACA
* * * *
13414311 TTATTAAT-CATTCATTTCATT-C-
1 TTATTATTCCCTTTA-TTAATTACA
** * *
13414333 TTATTATTTCTTTTTATTACTTATA
1 TTATTA-TTCCCTTTATTAATTACA
* *
13414358 TTATTATCCCCTTTATTAATTCCA
1 TTATTATTCCCTTTATTAATTACA
13414382 TTATTA
1 TTATTA
13414388 ATCATTCCTT
Statistics
Matches: 75, Mismatches: 21, Indels: 11
0.70 0.20 0.10
Matches are distributed among these distances:
22 6 0.08
23 10 0.13
24 41 0.55
25 18 0.24
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (24 bp):
TTATTATTCCCTTTATTAATTACA
Found at i:13414370 original size:71 final size:71
Alignment explanation
Indices: 13414250--13414409 Score: 266
Period size: 71 Copynumber: 2.2 Consensus size: 71
13414240 CCATCCTTAT
*
13414250 TTCATTTCATTCTTATTATTTCTTTTCATTAATTATATTATTATTCCCTTTATTAATTCCATTAT
1 TTCATTTCATTCTTATTATTTCTTTTCATTAATTATATTATTATCCCCTTTATTAATTCCATTAT
13414315 TAATCA
66 TAATCA
* *
13414321 TTCATTTCATTCTTATTATTTCTTTTTATTACTTATATTATTATCCCCTTTATTAATTCCATTAT
1 TTCATTTCATTCTTATTATTTCTTTTCATTAATTATATTATTATCCCCTTTATTAATTCCATTAT
13414386 TAATCA
66 TAATCA
* *
13414392 TTCCTTTCTTATCTTATT
1 TTCATTTCAT-TCTTATT
13414410 TTGCAGCCCA
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 76 0.92
72 7 0.08
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (71 bp):
TTCATTTCATTCTTATTATTTCTTTTCATTAATTATATTATTATCCCCTTTATTAATTCCATTAT
TAATCA
Found at i:13417244 original size:20 final size:20
Alignment explanation
Indices: 13417219--13417256 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
13417209 CATTCATTAA
13417219 CTCATGTCATGTTATTCTAG
1 CTCATGTCATGTTATTCTAG
13417239 CTCATGTCATGTTATTCT
1 CTCATGTCATGTTATTCT
13417257 TCATTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.47
Consensus pattern (20 bp):
CTCATGTCATGTTATTCTAG
Found at i:13417734 original size:19 final size:19
Alignment explanation
Indices: 13417692--13417731 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
13417682 TATCCCATCC
*
13417692 TTATTTCATTTCATTCTTA
1 TTATTTCATTTCATTATTA
*
13417711 TTATTTCTTTTCATTAATTA
1 TTATTTCATTTCATT-ATTA
13417731 T
1 T
13417732 ATTATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTTCATTTCATTATTA
Found at i:13417759 original size:24 final size:24
Alignment explanation
Indices: 13417708--13417833 Score: 78
Period size: 24 Copynumber: 5.2 Consensus size: 24
13417698 CATTTCATTC
* * *
13417708 TTATTATTTCTTTTCATTAATTATA
1 TTATTATTCCCTTT-ATTAATTACA
*
13417733 TTATTATTCCCTTTATTAATTCCA
1 TTATTATTCCCTTTATTAATTACA
* * * *
13417757 TTATTAAT-CATTCATTTCATT-C-
1 TTATTATTCCCTTTA-TTAATTACA
** * *
13417779 TTATTATTTCTTTTTATTACTTATA
1 TTATTA-TTCCCTTTATTAATTACA
* *
13417804 TTATTATCCCCTTTATTAATTCCA
1 TTATTATTCCCTTTATTAATTACA
13417828 TTATTA
1 TTATTA
13417834 ATCATTCCTT
Statistics
Matches: 75, Mismatches: 21, Indels: 11
0.70 0.20 0.10
Matches are distributed among these distances:
22 6 0.08
23 10 0.13
24 41 0.55
25 18 0.24
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (24 bp):
TTATTATTCCCTTTATTAATTACA
Found at i:13417816 original size:71 final size:71
Alignment explanation
Indices: 13417696--13417855 Score: 266
Period size: 71 Copynumber: 2.2 Consensus size: 71
13417686 CCATCCTTAT
*
13417696 TTCATTTCATTCTTATTATTTCTTTTCATTAATTATATTATTATTCCCTTTATTAATTCCATTAT
1 TTCATTTCATTCTTATTATTTCTTTTCATTAATTATATTATTATCCCCTTTATTAATTCCATTAT
13417761 TAATCA
66 TAATCA
* *
13417767 TTCATTTCATTCTTATTATTTCTTTTTATTACTTATATTATTATCCCCTTTATTAATTCCATTAT
1 TTCATTTCATTCTTATTATTTCTTTTCATTAATTATATTATTATCCCCTTTATTAATTCCATTAT
13417832 TAATCA
66 TAATCA
* *
13417838 TTCCTTTCTTATCTTATT
1 TTCATTTCAT-TCTTATT
13417856 TTGCAGCCCA
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 76 0.92
72 7 0.08
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (71 bp):
TTCATTTCATTCTTATTATTTCTTTTCATTAATTATATTATTATCCCCTTTATTAATTCCATTAT
TAATCA
Found at i:13420684 original size:20 final size:20
Alignment explanation
Indices: 13420659--13420696 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
13420649 CATTCATTAA
13420659 CTCATGTCATGTTATTCTAG
1 CTCATGTCATGTTATTCTAG
13420679 CTCATGTCATGTTATTCT
1 CTCATGTCATGTTATTCT
13420697 TCATTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.47
Consensus pattern (20 bp):
CTCATGTCATGTTATTCTAG
Found at i:13421252 original size:71 final size:71
Alignment explanation
Indices: 13421136--13421295 Score: 257
Period size: 71 Copynumber: 2.2 Consensus size: 71
13421126 CCATCCTTAT
*
13421136 TTCATTTTATTCTTATTATCTCTTTTCATTACTTATATTATTATCCCCTTTACTAATTCCATTAG
1 TTCATTTCATTCTTATTATCTCTTTTCATTACTTATATTATTATCCCCTTTACTAATTCCATTAG
13421201 TAATCA
66 TAATCA
* * *
13421207 TTCATTTCATTCTTATTATTTCTTTTCATTACTTATATTATTATCCCCTTTATTAATTCCATTAT
1 TTCATTTCATTCTTATTATCTCTTTTCATTACTTATATTATTATCCCCTTTACTAATTCCATTAG
13421272 TAATCA
66 TAATCA
* *
13421278 TTCCTTTCTTATCTTATT
1 TTCATTTCAT-TCTTATT
13421296 TTGCAGCCCA
Statistics
Matches: 82, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
71 75 0.91
72 7 0.09
ACGTcount: A:0.24, C:0.19, G:0.01, T:0.56
Consensus pattern (71 bp):
TTCATTTCATTCTTATTATCTCTTTTCATTACTTATATTATTATCCCCTTTACTAATTCCATTAG
TAATCA
Found at i:13421536 original size:26 final size:26
Alignment explanation
Indices: 13421507--13421556 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
13421497 GCAAAAAGAA
13421507 AGAAAAGACA-AAAAGAAAAAAAAATC
1 AGAAAAGA-AGAAAAGAAAAAAAAATC
*
13421533 AGAATAGAAGAAAAGAAAAAAAAA
1 AGAAAAGAAGAAAAGAAAAAAAAA
13421557 GAATTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.78, C:0.04, G:0.14, T:0.04
Consensus pattern (26 bp):
AGAAAAGAAGAAAAGAAAAAAAAATC
Found at i:13422290 original size:35 final size:36
Alignment explanation
Indices: 13422250--13422317 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
13422240 AATTAGAAGT
13422250 TGGTGATAATATAGGCGTGAT-ATAGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATAGTGATGGAATA
* *
13422285 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATAGTGATGGA
13422318 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 20 0.67
36 10 0.33
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATAGTGATGGAATA
Found at i:13425909 original size:12 final size:12
Alignment explanation
Indices: 13425892--13425928 Score: 65
Period size: 12 Copynumber: 3.0 Consensus size: 12
13425882 GGTAACTGGA
13425892 AGTAGCTGGGAG
1 AGTAGCTGGGAG
13425904 AGTAGCTGGGAG
1 AGTAGCTGGGAG
13425916 AGTAGCTGAGGAG
1 AGTAGCTG-GGAG
13425929 CTGAGAAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.27, C:0.08, G:0.49, T:0.16
Consensus pattern (12 bp):
AGTAGCTGGGAG
Found at i:13438407 original size:11 final size:11
Alignment explanation
Indices: 13438391--13438441 Score: 75
Period size: 11 Copynumber: 4.6 Consensus size: 11
13438381 TATTTTTTTT
*
13438391 CAAAAAATAAA
1 CAAAAAAAAAA
**
13438402 CAAAAAAAAGG
1 CAAAAAAAAAA
13438413 CAAAAAAAAAA
1 CAAAAAAAAAA
13438424 CAAAAAAAAAA
1 CAAAAAAAAAA
13438435 CAAAAAA
1 CAAAAAA
13438442 GCCAAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.84, C:0.10, G:0.04, T:0.02
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:13440122 original size:21 final size:21
Alignment explanation
Indices: 13440082--13440123 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13440072 TTCGAGAACA
* *
13440082 TTACCAAGGTACTTCATCCTC
1 TTACCAAGGTAATCCATCCTC
*
13440103 TTACCAAGGTAATCCTTCCTC
1 TTACCAAGGTAATCCATCCTC
13440124 GTCTTCTGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.33, G:0.10, T:0.33
Consensus pattern (21 bp):
TTACCAAGGTAATCCATCCTC
Found at i:13457604 original size:22 final size:21
Alignment explanation
Indices: 13457572--13457616 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
13457562 TGTATGAGTC
* *
13457572 TTTTTCTTTTCTTTTTGTTTT
1 TTTTTCTTTTCTTGTTGCTTT
13457593 TTTTTCTCTTTCTTGTTGCTTT
1 TTTTTCT-TTTCTTGTTGCTTT
13457615 TT
1 TT
13457617 GTTGTAGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (21 bp):
TTTTTCTTTTCTTGTTGCTTT
Found at i:13459735 original size:9 final size:9
Alignment explanation
Indices: 13459721--13459794 Score: 55
Period size: 9 Copynumber: 8.0 Consensus size: 9
13459711 TTTTTTTTTC
13459721 AAAACAAAA
1 AAAACAAAA
13459730 AAAACAAAA
1 AAAACAAAA
13459739 AAAA-AAGGCAA
1 AAAACAA---AA
*
13459750 AAAA-AAAT
1 AAAACAAAA
*
13459758 CAAA-AAAA
1 AAAACAAAA
13459766 AAAACAAAA
1 AAAACAAAA
13459775 AAAAGCCAAAA
1 AAAA--CAAAA
*
13459786 AAACCAAAA
1 AAAACAAAA
13459795 TTTAAAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
8 12 0.22
9 26 0.48
11 16 0.30
ACGTcount: A:0.82, C:0.12, G:0.04, T:0.01
Consensus pattern (9 bp):
AAAACAAAA
Found at i:13459742 original size:11 final size:11
Alignment explanation
Indices: 13459726--13459788 Score: 72
Period size: 11 Copynumber: 5.5 Consensus size: 11
13459716 TTTTCAAAAC
13459726 AAAAAAAACAA
1 AAAAAAAACAA
13459737 AAAAAAAAGGCAA
1 AAAAAAAA--CAA
*
13459750 AAAAAAATCAAA
1 AAAAAAAAC-AA
13459762 AAAAAAAACAA
1 AAAAAAAACAA
**
13459773 AAAAAAGCCAA
1 AAAAAAAACAA
13459784 AAAAA
1 AAAAA
13459789 CCAAAATTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
11 25 0.56
12 10 0.22
13 10 0.22
ACGTcount: A:0.84, C:0.10, G:0.05, T:0.02
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:13459743 original size:12 final size:12
Alignment explanation
Indices: 13459726--13459778 Score: 72
Period size: 12 Copynumber: 4.4 Consensus size: 12
13459716 TTTTCAAAAC
13459726 AAAAAAAACAAA
1 AAAAAAAACAAA
*
13459738 AAAAAAAGGC-AA
1 AAAAAAA-ACAAA
*
13459750 AAAAAAATCAAA
1 AAAAAAAACAAA
13459762 AAAAAAAACAAA
1 AAAAAAAACAAA
13459774 AAAAA
1 AAAAA
13459779 GCCAAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
11 1 0.03
12 34 0.94
13 1 0.03
ACGTcount: A:0.87, C:0.08, G:0.04, T:0.02
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:13459744 original size:13 final size:13
Alignment explanation
Indices: 13459720--13459778 Score: 61
Period size: 13 Copynumber: 4.7 Consensus size: 13
13459710 GTTTTTTTTT
13459720 CAAAACAAAAAAAA
1 CAAAA-AAAAAAAA
**
13459734 CAAAAAAAAAAGG
1 CAAAAAAAAAAAA
*
13459747 C--AAAAAAAAAT
1 CAAAAAAAAAAAA
13459758 C-AAAAAAAAAAA
1 CAAAAAAAAAAAA
13459770 CAAAAAAAA
1 CAAAAAAAA
13459779 GCCAAAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
11 9 0.24
12 10 0.26
13 14 0.37
14 5 0.13
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.02
Consensus pattern (13 bp):
CAAAAAAAAAAAA
Found at i:13459756 original size:23 final size:22
Alignment explanation
Indices: 13459721--13459788 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 22
13459711 TTTTTTTTTC
13459721 AAAAC-AAAAAAAACAAAAAAA
1 AAAACAAAAAAAAACAAAAAAA
*
13459742 AAAGGCAAAAAAAAATCAAAAAAA
1 AAA-ACAAAAAAAAA-CAAAAAAA
* *
13459766 AAAACAAAAAAAAGCCAAAAAA
1 AAAACAAAAAAAAACAAAAAAA
13459788 A
1 A
13459789 CCAAAATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 3 0.08
22 9 0.22
23 17 0.43
24 11 0.28
ACGTcount: A:0.84, C:0.10, G:0.04, T:0.01
Consensus pattern (22 bp):
AAAACAAAAAAAAACAAAAAAA
Found at i:13474382 original size:90 final size:91
Alignment explanation
Indices: 13474229--13474401 Score: 251
Period size: 90 Copynumber: 1.9 Consensus size: 91
13474219 AGGAAATGAT
* *
13474229 GCTTGGCTGAATAGGGAGAAAGCTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACAT-
1 GCTTGGCTGAATAGGGAGAAAACTCTTCATATTGGCGCCTAAATAAACCACATGCAAGGCACATG
*
13474293 GAGGCTGTTCACATGCAAAATACATG
66 GAGGCTGGTCACATGCAAAATACATG
* * *
13474319 GCTTGG-TCGAATAGGGAGAAAACTCTTGATATTGGCGCCTAAATGATCCACATGCAAGGCACAT
1 GCTTGGCT-GAATAGGGAGAAAACTCTTCATATTGGCGCCTAAATAAACCACATGCAAGGCACAT
* *
13474383 GGCGGCTGGTCATATGCAA
65 GGAGGCTGGTCACATGCAA
13474402 GGCACATGGG
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
89 1 0.01
90 57 0.78
91 15 0.21
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (91 bp):
GCTTGGCTGAATAGGGAGAAAACTCTTCATATTGGCGCCTAAATAAACCACATGCAAGGCACATG
GAGGCTGGTCACATGCAAAATACATG
Found at i:13476276 original size:13 final size:13
Alignment explanation
Indices: 13476254--13476283 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
13476244 ACTAAACACC
13476254 TTTC-ACATACCT
1 TTTCAACATACCT
13476266 TTTCAACATACCT
1 TTTCAACATACCT
13476279 TTTCA
1 TTTCA
13476284 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:13485421 original size:15 final size:17
Alignment explanation
Indices: 13485401--13485439 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
13485391 GTGCTTCAAC
13485401 TTTC-TTTCTTTT-TCT
1 TTTCTTTTCTTTTCTCT
13485416 TTTCTTTTCTTTTCTCT
1 TTTCTTTTCTTTTCTCT
13485433 TTT-TTTT
1 TTTCTTTT
13485440 TAAGTGCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.18
16 12 0.55
17 6 0.27
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTCTTTTCTTTTCTCT
Found at i:13485475 original size:28 final size:27
Alignment explanation
Indices: 13485426--13485493 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
13485416 TTTCTTTTCT
* *
13485426 TTTCTCTTTTT-TTTTAAGTGCTGGAA
1 TTTCTTTTTTTCTTTTAAGTGCTGCAA
* *
13485452 TTTCTTTTTTTCTTTTGGAGTGCTTCAA
1 TTTCTTTTTTTCTTTT-AAGTGCTGCAA
*
13485480 TTTCATTTTTTCTT
1 TTTCTTTTTTTCTT
13485494 ATTTTCTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 10 0.29
27 4 0.11
28 21 0.60
ACGTcount: A:0.12, C:0.13, G:0.12, T:0.63
Consensus pattern (27 bp):
TTTCTTTTTTTCTTTTAAGTGCTGCAA
Found at i:13485644 original size:5 final size:5
Alignment explanation
Indices: 13485630--13485659 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
13485620 GTGCTTCAAC
13485630 TTTC- TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
13485660 CTTTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:13485666 original size:15 final size:15
Alignment explanation
Indices: 13485629--13485666 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
13485619 AGTGCTTCAA
13485629 CTTTCTTTCTTTTCTT
1 CTTT-TTTCTTTTCTT
13485645 -TTCTTTTCTTTTCTT
1 CTT-TTTTCTTTTCTT
13485660 CTTTTTT
1 CTTTTTT
13485667 TTAAGTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
CTTTTTTCTTTTCTT
Found at i:13485701 original size:229 final size:225
Alignment explanation
Indices: 13485295--13485748 Score: 840
Period size: 229 Copynumber: 2.0 Consensus size: 225
13485285 AAGAAGAGAA
13485295 ATAAAAGGGTTACTTACACAAGTCACTTCCACCTTCTATCACCACAATCAGTTTAAAAGGCTTAC
1 ATAAAAGGGTTACTTACACAAGTCACTTCCACCTTCTATCACCACAATCAGTTTAAAAGGCTTAC
13485360 TTGAAAAGGCATGGTGATGAATTGTTGATGAGTGCTTCAACTTTCTTTCTTTTTCTTTTCTTTTC
66 TTGAAAAGGCATGGTGATGAATTGTTGATGAGTGCTTCAACTTTCTTTCTTTTTCTTTTCTTTTC
13485425 TTTTCTCTTTTTTTTTAAGTGCTGGAATTTCTTTTTTTCTTTTGGAGTGCTTCAATTTCATTTTT
131 TTTTCTCTTTTTTTTTAAGTGCTGGAATTTCTTTTTTTCTTTTGGAGTGCTTCAATTTCATTTTT
13485490 TCTTATTTTCTTTTTCTTTGACTTAGCACT
196 TCTTATTTTCTTTTTCTTTGACTTAGCACT
13485520 ATAAAAGGGTTACTTACACAAGTCACTTCACAACCTTCTATCACCACAATCAGTTTAAAAGGCTT
1 ATAAAAGGGTTACTTACACAAGTCACTTC-C-ACCTTCTATCACCACAATCAGTTTAAAAGGCTT
13485585 ACTTGAAAAGGCATGGTGATGAGAATTGTTGATGAGTGCTTCAACTTTCTTTC-TTTTCTTTTCT
64 ACTTGAAAAGGCATGGTGAT--GAATTGTTGATGAGTGCTTCAACTTTCTTTCTTTTTCTTTTCT
13485649 TTTCTTTTCT-TCTTTTTTTTAAGTGCTGGAATTTCTTTTTTTTCTTTTGGAGTGCTTCAATTTC
127 TTTCTTTTCTCT-TTTTTTTTAAGTGCTGGAATTTC-TTTTTTTCTTTTGGAGTGCTTCAATTTC
13485713 ATTTTTTCTTATTTTCTTTTTCTTTGACTTAGCACT
190 ATTTTTTCTTATTTTCTTTTTCTTTGACTTAGCACT
13485749 TTACTTTGCA
Statistics
Matches: 223, Mismatches: 0, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
225 29 0.13
226 1 0.00
227 54 0.24
228 44 0.20
229 95 0.43
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (225 bp):
ATAAAAGGGTTACTTACACAAGTCACTTCCACCTTCTATCACCACAATCAGTTTAAAAGGCTTAC
TTGAAAAGGCATGGTGATGAATTGTTGATGAGTGCTTCAACTTTCTTTCTTTTTCTTTTCTTTTC
TTTTCTCTTTTTTTTTAAGTGCTGGAATTTCTTTTTTTCTTTTGGAGTGCTTCAATTTCATTTTT
TCTTATTTTCTTTTTCTTTGACTTAGCACT
Found at i:13486610 original size:10 final size:10
Alignment explanation
Indices: 13486595--13486624 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
13486585 ATAACAGCAT
13486595 ATTCAGCTAC
1 ATTCAGCTAC
13486605 ATTCAGCTAC
1 ATTCAGCTAC
13486615 ATTCAGCTAC
1 ATTCAGCTAC
13486625 CTTTAACATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (10 bp):
ATTCAGCTAC
Found at i:13490917 original size:15 final size:16
Alignment explanation
Indices: 13490887--13490920 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
13490877 TTAAAGCTAG
13490887 TGAGCTAAACATAACA
1 TGAGCTAAACATAACA
*
13490903 TGAGCTAGA-ATAACA
1 TGAGCTAAACATAACA
13490918 TGA
1 TGA
13490921 CATGAGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.21
Consensus pattern (16 bp):
TGAGCTAAACATAACA
Found at i:13492534 original size:23 final size:23
Alignment explanation
Indices: 13492489--13492534 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
13492479 TTATACCTAT
*
13492489 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
13492512 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
13492535 TATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:13495825 original size:23 final size:23
Alignment explanation
Indices: 13495780--13495825 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
13495770 TTATACCTAT
*
13495780 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
13495803 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
13495826 TAGTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:13519685 original size:19 final size:18
Alignment explanation
Indices: 13519633--13519686 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
13519623 GTGTTGCAAC
* *
13519633 AAAAGAAACAAAAAGAGA
1 AAAAGAAAAAAAAAAAGA
*
13519651 AAAACAAAAAACAAAAAGA
1 AAAAGAAAAAA-AAAAAGA
13519670 AAAAGAAAAGAAAAAAA
1 AAAAGAAAA-AAAAAAA
13519687 CTCCTACATC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 9 0.30
19 19 0.63
20 2 0.07
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAAAAAAAGA
Found at i:13522594 original size:16 final size:16
Alignment explanation
Indices: 13522561--13522609 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
13522551 TAAGGTAATG
13522561 GAATAAGAATAGATGAAA
1 GAATAAGAA-A-ATGAAA
13522579 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* * *
13522595 TAGTAAGAAAGTGAA
1 GAATAAGAAAATGAA
13522610 GGTAACTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.16
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:13537050 original size:26 final size:24
Alignment explanation
Indices: 13536996--13537064 Score: 59
Period size: 24 Copynumber: 2.8 Consensus size: 24
13536986 AAATAAAGTG
*
13536996 AAGCACTCAAAAGAAAGAAAAATC
1 AAGCACTCAAAAGAAAGAAAAAGC
*
13537020 CAGCACTCAAAA-AAAGAAGAAAAGC
1 AAGCACTCAAAAGAAAG-A-AAAAGC
***
13537045 AAAGCAAAGAAAAGAAAGAA
1 -AAGCACTCAAAAGAAAGAA
13537065 GTTGAAGCAC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
23 4 0.11
24 12 0.34
25 6 0.17
26 9 0.26
27 4 0.11
ACGTcount: A:0.65, C:0.14, G:0.16, T:0.04
Consensus pattern (24 bp):
AAGCACTCAAAAGAAAGAAAAAGC
Found at i:13542181 original size:15 final size:15
Alignment explanation
Indices: 13542161--13542197 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
13542151 AGCCCACCTA
13542161 ATCACCCATACATTT
1 ATCACCCATACATTT
13542176 ATCACCCATACATTT
1 ATCACCCATACATTT
*
13542191 ACCACCC
1 ATCACCC
13542198 CTAACCATTC
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:0.32, C:0.41, G:0.00, T:0.27
Consensus pattern (15 bp):
ATCACCCATACATTT
Found at i:13546858 original size:21 final size:21
Alignment explanation
Indices: 13546833--13546875 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
13546823 ATAAATTATA
13546833 CTTGATAAGTCGATAAAAAGT
1 CTTGATAAGTCGATAAAAAGT
13546854 CTTGATAAGTCGATAAAAAGT
1 CTTGATAAGTCGATAAAAAGT
13546875 C
1 C
13546876 ACCATGACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28
Consensus pattern (21 bp):
CTTGATAAGTCGATAAAAAGT
Found at i:13550662 original size:15 final size:15
Alignment explanation
Indices: 13550627--13550655 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13550617 GTGCTTCAAC
13550627 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
13550641 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
13550656 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:13554875 original size:18 final size:18
Alignment explanation
Indices: 13554852--13554888 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
13554842 CTCGTTGCCA
13554852 TGTAAATGGTAAAGAATG
1 TGTAAATGGTAAAGAATG
*
13554870 TGTAAATGGTAAAGTATG
1 TGTAAATGGTAAAGAATG
13554888 T
1 T
13554889 CTTGTAGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (18 bp):
TGTAAATGGTAAAGAATG
Found at i:13555596 original size:24 final size:25
Alignment explanation
Indices: 13555545--13555610 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
13555535 GTCATTTCTT
* *
13555545 TTAAAATTCCAA-AAGATGTGTCAC
1 TTAAAATTCAAAGAACATGTGTCAC
13555569 TTAAAATTACAAAGAACATGT-TCA-
1 TTAAAATT-CAAAGAACATGTGTCAC
**
13555593 TTAACCTTCAAAGAACAT
1 TTAAAATTCAAAGAACAT
13555611 TCGCCTCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 10 0.28
24 14 0.39
25 6 0.17
26 6 0.17
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.29
Consensus pattern (25 bp):
TTAAAATTCAAAGAACATGTGTCAC
Found at i:13556842 original size:14 final size:14
Alignment explanation
Indices: 13556814--13556844 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13556804 AGGATTCAAC
13556814 CATGAAGATTCATT
1 CATGAAGATTCATT
*
13556828 CATGAAGATTTATT
1 CATGAAGATTCATT
13556842 CAT
1 CAT
13556845 TAATTCATCA
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:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (14 bp):
CATGAAGATTCATT
Found at i:13559026 original size:22 final size:22
Alignment explanation
Indices: 13558992--13559034 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
13558982 AAATCCAGCA
*
13558992 AAGAAAATCAAAGCACTCAAAG
1 AAGAAAATAAAAGCACTCAAAG
*
13559014 AAGAAATTAAAAGCACTCAAA
1 AAGAAAATAAAAGCACTCAAA
13559035 AAGGAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.16, G:0.12, T:0.12
Consensus pattern (22 bp):
AAGAAAATAAAAGCACTCAAAG
Found at i:13559048 original size:21 final size:22
Alignment explanation
Indices: 13559001--13559049 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
13558991 AAAGAAAATC
**
13559001 AAAGCACTCAAAGAAGAAATTA
1 AAAGCACTCAAAGAAGAAAGAA
*
13559023 AAAGCACTCAAA-AAGGAAGAA
1 AAAGCACTCAAAGAAGAAAGAA
13559044 AAAGCA
1 AAAGCA
13559050 AAGAAAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.61, C:0.14, G:0.16, T:0.08
Consensus pattern (22 bp):
AAAGCACTCAAAGAAGAAAGAA
Found at i:13564062 original size:23 final size:23
Alignment explanation
Indices: 13564031--13564081 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
13564021 TAAGGTTGGG
*
13564031 TCTTTGCTCTTTATAGCACAGGT
1 TCTTCGCTCTTTATAGCACAGGT
*
13564054 TCTTCGCTCTTTATAGCACTGGT
1 TCTTCGCTCTTTATAGCACAGGT
13564077 TCTTC
1 TCTTC
13564082 CTTGTTCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.14, C:0.25, G:0.16, T:0.45
Consensus pattern (23 bp):
TCTTCGCTCTTTATAGCACAGGT
Found at i:13571752 original size:19 final size:19
Alignment explanation
Indices: 13571730--13571785 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
13571720 CTCTTTTGAA
13571730 TTTCTTTTTCTTTTCTTTT
1 TTTCTTTTTCTTTTCTTTT
**
13571749 TTTCTGATTC--TTCTTTT
1 TTTCTTTTTCTTTTCTTTT
* *
13571766 TATCTTTTGCTTTTCTTTT
1 TTTCTTTTTCTTTTCTTTT
13571785 T
1 T
13571786 GCACTCCAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
17 13 0.45
19 16 0.55
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.77
Consensus pattern (19 bp):
TTTCTTTTTCTTTTCTTTT
Found at i:13577146 original size:19 final size:20
Alignment explanation
Indices: 13577109--13577146 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
13577099 TGAAAGTAAT
*
13577109 GAAATGGAAAGATAAATATG
1 GAAATGGAAAAATAAATATG
*
13577129 GAAAT-GAAAAATATATAT
1 GAAATGGAAAAATAAATAT
13577147 AAGTTGGTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (20 bp):
GAAATGGAAAAATAAATATG
Found at i:13580866 original size:72 final size:72
Alignment explanation
Indices: 13580744--13580882 Score: 233
Period size: 72 Copynumber: 1.9 Consensus size: 72
13580734 TTCACCACAC
* *
13580744 AGAGGACTACAAATATGGTTTAGGTTAAATTTTATGAATTCACACCTTTTCGCGAAGAGTTGCCA
1 AGAGAACTACAAATATGGTTTAGGTCAAATTTTATGAATTCACACCTTTTCGCGAAGAGTTGCCA
13580809 ATCCGGG
66 ATCCGGG
** *
13580816 AGAGAACTACAAATATGGTTTAGGTCAAATTTTATGAATTCGTACCTTTTCGTGAAGAGTTGCCA
1 AGAGAACTACAAATATGGTTTAGGTCAAATTTTATGAATTCACACCTTTTCGCGAAGAGTTGCCA
13580881 AT
66 AT
13580883 TCGAGAAGTG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (72 bp):
AGAGAACTACAAATATGGTTTAGGTCAAATTTTATGAATTCACACCTTTTCGCGAAGAGTTGCCA
ATCCGGG
Found at i:13581756 original size:35 final size:35
Alignment explanation
Indices: 13581673--13581788 Score: 151
Period size: 35 Copynumber: 3.3 Consensus size: 35
13581663 TACTATATGT
* * * *
13581673 TCATCACCATCTTCCATCACTATTTTCATGCTTATA
1 TCATCACCATCTTCTATCACCA-TTTCACGCCTATA
* * *
13581709 ACATCACTATCTTCTATCACCATTACACGCCTATA
1 TCATCACCATCTTCTATCACCATTTCACGCCTATA
13581744 TCATCACCATCTTCTATCACCATTTCACGCCTATA
1 TCATCACCATCTTCTATCACCATTTCACGCCTATA
*
13581779 TCATCCCCAT
1 TCATCACCAT
13581789 TCCCTTACCA
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
35 51 0.74
36 18 0.26
ACGTcount: A:0.27, C:0.35, G:0.03, T:0.35
Consensus pattern (35 bp):
TCATCACCATCTTCTATCACCATTTCACGCCTATA
Found at i:13584262 original size:30 final size:30
Alignment explanation
Indices: 13584228--13584284 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
13584218 TACAGTTGGG
* *
13584228 TGGAGCATTTTTGGA-AGACAAACAGCTTGT
1 TGGAGCA-TTTGGGAGACACAAACAGCTTGT
13584258 TGGAGCATTTGGGAGACACAAACAGCT
1 TGGAGCATTTGGGAGACACAAACAGCT
13584285 CAGAAGGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.25
Consensus pattern (30 bp):
TGGAGCATTTGGGAGACACAAACAGCTTGT
Found at i:13589379 original size:13 final size:13
Alignment explanation
Indices: 13589361--13589405 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
13589351 CATTCCCATT
*
13589361 TCATCATCATCCA
1 TCATCAACATCCA
*
13589374 TCATCAACATCCT
1 TCATCAACATCCA
*
13589387 TCATCAAGA-CCA
1 TCATCAACATCCA
13589399 TCATCAA
1 TCATCAA
13589406 TTCCATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.27
Consensus pattern (13 bp):
TCATCAACATCCA
Found at i:13589454 original size:18 final size:18
Alignment explanation
Indices: 13589427--13589463 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
13589417 CGCAACCATC
13589427 TCTATCATTTCTT-TATT
1 TCTATCATTTCTTATATT
13589444 TCTATTCATTTCTTATATT
1 TCTA-TCATTTCTTATATT
13589463 T
1 T
13589464 ATTATTTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (18 bp):
TCTATCATTTCTTATATT
Found at i:13589459 original size:17 final size:19
Alignment explanation
Indices: 13589427--13589471 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
13589417 CGCAACCATC
13589427 TCTA-TCATTTCTTTAT-T
1 TCTATTCATTTCTTTATAT
13589444 TCTATTCATTTC-TTATAT
1 TCTATTCATTTCTTTATAT
13589462 T-TATT-ATTTC
1 TCTATTCATTTC
13589472 ACTTATTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.19
17 12 0.46
18 9 0.35
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (19 bp):
TCTATTCATTTCTTTATAT
Found at i:13589747 original size:18 final size:17
Alignment explanation
Indices: 13589722--13589788 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 17
13589712 AAATTGGAGT
13589722 GAAAAAAGAAAAGAAAA
1 GAAAAAAGAAAAGAAAA
13589739 GATAAAAAGAAGAA-AAATTCA
1 GA-AAAAAGAA-AAGAAA---A
13589760 GAAAAGAAGAAAAGAAAA
1 GAAAA-AAGAAAAGAAAA
13589778 G-AAAAAGAAAA
1 GAAAAAAGAAAA
13589789 TCAAAAAGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
16 7 0.16
17 5 0.12
18 13 0.30
19 2 0.05
20 5 0.12
21 11 0.26
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.04
Consensus pattern (17 bp):
GAAAAAAGAAAAGAAAA
Found at i:13589778 original size:31 final size:30
Alignment explanation
Indices: 13589733--13589801 Score: 77
Period size: 34 Copynumber: 2.2 Consensus size: 30
13589723 AAAAAAGAAA
*
13589733 AGAAAAGATAAA-AAGAAGAAAAATTCAGAAAAG
1 AGAAAAGA-AAAGAAAAAG-AAAA-TCA-AAAAG
13589766 AAGAAAAGAAAAGAAAAAGAAAATCAAAAAG
1 -AGAAAAGAAAAGAAAAAGAAAATCAAAAAG
13589797 AGAAA
1 AGAAA
13589802 GCAAGCCAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
30 5 0.15
31 5 0.15
32 3 0.09
33 7 0.21
34 13 0.39
ACGTcount: A:0.74, C:0.03, G:0.17, T:0.06
Consensus pattern (30 bp):
AGAAAAGAAAAGAAAAAGAAAATCAAAAAG
Found at i:13603000 original size:17 final size:17
Alignment explanation
Indices: 13602975--13603016 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
13602965 TAGAATGCTT
*
13602975 ATGGTGTGGACTCCTTC
1 ATGGCGTGGACTCCTTC
13602992 ATGGCGTGGACTCCTTC
1 ATGGCGTGGACTCCTTC
13603009 ATGGCGTG
1 ATGGCGTG
13603017 AAGATGAGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.33, T:0.31
Consensus pattern (17 bp):
ATGGCGTGGACTCCTTC
Found at i:13606279 original size:26 final size:26
Alignment explanation
Indices: 13606249--13606300 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
13606239 ACAACAAGGA
*
13606249 TACCTCCTTCAAGTTTGATGTTGGGC
1 TACCTCCTTCAAGCTTGATGTTGGGC
13606275 TACCTCCTTCAAGCTTGATGTTGGGC
1 TACCTCCTTCAAGCTTGATGTTGGGC
13606301 AGATTGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.37
Consensus pattern (26 bp):
TACCTCCTTCAAGCTTGATGTTGGGC
Found at i:13621835 original size:17 final size:17
Alignment explanation
Indices: 13621813--13621853 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
13621803 GGGCTGAATT
*
13621813 CTAAAGGTCCTAAATAA
1 CTAAAGATCCTAAATAA
13621830 CTAAAGATCCTAAATAA
1 CTAAAGATCCTAAATAA
13621847 CTAAAGA
1 CTAAAGA
13621854 ATAAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.51, C:0.17, G:0.10, T:0.22
Consensus pattern (17 bp):
CTAAAGATCCTAAATAA
Found at i:13624662 original size:13 final size:13
Alignment explanation
Indices: 13624644--13624668 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13624634 TATAGGCGTG
13624644 ATATGGTGATGGA
1 ATATGGTGATGGA
13624657 ATATGGTGATGG
1 ATATGGTGATGG
13624669 TATAGGCTTG
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:0.28, C:0.00, G:0.40, T:0.32
Consensus pattern (13 bp):
ATATGGTGATGGA
Found at i:13629316 original size:6 final size:6
Alignment explanation
Indices: 13629305--13629353 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
13629295 AATTTTAGCT
**
13629305 TTTTTG TTTTTG TTTTTG TTTTT- TTTTTG -CCTT- TTTTTG TTTTT-
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
13629349 TTTTT
1 TTTTT
13629354 AAATAGCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
5 14 0.39
6 22 0.61
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:13629322 original size:12 final size:11
Alignment explanation
Indices: 13629304--13629353 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
13629294 AAATTTTAGC
13629304 TTTTTTGTTTT
1 TTTTTTGTTTT
13629315 TGTTTTTGTTTT
1 T-TTTTTGTTTT
**
13629327 TTTTTTG-CCT
1 TTTTTTGTTTT
13629337 TTTTTTGTTTT
1 TTTTTTGTTTT
13629348 TTTTTT
1 TTTTTT
13629354 AAATAGCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 8 0.24
11 14 0.42
12 11 0.33
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:13631210 original size:23 final size:24
Alignment explanation
Indices: 13631182--13631235 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
13631172 AAAATCAGCA
13631182 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
13631205 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
13631229 AAGAAAA
1 AAGAAAA
13631236 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:13631240 original size:24 final size:23
Alignment explanation
Indices: 13631182--13631241 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
13631172 AAAATCAGCA
13631182 AAGAAAATA-AAAGCACTCAAAAG
1 AAGAAAA-AGAAAGCACTCAAAAG
**
13631205 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
13631229 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
13631242 AAAGAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.63, C:0.10, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:13638149 original size:12 final size:13
Alignment explanation
Indices: 13638123--13638151 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
13638113 ATTGATTGTG
13638123 GTGATAGGAGGTT
1 GTGATAGGAGGTT
13638136 GTGATAGG-GGTT
1 GTGATAGGAGGTT
13638148 GTGA
1 GTGA
13638152 AGTGACTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.21, C:0.00, G:0.48, T:0.31
Consensus pattern (13 bp):
GTGATAGGAGGTT
Found at i:13640624 original size:91 final size:91
Alignment explanation
Indices: 13640442--13640615 Score: 285
Period size: 91 Copynumber: 1.9 Consensus size: 91
13640432 GGTAGTTGAT
*
13640442 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
13640507 GGGGATGATCACATGCAAAACACATG
66 GGGGATGATCACATGCAAAACACATG
* * *
13640533 GCTTGGCTGAATAGGGAGAGAACTTTTCATCTTGGCACCTAAATGACCCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
* * *
13640598 GGGGCTGGTCATATGCAA
66 GGGGATGATCACATGCAA
13640616 GGCGCATGGG
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 76 1.00
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
GGGGATGATCACATGCAAAACACATG
Found at i:13649514 original size:14 final size:14
Alignment explanation
Indices: 13649495--13649522 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13649485 GATGATGGAG
13649495 GATGGTGATGGAAA
1 GATGGTGATGGAAA
13649509 GATGGTGATGGAAA
1 GATGGTGATGGAAA
13649523 TAGATAGTAT
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:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (14 bp):
GATGGTGATGGAAA
Found at i:13658101 original size:13 final size:13
Alignment explanation
Indices: 13658083--13658108 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13658073 TGGCCAAAGA
13658083 TGAAAAGGTATGT
1 TGAAAAGGTATGT
13658096 TGAAAAGGTATGT
1 TGAAAAGGTATGT
13658109 GAGAGGTGTT
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:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:13661384 original size:24 final size:24
Alignment explanation
Indices: 13661335--13661384 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
13661325 AGGTACAAGT
* * *
13661335 GCCTTACATCAAGTGGCATTCGAA
1 GCCTTACATCAAGCGGCAATCAAA
*
13661359 GCCTTACATCAAGCGGTAATCAAA
1 GCCTTACATCAAGCGGCAATCAAA
13661383 GC
1 GC
13661385 TTTGGTGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (24 bp):
GCCTTACATCAAGCGGCAATCAAA
Found at i:13661504 original size:23 final size:25
Alignment explanation
Indices: 13661478--13661541 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 25
13661468 AAATCAAGCA
*
13661478 AAGAAAATCAAAGCACTC-AAAA-G
1 AAGAAAATCAAAGAACTCAAAAAGG
* *
13661501 AAGAAATTGAAAGAACTCAAAAAGG
1 AAGAAAATCAAAGAACTCAAAAAGG
*
13661526 AAGAAAAATAAAAGAA
1 AAG-AAAATCAAAGAA
13661542 AAGAAAAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
23 15 0.45
24 4 0.12
25 4 0.12
26 10 0.30
ACGTcount: A:0.66, C:0.09, G:0.16, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGAACTCAAAAAGG
Found at i:13673006 original size:24 final size:24
Alignment explanation
Indices: 13672957--13673006 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
13672947 AGGTACAAGT
* *
13672957 GCCTTACATCAAGTGGCATCAGAA
1 GCCTTACATCAAGCGGAATCAGAA
13672981 GCCTTACATCAAGCGGTAATCA-AA
1 GCCTTACATCAAGCGG-AATCAGAA
13673005 GC
1 GC
13673007 TTTGGTGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (24 bp):
GCCTTACATCAAGCGGAATCAGAA
Found at i:13680092 original size:36 final size:36
Alignment explanation
Indices: 13680011--13680126 Score: 164
Period size: 36 Copynumber: 3.2 Consensus size: 36
13680001 ATTTAGAAGT
*
13680011 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
13680046 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
* * *
13680082 T-GTTATTGATATAGGCATGATAATGGTGATGGAAGA
1 TGGTGA-TGATATAGGCGTGATAATGGTGATGGAATA
13680118 TGGTGATGA
1 TGGTGATGA
13680127 ACAGATTGTA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
35 23 0.32
36 45 0.63
37 3 0.04
ACGTcount: A:0.30, C:0.03, G:0.34, T:0.32
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:13685511 original size:13 final size:13
Alignment explanation
Indices: 13685450--13685517 Score: 91
Period size: 13 Copynumber: 5.2 Consensus size: 13
13685440 TGCGTCATAA
*
13685450 ATTTATGACACAC
1 ATTTATGACGCAC
*
13685463 ATTTATGACACAC
1 ATTTATGACGCAC
*
13685476 ATTTATGATGCAC
1 ATTTATGACGCAC
*
13685489 ATTTATGACGCTC
1 ATTTATGACGCAC
*
13685502 ATTTATGACGCTC
1 ATTTATGACGCAC
13685515 ATT
1 ATT
13685518 GCGCGTCATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (13 bp):
ATTTATGACGCAC
Found at i:13685590 original size:85 final size:84
Alignment explanation
Indices: 13685489--13685654 Score: 235
Period size: 85 Copynumber: 2.0 Consensus size: 84
13685479 TATGATGCAC
* * *
13685489 ATTTATGACGCTCATTTATGACGCT-CATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAGACG
1 ATTTATGACACGCATTTATGAC-CTACATTGCGCGTCATTGAAGCCCCCGCCATAAATGAAGACG
* *
13685553 ACACTCATTTGTGTGTCATAA
65 ACACACA-TTGTATGTCATAA
* * *
13685574 ATTTATGACACGCATTTATGACTTACATTGCGTGTCATTGAAGCCCCCGCCATAAATGAAGATGA
1 ATTTATGACACGCATTTATGACCTACATTGCGCGTCATTGAAGCCCCCGCCATAAATGAAGACGA
13685639 CACACATTGTATGTCA
66 CACACATTGTATGTCA
13685655 AAGAGTATAT
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
84 10 0.14
85 62 0.86
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (84 bp):
ATTTATGACACGCATTTATGACCTACATTGCGCGTCATTGAAGCCCCCGCCATAAATGAAGACGA
CACACATTGTATGTCATAA
Found at i:13689730 original size:64 final size:64
Alignment explanation
Indices: 13689659--13689778 Score: 152
Period size: 64 Copynumber: 1.9 Consensus size: 64
13689649 ATAAATCACC
* * * *
13689659 TTCGATGTTTTAATCTTAA-GAGGGTGCATCGATGCACTACTTGTACGTCGATACACTTATGGCA
1 TTCGATGTTTTAATCTTAATG-GAGTGCATCGATACACTACATGTACATCGATACACTTATGGCA
* * * *
13689723 TTCGATGTTTTTATTTTAATGGAGTGCATCGATACACTTCATGTGCATCGATACAC
1 TTCGATGTTTTAATCTTAATGGAGTGCATCGATACACTACATGTACATCGATACAC
13689779 CTTGAACAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
64 46 0.98
65 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (64 bp):
TTCGATGTTTTAATCTTAATGGAGTGCATCGATACACTACATGTACATCGATACACTTATGGCA
Found at i:13698557 original size:18 final size:18
Alignment explanation
Indices: 13698534--13698574 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
13698524 AGAGTCCCTT
13698534 GATTGGTGGGATTTATGA
1 GATTGGTGGGATTTATGA
13698552 GATTGGTGGGATTTATGA
1 GATTGGTGGGATTTATGA
13698570 GATTG
1 GATTG
13698575 TATTCGATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.39, T:0.39
Consensus pattern (18 bp):
GATTGGTGGGATTTATGA
Found at i:13700346 original size:46 final size:46
Alignment explanation
Indices: 13700292--13700443 Score: 225
Period size: 46 Copynumber: 3.3 Consensus size: 46
13700282 TTCATTTATG
*
13700292 GCATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAAT
* * *
13700338 GTATCCTTTCATACATTTCATTTCA-GACATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTCATTT-ATGGCATCCTTTCATGCCTTAAT
* * *
13700384 GCATCATTTCATGCATTTCATTTATGGAATCCTTTCACGCCTTAAT
1 GCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAAT
13700430 GCATCCTTTCATGC
1 GCATCCTTTCATGC
13700444 CTTAATGCAT
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
45 1 0.01
46 91 0.98
47 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.42
Consensus pattern (46 bp):
GCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAAT
Found at i:13700393 original size:20 final size:20
Alignment explanation
Indices: 13700365--13700463 Score: 108
Period size: 20 Copynumber: 4.7 Consensus size: 20
13700355 TCATTTCAGA
13700365 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
* *
13700385 CATCATTTCATGCATTTCATTTATGG
1 CATCCTTTCATGC----C-TTAAT-G
* *
13700411 AATCCTTTCACGCCTTAATG
1 CATCCTTTCATGCCTTAATG
13700431 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
13700451 CATCCTTTCATGC
1 CATCCTTTCATGC
13700464 ATTTCATTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
20 44 0.68
21 4 0.06
22 1 0.02
24 1 0.02
25 4 0.06
26 11 0.17
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.40
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATG
Found at i:13700906 original size:20 final size:20
Alignment explanation
Indices: 13700881--13700931 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
13700871 CTCAATAGTG
*
13700881 TCGATACCTCTACCATGGTA
1 TCGATACCTATACCATGGTA
*
13700901 TCGATACTTCTATACTATGGTA
1 TCGATAC--CTATACCATGGTA
*
13700923 CCGATACCT
1 TCGATACCT
13700932 TTCTCTCAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 9 0.35
22 17 0.65
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.33
Consensus pattern (20 bp):
TCGATACCTATACCATGGTA
Found at i:13704259 original size:3 final size:3
Alignment explanation
Indices: 13704251--13704276 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
13704241 TACCTACGTA
13704251 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
13704277 TAATAGAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:13706378 original size:25 final size:25
Alignment explanation
Indices: 13706344--13706393 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
13706334 TTGCCTCGAG
13706344 GCATAAGCCATAACTTTTCCATCTT
1 GCATAAGCCATAACTTTTCCATCTT
13706369 GCATAAGCCATAACTTTTCCATCTT
1 GCATAAGCCATAACTTTTCCATCTT
13706394 ACATCAGCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (25 bp):
GCATAAGCCATAACTTTTCCATCTT
Found at i:13709842 original size:46 final size:46
Alignment explanation
Indices: 13709791--13710110 Score: 450
Period size: 46 Copynumber: 7.0 Consensus size: 46
13709781 ATTATTGTTA
* * *
13709791 ATTTCATTTATGGTATCCTTTCATGTCTTAATACATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
** * *
13709837 ATTTCATTTATATCATCCTTTCATGCCTTAATGCATCCATTCATTAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCA-TGC
*
13709884 ATTTCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * * *
13709930 ATTTCATTTATAGCATCCTTTCATACCTTAATGCAACTTTTCATTC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
13709976 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
13710022 ATTTCATTTATGGCATCCTTTCATGCCTTAATGTATCCTTTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
13710068 ATTTCATTTATGGCATCATTTCAT---TT-ATGGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAAT-GCATCCTTTCATGC
13710111 CTTAATGCAT
Statistics
Matches: 244, Mismatches: 28, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
42 2 0.01
43 14 0.06
46 187 0.77
47 41 0.17
ACGTcount: A:0.22, C:0.23, G:0.09, T:0.46
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:13710089 original size:17 final size:17
Alignment explanation
Indices: 13710067--13710108 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
13710057 TCCTTTTATG
13710067 CATTTCATTTATGGCAT
1 CATTTCATTTATGGCAT
13710084 CATTTCATTTATGGCAT
1 CATTTCATTTATGGCAT
*
13710101 CCTTTCAT
1 CATTTCAT
13710109 GCCTTAATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (17 bp):
CATTTCATTTATGGCAT
Found at i:13710089 original size:63 final size:63
Alignment explanation
Indices: 13710021--13710143 Score: 219
Period size: 63 Copynumber: 2.0 Consensus size: 63
13710011 TCCTTTCATG
* * *
13710021 CATTTCATTTATGGCATCCTTTCATGCCTTAATGTATCCTTTTATGCATTTCATTTATGGCAT
1 CATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCAT
13710084 CATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGG
1 CATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGG
13710144 ATTCGTTTTA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.46
Consensus pattern (63 bp):
CATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCAT
Found at i:13710137 original size:138 final size:137
Alignment explanation
Indices: 13709791--13710110 Score: 385
Period size: 139 Copynumber: 2.3 Consensus size: 137
13709781 ATTATTGTTA
* * * * * * ** *
13709791 ATTTCATTTATGGTATCCTTTCATGTCTTAATACATCCTTTCATGCATTTCATTTATATCATCCT
1 ATTTCATTTATAGCATCATTTCA--TCTTAATGCAACCTTTCATGCATTTCATTCATGGCATCAT
13709856 TTCATGCCTTAATGCATCCATTCATTACATTTCATTTATGGCATCATTTCATGCCTTAATGCATC
64 TTCATGCCTTAATGCATCCATTCATTACATTTCATTTATGGCATCATTTCATGCCTTAATGCATC
13709921 CTTTCATGC
129 CTTTCATGC
* * * * *
13709930 ATTTCATTTATAGCATCCTTTCATACCTTAATGCAACTTTTCATTCATTTCATTTATGGCATCCT
1 ATTTCATTTATAGCATCATTTCAT--CTTAATGCAACCTTTCATGCATTTCATTCATGGCATCAT
* * * *
13709995 TTCATGCCTTAATGCATCCTTTCA-TGCATTTCATTTATGGCATCCTTTCATGCCTTAATGTATC
64 TTCATGCCTTAATGCATCCATTCATTACATTTCATTTATGGCATCATTTCATGCCTTAATGCATC
*
13710059 CTTTTATGC
129 CTTTCATGC
* *
13710068 ATTTCATTTATGGCATCATTTCAT-TT-ATGGCATCCTTTCATGC
1 ATTTCATTTATAGCATCATTTCATCTTAAT-GCAACCTTTCATGC
13710111 CTTAATGCAT
Statistics
Matches: 160, Mismatches: 18, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
134 2 0.01
135 13 0.08
137 1 0.01
138 67 0.42
139 77 0.48
ACGTcount: A:0.22, C:0.23, G:0.09, T:0.46
Consensus pattern (137 bp):
ATTTCATTTATAGCATCATTTCATCTTAATGCAACCTTTCATGCATTTCATTCATGGCATCATTT
CATGCCTTAATGCATCCATTCATTACATTTCATTTATGGCATCATTTCATGCCTTAATGCATCCT
TTCATGC
Found at i:13710589 original size:22 final size:22
Alignment explanation
Indices: 13710562--13710639 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
13710552 TACAAGTACC
13710562 ATGGTATCGATACTTCTATACT
1 ATGGTATCGATACTTCTATACT
*
13710584 ATGGTA-CTGATACCTT-TCT-CT
1 ATGGTATC-GATA-CTTCTATACT
* * *
13710605 -TAGTATCGATACTACTACACT
1 ATGGTATCGATACTTCTATACT
*
13710626 ATGGTATTGATACT
1 ATGGTATCGATACT
13710640 CCCTTTCGGT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
19 2 0.05
20 9 0.21
21 6 0.14
22 23 0.53
23 3 0.07
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (22 bp):
ATGGTATCGATACTTCTATACT
Found at i:13715615 original size:17 final size:18
Alignment explanation
Indices: 13715582--13715615 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13715572 TTAAAAAGTA
*
13715582 TAATGATTTATTTAAAAC
1 TAATCATTTATTTAAAAC
13715600 TAATCATTTA-TTAAAA
1 TAATCATTTATTTAAAA
13715616 TTATAATTTT
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:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (18 bp):
TAATCATTTATTTAAAAC
Found at i:13716288 original size:36 final size:35
Alignment explanation
Indices: 13716205--13716338 Score: 198
Period size: 36 Copynumber: 3.8 Consensus size: 35
13716195 AAATGAACAA
13716205 TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCAC
* * *
13716240 TTGAATCAAAAGTGCTGATGCTTTCTTCCGTTCTTC
1 TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTC-AC
*
13716276 TTGAATCGAAAGTGCCT-ATGCCTCCTTCCGTTCAC
1 TTGAATCGAAAGTG-CTGATGCTTCCTTCCGTTCAC
13716311 TTTGAATCGAAAGTGCTGATGCTTCCTT
1 -TTGAATCGAAAGTGCTGATGCTTCCTT
13716339 TCATTCTTCT
Statistics
Matches: 87, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
35 34 0.39
36 51 0.59
37 2 0.02
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.37
Consensus pattern (35 bp):
TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCAC
Found at i:13716375 original size:21 final size:19
Alignment explanation
Indices: 13716338--13716377 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
13716328 GATGCTTCCT
13716338 TTCATTCTTCTTATTCACC
1 TTCATTCTTCTTATTCACC
*
13716357 TTCATTTCTTTCTTCTTCACC
1 TTCA-TTC-TTCTTATTCACC
13716378 CTCTTTCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 3 0.17
21 11 0.61
ACGTcount: A:0.12, C:0.33, G:0.00, T:0.55
Consensus pattern (19 bp):
TTCATTCTTCTTATTCACC
Found at i:13718674 original size:49 final size:48
Alignment explanation
Indices: 13718600--13718693 Score: 125
Period size: 49 Copynumber: 1.9 Consensus size: 48
13718590 CCCCCTGAAT
* * * *
13718600 CGCGCTATACGCTGATTTGGTGCCACATGGGTATAGCGCGCCCCTGCCC
1 CGCGATATACGCTGATATGGCGCCACATGGGTATAACGC-CCCCTGCCC
* *
13718649 CGCGATATACGGTGATATGGCGCCACGTGGGTATAACGCCCCCTG
1 CGCGATATACGCTGATATGGCGCCACATGGGTATAACGCCCCCTG
13718694 ATTCGCGCTA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 6 0.15
49 33 0.85
ACGTcount: A:0.17, C:0.32, G:0.30, T:0.21
Consensus pattern (48 bp):
CGCGATATACGCTGATATGGCGCCACATGGGTATAACGCCCCCTGCCC
Found at i:13718844 original size:10 final size:10
Alignment explanation
Indices: 13718829--13718868 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
13718819 TTTATCACAC
13718829 CAAATTCTCT
1 CAAATTCTCT
13718839 CAAATTCTCT
1 CAAATTCTCT
13718849 -AAATTTCTCT
1 CAAA-TTCTCT
*
13718859 CAAATACTCT
1 CAAATTCTCT
13718869 ATCATTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:13720626 original size:18 final size:18
Alignment explanation
Indices: 13720603--13720638 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
13720593 CCCAACAGCC
13720603 ATCGCAGCCATATATGAT
1 ATCGCAGCCATATATGAT
13720621 ATCGCAGCCATATATGAT
1 ATCGCAGCCATATATGAT
13720639 GCCTCCATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (18 bp):
ATCGCAGCCATATATGAT
Found at i:13720992 original size:9 final size:9
Alignment explanation
Indices: 13720980--13721023 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
13720970 ACCTGCTCAG
*
13720980 GACGACGAC
1 GACGACGAT
13720989 GACGACGAT
1 GACGACGAT
*
13720998 GATGACGAT
1 GACGACGAT
* *
13721007 GACGATGGT
1 GACGACGAT
13721016 GACGACGA
1 GACGACGA
13721024 CGATGATGAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.32, C:0.20, G:0.36, T:0.11
Consensus pattern (9 bp):
GACGACGAT
Found at i:13721010 original size:15 final size:15
Alignment explanation
Indices: 13720986--13721032 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
13720976 TCAGGACGAC
13720986 GACGACGACGATGAT
1 GACGACGACGATGAT
* *
13721001 GACGATGACGATGGT
1 GACGACGACGATGAT
13721016 GACGACGACGATGAT
1 GACGACGACGATGAT
13721031 GA
1 GA
13721033 ATACAGCGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.32, C:0.17, G:0.36, T:0.15
Consensus pattern (15 bp):
GACGACGACGATGAT
Found at i:13722929 original size:37 final size:37
Alignment explanation
Indices: 13722835--13722940 Score: 124
Period size: 37 Copynumber: 2.9 Consensus size: 37
13722825 CATTTTCGTC
13722835 CTACTAGGATTCAAACTCCTAAAAATAGGATAATATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAATATT
* * * *
13722872 TTGCTAGGATTCAAACTCCTAAAAATATGATAGA-GTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATA-ATATT
* * * *
13722909 CTACTAAGATTTAAATTCCTAAATATAGGATA
1 CTACTAGGATTCAAACTCCTAAAAATAGGATA
13722941 CACAAGCACT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
37 56 0.98
38 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAATATT
Found at i:13723308 original size:15 final size:16
Alignment explanation
Indices: 13723290--13723322 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
13723280 ATATGGATAT
13723290 TTTATTCAT-TTATTA
1 TTTATTCATGTTATTA
13723305 TTTATTCATGTTATTA
1 TTTATTCATGTTATTA
13723321 TT
1 TT
13723323 ATATAGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTATTCATGTTATTA
Found at i:13723836 original size:125 final size:125
Alignment explanation
Indices: 13723460--13723836 Score: 327
Period size: 119 Copynumber: 3.0 Consensus size: 125
13723450 CGTATATATC
*
13723460 TTTTATACTTATAATAGTTTATTTATATACCCATTATATATATATATAT-ATAT-TCTTAATTAT
1 TTTTATACTTATAATAGTTTATTTATATA--TATTATATATATATATATAATATATCTTAATTA-
13723523 TTTTATTTGATTATTTCTTTATTTATGTAATATCTCTTATAACTTTATATATTATAGTATTTTTA
63 TTTTATTTGATTATTTCTTTATTTATGTAATA--TCTTATAAC-TT-TATA-TATAGTATTTTTA
13723588 TTA
123 TTA
* * ** * *
13723591 TTTCA-AATTATTTTCA-TTTATTTTTTACTATATT-TAT-TAT-TATATATATATATCTTTA-T
1 TTTTATACTTATAAT-AGTTTA-TTTATA-TATATTATATATATATATATA-ATATATCTTAATT
** * * * * * * * * **
13723650 ATTTTA-TT-A-TAAGTC-TAATATTA-CT-ATATATTGTAA--TTATCTTTATCTAGTCGTATA
62 ATTTTATTTGATTATTTCTTTAT-TTATGTAATATCTTATAACTTTATATATA-GTATTTTTAT-
13723707 TA
124 TA
*
13723709 TTTTATACTTATAATAGTTTATTTATATATATTAGATATATATATATAATATATCTTAATTATTT
1 TTTTATACTTATAATAGTTTATTTATATATATTATATATATATATATAATATATCTTAATTATTT
13723774 TATTTGATTATTTCTTTATTTATGTAATATCTTATAACTTTATATATAGTATTTTTATTA
66 TATTTGATTATTTCTTTATTTATGTAATATCTTATAACTTTATATATAGTATTTTTATTA
13723834 TTT
1 TTT
13723837 CATTTTTTTA
Statistics
Matches: 185, Mismatches: 38, Indels: 52
0.67 0.14 0.19
Matches are distributed among these distances:
116 3 0.02
117 15 0.08
118 15 0.08
119 23 0.12
120 13 0.07
121 8 0.04
122 1 0.01
123 10 0.05
124 8 0.04
125 21 0.11
126 7 0.04
127 14 0.08
128 8 0.04
129 9 0.05
130 18 0.10
131 10 0.05
132 2 0.01
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (125 bp):
TTTTATACTTATAATAGTTTATTTATATATATTATATATATATATATAATATATCTTAATTATTT
TATTTGATTATTTCTTTATTTATGTAATATCTTATAACTTTATATATAGTATTTTTATTA
Found at i:13724069 original size:2 final size:2
Alignment explanation
Indices: 13724058--13724095 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
13724048 TAATACTTTG
13724058 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13724096 TTTTTTTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:13728285 original size:191 final size:191
Alignment explanation
Indices: 13727957--13728342 Score: 675
Period size: 191 Copynumber: 2.0 Consensus size: 191
13727947 TGTAAATATG
13727957 AGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCAAAAGCCCTAGCTTTATGAATAGATCG
1 AGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCAAAAGCCCTAGCTTTATGAATAGATCG
* *
13728022 CATTCAAACCATGACATTGCTCGGACACTTGGCGATTCGGTGTTTGCTCCACTGCTTTTGTCAGG
66 CATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTACTCCACTGCTTTTGTCAGG
* * **
13728087 TTGAAGACTTTGTGATGAGATGAACCC-TCAGTTAAGCCTAATAAAGGTGATTATAATATTA
131 CTGAAGACTTTGTGATGAGATGAACCCTTCAGTTAAACCTAATAAAAAT-ATTATAATATTA
* *
13728148 AGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCAAAAGCCCTTGCTTTATGAATAGATTG
1 AGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCAAAAGCCCTAGCTTTATGAATAGATCG
13728213 CATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTACTCCACTGCTTTTGTCAGG
66 CATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTACTCCACTGCTTTTGTCAGG
*
13728278 CTGAAGACTTTGTGATGAGATGAACCCTTCAGTTAAACCTGATAAAAATATTATAATATTA
131 CTGAAGACTTTGTGATGAGATGAACCCTTCAGTTAAACCTAATAAAAATATTATAATATTA
13728339 AGCT
1 AGCT
13728343 GTCCCTCTAA
Statistics
Matches: 185, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
191 168 0.91
192 17 0.09
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (191 bp):
AGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCAAAAGCCCTAGCTTTATGAATAGATCG
CATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTACTCCACTGCTTTTGTCAGG
CTGAAGACTTTGTGATGAGATGAACCCTTCAGTTAAACCTAATAAAAATATTATAATATTA
Found at i:13729483 original size:36 final size:34
Alignment explanation
Indices: 13729443--13729550 Score: 92
Period size: 36 Copynumber: 3.0 Consensus size: 34
13729433 CACTCAAATT
13729443 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACA-A-TTTGTCTCACTTGAGAC
* * ** *
13729479 TGTTTTTCTTGAAAGA-AGATTTATTTCACTCAAGAT
1 TGTTTTTCTT-AAA-ACA-ATTTGTCTCACTTGAGAC
*
13729515 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAAC-A-ATTTGTCTCACTTGAGAC
13729551 CATTTTCACT
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
34 1 0.02
35 3 0.05
36 46 0.82
37 5 0.09
38 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.44
Consensus pattern (34 bp):
TGTTTTTCTTAAAACAATTTGTCTCACTTGAGAC
Found at i:13729751 original size:38 final size:38
Alignment explanation
Indices: 13729695--13729768 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
13729685 CCTTGAAATT
* *
13729695 AATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGA
1 AATTTTGTCTCTCCTGAGACAGTTTCCCTCGAAACAGA
* *
13729733 AATTTTGTCTC-CCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCTCC-TGAGACAGTTTCCCTCGAAACA
13729769 TAAACATTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 2 0.06
38 29 0.94
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.38
Consensus pattern (38 bp):
AATTTTGTCTCTCCTGAGACAGTTTCCCTCGAAACAGA
Found at i:13729868 original size:105 final size:103
Alignment explanation
Indices: 13729672--13729988 Score: 514
Period size: 105 Copynumber: 3.1 Consensus size: 103
13729662 ACAGTTTCTC
* *
13729672 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAAATT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAATT
13729737 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
13729775 TTGAAAACATTTCCCTTGAAATGATTTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
1 TTGAAAACATTTCCCTTGAAATGA-ATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAG-AAA
13729840 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
64 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * *
13729880 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G-AATT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAATT
** *
13729943 TTGTCTCCCTTGAGACAGTTTCTCTCCAAACAT-AACT
66 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
13729980 TTGAAAACA
1 TTGAAAACA
13729989 ATTTAAACGA
Statistics
Matches: 202, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
100 12 0.06
101 35 0.17
103 24 0.12
104 64 0.32
105 67 0.33
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (103 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAATT
TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:13729936 original size:36 final size:36
Alignment explanation
Indices: 13729889--13729964 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
13729879 ATTGAAAACA
* * *
13729889 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
13729925 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
13729961 TTTC
1 TTTC
13729965 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:13730324 original size:98 final size:100
Alignment explanation
Indices: 13730137--13730325 Score: 244
Period size: 98 Copynumber: 1.9 Consensus size: 100
13730127 ATCCGCGATT
* *
13730137 TCAACTCCACGACGGAGGATATCGTGACACTCGAGACAACACAAGCTCAAGTTCACAGAGAAGGG
1 TCAACTCCACGACGAAGGATATCGTGACACTCGAGACAACACAAGCTCAACTTCACAGAGAAGGG
13730202 GAAGCTGACTGTCAAAACATAATTTCGGAGCCAATC
66 GAAGCTGACTGTCAAAACA-AATTTCGGAGCCAATC
* * * *
13730238 TCAACTCCACGGCGAAGGATATTG-GAC-C-CGAGACAGCACAAGCTCAACTTCACAGCGAAGGG
1 TCAACTCCACGACGAAGGATATCGTGACACTCGAGACAACACAAGCTCAACTTCACAGAGAAGGG
*
13730300 G-CGACTGACTGTCGACAAAC-AATTTC
66 GAAG-CTGACTGTC-A-AAACAAATTTC
13730326 CCAGTTCCAG
Statistics
Matches: 78, Mismatches: 7, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
97 1 0.01
98 47 0.60
99 2 0.03
100 7 0.09
101 21 0.27
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.16
Consensus pattern (100 bp):
TCAACTCCACGACGAAGGATATCGTGACACTCGAGACAACACAAGCTCAACTTCACAGAGAAGGG
GAAGCTGACTGTCAAAACAAATTTCGGAGCCAATC
Done.