Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_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: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 24
Found at i:1177229 original size:21 final size:21
Alignment explanation
Indices: 1177203--1177275 Score: 128
Period size: 21 Copynumber: 3.5 Consensus size: 21
1177193 TATGCCATCT
1177203 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
1177224 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
* *
1177245 CCGCAGGGTTACATGCCTAGC
1 CCGCAGGGTTACATTCCGAGC
1177266 CCGCAGGGTT
1 CCGCAGGGTT
1177276 TTATACCATA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.18, C:0.33, G:0.30, T:0.19
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:1177825 original size:28 final size:28
Alignment explanation
Indices: 1177793--1177871 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
1177783 GATAAATGTT
* *
1177793 TTTAAAATACAAATTATATTATTCAAAA
1 TTTAAAATAAAAATAATATTATTCAAAA
1177821 TTTAAAATAAAAATAATATTATTCAAAA
1 TTTAAAATAAAAATAATATTATTCAAAA
*
1177849 TTTAAATTTAAAATATAA-ATTAT
1 TTTAAA-ATAAAA-ATAATATTAT
1177872 AGTATTCGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 32 0.70
29 10 0.22
30 4 0.09
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (28 bp):
TTTAAAATAAAAATAATATTATTCAAAA
Found at i:1177894 original size:34 final size:32
Alignment explanation
Indices: 1177794--1177894 Score: 111
Period size: 34 Copynumber: 3.2 Consensus size: 32
1177784 ATAAATGTTT
*
1177794 TTAAAATACAAATTATATTATTCAAAATTTAAA
1 TTAAAATATAAATTATA-TATTCAAAATTTAAA
*
1177827 ATAAAA-AT-AA-TAT-TATTCAAAATTTAAA
1 TTAAAATATAAATTATATATTCAAAATTTAAA
*
1177855 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATATAAATTATA-TATTCAAAATTTAA-A
1177890 TTAAA
1 TTAAA
1177895 TTTCAACTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
28 15 0.26
29 5 0.09
30 5 0.09
31 4 0.07
32 4 0.07
33 5 0.09
34 18 0.32
35 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (32 bp):
TTAAAATATAAATTATATATTCAAAATTTAAA
Found at i:1178516 original size:128 final size:128
Alignment explanation
Indices: 1178288--1178915 Score: 1109
Period size: 128 Copynumber: 4.9 Consensus size: 128
1178278 TTACCTGATT
*
1178288 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** **
1178353 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCT-GAAAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
* *
1178416 TACTGATATGA-ATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
1 TACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
1178480 CTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
65 CTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
1178544 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
1178609 TGACAAAATAATGGAAGACGTGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
1178672 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1178737 TGACAAAATAATGGAAGGCGTGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
1178800 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT-
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1178864 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
1178916 ACTCCGATTA
Statistics
Matches: 482, Mismatches: 15, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
127 53 0.11
128 428 0.89
129 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:1178999 original size:8 final size:8
Alignment explanation
Indices: 1178986--1179026 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1178976 TCACAAGCTT
1178986 TCAAATTC
1 TCAAATTC
1178994 TCAAATTC
1 TCAAATTC
* *
1179002 CCAAACTC
1 TCAAATTC
1179010 T-AAATTC
1 TCAAATTC
1179017 TCAAATTC
1 TCAAATTC
1179025 TC
1 TC
1179027 TAAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:1190493 original size:23 final size:22
Alignment explanation
Indices: 1190458--1190501 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1190448 GTAAGTTCTA
1190458 TTTATATAGTTTTGTTTTGTTTG
1 TTTATATAGTTTTG-TTTGTTTG
* *
1190481 TTTATTTATTTTTGTTTGTTT
1 TTTATATAGTTTTGTTTGTTT
1190502 AGTTAACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.11, C:0.00, G:0.14, T:0.75
Consensus pattern (22 bp):
TTTATATAGTTTTGTTTGTTTG
Found at i:1191336 original size:16 final size:18
Alignment explanation
Indices: 1191315--1191351 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
1191305 TTAATATTTT
1191315 ATTTTAAA-TAATTTA-A
1 ATTTTAAACTAATTTATA
1191331 ATTTTAAACTAATTTATA
1 ATTTTAAACTAATTTATA
1191349 ATT
1 ATT
1191352 ATATGTTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 7 0.37
18 4 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTAAACTAATTTATA
Found at i:1191431 original size:16 final size:16
Alignment explanation
Indices: 1191410--1191448 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
1191400 GGTGCTCAAC
*
1191410 GGTGCTCATCATTAGT
1 GGTGCTCATCATTAAT
1191426 GGTGCTCATCATTAAT
1 GGTGCTCATCATTAAT
1191442 GGTGCTC
1 GGTGCTC
1191449 GTCGAGCGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.36
Consensus pattern (16 bp):
GGTGCTCATCATTAAT
Found at i:1194655 original size:16 final size:16
Alignment explanation
Indices: 1194636--1194668 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1194626 TATATTTTAT
*
1194636 TTAAGATAAATTTAAA
1 TTAAGATAAATTAAAA
1194652 TTAAGATAAATTAAAA
1 TTAAGATAAATTAAAA
1194668 T
1 T
1194669 ATATATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (16 bp):
TTAAGATAAATTAAAA
Found at i:1194709 original size:18 final size:18
Alignment explanation
Indices: 1194676--1194727 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
1194666 AATATATATT
*
1194676 TTTAATGTTAAGATGTTAA
1 TTTAAT-TTAAGATGTGAA
*
1194695 TTTAATTTAATATGTGAA
1 TTTAATTTAAGATGTGAA
*
1194713 TTTAAGTTAAGATGT
1 TTTAATTTAAGATGT
1194728 AGTATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 23 0.79
19 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (18 bp):
TTTAATTTAAGATGTGAA
Found at i:1197731 original size:27 final size:27
Alignment explanation
Indices: 1197674--1197732 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
1197664 CTGAAGAGCT
* * *
1197674 TCCTCGTCTTCATCTTCCTCCCCCTCT
1 TCCTCGTCTTCATCTTCCACCCCCACA
* * *
1197701 TCCTTGTCTTCATCTTCCACTCCGACA
1 TCCTCGTCTTCATCTTCCACCCCCACA
1197728 TCCTC
1 TCCTC
1197733 TTCATCCTCT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.08, C:0.47, G:0.05, T:0.39
Consensus pattern (27 bp):
TCCTCGTCTTCATCTTCCACCCCCACA
Found at i:1199381 original size:29 final size:30
Alignment explanation
Indices: 1199300--1199365 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 30
1199290 GTGTAAGGAA
*
1199300 AAATAATTAAAATATGTTTTTTT-AAAGAT
1 AAATAATTAAATTATGTTTTTTTAAAAGAT
1199329 AAATAATTAAATTATGTTTTTTTAAAAGAT
1 AAATAATTAAATTATGTTTTTTTAAAAGAT
1199359 -AATAATT
1 AAATAATT
1199366 CATTATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 29 0.83
30 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (30 bp):
AAATAATTAAATTATGTTTTTTTAAAAGAT
Found at i:1199807 original size:12 final size:12
Alignment explanation
Indices: 1199790--1199832 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
1199780 GAAGGCGAAA
1199790 AAATAAACTAAT
1 AAATAAACTAAT
1199802 AAATAAAAGC-AA-
1 AAAT-AAA-CTAAT
1199814 AAATAAACTAAT
1 AAATAAACTAAT
1199826 AAATAAA
1 AAATAAA
1199833 AGCAAAGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 1 0.04
11 5 0.19
12 15 0.56
13 5 0.19
14 1 0.04
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.19
Consensus pattern (12 bp):
AAATAAACTAAT
Found at i:1199815 original size:24 final size:24
Alignment explanation
Indices: 1199788--1199838 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
1199778 TGGAAGGCGA
1199788 AAAAATAAACTAATAAATAAAAGC
1 AAAAATAAACTAATAAATAAAAGC
1199812 AAAAATAAACTAATAAATAAAAGC
1 AAAAATAAACTAATAAATAAAAGC
1199836 AAA
1 AAA
1199839 GCTAGGTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.73, C:0.08, G:0.04, T:0.16
Consensus pattern (24 bp):
AAAAATAAACTAATAAATAAAAGC
Found at i:1201128 original size:16 final size:16
Alignment explanation
Indices: 1201107--1201137 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1201097 ATATTCGACC
1201107 CATACCCAACTCAAAT
1 CATACCCAACTCAAAT
*
1201123 CATACCCAATTCAAA
1 CATACCCAACTCAAA
1201138 ATTTAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.19
Consensus pattern (16 bp):
CATACCCAACTCAAAT
Found at i:1201284 original size:16 final size:17
Alignment explanation
Indices: 1201248--1201291 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1201238 GTTGAAATTG
*
1201248 ATAAAAATTATTAATCG
1 ATAAAAATTATTAATCA
*
1201265 ATAAAAATTATT-TTCA
1 ATAAAAATTATTAATCA
1201281 ATAATAAATTA
1 ATAA-AAATTA
1201292 ACTTAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (17 bp):
ATAAAAATTATTAATCA
Found at i:1201375 original size:17 final size:17
Alignment explanation
Indices: 1201339--1201376 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1201329 TTTATAATAA
1201339 AATAATATAAAGTTTAAG
1 AATAATATAAAG-TTAAG
1201357 AATAATATAAAAG-TAAG
1 AATAATAT-AAAGTTAAG
1201374 AAT
1 AAT
1201377 CTAATTGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 8 0.42
19 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (17 bp):
AATAATATAAAGTTAAG
Found at i:1202465 original size:14 final size:13
Alignment explanation
Indices: 1202434--1202468 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1202424 TATAAACAAC
1202434 TTTTAAAATTATT
1 TTTTAAAATTATT
*
1202447 TTTTATAATTATAT
1 TTTTAAAATTAT-T
1202461 TTTTAAAA
1 TTTTAAAA
1202469 ATATAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAAATTATT
Found at i:1202473 original size:14 final size:14
Alignment explanation
Indices: 1202434--1202473 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1202424 TATAAACAAC
1202434 TTTTAAAATTAT-T
1 TTTTAAAATTATAT
*
1202447 TTTTATAATTATAT
1 TTTTAAAATTATAT
*
1202461 TTTTAAAAATATA
1 TTTTAAAATTATA
1202474 ATTATTCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTAAAATTATAT
Found at i:1202500 original size:26 final size:27
Alignment explanation
Indices: 1202434--1202500 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 27
1202424 TATAAACAAC
* *
1202434 TTTTAAAATTATTTTTTATAATTATAT
1 TTTTAAAATAATTTTCTATAATTATAT
1202461 TTTTAAAAATATAATTATTCT-TAATT-TAT
1 TTTT--AAA-ATAATT-TTCTATAATTATAT
1202490 TTTTAAAATAA
1 TTTTAAAATAA
1202501 AAATAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
26 4 0.12
27 7 0.21
29 10 0.29
30 10 0.29
31 3 0.09
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTTAAAATAATTTTCTATAATTATAT
Found at i:1203484 original size:15 final size:14
Alignment explanation
Indices: 1203455--1203481 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1203445 ATCGAAACAA
1203455 AAATAAAATTTTTG
1 AAATAAAATTTTTG
1203469 AAATAAAATTTTT
1 AAATAAAATTTTT
1203482 TGAGTTTGAG
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:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
AAATAAAATTTTTG
Found at i:1214427 original size:17 final size:17
Alignment explanation
Indices: 1214405--1214454 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1214395 AAATTCTTCT
1214405 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
*
1214422 AACATT--T--ATACTCA
1 AACATTCATAGAAAC-CA
1214436 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
1214453 AA
1 AA
1214455 ACATAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 3 0.12
14 8 0.31
15 1 0.04
16 1 0.04
17 10 0.38
18 3 0.12
ACGTcount: A:0.52, C:0.22, G:0.04, T:0.22
Consensus pattern (17 bp):
AACATTCATAGAAACCA
Found at i:1223879 original size:20 final size:20
Alignment explanation
Indices: 1223854--1223903 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1223844 AGAGAGTAAG
1223854 GCAGCTTTGTTGCGTTGAGA
1 GCAGCTTTGTTGCGTTGAGA
1223874 GCAGCTTTGTTGCGTTGAGA
1 GCAGCTTTGTTGCGTTGAGA
1223894 GCAGCTTTGT
1 GCAGCTTTGT
1223904 CTCTAAGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.14, C:0.16, G:0.34, T:0.36
Consensus pattern (20 bp):
GCAGCTTTGTTGCGTTGAGA
Found at i:1224495 original size:200 final size:204
Alignment explanation
Indices: 1224116--1224502 Score: 665
Period size: 200 Copynumber: 1.9 Consensus size: 204
1224106 AATTAATATT
1224116 AATTAATTTAATTATTTAAATGTTTGTTAATATTTTAATAAAATAAAGAATTTAATCCCTTAATG
1 AATTAATTTAATTATTTAAATGTTTGTTAATATTTTAATAAAATAAAGAATTTAATCCCTTAATG
1224181 TTTTTTTTTATAAAATAGTTTAATCCCTTAATCACTCAGATTTGAATGTATTATACTTCTTTTAC
66 -TTTTTTTTATAAAATAGTTTAATCCCTTAATCACTCAGATTTGAATGTATTATACTTCTTTTAC
*
1224246 AAGTTACATTTTCGCTGTCATTTTTTCATCTACCAAAGTCTTTAAAATTCTTTAAAACATTTGAT
130 AAGTTACATTTTCGCTGTCATTTTTTCATATACCAAAGTCTTTAAAATTCTTTAAAACATTTGAT
1224311 TTATAATTTA
195 TTATAATTTA
*
1224321 AATTAATTTAATTATTTAAATGTTTGTTAATATTTTAATAAAATAAAGAATTTAATCCCTTCATG
1 AATTAATTTAATTATTTAAATGTTTGTTAATATTTTAATAAAATAAAGAATTTAATCCCTTAATG
* * * *
1224386 -TTTTTTT-T-AAATTGTTTAAT-CCTTGATCACTTAGATTTGAATGTATTATATTTCTTTTACA
66 TTTTTTTTATAAAATAGTTTAATCCCTTAATCACTCAGATTTGAATGTATTATACTTCTTTTACA
* *
1224447 AGTTACATTTTTGCTGTCATTTTTTCATATATCAAAGTCTTTAAAATTCTTTAAAA
131 AGTTACATTTTCGCTGTCATTTTTTCATATACCAAAGTCTTTAAAATTCTTTAAAA
1224503 GTGTAACGAT
Statistics
Matches: 174, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
200 91 0.52
201 11 0.06
202 1 0.01
203 7 0.04
205 64 0.37
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (204 bp):
AATTAATTTAATTATTTAAATGTTTGTTAATATTTTAATAAAATAAAGAATTTAATCCCTTAATG
TTTTTTTTATAAAATAGTTTAATCCCTTAATCACTCAGATTTGAATGTATTATACTTCTTTTACA
AGTTACATTTTCGCTGTCATTTTTTCATATACCAAAGTCTTTAAAATTCTTTAAAACATTTGATT
TATAATTTA
Found at i:1226622 original size:213 final size:214
Alignment explanation
Indices: 1226199--1226626 Score: 849
Period size: 213 Copynumber: 2.0 Consensus size: 214
1226189 TATTTATACC
1226199 AACTTAATAACATGCATAACATTCAATTAATTGAATGATCTAACTTTTTAAAAGTCAATTATCCA
1 AACTTAATAACATGCATAACATTCAATTAATTGAATGATCTAACTTTTTAAAAGTCAATTATCCA
1226264 TTTATAATTTTACTAATAATTGAATAAATCATTGCATTTTACCCAATATTTTATTCTTATGTTAT
66 TTTATAATTTTACTAATAATTGAATAAATCATTGCATTTTACCCAATATTTTATTCTTATGTTAT
1226329 TTGAATTTGATAAAAAAATAATACAAATTTCATTTTTCATAAATTTTGAGTCGATTTCAATTATT
131 TTGAATTTGATAAAAAAATAATACAAATTTCATTTTTCATAAATTTTGAGTCGATTTCAATTATT
1226394 TAACGAATCAAATTAGAGT
196 TAACGAATCAAATTAGAGT
1226413 AACTTAATAACATGCATAACATTCAATTAATTGAATGATCTAACTTTTTAAAAGTCAATTATCCA
1 AACTTAATAACATGCATAACATTCAATTAATTGAATGATCTAACTTTTTAAAAGTCAATTATCCA
1226478 TTTATAATTTTACTAATAATTGAATAAATCATTGCATTTT-CCCAATATTTTATTCTTATGTTAT
66 TTTATAATTTTACTAATAATTGAATAAATCATTGCATTTTACCCAATATTTTATTCTTATGTTAT
1226542 TTGAATTTGATAAAAAAATAATACAAATTTCATTTTTCATAAATTTTGAGTCGATTTCAATTATT
131 TTGAATTTGATAAAAAAATAATACAAATTTCATTTTTCATAAATTTTGAGTCGATTTCAATTATT
1226607 TAACGAATCAAATTAGAGT
196 TAACGAATCAAATTAGAGT
1226626 A
1 A
1226627 TTTTAATATT
Statistics
Matches: 214, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
213 109 0.51
214 105 0.49
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (214 bp):
AACTTAATAACATGCATAACATTCAATTAATTGAATGATCTAACTTTTTAAAAGTCAATTATCCA
TTTATAATTTTACTAATAATTGAATAAATCATTGCATTTTACCCAATATTTTATTCTTATGTTAT
TTGAATTTGATAAAAAAATAATACAAATTTCATTTTTCATAAATTTTGAGTCGATTTCAATTATT
TAACGAATCAAATTAGAGT
Found at i:1228251 original size:17 final size:18
Alignment explanation
Indices: 1228229--1228263 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1228219 CACCAAAGCT
1228229 GCCTCCA-TTTCGAATCA
1 GCCTCCATTTTCGAATCA
1228246 GCCTCCATTTTCGAATCA
1 GCCTCCATTTTCGAATCA
1228264 AGAAGCGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.23, C:0.34, G:0.11, T:0.31
Consensus pattern (18 bp):
GCCTCCATTTTCGAATCA
Found at i:1239189 original size:23 final size:23
Alignment explanation
Indices: 1239189--1239285 Score: 106
Period size: 26 Copynumber: 4.0 Consensus size: 23
1239179 ATAACTATCT
1239189 TATC-TCTTTATTAAGAGATAAC
1 TATCTTCTTTATTAAGAGATAAC
1239211 TATCTATCTCTTTATTAAGAGATAAC
1 TATC--T-TCTTTATTAAGAGATAAC
* *
1239237 TATATTATTTATTAAGAGATAAC
1 TATCTTCTTTATTAAGAGATAAC
1239260 TATCTTATCTCTTTATTAAGAGATAA
1 TATC---T-TCTTTATTAAGAGATAA
1239286 GCAGGTGAGG
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
22 4 0.06
23 20 0.32
24 1 0.02
26 22 0.35
27 16 0.25
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.43
Consensus pattern (23 bp):
TATCTTCTTTATTAAGAGATAAC
Found at i:1239225 original size:26 final size:27
Alignment explanation
Indices: 1239167--1239285 Score: 176
Period size: 27 Copynumber: 4.6 Consensus size: 27
1239157 AAATGGTCTT
*
1239167 TTTATCTAAAAGATAACTATCTTATCTC
1 TTTAT-TAAGAGATAACTATCTTATCTC
1239195 TTTATTAAGAGATAACTATC-TATCTC
1 TTTATTAAGAGATAACTATCTTATCTC
*
1239221 TTTATTAAGAGATAACTA---TAT-TA
1 TTTATTAAGAGATAACTATCTTATCTC
1239244 TTTATTAAGAGATAACTATCTTATCTC
1 TTTATTAAGAGATAACTATCTTATCTC
1239271 TTTATTAAGAGATAA
1 TTTATTAAGAGATAA
1239286 GCAGGTGAGG
Statistics
Matches: 84, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
23 19 0.23
24 3 0.04
26 27 0.32
27 30 0.36
28 5 0.06
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.43
Consensus pattern (27 bp):
TTTATTAAGAGATAACTATCTTATCTC
Found at i:1241121 original size:22 final size:22
Alignment explanation
Indices: 1241091--1241141 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1241081 CGGGACATAT
* *
1241091 ACAATATACAGAGGTCCTTCAGG
1 ACAA-ATACAGAAGTCATTCAGG
* *
1241114 ACAAATACATAAGTCATTCGGG
1 ACAAATACAGAAGTCATTCAGG
1241136 ACAAAT
1 ACAAAT
1241142 TTCACATGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (22 bp):
ACAAATACAGAAGTCATTCAGG
Found at i:1241858 original size:21 final size:21
Alignment explanation
Indices: 1241832--1241972 Score: 212
Period size: 21 Copynumber: 6.7 Consensus size: 21
1241822 AGATGAAGTT
*
1241832 ACTGTAGCAGTACATCGATAC
1 ACTGTAGCAGTGCATCGATAC
*
1241853 ACTGTAGCAGTGCATCGGTAC
1 ACTGTAGCAGTGCATCGATAC
*
1241874 ACTGTAGCAGTGCATTGATAC
1 ACTGTAGCAGTGCATCGATAC
*
1241895 ACTGTAGCAGTGCATCAATAC
1 ACTGTAGCAGTGCATCGATAC
*
1241916 ACTGTAGCAGTGCATCAATAC
1 ACTGTAGCAGTGCATCGATAC
*
1241937 ACTGTATCAGTGCATC-AGTAC
1 ACTGTAGCAGTGCATCGA-TAC
1241958 ACTGTAGCAGTGCAT
1 ACTGTAGCAGTGCAT
1241973 TAGTACACTA
Statistics
Matches: 111, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
20 1 0.01
21 110 0.99
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.26
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATAC
Found at i:1248249 original size:23 final size:23
Alignment explanation
Indices: 1248223--1248291 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
1248213 GTCACCACAG
*
1248223 CTCGTATAATTGCACCGAAGTGC
1 CTCGTAGAATTGCACCGAAGTGC
1248246 CTCGTAGAATTGCACC-AGAGTGC
1 CTCGTAGAATTGCACCGA-AGTGC
* *
1248269 CGCGTAGAA-TGCACCGTAGTGC
1 CTCGTAGAATTGCACCGAAGTGC
1248291 C
1 C
1248292 ATATAATGTC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 13 0.32
23 28 0.68
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.22
Consensus pattern (23 bp):
CTCGTAGAATTGCACCGAAGTGC
Found at i:1248469 original size:103 final size:100
Alignment explanation
Indices: 1248291--1248518 Score: 386
Period size: 103 Copynumber: 2.2 Consensus size: 100
1248281 ACCGTAGTGC
** *
1248291 CATATAATGTCCATAAGGA-CACATATCATTCCTTAAGAATCATATCATACTAAGGATCAAGTAT
1 CATAT-ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATCATACCAAGGATCAAGTAT
1248355 GTGTCTCACCAGACTTCACACATGTTCCAAAGAATA
65 GTGTCTCACCAGACTTCACACATGTTCCAAAGAATA
1248391 CATATATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGT
1 CATATATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATAT-CATA--CCAAGGATCAAGT
1248456 ATGTGTCTCACCAGACTTCACACATGTTCCAAAGAATA
63 ATGTGTCTCACCAGACTTCACACATGTTCCAAAGAATA
1248494 CATATATGTCCCGAAGGACCACATA
1 CATATATGTCCCGAAGGACCACATA
1248519 GACCCTCGAC
Statistics
Matches: 121, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
99 11 0.09
100 31 0.26
101 4 0.03
103 75 0.62
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (100 bp):
CATATATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATCATACCAAGGATCAAGTATG
TGTCTCACCAGACTTCACACATGTTCCAAAGAATA
Found at i:1250159 original size:12 final size:12
Alignment explanation
Indices: 1250142--1250185 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
1250132 TTGACAAGTC
1250142 AAATTCAACTTA
1 AAATTCAACTTA
1250154 AAATTCAACTT-
1 AAATTCAACTTA
1250165 --A-TCAACTTA
1 AAATTCAACTTA
1250174 AAATTCAACTTA
1 AAATTCAACTTA
1250186 TCAACTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
8 7 0.25
9 1 0.04
11 1 0.04
12 19 0.68
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (12 bp):
AAATTCAACTTA
Found at i:1250171 original size:20 final size:20
Alignment explanation
Indices: 1250146--1250192 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
1250136 CAAGTCAAAT
1250146 TCAACTTAAAATTCAACTTA
1 TCAACTTAAAATTCAACTTA
1250166 TCAACTTAAAATTCAACTTA
1 TCAACTTAAAATTCAACTTA
1250186 TCAACTT
1 TCAACTT
1250193 TATTTCAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (20 bp):
TCAACTTAAAATTCAACTTA
Found at i:1252042 original size:24 final size:24
Alignment explanation
Indices: 1252014--1252066 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1252004 TGTAGTTCTT
* * *
1252014 TCACATAGCTCATCGTCATATAAA
1 TCACATAGCCCATAGACATATAAA
*
1252038 TCACATATCCCATAGACATATAAA
1 TCACATAGCCCATAGACATATAAA
1252062 -CACAT
1 TCACAT
1252067 GGTTCACTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (24 bp):
TCACATAGCCCATAGACATATAAA
Found at i:1257185 original size:16 final size:17
Alignment explanation
Indices: 1257164--1257205 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1257154 ATTATATATA
1257164 TATATATATAATATT-T
1 TATATATATAATATTAT
* *
1257180 TATATATTTTATATTAAT
1 TATATATATAATATT-AT
1257198 TATATATA
1 TATATATA
1257206 ATACAAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 13 0.62
18 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATATATAATATTAT
Found at i:1264378 original size:21 final size:22
Alignment explanation
Indices: 1264354--1264394 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1264344 AAAAAATAAT
*
1264354 CAAACGACA-AAAAAAATATGC
1 CAAAAGACAGAAAAAAATATGC
1264375 CAAAAGACAGAAAAAAATAT
1 CAAAAGACAGAAAAAAATAT
1264395 ATGAAGGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.66, C:0.15, G:0.10, T:0.10
Consensus pattern (22 bp):
CAAAAGACAGAAAAAAATATGC
Found at i:1268373 original size:24 final size:24
Alignment explanation
Indices: 1268346--1268429 Score: 107
Period size: 24 Copynumber: 3.5 Consensus size: 24
1268336 TGAATTTTGT
* *
1268346 TATGGTACCTGACCTGGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
* *
1268370 TATGATA-TTGACATGGATTATGA
1 TATGATACTTGACCTGGATTCTGA
* *
1268393 TCTGATACATGACCTGGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
1268417 TATGATACTTGAC
1 TATGATACTTGAC
1268430 TTGAATTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
23 19 0.39
24 30 0.61
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (24 bp):
TATGATACTTGACCTGGATTCTGA
Found at i:1270832 original size:3 final size:3
Alignment explanation
Indices: 1270824--1270852 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1270814 TTAGGAACGT
1270824 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1270853 TTATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1270857 original size:3 final size:3
Alignment explanation
Indices: 1270851--1270881 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1270841 ATAATAATAA
1270851 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1270882 CATTTACACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1271872 original size:17 final size:15
Alignment explanation
Indices: 1271836--1271866 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1271826 AAATTCTAAA
1271836 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
1271851 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
1271866 T
1 T
1271867 TTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:1273119 original size:22 final size:22
Alignment explanation
Indices: 1273094--1273136 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1273084 ACTTCTAAAT
*
1273094 TTCATCATGTATTCAATTTAAG
1 TTCATCACGTATTCAATTTAAG
*
1273116 TTCATCACGTGTTCAATTTAA
1 TTCATCACGTATTCAATTTAA
1273137 TTCCTACATC
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:0.30, C:0.16, G:0.09, T:0.44
Consensus pattern (22 bp):
TTCATCACGTATTCAATTTAAG
Found at i:1274800 original size:21 final size:21
Alignment explanation
Indices: 1274774--1274831 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
1274764 ATTTACCGTG
1274774 ATTGCGGCCGTCGC-GAGCGCT
1 ATTGCGGCCGTCGCGGA-CGCT
*
1274795 ATTGCGGTCGTCGCGGACGCT
1 ATTGCGGCCGTCGCGGACGCT
1274816 ATTGCGGCCGTCGCGG
1 ATTGCGGCCGTCGCGG
1274832 GTAACTCGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 32 0.94
22 2 0.06
ACGTcount: A:0.09, C:0.31, G:0.40, T:0.21
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGACGCT
Found at i:1281446 original size:200 final size:202
Alignment explanation
Indices: 1281100--1281575 Score: 536
Period size: 200 Copynumber: 2.4 Consensus size: 202
1281090 ATTACAAGTG
* * * *
1281100 TTTATAGGCACATTTGAGAGGCATTTTCAGGTAGTTAATTTAAAATTTTTTCGTAATTTATATAT
1 TTTATAGGCACATTCGAGAGGTATTTTCGGGTAGTTAATCTAAAATTTTTT-GTAATTTATA-A-
* **
1281165 GATTA-GAGGCGTAGTATTAAAATTTATTTTTCAATTAAGGCCAATATCAACACATACAAGATAT
63 GATTAGGAGGCGTAGTATTAAAACTTATTTTTCAACCAAGGCCAATATCAACACATACAAGATAT
* *
1281229 TGTAAGCATGTTAAAAATCGCATTGAAAATGGCTCCAAAG-TTTATTTTGTGCTTGAAGAAAAAA
128 TGTAAGCATGTTAAAAATCACATTGAAAATGGCTCCAAAGCTTGATTTTGTGCTTGAAGAAAAAA
1281293 CTAAAA-TGA
193 CTAAAATTGA
* *
1281302 TTTTATAGGCACAATCGAGAGGTTTTTTCGGGTAGTTAATCTAAAATTTTTTGTAATTTATAAGA
1 -TTTATAGGCACATTCGAGAGGTATTTTCGGGTAGTTAATCTAAAATTTTTTGTAATTTATAAGA
* * ** *
1281367 TTAGGA-GCGTAGTATTATAACTTATTTTTCAACCGAGGGTAATATCAATACATACAAGATATTG
65 TTAGGAGGCGTAGTATTAAAACTTATTTTTCAACCAAGGCCAATATCAACACATACAAGATATTG
* * * ** * * **
1281431 TAAGC-GGTTTAAAAATCACGTTGAAAATGGTTCTGAAGCTTGGTTTTGTTCTTGAAGAAAATGC
130 TAAGCATG-TTAAAAATCACATTGAAAATGGCTCCAAAGCTTGATTTTGTGCTTGAAGAAAAAAC
1281495 TAAAATTGA
194 TAAAATTGA
* ** ** * * *
1281504 TTGATAAACATGTTC-AGGGAGTATTTTCGGGAAGTTAATCT-AAATGTTTTCGTAATTTATAAG
1 TTTATAGGCACATTCGAGAG-GTATTTTCGGGTAGTTAATCTAAAAT-TTTTTGTAATTTATAAG
1281567 ATTA-GAGGC
64 ATTAGGAGGC
1281576 ATAATATTTT
Statistics
Matches: 231, Mismatches: 35, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
199 1 0.00
200 94 0.41
201 78 0.34
202 13 0.06
203 45 0.19
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (202 bp):
TTTATAGGCACATTCGAGAGGTATTTTCGGGTAGTTAATCTAAAATTTTTTGTAATTTATAAGAT
TAGGAGGCGTAGTATTAAAACTTATTTTTCAACCAAGGCCAATATCAACACATACAAGATATTGT
AAGCATGTTAAAAATCACATTGAAAATGGCTCCAAAGCTTGATTTTGTGCTTGAAGAAAAAACTA
AAATTGA
Found at i:1283937 original size:21 final size:21
Alignment explanation
Indices: 1283911--1283955 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1283901 GATTTCTGGG
* *
1283911 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1283932 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1283953 CAA
1 CAA
1283956 ACGAACAAGA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1284703 original size:2 final size:2
Alignment explanation
Indices: 1284696--1284747 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1284686 TTAGATTATG
1284696 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1284738 TA TA TA TA TA
1 TA TA TA TA TA
1284748 GAAATAATAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1285661 original size:140 final size:148
Alignment explanation
Indices: 1285471--1285767 Score: 425
Period size: 146 Copynumber: 2.1 Consensus size: 148
1285461 GAGTCGAGGG
* *
1285471 TCTACGCGCGTCCTTCGGGATATATATATTCTTTTGGAATATGTGTGAAGTCT-G-ATGACACAT
1 TCTACGCGCGTCCTTCGGGACATATATATTCTTTTGGAATATGTGTGAAGTCTGGAAAGACACAT
* *
1285534 A-TATGATCCCTAG-CATATGTAT-ATTCTTAA-GAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTA-AATCCCTAGACATATATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
*
1285595 TATGGCACT-CCGTGCAAT
130 TATGACACTACCGTGCAAT
*
1285613 TCTAC-CG-GTCCTTCGGGACATATGTTATTC-TTTGGAATATGTGTGAAGTCTGGAAAGACACA
1 TCTACGCGCGTCCTTCGGGACATAT-ATATTCTTTTGGAATATGTGTGAAGTCTGGAAAGACACA
*
1285675 TACTAAATCCCTAGTATATATATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
65 TACTAAATCCCTAG-ACATATATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
*
1285740 ATATGACACTACGGTGCAAT
129 ATATGACACTACCGTGCAAT
1285760 TCTACGCG
1 TCTACGCG
1285768 GCACTTCGGT
Statistics
Matches: 137, Mismatches: 8, Indels: 14
0.86 0.05 0.09
Matches are distributed among these distances:
140 36 0.26
141 8 0.06
142 22 0.16
143 2 0.01
144 7 0.05
145 8 0.06
146 39 0.28
147 13 0.09
148 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (148 bp):
TCTACGCGCGTCCTTCGGGACATATATATTCTTTTGGAATATGTGTGAAGTCTGGAAAGACACAT
ACTAAATCCCTAGACATATATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTAT
ATGACACTACCGTGCAAT
Found at i:1287700 original size:11 final size:11
Alignment explanation
Indices: 1287684--1287736 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
1287674 AAAATTCAGG
*
1287684 AGCTCGATTGA
1 AGCTCGATTCA
* *
1287695 AGCTCGAGACTCG
1 AGCTC--GATTCA
1287708 AGCTCGATTCA
1 AGCTCGATTCA
1287719 AGCTCGATTCA
1 AGCTCGATTCA
1287730 AGCTCGA
1 AGCTCGA
1287737 ACTCAAAACT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 27 0.77
13 8 0.23
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:1289895 original size:16 final size:17
Alignment explanation
Indices: 1289874--1289909 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1289864 AGATGATAGT
1289874 TTTAGTTAAT-ATTAGG
1 TTTAGTTAATAATTAGG
*
1289890 TTTAGTTTATAATTAGG
1 TTTAGTTAATAATTAGG
1289907 TTT
1 TTT
1289910 TTATATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.56
Consensus pattern (17 bp):
TTTAGTTAATAATTAGG
Found at i:1290193 original size:7 final size:7
Alignment explanation
Indices: 1290183--1290226 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
1290173 GTTAAATTTG
1290183 TAAATCC
1 TAAATCC
1290190 TAAATCC
1 TAAATCC
* *
1290197 TACATCT
1 TAAATCC
*
1290204 TAAACCC
1 TAAATCC
1290211 TAAATCC
1 TAAATCC
*
1290218 TAAACCC
1 TAAATCC
1290225 TA
1 TA
1290227 TCACTTAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAATCC
Found at i:1290212 original size:14 final size:14
Alignment explanation
Indices: 1290183--1290226 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1290173 GTTAAATTTG
*
1290183 TAAATCCTAAATCC
1 TAAATCCTAAACCC
* *
1290197 TACATCTTAAACCC
1 TAAATCCTAAACCC
1290211 TAAATCCTAAACCC
1 TAAATCCTAAACCC
1290225 TA
1 TA
1290227 TCACTTAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAATCCTAAACCC
Found at i:1290661 original size:5 final size:5
Alignment explanation
Indices: 1290651--1290682 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1290641 ATCATATTTT
1290651 TATTA TATTA TATTA TATT- TATTA TATT- TATT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATT
1290683 GTGAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
TATTA
Found at i:1290675 original size:9 final size:9
Alignment explanation
Indices: 1290649--1290682 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
1290639 GAATCATATT
1290649 TTTATTATA
1 TTTATTATA
1290658 TTATATTATA
1 TT-TATTATA
1290668 TTTATTATA
1 TTTATTATA
1290677 TTTATT
1 TTTATT
1290683 GTGAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTATTATA
Found at i:1292561 original size:73 final size:72
Alignment explanation
Indices: 1292443--1292596 Score: 245
Period size: 73 Copynumber: 2.1 Consensus size: 72
1292433 TCTCAAACTT
* * * *
1292443 TTTTTTGGGCCCCTATTTTTTGGGCTTCTTAATGGCAACAACTGATAGATATACTTGATTTCGGG
1 TTTTTTGGGCCCATATTTTTAGGGCTTCTTAATGGCAACAACTGATAGATAGACTCGATTTCGGG
*
1292508 GCTCCTA
66 GCCCCTA
*
1292515 TTTTTTGGGCCCATATTATTTAGGGCTTCTTAATGGCAACATCTGATAGATAGACTCGATTTCGG
1 TTTTTTGGGCCCATATT-TTTAGGGCTTCTTAATGGCAACAACTGATAGATAGACTCGATTTCGG
1292580 GGCCCCTA
65 GGCCCCTA
1292588 TTTTTTGGG
1 TTTTTTGGG
1292597 GCCCTGCGCA
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
72 16 0.21
73 59 0.79
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (72 bp):
TTTTTTGGGCCCATATTTTTAGGGCTTCTTAATGGCAACAACTGATAGATAGACTCGATTTCGGG
GCCCCTA
Found at i:1312242 original size:23 final size:26
Alignment explanation
Indices: 1312216--1312266 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 26
1312206 ATTTATTTTA
1312216 ATTTTTTA-AAAAAAATAAA-A-AAT
1 ATTTTTTATAAAAAAATAAATATAAT
*
1312239 A-TTTTTATTAAAAAATAAATATAAT
1 ATTTTTTATAAAAAAATAAATATAAT
1312264 ATT
1 ATT
1312267 AAAAAAAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
22 6 0.26
23 11 0.48
24 1 0.04
25 4 0.17
26 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
ATTTTTTATAAAAAAATAAATATAAT
Found at i:1312245 original size:22 final size:21
Alignment explanation
Indices: 1312218--1312274 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
1312208 TTATTTTAAT
1312218 TTTTTAAAAAAAATAAAAAATA
1 TTTTTAAAAAAAAT-AAAAATA
* *
1312240 TTTTTATTAAAAAATAAATATA
1 TTTTTA-AAAAAAATAAAAATA
* *
1312262 ATATTAAAAAAAA
1 TTTTTAAAAAAAA
1312275 CCTTTTTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 6 0.21
22 16 0.55
23 7 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TTTTTAAAAAAAATAAAAATA
Found at i:1312753 original size:22 final size:23
Alignment explanation
Indices: 1312727--1312774 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
1312717 CCAAAAATTG
1312727 AAAAATATAAC-GATAGAAAC-TT
1 AAAAATATAACTGATA-AAACGTT
1312749 AAAAATATAACTGATAAAACGTT
1 AAAAATATAACTGATAAAACGTT
1312772 AAA
1 AAA
1312775 CACTTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.23
Consensus pattern (23 bp):
AAAAATATAACTGATAAAACGTT
Found at i:1313478 original size:330 final size:331
Alignment explanation
Indices: 1312862--1313525 Score: 1240
Period size: 330 Copynumber: 2.0 Consensus size: 331
1312852 AATTTATATT
*
1312862 TAATTGATTTATAGGTAAGTTTAAATAATTTAATAATTGAATTTGATATGTCATATGATGATTAG
1 TAATTGATTTATAGGTAAGTTTAAATAATTTAATAATTGAATTTAATATGTCATATGATGATTAG
**
1312927 ACTTATTATGGACAATTTTGCAACTATGACTACGTCATGACATGGTATGCCCCCACTGTTTCCTC
66 ACTTATTATGGACAATCATGCAACTATGACTACGTCATGACATGGTATGCCCCCACTGTTTCCTC
1312992 TGTTCTGTTCCTTGAATTTTGGGACCCTCAAGACAAACCCCAACCAAAGGTGCATTGAATTGGGC
131 TGTTCTGTTCCTTGAATTTTGGGACCCTCAAGACAAACCCCAACCAAAGGTGCATTGAATTGGGC
1313057 ATTTCATTGTCCTAATTAGCTGCACATATAGACCGAATAATATTACATGATACCATTATATAATT
196 ATTTCATTGTCCTAATTAGCTGCACATATAGACCGAATAATATTACATGATACCATTATATAATT
* *
1313122 ACCGGAAAATTCTATAATGTTATACGAGCATTATACGTATCATTAATAATGAGTATTATTAATTT
261 ACCGGAAAATTCTATAATGCTATACGAGCATCATACGTATCATTAATAATGAGTATTATTAATTT
1313187 AATTTA
326 AATTTA
* *
1313193 TAATTGTTTTATAGTTAAGTTTAAATAATTTAATAATTGAATTTAATATGTCATATGATGATTAG
1 TAATTGATTTATAGGTAAGTTTAAATAATTTAATAATTGAATTTAATATGTCATATGATGATTAG
1313258 ACTTATTATGGACAATCATGCAAC-ATGACTACGTCATGACATGGTATGCCCCCACTGTTTCCTC
66 ACTTATTATGGACAATCATGCAACTATGACTACGTCATGACATGGTATGCCCCCACTGTTTCCTC
*
1313322 TGTTCTGTTCCTTGAATTTTGGGACCCTCGAGACAAACCCCAACCAAAGGTGCATTGAATTGGGC
131 TGTTCTGTTCCTTGAATTTTGGGACCCTCAAGACAAACCCCAACCAAAGGTGCATTGAATTGGGC
1313387 ATTTCATTGTCCTAATTAGCTGCACATATAGACCGAATAATATTACATGATACCATTATATAATT
196 ATTTCATTGTCCTAATTAGCTGCACATATAGACCGAATAATATTACATGATACCATTATATAATT
*
1313452 ATCGGAAAATTCTATAATGCTATACGAGCATCATACGTATCATTAATAATGAGTATTATTAATTT
261 ACCGGAAAATTCTATAATGCTATACGAGCATCATACGTATCATTAATAATGAGTATTATTAATTT
1313517 AATTTA
326 AATTTA
1313523 TAA
1 TAA
1313526 AAAATTAAAT
Statistics
Matches: 324, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
330 240 0.74
331 84 0.26
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (331 bp):
TAATTGATTTATAGGTAAGTTTAAATAATTTAATAATTGAATTTAATATGTCATATGATGATTAG
ACTTATTATGGACAATCATGCAACTATGACTACGTCATGACATGGTATGCCCCCACTGTTTCCTC
TGTTCTGTTCCTTGAATTTTGGGACCCTCAAGACAAACCCCAACCAAAGGTGCATTGAATTGGGC
ATTTCATTGTCCTAATTAGCTGCACATATAGACCGAATAATATTACATGATACCATTATATAATT
ACCGGAAAATTCTATAATGCTATACGAGCATCATACGTATCATTAATAATGAGTATTATTAATTT
AATTTA
Found at i:1315626 original size:13 final size:13
Alignment explanation
Indices: 1315608--1315653 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
1315598 TTTAAATATT
1315608 ATAAAAAATATAA
1 ATAAAAAATATAA
*
1315621 ATAAAATATATAA
1 ATAAAAAATATAA
1315634 ATAACCAAAATATAA
1 ATAA--AAAATATAA
1315649 TATAA
1 -ATAA
1315654 CCTATGATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 16 0.57
15 8 0.29
16 4 0.14
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (13 bp):
ATAAAAAATATAA
Found at i:1317452 original size:21 final size:21
Alignment explanation
Indices: 1317409--1317452 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1317399 TTTGATATAT
*** *
1317409 AAAACAACTTTTATTTAATAA
1 AAAACAACTTTTAACCAAAAA
1317430 AAAACAACTTTTAACCAAAAA
1 AAAACAACTTTTAACCAAAAA
1317451 AA
1 AA
1317453 TATTTGATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAACAACTTTTAACCAAAAA
Found at i:1324429 original size:3 final size:3
Alignment explanation
Indices: 1324421--1324450 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1324411 CGAGTTTTCA
*
1324421 ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1324451 CACATCTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1324789 original size:21 final size:22
Alignment explanation
Indices: 1324754--1324808 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
1324744 AAATAATAAT
* *
1324754 AAAATAT-TATTTTTATTCAATA
1 AAAATATATA-TTTAATTCAAAA
*
1324776 AAAATATATATTTAATTGAAAA
1 AAAATATATATTTAATTCAAAA
1324798 AATAATATATA
1 AA-AATATATA
1324809 GAGGAGTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AAAATATATATTTAATTCAAAA
Found at i:1325235 original size:2 final size:2
Alignment explanation
Indices: 1325228--1325272 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1325218 ATTAAAATCT
1325228 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1325270 TA T
1 TA T
1325273 TGTAAATAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1325461 original size:21 final size:20
Alignment explanation
Indices: 1325414--1325452 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1325404 CCCAAAATCC
**
1325414 CTATAATTTTAAATTTTCAA
1 CTATAATTTTAAAAATTCAA
1325434 CTATAATTTTAAAAATTCA
1 CTATAATTTTAAAAATTCA
1325453 TATTATAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (20 bp):
CTATAATTTTAAAAATTCAA
Found at i:1331690 original size:105 final size:105
Alignment explanation
Indices: 1331569--1331776 Score: 371
Period size: 105 Copynumber: 2.0 Consensus size: 105
1331559 CAAATCCTGG
* * *
1331569 TTGAACCGGCCTTTCTTTTGTCTTTGTGCCAGACATGGTCTTGAAGTCTGCTATCAATAACCAAA
1 TTGAACCGGCCTTTCTTTTGTATTTGGGCCAGACATGGTCTTGAAATCTGCTATCAATAACCAAA
*
1331634 TATATATCTTTTCGATGTGATCAATTCATCAAACATGGTC
66 AATATATCTTTTCGATGTGATCAATTCATCAAACATGGTC
1331674 TTGAACCGGCCTTTCTTTTGTATTTGGGCCAGACATGGTCTTGAAATCTGCTATCAATAACCAAA
1 TTGAACCGGCCTTTCTTTTGTATTTGGGCCAGACATGGTCTTGAAATCTGCTATCAATAACCAAA
*
1331739 AATATATCTTTTCGATGTGATCGATTCATCAAACATGG
66 AATATATCTTTTCGATGTGATCAATTCATCAAACATGG
1331777 ACAATCTATT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 98 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (105 bp):
TTGAACCGGCCTTTCTTTTGTATTTGGGCCAGACATGGTCTTGAAATCTGCTATCAATAACCAAA
AATATATCTTTTCGATGTGATCAATTCATCAAACATGGTC
Found at i:1331881 original size:17 final size:19
Alignment explanation
Indices: 1331859--1331894 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
1331849 ACTTCCGGTT
1331859 TTTTGAAA-AAAA-ATTAC
1 TTTTGAAATAAAATATTAC
1331876 TTTTGAAATAAAATATTAC
1 TTTTGAAATAAAATATTAC
1331895 CTATCAGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 4 0.24
19 5 0.29
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (19 bp):
TTTTGAAATAAAATATTAC
Found at i:1332278 original size:17 final size:17
Alignment explanation
Indices: 1332256--1332292 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1332246 TAGTTTTTAG
1332256 TAATTTTATTA-TTATTT
1 TAATTTT-TTATTTATTT
1332273 TAATTTTTTATTTATTT
1 TAATTTTTTATTTATTT
1332290 TAA
1 TAA
1332293 ACTAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TAATTTTTTATTTATTT
Found at i:1333265 original size:21 final size:24
Alignment explanation
Indices: 1333241--1333283 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1333231 TCAAGAGTAA
1333241 ATTTATT-TT-TA-AATAATATTT
1 ATTTATTATTATAGAATAATATTT
1333262 ATTTATTATTATAGAATAATAT
1 ATTTATTATTATAGAATAATAT
1333284 ATATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 2 0.11
23 2 0.11
24 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTTATTATTATAGAATAATATTT
Found at i:1333287 original size:2 final size:2
Alignment explanation
Indices: 1333280--1333329 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1333270 TTATAGAATA
1333280 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1333322 AT AT AT AT
1 AT AT AT AT
1333330 TAGGTGGTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1334667 original size:22 final size:22
Alignment explanation
Indices: 1334625--1334674 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1334615 TATTTCTTTA
* *
1334625 TTATGTATTTGAATCTTATTTT
1 TTATGTATTTGAATCTAATTTG
*
1334647 TTATGTATTTTGTATC-AATTTG
1 TTATGTA-TTTGAATCTAATTTG
1334669 TTATGT
1 TTATGT
1334675 TTCTCTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.22, C:0.04, G:0.12, T:0.62
Consensus pattern (22 bp):
TTATGTATTTGAATCTAATTTG
Found at i:1336566 original size:82 final size:83
Alignment explanation
Indices: 1336419--1336611 Score: 221
Period size: 82 Copynumber: 2.3 Consensus size: 83
1336409 AGGGGATGCA
* *
1336419 TTTTTCCATTATTATTCAGAGAATATCTGGATTATAATAATAATCTATCTCATCCAAAATAAAAG
1 TTTTTCCATTATTATTCAAAGAATATCTGGATTATAATAATAATCTATCCCATCCAAAATAAAAG
* *
1336484 GCGCGTTCAAG-GA-ATTG
66 GCGCGTT-AAGAGATAATC
* * ** *
1336501 TTTTTCCATTATTATTCAAAGAATATCTGGATTATAATAGTGATAC-ATCCCATCTGAAATGAAA
1 TTTTTCCATTATTATTCAAAGAATATCTGGATTATAATAATAAT-CTATCCCATCCAAAATAAAA
* * **
1336565 GGTGTGTTTTGAGATAATC
65 GGCGCGTTAAGAGATAATC
*
1336584 ATTTTCCATTATTATTCAAAGAATATCT
1 TTTTTCCATTATTATTCAAAGAATATCT
1336612 ATCGTGTCAG
Statistics
Matches: 94, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
81 1 0.01
82 63 0.67
83 30 0.32
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (83 bp):
TTTTTCCATTATTATTCAAAGAATATCTGGATTATAATAATAATCTATCCCATCCAAAATAAAAG
GCGCGTTAAGAGATAATC
Found at i:1336701 original size:81 final size:81
Alignment explanation
Indices: 1336502--1336857 Score: 308
Period size: 83 Copynumber: 4.3 Consensus size: 81
1336492 AAGGAATTGT
* * * * * * *
1336502 TTTTCCATTATTATTCAAAGAATATCTG-GATTATAATAGTGATACATCCCATCTGAAATGAAAG
1 TTTTCCATTATTATTCAAAGAATCTCTGTCA-TGTCAGAGTGTTCCATCCCATCTGAAAT-AAAG
** * * *
1336566 GTGTGTTT-TGAGATAATCA
64 ACGCGTTTCAGGGA-AA-CA
* * * * *
1336585 TTTTCCATTATTATTCAAAGAATATCTATCGTGTCAGAGTGTTCCATCCTATATGAAATAAAGAC
1 TTTTCCATTATTATTCAAAGAATCTCTGTCATGTCAGAGTGTTCCATCCCATCTGAAATAAAGAC
1336650 GCGTTTC-GGGAAAGCA
66 GCGTTTCAGGGAAA-CA
* *
1336666 TTTTCCATTATTATTCAGAGAATCTCTGTCATGTCATAGTGTTCCATCCCATCT-AAATTAAA-A
1 TTTTCCATTATTATTCAAAGAATCTCTGTCATGTCAGAGTGTTCCATCCCATCTGAAA-TAAAGA
* * *
1336729 GGCGTATTTCGGGGCAAACT
65 CGCG--TTTCAGGG-AAACA
* * * * *
1336749 TTTTTCATTATTATTTAAAGAATCTTTGCCATGTCAGAGTGTTCCATCCCATCCGAAATGAAAGA
1 TTTTCCATTATTATTCAAAGAATCTCTGTCATGTCAGAGTGTTCCATCCCATCTGAAAT-AAAGA
* *
1336814 TGCGTTTCATGGAAACA
65 CGCGTTTCAGGGAAACA
* *
1336831 TTTTCTATTATTATTCATAGAATCTCT
1 TTTTCCATTATTATTCAAAGAATCTCT
1336858 ACCACTTTAC
Statistics
Matches: 223, Mismatches: 40, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
80 7 0.03
81 55 0.25
82 42 0.19
83 106 0.48
84 9 0.04
85 4 0.02
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (81 bp):
TTTTCCATTATTATTCAAAGAATCTCTGTCATGTCAGAGTGTTCCATCCCATCTGAAATAAAGAC
GCGTTTCAGGGAAACA
Found at i:1336915 original size:8 final size:8
Alignment explanation
Indices: 1336896--1336951 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
1336886 TCCCTAGCCC
1336896 TAAACATCT
1 TAAAC-TCT
1336905 TAAACTCT
1 TAAACTCT
*
1336913 TAAATTCT
1 TAAACTCT
* *
1336921 AAAACTCA
1 TAAACTCT
*
1336929 TCAACTC-
1 TAAACTCT
1336936 TAAACTCT
1 TAAACTCT
*
1336944 CAAACTCT
1 TAAACTCT
1336952 CAAAACTTCA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
7 6 0.16
8 27 0.71
9 5 0.13
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.32
Consensus pattern (8 bp):
TAAACTCT
Found at i:1336940 original size:15 final size:15
Alignment explanation
Indices: 1336905--1336951 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1336895 CTAAACATCT
* *
1336905 TAAACTCTTAAATTC
1 TAAACTCTCAAACTC
1336920 TAAAACTCATC-AACTC
1 T-AAACTC-TCAAACTC
1336936 TAAACTCTCAAACTC
1 TAAACTCTCAAACTC
1336951 T
1 T
1336952 CAAAACTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 2 0.07
15 13 0.48
16 11 0.41
17 1 0.04
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAACTCTCAAACTC
Found at i:1336952 original size:8 final size:8
Alignment explanation
Indices: 1336906--1336974 Score: 54
Period size: 8 Copynumber: 8.6 Consensus size: 8
1336896 TAAACATCTT
*
1336906 AAACTCTT
1 AAACTCTC
* *
1336914 AAATTCTA
1 AAACTCTC
1336922 AAACTCATC
1 AAACTC-TC
1336931 -AACTCT-
1 AAACTCTC
1336937 AAACTCTC
1 AAACTCTC
1336945 AAACTCTC
1 AAACTCTC
1336953 AAAACT-TC
1 -AAACTCTC
*
1336961 AAAACACTC
1 -AAACTCTC
1336970 AAACT
1 AAACT
1336975 ACGAAAATGG
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
7 7 0.14
8 35 0.70
9 8 0.16
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (8 bp):
AAACTCTC
Found at i:1341287 original size:20 final size:20
Alignment explanation
Indices: 1341248--1341296 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1341238 ATCTAATTTT
*
1341248 ATTTAATATTTTATATAATA
1 ATTTAATATTTTAAATAATA
1341268 ATTTAA-ATTTTAAATCAAT-
1 ATTTAATATTTTAAAT-AATA
*
1341287 ATTTTATATT
1 ATTTAATATT
1341297 AATTTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTAATATTTTAAATAATA
Found at i:1341302 original size:30 final size:31
Alignment explanation
Indices: 1341252--1341311 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 31
1341242 AATTTTATTT
*
1341252 AATATTTTATATAATAATTTAAATTTTAAATC
1 AATATTTTATAT-ATAATTTAAATTATAAATC
1341284 AATATTTTATAT-TAATTTAAATTATAAA
1 AATATTTTATATATAATTTAAATTATAAA
1341312 CAAATAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 15 0.56
32 12 0.44
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (31 bp):
AATATTTTATATATAATTTAAATTATAAATC
Found at i:1343292 original size:19 final size:19
Alignment explanation
Indices: 1343265--1343302 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1343255 CCAAAGTTCG
*
1343265 CGTTGCGATTTTCCAAATT
1 CGTTACGATTTTCCAAATT
1343284 CGTTACGATTTTCCAAATT
1 CGTTACGATTTTCCAAATT
1343303 TACGTTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (19 bp):
CGTTACGATTTTCCAAATT
Found at i:1343343 original size:21 final size:21
Alignment explanation
Indices: 1343319--1343369 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1343309 AGTTCAAATT
*
1343319 CGTTGCGATAGTCTAAGTTCA
1 CGTTGCGATAGTCGAAGTTCA
*
1343340 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCGAAGTTCA
*
1343361 CATTGCGAT
1 CGTTGCGAT
1343370 TTTTCAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (21 bp):
CGTTGCGATAGTCGAAGTTCA
Found at i:1343813 original size:19 final size:19
Alignment explanation
Indices: 1343789--1343897 Score: 94
Period size: 19 Copynumber: 5.4 Consensus size: 19
1343779 TTATTTTGGA
1343789 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
*
1343808 TTTTTCACTATCACAACAACAC
1 TTTTTCACTAT--C-GCAACAC
*
1343830 GTTTTTCAAACTCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* *
1343852 ATTTTAACTATCGCAACA-
1 TTTTTCACTATCGCAACAC
*
1343870 TATTTTAACTATCGCAACAC
1 T-TTTTCACTATCGCAACAC
1343890 ATTTTTCA
1 -TTTTTCA
1343898 AAACCGCGTT
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
19 39 0.53
20 5 0.07
21 6 0.08
22 12 0.16
23 7 0.10
25 4 0.05
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.36
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:1345565 original size:111 final size:110
Alignment explanation
Indices: 1345371--1345703 Score: 567
Period size: 111 Copynumber: 3.0 Consensus size: 110
1345361 TTGAAATCAT
* * * *
1345371 ATATCTCTACACTTTACTGATATGGTAACATTTTACCGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
1345436 TATTTAGTTTATTTATTTAATGCATGATTATTATATTAAGAATTAA
66 TAATTAG-TTATTTATTTAATGCATGATTATTAGATTAAGAATTAA
1345482 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1345547 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTT-ATTTATTTAATGCATGATTATTAGATTAAGAATTAA
1345593 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
1345658 TAATTAGTTATTTTATTTAATGCATGATTATTAGAGTATGAATTAA
66 TAATTAGTTA-TTTATTTAATGCATGATTATTAGATTAAGAATTAA
1345704 TTTTTGTAAT
Statistics
Matches: 212, Mismatches: 8, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
110 3 0.01
111 209 0.99
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (110 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:1347239 original size:18 final size:18
Alignment explanation
Indices: 1347211--1347251 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1347201 CCCAGCAGCC
1347211 ACCGCAACCATATATGAT
1 ACCGCAACCATATATGAT
* *
1347229 GCCGCATCCATATATGAT
1 ACCGCAACCATATATGAT
1347247 ACCGC
1 ACCGC
1347252 CATCGCCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.22
Consensus pattern (18 bp):
ACCGCAACCATATATGAT
Found at i:1347626 original size:9 final size:9
Alignment explanation
Indices: 1347584--1347631 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
1347574 ACTTGCTCAG
*
1347584 GACGACGAC
1 GACGACGAT
*
1347593 GACGACGAC
1 GACGACGAT
*
1347602 GACGATGAT
1 GACGACGAT
**
1347611 GGTGACGAT
1 GACGACGAT
1347620 GACGACGAT
1 GACGACGAT
1347629 GAC
1 GAC
1347632 AGCGAGGAGT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.31, C:0.23, G:0.35, T:0.10
Consensus pattern (9 bp):
GACGACGAT
Found at i:1347882 original size:35 final size:33
Alignment explanation
Indices: 1347842--1347926 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
1347832 ATATTTCAGT
1347842 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
1347877 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
1347912 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
1347927 TAAATACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:1361746 original size:85 final size:83
Alignment explanation
Indices: 1361499--1361915 Score: 312
Period size: 85 Copynumber: 4.9 Consensus size: 83
1361489 GAAAATGATT
* * * **
1361499 AAATTAGGGGCTTAAATTATAAAAGTAAAAAGT-ATTATTG-AAAAATTAGGGATCTCAATTATA
1 AAATTA-GGGCATCAATTATAAAAGTAAAAAGTGA-GATTGAAAAAATTAGGGGCCTCAATTATA
*
1361562 AAGTCAAAAAGTGAGATTAAA
64 AAGT-AAAAAGTGAGATGAAA
* * * *
1361583 AAATTTAGGGTC-TCAATT-T-AAAGTAAAAAGTGAGATTGAAAATATTTAAGGGCTTAAATTAT
1 AAA-TTAGGG-CATCAATTATAAAAGTAAAAAGTGAGATTGAAAA-AATTAGGGGCCTCAATTAT
1361645 ATAAGTAAAAAGTGAGATCGAAA
63 A-AAGTAAAAAGTGAGAT-GAAA
*
1361668 AAATTAGGGCATCAATTATAAAAGTAAAAGGTGAGATTGAAAAAATTAGGGGCCTCAATTATAAA
1 AAATTAGGGCATCAATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGGGCCTCAATTATAAA
*
1361733 GGTAGAAAGTGAGATTGAAA
66 -GTAAAAAGTGAGA-TGAAA
* * * * * *** *
1361753 AAAATA-GGAACTCAATTATAAAAGTACAAAGTGGGATTGAAAAACTTAGTATCATCAATTATAA
1 AAATTAGGGCA-TCAATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGGGCCTCAATTATAA
*
1361817 ATATAAAAAAAAGT-AGGAGTGAAAA
65 A-GT---AAAAAGTGA-GA-TG-AAA
* * * * * * *
1361842 AAATTAAAGGCCTTAATTAT-AAAGATAAAAAATAAGGTT-ACAAAAATTAGGGGTCTCAATTAT
1 AAATT-AGGGCATCAATTATAAAAG-TAAAAAGTGAGATTGA-AAAAATTAGGGGCCTCAATTAT
1361905 AAAGATAAAAA
63 AAAG-TAAAAA
1361916 AAATTAAAAG
Statistics
Matches: 265, Mismatches: 45, Indels: 43
0.75 0.13 0.12
Matches are distributed among these distances:
82 16 0.06
83 6 0.02
84 54 0.20
85 99 0.37
86 23 0.09
87 6 0.02
88 10 0.04
89 12 0.05
90 37 0.14
91 2 0.01
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (83 bp):
AAATTAGGGCATCAATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGGGCCTCAATTATAAA
GTAAAAAGTGAGATGAAA
Found at i:1361817 original size:43 final size:42
Alignment explanation
Indices: 1361499--1361801 Score: 314
Period size: 42 Copynumber: 7.2 Consensus size: 42
1361489 GAAAATGATT
* *
1361499 AAATTAGGGGCTTAAATTATAAAAGTAAAAAGT-ATTATTG-AA
1 AAATTAGGGGC-TCAATTATAAAAGTAAAAAGTGA-GATTGAAA
*
1361541 AAATTAGGGATCTCAATTAT-AAAGTCAAAAAGTGAGATT-AAA
1 AAATTAGGG-GCTCAATTATAAAAGT-AAAAAGTGAGATTGAAA
*
1361583 AAATTTAGGGTCTCAATT-T-AAAGTAAAAAGTGAGATTGAAA
1 AAA-TTAGGGGCTCAATTATAAAAGTAAAAAGTGAGATTGAAA
* * * * *
1361624 ATATTTAAGGGCTTAAATTATATAAGTAAAAAGTGAGATCGAAA
1 A-AATTAGGGGC-TCAATTATAAAAGTAAAAAGTGAGATTGAAA
*
1361668 AAATTA-GGGCATCAATTATAAAAGTAAAAGGTGAGATTGAAA
1 AAATTAGGGGC-TCAATTATAAAAGTAAAAAGTGAGATTGAAA
* *
1361710 AAATTAGGGGCCTCAATTATAAAGGTAGAAAGTGAGATTGAAA
1 AAATTAGGGG-CTCAATTATAAAAGTAAAAAGTGAGATTGAAA
* ** * *
1361753 AAAATAGGAACTCAATTATAAAAGTACAAAGTGGGATTGAAA
1 AAATTAGGGGCTCAATTATAAAAGTAAAAAGTGAGATTGAAA
*
1361795 AACTTAG
1 AAATTAG
1361802 TATCATCAAT
Statistics
Matches: 223, Mismatches: 26, Indels: 24
0.82 0.10 0.09
Matches are distributed among these distances:
40 13 0.06
41 21 0.09
42 116 0.52
43 51 0.23
44 22 0.10
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (42 bp):
AAATTAGGGGCTCAATTATAAAAGTAAAAAGTGAGATTGAAA
Found at i:1363257 original size:22 final size:22
Alignment explanation
Indices: 1363214--1363302 Score: 160
Period size: 22 Copynumber: 4.0 Consensus size: 22
1363204 CTCGTATAAA
1363214 TGCACCGAAGTGCCTCGTAGAAT
1 TGCACCGAAGTGCC-CGTAGAAT
1363237 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1363259 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
1363281 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1363303 GATGTCCATA
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
22 51 0.78
23 14 0.22
ACGTcount: A:0.26, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1363290 original size:13 final size:13
Alignment explanation
Indices: 1363229--1363290 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 13
1363219 CGAAGTGCCT
1363229 CGTAGAATTGCAC
1 CGTAGAATTGCAC
*
1363242 C---GAAGTGC-C
1 CGTAGAATTGCAC
1363251 CGTAGAATTGCAC
1 CGTAGAATTGCAC
*
1363264 C---GAAGTGC-C
1 CGTAGAATTGCAC
1363273 CGTAGAATTGCAC
1 CGTAGAATTGCAC
1363286 CGTAG
1 CGTAG
1363291 TGCCCGTAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 16
0.65 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 9 0.24
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.19
Consensus pattern (13 bp):
CGTAGAATTGCAC
Found at i:1365037 original size:21 final size:21
Alignment explanation
Indices: 1365013--1365057 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1365003 TCTTGTTCGT
* *
1365013 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1365034 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1365055 TTG
1 TTG
1365058 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1368234 original size:22 final size:22
Alignment explanation
Indices: 1368193--1368281 Score: 160
Period size: 22 Copynumber: 4.0 Consensus size: 22
1368183 CTCGTATAAA
1368193 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1368216 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1368238 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
1368260 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1368282 GATGTCCATA
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
22 53 0.82
23 12 0.18
ACGTcount: A:0.26, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1368269 original size:13 final size:13
Alignment explanation
Indices: 1368207--1368269 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
1368197 CCGAAGTGCC
1368207 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
1368220 CC---GAAGTGC-
1 CCGTAGAATTGCA
1368229 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
1368242 CC---GAAGTGC-
1 CCGTAGAATTGCA
1368251 CCGTAGAATTGCA
1 CCGTAGAATTGCA
1368264 CCGTAG
1 CCGTAG
1368270 TGCCCGTAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:1370021 original size:21 final size:21
Alignment explanation
Indices: 1369997--1370041 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1369987 TCTTGTTCGT
* *
1369997 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1370018 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1370039 TTG
1 TTG
1370042 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1372346 original size:18 final size:18
Alignment explanation
Indices: 1372323--1372357 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1372313 ACTGAATATT
*
1372323 TGTCCCAAATGACCACTA
1 TGTCCCAAAGGACCACTA
*
1372341 TGTCCCGAAGGACCACT
1 TGTCCCAAAGGACCACT
1372358 GATAATCTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:1383042 original size:7 final size:7
Alignment explanation
Indices: 1383030--1383054 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1383020 GAAGGAATGA
1383030 ATGTTGT
1 ATGTTGT
1383037 ATGTTGT
1 ATGTTGT
1383044 ATGTTGT
1 ATGTTGT
1383051 ATGT
1 ATGT
1383055 GCATCAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (7 bp):
ATGTTGT
Found at i:1383826 original size:2 final size:2
Alignment explanation
Indices: 1383819--1383846 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1383809 GTTCATCAAA
1383819 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
1383847 CAAACCCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1383930 original size:24 final size:22
Alignment explanation
Indices: 1383903--1383947 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
1383893 CATCAAGTTC
1383903 AAACTCTAATAAAGCCTCATTTAA
1 AAACTCTAATAAA-CCTC-TTTAA
*
1383927 AAACTCTGATAAACCTCTTTA
1 AAACTCTAATAAACCTCTTTA
1383948 TGTACGATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 4 0.20
24 12 0.60
ACGTcount: A:0.42, C:0.22, G:0.04, T:0.31
Consensus pattern (22 bp):
AAACTCTAATAAACCTCTTTAA
Found at i:1384580 original size:259 final size:255
Alignment explanation
Indices: 1384072--1384586 Score: 953
Period size: 259 Copynumber: 2.0 Consensus size: 255
1384062 TTTTGAATTT
1384072 TAGAATTGTCTCATTCAAAATGTTTTATTAAAAAAATTAACAAACAACAATATTTACATTCTTTT
1 TAGAATTGTCTCATTCAAAATGTTTTATTAAAAAAATTAACAAACAACAATATTTACATTCTTTT
1384137 TTACCCTTTATATCATATTATTTACATTACATCAAAACAATATGTTAAATTCATTAATTGTCTTT
66 TTACCCTTTATATCATATTATTTACATTACATCAAAACAATATGTTAAATTCATTAATTGTCTTT
1384202 TACGAATAATTTAATAATTTTTTTAATTATAATACTAAAATTACGTGATAATTAATATAAAACAA
131 TACGAATAATTTAATAATTTTTTTAATTATAATACTAAAATTACGTGATAATTAATATAAAACAA
*
1384267 AGGACGGAATGAATAATAAACACAAGGGAGAAAAAAAGTATATAATATTATTAGTAGATC
196 AGGACGGAATGAATAATAAACACAAGGGAGAAAAAAAGTATATAATAATATTAGTAGATC
1384327 TAGAATTGTCTCATTCAAAATGTTTTATTAAAAAAATTAACAAACAACAATATTTACATTTCTTT
1 TAGAATTGTCTCATTCAAAATGTTTTATTAAAAAAATTAACAAACAACAATATTTACA-TTCTTT
1384392 TTTACCCTTTATATCATATTATTTTACA-TACATCAAAACAAATATGTTAAATTCATTAATTGTC
65 TTTACCCTTTATATCATATTA-TTTACATTACATCAAAAC-AATATGTTAAATTCATTAATTGTC
1384456 TTTTACGAATAATTTAATAATTTTTTTTAATT-TATATACTAAAATTACGTGTATAATTAATATA
128 TTTTACGAATAATTTAATAA-TTTTTTTAATTATA-ATACTAAAATTACGTG-ATAATTAATATA
1384520 AAACAAAGGACGGAATGAATAATAAACACAAGGGAGAAAAAAAGTATATAATAATATTAGTAGAT
190 AAACAAAGGACGGAATGAATAATAAACACAAGGGAGAAAAAAAGTATATAATAATATTAGTAGAT
1384585 C
255 C
1384586 T
1 T
1384587 TAATGGATAA
Statistics
Matches: 253, Mismatches: 1, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
255 58 0.23
256 38 0.15
257 52 0.21
258 27 0.11
259 78 0.31
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (255 bp):
TAGAATTGTCTCATTCAAAATGTTTTATTAAAAAAATTAACAAACAACAATATTTACATTCTTTT
TTACCCTTTATATCATATTATTTACATTACATCAAAACAATATGTTAAATTCATTAATTGTCTTT
TACGAATAATTTAATAATTTTTTTAATTATAATACTAAAATTACGTGATAATTAATATAAAACAA
AGGACGGAATGAATAATAAACACAAGGGAGAAAAAAAGTATATAATAATATTAGTAGATC
Found at i:1385772 original size:28 final size:27
Alignment explanation
Indices: 1385741--1385817 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
1385731 ATAATATTCA
* *
1385741 TTTTGATCCCACAATTGTAATTAAAAGT
1 TTTTGATCCCGCAATTCTAATT-AAAGT
* *
1385769 TTTTGATCCCGCAGTTTTAATTAAAGT
1 TTTTGATCCCGCAATTCTAATTAAAGT
1385796 TTTTGATCCCGCAATTCTAATT
1 TTTTGATCCCGCAATTCTAATT
1385818 TTATTAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (27 bp):
TTTTGATCCCGCAATTCTAATTAAAGT
Found at i:1389814 original size:21 final size:21
Alignment explanation
Indices: 1389763--1389815 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1389753 GCGATGGTAC
*
1389763 TGATACTAAGCCCTTTAGTAT
1 TGATACTAATCCCTTTAGTAT
1389784 TGATACTAATCCCTTTAGTAT
1 TGATACTAATCCCTTTAGTAT
1389805 TGATACTAATC
1 TGATACTAATC
1389816 TATCAATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (21 bp):
TGATACTAATCCCTTTAGTAT
Found at i:1399559 original size:32 final size:32
Alignment explanation
Indices: 1399523--1399586 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1399513 TGGAAGATAC
1399523 GAATGATGGACTCAGAATCGCTAGATGCTGCA
1 GAATGATGGACTCAGAATCGCTAGATGCTGCA
1399555 GAATGATGGACTCAGAATCGCTAGATGCTGCA
1 GAATGATGGACTCAGAATCGCTAGATGCTGCA
1399587 ACGGAAGCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (32 bp):
GAATGATGGACTCAGAATCGCTAGATGCTGCA
Found at i:1401629 original size:81 final size:81
Alignment explanation
Indices: 1401486--1401727 Score: 430
Period size: 81 Copynumber: 3.0 Consensus size: 81
1401476 TATTTTTGGA
* *
1401486 CTCCCGTTCGGTTGCTTGTCTTAAATTCTCTGTTTCAAACATCTAATACATACAGTACACTTATT
1 CTCCCGTTCGGTTGCTTGTCTTAAACTCTCTGTTTCAAACATCTAATACATACACTACACTTATT
1401551 CACTTTCATTAGTAAC
66 CACTTTCATTAGTAAC
*
1401567 CTCCCGTTCGGTTGCTTGTCTTAAACTCTCTGTTTCAAACATCTAATACATACACTATACTTATT
1 CTCCCGTTCGGTTGCTTGTCTTAAACTCTCTGTTTCAAACATCTAATACATACACTACACTTATT
1401632 CACTTTCATTAGTAAC
66 CACTTTCATTAGTAAC
* *
1401648 CTCCCGTTCGGTTGCTTGCCTTAAACTCTCTGTTTCAAACTTCTAATACATACACTACACTTATT
1 CTCCCGTTCGGTTGCTTGTCTTAAACTCTCTGTTTCAAACATCTAATACATACACTACACTTATT
*
1401713 CACTTTCACTAGTAA
66 CACTTTCATTAGTAA
1401728 GGAGTGACAT
Statistics
Matches: 154, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 154 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.39
Consensus pattern (81 bp):
CTCCCGTTCGGTTGCTTGTCTTAAACTCTCTGTTTCAAACATCTAATACATACACTACACTTATT
CACTTTCATTAGTAAC
Found at i:1405221 original size:20 final size:20
Alignment explanation
Indices: 1405173--1405227 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1405163 CAACATGAAA
*
1405173 TTTCAAATTCGCAACTCGAT
1 TTTCAAATTCGCAACGCGAT
**
1405193 TTTTGAATTCGCAACGCGAT
1 TTTCAAATTCGCAACGCGAT
*
1405213 TTTCAAATTTGCAAC
1 TTTCAAATTCGCAAC
1405228 ACGAACTCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (20 bp):
TTTCAAATTCGCAACGCGAT
Found at i:1406036 original size:24 final size:24
Alignment explanation
Indices: 1406009--1406062 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1405999 GTATTCAAAA
* *
1406009 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGCTCAATACTCAGAC
*
1406033 TTTGATCTTGCTCAATACTCAGAT
1 TTTGATCTTGCTCAATACTCAGAC
1406057 TTTGAT
1 TTTGAT
1406063 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGCTCAATACTCAGAC
Found at i:1408318 original size:18 final size:18
Alignment explanation
Indices: 1408292--1408327 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1408282 AAGCAAAAAG
*
1408292 AAATAAAAATCGCAATCA
1 AAATAAAAATCCCAATCA
*
1408310 AAATCAAAATCCCAATCA
1 AAATAAAAATCCCAATCA
1408328 CAACCGCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.22, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATAAAAATCCCAATCA
Found at i:1408643 original size:20 final size:20
Alignment explanation
Indices: 1408620--1408662 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1408610 GAAAATCGAA
1408620 TTCGCAACGCGAATTTGATT
1 TTCGCAACGCGAATTTGATT
***
1408640 TTCGCGTTGCGAATTTGATT
1 TTCGCAACGCGAATTTGATT
1408660 TTC
1 TTC
1408663 TTAAAGGTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (20 bp):
TTCGCAACGCGAATTTGATT
Found at i:1410206 original size:21 final size:21
Alignment explanation
Indices: 1410182--1410232 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1410172 AGGTGGATCA
1410182 TGAACGATGGGAAGGGCCTCT
1 TGAACGATGGGAAGGGCCTCT
** *
1410203 TGAACGATGGGGTGTGCCTCT
1 TGAACGATGGGAAGGGCCTCT
1410224 TGAACGATG
1 TGAACGATG
1410233 ACAAGTGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.24
Consensus pattern (21 bp):
TGAACGATGGGAAGGGCCTCT
Found at i:1410266 original size:21 final size:21
Alignment explanation
Indices: 1410242--1410285 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1410232 GACAAGTGAT
1410242 TCCTGAACAATGGAAGGTGGA
1 TCCTGAACAATGGAAGGTGGA
*
1410263 TCCTGAACAATGGTAGGTGGA
1 TCCTGAACAATGGAAGGTGGA
1410284 TC
1 TC
1410286 GGGCTTCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.23
Consensus pattern (21 bp):
TCCTGAACAATGGAAGGTGGA
Found at i:1410593 original size:21 final size:21
Alignment explanation
Indices: 1410569--1410619 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1410559 TAAAACAATC
* *
1410569 TCACGTAGAGCAGCTACCTCA
1 TCACGTAAAGCAGATACCTCA
*
1410590 TCACGTAAAGCATATACCTCA
1 TCACGTAAAGCAGATACCTCA
*
1410611 CCACGTAAA
1 TCACGTAAA
1410620 TCACCATTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.31, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCAGATACCTCA
Found at i:1410675 original size:42 final size:43
Alignment explanation
Indices: 1410582--1410678 Score: 119
Period size: 42 Copynumber: 2.3 Consensus size: 43
1410572 CGTAGAGCAG
*
1410582 CTACCTCATCACGTAAAGCATATACCTCACCACGTAAATCACC
1 CTACCTCATCACGTAAAACATATACCTCACCACGTAAATCACC
* ** *
1410625 AT-TGTCATCACGTAAAACA-ACTACCTCACCATGTAAAT-ACC
1 CTACCTCATCACGTAAAACATA-TACCTCACCACGTAAATCACC
1410666 CTACCTCATCACG
1 CTACCTCATCACG
1410679 CCATGCACCA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
41 5 0.11
42 38 0.86
43 1 0.02
ACGTcount: A:0.35, C:0.35, G:0.07, T:0.23
Consensus pattern (43 bp):
CTACCTCATCACGTAAAACATATACCTCACCACGTAAATCACC
Found at i:1410719 original size:21 final size:21
Alignment explanation
Indices: 1410695--1410738 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1410685 ACCATTGTCG
*
1410695 TCACATAAAGCACCGACCTCA
1 TCACATAAAGCACCGAACTCA
*
1410716 TCACATAAAGCACCTAACTCA
1 TCACATAAAGCACCGAACTCA
1410737 TC
1 TC
1410739 CCGTGGAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.36, G:0.07, T:0.18
Consensus pattern (21 bp):
TCACATAAAGCACCGAACTCA
Found at i:1410899 original size:42 final size:42
Alignment explanation
Indices: 1410837--1410985 Score: 172
Period size: 42 Copynumber: 3.5 Consensus size: 42
1410827 TGTGATGGAA
* **
1410837 TAGGTGATGGCTCTTAGTGTCGAGGTGTAGAATCGACTCGAT
1 TAGGTGATGGATCTCGGTGTCGAGGTGTAGAATCGACTCGAT
* * *
1410879 TAGGTGATGGCTCTCGGTGTCGAGGTGTAGAATCGTCTTGAT
1 TAGGTGATGGATCTCGGTGTCGAGGTGTAGAATCGACTCGAT
* * * * ** *
1410921 CATGTGATGGATCTCGGTGTCGAAGTGGAGAAGAGGCTCGAT
1 TAGGTGATGGATCTCGGTGTCGAGGTGTAGAATCGACTCGAT
*
1410963 GAGGTGATGGATCTCGGTGTCGA
1 TAGGTGATGGATCTCGGTGTCGA
1410986 AGTGGGGGTG
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 92 1.00
ACGTcount: A:0.20, C:0.14, G:0.37, T:0.29
Consensus pattern (42 bp):
TAGGTGATGGATCTCGGTGTCGAGGTGTAGAATCGACTCGAT
Found at i:1412534 original size:14 final size:14
Alignment explanation
Indices: 1412517--1412548 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1412507 ACTCGAAAAT
1412517 GAAATTCGCAACAC
1 GAAATTCGCAACAC
*
1412531 GAAATTCGCAACGC
1 GAAATTCGCAACAC
1412545 GAAA
1 GAAA
1412549 ACTAAAATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.25, G:0.19, T:0.12
Consensus pattern (14 bp):
GAAATTCGCAACAC
Found at i:1412548 original size:34 final size:34
Alignment explanation
Indices: 1412484--1412549 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
1412474 CTTGAAACTT
* * *
1412484 AAATTTGCAACATGAAAATCCTAACTCGAAAATG
1 AAATTCGCAACACGAAAATCCTAACGCGAAAATG
*
1412518 AAATTCGCAACACGAAATTCGC-AACGCGAAAA
1 AAATTCGCAACACGAAAATC-CTAACGCGAAAA
1412550 CTAAAATCGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 26 0.96
35 1 0.04
ACGTcount: A:0.47, C:0.21, G:0.14, T:0.18
Consensus pattern (34 bp):
AAATTCGCAACACGAAAATCCTAACGCGAAAATG
Found at i:1412948 original size:22 final size:22
Alignment explanation
Indices: 1412923--1412994 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
1412913 GATGGAGGGG
* * *
1412923 GTCGCCGGATATGGGGACGGAT
1 GTCGCCAGAGATGGGGACGAAT
1412945 GTCGCCAGAGATGGGGACGAAT
1 GTCGCCAGAGATGGGGACGAAT
1412967 GTCGCCAGAGATGGGGACGAAT
1 GTCGCCAGAGATGGGGACGAAT
1412989 GTCGCC
1 GTCGCC
1412995 GTAGAGAGTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.22, C:0.21, G:0.42, T:0.15
Consensus pattern (22 bp):
GTCGCCAGAGATGGGGACGAAT
Found at i:1413061 original size:27 final size:27
Alignment explanation
Indices: 1413022--1413089 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
1413012 AAGATGAGAC
1413022 TGAGTTGCGATTTAGAGTTTTAGGTTA
1 TGAGTTGCGATTTAGAGTTTTAGGTTA
* *
1413049 TGAGTTGCTATTTAGGGTTTTAGGTTA
1 TGAGTTGCGATTTAGAGTTTTAGGTTA
*
1413076 TGAGTTGTGATTTA
1 TGAGTTGCGATTTA
1413090 CGGGATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.21, C:0.03, G:0.29, T:0.47
Consensus pattern (27 bp):
TGAGTTGCGATTTAGAGTTTTAGGTTA
Found at i:1413266 original size:20 final size:21
Alignment explanation
Indices: 1413231--1413269 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1413221 GCGAAAAAAG
*
1413231 AAATTCGAGTTGCGAATTTCA
1 AAATTCGAGATGCGAATTTCA
1413252 AAATT-GAGATGCGAATTT
1 AAATTCGAGATGCGAATTT
1413270 GGAAACTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (21 bp):
AAATTCGAGATGCGAATTTCA
Found at i:1423726 original size:30 final size:31
Alignment explanation
Indices: 1423692--1423761 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
1423682 GTGACCCAAC
* *
1423692 GATCAAAATGT-A-ACAATCGATATTATAAAT
1 GATCAAAATGTAATAAAAT-GATAATATAAAT
*
1423722 GATCAAAATTTAATAAAATGATAATATAAAT
1 GATCAAAATGTAATAAAATGATAATATAAAT
*
1423753 GATTAAAAT
1 GATCAAAAT
1423762 TTATTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.29
31 20 0.59
32 4 0.12
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.31
Consensus pattern (31 bp):
GATCAAAATGTAATAAAATGATAATATAAAT
Found at i:1425894 original size:24 final size:24
Alignment explanation
Indices: 1425849--1425894 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1425839 GATCACTCGG
* *
1425849 TGTACAAAGGGCACCAGGTATTCT
1 TGTACAAAGAGCACCAGATATTCT
1425873 TGTACAAAAGAGCA-CAGATATT
1 TGTAC-AAAGAGCACCAGATATT
1425895 TGCTGCCGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (24 bp):
TGTACAAAGAGCACCAGATATTCT
Found at i:1426521 original size:13 final size:13
Alignment explanation
Indices: 1426503--1426530 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1426493 TTTATGTTTA
1426503 ATAGGTTCTAAGG
1 ATAGGTTCTAAGG
1426516 ATAGGTTCTAAGG
1 ATAGGTTCTAAGG
1426529 AT
1 AT
1426531 TACAGTTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.29, T:0.32
Consensus pattern (13 bp):
ATAGGTTCTAAGG
Found at i:1426801 original size:24 final size:24
Alignment explanation
Indices: 1426775--1426820 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1426765 TAATTGAACA
* *
1426775 AAAATTAATTT-TTTATATAATTT
1 AAAATAAATTTATATATATAATTT
1426798 AAAATAAATTTATATATATAATT
1 AAAATAAATTTATATATATAATT
1426821 ATATTAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AAAATAAATTTATATATATAATTT
Done.