Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 5 of 226
Found at i:1594397 original size:162 final size:162
Alignment explanation
Indices: 1594130--1594454 Score: 596
Period size: 162 Copynumber: 2.0 Consensus size: 162
1594120 TGATTGTCAC
*
1594130 TGCAAGCTTTGATGGACGCATTCGAACCTACCTCAATTACGGGTTGCCAATTCGAGTATAAGAAC
1 TGCAAGCTTTGATGGACGCATTCGAACCTACCTCAATTACGGGTTACCAATTCGAGTATAAGAAC
*
1594195 CTCTCCATCCCTAAAGATACAGCAACACAACACATATACGAATATAGGTATAACTGTGCGGTCTG
66 CTCTCCATCCCTAAAGATACAGCAACACAACACATATACGAATATAGGTATAACTGTGCCGTCTG
1594260 GTTTTAAACACATACATGTCTTTGAACACTCA
131 GTTTTAAACACATACATGTCTTTGAACACTCA
*
1594292 TGCAAGCTTTGATGGACGCATTCGAACCTACCTCAATTATGGGTTACCAATTCGAGTATAAGAAC
1 TGCAAGCTTTGATGGACGCATTCGAACCTACCTCAATTACGGGTTACCAATTCGAGTATAAGAAC
*
1594357 CTCTCCGTCCCTAAAGATACAGCAACACAACACATATACGAATATAGGTATAACTGTGCCGTCTG
66 CTCTCCATCCCTAAAGATACAGCAACACAACACATATACGAATATAGGTATAACTGTGCCGTCTG
* *
1594422 GTTTTAAGCACATGCATGTCTTTGAACACTCA
131 GTTTTAAACACATACATGTCTTTGAACACTCA
1594454 T
1 T
1594455 TTTCGAATTC
Statistics
Matches: 157, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
162 157 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (162 bp):
TGCAAGCTTTGATGGACGCATTCGAACCTACCTCAATTACGGGTTACCAATTCGAGTATAAGAAC
CTCTCCATCCCTAAAGATACAGCAACACAACACATATACGAATATAGGTATAACTGTGCCGTCTG
GTTTTAAACACATACATGTCTTTGAACACTCA
Found at i:1605382 original size:9 final size:9
Alignment explanation
Indices: 1605368--1605422 Score: 58
Period size: 9 Copynumber: 6.0 Consensus size: 9
1605358 ACTTCATACT
1605368 AATTTTTTA
1 AATTTTTTA
1605377 AATTTTTTA
1 AATTTTTTA
*
1605386 TATATTTTTA
1 AAT-TTTTTA
*
1605396 ATATTTTTTT
1 A-ATTTTTTA
1605406 AA-TTTTTA
1 AATTTTTTA
*
1605414 AATTATTTA
1 AATTTTTTA
1605423 TTGACATGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
8 7 0.18
9 17 0.45
10 12 0.32
11 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
AATTTTTTA
Found at i:1605410 original size:18 final size:19
Alignment explanation
Indices: 1605371--1605423 Score: 74
Period size: 18 Copynumber: 2.8 Consensus size: 19
1605361 TCATACTAAT
1605371 TTTTTAAATTTTTTATATA
1 TTTTTAAATTTTTTATATA
1605390 TTTTTAATATTTTTT-TA-A
1 TTTTTAA-ATTTTTTATATA
*
1605408 TTTTTAAATTATTTAT
1 TTTTTAAATTTTTTAT
1605424 TGACATGACA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 6 0.19
18 9 0.29
19 9 0.29
20 7 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTAAATTTTTTATATA
Found at i:1608575 original size:17 final size:18
Alignment explanation
Indices: 1608550--1608583 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1608540 GCATTTGTAC
*
1608550 AAGT-TTTTTTAATAATG
1 AAGTATTTTATAATAATG
1608567 AAGTATTTTATAATAAT
1 AAGTATTTTATAATAAT
1608584 TTAACTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (18 bp):
AAGTATTTTATAATAATG
Found at i:1609302 original size:22 final size:22
Alignment explanation
Indices: 1609271--1609313 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1609261 CCTACTCTTT
*
1609271 TTGTTGTTTTCCCACTGTTTTC
1 TTGTTATTTTCCCACTGTTTTC
* *
1609293 TTGTTATTTTTCTACTGTTTT
1 TTGTTATTTTCCCACTGTTTT
1609314 GTTGACTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.07, C:0.16, G:0.12, T:0.65
Consensus pattern (22 bp):
TTGTTATTTTCCCACTGTTTTC
Found at i:1614526 original size:33 final size:33
Alignment explanation
Indices: 1614489--1614554 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1614479 AGCCGCCATT
*
1614489 GGAGGTCTCTCTGATAGTAGTGAAAGTAGGTGA
1 GGAGGTCTCTCCGATAGTAGTGAAAGTAGGTGA
*
1614522 GGAGGTCTCTCCGATAGTAGTTAAAGTAGGTGA
1 GGAGGTCTCTCCGATAGTAGTGAAAGTAGGTGA
1614555 TAGATGACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.11, G:0.35, T:0.27
Consensus pattern (33 bp):
GGAGGTCTCTCCGATAGTAGTGAAAGTAGGTGA
Found at i:1619301 original size:22 final size:22
Alignment explanation
Indices: 1619276--1619317 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1619266 TGTTTATGTT
* *
1619276 TTACTGTAATTTTGTTATTATA
1 TTACTATAATTTTATTATTATA
*
1619298 TTACTATTATTTTATTATTA
1 TTACTATAATTTTATTATTA
1619318 GTGTTTAGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (22 bp):
TTACTATAATTTTATTATTATA
Found at i:1625186 original size:34 final size:34
Alignment explanation
Indices: 1625143--1625211 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
1625133 TCAATCACTG
1625143 TTAGATGCTCGTAAAAAACAAGGGTCTATGTCCA
1 TTAGATGCTCGTAAAAAACAAGGGTCTATGTCCA
1625177 TTAGATGCTCGTAAAAAACAAGGGTCTATGTCCA
1 TTAGATGCTCGTAAAAAACAAGGGTCTATGTCCA
1625211 T
1 T
1625212 CTTAGAGCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (34 bp):
TTAGATGCTCGTAAAAAACAAGGGTCTATGTCCA
Found at i:1633551 original size:33 final size:33
Alignment explanation
Indices: 1633509--1633577 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
1633499 AAAGGAAAAG
1633509 TTGGTGCCAAAAAGCCTAGTCTTCGCCATGTAT
1 TTGGTGCCAAAAAGCCTAGTCTTCGCCATGTAT
1633542 TTGGTGCCAAAAAGCCTAGTCTTCGCCATGTAT
1 TTGGTGCCAAAAAGCCTAGTCTTCGCCATGTAT
1633575 TTG
1 TTG
1633578 AAGGAGAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (33 bp):
TTGGTGCCAAAAAGCCTAGTCTTCGCCATGTAT
Found at i:1638794 original size:16 final size:17
Alignment explanation
Indices: 1638773--1638806 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1638763 TACTACTAAA
1638773 AATTTA-TTTTTACTTT
1 AATTTAGTTTTTACTTT
*
1638789 AATTTAGTTTTTATTTT
1 AATTTAGTTTTTACTTT
1638806 A
1 A
1638807 TTTTGGGGCC
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:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
AATTTAGTTTTTACTTT
Found at i:1639293 original size:22 final size:22
Alignment explanation
Indices: 1639265--1639308 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1639255 GGCCTCAAAC
1639265 TCGATATTTTAACTAAGAAAAA
1 TCGATATTTTAACTAAGAAAAA
1639287 TCGATATTTTAACTAAGAAAAA
1 TCGATATTTTAACTAAGAAAAA
1639309 ATGTAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (22 bp):
TCGATATTTTAACTAAGAAAAA
Found at i:1649431 original size:58 final size:59
Alignment explanation
Indices: 1649357--1649493 Score: 149
Period size: 59 Copynumber: 2.4 Consensus size: 59
1649347 GCGACAATGT
* * *
1649357 CCAC-ATTAGGGTTTGAA-TTTTTTTTGTATAAGTT-AGTCCCTGAACTTGGTAATTGTTC
1 CCACGATTAGGGCTTGAACTTTTTTTT-T-TAAGTTAAGTCCCTGAACTTGGTAACTATTC
** *
1649415 CCA-GATTAGGGCTTGAACTTTTTTTTTTCTGTTCAAGTCTCTGAACTTGGTAACTATTC
1 CCACGATTAGGGCTTGAACTTTTTTTTTTAAGTT-AAGTCCCTGAACTTGGTAACTATTC
*
1649474 CCACG-TTAGGGCTTTAACTT
1 CCACGATTAGGGCTTGAACTT
1649494 AAAGGTTTTC
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
57 4 0.06
58 16 0.24
59 46 0.69
60 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (59 bp):
CCACGATTAGGGCTTGAACTTTTTTTTTTAAGTTAAGTCCCTGAACTTGGTAACTATTC
Found at i:1653200 original size:33 final size:33
Alignment explanation
Indices: 1653158--1653225 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
1653148 ACAAAACATA
* *
1653158 TACGAAGTTCTCGAATCCTAACTGTTGACCTAG
1 TACGAAGTTCTCGAATCCTAACTCTTGACCAAG
*
1653191 TACGAAGTTCTCGAATTCTAACTCTTGACCAAG
1 TACGAAGTTCTCGAATCCTAACTCTTGACCAAG
1653224 TA
1 TA
1653226 GCATTGGGCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (33 bp):
TACGAAGTTCTCGAATCCTAACTCTTGACCAAG
Found at i:1656148 original size:7 final size:7
Alignment explanation
Indices: 1656136--1656211 Score: 152
Period size: 7 Copynumber: 10.9 Consensus size: 7
1656126 CAAACAATTA
1656136 AATTACT
1 AATTACT
1656143 AATTACT
1 AATTACT
1656150 AATTACT
1 AATTACT
1656157 AATTACT
1 AATTACT
1656164 AATTACT
1 AATTACT
1656171 AATTACT
1 AATTACT
1656178 AATTACT
1 AATTACT
1656185 AATTACT
1 AATTACT
1656192 AATTACT
1 AATTACT
1656199 AATTACT
1 AATTACT
1656206 AATTAC
1 AATTAC
1656212 AGTTCTATTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 69 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.42
Consensus pattern (7 bp):
AATTACT
Found at i:1656247 original size:18 final size:18
Alignment explanation
Indices: 1656224--1656259 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1656214 TTCTATTTCA
1656224 GTGAACCAAACTTTGCTT
1 GTGAACCAAACTTTGCTT
1656242 GTGAACCAAACTTTGCTT
1 GTGAACCAAACTTTGCTT
1656260 ACTCAACACA
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:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (18 bp):
GTGAACCAAACTTTGCTT
Found at i:1658096 original size:15 final size:15
Alignment explanation
Indices: 1658076--1658126 Score: 93
Period size: 15 Copynumber: 3.4 Consensus size: 15
1658066 AGCCCCCAGA
1658076 ACCACCGAAGGGGTC
1 ACCACCGAAGGGGTC
*
1658091 ACCACCGAAGAGGTC
1 ACCACCGAAGGGGTC
1658106 ACCACCGAAGGGGTC
1 ACCACCGAAGGGGTC
1658121 ACCACC
1 ACCACC
1658127 AAAATTGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.29, C:0.37, G:0.27, T:0.06
Consensus pattern (15 bp):
ACCACCGAAGGGGTC
Found at i:1661390 original size:3 final size:3
Alignment explanation
Indices: 1661382--1661416 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1661372 TTACACATAA
*
1661382 AAC AAC AAC AAC AGC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1661417 TGACAACTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.31, G:0.03, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1675988 original size:123 final size:122
Alignment explanation
Indices: 1675781--1676117 Score: 444
Period size: 123 Copynumber: 2.7 Consensus size: 122
1675771 GGTATGGGAA
* *
1675781 GAAATAATTTTTTTGACCTTTCTGAGCAAATAGTATAAAATCGCATATAGCAGGATGCTATTTGA
1 GAAATAATTTTTTTGACATTTCTGAGCAAATAGTATAAAATCGC-TCTAGCAGGATGCTATTTGA
* * **
1675846 GAATAAATTT-TGAAATCGCGCCCTCGTTAACGC-GCTCTTGCTACAGTAGGTCATGGAT
65 GAA-AAATTTGTAAAATCGCGCCCTCGTGAACGCTG-AATTGCTACAGTAGGTCATGGAT
* * * *
1675904 GAAATATTTTTTTTGACGTTTCTGAGCAAATAGTATAAATTCGCTCCTAGCAGGATTCTATTTGA
1 GAAATAATTTTTTTGACATTTCTGAGCAAATAGTATAAAATCGCT-CTAGCAGGATGCTATTTGA
* *
1675969 GAAGAATTTGTAAAATCGCGCCCTCGTGGACGCTGAATTGCTACAGTAGGTCATGGAT
65 GAAAAATTTGTAAAATCGCGCCCTCGTGAACGCTGAATTGCTACAGTAGGTCATGGAT
* * * *
1676027 GAAATAAATTTTTTGACATTTCTAAGCAAATAGTATAAAATCGCTTCTAGCAGTATGCTATTTGG
1 GAAATAATTTTTTTGACATTTCTGAGCAAATAGTATAAAATCGC-TCTAGCAGGATGCTATTTGA
* *
1676092 GAACAATTTGTGAAAATCGCACCCTC
65 GAAAAATTTGT-AAAATCGCGCCCTC
1676118 AGGGACGCAT
Statistics
Matches: 188, Mismatches: 21, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
122 6 0.03
123 167 0.89
124 15 0.08
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (122 bp):
GAAATAATTTTTTTGACATTTCTGAGCAAATAGTATAAAATCGCTCTAGCAGGATGCTATTTGAG
AAAAATTTGTAAAATCGCGCCCTCGTGAACGCTGAATTGCTACAGTAGGTCATGGAT
Found at i:1679306 original size:44 final size:43
Alignment explanation
Indices: 1679256--1679582 Score: 211
Period size: 44 Copynumber: 7.3 Consensus size: 43
1679246 GAATGTTAAG
*
1679256 GGTTAGGGTTTTTAAGTTTAGAGTTAGGGTTTTTAACTTAATTA
1 GGTTAGGGTTTTTAAGTTTAG-GTTAGGGTTTTCAACTTAATTA
* * *** *
1679300 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTAGGATTTAATTA
1 GGTTAGGGTTTTTAA-GT--TTAGGTTAGGGTTTTCAACTTAATTA
** * * * *
1679346 GGTTAGGGTTTAGAATTTAATTAAGTTAGGGTTTTTAA-GT--TTA
1 GGTTAGGGTTTTTAA-GT--TTAGGTTAGGGTTTTCAACTTAATTA
** * * *
1679389 GGGTTAGAATTTTCAACTTAATTAGGTTAGGGGTTTT-AA-GT--TTA
1 -GGTTAGGGTTTTTAA-GT--TTAGGTTA-GGGTTTTCAACTTAATTA
* * *
1679433 GGGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTGTCAACTTAATTA
1 -GGTTAGGGTTTTTAA-GT--TTAGGTTAGGGTTTTCAACTTAATTA
1679480 GGTTAGGGTTTTTAAGTTTAGGGTTAGGGTTTTCAACTTAATTA
1 GGTTAGGGTTTTTAAGTTTA-GGTTAGGGTTTTCAACTTAATTA
* * *
1679524 GG-TCGGGATTTTTAAGTTTAGGGTCAAGGTTTTCAACTTAATTA
1 GGTTAGGG-TTTTTAAGTTTA-GGTTAGGGTTTTCAACTTAATTA
1679568 GGTTAGGGTTTTTAA
1 GGTTAGGGTTTTTAA
1679583 TTTTTATCAC
Statistics
Matches: 240, Mismatches: 31, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
43 16 0.07
44 139 0.58
45 15 0.06
46 63 0.26
47 7 0.03
ACGTcount: A:0.25, C:0.05, G:0.26, T:0.44
Consensus pattern (43 bp):
GGTTAGGGTTTTTAAGTTTAGGTTAGGGTTTTCAACTTAATTA
Found at i:1679308 original size:23 final size:23
Alignment explanation
Indices: 1679256--1679582 Score: 254
Period size: 23 Copynumber: 14.7 Consensus size: 23
1679246 GAATGTTAAG
*
1679256 GGTTAGGGTTTTTAA-GT--TTA
1 GGTTAGGGTTTTTAACTTAATTA
1679276 GAGTTAGGGTTTTTAACTTAATTA
1 G-GTTAGGGTTTTTAACTTAATTA
*
1679300 GGTTAGGGTTTTCAACTTAATTA
1 GGTTAGGGTTTTTAACTTAATTA
*** *
1679323 GGTTAGGGTTTAGGATTTAATTA
1 GGTTAGGGTTTTTAACTTAATTA
** *
1679346 GGTTAGGGTTTAGAATTTAATTA
1 GGTTAGGGTTTTTAACTTAATTA
* *
1679369 AGTTAGGGTTTTTAA-GT--TTA
1 GGTTAGGGTTTTTAACTTAATTA
** *
1679389 GGGTTAGAATTTTCAACTTAATTA
1 -GGTTAGGGTTTTTAACTTAATTA
* *
1679413 GGTTAGGGGTTTTAA-GT--TTA
1 GGTTAGGGTTTTTAACTTAATTA
*
1679433 GGGTTAGGGTTTTCAACTTAATTA
1 -GGTTAGGGTTTTTAACTTAATTA
* *
1679457 GGTTAGGGTTGTCAACTTAATTA
1 GGTTAGGGTTTTTAACTTAATTA
*
1679480 GGTTAGGGTTTTTAA-GT--TTA
1 GGTTAGGGTTTTTAACTTAATTA
*
1679500 GGGTTAGGGTTTTCAACTTAATTA
1 -GGTTAGGGTTTTTAACTTAATTA
* *
1679524 GG-TCGGGATTTTTAA-GT--TTA
1 GGTTAGGG-TTTTTAACTTAATTA
* * *
1679544 GGGTCAAGGTTTTCAACTTAATTA
1 -GGTTAGGGTTTTTAACTTAATTA
1679568 GGTTAGGGTTTTTAA
1 GGTTAGGGTTTTTAA
1679583 TTTTTATCAC
Statistics
Matches: 244, Mismatches: 41, Indels: 41
0.75 0.13 0.13
Matches are distributed among these distances:
20 13 0.05
21 60 0.25
22 15 0.06
23 140 0.57
24 16 0.07
ACGTcount: A:0.25, C:0.05, G:0.26, T:0.44
Consensus pattern (23 bp):
GGTTAGGGTTTTTAACTTAATTA
Found at i:1679461 original size:67 final size:67
Alignment explanation
Indices: 1679300--1679526 Score: 257
Period size: 67 Copynumber: 3.4 Consensus size: 67
1679290 AACTTAATTA
*** * *
1679300 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTAGGATTTAATTAGGTTA-GGG-TTTAGAATT
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTAGGTTAGGGGTTTTA-AGTT
*
1679363 TAATTA
65 T-A--G
* * * **
1679369 AGTTAGGGTTTTTAA-GT--TTAGGGTTAGAATTTTCAACTTAATTAGGTTAGGGGTTTTAAGTT
1 GGTTAGGGTTTTCAACTTAATTA-GGTTAGGGTTTTCAACTTAATTAGGTTAGGGGTTTTAAGTT
1679431 TAG
65 TAG
* *
1679434 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTGTCAACTTAATTAGGTTAGGGTTTTTAAGTTT
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTAGGTTAGGGGTTTTAAGTTT
1679499 AG
66 AG
1679501 GGTTAGGGTTTTCAACTTAATTAGGT
1 GGTTAGGGTTTTCAACTTAATTAGGT
1679527 CGGGATTTTT
Statistics
Matches: 134, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
65 13 0.10
66 4 0.03
67 89 0.66
68 11 0.08
69 17 0.13
ACGTcount: A:0.26, C:0.04, G:0.26, T:0.44
Consensus pattern (67 bp):
GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTAGGTTAGGGGTTTTAAGTTT
AG
Found at i:1679488 original size:111 final size:111
Alignment explanation
Indices: 1679256--1679578 Score: 420
Period size: 111 Copynumber: 2.9 Consensus size: 111
1679246 GAATGTTAAG
* * *
1679256 GGTTAGGGTTTTTAAGTTTAGAGTTAGGGTTTTTAACTTAATTAGGTTA-GGGTTTTCAACTTAA
1 GGTTAGGGTTTTTAAGTTTAGGGTTAGGGTTTTCAACTTAATTAGGTTAGGGGTTTT-AA-GT--
*** * * *
1679320 TTA-GGTTAGGGTTTAGGATTTAATTAGGTTAGGGTTTAGAATTTAATTA
62 TTAGGGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTACAACTTAATTA
* **
1679369 AGTTAGGGTTTTTAAGTTTAGGGTTAGAATTTTCAACTTAATTAGGTTAGGGGTTTTAAGTTTAG
1 GGTTAGGGTTTTTAAGTTTAGGGTTAGGGTTTTCAACTTAATTAGGTTAGGGGTTTTAAGTTTAG
1679434 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTGT-CAACTTAATTA
66 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTT-TACAACTTAATTA
* *
1679480 GGTTAGGGTTTTTAAGTTTAGGGTTAGGGTTTTCAACTTAATTAGG-TCGGGATTTTTAAGTTTA
1 GGTTAGGGTTTTTAAGTTTAGGGTTAGGGTTTTCAACTTAATTAGGTTAGGG-GTTTTAAGTTTA
* *
1679544 GGGTCAAGGTTTTCAACTTAATTAGGTTAGGGTTT
65 GGGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTT
1679579 TTAATTTTTA
Statistics
Matches: 187, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
110 8 0.04
111 124 0.66
112 2 0.01
113 46 0.25
114 7 0.04
ACGTcount: A:0.25, C:0.05, G:0.26, T:0.44
Consensus pattern (111 bp):
GGTTAGGGTTTTTAAGTTTAGGGTTAGGGTTTTCAACTTAATTAGGTTAGGGGTTTTAAGTTTAG
GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTACAACTTAATTA
Found at i:1679619 original size:25 final size:25
Alignment explanation
Indices: 1679584--1679751 Score: 181
Period size: 25 Copynumber: 6.9 Consensus size: 25
1679574 GGTTTTTAAT
*
1679584 TTTTATCACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
*
1679609 TTTTATTACATCATATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
1679634 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
1679659 TTTTATTACATCAAAT-AA-TATC-A
1 TTTTATTACATCAAATAAACT-TCTA
** * * *
1679682 --AAATAAC-TCAAA-AAAATTCAA
1 TTTTATTACATCAAATAAACTTCTA
1679703 TTTTTATTACATC-AATAAAACTTCTA
1 -TTTTATTACATCAAAT-AAACTTCTA
*
1679729 TTTTATTACATCAAACAAACTTC
1 TTTTATTACATCAAATAAACTTC
1679752 AAAATATTCA
Statistics
Matches: 120, Mismatches: 12, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
20 9 0.08
21 6 0.05
23 2 0.02
24 10 0.08
25 84 0.70
26 9 0.08
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTCTA
Found at i:1680200 original size:18 final size:18
Alignment explanation
Indices: 1680177--1680214 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1680167 CTCGGAAAAT
*
1680177 GATACATATAAGGGTTAG
1 GATACATATAAGGGATAG
*
1680195 GATACATGTAAGGGATAG
1 GATACATATAAGGGATAG
1680213 GA
1 GA
1680215 AACGCACCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.32, T:0.24
Consensus pattern (18 bp):
GATACATATAAGGGATAG
Found at i:1681069 original size:20 final size:20
Alignment explanation
Indices: 1681032--1681069 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1681022 TTTATTTTTA
*
1681032 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
1681052 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
1681070 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:1682116 original size:10 final size:11
Alignment explanation
Indices: 1682103--1682153 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
1682093 ATGAGAATTT
1682103 TTGA-AGGAAA
1 TTGAGAGGAAA
*
1682113 TTGAGAGAAAA
1 TTGAGAGGAAA
1682124 TTGAGAGGAAA
1 TTGAGAGGAAA
* *
1682135 TTGATAGAAAA
1 TTGAGAGGAAA
1682146 TATGAGAG
1 T-TGAGAG
1682154 AGGATTTGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
10 4 0.12
11 25 0.74
12 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:1682121 original size:22 final size:22
Alignment explanation
Indices: 1682103--1682153 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
1682093 ATGAGAATTT
1682103 TTGA-AGGAAATTGAGAGAAAA
1 TTGAGAGGAAATTGAGAGAAAA
*
1682124 TTGAGAGGAAATTGATAGAAAA
1 TTGAGAGGAAATTGAGAGAAAA
1682146 TATGAGAG
1 T-TGAGAG
1682154 AGGATTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 4 0.15
22 17 0.63
23 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (22 bp):
TTGAGAGGAAATTGAGAGAAAA
Found at i:1682126 original size:11 final size:11
Alignment explanation
Indices: 1682110--1682154 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
1682100 TTTTTGAAGG
1682110 AAATTGAGAGA
1 AAATTGAGAGA
*
1682121 AAATTGAGAGG
1 AAATTGAGAGA
*
1682132 AAATTGATAGA
1 AAATTGAGAGA
1682143 AAATATGAGAGA
1 AAAT-TGAGAGA
1682155 GGATTTGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 23 0.79
12 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.27, T:0.20
Consensus pattern (11 bp):
AAATTGAGAGA
Found at i:1682126 original size:51 final size:51
Alignment explanation
Indices: 1682004--1682127 Score: 162
Period size: 51 Copynumber: 2.4 Consensus size: 51
1681994 TATTTTAAAA
* *
1682004 AAGGAAATTGAGAGCAAATTAAAAATAAATATGGGTTTGAGAGATTTTTGG
1 AAGGAAATTGAGAGAAAATTGAAAATAAATATGGGTTTGAGAGATTTTTGG
* * * *
1682055 AATGAAATTGAGAGGAAATTGAAATTAAATATGGATTT-ATGAGAATTTTT-G
1 AAGGAAATTGAGAGAAAATTGAAAATAAATATGGGTTTGA-GAG-ATTTTTGG
1682106 AAGGAAATTGAGAGAAAATTGA
1 AAGGAAATTGAGAGAAAATTGA
1682128 GAGGAAATTG
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
50 1 0.02
51 57 0.89
52 6 0.09
ACGTcount: A:0.45, C:0.01, G:0.24, T:0.30
Consensus pattern (51 bp):
AAGGAAATTGAGAGAAAATTGAAAATAAATATGGGTTTGAGAGATTTTTGG
Found at i:1696059 original size:24 final size:25
Alignment explanation
Indices: 1696027--1696073 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1696017 ACCCTAAATA
1696027 TGTCAGTATTAATTCTT-TTGAAGG
1 TGTCAGTATTAATTCTTGTTGAAGG
*
1696051 TGTCAGTATTAATTTTTGTTGAA
1 TGTCAGTATTAATTCTTGTTGAA
1696074 CCTACAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.49
Consensus pattern (25 bp):
TGTCAGTATTAATTCTTGTTGAAGG
Found at i:1696474 original size:14 final size:14
Alignment explanation
Indices: 1696439--1696468 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1696429 TTAGATTATC
1696439 ATACATTAATCAAA
1 ATACATTAATCAAA
1696453 ATACATTAATCAAA
1 ATACATTAATCAAA
1696467 AT
1 AT
1696469 TGATTAGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (14 bp):
ATACATTAATCAAA
Found at i:1709900 original size:18 final size:18
Alignment explanation
Indices: 1709877--1709947 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 18
1709867 CCAACTACTG
*
1709877 TATACGTGAACAGTACCA
1 TATACGTGAATAGTACCA
*
1709895 TATACGTGAATAGTACCG
1 TATACGTGAATAGTACCA
* ***
1709913 CATACGTGAATAGTATTG
1 TATACGTGAATAGTACCA
*
1709931 TATACATGAATAGTACC
1 TATACGTGAATAGTACC
1709948 GTAAACGGTC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (18 bp):
TATACGTGAATAGTACCA
Found at i:1720569 original size:282 final size:282
Alignment explanation
Indices: 1720065--1720583 Score: 896
Period size: 282 Copynumber: 1.8 Consensus size: 282
1720055 ATACGGCGAT
*
1720065 CAAAGCCTGATATATTGGAATAAGCATAGAATAAGAATCTAAACCGCTAGTTATAGCCGTTGTAA
1 CAAAGCCTGATATATTGGAATAAGCATAGAATAAGAATCTAAACCGATAGTTATAGCCGTTGTAA
*
1720130 CGACCGACAATTAAATAAGTCTACCGATCAAATTTTCAACAAGCATCTTACTCACATATCAATCG
66 CGACCGACAATTAAATAAGTCCACCGATCAAATTTTCAACAAGCATCTTACTCACATATCAATCG
* *
1720195 GTCATACCGAAAATGCATGATCTACTGCCGTAACCACTTATAAACCTCAACACGATACATAATCT
131 ATCATACAGAAAATGCATGATCTACTGCCGTAACCACTTATAAACCTCAACACGATACATAATCT
1720260 AAGTTCTTAATTAGGCCAATCAACACTAATTGCCAACACATAATCTATAAGTCCTATTCTAGCCT
196 AAGTTCTTAATTAGGCCAATCAACACTAATTGCCAACACATAATCTATAAGTCCTATTCTAGCCT
1720325 TGTTTACTCAAAATATGACGAA
261 TGTTTACTCAAAATATGACGAA
* *
1720347 CAAAGCCTGATATGTTGGAATAAGCATAGAATAAGAATCTAAACTGATAGTTATAGCCGTTGTAA
1 CAAAGCCTGATATATTGGAATAAGCATAGAATAAGAATCTAAACCGATAGTTATAGCCGTTGTAA
* * * *
1720412 CGGCCGACAATTAAATAAGTCCACTGATCAAATTTTCAACAAGCATCTTACTCACATATCGATTG
66 CGACCGACAATTAAATAAGTCCACCGATCAAATTTTCAACAAGCATCTTACTCACATATCAATCG
**
1720477 ATCATA-AGAAAAATGCATGATCTACTGCCGTAACCACTTATAAACCTTGACACGATACATAATC
131 ATCATACAG-AAAATGCATGATCTACTGCCGTAACCACTTATAAACCTCAACACGATACATAATC
* *
1720541 TAGGTTTTTAATTAGGCCAATCAACACTAATTGCCAACACATA
195 TAAGTTCTTAATTAGGCCAATCAACACTAATTGCCAACACATA
1720584 TCTGAGTTCT
Statistics
Matches: 222, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
281 1 0.00
282 221 1.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (282 bp):
CAAAGCCTGATATATTGGAATAAGCATAGAATAAGAATCTAAACCGATAGTTATAGCCGTTGTAA
CGACCGACAATTAAATAAGTCCACCGATCAAATTTTCAACAAGCATCTTACTCACATATCAATCG
ATCATACAGAAAATGCATGATCTACTGCCGTAACCACTTATAAACCTCAACACGATACATAATCT
AAGTTCTTAATTAGGCCAATCAACACTAATTGCCAACACATAATCTATAAGTCCTATTCTAGCCT
TGTTTACTCAAAATATGACGAA
Found at i:1725878 original size:57 final size:57
Alignment explanation
Indices: 1725790--1725903 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
1725780 ATTTCATATT
1725790 CATATTTTTTTATCGTATTAGTAGAGGTGGTGTTTTATTGGAGTCTCAAAATTTTGA
1 CATATTTTTTTATCGTATTAGTAGAGGTGGTGTTTTATTGGAGTCTCAAAATTTTGA
1725847 CATATTTTTTTATCGTATTAGTAGAGGTGGTGTTTTATTGGAGTCTCAAAATTTTGA
1 CATATTTTTTTATCGTATTAGTAGAGGTGGTGTTTTATTGGAGTCTCAAAATTTTGA
1725904 GAAATTTTCG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.47
Consensus pattern (57 bp):
CATATTTTTTTATCGTATTAGTAGAGGTGGTGTTTTATTGGAGTCTCAAAATTTTGA
Found at i:1728690 original size:14 final size:14
Alignment explanation
Indices: 1728671--1728698 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1728661 TCAAATTCAA
1728671 TAGTTTATGTGCTC
1 TAGTTTATGTGCTC
1728685 TAGTTTATGTGCTC
1 TAGTTTATGTGCTC
1728699 GGCCACTCGG
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:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (14 bp):
TAGTTTATGTGCTC
Found at i:1736661 original size:4 final size:4
Alignment explanation
Indices: 1736652--1736722 Score: 142
Period size: 4 Copynumber: 17.8 Consensus size: 4
1736642 ATCAATTTTA
1736652 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1736700 ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACA
1736723 CAGACACGCA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 67 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:1738486 original size:31 final size:31
Alignment explanation
Indices: 1738424--1738487 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
1738414 GATCTCTGAT
* *
1738424 CTATTTAAAAGTTTTTACTCAAGTTAGTAAA
1 CTATTTAAAAGCTTTTACTCAAGTCAGTAAA
* * * *
1738455 CTATTTGAAAGCTTTTATTTAAGTCATTAAA
1 CTATTTAAAAGCTTTTACTCAAGTCAGTAAA
1738486 CT
1 CT
1738488 GTTAAGGTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (31 bp):
CTATTTAAAAGCTTTTACTCAAGTCAGTAAA
Found at i:1753196 original size:14 final size:14
Alignment explanation
Indices: 1753177--1753203 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1753167 CAATTTTTAA
1753177 ATTTTAGTGAAATG
1 ATTTTAGTGAAATG
1753191 ATTTTAGTGAAAT
1 ATTTTAGTGAAAT
1753204 TGCTCGCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (14 bp):
ATTTTAGTGAAATG
Found at i:1753333 original size:17 final size:17
Alignment explanation
Indices: 1753292--1753364 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 17
1753282 AATCATGTAT
1753292 AATTTATAAAAATTAAAAA
1 AATTTA-AAAAA-TAAAAA
*
1753311 ATATTTAAAAAATAAACA
1 A-ATTTAAAAAATAAAAA
1753329 AATTTAAAAAATTTAATAAAA
1 AATTTAAAAAA--T-A-AAAA
1753350 ACATTTAAAAAATAA
1 A-ATTTAAAAAATAA
1753365 TTCCATATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
17 10 0.22
18 7 0.15
19 8 0.17
20 7 0.15
21 4 0.09
22 10 0.22
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
AATTTAAAAAATAAAAA
Found at i:1753349 original size:10 final size:9
Alignment explanation
Indices: 1753292--1753349 Score: 57
Period size: 10 Copynumber: 6.2 Consensus size: 9
1753282 AATCATGTAT
1753292 AATTTATAAA
1 AATTTA-AAA
*
1753302 AATTAAAAA
1 AATTTAAAA
1753311 ATATTTAAAA
1 A-ATTTAAAA
1753321 AA--TAAACA
1 AATTTAAA-A
1753329 AATTTAAAA
1 AATTTAAAA
1753338 AATTTAATAA
1 AATTTAA-AA
1753348 AA
1 AA
1753350 ACATTTAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
7 4 0.10
8 3 0.07
9 13 0.32
10 21 0.51
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (9 bp):
AATTTAAAA
Found at i:1753355 original size:22 final size:22
Alignment explanation
Indices: 1753321--1753362 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1753311 ATATTTAAAA
1753321 AATAAACAAATTTAAAAAATTT
1 AATAAACAAATTTAAAAAATTT
1753343 AATAAA-AACATTTAAAAAAT
1 AATAAACAA-ATTTAAAAAAT
1753363 AATTCCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (22 bp):
AATAAACAAATTTAAAAAATTT
Found at i:1758376 original size:32 final size:34
Alignment explanation
Indices: 1758334--1758402 Score: 90
Period size: 32 Copynumber: 2.1 Consensus size: 34
1758324 AAAAATATCA
1758334 TTTACA-TTTTTAAAATTTTTATAAATAATTT-TT
1 TTTACATTTTTTAAAA-TTTTATAAATAATTTCTT
**
1758367 TTTA-ATTTTTTATGATTTTATAAATAATTTCTT
1 TTTACATTTTTTAAAATTTTATAAATAATTTCTT
1758400 TTT
1 TTT
1758403 GTTTGGAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 16 0.50
33 16 0.50
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (34 bp):
TTTACATTTTTTAAAATTTTATAAATAATTTCTT
Found at i:1759623 original size:16 final size:18
Alignment explanation
Indices: 1759587--1759623 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
1759577 AATTTTCGTT
*
1759587 TAAATATTTTATAATTTA
1 TAAATATTTTATAATTAA
1759605 TAAA-ATTTTA-AATTAA
1 TAAATATTTTATAATTAA
1759621 TAA
1 TAA
1759624 TAATAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 6 0.33
18 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAATATTTTATAATTAA
Found at i:1767110 original size:22 final size:22
Alignment explanation
Indices: 1767080--1767122 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1767070 CAAACGTAAC
* *
1767080 AACAAAATAGTGAAATGATAGT
1 AACAAAATAATAAAATGATAGT
*
1767102 AACATAATAATAAAATGATAG
1 AACAAAATAATAAAATGATAG
1767123 CAAAACAGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.05, G:0.14, T:0.23
Consensus pattern (22 bp):
AACAAAATAATAAAATGATAGT
Found at i:1775382 original size:30 final size:30
Alignment explanation
Indices: 1775348--1775409 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
1775338 CTTAACAAGT
1775348 AAATGCCTCT-AAAATAATAACAAAATTAAC
1 AAATG-CTCTAAAAATAATAACAAAATTAAC
* *
1775378 AAATGCTTTAAAAATATTAACAAAATTAAC
1 AAATGCTCTAAAAATAATAACAAAATTAAC
1775408 AA
1 AA
1775410 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (30 bp):
AAATGCTCTAAAAATAATAACAAAATTAAC
Found at i:1776892 original size:18 final size:18
Alignment explanation
Indices: 1776869--1776911 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1776859 CACGGAGGAA
1776869 GAAGAAGAAGAACCAGAG
1 GAAGAAGAAGAACCAGAG
*
1776887 GAAGAAGAGGAACCAGAG
1 GAAGAAGAAGAACCAGAG
1776905 GAAGAAG
1 GAAGAAG
1776912 GAGTTCAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.53, C:0.09, G:0.37, T:0.00
Consensus pattern (18 bp):
GAAGAAGAAGAACCAGAG
Found at i:1783627 original size:29 final size:30
Alignment explanation
Indices: 1783593--1783651 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
1783583 TTTAGCCTAA
* *
1783593 TGTGTAATTTTGTAC-TTAAATTTTGATTT
1 TGTGTAATTTTATACATAAAATTTTGATTT
1783622 TGTGTAATTTTATACATAAAATTTTGATTT
1 TGTGTAATTTTATACATAAAATTTTGATTT
1783652 GATCCAGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.29, C:0.03, G:0.12, T:0.56
Consensus pattern (30 bp):
TGTGTAATTTTATACATAAAATTTTGATTT
Found at i:1784394 original size:24 final size:25
Alignment explanation
Indices: 1784357--1784414 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
1784347 ATTATATTTT
* * *
1784357 TATTTATGTAAATATATTTATTAAAA
1 TATTTATATAAATA-ATTAAATAAAA
1784383 -ATTTATAT-AATAATTAAATAAAA
1 TATTTATATAAATAATTAAATAAAA
1784406 TATTTATAT
1 TATTTATAT
1784415 GGAATTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 9 0.32
24 12 0.43
25 7 0.25
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
TATTTATATAAATAATTAAATAAAA
Found at i:1787029 original size:28 final size:29
Alignment explanation
Indices: 1786996--1787052 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
1786986 ATAAGAAAAT
1786996 ATCATTAAAATAACATAAAAAAAA-AACA
1 ATCATTAAAATAACATAAAAAAAACAACA
1787024 ATCATTAAAATAACATAAAAAAAACAACA
1 ATCATTAAAATAACATAAAAAAAACAACA
1787053 TTTTTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (29 bp):
ATCATTAAAATAACATAAAAAAAACAACA
Found at i:1787047 original size:14 final size:14
Alignment explanation
Indices: 1787002--1787053 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
1786992 AAATATCATT
1787002 AAAATAACATAAAA
1 AAAATAACATAAAA
* **
1787016 AAAA-AACAATCATT
1 AAAATAAC-ATAAAA
1787030 AAAATAACATAAAA
1 AAAATAACATAAAA
*
1787044 AAAACAACAT
1 AAAATAACAT
1787054 TTTTTTTTGT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 3 0.10
14 23 0.79
15 3 0.10
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAATAACATAAAA
Found at i:1790255 original size:30 final size:32
Alignment explanation
Indices: 1790216--1790276 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
1790206 TCTTGAATTT
*
1790216 GACACA-TTTTCCTAATTTGGTACTTAAACTA
1 GACACATTTTTCCTAAGTTGGTACTTAAACTA
*
1790247 GACA-ATTTTTCTTAAGTTGGTACTTAAACT
1 GACACATTTTTCCTAAGTTGGTACTTAAACT
1790277 GTTTGGGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.41
Consensus pattern (32 bp):
GACACATTTTTCCTAAGTTGGTACTTAAACTA
Found at i:1790701 original size:22 final size:23
Alignment explanation
Indices: 1790661--1790708 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
1790651 TTTAAAATTT
*
1790661 AATATGCTATTTTC-TTTTTTAA
1 AATATGCTATTTTCGTTTTGTAA
*
1790683 AATATGCTATTTTGGTTTTGTAA
1 AATATGCTATTTTCGTTTTGTAA
1790706 AAT
1 AAT
1790709 TTAATATGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.54
Consensus pattern (23 bp):
AATATGCTATTTTCGTTTTGTAA
Found at i:1791198 original size:56 final size:57
Alignment explanation
Indices: 1791113--1791232 Score: 161
Period size: 56 Copynumber: 2.1 Consensus size: 57
1791103 ATTAAACCTA
* * * *
1791113 AAAAAAAGCTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGGTATCAAATTGGG
1 AAAAAAAGCTTAGGTACCAAATTAAGAAAAAATGTCAAATTCAAGTATCAAATTGAG
* * * *
1791170 AAAAAAA-TTTAGGTACCAATTTAAGAAAAATTGTCAAATTCAAGTATCGAATTGAG
1 AAAAAAAGCTTAGGTACCAAATTAAGAAAAAATGTCAAATTCAAGTATCAAATTGAG
1791226 AAAAAAA
1 AAAAAAA
1791233 AAATTGTTAC
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
56 48 0.87
57 7 0.13
ACGTcount: A:0.50, C:0.09, G:0.17, T:0.24
Consensus pattern (57 bp):
AAAAAAAGCTTAGGTACCAAATTAAGAAAAAATGTCAAATTCAAGTATCAAATTGAG
Found at i:1791253 original size:56 final size:55
Alignment explanation
Indices: 1791112--1791256 Score: 157
Period size: 56 Copynumber: 2.6 Consensus size: 55
1791102 AATTAAACCT
* * *
1791112 AAAAAAAAGCTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGGTATCAAATTGG
1 AAAAAAAA-ATTAGGTACCAAATTA-GAAAAAATGTCAAATTCAAGTATCAAATTGG
* * * * *
1791169 GAAAAAAATTTAGGTACCAATTTAAGAAAAATTGTCAAATTCAAGTATCGAATTGAG
1 AAAAAAAAATTAGGTACCAAATT-AGAAAAAATGTCAAATTCAAGTATCAAATTG-G
*
1791226 AAAAAAAAAATT-GTTACCAAATTAGAAAAAA
1 -AAAAAAAAATTAGGTACCAAATTAGAAAAAA
1791257 AACATAGGTT
Statistics
Matches: 73, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
56 46 0.63
57 18 0.25
58 9 0.12
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (55 bp):
AAAAAAAAATTAGGTACCAAATTAGAAAAAATGTCAAATTCAAGTATCAAATTGG
Found at i:1809335 original size:31 final size:31
Alignment explanation
Indices: 1809300--1809358 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1809290 CAAAATAGTT
*
1809300 ATTGAATTATTCGA-AGGTTTTTATTTAAATA
1 ATTGAACTATTCGATA-GTTTTTATTTAAATA
* *
1809331 ATTGAGCTATTTGATAGTTTTTATTTAA
1 ATTGAACTATTCGATAGTTTTTATTTAA
1809359 GTCATTGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.96
32 1 0.04
ACGTcount: A:0.32, C:0.03, G:0.14, T:0.51
Consensus pattern (31 bp):
ATTGAACTATTCGATAGTTTTTATTTAAATA
Found at i:1818080 original size:44 final size:43
Alignment explanation
Indices: 1818028--1818131 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 43
1818018 CACTCCATTA
* * *
1818028 CAACTTTAGGGAGATAGAATTTGTTCATTCAGTCTG-TCCCACTG
1 CAACTTTAGGGAGATAGAATTTCTT-ACTCAGCCTGCT-CCACTG
* * *
1818072 CAATTTTAGGGGGATAAGACTTTCTTACTCAGCCTGCTCCACTG
1 CAACTTTAGGGAGAT-AGAATTTCTTACTCAGCCTGCTCCACTG
*
1818116 CAACTTCAGGGAGATA
1 CAACTTTAGGGAGATA
1818132 AGACCAGATG
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
43 1 0.02
44 39 0.80
45 9 0.18
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (43 bp):
CAACTTTAGGGAGATAGAATTTCTTACTCAGCCTGCTCCACTG
Found at i:1818839 original size:9 final size:9
Alignment explanation
Indices: 1818820--1818849 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1818810 AAGCGATTTT
1818820 GAGTGAAAAC
1 GAGT-AAAAC
1818830 GAGTAAAAC
1 GAGTAAAAC
1818839 GAGTAAAAC
1 GAGTAAAAC
1818848 GA
1 GA
1818850 CATAATCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.80
10 4 0.20
ACGTcount: A:0.53, C:0.10, G:0.27, T:0.10
Consensus pattern (9 bp):
GAGTAAAAC
Found at i:1819320 original size:51 final size:50
Alignment explanation
Indices: 1819264--1819562 Score: 314
Period size: 51 Copynumber: 5.9 Consensus size: 50
1819254 AGTGAAAGTG
* *
1819264 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAAT
1 TTGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAAT
* * * * * * *
1819314 AATGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTATCGAGAAGCT
1 -TTGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAA-AT
* * *
1819366 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAAT
1 TTGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAAT
* * * * * *
1819416 GATGGTCACATGTGTAGTACTAAGCGAAGGCTACTATGTGTACCGA-AAAGCT
1 -TTGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAA--T
* * *
1819468 TTAGTCACATATGTAGTACTATGTGAAGGCTACTACGTGAATCG-TAAAAC
1 TTGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAATCGAT-AAAT
* * *
1819518 TTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 TTGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
1819563 ATGATAATAG
Statistics
Matches: 199, Mismatches: 42, Indels: 14
0.78 0.16 0.05
Matches are distributed among these distances:
50 43 0.22
51 151 0.76
52 5 0.03
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (50 bp):
TTGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAAT
Found at i:1819445 original size:102 final size:102
Alignment explanation
Indices: 1819264--1819563 Score: 442
Period size: 102 Copynumber: 3.0 Consensus size: 102
1819254 AGTGAAAGTG
1819264 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
* *
1819329 AGTACTAAGTGAAGGCTACAATGTGTATCGAGAAGCT
66 AGTACTAAGTGAAGGCTACTATGTGTATCGAAAAGCT
* *
1819366 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
* *
1819431 AGTACTAAGCGAAGGCTACTATGTGTACCGAAAAGCT
66 AGTACTAAGTGAAGGCTACTATGTGTATCGAAAAGCT
* * * * * * *
1819468 TTAGTCACATATGTAGTACTATGTGAAGGCTACTACGTGAATCG-TAAA-ACTTGATCACGTGTG
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTG
* *
1819531 TAGTACTATGTGAAGGCTACTACGTGTATCGAA
65 TAGTACTAAGTGAAGGCTACTATGTGTATCGAA
1819564 TGATAATAGT
Statistics
Matches: 178, Mismatches: 19, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
101 43 0.24
102 135 0.76
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (102 bp):
TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
AGTACTAAGTGAAGGCTACTATGTGTATCGAAAAGCT
Found at i:1819738 original size:14 final size:15
Alignment explanation
Indices: 1819714--1819742 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1819704 TTTTTCTGTG
1819714 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
1819729 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
1819743 AGTTTCGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:1819961 original size:15 final size:14
Alignment explanation
Indices: 1819937--1819990 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
1819927 AGTTTTTATA
*
1819937 ATAATTATAAAGGTT
1 ATAATAATAAA-GTT
*
1819952 ATAATAATAAA-TA
1 ATAATAATAAAGTT
*
1819965 ATATATTATAAAGTT
1 ATA-ATAATAAAGTT
1819980 ATAATAATAAA
1 ATAATAATAAA
1819991 AACAAACATA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 4 0.12
14 14 0.44
15 14 0.44
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (14 bp):
ATAATAATAAAGTT
Found at i:1819980 original size:28 final size:28
Alignment explanation
Indices: 1819934--1819990 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 28
1819924 TATAGTTTTT
1819934 ATAATAATTATAAAGGTTATAATAATAA
1 ATAATAATTATAAAGGTTATAATAATAA
1819962 ATAATATATTATAAA-GTTATAATAATAA
1 ATAATA-ATTATAAAGGTTATAATAATAA
1819990 A
1 A
1819991 AACAAACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (28 bp):
ATAATAATTATAAAGGTTATAATAATAA
Found at i:1821804 original size:41 final size:41
Alignment explanation
Indices: 1821759--1821897 Score: 224
Period size: 41 Copynumber: 3.4 Consensus size: 41
1821749 GTCTTTAAGT
* *
1821759 CTAGCAGGCTAAGTGTCAGTGATCTAAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAAAC
* *
1821800 CTAGCAAGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAAAC
* *
1821841 CTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAAAC
1821882 CTAGCAGGCTAAGTGC
1 CTAGCAGGCTAAGTGC
1821898 TGGTGAATAT
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 90 1.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAAAC
Found at i:1824258 original size:44 final size:44
Alignment explanation
Indices: 1824188--1824287 Score: 146
Period size: 44 Copynumber: 2.3 Consensus size: 44
1824178 TCTGTAACTT
* * *
1824188 CAGGGAGATAAGATTCTCAATCTTCAACGTATTCCCCTGCTGAC
1 CAGGGAGATAAGATTCACAATCTTCAACCTATTCCACTGCTGAC
* * *
1824232 CAGGGAGGTAGGATTCACAATTTTCAACCTATTCCACTGCTGAC
1 CAGGGAGATAAGATTCACAATCTTCAACCTATTCCACTGCTGAC
1824276 CAGGGAGATAAG
1 CAGGGAGATAAG
1824288 GCTGGGGACT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (44 bp):
CAGGGAGATAAGATTCACAATCTTCAACCTATTCCACTGCTGAC
Found at i:1824345 original size:87 final size:87
Alignment explanation
Indices: 1824250--1824459 Score: 267
Period size: 87 Copynumber: 2.4 Consensus size: 87
1824240 TAGGATTCAC
* *
1824250 AATTTTCAACCTATTCCACTGCTGACCAGGGAGATAAGGCTGGGGACTTCGATCTGCTCCACTAC
1 AATTTTCAACCTACTCCACTGCTGACCAGGGAGATAAGGCTGGGGACTTCGATCTACTCCACTAC
* *
1824315 TGCTTAGGGAGATAAGATCTAT
66 TGCTTAAGGAGATAAGATATAT
** *** * * ** *
1824337 AATTTTCAACCTACTCCACTATTGTTTAGGGAGACAAGGTTGGGGTTTTTGATCTACTCCACTAC
1 AATTTTCAACCTACTCCACTGCTGACCAGGGAGATAAGGCTGGGGACTTCGATCTACTCCACTAC
* *
1824402 TGCTTAAGGAGATATGATATGT
66 TGCTTAAGGAGATAAGATATAT
*
1824424 AATTTTTAACCTACTCCACTGCTGACCAGGGAGATA
1 AATTTTCAACCTACTCCACTGCTGACCAGGGAGATA
1824460 GGATTCACAA
Statistics
Matches: 100, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
87 100 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (87 bp):
AATTTTCAACCTACTCCACTGCTGACCAGGGAGATAAGGCTGGGGACTTCGATCTACTCCACTAC
TGCTTAAGGAGATAAGATATAT
Found at i:1824443 original size:44 final size:43
Alignment explanation
Indices: 1824306--1824443 Score: 141
Period size: 44 Copynumber: 3.2 Consensus size: 43
1824296 CTTCGATCTG
* *
1824306 CTCCACTACTGCTTAGGGAGATAAGATCTATAATTTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGAT-TGTAATTTTTAACCTA
* * * * *** * *
1824350 CTCCACTATTGTTTAGGGAGACAAGGTTGGGGTTTTTGATCTA
1 CTCCACTACTGCTTAGGGAGATAAGATTGTAATTTTTAACCTA
* *
1824393 CTCCACTACTGCTTAAGGAGATATGATATGTAATTTTTAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGAT-TGTAATTTTTAACCTA
1824437 CTCCACT
1 CTCCACT
1824444 GCTGACCAGG
Statistics
Matches: 71, Mismatches: 22, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
43 30 0.42
44 41 0.58
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (43 bp):
CTCCACTACTGCTTAGGGAGATAAGATTGTAATTTTTAACCTA
Found at i:1824631 original size:88 final size:88
Alignment explanation
Indices: 1824516--1825036 Score: 742
Period size: 88 Copynumber: 5.9 Consensus size: 88
1824506 GTTGGGGTCA
* * * * *
1824516 TCGATCTGCTTCGTTGTCGGTGCAGGAAGGCAAGATATGCTATTTTTAACCTGCTCCACTACAAC
1 TCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAAC
1824581 CCAGGGAGGCAAGGCTGGTATCT
66 CCAGGGAGGCAAGGCTGGTATCT
* *
1824604 TCGATCTGCTTCGCTGTCGATGCAGGAAGACAAGATCTGCTATCTTCAACTTGCTCCACTACAAC
1 TCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAAC
*
1824669 CTA-GGAGGGCAAGGCTGGTATCT
66 CCAGGGA-GGCAAGGCTGGTATCT
* * *
1824692 TCGATCTGCTTAGCTGTCGATGCAGGAAGGCAAGATCTGCTATATTCAACCTGCTCCACTGCAAC
1 TCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAAC
*
1824757 CCAGGGAGGCAAGGTTGGTATCT
66 CCAGGGAGGCAAGGCTGGTATCT
* *
1824780 TCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATATGCTATCTTCAACCTGCTCCACGACAAC
1 TCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAAC
* * * *
1824845 CCAAGGATGCAAGACTGGTATCG
66 CCAGGGAGGCAAGGCTGGTATCT
1824868 TCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAAC
1 TCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAAC
* *
1824933 CCAAGTAGGCAAGGCTGGTATCT
66 CCAGGGAGGCAAGGCTGGTATCT
* * * * * *
1824956 TCGATCTGTTTCGCCT-TC-AGTACATGAAGGCAAGATCTGTTATTTTCAACCTGCTCCACTGCA
1 TCGATCTGCTTCG-CTGTCGA-TGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
* *
1825019 AACCAGGAAGGCAAGGCT
64 ACCCAGGGAGGCAAGGCT
1825037 TTGTGATTTC
Statistics
Matches: 389, Mismatches: 40, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
87 4 0.01
88 380 0.98
89 5 0.01
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAAC
CCAGGGAGGCAAGGCTGGTATCT
Found at i:1831316 original size:24 final size:26
Alignment explanation
Indices: 1831274--1831331 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 26
1831264 AGTTGGAAAG
1831274 AAAAAATATATATAAATAT-G-TATA
1 AAAAAATATATATAAATATAGATATA
** *
1831298 AAAAAATATATATGTATATAGATTTA
1 AAAAAATATATATAAATATAGATATA
1831324 AAAAAATA
1 AAAAAATA
1831332 ATTACATATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 17 0.59
25 1 0.03
26 11 0.38
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAAAATATATATAAATATAGATATA
Found at i:1833456 original size:25 final size:28
Alignment explanation
Indices: 1833390--1833462 Score: 146
Period size: 28 Copynumber: 2.6 Consensus size: 28
1833380 ATAAAGGGAC
1833390 AGTCAAATATTATTTTTTTCCTAGAATA
1 AGTCAAATATTATTTTTTTCCTAGAATA
1833418 AGTCAAATATTATTTTTTTCCTAGAATA
1 AGTCAAATATTATTTTTTTCCTAGAATA
1833446 AGTCAAATATTATTTTT
1 AGTCAAATATTATTTTT
1833463 ATTCATTTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.48
Consensus pattern (28 bp):
AGTCAAATATTATTTTTTTCCTAGAATA
Found at i:1836613 original size:2 final size:2
Alignment explanation
Indices: 1836606--1836635 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1836596 ATTACTATGC
1836606 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
1836636 TTATGGATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1844483 original size:19 final size:19
Alignment explanation
Indices: 1844433--1844484 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
1844423 TTTTATATTA
*
1844433 TTAAATTTAATTATTATCC
1 TTAAACTTAATTATTATCC
*
1844452 TTAATACAT-ATTATTAAT-C
1 TTAA-ACTTAATTATT-ATCC
1844471 TTAAACTTAATTAT
1 TTAAACTTAATTAT
1844485 ATCTTGAGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 3 0.11
19 20 0.74
20 4 0.15
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAAACTTAATTATTATCC
Found at i:1848511 original size:31 final size:31
Alignment explanation
Indices: 1848438--1848511 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
1848428 TAATTTGCTC
* ** *
1848438 AATTTTAGTCCCTATGTTTTTTGAATTAGTC
1 AATTTTAGTCCTTATACTTTTTGAATTAGTA
1848469 AATTTTAGTCCTTATACTTTTTGAATTA-TGA
1 AATTTTAGTCCTTATACTTTTTGAATTAGT-A
1848500 AATTTTAGTCCT
1 AATTTTAGTCCT
1848512 GACTTGGTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 1 0.03
31 37 0.97
ACGTcount: A:0.26, C:0.12, G:0.11, T:0.51
Consensus pattern (31 bp):
AATTTTAGTCCTTATACTTTTTGAATTAGTA
Found at i:1855202 original size:11 final size:11
Alignment explanation
Indices: 1855186--1855214 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1855176 CAAGTGTAGG
1855186 TAAAAGTATCA
1 TAAAAGTATCA
1855197 TAAAAGTATCA
1 TAAAAGTATCA
1855208 TAAAAGT
1 TAAAAGT
1855215 TTTTATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.28
Consensus pattern (11 bp):
TAAAAGTATCA
Found at i:1855237 original size:26 final size:26
Alignment explanation
Indices: 1855201--1855255 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
1855191 GTATCATAAA
*
1855201 AGTATCATAAAAGTTTTTATATTAAG
1 AGTATCATAAAAATTTTTATATTAAG
1855227 AGTATCATAAAAATTTTTATATTAAG
1 AGTATCATAAAAATTTTTATATTAAG
1855253 AGT
1 AGT
1855256 CAAATTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.42
Consensus pattern (26 bp):
AGTATCATAAAAATTTTTATATTAAG
Found at i:1857036 original size:3 final size:3
Alignment explanation
Indices: 1857028--1857054 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1857018 CAAAAGGATT
1857028 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1857055 CAATTTTACA
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):
TTA
Found at i:1865299 original size:17 final size:18
Alignment explanation
Indices: 1865278--1865318 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1865268 TGTTGATTTT
* *
1865278 TTATTTTTTATTTTTAAA
1 TTATTTTATAATTTTAAA
1865296 -TATTTTATAATTTTAAA
1 TTATTTTATAATTTTAAA
1865313 TTATTT
1 TTATTT
1865319 GTTAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTTTATAATTTTAAA
Found at i:1865324 original size:18 final size:17
Alignment explanation
Indices: 1865282--1865324 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1865272 GATTTTTTAT
*
1865282 TTTTTATTTTTAAA-TA
1 TTTTTAATTTTAAATTA
1865298 TTTTATAATTTTAAATTA
1 TTTT-TAATTTTAAATTA
1865316 TTTGTTAAT
1 TTT-TTAAT
1865325 GATATAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 4 0.17
17 9 0.39
18 9 0.39
19 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTTAATTTTAAATTA
Found at i:1869649 original size:20 final size:21
Alignment explanation
Indices: 1869624--1869675 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1869614 AAGATTAAAA
*
1869624 TATAATTTTATA-TATCATTT
1 TATAATTTTATAGTATAATTT
*
1869644 TATAA-TTTAAAGTATAATTT
1 TATAATTTTATAGTATAATTT
1869664 TATAATTTTATA
1 TATAATTTTATA
1869676 AATTTATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.19
20 17 0.63
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TATAATTTTATAGTATAATTT
Found at i:1871025 original size:7 final size:7
Alignment explanation
Indices: 1871010--1871040 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1871000 TTTAGGACTA
1871010 AAATTTC
1 AAATTTC
*
1871017 AAATCTC
1 AAATTTC
1871024 AAATTTC
1 AAATTTC
1871031 AAATTTC
1 AAATTTC
1871038 AAA
1 AAA
1871041 AAGCATAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (7 bp):
AAATTTC
Found at i:1873377 original size:12 final size:13
Alignment explanation
Indices: 1873355--1873383 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1873345 TCCCATTACA
1873355 GTTTCCTGTTTCT
1 GTTTCCTGTTTCT
1873368 GTTT-CTGTTTCT
1 GTTTCCTGTTTCT
1873380 GTTT
1 GTTT
1873384 GGCCCTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.00, C:0.17, G:0.17, T:0.66
Consensus pattern (13 bp):
GTTTCCTGTTTCT
Found at i:1883199 original size:21 final size:20
Alignment explanation
Indices: 1883169--1883230 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
1883159 GTCATAATAA
*
1883169 AAAAACATATTAATTAATTAT
1 AAAAATATATTAATTAATT-T
* *
1883190 AAAAATATATAAATATTATTT
1 AAAAATATATTAAT-TAATTT
*
1883211 AAAAATA-ATTAAATAATTT
1 AAAAATATATTAATTAATTT
1883230 A
1 A
1883231 TATTTTATGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 6 0.18
20 4 0.12
21 20 0.59
22 4 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATATATTAATTAATTT
Found at i:1892270 original size:42 final size:43
Alignment explanation
Indices: 1892222--1892309 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
1892212 TCAATAGCCA
*
1892222 TTCAACGTTCATCTTA-AATTTGAATTTTGAAAAATCAGACCG
1 TTCAACGTTCATCTTATAATTTGAATTTTGAAAAACCAGACCG
*
1892264 TTCAACGTTCATCTTATATTTTGAATTTTGAAAAACCAGACCG
1 TTCAACGTTCATCTTATAATTTGAATTTTGAAAAACCAGACCG
1892307 TTC
1 TTC
1892310 CTCACCCCGT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
42 16 0.37
43 27 0.63
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (43 bp):
TTCAACGTTCATCTTATAATTTGAATTTTGAAAAACCAGACCG
Found at i:1893332 original size:12 final size:12
Alignment explanation
Indices: 1893317--1893349 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1893307 GAAGAAGCTG
1893317 AGAAAGAAACCA
1 AGAAAGAAACCA
*
1893329 AGAAAAAAACCA
1 AGAAAGAAACCA
1893341 AGAAAGAAA
1 AGAAAGAAA
1893350 GGGATCCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.73, C:0.12, G:0.15, T:0.00
Consensus pattern (12 bp):
AGAAAGAAACCA
Found at i:1897160 original size:9 final size:9
Alignment explanation
Indices: 1897146--1897233 Score: 83
Period size: 9 Copynumber: 9.8 Consensus size: 9
1897136 CTTGCCATGG
1897146 AAAGAAGGA
1 AAAGAAGGA
1897155 AAAGAA-G-
1 AAAGAAGGA
* *
1897162 -ATGAAAGA
1 AAAGAAGGA
*
1897170 CAAGAAGGA
1 AAAGAAGGA
1897179 GAAAGACAAGGA
1 -AAAG--AAGGA
*
1897191 CAAGAAGGA
1 AAAGAAGGA
*
1897200 AAAGAAAGA
1 AAAGAAGGA
1897209 AAAGAAGGA
1 AAAGAAGGA
1897218 AAAGAAGGA
1 AAAGAAGGA
1897227 AAAGAAG
1 AAAGAAG
1897234 ACCGAGAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
6 4 0.06
7 1 0.02
8 1 0.02
9 48 0.74
10 3 0.05
11 3 0.05
12 5 0.08
ACGTcount: A:0.65, C:0.03, G:0.31, T:0.01
Consensus pattern (9 bp):
AAAGAAGGA
Found at i:1897265 original size:18 final size:18
Alignment explanation
Indices: 1897220--1897267 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1897210 AAGAAGGAAA
*
1897220 AGAAGGAAAAGAAGACCG
1 AGAAGGAGAAGAAGACCG
* *
1897238 AG-AGCAAGAAGAAGCCCG
1 AGAAG-GAGAAGAAGACCG
1897256 AGAAGGAGAAGA
1 AGAAGGAGAAGA
1897268 GTAAGCACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
18 20 0.83
19 2 0.08
ACGTcount: A:0.52, C:0.12, G:0.35, T:0.00
Consensus pattern (18 bp):
AGAAGGAGAAGAAGACCG
Found at i:1929021 original size:24 final size:24
Alignment explanation
Indices: 1928985--1929049 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
1928975 TATTTTATGT
*
1928985 ATAAAGATATTTTTTAACAGTAAAA
1 ATAAATATATTTTTTAACA-TAAAA
*
1929010 ATAAATAT-TTTTTTAATATAAAA
1 ATAAATATATTTTTTAACATAAAA
*
1929033 ATTAAAT-TATTATTTAA
1 A-TAAATATATTTTTTAA
1929050 TCTAATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 7 0.20
24 21 0.60
25 7 0.20
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.45
Consensus pattern (24 bp):
ATAAATATATTTTTTAACATAAAA
Found at i:1933952 original size:2 final size:2
Alignment explanation
Indices: 1933945--1933969 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1933935 AATTCTTATC
1933945 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
1933970 ATGCTTATAA
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:1938039 original size:186 final size:188
Alignment explanation
Indices: 1937665--1938226 Score: 952
Period size: 186 Copynumber: 3.0 Consensus size: 188
1937655 CATTAGAGAG
* * * *
1937665 ATGTTTAATTCGTGTATACATGCCTTAGCTCATGTCCTTTTCATGTAAACCGTGTA-AATATAAA
1 ATGTTTAATTCGTGTATACATCCCTTAGCTCATGTTCTTTTCGTGTAAACCGTG-AGAGTATAAA
* * * *
1937729 TTCAATACAAATTATTATGTGTCAAAATCCTAAATACGAGTACAATAAATGTA-CTAAATGTGTT
65 TTCAATACAAATTATTATGTGTCAAGATCCTAAATATGAGTACAATAAATGTACCAAAATGCGTT
*
1937793 GTGTTTATGTCATGTTTTCAGATCGTCAAATCTAGAAAAGAAACCCGAGCAAAAAATGA
130 GTGTTTATGTCATGTTTTCATATCGTCAAATCTAGAAAAGAAACCCGAGCAAAAAATGA
*
1937852 ATGTTTAATTCGTGTATACATCCCTTAGCTCCTGTTCTTTTCGTGTAAACCGTGAGAGTATAAAT
1 ATGTTTAATTCGTGTATACATCCCTTAGCTCATGTTCTTTTCGTGTAAACCGTGAGAGTATAAAT
1937917 TCAATACAAATTA-T-TGTGTCAAGATCCTAAATATGAGTACAATAAATGTACCAAAATGCGTTG
66 TCAATACAAATTATTATGTGTCAAGATCCTAAATATGAGTACAATAAATGTACCAAAATGCGTTG
1937980 TGTTTATGTCATGTTTTCATATCGTCAAATCTAGAAAAGAAACCCGAGCAAAAAATGA
131 TGTTTATGTCATGTTTTCATATCGTCAAATCTAGAAAAGAAACCCGAGCAAAAAATGA
*
1938038 ATGTTTAATTCCTGTATACATCCCTTAGCTCATGTTCTTTTCGTGTAAACCGTGAGAGTATAAAT
1 ATGTTTAATTCGTGTATACATCCCTTAGCTCATGTTCTTTTCGTGTAAACCGTGAGAGTATAAAT
*
1938103 TCAATACAAATTATTATGTGTCATGATCCTAAATATGAGTACAATAAATGTACCAAAATGCGTTG
66 TCAATACAAATTATTATGTGTCAAGATCCTAAATATGAGTACAATAAATGTACCAAAATGCGTTG
***
1938168 TGTTTATGTCATGTTTTCATATCGTCAAATCTAGAAAAGAAGTGCGAGCAAAAAATGA
131 TGTTTATGTCATGTTTTCATATCGTCAAATCTAGAAAAGAAACCCGAGCAAAAAATGA
1938226 A
1 A
1938227 GGTACCTGAT
Statistics
Matches: 355, Mismatches: 16, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
185 34 0.10
186 145 0.41
187 72 0.20
188 104 0.29
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (188 bp):
ATGTTTAATTCGTGTATACATCCCTTAGCTCATGTTCTTTTCGTGTAAACCGTGAGAGTATAAAT
TCAATACAAATTATTATGTGTCAAGATCCTAAATATGAGTACAATAAATGTACCAAAATGCGTTG
TGTTTATGTCATGTTTTCATATCGTCAAATCTAGAAAAGAAACCCGAGCAAAAAATGA
Found at i:1955208 original size:116 final size:116
Alignment explanation
Indices: 1955055--1955288 Score: 432
Period size: 116 Copynumber: 2.0 Consensus size: 116
1955045 TAATTACCCA
* *
1955055 CAAAATTTCCGTGACGTAATAATTATGATCCCTAATTAAAGGCGGATTTGAAATCTAATTATTGT
1 CAAAACTTCCGTGACGTAATAATTATGATCCCTAATTAAAGACGGATTTGAAATCTAATTATTGT
1955120 ACAATTGATAGAAACTTAAAATCCGCCTTTCCCACGGTCTTATATAAGTAT
66 ACAATTGATAGAAACTTAAAATCCGCCTTTCCCACGGTCTTATATAAGTAT
1955171 CAAAACTTCCGTGACGTAATAATTATGATCCCTAATTAAAGACGGATTTGAAATCTAATTATTGT
1 CAAAACTTCCGTGACGTAATAATTATGATCCCTAATTAAAGACGGATTTGAAATCTAATTATTGT
* *
1955236 ATAATTGATATAAACTTAAAATCCGCCTTTCCCACGGTCTTATATAAGTAT
66 ACAATTGATAGAAACTTAAAATCCGCCTTTCCCACGGTCTTATATAAGTAT
1955287 CA
1 CA
1955289 GTTTCTTTTC
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 114 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.34
Consensus pattern (116 bp):
CAAAACTTCCGTGACGTAATAATTATGATCCCTAATTAAAGACGGATTTGAAATCTAATTATTGT
ACAATTGATAGAAACTTAAAATCCGCCTTTCCCACGGTCTTATATAAGTAT
Found at i:1958573 original size:26 final size:26
Alignment explanation
Indices: 1958543--1958626 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 26
1958533 GAAGTTATTT
1958543 ATATTTATAAATTCATATATACTTTA
1 ATATTTATAAATTCATATATACTTTA
***
1958569 ATA-TT-TAAA-TCATGATACTAAAGTA
1 ATATTTATAAATTCAT-ATA-TACTTTA
* *
1958594 A-ATATTAGAAATACATATATACTTTA
1 ATAT-TTATAAATTCATATATACTTTA
1958620 ATATTTA
1 ATATTTA
1958627 AATATTAAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
23 4 0.09
24 8 0.19
25 7 0.16
26 13 0.30
27 8 0.19
28 3 0.07
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (26 bp):
ATATTTATAAATTCATATATACTTTA
Found at i:1958624 original size:25 final size:23
Alignment explanation
Indices: 1958555--1958629 Score: 60
Period size: 25 Copynumber: 3.0 Consensus size: 23
1958545 ATTTATAAAT
*
1958555 TCATATATACTTTAATATTTAAA
1 TCATATATACTTTAATATTGAAA
** *
1958578 TCATGATACTAAAGTAAATATTAGAAA
1 TCAT-ATA-T-ACTTTAATATT-GAAA
*
1958605 TACATATATACTTTAATATTTAAA
1 T-CATATATACTTTAATATTGAAA
1958629 T
1 T
1958630 ATTAAAGTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
23 4 0.10
24 7 0.18
25 9 0.23
26 9 0.23
27 7 0.18
28 3 0.08
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (23 bp):
TCATATATACTTTAATATTGAAA
Found at i:1958656 original size:12 final size:12
Alignment explanation
Indices: 1958641--1958668 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1958631 TTAAAGTAAA
1958641 TATGCTAATAAC
1 TATGCTAATAAC
1958653 TATGCTAATAAC
1 TATGCTAATAAC
1958665 TATG
1 TATG
1958669 TGTTTAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (12 bp):
TATGCTAATAAC
Found at i:1962780 original size:25 final size:25
Alignment explanation
Indices: 1962733--1962781 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1962723 TGAGTATACT
* ** *
1962733 TTAAGTACCAAATTGGGATAAAAAA
1 TTAAGTACCAAAATGAAAAAAAAAA
1962758 TTAAGTACCAAAATGAAAAAAAAA
1 TTAAGTACCAAAATGAAAAAAAAA
1962782 TATTTTAGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.59, C:0.08, G:0.12, T:0.20
Consensus pattern (25 bp):
TTAAGTACCAAAATGAAAAAAAAAA
Found at i:1966964 original size:17 final size:18
Alignment explanation
Indices: 1966936--1966970 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1966926 CTGTAATCTA
*
1966936 AATTTTTAATAATATATT
1 AATTTTTAATAAAATATT
1966954 AATTTTT-ATAAAATATT
1 AATTTTTAATAAAATATT
1966971 TAAAAATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTTTTAATAAAATATT
Found at i:1966973 original size:18 final size:18
Alignment explanation
Indices: 1966936--1966973 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1966926 CTGTAATCTA
*
1966936 AATTTTTAATAATATATT
1 AATTTTTAAAAATATATT
1966954 AATTTTTATAAAATAT-TT
1 AATTTTTA-AAAATATATT
1966972 AA
1 AA
1966974 AAATATGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTTTTAAAAATATATT
Found at i:1974999 original size:2 final size:2
Alignment explanation
Indices: 1974992--1975017 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1974982 AATGTCCTGG
1974992 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
1975018 CACATATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1975564 original size:4 final size:4
Alignment explanation
Indices: 1975555--1975627 Score: 146
Period size: 4 Copynumber: 18.2 Consensus size: 4
1975545 CCTGTGGCTG
1975555 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1975603 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
1975628 CCATGCATGT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 69 1.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:1986600 original size:31 final size:31
Alignment explanation
Indices: 1986523--1986600 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 31
1986513 GTAATAAAAT
*
1986523 AGTTATTAAATTATTTGATAATTTTTATTTA
1 AGTTATTAAATTTTTTGATAATTTTTATTTA
* * * *
1986554 AATCATTAAAATTTTTTTATATTTTTTATTTA
1 AGTTATT-AAATTTTTTGATAATTTTTATTTA
*
1986586 AGTTATTAAGTTTTT
1 AGTTATTAAATTTTT
1986601 AAGATTTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 12 0.32
32 26 0.68
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.60
Consensus pattern (31 bp):
AGTTATTAAATTTTTTGATAATTTTTATTTA
Found at i:1990300 original size:13 final size:13
Alignment explanation
Indices: 1990284--1990308 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1990274 AATGGATAAT
1990284 TAAAAATAAAAAA
1 TAAAAATAAAAAA
1990297 TAAAAATAAAAA
1 TAAAAATAAAAA
1990309 CTTTGGGTTG
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:1999254 original size:45 final size:45
Alignment explanation
Indices: 1999171--1999310 Score: 178
Period size: 45 Copynumber: 3.1 Consensus size: 45
1999161 TATTGCCGGC
* * *
1999171 TTACTGATT-AGGCAC-TTATGTGCCGACTACTGTTACTGTTACTG
1 TTACTGATTCA-GCACTTTGTGTGTCGAATACTGTTACTGTTACTG
* *
1999215 TTACTGATTC-GATACTTTGTGTGTCGAATATTGTTACTGTTACTG
1 TTACTGATTCAG-CACTTTGTGTGTCGAATACTGTTACTGTTACTG
* *
1999260 TTACAGATTCAGCACTTTGTGTGTTGAATACTGTTACTGTTACTG
1 TTACTGATTCAGCACTTTGTGTGTCGAATACTGTTACTGTTACTG
1999305 TTACTG
1 TTACTG
1999311 CTACCGTTAC
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
43 1 0.01
44 11 0.13
45 69 0.84
46 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (45 bp):
TTACTGATTCAGCACTTTGTGTGTCGAATACTGTTACTGTTACTG
Found at i:1999299 original size:6 final size:6
Alignment explanation
Indices: 1999288--1999329 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
1999278 GTGTGTTGAA
* *
1999288 TACTGT TACTGT TACTGT TACTGC TACCGT TACTGTT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTG
1999330 ATCAGGTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (6 bp):
TACTGT
Found at i:2001155 original size:13 final size:13
Alignment explanation
Indices: 2001139--2001166 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2001129 CAATCTCTTT
2001139 TGGGTATTCTATA
1 TGGGTATTCTATA
2001152 TGGGTATTCTATA
1 TGGGTATTCTATA
2001165 TG
1 TG
2001167 TTCTTTTATC
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:0.21, C:0.07, G:0.25, T:0.46
Consensus pattern (13 bp):
TGGGTATTCTATA
Found at i:2003999 original size:45 final size:45
Alignment explanation
Indices: 2003916--2004055 Score: 178
Period size: 45 Copynumber: 3.1 Consensus size: 45
2003906 TATTGCCGGC
* * *
2003916 TTACTGATT-AGGCAC-TTATGTGCCGACTACTGTTACTGTTACTG
1 TTACTGATTCA-GCACTTTGTGTGTCGAATACTGTTACTGTTACTG
* *
2003960 TTACTGATTC-GATACTTTGTGTGTCGAATATTGTTACTGTTACTG
1 TTACTGATTCAG-CACTTTGTGTGTCGAATACTGTTACTGTTACTG
* *
2004005 TTACAGATTCAGCACTTTGTGTGTTGAATACTGTTACTGTTACTG
1 TTACTGATTCAGCACTTTGTGTGTCGAATACTGTTACTGTTACTG
2004050 TTACTG
1 TTACTG
2004056 CTACCGTTAC
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
43 1 0.01
44 11 0.13
45 69 0.84
46 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (45 bp):
TTACTGATTCAGCACTTTGTGTGTCGAATACTGTTACTGTTACTG
Found at i:2004044 original size:6 final size:6
Alignment explanation
Indices: 2004033--2004074 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
2004023 GTGTGTTGAA
* *
2004033 TACTGT TACTGT TACTGT TACTGC TACCGT TACTGTT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTG
2004075 ATCAGGTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (6 bp):
TACTGT
Found at i:2007744 original size:16 final size:16
Alignment explanation
Indices: 2007725--2007792 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
2007715 GATTTGCTAT
* *
2007725 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
2007741 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2007757 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2007773 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2007789 TACA
1 TACA
2007793 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:2010304 original size:27 final size:27
Alignment explanation
Indices: 2010266--2010320 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2010256 GATCATGACG
2010266 TGGGTAAGAAATATCATGTAATAAATT
1 TGGGTAAGAAATATCATGTAATAAATT
2010293 TGGGTAAGAAATATCATGTAATAAATT
1 TGGGTAAGAAATATCATGTAATAAATT
2010320 T
1 T
2010321 TTAAAAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.35
Consensus pattern (27 bp):
TGGGTAAGAAATATCATGTAATAAATT
Found at i:2024276 original size:23 final size:23
Alignment explanation
Indices: 2024250--2024325 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
2024240 ATAAGTGCCA
2024250 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
2024273 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
2024296 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
2024319 CACTGAT
1 CACTGAT
2024326 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:2024563 original size:18 final size:17
Alignment explanation
Indices: 2024537--2024575 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2024527 ATTTTCCTTC
2024537 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
2024554 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
2024572 CACA
1 CACA
2024576 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:2025855 original size:21 final size:21
Alignment explanation
Indices: 2025831--2025875 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2025821 AACACAAAAT
* *
2025831 AACCCATTTCCAACAGACCCA
1 AACCCATTACCAAAAGACCCA
*
2025852 AACCCATTACCAAAATACCCA
1 AACCCATTACCAAAAGACCCA
2025873 AAC
1 AAC
2025876 TAAACCCACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.40, G:0.02, T:0.13
Consensus pattern (21 bp):
AACCCATTACCAAAAGACCCA
Found at i:2027023 original size:23 final size:23
Alignment explanation
Indices: 2026980--2027024 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2026970 CCTACATTTT
* *
2026980 GGTTATTTATTTATTTGTTTTAA
1 GGTTATATATTTATTTATTTTAA
2027003 GGTTATATATATTA-TTATTTTA
1 GGTTATATAT-TTATTTATTTTA
2027025 TATATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.62
Consensus pattern (23 bp):
GGTTATATATTTATTTATTTTAA
Found at i:2027813 original size:18 final size:18
Alignment explanation
Indices: 2027775--2027813 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2027765 AAATATCATA
*
2027775 TTTCAAAAAAGGAAATTT
1 TTTCAAAAAAGGAAATGT
* *
2027793 TTTCAAATAAGGCAATGT
1 TTTCAAAAAAGGAAATGT
2027811 TTT
1 TTT
2027814 GCGTTTGGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (18 bp):
TTTCAAAAAAGGAAATGT
Found at i:2027982 original size:109 final size:109
Alignment explanation
Indices: 2027791--2028079 Score: 456
Period size: 109 Copynumber: 2.7 Consensus size: 109
2027781 AAAAGGAAAT
* * *
2027791 TTTTTCAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGTTGGGTG
1 TTTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTG
*
2027856 TCGATTTTTCTCGTTCAACCAAATGG-TTAAATATCCTTTTAAAA
66 TCGATTTTTCTCATTCAACCAAATGGCTT-AATATCCTTTTAAAA
* *
2027900 TTTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTACCCTAAGGTGCTGGGTG
1 TTTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTG
2027965 TCGATTTTTCTCATTCAACCAAATGGCTTAATATCCTTTTAAAA
66 TCGATTTTTCTCATTCAACCAAATGGCTTAATATCCTTTTAAAA
* * * * *
2028009 ATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-AAACGTGCCCTAATGTGCTGAGTT
1 TTTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTG
2028073 TCGATTT
66 TCGATTT
2028080 CTCGTTTAAC
Statistics
Matches: 166, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
108 27 0.16
109 137 0.83
110 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (109 bp):
TTTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTG
TCGATTTTTCTCATTCAACCAAATGGCTTAATATCCTTTTAAAA
Found at i:2030255 original size:15 final size:15
Alignment explanation
Indices: 2030237--2030270 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2030227 CCCAAAATAA
2030237 CAAACCACCTAAACC
1 CAAACCACCTAAACC
*
2030252 CAAACCACTTAAACC
1 CAAACCACCTAAACC
2030267 CAAA
1 CAAA
2030271 ACCCAATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.41, G:0.00, T:0.09
Consensus pattern (15 bp):
CAAACCACCTAAACC
Found at i:2033213 original size:37 final size:37
Alignment explanation
Indices: 2033152--2033297 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
2033142 TACGTATGAT
* *
2033152 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
2033187 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
2033224 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
2033261 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
2033298 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:2033314 original size:46 final size:46
Alignment explanation
Indices: 2033261--2033529 Score: 358
Period size: 46 Copynumber: 5.6 Consensus size: 46
2033251 TAAGTGTAGC
* **
2033261 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
2033307 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
2033353 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
2033405 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
2033457 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
2033503 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
2033530 AGTACTCAAA
Statistics
Matches: 207, Mismatches: 9, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
46 112 0.54
49 1 0.00
50 1 0.00
51 3 0.01
52 90 0.43
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:2033380 original size:52 final size:52
Alignment explanation
Indices: 2033304--2033523 Score: 326
Period size: 52 Copynumber: 4.3 Consensus size: 52
2033294 TAGCTAAAGC
* *
2033304 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
2033357 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * *
2033409 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
2033461 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
2033507 TATCACTTTATCACTTG
1 TATCACTTT-TCACTTG
2033524 ATCAGAAGTA
Statistics
Matches: 152, Mismatches: 8, Indels: 14
0.87 0.05 0.08
Matches are distributed among these distances:
46 43 0.28
50 1 0.01
52 93 0.61
53 15 0.10
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:2033472 original size:98 final size:94
Alignment explanation
Indices: 2033261--2033529 Score: 348
Period size: 98 Copynumber: 2.8 Consensus size: 94
2033251 TAAGTGTAGC
* ** *
2033261 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCAC--TTTGTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTTGTCA
2033324 CTTGATCAGATAAGTATAGCCGAAGCTAT
66 CTTGATCAGATAAGTATAGCCGAAGCTAT
2033353 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
* *
2033418 CCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
60 ----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
2033457 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCAC--TTTATCA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTTGTCA
2033520 CTTGATCAGA
66 CTTGATCAGA
2033530 AGTACTCAAA
Statistics
Matches: 157, Mismatches: 8, Indels: 24
0.83 0.04 0.13
Matches are distributed among these distances:
92 25 0.16
95 1 0.01
96 1 0.01
98 86 0.55
100 1 0.01
101 1 0.01
104 42 0.27
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (94 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTTGTCA
CTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:2035919 original size:35 final size:35
Alignment explanation
Indices: 2035843--2035911 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
2035833 ATGATTAAAC
**
2035843 AATTTAATAATATAAATAGTAAAAATGTGAAATTT
1 AATTTAATAATATAAATAGTAAAAATGAAAAATTT
* *
2035878 AATTTAATAATATAAATAGTAGACAT-AAAAATTT
1 AATTTAATAATATAAATAGTAAAAATGAAAAATTT
2035912 TTTTTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 6 0.20
35 24 0.80
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.36
Consensus pattern (35 bp):
AATTTAATAATATAAATAGTAAAAATGAAAAATTT
Found at i:2036124 original size:9 final size:9
Alignment explanation
Indices: 2036110--2036140 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2036100 GTTAAACGAA
2036110 TCGAGTTAT
1 TCGAGTTAT
*
2036119 TCGAGTTAA
1 TCGAGTTAT
2036128 TCGAGTTAT
1 TCGAGTTAT
2036137 TCGA
1 TCGA
2036141 ATCAACTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:2036212 original size:9 final size:9
Alignment explanation
Indices: 2036195--2036231 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
2036185 TGAGTTTTCG
2036195 AATTCGAAT
1 AATTCGAAT
*
2036204 AACTCGAAT
1 AATTCGAAT
2036213 AATTCGAAT
1 AATTCGAAT
2036222 AATTCGAAT
1 AATTCGAAT
2036231 A
1 A
2036232 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Done.